0s autopkgtest [17:50:10]: starting date and time: 2024-03-16 17:50:10+0000 0s autopkgtest [17:50:10]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:50:10]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.v6xiyi9c/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-ape --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-arm64-2.secgroup --name adt-noble-arm64-r-cran-ape-20240316-175010-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/ 116s autopkgtest [17:52:06]: testbed dpkg architecture: arm64 116s autopkgtest [17:52:06]: testbed apt version: 2.7.12 116s autopkgtest [17:52:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 117s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 117s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [473 kB] 117s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 117s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 117s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3670 kB] 117s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 117s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 117s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 117s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 117s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3995 kB] 117s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 117s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 117s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 119s Fetched 9060 kB in 2s (5587 kB/s) 119s Reading package lists... 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 123s Calculating upgrade... 124s The following packages will be REMOVED: 124s libglib2.0-0 libssl3 124s The following NEW packages will be installed: 124s libglib2.0-0t64 libssl3t64 xdg-user-dirs 124s The following packages have been kept back: 124s curl 124s The following packages will be upgraded: 124s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 124s ubuntu-minimal ubuntu-standard 124s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 124s Need to get 4613 kB of archives. 124s After this operation, 211 kB of additional disk space will be used. 124s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 124s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 125s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 125s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 125s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 125s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 125s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 125s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 125s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 125s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 126s Fetched 4613 kB in 1s (6266 kB/s) 126s (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.) 126s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 126s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 127s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 127s udisks2 depends on libglib2.0-0 (>= 2.77.0). 127s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 127s python3-gi depends on libglib2.0-0 (>= 2.77.0). 127s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 127s netplan.io depends on libglib2.0-0 (>= 2.70.0). 127s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 127s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 127s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 127s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 127s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 127s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 127s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 127s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 127s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 127s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 127s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 127s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 127s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 127s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 127s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 127s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 127s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 127s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 127s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 127s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 127s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 127s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 127s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 127s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 127s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 127s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 127s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 127s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 127s fwupd depends on libglib2.0-0 (>= 2.79.0). 127s bolt depends on libglib2.0-0 (>= 2.56.0). 127s 127s (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.) 127s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 127s Selecting previously unselected package libglib2.0-0t64:arm64. 127s (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.) 127s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 127s 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... 127s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 127s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 127s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 127s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 127s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 127s wget depends on libssl3 (>= 3.0.0). 127s u-boot-tools depends on libssl3 (>= 3.0.0). 127s tnftp depends on libssl3 (>= 3.0.0). 127s tcpdump depends on libssl3 (>= 3.0.0). 127s systemd-resolved depends on libssl3 (>= 3.0.0). 127s systemd depends on libssl3 (>= 3.0.0). 127s sudo depends on libssl3 (>= 3.0.0). 127s sbsigntool depends on libssl3 (>= 3.0.0). 127s rsync depends on libssl3 (>= 3.0.0). 127s python3-cryptography depends on libssl3 (>= 3.0.0). 127s openssh-server depends on libssl3 (>= 3.0.10). 127s openssh-client depends on libssl3 (>= 3.0.10). 127s mtd-utils depends on libssl3 (>= 3.0.0). 127s mokutil depends on libssl3 (>= 3.0.0). 127s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 127s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 127s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 127s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 127s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 127s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 127s libnvme1 depends on libssl3 (>= 3.0.0). 127s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 127s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 127s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 127s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 127s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 127s kmod depends on libssl3 (>= 3.0.0). 127s dhcpcd-base depends on libssl3 (>= 3.0.0). 127s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 127s 127s (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.) 127s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 127s Selecting previously unselected package libssl3t64:arm64. 127s (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.) 127s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 127s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 128s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 128s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 128s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ... 128s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 128s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ... 128s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 128s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ... 128s Unpacking ubuntu-minimal (1.536) over (1.535) ... 128s Selecting previously unselected package xdg-user-dirs. 128s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ... 128s Unpacking xdg-user-dirs (0.18-1) ... 128s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ... 128s Unpacking ubuntu-standard (1.536) over (1.535) ... 128s Setting up ubuntu-minimal (1.536) ... 128s Setting up xdg-user-dirs (0.18-1) ... 128s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 128s Setting up libtirpc-common (1.3.4+ds-1.1) ... 128s Setting up ubuntu-standard (1.536) ... 128s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 128s No schema files found: doing nothing. 128s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 128s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 128s Setting up openssl (3.0.13-0ubuntu1) ... 128s Setting up readline-common (8.2-3.1) ... 128s Processing triggers for man-db (2.12.0-3) ... 129s Processing triggers for install-info (7.1-3) ... 129s Processing triggers for libc-bin (2.39-0ubuntu2) ... 129s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 131s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 131s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 131s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 131s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 132s Reading package lists... 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s Calculating upgrade... 134s The following packages have been kept back: 134s curl 134s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 134s Reading package lists... 135s Building dependency tree... 135s Reading state information... 135s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 138s autopkgtest [17:52:28]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 139s autopkgtest [17:52:29]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-ape 141s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-ape 5.7-1-1 (dsc) [2114 B] 141s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-ape 5.7-1-1 (tar) [1577 kB] 141s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-ape 5.7-1-1 (diff) [5536 B] 141s gpgv: Signature made Fri Jun 9 19:08:51 2023 UTC 141s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 141s gpgv: issuer "tille@debian.org" 141s gpgv: Can't check signature: No public key 141s dpkg-source: warning: cannot verify inline signature for ./r-cran-ape_5.7-1-1.dsc: no acceptable signature found 141s autopkgtest [17:52:31]: testing package r-cran-ape version 5.7-1-1 142s autopkgtest [17:52:32]: build not needed 143s autopkgtest [17:52:33]: test run-unit-test: preparing testbed 145s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s Starting pkgProblemResolver with broken count: 0 146s Starting 2 pkgProblemResolver with broken count: 0 146s Done 147s The following additional packages will be installed: 147s curl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 147s libblas3 libcairo2 libcurl4t64 libdatrie1 libdeflate0 libfontconfig1 147s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 147s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 147s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 147s libpng16-16t64 libpsl5t64 libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 147s libthai-data libthai0 libtiff6 libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 147s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler r-base-core 147s r-cran-ape r-cran-cli r-cran-cpp11 r-cran-digest r-cran-fastmatch 147s r-cran-generics r-cran-glue r-cran-igraph r-cran-lattice r-cran-lifecycle 147s r-cran-littler r-cran-magrittr r-cran-matrix r-cran-nlme r-cran-phangorn 147s r-cran-pkgconfig r-cran-pkgkitten r-cran-quadprog r-cran-rcpp r-cran-rlang 147s unzip x11-common xdg-utils zip 147s Suggested packages: 147s tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 147s r-cran-gee r-cran-expm clustalw muscle phyml t-coffee r-cran-covr 147s r-cran-tibble r-cran-withr r-cran-getopt r-cran-knitr r-cran-rmarkdown 147s r-bioc-biostrings r-cran-magick r-cran-rgl r-cran-seqinr r-bioc-seqlogo 147s r-cran-xtable r-cran-testthat r-cran-inline 147s Recommended packages: 147s r-recommended r-base-dev r-doc-html r-cran-callr r-cran-covr r-cran-crayon 147s r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-mockery 147s r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot 147s r-cran-rstudioapi r-cran-testthat r-cran-tibble r-cran-whoami r-cran-withr 147s r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-ggplot2 147s r-cran-lobstr r-cran-progress r-cran-scales r-cran-vctrs r-cran-pkgload 147s r-cran-dbi r-cran-dplyr r-cran-rsqlite r-cran-waldo r-bioc-graph r-cran-rgl 147s r-cran-vdiffr r-cran-lintr r-cran-tidyverse r-cran-tinytest r-cran-fs 147s r-cran-pillar r-cran-usethis libfile-mimeinfo-perl libnet-dbus-perl 147s libx11-protocol-perl x11-utils x11-xserver-utils 147s The following packages will be REMOVED: 147s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 147s The following NEW packages will be installed: 147s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 147s fonts-dejavu-mono libblas3 libcairo2 libcurl4t64 libdatrie1 libdeflate0 147s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 147s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 147s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 147s libpng16-16t64 libpsl5t64 libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 147s libthai-data libthai0 libtiff6 libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 147s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler r-base-core 147s r-cran-ape r-cran-cli r-cran-cpp11 r-cran-digest r-cran-fastmatch 147s r-cran-generics r-cran-glue r-cran-igraph r-cran-lattice r-cran-lifecycle 147s r-cran-littler r-cran-magrittr r-cran-matrix r-cran-nlme r-cran-phangorn 147s r-cran-pkgconfig r-cran-pkgkitten r-cran-quadprog r-cran-rcpp r-cran-rlang 147s unzip x11-common xdg-utils zip 147s The following packages will be upgraded: 147s curl 147s 1 upgraded, 71 newly installed, 5 to remove and 0 not upgraded. 147s Need to get 60.1 MB/60.1 MB of archives. 147s After this operation, 118 MB of additional disk space will be used. 147s Get:1 /tmp/autopkgtest.cXaMz9/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 148s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 148s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 148s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 148s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 148s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 148s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 148s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 148s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 148s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 148s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 148s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 148s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 148s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 148s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 148s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 148s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 148s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 148s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 148s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 148s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 148s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 148s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 148s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 148s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 148s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 148s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 148s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 148s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 148s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 148s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 148s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 148s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 148s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 148s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 148s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 148s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 149s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 149s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 149s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 149s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 149s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 149s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 149s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 149s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 149s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 149s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 149s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 149s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 149s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 149s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 149s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 149s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 149s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 149s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 149s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 149s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 149s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-digest arm64 0.6.34-1 [182 kB] 149s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ape arm64 5.7-1-1 [2879 kB] 149s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB] 149s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cpp11 all 0.4.7-1 [266 kB] 149s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fastmatch arm64 1.1-4-1 [34.6 kB] 149s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 149s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB] 149s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB] 150s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 150s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 150s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 150s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 150s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-igraph arm64 1.6.0-1 [4329 kB] 150s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-quadprog arm64 1.5-8-1build1 [29.8 kB] 150s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-phangorn arm64 2.11.1+dfsg-1 [1668 kB] 151s Preconfiguring packages ... 151s Fetched 60.1 MB in 2s (24.5 MB/s) 151s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 151s wget depends on libpsl5 (>= 0.16.0). 151s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 151s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 151s 151s (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.) 151s Removing libpsl5:arm64 (0.21.2-1build1) ... 151s Selecting previously unselected package libpsl5t64:arm64. 151s (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.) 151s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 151s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 151s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 151s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 151s (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.) 151s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 151s Selecting previously unselected package libcurl4t64:arm64. 151s (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.) 151s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 151s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 152s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 152s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 152s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 152s 152s (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.) 152s Removing libpng16-16:arm64 (1.6.43-1) ... 152s Selecting previously unselected package libpng16-16t64:arm64. 152s (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.) 152s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 152s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 152s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 152s parted depends on libreadline8 (>= 6.0). 152s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 152s gpgsm depends on libreadline8 (>= 6.0). 152s gpgconf depends on libreadline8 (>= 6.0). 152s gpg depends on libreadline8 (>= 6.0). 152s gawk depends on libreadline8 (>= 6.0). 152s fdisk depends on libreadline8 (>= 6.0). 152s 152s (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.) 152s Removing libreadline8:arm64 (8.2-3) ... 152s Selecting previously unselected package libreadline8t64:arm64. 152s (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.) 152s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 152s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 152s 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' 152s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 152s 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' 152s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 152s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 152s lsof depends on libtirpc3 (>= 1.0.2). 152s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 152s libnss-nisplus:arm64 depends on libtirpc3 (>= 1.0.2). 152s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 152s iproute2 depends on libtirpc3 (>= 1.0.2). 152s 152s (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.) 152s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 152s Selecting previously unselected package libtirpc3t64:arm64. 152s (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.) 152s Preparing to unpack .../00-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 152s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 152s 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' 152s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 152s Selecting previously unselected package fonts-dejavu-mono. 152s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 152s Unpacking fonts-dejavu-mono (2.37-8) ... 152s Selecting previously unselected package fonts-dejavu-core. 152s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 152s Unpacking fonts-dejavu-core (2.37-8) ... 152s Selecting previously unselected package fontconfig-config. 152s Preparing to unpack .../03-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 152s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 152s Selecting previously unselected package libfontconfig1:arm64. 152s Preparing to unpack .../04-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 152s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 152s Selecting previously unselected package fontconfig. 152s Preparing to unpack .../05-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 152s Unpacking fontconfig (2.15.0-1ubuntu1) ... 152s Selecting previously unselected package libblas3:arm64. 152s Preparing to unpack .../06-libblas3_3.12.0-3_arm64.deb ... 152s Unpacking libblas3:arm64 (3.12.0-3) ... 152s Selecting previously unselected package libpixman-1-0:arm64. 153s Preparing to unpack .../07-libpixman-1-0_0.42.2-1_arm64.deb ... 153s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 153s Selecting previously unselected package libxcb-render0:arm64. 153s Preparing to unpack .../08-libxcb-render0_1.15-1_arm64.deb ... 153s Unpacking libxcb-render0:arm64 (1.15-1) ... 153s Selecting previously unselected package libxcb-shm0:arm64. 153s Preparing to unpack .../09-libxcb-shm0_1.15-1_arm64.deb ... 153s Unpacking libxcb-shm0:arm64 (1.15-1) ... 153s Selecting previously unselected package libxrender1:arm64. 153s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 153s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 153s Selecting previously unselected package libcairo2:arm64. 153s Preparing to unpack .../11-libcairo2_1.18.0-1_arm64.deb ... 153s Unpacking libcairo2:arm64 (1.18.0-1) ... 153s Selecting previously unselected package libdatrie1:arm64. 153s Preparing to unpack .../12-libdatrie1_0.2.13-3_arm64.deb ... 153s Unpacking libdatrie1:arm64 (0.2.13-3) ... 153s Selecting previously unselected package libdeflate0:arm64. 153s Preparing to unpack .../13-libdeflate0_1.19-1_arm64.deb ... 153s Unpacking libdeflate0:arm64 (1.19-1) ... 153s Selecting previously unselected package libgfortran5:arm64. 153s Preparing to unpack .../14-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 153s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 153s Selecting previously unselected package libgomp1:arm64. 153s Preparing to unpack .../15-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 153s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 153s Selecting previously unselected package libgraphite2-3:arm64. 153s Preparing to unpack .../16-libgraphite2-3_1.3.14-2_arm64.deb ... 153s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 153s Selecting previously unselected package libharfbuzz0b:arm64. 153s Preparing to unpack .../17-libharfbuzz0b_8.3.0-2_arm64.deb ... 153s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 153s Selecting previously unselected package x11-common. 153s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu2_all.deb ... 153s Unpacking x11-common (1:7.7+23ubuntu2) ... 153s Selecting previously unselected package libice6:arm64. 153s Preparing to unpack .../19-libice6_2%3a1.0.10-1build2_arm64.deb ... 153s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 153s Selecting previously unselected package libjpeg-turbo8:arm64. 153s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 153s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 153s Selecting previously unselected package libjpeg8:arm64. 153s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_arm64.deb ... 153s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 153s Selecting previously unselected package liblapack3:arm64. 153s Preparing to unpack .../22-liblapack3_3.12.0-3_arm64.deb ... 153s Unpacking liblapack3:arm64 (3.12.0-3) ... 153s Selecting previously unselected package liblerc4:arm64. 153s Preparing to unpack .../23-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 153s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 153s Selecting previously unselected package libthai-data. 153s Preparing to unpack .../24-libthai-data_0.1.29-2_all.deb ... 153s Unpacking libthai-data (0.1.29-2) ... 153s Selecting previously unselected package libthai0:arm64. 153s Preparing to unpack .../25-libthai0_0.1.29-2_arm64.deb ... 153s Unpacking libthai0:arm64 (0.1.29-2) ... 153s Selecting previously unselected package libpango-1.0-0:arm64. 153s Preparing to unpack .../26-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 153s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 153s Selecting previously unselected package libpangoft2-1.0-0:arm64. 153s Preparing to unpack .../27-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 153s Unpacking libpangoft2-1.0-0:arm64 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(4.3.3-2build1) ... 161s 161s Creating config file /etc/R/Renviron with new version 161s Setting up r-cran-fastmatch (1.1-4-1) ... 161s Setting up r-cran-lattice (0.22-5-1) ... 161s Setting up r-cran-nlme (3.1.164-1) ... 161s Setting up r-cran-pkgkitten (0.2.3-1) ... 161s Setting up r-cran-magrittr (2.0.3-1) ... 161s Setting up r-cran-quadprog (1.5-8-1build1) ... 161s Setting up r-cran-littler (0.3.19-1) ... 161s Setting up r-cran-rcpp (1.0.12-1) ... 161s Setting up r-cran-rlang (1.1.3-1) ... 161s Setting up littler (0.3.19-1) ... 161s Setting up r-cran-generics (0.1.3-1) ... 161s Setting up r-cran-digest (0.6.34-1) ... 161s Setting up r-cran-ape (5.7-1-1) ... 161s Setting up r-cran-glue (1.7.0-1) ... 161s Setting up r-cran-cli (3.6.2-1) ... 161s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 161s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 161s Setting up r-cran-cpp11 (0.4.7-1) ... 161s Setting up r-cran-matrix (1.6-5-1) ... 161s Setting up r-cran-igraph (1.6.0-1) ... 161s Setting up r-cran-phangorn (2.11.1+dfsg-1) ... 161s Setting up autopkgtest-satdep (0) ... 161s Processing triggers for man-db (2.12.0-3) ... 162s Processing triggers for install-info (7.1-3) ... 162s Processing triggers for libc-bin (2.39-0ubuntu2) ... 168s (Reading database ... 79396 files and directories currently installed.) 168s Removing autopkgtest-satdep (0) ... 169s autopkgtest [17:52:59]: test run-unit-test: [----------------------- 169s 169s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 169s Copyright (C) 2024 The R Foundation for Statistical Computing 169s Platform: aarch64-unknown-linux-gnu (64-bit) 169s 169s R is free software and comes with ABSOLUTELY NO WARRANTY. 169s You are welcome to redistribute it under certain conditions. 169s Type 'license()' or 'licence()' for distribution details. 169s 169s R is a collaborative project with many contributors. 169s Type 'contributors()' for more information and 169s 'citation()' on how to cite R or R packages in publications. 169s 169s Type 'demo()' for some demos, 'help()' for on-line help, or 169s 'help.start()' for an HTML browser interface to help. 169s Type 'q()' to quit R. 169s 170s > Stangle("DrawingPhylogenies.Rnw") 170s Writing to file DrawingPhylogenies.R 170s > source("DrawingPhylogenies.R", echo=TRUE) 170s 170s > options(width = 80, prompt = "> ") 170s 170s > library(ape) 170s 170s > mytr <- read.tree(text = "((Pan:5,Homo:5):2,Gorilla:7);") 170s 170s > foo <- function() { 170s + col <- "green" 170s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 170s + las = 1) 170s + box(lty .... [TRUNCATED] 170s 170s > layout(matrix(1:4, 2, 2, byrow = TRUE)) 170s 170s > plot(mytr) 170s 170s > foo() 170s 170s > plot(mytr, "c", FALSE) 170s 170s > foo() 170s 170s > plot(mytr, "u") 170s 170s > foo() 170s 170s > par(xpd = TRUE) 170s 170s > plot(mytr, "f") 170s 170s > foo() 170s 170s > box("outer") 170s 170s > tr <- compute.brlen(stree(8, "l"), 0.1) 170s 170s > tr$tip.label[] <- "" 170s 170s > foo <- function() { 170s + col <- "green" 170s + axis(1, col = col, col.ticks = col, col.axis = col) 170s + axis(2, col = col, col.ticks = col, col.axi .... [TRUNCATED] 170s 170s > layout(matrix(1:12, 6, 2)) 170s 170s > par(mar = c(2, 2, 0.3, 0)) 170s 170s > for (type in c("p", "c")) { 170s + plot(tr, type) 170s + foo() 170s + plot(tr, type, node.pos = 2) 170s + foo() 170s + plot(tr, type, FALSE) 170s + foo() 170s .... [TRUNCATED] 170s 170s > foo <- function() { 170s + col <- "green" 170s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 170s + las = 1) 170s + box(lty .... [TRUNCATED] 170s 170s > layout(matrix(1:4, 2, 2)) 170s 170s > par(las = 1) 170s 170s > plot(tr, "u") 170s 170s > foo() 170s 170s > plot(tr, "u", FALSE) 170s 170s > foo() 170s 170s > plot(tr, "f") 170s 170s > foo() 170s 170s > plot(tr, "f", FALSE) 170s 170s > foo() 170s 170s > args(node.depth.edgelength) 170s function (phy) 170s NULL 170s 170s > args(node.depth) 170s function (phy, method = 1) 170s NULL 170s 170s > args(node.height) 170s function (phy, clado.style = FALSE) 170s NULL 170s 170s > args(unrooted.xy) 170s function (Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree) 170s NULL 170s 170s > args(phylogram.plot) 170s function (edge, Ntip, Nnode, xx, yy, horizontal, edge.color = NULL, 170s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 170s node.lty = NULL) 170s NULL 170s 170s > args(cladogram.plot) 170s function (edge, xx, yy, edge.color, edge.width, edge.lty) 170s NULL 170s 170s > args(circular.plot) 170s function (edge, Ntip, Nnode, xx, yy, theta, r, edge.color, edge.width, 170s edge.lty) 170s NULL 170s 170s > args(plot.phylo) 170s function (x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL, 170s show.tip.label = TRUE, show.node.label = FALSE, edge.color = NULL, 170s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 170s node.lty = NULL, font = 3, cex = par("cex"), adj = NULL, 170s srt = 0, no.margin = FALSE, root.edge = FALSE, label.offset = 0, 170s underscore = FALSE, x.lim = NULL, y.lim = NULL, direction = "rightwards", 170s lab4ut = NULL, tip.color = par("col"), plot = TRUE, rotate.tree = 0, 170s open.angle = 0, node.depth = 1, align.tip.label = FALSE, 170s ...) 170s NULL 170s 170s > geo <- factor(c("Africa", "World", "Africa")) 170s 170s > (mycol <- c("blue", "red")[geo]) 170s [1] "blue" "red" "blue" 170s 170s > plot(mytr, tip.color = mycol) 170s 170s > par(xpd = TRUE) 170s 170s > plot(mytr, tip.color = mycol, cex = c(1, 1, 1.5)) 170s 170s > args(def) 170s function (x, ..., default = NULL, regexp = FALSE) 170s NULL 170s 170s > mycol2 <- def(mytr$tip.label, Homo = "red", default = "blue") 170s 170s > identical(mycol, mycol2) 170s [1] TRUE 170s 170s > (i <- which.edge(mytr, c("Homo", "Pan"))) 170s [1] 2 3 170s 170s > co <- rep("black", Nedge(mytr)) 170s 170s > co[i] <- "blue" 170s 170s > par(xpd = TRUE) 170s 170s > plot(mytr, edge.col = co) 170s 170s > edgelabels() 170s 170s > args(axisPhylo) 170s function (side = 1, root.time = NULL, backward = TRUE, ...) 170s NULL 170s 170s > args(add.scale.bar) 170s function (x, y, length = NULL, ask = FALSE, lwd = 1, lcol = "black", 170s ...) 170s NULL 170s 170s > plot(mytr) 170s 170s > add.scale.bar() 170s 170s > axisPhylo() 170s 170s > axis(3) 170s 170s > args(nodelabels) 170s function (text, node, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 170s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 170s bg = "lightblue", horiz = FALSE, width = NULL, height = NULL, 170s ...) 170s NULL 170s 170s > args(tiplabels) 170s function (text, tip, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 170s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 170s bg = "yellow", horiz = FALSE, width = NULL, height = NULL, 170s offset = 0, ...) 170s NULL 170s 170s > args(edgelabels) 170s function (text, edge, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 170s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 170s bg = "lightgreen", horiz = FALSE, width = NULL, height = NULL, 170s date = NULL, ...) 170s NULL 170s 170s > par(xpd = TRUE) 170s 170s > plot(mytr) 170s 170s > nodelabels() 170s 170s > tiplabels() 170s 170s > edgelabels() 170s 170s > plot(rep(1:5, 5), rep(1:5, each = 5), pch = 1:25, 170s + xlim = c(1, 5.2), col = "blue", bg = "yellow", cex = 2) 170s 170s > text(rep(1:5, 5) + 0.2, rep(1:5, each = 5), 1:25) 170s 170s > v <- c(0, 0.5, 1) 170s 170s > layout(matrix(1:9, 3, 3)) 170s 170s > par(mar = c(3, 3, 3, 0), las = 1) 170s 170s > for (i in v) { 170s + for (j in v) { 170s + plot(0, 0, "n", main = paste0("adj = c(", i, ", ", j, 170s + ")")) 170s + abline(v = 0, h = .... [TRUNCATED] 170s 170s > plot(rep(0, 3), 0:2, "n", las = 1) 170s 170s > abline(v = 0, h = 0:2, lty = 3) 170s 170s > text(0, 0:2, mytr$tip.label, adj = -1) 170s 170s > text(0, 0:2, mytr$tip.label, adj = 2, font = 2) 170s 170s > args(phydataplot) 170s function (x, phy, style = "bars", offset = 1, scaling = 1, continuous = FALSE, 170s width = NULL, legend = "below", funcol = rainbow, ...) 170s NULL 170s 170s > args(ring) 170s function (x, phy, style = "ring", offset = 1, ...) 170s NULL 170s 170s > x <- matrix(1:6, 3, 10) 170s 170s > dimnames(x) <- list(c("Homo", "Gorilla", "Pan"), LETTERS[1:ncol(x)]) 170s 170s > x 170s A B C D E F G H I J 170s Homo 1 4 1 4 1 4 1 4 1 4 170s Gorilla 2 5 2 5 2 5 2 5 2 5 170s Pan 3 6 3 6 3 6 3 6 3 6 170s 170s > mytr$tip.label 170s [1] "Pan" "Homo" "Gorilla" 170s 170s > par(mar = c(10, 2, 5, 5)) 170s 170s > plot(mytr, x.lim = 30) 170s 170s > phydataplot(x, mytr, "m", border = "white", offset = 2, 170s + width = 1) 170s 170s > phydataplot(x, mytr, "m", border = "white", offset = 15, 170s + width = 1, continuous = 2) 170s 170s > n <- 100 170s 170s > p <- 3 170s 170s > set.seed(3) 170s 170s > tr <- rcoal(n) 170s 170s > x <- matrix(runif(p * n), n, p) 170s 170s > rownames(x) <- tr$tip.label 170s 170s > COL <- c("red", "green", "blue") 170s 170s > par(xpd = TRUE) 170s 170s > plot(tr, "f", x.lim = c(-5, 5), show.tip.label = FALSE, 170s + no.margin = TRUE) 170s 170s > for (j in 1:p) ring(x[, j], tr, offset = j - 1 + 0.1, 170s + col = COL[j]) 170s 170s > tree <- rtree(10) 170s 170s > tree$edge.length[1] <- 1000 170s 170s > layout(matrix(1:2, 1)) 170s 170s > plot(tree) 170s 170s > axisPhylo() 170s 170s > plotBreakLongEdges(tree) 170s 170s > axisPhylo() 170s 170s > el <- tree$edge.length 170s 170s > sum(el > mean(el) + 2 * sd(el)) 170s [1] 1 170s 170s > tree$edge.length[8] <- 1000 170s 170s > el <- tree$edge.length 170s 170s > sum(el > mean(el) + 2 * sd(el)) 170s [1] 2 170s 170s > layout(matrix(1:2, 1)) 170s 170s > plotBreakLongEdges(tree) 170s 170s > plotBreakLongEdges(tree, n = 2) 170s 170s > TR <- replicate(10, rcoal(sample(11:20, size = 1)), 170s + simplify = FALSE) 170s 170s > kronoviz(TR, type = "c", show.tip.label = FALSE) 171s 171s > dates <- as.Date(.leap.seconds) 171s 171s > tr <- rcoal(length(dates)) 171s 171s > plotTreeTime(tr, dates) 171s 171s > par(oma = rep(2, 4)) 171s 171s > plot(mytr) 171s 171s > box(lty = 3) 171s 171s > box("figure", col = "blue") 171s 171s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 171s + font = 2, col = "blue") 171s 171s > box("outer") 171s 171s > layout(matrix(1:4, 2, 2)) 171s 171s > par(oma = rep(2, 4)) 171s 171s > for (i in 1:4) { 171s + par(mar = rep(i, 4)) 171s + plot(mytr) 171s + box(lty = 3) 171s + box("figure", col = "blue") 171s + } 171s 171s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 171s + font = 2, col = "blue") 171s 171s > box("outer") 171s 171s > layout(matrix(c(1, 2, 1, 3), 2, 2)) 171s 171s > for (i in 1:3) plot(rtree(5)) 171s 171s > (pp <- get("last_plot.phylo", envir = .PlotPhyloEnv)) 171s $type 171s [1] "phylogram" 171s 171s $use.edge.length 171s [1] TRUE 171s 171s $node.pos 171s [1] 1 171s 171s $node.depth 171s [1] 1 171s 171s $show.tip.label 171s [1] TRUE 171s 171s $show.node.label 171s [1] FALSE 171s 171s $font 171s [1] 3 171s 171s $cex 171s [1] 0.83 171s 171s $adj 171s [1] 0 171s 171s $srt 171s [1] 0 171s 171s $no.margin 171s [1] FALSE 171s 171s $label.offset 171s [1] 0 171s 171s $x.lim 171s [1] 0.00000 3.13046 171s 171s $y.lim 171s [1] 1 5 171s 171s $direction 171s [1] "rightwards" 171s 171s $tip.color 171s [1] "black" 171s 171s $Ntip 171s [1] 5 171s 171s $Nnode 171s [1] 4 171s 171s $root.time 171s NULL 171s 171s $align.tip.label 171s [1] FALSE 171s 171s $edge 171s [,1] [,2] 171s [1,] 6 1 171s [2,] 6 7 171s [3,] 7 2 171s [4,] 7 8 171s [5,] 8 3 171s [6,] 8 9 171s [7,] 9 4 171s [8,] 9 5 171s 171s $xx 171s [1] 0.3967457 1.7260289 2.2158455 2.9728029 2.8310192 0.0000000 0.8134181 171s [8] 1.3631198 1.9857132 171s 171s $yy 171s [1] 1.0000 2.0000 3.0000 4.0000 5.0000 1.9375 2.8750 3.7500 4.5000 171s 171s 171s > layout(matrix(1:2, 2)) 171s 171s > plot(rtree(4)) 171s 171s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 171s 171s > x <- pp$xx[1] 171s 171s > y <- pp$yy[1] 171s 171s > (pu <- par("usr")) 171s [1] -0.06364557 1.65478492 0.88000000 4.12000000 171s 171s > (x - pu[1])/(pu[2] - pu[1]) 171s [1] 0.9349839 171s 171s > (y - pu[3])/(pu[4] - pu[3]) 171s [1] 0.03703704 171s 171s > pi <- par("pin") 171s 171s > mi <- par("mai") 171s 171s > xi1 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 171s 171s > yi1 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 171s 171s > plot(rtree(4)) 171s 171s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 171s 171s > x <- pp$xx[5] 171s 171s > y <- pp$yy[5] 171s 171s > pu <- par("usr") 171s 171s > pi <- par("pin") 171s 171s > mi <- par("mai") 171s 171s > xi2 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 171s 171s > yi2 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 171s 171s > yi1 <- yi1 + par("fin")[2] 171s 171s > di <- par("din") 171s 171s > layout(1) 171s 171s > par(new = TRUE, mai = rep(0, 4)) 171s 171s > plot(NA, type = "n", ann = FALSE, axes = FALSE, xlim = 0:1, 171s + ylim = 0:1, xaxs = "i", yaxs = "i") 171s 171s > fancyarrows(xi1/di[1], yi1/di[2], xi2/di[1], yi2/di[2], 171s + 1, lwd = 10, col = rgb(1, 0.5, 0, 0.5), type = "h") 171s 171s > foo <- function(phy1, phy2, from) { 171s + layout(matrix(1:2, 2)) 171s + plot(phy1, font = 1) 171s + pp <- get("last_plot.phylo", envir = .PlotPhyloEnv .... [TRUNCATED] 171s 171s > trb <- read.tree(text = "((Primates,Carnivora),Monotremata);") 171s 171s > par(xpd = TRUE) 171s 171s > foo(trb, mytr, "Primates") 171s 171s > plot(mytr, plot = FALSE) 171s 171s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 171s 171s > rect(pp$xx[5] - 0.1, pp$yy[1] - 0.1, pp$xx[1] + 2, 171s + pp$yy[2] + 0.1, col = "yellow", border = NA) 171s 171s > par(new = TRUE) 171s 171s > plot(mytr) 171s > 171s 171s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 171s Copyright (C) 2024 The R Foundation for Statistical Computing 171s Platform: aarch64-unknown-linux-gnu (64-bit) 171s 171s R is free software and comes with ABSOLUTELY NO WARRANTY. 171s You are welcome to redistribute it under certain conditions. 171s Type 'license()' or 'licence()' for distribution details. 171s 171s R is a collaborative project with many contributors. 171s Type 'contributors()' for more information and 171s 'citation()' on how to cite R or R packages in publications. 171s 171s Type 'demo()' for some demos, 'help()' for on-line help, or 171s 'help.start()' for an HTML browser interface to help. 171s Type 'q()' to quit R. 171s 171s > Stangle("MoranI.Rnw") 171s Writing to file MoranI.R 171s > source("MoranI.R", echo=TRUE) 171s 171s > options(width = 80, prompt = "> ") 171s 171s > body <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) 171s 171s > longevity <- c(4.74493, 3.3322, 3.3673, 2.89037, 2.30259) 171s 171s > names(body) <- names(longevity) <- c("Homo", "Pongo", 171s + "Macaca", "Ateles", "Galago") 171s 171s > library(ape) 171s 171s > trnwk <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62)" 171s 171s > trnwk[2] <- ":0.38,Galago:1.00);" 171s 171s > tr <- read.tree(text = trnwk) 171s 171s > plot(tr) 171s 171s > axisPhylo() 171s 171s > w <- 1/cophenetic(tr) 171s 171s > w 171s Homo Pongo Macaca Ateles Galago 171s Homo Inf 2.3809524 1.0204082 0.8064516 0.5 171s Pongo 2.3809524 Inf 1.0204082 0.8064516 0.5 171s Macaca 1.0204082 1.0204082 Inf 0.8064516 0.5 171s Ateles 0.8064516 0.8064516 0.8064516 Inf 0.5 171s Galago 0.5000000 0.5000000 0.5000000 0.5000000 Inf 171s 171s > diag(w) <- 0 171s 171s > Moran.I(body, w) 171s $observed 171s [1] -0.07312179 171s 171s $expected 171s [1] -0.25 171s 171s $sd 171s [1] 0.08910814 171s 171s $p.value 171s [1] 0.04714628 171s 171s 171s > Moran.I(body, w, alt = "greater") 171s $observed 171s [1] -0.07312179 171s 171s $expected 171s [1] -0.25 171s 171s $sd 171s [1] 0.08910814 171s 171s $p.value 171s [1] 0.02357314 171s 171s 171s > Moran.I(longevity, w) 171s $observed 171s [1] -0.1837739 171s 171s $expected 171s [1] -0.25 171s 171s $sd 171s [1] 0.09114549 171s 171s $p.value 171s [1] 0.4674727 171s 171s 171s > data(carnivora) 171s 171s > carnivora$log10SW <- log10(carnivora$SW) 171s 171s > carnivora$log10FW <- log10(carnivora$FW) 171s 171s > fm1.carn <- log10SW ~ Order/SuperFamily/Family/Genus 171s 171s > co1 <- correlogram.formula(fm1.carn, data = carnivora) 171s 171s > plot(co1) 171s 171s > fm2.carn <- log10SW + log10FW ~ Order/SuperFamily/Family/Genus 171s 171s > co2 <- correlogram.formula(fm2.carn, data = carnivora) 171s 171s > print(plot(co2)) 171s 171s > plot(co2, FALSE) 171s > 171s 171s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 171s Copyright (C) 2024 The R Foundation for Statistical Computing 171s Platform: aarch64-unknown-linux-gnu (64-bit) 171s 171s R is free software and comes with ABSOLUTELY NO WARRANTY. 171s You are welcome to redistribute it under certain conditions. 171s Type 'license()' or 'licence()' for distribution details. 171s 171s R is a collaborative project with many contributors. 171s Type 'contributors()' for more information and 171s 'citation()' on how to cite R or R packages in publications. 171s 171s Type 'demo()' for some demos, 'help()' for on-line help, or 171s 'help.start()' for an HTML browser interface to help. 171s Type 'q()' to quit R. 171s 171s > Stangle("RandomTopologies.Rnw") 172s Writing to file RandomTopologies.R 172s > source("RandomTopologies.R", echo=TRUE) 172s 172s > options(width = 80, prompt = "> ") 172s 172s > library(ape) 172s 172s > n <- 1:10 172s 172s > data.frame(N.topo = sapply(n, howmanytrees)) 172s N.topo 172s 1 1 172s 2 1 172s 3 3 172s 4 15 172s 5 105 172s 6 945 172s 7 10395 172s 8 135135 172s 9 2027025 172s 10 34459425 172s 172s > howmanytrees(25) 172s [1] 1.192568e+30 172s 172s > howmanytrees(25) * 0.21 172s [1] 2.504393e+29 172s 172s > data.frame(N.topo = sapply(n, howmanytrees, labeled = FALSE)) 172s N.topo 172s 1 1 172s 2 1 172s 3 1 172s 4 2 172s 5 3 172s 6 6 172s 7 11 172s 8 23 172s 9 46 172s 10 98 172s 172s > n2 <- c(50, 100, 200) 172s 172s > data.frame(N.topo = sapply(n2, howmanytrees, labeled = FALSE), 172s + row.names = n2) 172s N.topo 172s 50 5.150149e+16 172s 100 1.019560e+36 172s 200 1.141703e+75 172s 172s > 1/howmanytrees(50) 172s [1] 3.632505e-77 172s 172s > 1/sapply(n, howmanytrees) 172s [1] 1.000000e+00 1.000000e+00 3.333333e-01 6.666667e-02 9.523810e-03 172s [6] 1.058201e-03 9.620010e-05 7.400007e-06 4.933338e-07 2.901964e-08 172s 172s > 1/sapply(n, howmanytrees, labeled = FALSE) 172s [1] 1.00000000 1.00000000 1.00000000 0.50000000 0.33333333 0.16666667 172s [7] 0.09090909 0.04347826 0.02173913 0.01020408 172s 172s > library(phangorn) 173s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 173s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 173s 173s > TR <- allTrees(4, rooted = TRUE) 173s 173s > TR 173s 15 phylogenetic trees 173s 173s > layout(matrix(1:15, 3, 5)) 173s 173s > par(mar = rep(1.5, 4), xpd = TRUE) 173s 173s > for (i in 1:15) plot(TR[[i]], "c", cex = 1.2, font = 1) 173s 173s > K <- 100 173s 173s > n <- 50 173s 173s > N <- howmanytrees(n, labeled = FALSE) 173s 173s > p <- 1/N 173s 173s > 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 173s [1] 0 173s 173s > 1 - dbinom(0, K, p) - dbinom(1, K, p) 173s [1] -5.431212e-17 173s 173s > f <- function(n, K) { 173s + N <- howmanytrees(n, labeled = FALSE) 173s + p <- 1/N 173s + 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 173s + } 173s 173s > DF <- expand.grid(n = 4:20, K = c(2, 5, 10, 100, 1000, 173s + 10000)) 173s 173s > DF$P <- mapply(f, n = DF$n, K = DF$K) 173s 173s > library(lattice) 173s 173s > xyplot(P ~ n, DF, groups = K, panel = panel.superpose, 173s + type = "b", auto.key = list(x = 0.8, y = 0.9, title = "K")) 173s 173s > subset(DF, n == 20) 173s n K P 173s 17 20 2 1.160494e-11 173s 34 20 5 1.160491e-10 173s 51 20 10 5.222149e-10 173s 68 20 100 5.743191e-08 173s 85 20 1000 5.783570e-06 173s 102 20 10000 5.671842e-04 173s 173s > f(20, 1e+05) 173s [1] 0.04638755 173s 173s > f(30, 1e+06) 173s [1] 2.525152e-07 173s 173s > txt <- c("((,),((,),));", "(((,),(,)),);", "((((,),),),);") 173s 173s > TR5 <- read.tree(text = txt) 173s 173s > layout(matrix(1:3, 1)) 173s 173s > for (i in 1:3) plot(TR5[[i]], "c", cex = 1.2, main = LETTERS[i]) 173s 173s > howmanytrees(1, labeled = FALSE) * howmanytrees(4, 173s + labeled = FALSE) 173s [1] 2 173s 173s > howmanytrees(2, labeled = FALSE) * howmanytrees(3, 173s + labeled = FALSE) 173s [1] 1 173s 173s > howmanytrees(400, labeled = FALSE) * howmanytrees(403, 173s + labeled = FALSE) 173s [1] Inf 173s 173s > TR <- list(rmtopology(1000, 4, TRUE, br = NULL), rmtree(1000, 173s + 4, TRUE, br = NULL), rmtree(1000, 4, TRUE, br = NULL, equiprob = TRUE)) 174s 174s > foo.test <- function(x, labeled = TRUE) { 174s + uTR <- unique(x, use.tip.label = labeled) 174s + f <- integer(length(uTR)) 174s + for (j in seq_along( .... [TRUNCATED] 174s 174s > lapply(TR, foo.test) 179s [1] 64 64 78 60 74 54 69 76 60 70 68 80 61 56 66 183s [1] 129 49 60 58 46 53 69 89 43 57 115 55 69 58 50 186s [1] 156 38 50 152 36 175 47 53 50 39 42 42 40 42 38 186s [[1]] 186s 186s Chi-squared test for given probabilities 186s 186s data: f 186s X-squared = 13.13, df = 14, p-value = 0.5163 186s 186s 186s [[2]] 186s 186s Chi-squared test for given probabilities 186s 186s data: f 186s X-squared = 133.79, df = 14, p-value < 2.2e-16 186s 186s 186s [[3]] 186s 186s Chi-squared test for given probabilities 186s 186s data: f 186s X-squared = 510.2, df = 14, p-value < 2.2e-16 186s 186s 186s 186s > lapply(TR, foo.test, labeled = FALSE) 186s [1] 782 218 187s [1] 333 667 188s [1] 483 517 188s [[1]] 188s 188s Chi-squared test for given probabilities 188s 188s data: f 188s X-squared = 318.1, df = 1, p-value < 2.2e-16 188s 188s 188s [[2]] 188s 188s Chi-squared test for given probabilities 188s 188s data: f 188s X-squared = 111.56, df = 1, p-value < 2.2e-16 188s 188s 188s [[3]] 188s 188s Chi-squared test for given probabilities 188s 188s data: f 188s X-squared = 1.156, df = 1, p-value = 0.2823 188s 188s 188s 188s > .Machine$double.xmax 188s [1] 1.797693e+308 188s 188s > howmanytrees(151) 188s [1] 3.753274e+306 188s 188s > howmanytrees(792, labeled = FALSE) 188s [1] 1.029038e+308 188s 188s > (N <- howmanytrees(2e+06)) 188s approximately 3.692364 * 10^12335524 188s 188s > N[2] + 1 188s n 188s 12335525 188s 188s > ceiling((N[2] + 1)/3000) 188s n 188s 4112 188s 188s > n <- 1:792 188s 188s > N <- howmanytrees(792, labeled = FALSE, detail = TRUE) 188s 188s > lN <- log10(N) 188s 188s > summary(lm(lN ~ n)) 188s 188s Call: 188s lm(formula = lN ~ n) 188s 188s Residuals: 188s Min 1Q Median 3Q Max 188s -0.25968 -0.21424 -0.08311 0.12406 2.82605 188s 188s Coefficients: 188s Estimate Std. Error t value Pr(>|t|) 188s (Intercept) -3.219e+00 2.258e-02 -142.5 <2e-16 *** 188s n 3.926e-01 4.934e-05 7956.3 <2e-16 *** 188s --- 188s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 188s 188s Residual standard error: 0.3175 on 790 degrees of freedom 188s Multiple R-squared: 1, Adjusted R-squared: 1 188s F-statistic: 6.33e+07 on 1 and 790 DF, p-value: < 2.2e-16 188s 188s 188s > s <- n > 700 188s 188s > summary(lm(lN[s] ~ n[s])) 188s 188s Call: 188s lm(formula = lN[s] ~ n[s]) 188s 188s Residuals: 188s Min 1Q Median 3Q Max 188s -0.0004133 -0.0003323 -0.0001032 0.0002834 0.0008197 188s 188s Coefficients: 188s Estimate Std. Error t value Pr(>|t|) 188s (Intercept) -4.153e+00 1.096e-03 -3788 <2e-16 *** 188s n[s] 3.941e-01 1.468e-06 268567 <2e-16 *** 188s --- 188s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 188s 188s Residual standard error: 0.0003738 on 90 degrees of freedom 188s Multiple R-squared: 1, Adjusted R-squared: 1 188s F-statistic: 7.213e+10 on 1 and 90 DF, p-value: < 2.2e-16 188s 188s 188s > n <- 788:792 188s 188s > log10(sapply(n, howmanytrees, labeled = FALSE)) 188s [1] 306.4356 306.8298 307.2240 307.6182 308.0124 188s 188s > 0.3941 * n - 4.153 188s [1] 306.3978 306.7919 307.1860 307.5801 307.9742 188s 188s > xi <- 2.477993 188s 188s > lxi <- log10(xi) 188s 188s > n <- 1000 188s 188s > (n - 1) * lxi 188s [1] 393.706 188s 188s > for (k in 2:11) print((n - k) * lxi + log10(sum(xi^(0:(k - 188s + 1))))) 188s [1] 393.8532 188s [1] 393.9009 188s [1] 393.9187 188s [1] 393.9257 188s [1] 393.9285 188s [1] 393.9296 188s [1] 393.9301 188s [1] 393.9303 188s [1] 393.9304 188s [1] 393.9304 188s > 189s autopkgtest [17:53:19]: test run-unit-test: -----------------------] 189s run-unit-test PASS 189s autopkgtest [17:53:19]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 190s autopkgtest [17:53:20]: test pkg-r-autopkgtest: preparing testbed 191s Reading package lists... 191s Building dependency tree... 191s Reading state information... 192s Starting pkgProblemResolver with broken count: 0 192s Starting 2 pkgProblemResolver with broken count: 0 192s Done 193s The following additional packages will be installed: 193s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 193s dctrl-tools g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 193s gcc-13 gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-13 193s gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 193s libasan8 libatomic1 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 193s libcrypt-dev libgcc-13-dev libgfortran-13-dev libhwasan0 libicu-dev libisl23 193s libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 193s liblzma-dev libmpc3 libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 193s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev 193s libstdc++-13-dev libtirpc-dev libtsan2 libubsan1 linux-libc-dev pkg-config 193s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev r-cran-expm r-cran-gee 193s rpcsvc-proto zlib1g-dev 193s Suggested packages: 193s cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib 193s manpages-dev autoconf automake libtool flex bison gdb gcc-doc 193s gdb-aarch64-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev 193s liblapack-doc glibc-doc icu-doc liblzma-doc ncurses-doc readline-doc 193s libstdc++-13-doc texlive-base texlive-latex-base texlive-plain-generic 193s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils 193s texlive-latex-recommended texlive-latex-extra texinfo 193s Recommended packages: 193s bzip2-doc manpages manpages-dev libc-devtools libpng-tools 193s r-cran-rcolorbrewer r-cran-sfsmisc r-cran-rmpfr r-cran-mass 193s The following NEW packages will be installed: 193s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu 193s cpp-aarch64-linux-gnu dctrl-tools g++ g++-13 g++-13-aarch64-linux-gnu 193s g++-aarch64-linux-gnu gcc gcc-13 gcc-13-aarch64-linux-gnu 193s gcc-aarch64-linux-gnu gfortran gfortran-13 gfortran-13-aarch64-linux-gnu 193s gfortran-aarch64-linux-gnu icu-devtools libasan8 libatomic1 libblas-dev 193s libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libgcc-13-dev 193s libgfortran-13-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 193s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 193s libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev 193s libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev libstdc++-13-dev 193s libtirpc-dev libtsan2 libubsan1 linux-libc-dev pkg-config pkg-r-autopkgtest 193s pkgconf pkgconf-bin r-base-dev r-cran-expm r-cran-gee rpcsvc-proto 193s zlib1g-dev 193s 0 upgraded, 64 newly installed, 0 to remove and 0 not upgraded. 193s Need to get 93.1 MB/93.1 MB of archives. 193s After this operation, 343 MB of additional disk space will be used. 193s Get:1 /tmp/autopkgtest.cXaMz9/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [740 B] 193s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 193s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 194s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 194s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1 [201 kB] 194s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 194s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 194s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 194s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 194s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 194s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 194s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 194s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 194s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 194s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 194s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 194s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 194s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 194s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 194s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 194s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 194s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 194s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 194s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 195s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 195s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 195s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 195s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 195s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 195s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 195s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 195s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 195s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 195s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 dctrl-tools arm64 2.24-3build2 [65.2 kB] 195s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-17ubuntu2 [478 kB] 195s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.8 MB] 195s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-17ubuntu2 [10.3 kB] 195s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1022 B] 195s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B] 195s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB] 195s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB] 195s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 195s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB] 196s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu1 [304 kB] 196s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 196s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 196s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB] 196s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses-dev arm64 6.4+20240113-1ubuntu1 [385 kB] 196s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu1 [195 kB] 196s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu1 [183 kB] 196s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-posix3 arm64 10.42-4ubuntu1 [6654 B] 196s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-dev arm64 10.42-4ubuntu1 [679 kB] 196s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB] 196s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 196s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng-dev arm64 1.6.43-3 [267 kB] 196s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline-dev arm64 8.2-3.1 [177 kB] 196s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB] 196s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] 196s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B] 196s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB] 196s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-dev all 4.3.3-2build1 [4334 B] 196s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 196s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-expm arm64 0.999-9-1 [217 kB] 196s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gee arm64 4.13-26-1 [72.3 kB] 197s Fetched 93.1 MB in 3s (31.9 MB/s) 197s Selecting previously unselected package libc-dev-bin. 197s (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 ... 79396 files and directories currently installed.) 197s Preparing to unpack .../00-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 197s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 197s Selecting previously unselected package linux-libc-dev:arm64. 197s Preparing to unpack .../01-linux-libc-dev_6.8.0-11.11_arm64.deb ... 197s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 197s Selecting previously unselected package libcrypt-dev:arm64. 197s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 197s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 197s Selecting previously unselected package libtirpc-dev:arm64. 197s Preparing to unpack .../03-libtirpc-dev_1.3.4+ds-1.1_arm64.deb ... 197s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 197s Selecting previously unselected package libnsl-dev:arm64. 197s Preparing to unpack .../04-libnsl-dev_1.3.0-3_arm64.deb ... 197s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 197s Selecting previously unselected package rpcsvc-proto. 197s Preparing to unpack .../05-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 197s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 197s Selecting previously unselected package libc6-dev:arm64. 197s Preparing to unpack .../06-libc6-dev_2.39-0ubuntu2_arm64.deb ... 197s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 197s Selecting previously unselected package libisl23:arm64. 197s Preparing to unpack .../07-libisl23_0.26-3_arm64.deb ... 197s Unpacking libisl23:arm64 (0.26-3) ... 197s Selecting previously unselected package libmpc3:arm64. 197s Preparing to unpack .../08-libmpc3_1.3.1-1_arm64.deb ... 197s Unpacking libmpc3:arm64 (1.3.1-1) ... 198s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 198s Preparing to unpack .../09-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 198s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 198s Selecting previously unselected package cpp-13. 198s Preparing to unpack .../10-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 198s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 198s Selecting previously unselected package cpp-aarch64-linux-gnu. 198s Preparing to unpack .../11-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 198s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 198s Selecting previously unselected package cpp. 198s Preparing to unpack .../12-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 198s Unpacking cpp (4:13.2.0-7ubuntu1) ... 198s Selecting previously unselected package libcc1-0:arm64. 198s Preparing to unpack .../13-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 198s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 198s Selecting previously unselected package libitm1:arm64. 198s Preparing to unpack .../14-libitm1_14-20240303-1ubuntu1_arm64.deb ... 198s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 198s Selecting previously unselected package libatomic1:arm64. 198s Preparing to unpack .../15-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 198s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 198s Selecting previously unselected package libasan8:arm64. 198s Preparing to unpack .../16-libasan8_14-20240303-1ubuntu1_arm64.deb ... 198s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 198s Selecting previously unselected package liblsan0:arm64. 198s Preparing to unpack .../17-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 198s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 199s Selecting previously unselected package libtsan2:arm64. 199s Preparing to unpack .../18-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 199s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 199s Selecting previously unselected package libubsan1:arm64. 199s Preparing to unpack .../19-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 199s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 199s Selecting previously unselected package libhwasan0:arm64. 199s Preparing to unpack .../20-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 199s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 199s Selecting previously unselected package libgcc-13-dev:arm64. 199s Preparing to unpack .../21-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 199s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 199s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 199s Preparing to unpack .../22-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 199s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 199s Selecting previously unselected package gcc-13. 199s Preparing to unpack .../23-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 199s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 199s Selecting previously unselected package gcc-aarch64-linux-gnu. 199s Preparing to unpack .../24-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 199s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 200s Selecting previously unselected package gcc. 200s Preparing to unpack .../25-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 200s Unpacking gcc (4:13.2.0-7ubuntu1) ... 200s Selecting previously unselected package libstdc++-13-dev:arm64. 200s Preparing to unpack .../26-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 200s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 200s Selecting previously unselected package g++-13-aarch64-linux-gnu. 200s Preparing to unpack .../27-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 200s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 200s Selecting previously unselected package g++-13. 200s Preparing to unpack .../28-g++-13_13.2.0-17ubuntu2_arm64.deb ... 200s Unpacking g++-13 (13.2.0-17ubuntu2) ... 200s Selecting previously unselected package g++-aarch64-linux-gnu. 200s Preparing to unpack .../29-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 200s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 200s Selecting previously unselected package g++. 200s Preparing to unpack .../30-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 200s Unpacking g++ (4:13.2.0-7ubuntu1) ... 200s Selecting previously unselected package build-essential. 200s Preparing to unpack .../31-build-essential_12.10ubuntu1_arm64.deb ... 200s Unpacking build-essential (12.10ubuntu1) ... 200s Selecting previously unselected package dctrl-tools. 200s Preparing to unpack .../32-dctrl-tools_2.24-3build2_arm64.deb ... 200s Unpacking dctrl-tools (2.24-3build2) ... 200s Selecting previously unselected package libgfortran-13-dev:arm64. 200s Preparing to unpack .../33-libgfortran-13-dev_13.2.0-17ubuntu2_arm64.deb ... 200s Unpacking libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 201s Selecting previously unselected package gfortran-13-aarch64-linux-gnu. 201s Preparing to unpack .../34-gfortran-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 201s Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 201s Selecting previously unselected package gfortran-13. 201s Preparing to unpack .../35-gfortran-13_13.2.0-17ubuntu2_arm64.deb ... 201s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 201s Selecting previously unselected package gfortran-aarch64-linux-gnu. 201s Preparing to unpack .../36-gfortran-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 201s Unpacking gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 201s Selecting previously unselected package gfortran. 201s Preparing to unpack .../37-gfortran_4%3a13.2.0-7ubuntu1_arm64.deb ... 201s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 201s Selecting previously unselected package icu-devtools. 201s Preparing to unpack .../38-icu-devtools_74.2-1ubuntu1_arm64.deb ... 201s Unpacking icu-devtools (74.2-1ubuntu1) ... 201s Selecting previously unselected package libblas-dev:arm64. 201s Preparing to unpack .../39-libblas-dev_3.12.0-3_arm64.deb ... 201s Unpacking libblas-dev:arm64 (3.12.0-3) ... 201s Selecting previously unselected package libbz2-dev:arm64. 201s Preparing to unpack .../40-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 201s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 201s Selecting previously unselected package libicu-dev:arm64. 201s Preparing to unpack .../41-libicu-dev_74.2-1ubuntu1_arm64.deb ... 201s Unpacking libicu-dev:arm64 (74.2-1ubuntu1) ... 202s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 202s Preparing to unpack .../42-libjpeg-turbo8-dev_2.1.5-2ubuntu1_arm64.deb ... 202s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 202s Selecting previously unselected package libjpeg8-dev:arm64. 202s Preparing to unpack .../43-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 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Unpacking r-base-dev (4.3.3-2build1) ... 203s Selecting previously unselected package pkg-r-autopkgtest. 203s Preparing to unpack .../60-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 203s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 203s Selecting previously unselected package r-cran-expm. 203s Preparing to unpack .../61-r-cran-expm_0.999-9-1_arm64.deb ... 203s Unpacking r-cran-expm (0.999-9-1) ... 203s Selecting previously unselected package r-cran-gee. 203s Preparing to unpack .../62-r-cran-gee_4.13-26-1_arm64.deb ... 203s Unpacking r-cran-gee (4.13-26-1) ... 203s Selecting previously unselected package autopkgtest-satdep. 203s Preparing to unpack .../63-2-autopkgtest-satdep.deb ... 203s Unpacking autopkgtest-satdep (0) ... 203s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 203s Setting up r-cran-expm (0.999-9-1) ... 203s Setting up libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 203s Setting up libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 203s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 203s Setting up libpkgconf3:arm64 (1.8.1-2) ... 203s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 203s Setting up libmpc3:arm64 (1.3.1-1) ... 203s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 203s Setting up icu-devtools (74.2-1ubuntu1) ... 203s Setting up pkgconf-bin (1.8.1-2) ... 203s Setting up liblzma-dev:arm64 (5.4.5-0.3) ... 203s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 203s Setting up libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 203s Setting up libnsl-dev:arm64 (1.3.0-3) ... 203s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 203s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 203s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 203s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 203s Setting up r-cran-gee (4.13-26-1) ... 203s Setting up libisl23:arm64 (0.26-3) ... 203s Setting up libc-dev-bin (2.39-0ubuntu2) ... 203s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 203s Setting up liblsan0:arm64 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(74.2-1ubuntu1) ... 203s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 203s Setting up libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 203s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 203s Setting up libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 203s Setting up libpcre2-dev:arm64 (10.42-4ubuntu1) ... 203s Setting up cpp-13 (13.2.0-17ubuntu2) ... 203s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 203s Setting up libreadline-dev:arm64 (8.2-3.1) ... 203s Setting up gcc-13 (13.2.0-17ubuntu2) ... 203s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 203s Setting up cpp (4:13.2.0-7ubuntu1) ... 203s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 203s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 203s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 203s Setting up g++-13 (13.2.0-17ubuntu2) ... 203s Setting up libpng-dev:arm64 (1.6.43-3) ... 203s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 203s Setting up gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 203s Setting up gcc (4:13.2.0-7ubuntu1) ... 203s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 203s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 203s Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 203s Setting up gfortran (4:13.2.0-7ubuntu1) ... 203s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 203s 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 203s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 203s 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 203s Setting up g++ (4:13.2.0-7ubuntu1) ... 203s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 203s Setting up build-essential (12.10ubuntu1) ... 203s Setting up r-base-dev (4.3.3-2build1) ... 203s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 203s Setting up autopkgtest-satdep (0) ... 203s Processing triggers for man-db (2.12.0-3) ... 204s Processing triggers for install-info (7.1-3) ... 204s Processing triggers for libc-bin (2.39-0ubuntu2) ... 207s (Reading database ... 83064 files and directories currently installed.) 207s Removing autopkgtest-satdep (0) ... 208s autopkgtest [17:53:38]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 208s autopkgtest [17:53:38]: test pkg-r-autopkgtest: [----------------------- 208s Test: Try to load the R library ape 208s 208s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 208s Copyright (C) 2024 The R Foundation for Statistical Computing 208s Platform: aarch64-unknown-linux-gnu (64-bit) 208s 208s R is free software and comes with ABSOLUTELY NO WARRANTY. 208s You are welcome to redistribute it under certain conditions. 208s Type 'license()' or 'licence()' for distribution details. 208s 208s R is a collaborative project with many contributors. 208s Type 'contributors()' for more information and 208s 'citation()' on how to cite R or R packages in publications. 208s 208s Type 'demo()' for some demos, 'help()' for on-line help, or 208s 'help.start()' for an HTML browser interface to help. 208s Type 'q()' to quit R. 208s 208s > library('ape') 209s > 209s > 209s Other tests are currently unsupported! 209s They will be progressively added. 209s autopkgtest [17:53:39]: test pkg-r-autopkgtest: -----------------------] 210s pkg-r-autopkgtest PASS 210s autopkgtest [17:53:40]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 210s autopkgtest [17:53:40]: @@@@@@@@@@@@@@@@@@@@ summary 210s run-unit-test PASS 210s pkg-r-autopkgtest PASS 221s Creating nova instance adt-noble-arm64-r-cran-ape-20240316-175010-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...