0s autopkgtest [20:34:56]: starting date and time: 2024-03-16 20:34:56+0000 0s autopkgtest [20:34:56]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [20:34:56]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pjbh4_6f/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade r-cran-vegan --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-9.secgroup --name adt-noble-arm64-r-cran-vegan-20240316-203456-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 202s autopkgtest [20:38:18]: testbed dpkg architecture: arm64 202s autopkgtest [20:38:18]: testbed apt version: 2.7.12 202s autopkgtest [20:38:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 203s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 203s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3704 kB] 204s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 204s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 204s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 204s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 204s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 204s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 204s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 204s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4012 kB] 204s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 204s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 204s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 205s Fetched 9112 kB in 2s (5425 kB/s) 206s Reading package lists... 208s Reading package lists... 209s Building dependency tree... 209s Reading state information... 209s Calculating upgrade... 209s The following packages will be REMOVED: 209s libglib2.0-0 libssl3 209s The following NEW packages will be installed: 209s libglib2.0-0t64 libssl3t64 xdg-user-dirs 209s The following packages have been kept back: 209s curl 209s The following packages will be upgraded: 209s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 209s ubuntu-minimal ubuntu-standard 210s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 210s Need to get 4613 kB of archives. 210s After this operation, 211 kB of additional disk space will be used. 210s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 210s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 211s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 211s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 211s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 211s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 211s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 211s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 211s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 211s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 211s Fetched 4613 kB in 1s (6034 kB/s) 211s (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 ... 74758 files and directories currently installed.) 211s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 211s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 211s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 211s udisks2 depends on libglib2.0-0 (>= 2.77.0). 211s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 211s python3-gi depends on libglib2.0-0 (>= 2.77.0). 211s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 211s netplan.io depends on libglib2.0-0 (>= 2.70.0). 211s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 211s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 211s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 211s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 211s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 211s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 211s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 211s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 211s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 211s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 211s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 211s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 211s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 211s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 211s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 211s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 211s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 211s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 211s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 211s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 211s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 211s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 211s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 211s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 211s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 211s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 211s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 211s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 211s fwupd depends on libglib2.0-0 (>= 2.79.0). 211s bolt depends on libglib2.0-0 (>= 2.56.0). 211s 211s (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 ... 74758 files and directories currently installed.) 211s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 211s Selecting previously unselected package libglib2.0-0t64:arm64. 211s (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 ... 74733 files and directories currently installed.) 211s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 211s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 211s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 211s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 211s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 211s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 211s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 211s wget depends on libssl3 (>= 3.0.0). 211s u-boot-tools depends on libssl3 (>= 3.0.0). 211s tnftp depends on libssl3 (>= 3.0.0). 211s tcpdump depends on libssl3 (>= 3.0.0). 211s systemd-resolved depends on libssl3 (>= 3.0.0). 211s systemd depends on libssl3 (>= 3.0.0). 211s sudo depends on libssl3 (>= 3.0.0). 211s sbsigntool depends on libssl3 (>= 3.0.0). 211s rsync depends on libssl3 (>= 3.0.0). 211s python3-cryptography depends on libssl3 (>= 3.0.0). 211s openssh-server depends on libssl3 (>= 3.0.10). 211s openssh-client depends on libssl3 (>= 3.0.10). 211s mtd-utils depends on libssl3 (>= 3.0.0). 211s mokutil depends on libssl3 (>= 3.0.0). 211s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 211s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 211s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 211s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 211s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 211s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 211s libnvme1 depends on libssl3 (>= 3.0.0). 211s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 211s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 211s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 211s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 211s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 211s kmod depends on libssl3 (>= 3.0.0). 211s dhcpcd-base depends on libssl3 (>= 3.0.0). 211s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 211s 211s (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 ... 74758 files and directories currently installed.) 211s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 211s Selecting previously unselected package libssl3t64:arm64. 211s (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 ... 74747 files and directories currently installed.) 211s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 211s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 212s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 212s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 212s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ... 212s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 212s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ... 212s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 212s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ... 212s Unpacking ubuntu-minimal (1.536) over (1.535) ... 212s Selecting previously unselected package xdg-user-dirs. 212s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ... 212s Unpacking xdg-user-dirs (0.18-1) ... 212s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ... 212s Unpacking ubuntu-standard (1.536) over (1.535) ... 212s Setting up ubuntu-minimal (1.536) ... 212s Setting up xdg-user-dirs (0.18-1) ... 212s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 212s Setting up libtirpc-common (1.3.4+ds-1.1) ... 212s Setting up ubuntu-standard (1.536) ... 212s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 212s No schema files found: doing nothing. 212s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 212s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 212s Setting up openssl (3.0.13-0ubuntu1) ... 212s Setting up readline-common (8.2-3.1) ... 212s Processing triggers for man-db (2.12.0-3) ... 212s Processing triggers for install-info (7.1-3) ... 213s Processing triggers for libc-bin (2.39-0ubuntu2) ... 213s Reading package lists... 213s Building dependency tree... 213s Reading state information... 214s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 214s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 214s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 215s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 215s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 216s Reading package lists... 216s Reading package lists... 216s Building dependency tree... 216s Reading state information... 217s Calculating upgrade... 217s The following packages have been kept back: 217s curl 217s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 217s Reading package lists... 218s Building dependency tree... 218s Reading state information... 218s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 221s autopkgtest [20:38:37]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 221s autopkgtest [20:38:37]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 223s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-vegan 2.6-4+dfsg-1 (dsc) [2154 B] 223s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-vegan 2.6-4+dfsg-1 (tar) [1198 kB] 223s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-vegan 2.6-4+dfsg-1 (diff) [6176 B] 224s gpgv: Signature made Fri Oct 14 13:21:08 2022 UTC 224s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 224s gpgv: issuer "tille@debian.org" 224s gpgv: Can't check signature: No public key 224s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-4+dfsg-1.dsc: no acceptable signature found 224s autopkgtest [20:38:40]: testing package r-cran-vegan version 2.6-4+dfsg-1 225s autopkgtest [20:38:41]: build not needed 226s autopkgtest [20:38:42]: test run-unit-test: preparing testbed 227s Reading package lists... 227s Building dependency tree... 227s Reading state information... 228s Starting pkgProblemResolver with broken count: 0 228s Starting 2 pkgProblemResolver with broken count: 0 228s Done 228s The following additional packages will be installed: 228s curl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 228s libblas3 libcairo2 libcurl4t64 libdatrie1 libdeflate0 libfontconfig1 228s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 228s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 228s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 228s libpng16-16t64 libpsl5t64 libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 228s libthai-data libthai0 libtiff6 libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 228s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-cluster 228s r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme 228s r-cran-permute r-cran-vegan unzip x11-common xdg-utils zip 228s Suggested packages: 228s tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 228s r-cran-knitr r-cran-rmarkdown r-cran-bookdown r-cran-sessioninfo 228s r-cran-markdown 228s Recommended packages: 228s r-recommended r-base-dev r-doc-html r-cran-testthat libfile-mimeinfo-perl 228s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 228s The following packages will be REMOVED: 228s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 228s The following NEW packages will be installed: 228s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 228s fonts-dejavu-mono libblas3 libcairo2 libcurl4t64 libdatrie1 libdeflate0 228s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 228s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 228s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 228s libpng16-16t64 libpsl5t64 libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 228s libthai-data libthai0 libtiff6 libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 228s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-cluster 228s r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme 228s r-cran-permute r-cran-vegan unzip x11-common xdg-utils zip 228s The following packages will be upgraded: 228s curl 228s 1 upgraded, 58 newly installed, 5 to remove and 0 not upgraded. 228s Need to get 53.3 MB/53.3 MB of archives. 228s After this operation, 97.0 MB of additional disk space will be used. 228s Get:1 /tmp/autopkgtest.9uXNFN/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 229s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 229s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 229s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 229s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 229s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 229s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 229s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 229s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 229s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 229s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 229s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 229s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 229s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 229s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 229s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 229s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 229s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 229s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 229s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 229s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 229s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 229s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 229s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 229s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 229s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 229s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 229s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 229s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 229s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 229s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 229s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 229s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 229s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 229s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 229s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 229s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 230s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 230s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 230s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 230s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 230s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 230s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 230s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 230s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 230s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 230s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 230s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 230s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 230s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 230s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 230s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cluster arm64 2.1.6-1 [552 kB] 230s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 230s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 230s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 230s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 230s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 231s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-permute all 0.9-7-1 [228 kB] 231s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vegan arm64 2.6-4+dfsg-1 [3088 kB] 231s Preconfiguring packages ... 231s Fetched 53.3 MB in 2s (23.7 MB/s) 231s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 231s wget depends on libpsl5 (>= 0.16.0). 231s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 231s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 231s 231s (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 ... 74774 files and directories currently installed.) 231s Removing libpsl5:arm64 (0.21.2-1build1) ... 231s Selecting previously unselected package libpsl5t64:arm64. 231s (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 ... 74769 files and directories currently installed.) 231s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 232s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 232s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 232s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 232s (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 ... 74775 files and directories currently installed.) 232s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 232s Selecting previously unselected package libcurl4t64:arm64. 232s (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 ... 74770 files and directories currently installed.) 232s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 232s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 232s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 232s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 232s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 232s 232s (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 ... 74776 files and directories currently installed.) 232s Removing libpng16-16:arm64 (1.6.43-1) ... 232s Selecting previously unselected package libpng16-16t64:arm64. 232s (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 ... 74766 files and directories currently installed.) 232s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 232s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 232s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 232s parted depends on libreadline8 (>= 6.0). 232s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 232s gpgsm depends on libreadline8 (>= 6.0). 232s gpgconf depends on libreadline8 (>= 6.0). 232s gpg depends on libreadline8 (>= 6.0). 232s gawk depends on libreadline8 (>= 6.0). 232s fdisk depends on libreadline8 (>= 6.0). 232s 232s (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 ... 74777 files and directories currently installed.) 232s Removing libreadline8:arm64 (8.2-3) ... 232s Selecting previously unselected package libreadline8t64:arm64. 232s (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 ... 74765 files and directories currently installed.) 232s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 232s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 232s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' 232s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 232s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' 232s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 232s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 232s lsof depends on libtirpc3 (>= 1.0.2). 232s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 232s libnss-nisplus:arm64 depends on libtirpc3 (>= 1.0.2). 232s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 232s iproute2 depends on libtirpc3 (>= 1.0.2). 232s 232s (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 ... 74785 files and directories currently installed.) 232s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 232s Selecting previously unselected package libtirpc3t64:arm64. 232s (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 ... 74779 files and directories currently installed.) 232s Preparing to unpack .../00-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 232s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 232s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 232s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 232s Selecting previously unselected package fonts-dejavu-mono. 232s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 232s Unpacking fonts-dejavu-mono (2.37-8) ... 232s Selecting previously unselected package fonts-dejavu-core. 232s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 232s Unpacking fonts-dejavu-core (2.37-8) ... 232s Selecting previously unselected package fontconfig-config. 232s Preparing to unpack .../03-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 233s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 233s Selecting previously unselected package libfontconfig1:arm64. 233s Preparing to unpack .../04-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 233s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 233s Selecting previously unselected package fontconfig. 233s Preparing to unpack .../05-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 233s Unpacking fontconfig (2.15.0-1ubuntu1) ... 233s Selecting previously unselected package libblas3:arm64. 233s Preparing to unpack .../06-libblas3_3.12.0-3_arm64.deb ... 233s Unpacking libblas3:arm64 (3.12.0-3) ... 233s Selecting previously unselected package libpixman-1-0:arm64. 233s Preparing to unpack .../07-libpixman-1-0_0.42.2-1_arm64.deb ... 233s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 233s Selecting previously unselected package libxcb-render0:arm64. 233s Preparing to unpack .../08-libxcb-render0_1.15-1_arm64.deb ... 233s Unpacking libxcb-render0:arm64 (1.15-1) ... 233s Selecting previously unselected package libxcb-shm0:arm64. 233s Preparing to unpack .../09-libxcb-shm0_1.15-1_arm64.deb ... 233s Unpacking libxcb-shm0:arm64 (1.15-1) ... 233s Selecting previously unselected package libxrender1:arm64. 233s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 233s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 233s Selecting previously unselected package libcairo2:arm64. 233s Preparing to unpack .../11-libcairo2_1.18.0-1_arm64.deb ... 233s Unpacking libcairo2:arm64 (1.18.0-1) ... 233s Selecting previously unselected package libdatrie1:arm64. 233s Preparing to unpack .../12-libdatrie1_0.2.13-3_arm64.deb ... 233s Unpacking libdatrie1:arm64 (0.2.13-3) ... 233s Selecting previously unselected package libdeflate0:arm64. 233s Preparing to unpack .../13-libdeflate0_1.19-1_arm64.deb ... 233s Unpacking libdeflate0:arm64 (1.19-1) ... 233s Selecting previously unselected package libgfortran5:arm64. 233s Preparing to unpack .../14-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 233s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 233s Selecting previously unselected package libgomp1:arm64. 233s Preparing to unpack .../15-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 233s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 233s Selecting previously unselected package libgraphite2-3:arm64. 233s Preparing to unpack .../16-libgraphite2-3_1.3.14-2_arm64.deb ... 233s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 233s Selecting previously unselected package libharfbuzz0b:arm64. 233s Preparing to unpack .../17-libharfbuzz0b_8.3.0-2_arm64.deb ... 233s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 233s Selecting previously unselected package x11-common. 233s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu2_all.deb ... 233s Unpacking x11-common (1:7.7+23ubuntu2) ... 233s Selecting previously unselected package libice6:arm64. 233s Preparing to unpack .../19-libice6_2%3a1.0.10-1build2_arm64.deb ... 233s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 233s Selecting previously unselected package libjpeg-turbo8:arm64. 233s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 233s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 233s Selecting previously unselected package libjpeg8:arm64. 233s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_arm64.deb ... 233s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 233s Selecting previously unselected package liblapack3:arm64. 233s Preparing to unpack .../22-liblapack3_3.12.0-3_arm64.deb ... 233s Unpacking liblapack3:arm64 (3.12.0-3) ... 233s Selecting previously unselected package liblerc4:arm64. 233s Preparing to unpack .../23-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 233s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 233s Selecting previously unselected package libthai-data. 233s Preparing to unpack .../24-libthai-data_0.1.29-2_all.deb ... 233s Unpacking libthai-data (0.1.29-2) ... 233s Selecting previously unselected package libthai0:arm64. 233s Preparing to unpack .../25-libthai0_0.1.29-2_arm64.deb ... 233s Unpacking libthai0:arm64 (0.1.29-2) ... 233s Selecting previously unselected package libpango-1.0-0:arm64. 233s Preparing to unpack .../26-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 233s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 233s Selecting previously unselected package libpangoft2-1.0-0:arm64. 233s Preparing to unpack .../27-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 233s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 233s Selecting previously unselected package libpangocairo-1.0-0:arm64. 233s Preparing to unpack .../28-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 233s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 233s Selecting previously unselected package libpaper1:arm64. 233s Preparing to unpack .../29-libpaper1_1.1.29_arm64.deb ... 233s Unpacking libpaper1:arm64 (1.1.29) ... 233s Selecting previously unselected package libpaper-utils. 233s Preparing to unpack .../30-libpaper-utils_1.1.29_arm64.deb ... 233s Unpacking libpaper-utils (1.1.29) ... 233s Selecting previously unselected package libsharpyuv0:arm64. 233s Preparing to unpack .../31-libsharpyuv0_1.3.2-0.4_arm64.deb ... 233s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 233s Selecting previously unselected package libsm6:arm64. 233s Preparing to unpack .../32-libsm6_2%3a1.2.3-1build2_arm64.deb ... 233s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 233s Selecting previously unselected package libtcl8.6:arm64. 234s Preparing to unpack .../33-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 234s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 234s Selecting previously unselected package libjbig0:arm64. 234s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 234s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 234s Selecting previously unselected package libwebp7:arm64. 234s Preparing to unpack .../35-libwebp7_1.3.2-0.4_arm64.deb ... 234s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 234s Selecting previously unselected package libtiff6:arm64. 234s Preparing to unpack .../36-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 234s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 234s Selecting previously unselected package libxft2:arm64. 234s Preparing to unpack .../37-libxft2_2.3.6-1_arm64.deb ... 234s Unpacking libxft2:arm64 (2.3.6-1) ... 234s Selecting previously unselected package libxss1:arm64. 234s Preparing to unpack .../38-libxss1_1%3a1.2.3-1build2_arm64.deb ... 234s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 234s Selecting previously unselected package libtk8.6:arm64. 234s Preparing to unpack .../39-libtk8.6_8.6.13-2_arm64.deb ... 234s Unpacking libtk8.6:arm64 (8.6.13-2) ... 234s Selecting previously unselected package libxt6t64:arm64. 234s Preparing to unpack .../40-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... 234s Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... 234s Selecting previously unselected package zip. 234s Preparing to unpack .../41-zip_3.0-13_arm64.deb ... 234s Unpacking zip (3.0-13) ... 234s Selecting previously unselected package unzip. 234s Preparing to unpack .../42-unzip_6.0-28ubuntu3_arm64.deb ... 234s Unpacking unzip (6.0-28ubuntu3) ... 234s Selecting previously unselected package xdg-utils. 234s Preparing to unpack .../43-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 234s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 234s Selecting previously unselected package r-base-core. 234s Preparing to unpack .../44-r-base-core_4.3.3-2build1_arm64.deb ... 234s Unpacking r-base-core (4.3.3-2build1) ... 234s Selecting previously unselected package r-cran-cluster. 234s Preparing to unpack .../45-r-cran-cluster_2.1.6-1_arm64.deb ... 234s Unpacking r-cran-cluster (2.1.6-1) ... 234s Selecting previously unselected package r-cran-lattice. 234s Preparing to unpack .../46-r-cran-lattice_0.22-5-1_arm64.deb ... 234s Unpacking r-cran-lattice (0.22-5-1) ... 234s Selecting previously unselected package r-cran-mass. 234s Preparing to unpack .../47-r-cran-mass_7.3-60.0.1-1_arm64.deb ... 234s Unpacking r-cran-mass (7.3-60.0.1-1) ... 234s Selecting previously unselected package r-cran-matrix. 234s Preparing to unpack .../48-r-cran-matrix_1.6-5-1_arm64.deb ... 234s Unpacking r-cran-matrix (1.6-5-1) ... 234s Selecting previously unselected package r-cran-nlme. 234s Preparing to unpack .../49-r-cran-nlme_3.1.164-1_arm64.deb ... 234s Unpacking r-cran-nlme (3.1.164-1) ... 234s Selecting previously unselected package r-cran-mgcv. 234s Preparing to unpack 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r-cran-matrix (1.6-5-1) ... 238s Setting up r-cran-mgcv (1.9-1-1) ... 238s Setting up r-cran-vegan (2.6-4+dfsg-1) ... 238s Setting up autopkgtest-satdep (0) ... 238s Processing triggers for man-db (2.12.0-3) ... 239s Processing triggers for install-info (7.1-3) ... 239s Processing triggers for libc-bin (2.39-0ubuntu2) ... 244s (Reading database ... 77384 files and directories currently installed.) 244s Removing autopkgtest-satdep (0) ... 244s autopkgtest [20:39:00]: test run-unit-test: [----------------------- 245s 245s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 245s Copyright (C) 2024 The R Foundation for Statistical Computing 245s Platform: aarch64-unknown-linux-gnu (64-bit) 245s 245s R is free software and comes with ABSOLUTELY NO WARRANTY. 245s You are welcome to redistribute it under certain conditions. 245s Type 'license()' or 'licence()' for distribution details. 245s 245s R is a collaborative project with many contributors. 245s Type 'contributors()' for more information and 245s 'citation()' on how to cite R or R packages in publications. 245s 245s Type 'demo()' for some demos, 'help()' for on-line help, or 245s 'help.start()' for an HTML browser interface to help. 245s Type 'q()' to quit R. 245s 245s > Stangle("decision-vegan.Rnw") 245s Writing to file decision-vegan.R 245s > source("decision-vegan.R", echo=TRUE) 245s 245s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 245s 245s > options(SweaveHooks = list(fig = figset)) 245s 245s > options(prompt = "> ", continue = " ") 245s 245s > options(width = 55) 245s 245s > require(vegan) 245s Loading required package: vegan 245s Loading required package: permute 245s Loading required package: lattice 246s This is vegan 2.6-4 246s 246s > data(sipoo) 246s 246s > mod <- nestedtemp(sipoo) 246s 246s > plot(mod, "i") 246s 246s > x <- mod$c["Falcsubb"] 246s 246s > y <- 1 - mod$r["Svartholm"] 246s 246s > points(x, y, pch = 16, cex = 1.5) 246s 246s > abline(x + y, -1, lty = 2) 246s 246s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 246s 246s > cross <- function(x, a, p) f(x, p) - a + x 246s 246s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 246s 246s > arrows(x, y, r, f(r, mod$p), lwd = 4) 246s 246s > library(vegan) 246s 246s > data(varespec) 246s 246s > data(varechem) 246s 246s > orig <- cca(varespec ~ Al + K, varechem) 246s 246s > plot(orig, dis = c("lc", "bp")) 247s 247s > plot(orig, dis = c("lc", "bp")) 247s 247s > i <- sample(nrow(varespec)) 247s 247s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 247s 247s > plot(shuff, dis = c("lc", "bp")) 247s 247s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 247s + dis = "lc"))) 247s 247s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 247s + dis = "lc"))) 247s 247s > tmp1 <- rda(varespec ~ Al + K, varechem) 247s 247s > i <- sample(nrow(varespec)) 247s 247s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 247s 247s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 247s + dis = "lc"))) 247s 247s > orig 247s Call: cca(formula = varespec ~ Al + K, data = 247s varechem) 247s 247s Inertia Proportion Rank 247s Total 2.0832 1.0000 247s Constrained 0.4760 0.2285 2 247s Unconstrained 1.6072 0.7715 21 247s Inertia is scaled Chi-square 247s 247s Eigenvalues for constrained axes: 247s CCA1 CCA2 247s 0.3608 0.1152 247s 247s Eigenvalues for unconstrained axes: 247s CA1 CA2 CA3 CA4 CA5 CA6 CA7 247s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 247s CA8 247s 0.0757 247s (Showing 8 of 21 unconstrained eigenvalues) 247s 247s 247s > shuff 247s Call: cca(formula = varespec[i, ] ~ Al + K, data 247s = varechem) 247s 247s Inertia Proportion Rank 247s Total 2.08320 1.00000 247s Constrained 0.10817 0.05192 2 247s Unconstrained 1.97503 0.94808 21 247s Inertia is scaled Chi-square 247s 247s Eigenvalues for constrained axes: 247s CCA1 CCA2 247s 0.06975 0.03842 247s 247s Eigenvalues for unconstrained axes: 247s CA1 CA2 CA3 CA4 CA5 CA6 CA7 247s 0.5176 0.3548 0.2287 0.1901 0.1682 0.1181 0.1076 247s CA8 247s 0.0786 247s (Showing 8 of 21 unconstrained eigenvalues) 247s 247s 247s > plot(procrustes(orig, shuff)) 247s 247s > tmp1 <- rda(varespec ~ ., varechem) 247s 247s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 247s 247s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 247s + scores(tmp2, dis = "lc", choi = 1:14)) 247s 247s > max(residuals(proc)) 247s [1] 3.392982e-14 247s 247s > data(dune) 247s 247s > data(dune.env) 247s 247s > orig <- cca(dune ~ Moisture, dune.env) 247s 247s > plot(orig, dis = "lc") 247s 247s > plot(orig, display = "wa", type = "points") 247s 247s > ordispider(orig, col = "red") 247s 247s > text(orig, dis = "cn", col = "blue") 247s 247s > plot(orig, display = "wa", type = "points") 247s 247s > ordispider(orig, col = "red") 247s 247s > text(orig, dis = "cn", col = "blue") 247s > 247s 247s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 247s Copyright (C) 2024 The R Foundation for Statistical Computing 247s Platform: aarch64-unknown-linux-gnu (64-bit) 247s 247s R is free software and comes with ABSOLUTELY NO WARRANTY. 247s You are welcome to redistribute it under certain conditions. 247s Type 'license()' or 'licence()' for distribution details. 247s 247s R is a collaborative project with many contributors. 247s Type 'contributors()' for more information and 247s 'citation()' on how to cite R or R packages in publications. 247s 247s Type 'demo()' for some demos, 'help()' for on-line help, or 247s 'help.start()' for an HTML browser interface to help. 247s Type 'q()' to quit R. 247s 247s > Stangle("diversity-vegan.Rnw") 247s Writing to file diversity-vegan.R 247s > source("diversity-vegan.R", echo=TRUE) 247s 247s > par(mfrow = c(1, 1)) 247s 247s > options(width = 55) 247s 247s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 247s 247s > options(SweaveHooks = list(fig = figset)) 247s 247s > options(prompt = "> ", continue = " ") 247s 247s > library(vegan) 247s Loading required package: permute 247s Loading required package: lattice 248s This is vegan 2.6-4 248s 248s > data(BCI) 248s 248s > H <- diversity(BCI) 248s 248s > J <- H/log(specnumber(BCI)) 248s 248s > k <- sample(nrow(BCI), 6) 248s 248s > R <- renyi(BCI[k, ]) 248s 248s > print(plot(R)) 248s 248s > alpha <- fisher.alpha(BCI) 248s 248s > quantile(rowSums(BCI)) 248s 0% 25% 50% 75% 100% 248s 340.0 409.0 428.0 443.5 601.0 248s 248s > Srar <- rarefy(BCI, min(rowSums(BCI))) 248s 248s > S2 <- rarefy(BCI, 2) 248s 248s > all(rank(Srar) == rank(S2)) 248s [1] FALSE 248s 248s > range(diversity(BCI, "simp") - (S2 - 1)) 248s [1] -0.002868298 -0.001330663 248s 248s > data(dune) 248s 248s > data(dune.taxon) 248s 248s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 248s 248s > mod <- taxondive(dune, taxdis) 248s 248s > plot(mod) 248s 248s > tr <- hclust(taxdis, "aver") 248s 248s > mod <- treedive(dune, tr) 248s 248s > k <- sample(nrow(BCI), 1) 248s 248s > fish <- fisherfit(BCI[k, ]) 248s forced matching of 'tree' labels and 'comm' names 248s 248s > fish 248s 248s Fisher log series model 248s No. of species: 82 248s Fisher alpha: 30.58383 248s 248s 248s > plot(fish) 248s 248s > prestondistr(BCI[k, ]) 248s 248s Preston lognormal model 248s Method: maximized likelihood to log2 abundances 248s No. of species: 82 248s 248s mode width S0 248s 1.184636 1.724112 21.142298 248s 248s Frequencies by Octave 248s 0 1 2 3 4 248s Observed 14.0000 21.50000 16.00000 17.00000 6.500000 248s Fitted 16.6969 21.02141 18.90544 12.14537 5.573573 248s 5 6 248s Observed 6.000000 1.0000000 248s Fitted 1.827072 0.4278351 248s 248s 248s > rad <- radfit(BCI[k, ]) 248s 248s > rad 248s 248s RAD models, family poisson 248s No. of species 82, total abundance 416 248s 248s par1 par2 par3 Deviance 248s Null 44.1321 248s Preemption 0.050871 35.5813 248s Lognormal 1.0473 1.0934 15.0446 248s Zipf 0.1343 -0.81154 37.1297 248s Mandelbrot 4.4331 -1.6963 9.5855 6.8295 248s AIC BIC 248s Null 288.5829 288.5829 248s Preemption 282.0320 284.4388 248s Lognormal 263.4954 268.3088 248s Zipf 285.5805 290.3940 248s Mandelbrot 257.2803 264.5004 248s 248s > print(radlattice(rad)) 248s 248s > sac <- specaccum(BCI) 248s 248s > plot(sac, ci.type = "polygon", ci.col = "yellow") 248s 248s > sac <- specaccum(BCI) 248s 248s > plot(sac, ci.type = "polygon", ci.col = "yellow") 248s 248s > ncol(BCI)/mean(specnumber(BCI)) - 1 248s [1] 1.478519 248s 248s > beta <- vegdist(BCI, binary = TRUE) 248s 248s > mean(beta) 248s [1] 0.3399075 248s 248s > betadiver(help = TRUE) 248s 1 "w" = (b+c)/(2*a+b+c) 248s 2 "-1" = (b+c)/(2*a+b+c) 248s 3 "c" = (b+c)/2 248s 4 "wb" = b+c 248s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 248s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 248s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 248s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 248s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 248s (2*a+b+c))-1 248s 8 "t" = (b+c)/(2*a+b+c) 248s 9 "me" = (b+c)/(2*a+b+c) 248s 10 "j" = a/(a+b+c) 248s 11 "sor" = 2*a/(2*a+b+c) 248s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 248s 13 "-2" = pmin(b,c)/(pmax(b,c)+a) 248s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 248s 15 "cc" = (b+c)/(a+b+c) 248s 16 "g" = (b+c)/(a+b+c) 248s 17 "-3" = pmin(b,c)/(a+b+c) 248s 18 "l" = (b+c)/2 248s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 248s 20 "hk" = (b+c)/(2*a+b+c) 248s 21 "rlb" = a/(a+c) 248s 22 "sim" = pmin(b,c)/(pmin(b,c)+a) 248s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 248s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 248s 248s > z <- betadiver(BCI, "z") 248s 248s > quantile(z) 248s 0% 25% 50% 75% 100% 248s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 248s 248s > data(dune) 248s 248s > data(dune.env) 248s 248s > z <- betadiver(dune, "z") 248s 248s > mod <- with(dune.env, betadisper(z, Management)) 248s 248s > mod 248s 248s Homogeneity of multivariate dispersions 248s 248s Call: betadisper(d = z, group = Management) 248s 248s No. of Positive Eigenvalues: 12 248s No. of Negative Eigenvalues: 7 248s 248s Average distance to median: 248s BF HF NM SF 248s 0.2532 0.2512 0.4406 0.3635 248s 248s Eigenvalues for PCoA axes: 248s (Showing 8 of 19 eigenvalues) 248s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 248s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 248s PCoA7 PCoA8 248s 0.16128 0.08099 248s 248s > boxplot(mod) 248s 248s > specpool(BCI) 248s Species chao chao.se jack1 jack1.se jack2 248s All 225 236.3732 6.54361 245.58 5.650522 247.8722 248s boot boot.se n 248s All 235.6862 3.468888 50 248s 248s > s <- sample(nrow(BCI), 25) 248s 248s > specpool(BCI[s, ]) 248s Species chao chao.se jack1 jack1.se jack2 248s All 207 232.088 12.52852 233.88 7.892072 246.415 248s boot boot.se n 248s All 219.6213 4.24539 25 248s 248s > estimateR(BCI[k, ]) 248s 7 248s S.obs 82.000000 248s S.chao1 105.625000 248s se.chao1 11.789446 248s S.ACE 108.315823 248s se.ACE 4.913317 248s 248s > veiledspec(prestondistr(BCI[k, ])) 249s Extrapolated Observed Veiled 249s 91.370848 82.000000 9.370848 249s 249s > veiledspec(BCI[k, ]) 249s Extrapolated Observed Veiled 249s 97.93917 82.00000 15.93917 249s 249s > smo <- beals(BCI) 249s 249s > j <- which(colnames(BCI) == "Ceiba.pentandra") 249s 249s > plot(beals(BCI, species = j, include = FALSE), BCI[, 249s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 249s 249s > j <- which(colnames(BCI) == "Ceiba.pentandra") 249s 249s > plot(beals(BCI, species = j, include = FALSE), BCI[, 249s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 249s > 249s Warning messages: 249s 1: In cor(x > 0) : the standard deviation is zero 249s 2: In cor(x > 0) : the standard deviation is zero 249s 3: In betadisper(z, Management) : 249s some squared distances are negative and changed to zero 249s 249s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 249s Copyright (C) 2024 The R Foundation for Statistical Computing 249s Platform: aarch64-unknown-linux-gnu (64-bit) 249s 249s R is free software and comes with ABSOLUTELY NO WARRANTY. 249s You are welcome to redistribute it under certain conditions. 249s Type 'license()' or 'licence()' for distribution details. 249s 249s R is a collaborative project with many contributors. 249s Type 'contributors()' for more information and 249s 'citation()' on how to cite R or R packages in publications. 249s 249s Type 'demo()' for some demos, 'help()' for on-line help, or 249s 'help.start()' for an HTML browser interface to help. 249s Type 'q()' to quit R. 249s 249s > Stangle("intro-vegan.Rnw") 249s Writing to file intro-vegan.R 249s > source("intro-vegan.R", echo=TRUE) 249s 249s > par(mfrow = c(1, 1)) 249s 249s > options(width = 72) 249s 249s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 249s 249s > options(SweaveHooks = list(fig = figset)) 249s 249s > options(prompt = "> ", continue = " ") 249s 249s > library(vegan) 249s Loading required package: permute 249s Loading required package: lattice 250s This is vegan 2.6-4 250s 250s > data(dune) 250s 250s > ord <- decorana(dune) 250s 250s > ord 250s 250s Call: 250s decorana(veg = dune) 250s 250s Detrended correspondence analysis with 26 segments. 250s Rescaling of axes with 4 iterations. 250s Total inertia (scaled Chi-square): 2.1153 250s 250s DCA1 DCA2 DCA3 DCA4 250s Eigenvalues 0.5117 0.3036 0.12125 0.14267 250s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 250s Decorana values 0.5360 0.2869 0.08136 0.04814 250s Axis lengths 3.7004 3.1166 1.30055 1.47888 250s 250s 250s > ord <- metaMDS(dune) 250s Run 0 stress 0.1192678 250s Run 1 stress 0.1183186 250s ... New best solution 250s ... Procrustes: rmse 0.02027015 max resid 0.06496105 250s Run 2 stress 0.1183186 250s ... Procrustes: rmse 3.339011e-06 max resid 8.202787e-06 250s ... Similar to previous best 250s Run 3 stress 0.1183186 250s ... Procrustes: rmse 1.125032e-05 max resid 3.740691e-05 250s ... Similar to previous best 250s Run 4 stress 0.1183186 250s ... Procrustes: rmse 1.783048e-05 max resid 5.89955e-05 250s ... Similar to previous best 250s Run 5 stress 0.1183186 250s ... Procrustes: rmse 7.810942e-06 max resid 2.733103e-05 250s ... Similar to previous best 250s Run 6 stress 0.1192678 250s Run 7 stress 0.1183186 250s ... Procrustes: rmse 3.80979e-06 max resid 1.090851e-05 250s ... Similar to previous best 250s Run 8 stress 0.1808911 250s Run 9 stress 0.1192678 250s Run 10 stress 0.1183186 250s ... Procrustes: rmse 2.299342e-05 max resid 7.202725e-05 250s ... Similar to previous best 250s Run 11 stress 0.1901489 250s Run 12 stress 0.1192678 250s Run 13 stress 0.1192678 250s Run 14 stress 0.1183186 250s ... Procrustes: rmse 2.681e-06 max resid 6.929722e-06 250s ... Similar to previous best 250s Run 15 stress 0.1183186 250s ... Procrustes: rmse 3.335787e-06 max resid 1.07942e-05 250s ... Similar to previous best 250s Run 16 stress 0.1808911 250s Run 17 stress 0.1192678 250s Run 18 stress 0.1809577 250s Run 19 stress 0.1183186 250s ... Procrustes: rmse 1.444978e-05 max resid 4.520106e-05 250s ... Similar to previous best 250s Run 20 stress 0.1192679 250s *** Best solution repeated 9 times 250s 250s > ord 250s 250s Call: 250s metaMDS(comm = dune) 250s 250s global Multidimensional Scaling using monoMDS 250s 250s Data: dune 250s Distance: bray 250s 250s Dimensions: 2 250s Stress: 0.1183186 250s Stress type 1, weak ties 250s Best solution was repeated 9 times in 20 tries 250s The best solution was from try 1 (random start) 250s Scaling: centring, PC rotation, halfchange scaling 250s Species: expanded scores based on ‘dune’ 250s 250s 250s > plot(ord) 250s 250s > plot(ord) 250s 250s > plot(ord, type = "n") 250s 250s > points(ord, display = "sites", cex = 0.8, pch = 21, 250s + col = "red", bg = "yellow") 250s 250s > text(ord, display = "spec", cex = 0.7, col = "blue") 250s 250s > plot(ord, type = "n") 250s 250s > points(ord, display = "sites", cex = 0.8, pch = 21, 250s + col = "red", bg = "yellow") 250s 250s > text(ord, display = "spec", cex = 0.7, col = "blue") 250s 250s > data(dune.env) 250s 250s > attach(dune.env) 250s 250s > plot(ord, disp = "sites", type = "n") 250s 250s > ordihull(ord, Management, col = 1:4, lwd = 3) 250s 250s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 250s + lwd = 3) 250s 250s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 250s 250s > ordispider(ord, Management, col = 1:4, label = TRUE) 250s 250s > points(ord, disp = "sites", pch = 21, col = "red", 250s + bg = "yellow", cex = 1.3) 250s 250s > plot(ord, disp = "sites", type = "n") 250s 250s > ordihull(ord, Management, col = 1:4, lwd = 3) 250s 250s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 250s + lwd = 3) 250s 250s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 250s 250s > ordispider(ord, Management, col = 1:4, label = TRUE) 250s 250s > points(ord, disp = "sites", pch = 21, col = "red", 250s + bg = "yellow", cex = 1.3) 250s 250s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 250s + perm = 999) 250s 250s > ord.fit 250s 250s ***VECTORS 250s 250s NMDS1 NMDS2 r2 Pr(>r) 250s A1 0.96473 0.26323 0.3649 0.018 * 250s --- 250s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 250s Permutation: free 250s Number of permutations: 999 250s 250s ***FACTORS: 250s 250s Centroids: 250s NMDS1 NMDS2 250s ManagementBF -0.4534 -0.0102 250s ManagementHF -0.2636 -0.1282 250s ManagementNM 0.2958 0.5790 250s ManagementSF 0.1506 -0.4670 250s 250s Goodness of fit: 250s r2 Pr(>r) 250s Management 0.4134 0.007 ** 250s --- 250s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 250s Permutation: free 250s Number of permutations: 999 250s 250s 250s 250s > plot(ord, dis = "site") 250s 250s > plot(ord.fit) 250s 250s > ordisurf(ord, A1, add = TRUE) 250s 250s Family: gaussian 250s Link function: identity 250s 250s Formula: 250s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 250s 250s Estimated degrees of freedom: 250s 1.59 total = 2.59 250s 250s REML score: 41.58727 250s 250s > plot(ord, dis = "site") 250s 250s > plot(ord.fit) 250s 250s > ordisurf(ord, A1, add = TRUE) 250s 250s Family: gaussian 250s Link function: identity 250s 250s Formula: 250s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 250s 250s Estimated degrees of freedom: 250s 1.59 total = 2.59 250s 250s REML score: 41.58727 250s 250s > ord <- cca(dune ~ A1 + Management, data = dune.env) 250s 250s > ord 250s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 250s 250s Inertia Proportion Rank 250s Total 2.1153 1.0000 250s Constrained 0.7798 0.3686 4 250s Unconstrained 1.3355 0.6314 15 250s Inertia is scaled Chi-square 250s 250s Eigenvalues for constrained axes: 250s CCA1 CCA2 CCA3 CCA4 250s 0.3187 0.2372 0.1322 0.0917 250s 250s Eigenvalues for unconstrained axes: 250s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 250s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 250s CA11 CA12 CA13 CA14 CA15 250s 0.0317 0.0178 0.0116 0.0087 0.0047 250s 250s 250s > plot(ord) 250s 250s > plot(ord) 250s 250s > cca(dune ~ ., data = dune.env) 250s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 250s Manure, data = dune.env) 250s 250s Inertia Proportion Rank 250s Total 2.1153 1.0000 250s Constrained 1.5032 0.7106 12 250s Unconstrained 0.6121 0.2894 7 250s Inertia is scaled Chi-square 250s Some constraints or conditions were aliased because they were redundant 250s 250s Eigenvalues for constrained axes: 250s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 250s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 250s CCA11 CCA12 250s 0.0228 0.0108 250s 250s Eigenvalues for unconstrained axes: 250s CA1 CA2 CA3 CA4 CA5 CA6 CA7 250s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 250s 250s 250s > anova(ord) 250s Permutation test for cca under reduced model 250s Permutation: free 250s Number of permutations: 999 250s 250s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 250s Df ChiSquare F Pr(>F) 250s Model 4 0.77978 2.1896 0.001 *** 250s Residual 15 1.33549 250s --- 250s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 250s 250s > anova(ord, by = "term", permutations = 199) 250s Permutation test for cca under reduced model 250s Terms added sequentially (first to last) 250s Permutation: free 250s Number of permutations: 199 250s 250s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 250s Df ChiSquare F Pr(>F) 250s A1 1 0.22476 2.5245 0.015 * 250s Management 3 0.55502 2.0780 0.010 ** 250s Residual 15 1.33549 250s --- 250s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 250s 250s > anova(ord, by = "mar", permutations = 199) 250s Permutation test for cca under reduced model 250s Marginal effects of terms 250s Permutation: free 250s Number of permutations: 199 250s 250s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 250s Df ChiSquare F Pr(>F) 250s A1 1 0.17594 1.9761 0.040 * 250s Management 3 0.55502 2.0780 0.005 ** 250s Residual 15 1.33549 250s --- 250s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 250s 250s > anova(ord, by = "axis", permutations = 499) 250s Permutation test for cca under reduced model 250s Forward tests for axes 250s Permutation: free 250s Number of permutations: 499 250s 250s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 250s Df ChiSquare F Pr(>F) 250s CCA1 1 0.31875 3.5801 0.006 ** 250s CCA2 1 0.23718 2.6640 0.058 . 250s CCA3 1 0.13217 1.4845 0.294 250s CCA4 1 0.09168 1.0297 0.396 250s Residual 15 1.33549 250s --- 250s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 250s 250s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 250s + data = dune.env) 250s 250s > ord 250s Call: cca(formula = dune ~ A1 + Management + 250s Condition(Moisture), data = dune.env) 250s 250s Inertia Proportion Rank 250s Total 2.1153 1.0000 250s Conditional 0.6283 0.2970 3 250s Constrained 0.5109 0.2415 4 250s Unconstrained 0.9761 0.4615 12 250s Inertia is scaled Chi-square 250s 250s Eigenvalues for constrained axes: 250s CCA1 CCA2 CCA3 CCA4 250s 0.24932 0.12090 0.08160 0.05904 250s 250s Eigenvalues for unconstrained axes: 250s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 250s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 250s CA10 CA11 CA12 250s 0.02102 0.01254 0.00928 250s 250s 250s > anova(ord, by = "term", permutations = 499) 250s Permutation test for cca under reduced model 250s Terms added sequentially (first to last) 250s Permutation: free 250s Number of permutations: 499 250s 250s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 250s Df ChiSquare F Pr(>F) 250s A1 1 0.11543 1.4190 0.142 250s Management 3 0.39543 1.6205 0.036 * 250s Residual 12 0.97610 250s --- 250s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 250s 250s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 250s 250s > anova(ord, by = "term", permutations = how) 251s Permutation test for cca under reduced model 251s Terms added sequentially (first to last) 251s Plots: dune.env$Moisture, plot permutation: none 251s Permutation: free 251s Number of permutations: 499 251s 251s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 251s Df ChiSquare F Pr(>F) 251s A1 1 0.11543 1.4190 0.274 251s Management 3 0.39543 1.6205 0.008 ** 251s Residual 12 0.97610 251s --- 251s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 251s 251s > detach(dune.env) 251s > 251s 251s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 251s Copyright (C) 2024 The R Foundation for Statistical Computing 251s Platform: aarch64-unknown-linux-gnu (64-bit) 251s 251s R is free software and comes with ABSOLUTELY NO WARRANTY. 251s You are welcome to redistribute it under certain conditions. 251s Type 'license()' or 'licence()' for distribution details. 251s 251s R is a collaborative project with many contributors. 251s Type 'contributors()' for more information and 251s 'citation()' on how to cite R or R packages in publications. 251s 251s Type 'demo()' for some demos, 'help()' for on-line help, or 251s 'help.start()' for an HTML browser interface to help. 251s Type 'q()' to quit R. 251s 251s > Stangle("partitioning.Rnw") 251s Writing to file partitioning.R 251s > source("partitioning.R", echo=TRUE) 251s 251s > par(mfrow = c(1, 1)) 251s 251s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 251s 251s > options(SweaveHooks = list(fig = figset)) 251s 251s > library(vegan) 251s Loading required package: permute 251s Loading required package: lattice 252s This is vegan 2.6-4 252s 252s > labs <- paste("Table", 1:4) 252s 252s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 252s 252s > showvarparts(2, bg = cls, Xnames = labs) 252s 252s > showvarparts(3, bg = cls, Xnames = labs) 252s 252s > showvarparts(4, bg = cls, Xnames = labs) 252s > 260s Test cca-object-tests passed 261s Test oecosimu-tests passed 264s Test vegan-tests passed 265s autopkgtest [20:39:21]: test run-unit-test: -----------------------] 265s autopkgtest [20:39:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 265s run-unit-test PASS 266s autopkgtest [20:39:22]: test pkg-r-autopkgtest: preparing testbed 267s Reading package lists... 267s Building dependency tree... 267s Reading state information... 268s Starting pkgProblemResolver with broken count: 0 268s Starting 2 pkgProblemResolver with broken count: 0 268s Done 268s The following additional packages will be installed: 268s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 268s dctrl-tools fonts-glyphicons-halflings fonts-mathjax g++ g++-13 268s g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 268s gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-13 268s gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 268s libasan8 libatomic1 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 268s libcrypt-dev libgcc-13-dev libgfortran-13-dev libhwasan0 libicu-dev libisl23 268s libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev libjs-bootstrap 268s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 268s liblapack-dev liblsan0 liblzma-dev libmpc3 libncurses-dev libnsl-dev 268s libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 268s libpng-dev libreadline-dev libstdc++-13-dev libtirpc-dev libtsan2 libubsan1 268s linux-libc-dev node-normalize.css pkg-config pkg-r-autopkgtest pkgconf 268s pkgconf-bin r-base-dev r-cran-commonmark r-cran-evaluate r-cran-highr 268s r-cran-knitr r-cran-markdown r-cran-xfun r-cran-yaml rpcsvc-proto zlib1g-dev 268s Suggested packages: 268s cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib 268s manpages-dev autoconf automake libtool flex bison gdb gcc-doc 268s gdb-aarch64-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev 268s liblapack-doc glibc-doc icu-doc fonts-mathjax-extras fonts-stix 268s libjs-mathjax-doc liblzma-doc ncurses-doc readline-doc libstdc++-13-doc 268s libjs-html5shiv texlive-base texlive-latex-base texlive-plain-generic 268s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils 268s texlive-latex-recommended texlive-latex-extra texinfo 268s Recommended packages: 268s bzip2-doc manpages manpages-dev libc-devtools javascript-common libpng-tools 268s r-cran-curl r-cran-testthat r-cran-xml2 r-cran-covr r-cran-ggplot2 268s r-cran-rlang r-cran-withr r-cran-testit r-cran-bslib r-cran-codetools 268s r-cran-dbi r-cran-digest r-cran-formatr r-cran-gridsvg r-cran-htmlwidgets 268s r-cran-jpeg r-cran-magick r-cran-png r-cran-ragg r-cran-reticulate 268s r-cran-rgl r-cran-rmarkdown r-cran-sass r-cran-tibble r-cran-tikzdevice 268s r-cran-tinytex r-cran-webshot r-cran-rstudioapi r-cran-svglite 268s node-highlight.js r-cran-rcurl r-cran-mime r-cran-htmltools r-cran-remotes 268s r-cran-renv r-cran-jsonlite r-cran-runit 268s The following NEW packages will be installed: 268s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu 268s cpp-aarch64-linux-gnu dctrl-tools fonts-glyphicons-halflings fonts-mathjax 268s g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 268s gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-13 268s gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 268s libasan8 libatomic1 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 268s libcrypt-dev libgcc-13-dev libgfortran-13-dev libhwasan0 libicu-dev libisl23 268s libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev libjs-bootstrap 268s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 268s liblapack-dev liblsan0 liblzma-dev libmpc3 libncurses-dev libnsl-dev 268s libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 268s libpng-dev libreadline-dev libstdc++-13-dev libtirpc-dev libtsan2 libubsan1 268s linux-libc-dev node-normalize.css pkg-config pkg-r-autopkgtest pkgconf 268s pkgconf-bin r-base-dev r-cran-commonmark r-cran-evaluate r-cran-highr 268s r-cran-knitr r-cran-markdown r-cran-xfun r-cran-yaml rpcsvc-proto zlib1g-dev 268s 0 upgraded, 77 newly installed, 0 to remove and 0 not upgraded. 268s Need to get 104 MB/104 MB of archives. 268s After this operation, 399 MB of additional disk space will be used. 268s Get:1 /tmp/autopkgtest.9uXNFN/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [732 B] 269s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 269s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 269s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 269s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1 [201 kB] 269s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 269s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 269s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 269s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 269s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 269s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 270s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 270s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 270s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 270s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 270s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 270s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 270s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 270s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 270s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 270s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 270s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 270s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 270s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 271s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 271s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 271s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 271s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 271s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 271s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 271s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 271s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 271s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 271s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 dctrl-tools arm64 2.24-3build2 [65.2 kB] 271s Get:35 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 271s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 271s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-17ubuntu2 [478 kB] 271s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.8 MB] 271s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-17ubuntu2 [10.3 kB] 271s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1022 B] 271s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B] 271s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB] 271s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB] 271s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 271s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB] 272s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu1 [304 kB] 272s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 272s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 272s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 272s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 272s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 272s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 272s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB] 272s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses-dev arm64 6.4+20240113-1ubuntu1 [385 kB] 272s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu1 [195 kB] 272s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu1 [183 kB] 272s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-posix3 arm64 10.42-4ubuntu1 [6654 B] 272s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-dev arm64 10.42-4ubuntu1 [679 kB] 272s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB] 272s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 272s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng-dev arm64 1.6.43-3 [267 kB] 272s Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline-dev arm64 8.2-3.1 [177 kB] 272s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB] 272s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB] 272s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] 272s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B] 272s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB] 272s Get:68 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-dev all 4.3.3-2build1 [4334 B] 272s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 272s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-commonmark arm64 1.9.1-1 [127 kB] 272s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-evaluate all 0.23-1 [90.2 kB] 272s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xfun arm64 0.41+dfsg-1 [415 kB] 272s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-highr all 0.10+dfsg-1 [38.3 kB] 272s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-yaml arm64 2.3.8-1 [107 kB] 272s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 272s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-knitr all 1.45+dfsg-1 [917 kB] 272s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-markdown all 1.12+dfsg-1 [179 kB] 273s Fetched 104 MB in 4s (26.9 MB/s) 273s Selecting previously unselected package libc-dev-bin. 273s (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 ... 77384 files and directories currently installed.) 273s Preparing to unpack .../00-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 273s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 273s Selecting previously unselected package linux-libc-dev:arm64. 273s Preparing to unpack .../01-linux-libc-dev_6.8.0-11.11_arm64.deb ... 273s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 273s Selecting previously unselected package libcrypt-dev:arm64. 273s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 273s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 273s Selecting previously unselected package libtirpc-dev:arm64. 273s Preparing to unpack .../03-libtirpc-dev_1.3.4+ds-1.1_arm64.deb ... 273s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 273s Selecting previously unselected package libnsl-dev:arm64. 273s Preparing to unpack .../04-libnsl-dev_1.3.0-3_arm64.deb ... 273s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 273s Selecting previously unselected package rpcsvc-proto. 273s Preparing to unpack .../05-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 273s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 273s Selecting previously unselected package libc6-dev:arm64. 273s Preparing to unpack .../06-libc6-dev_2.39-0ubuntu2_arm64.deb ... 273s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 273s Selecting previously unselected package libisl23:arm64. 273s Preparing to unpack .../07-libisl23_0.26-3_arm64.deb ... 273s Unpacking libisl23:arm64 (0.26-3) ... 273s Selecting previously unselected package libmpc3:arm64. 273s Preparing to unpack .../08-libmpc3_1.3.1-1_arm64.deb ... 273s Unpacking libmpc3:arm64 (1.3.1-1) ... 273s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 273s Preparing to unpack .../09-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 273s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 274s Selecting previously unselected package cpp-13. 274s Preparing to unpack .../10-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 274s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 274s Selecting previously unselected package cpp-aarch64-linux-gnu. 274s Preparing to unpack .../11-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 274s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 274s Selecting previously unselected package cpp. 274s Preparing to unpack .../12-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 274s Unpacking cpp (4:13.2.0-7ubuntu1) ... 274s Selecting previously unselected package libcc1-0:arm64. 274s Preparing to unpack .../13-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 274s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 274s Selecting previously unselected package libitm1:arm64. 274s Preparing to unpack .../14-libitm1_14-20240303-1ubuntu1_arm64.deb ... 274s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 274s Selecting previously unselected package libatomic1:arm64. 274s Preparing to unpack .../15-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 274s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 274s Selecting previously unselected package libasan8:arm64. 274s Preparing to unpack .../16-libasan8_14-20240303-1ubuntu1_arm64.deb ... 274s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 274s Selecting previously unselected package liblsan0:arm64. 274s Preparing to unpack .../17-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 274s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 274s Selecting previously unselected package libtsan2:arm64. 274s Preparing to unpack .../18-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 274s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 274s Selecting previously unselected package libubsan1:arm64. 274s Preparing to unpack .../19-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 274s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 274s Selecting previously unselected package libhwasan0:arm64. 274s Preparing to unpack .../20-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 274s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 274s Selecting previously unselected package libgcc-13-dev:arm64. 274s Preparing to unpack .../21-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 274s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 274s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 274s Preparing to unpack .../22-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 274s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 275s Selecting previously unselected package gcc-13. 275s Preparing to unpack .../23-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 275s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 275s Selecting previously unselected package gcc-aarch64-linux-gnu. 275s Preparing to unpack .../24-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 275s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 275s Selecting previously unselected package gcc. 275s Preparing to unpack .../25-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 275s Unpacking gcc (4:13.2.0-7ubuntu1) ... 275s Selecting previously unselected package libstdc++-13-dev:arm64. 275s Preparing to unpack .../26-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 275s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 275s Selecting previously unselected package g++-13-aarch64-linux-gnu. 275s Preparing to unpack .../27-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 275s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 275s Selecting previously unselected package g++-13. 275s Preparing to unpack .../28-g++-13_13.2.0-17ubuntu2_arm64.deb ... 275s Unpacking g++-13 (13.2.0-17ubuntu2) ... 275s Selecting previously unselected package g++-aarch64-linux-gnu. 275s Preparing to unpack .../29-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 275s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 275s Selecting previously unselected package g++. 275s Preparing to unpack .../30-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 275s Unpacking g++ (4:13.2.0-7ubuntu1) ... 275s Selecting previously unselected package build-essential. 275s Preparing to unpack .../31-build-essential_12.10ubuntu1_arm64.deb ... 275s Unpacking build-essential (12.10ubuntu1) ... 275s Selecting previously unselected package dctrl-tools. 275s Preparing to unpack .../32-dctrl-tools_2.24-3build2_arm64.deb ... 275s Unpacking dctrl-tools (2.24-3build2) ... 275s Selecting previously unselected package fonts-glyphicons-halflings. 275s Preparing to unpack .../33-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 275s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 275s Selecting previously unselected package fonts-mathjax. 275s Preparing to unpack .../34-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 275s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 275s Selecting previously unselected package libgfortran-13-dev:arm64. 275s Preparing to unpack .../35-libgfortran-13-dev_13.2.0-17ubuntu2_arm64.deb ... 275s Unpacking libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 275s Selecting previously unselected package gfortran-13-aarch64-linux-gnu. 275s Preparing to unpack .../36-gfortran-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 275s Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 276s Selecting previously unselected package gfortran-13. 276s Preparing to unpack .../37-gfortran-13_13.2.0-17ubuntu2_arm64.deb ... 276s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 276s Selecting previously unselected package gfortran-aarch64-linux-gnu. 276s Preparing to unpack .../38-gfortran-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 276s Unpacking gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 276s Selecting previously unselected package gfortran. 276s Preparing to unpack .../39-gfortran_4%3a13.2.0-7ubuntu1_arm64.deb ... 276s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 276s Selecting previously unselected package icu-devtools. 276s Preparing to unpack .../40-icu-devtools_74.2-1ubuntu1_arm64.deb ... 276s Unpacking icu-devtools (74.2-1ubuntu1) ... 276s Selecting previously unselected package libblas-dev:arm64. 276s Preparing to unpack .../41-libblas-dev_3.12.0-3_arm64.deb ... 276s Unpacking libblas-dev:arm64 (3.12.0-3) ... 276s Selecting previously unselected package libbz2-dev:arm64. 276s Preparing to unpack .../42-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 276s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 276s Selecting previously unselected package libicu-dev:arm64. 276s Preparing to unpack .../43-libicu-dev_74.2-1ubuntu1_arm64.deb ... 276s Unpacking libicu-dev:arm64 (74.2-1ubuntu1) ... 276s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 276s Preparing to unpack .../44-libjpeg-turbo8-dev_2.1.5-2ubuntu1_arm64.deb ... 276s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 276s Selecting previously unselected package libjpeg8-dev:arm64. 276s Preparing to unpack .../45-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 276s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 276s Selecting previously unselected package libjpeg-dev:arm64. 276s Preparing to unpack .../46-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 276s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 276s Selecting previously unselected package libjs-bootstrap. 276s Preparing to unpack .../47-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 276s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 276s Selecting previously unselected package libjs-highlight.js. 276s Preparing to unpack .../48-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 276s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 276s Selecting previously unselected package libjs-jquery. 276s Preparing to unpack .../49-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 276s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 276s Selecting previously unselected package libjs-jquery-datatables. 276s Preparing to unpack .../50-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 276s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 276s Selecting previously unselected package liblapack-dev:arm64. 276s Preparing to unpack .../51-liblapack-dev_3.12.0-3_arm64.deb ... 276s Unpacking liblapack-dev:arm64 (3.12.0-3) ... 277s Selecting previously unselected package libncurses-dev:arm64. 277s Preparing to unpack .../52-libncurses-dev_6.4+20240113-1ubuntu1_arm64.deb ... 277s Unpacking libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 277s Selecting previously unselected package libpcre2-16-0:arm64. 277s Preparing to unpack .../53-libpcre2-16-0_10.42-4ubuntu1_arm64.deb ... 277s Unpacking libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 277s Selecting previously unselected package libpcre2-32-0:arm64. 277s Preparing to unpack .../54-libpcre2-32-0_10.42-4ubuntu1_arm64.deb ... 277s Unpacking libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 277s Selecting previously unselected package libpcre2-posix3:arm64. 277s Preparing to unpack .../55-libpcre2-posix3_10.42-4ubuntu1_arm64.deb ... 277s Unpacking libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 277s Selecting previously unselected package libpcre2-dev:arm64. 277s Preparing to unpack .../56-libpcre2-dev_10.42-4ubuntu1_arm64.deb ... 277s Unpacking libpcre2-dev:arm64 (10.42-4ubuntu1) ... 277s Selecting previously unselected package libpkgconf3:arm64. 277s Preparing to unpack .../57-libpkgconf3_1.8.1-2_arm64.deb ... 277s Unpacking libpkgconf3:arm64 (1.8.1-2) ... 277s Selecting previously unselected package zlib1g-dev:arm64. 277s Preparing to unpack .../58-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 277s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 277s Selecting previously unselected package libpng-dev:arm64. 277s Preparing to unpack .../59-libpng-dev_1.6.43-3_arm64.deb ... 277s Unpacking libpng-dev:arm64 (1.6.43-3) ... 277s Selecting previously unselected package libreadline-dev:arm64. 277s Preparing to unpack .../60-libreadline-dev_8.2-3.1_arm64.deb ... 277s Unpacking libreadline-dev:arm64 (8.2-3.1) ... 277s Selecting previously unselected package node-normalize.css. 277s Preparing to unpack .../61-node-normalize.css_8.0.1-5_all.deb ... 277s Unpacking node-normalize.css (8.0.1-5) ... 277s Selecting previously unselected package pkgconf-bin. 277s Preparing to unpack .../62-pkgconf-bin_1.8.1-2_arm64.deb ... 277s Unpacking pkgconf-bin (1.8.1-2) ... 277s Selecting previously unselected package pkgconf:arm64. 277s Preparing to unpack .../63-pkgconf_1.8.1-2_arm64.deb ... 277s Unpacking pkgconf:arm64 (1.8.1-2) ... 277s Selecting previously unselected package pkg-config:arm64. 277s Preparing to unpack .../64-pkg-config_1.8.1-2_arm64.deb ... 277s Unpacking pkg-config:arm64 (1.8.1-2) ... 277s Selecting previously unselected package liblzma-dev:arm64. 277s Preparing to unpack .../65-liblzma-dev_5.4.5-0.3_arm64.deb ... 277s Unpacking liblzma-dev:arm64 (5.4.5-0.3) ... 277s Selecting previously unselected package r-base-dev. 277s Preparing to unpack .../66-r-base-dev_4.3.3-2build1_all.deb ... 277s Unpacking r-base-dev (4.3.3-2build1) ... 277s Selecting previously unselected package pkg-r-autopkgtest. 277s Preparing to unpack .../67-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 277s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 277s Selecting previously unselected package r-cran-commonmark. 277s Preparing to unpack .../68-r-cran-commonmark_1.9.1-1_arm64.deb ... 277s Unpacking r-cran-commonmark (1.9.1-1) ... 277s Selecting previously unselected package r-cran-evaluate. 277s Preparing to unpack .../69-r-cran-evaluate_0.23-1_all.deb ... 277s Unpacking r-cran-evaluate (0.23-1) ... 277s Selecting previously unselected package r-cran-xfun. 277s Preparing to unpack .../70-r-cran-xfun_0.41+dfsg-1_arm64.deb ... 277s Unpacking r-cran-xfun (0.41+dfsg-1) ... 278s Selecting previously unselected package r-cran-highr. 278s Preparing to unpack .../71-r-cran-highr_0.10+dfsg-1_all.deb ... 278s Unpacking r-cran-highr (0.10+dfsg-1) ... 278s Selecting previously unselected package r-cran-yaml. 278s Preparing to unpack .../72-r-cran-yaml_2.3.8-1_arm64.deb ... 278s Unpacking r-cran-yaml (2.3.8-1) ... 278s Selecting previously unselected package libjs-mathjax. 278s Preparing to unpack .../73-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 278s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 278s Selecting previously unselected package r-cran-knitr. 278s Preparing to unpack .../74-r-cran-knitr_1.45+dfsg-1_all.deb ... 278s Unpacking r-cran-knitr (1.45+dfsg-1) ... 278s Selecting previously unselected package r-cran-markdown. 278s Preparing to unpack .../75-r-cran-markdown_1.12+dfsg-1_all.deb ... 278s Unpacking r-cran-markdown (1.12+dfsg-1) ... 278s Selecting previously unselected package autopkgtest-satdep. 278s Preparing to unpack .../76-2-autopkgtest-satdep.deb ... 278s Unpacking autopkgtest-satdep (0) ... 278s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 278s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 278s Setting up r-cran-xfun (0.41+dfsg-1) ... 278s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 278s Setting up r-cran-yaml (2.3.8-1) ... 278s Setting up r-cran-evaluate (0.23-1) ... 278s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 278s Setting up libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 278s Setting up libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 278s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 278s Setting up libpkgconf3:arm64 (1.8.1-2) ... 278s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 278s Setting up libmpc3:arm64 (1.3.1-1) ... 278s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 278s Setting up icu-devtools (74.2-1ubuntu1) ... 278s Setting up pkgconf-bin (1.8.1-2) ... 278s Setting up liblzma-dev:arm64 (5.4.5-0.3) ... 278s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 278s Setting up libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 278s Setting up libjs-highlight.js (9.18.5+dfsg1-2) ... 278s Setting up libnsl-dev:arm64 (1.3.0-3) ... 278s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 278s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 278s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 278s Setting up r-cran-commonmark (1.9.1-1) ... 278s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 278s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 278s Setting up libisl23:arm64 (0.26-3) ... 278s Setting up libc-dev-bin (2.39-0ubuntu2) ... 278s Setting up node-normalize.css (8.0.1-5) ... 278s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 278s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 278s Setting up libblas-dev:arm64 (3.12.0-3) ... 278s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide 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Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 278s Setting up gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 278s Setting up gcc (4:13.2.0-7ubuntu1) ... 278s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 278s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 278s Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 278s Setting up gfortran (4:13.2.0-7ubuntu1) ... 278s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 278s 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 278s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 278s 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 278s Setting up g++ (4:13.2.0-7ubuntu1) ... 278s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 278s Setting up build-essential (12.10ubuntu1) ... 278s Setting up r-base-dev (4.3.3-2build1) ... 278s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 278s Setting up autopkgtest-satdep (0) ... 278s Processing triggers for man-db (2.12.0-3) ... 279s Processing triggers for install-info (7.1-3) ... 279s Processing triggers for fontconfig (2.15.0-1ubuntu1) ... 279s Processing triggers for libc-bin (2.39-0ubuntu2) ... 282s (Reading database ... 86120 files and directories currently installed.) 282s Removing autopkgtest-satdep (0) ... 283s autopkgtest [20:39:39]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 283s autopkgtest [20:39:39]: test pkg-r-autopkgtest: [----------------------- 283s Test: Try to load the R library vegan 283s 283s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 283s Copyright (C) 2024 The R Foundation for Statistical Computing 283s Platform: aarch64-unknown-linux-gnu (64-bit) 283s 283s R is free software and comes with ABSOLUTELY NO WARRANTY. 283s You are welcome to redistribute it under certain conditions. 283s Type 'license()' or 'licence()' for distribution details. 283s 283s R is a collaborative project with many contributors. 283s Type 'contributors()' for more information and 283s 'citation()' on how to cite R or R packages in publications. 283s 283s Type 'demo()' for some demos, 'help()' for on-line help, or 283s 'help.start()' for an HTML browser interface to help. 283s Type 'q()' to quit R. 283s 283s > library('vegan') 283s Loading required package: permute 283s Loading required package: lattice 284s This is vegan 2.6-4 284s > 284s > 284s Other tests are currently unsupported! 284s They will be progressively added. 285s autopkgtest [20:39:41]: test pkg-r-autopkgtest: -----------------------] 285s pkg-r-autopkgtest PASS 285s autopkgtest [20:39:41]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 286s autopkgtest [20:39:42]: @@@@@@@@@@@@@@@@@@@@ summary 286s run-unit-test PASS 286s pkg-r-autopkgtest PASS 297s Creating nova instance adt-noble-arm64-r-cran-vegan-20240316-203456-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...