0s autopkgtest [19:32:46]: starting date and time: 2024-03-16 19:32:46+0000 0s autopkgtest [19:32:46]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [19:32:46]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qdf07t_1/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-prabclus --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-arm64-11.secgroup --name adt-noble-arm64-r-cran-prabclus-20240316-193246-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/ 223s autopkgtest [19:36:29]: testbed dpkg architecture: arm64 223s autopkgtest [19:36:29]: testbed apt version: 2.7.12 223s autopkgtest [19:36:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 223s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 224s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 224s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 224s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3657 kB] 224s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 224s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 224s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 224s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 224s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 224s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4013 kB] 224s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 224s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 224s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 226s Fetched 9065 kB in 2s (5485 kB/s) 226s Reading package lists... 229s Reading package lists... 230s Building dependency tree... 230s Reading state information... 230s Calculating upgrade... 231s The following packages will be REMOVED: 231s libglib2.0-0 libssl3 231s The following NEW packages will be installed: 231s libglib2.0-0t64 libssl3t64 xdg-user-dirs 231s The following packages have been kept back: 231s curl 231s The following packages will be upgraded: 231s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 231s ubuntu-minimal ubuntu-standard 231s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 231s Need to get 4613 kB of archives. 231s After this operation, 211 kB of additional disk space will be used. 231s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 231s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 231s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 231s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 231s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 231s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 231s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 231s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 231s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 231s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 232s Fetched 4613 kB in 1s (6561 kB/s) 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 ... 74758 files and directories currently installed.) 232s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 232s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 232s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 232s udisks2 depends on libglib2.0-0 (>= 2.77.0). 232s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 232s python3-gi depends on libglib2.0-0 (>= 2.77.0). 232s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 232s netplan.io depends on libglib2.0-0 (>= 2.70.0). 232s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 232s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 232s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 232s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 232s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 232s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 232s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 232s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 232s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 232s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 232s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 232s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 232s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 232s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 232s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 232s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 232s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 232s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 232s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 232s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 232s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 232s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 232s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 232s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 232s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 232s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 232s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 232s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 232s fwupd depends on libglib2.0-0 (>= 2.79.0). 232s bolt depends on libglib2.0-0 (>= 2.56.0). 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 ... 74758 files and directories currently installed.) 232s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 232s Selecting previously unselected package libglib2.0-0t64: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 ... 74733 files and directories currently installed.) 232s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 232s 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... 232s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 232s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 232s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 232s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 232s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 232s wget depends on libssl3 (>= 3.0.0). 232s u-boot-tools depends on libssl3 (>= 3.0.0). 232s tnftp depends on libssl3 (>= 3.0.0). 232s tcpdump depends on libssl3 (>= 3.0.0). 232s systemd-resolved depends on libssl3 (>= 3.0.0). 232s systemd depends on libssl3 (>= 3.0.0). 232s sudo depends on libssl3 (>= 3.0.0). 232s sbsigntool depends on libssl3 (>= 3.0.0). 232s rsync depends on libssl3 (>= 3.0.0). 232s python3-cryptography depends on libssl3 (>= 3.0.0). 232s openssh-server depends on libssl3 (>= 3.0.10). 232s openssh-client depends on libssl3 (>= 3.0.10). 232s mtd-utils depends on libssl3 (>= 3.0.0). 232s mokutil depends on libssl3 (>= 3.0.0). 232s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 232s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 232s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 232s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 232s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 232s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 232s libnvme1 depends on libssl3 (>= 3.0.0). 232s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 232s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 232s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 232s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 232s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 232s kmod depends on libssl3 (>= 3.0.0). 232s dhcpcd-base depends on libssl3 (>= 3.0.0). 232s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 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 ... 74758 files and directories currently installed.) 232s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 233s Selecting previously unselected package libssl3t64:arm64. 233s (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.) 233s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 233s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 233s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 233s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 233s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ... 233s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 233s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ... 233s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 233s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ... 233s Unpacking ubuntu-minimal (1.536) over (1.535) ... 233s Selecting previously unselected package xdg-user-dirs. 233s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ... 233s Unpacking xdg-user-dirs (0.18-1) ... 233s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ... 233s Unpacking ubuntu-standard (1.536) over (1.535) ... 233s Setting up ubuntu-minimal (1.536) ... 233s Setting up xdg-user-dirs (0.18-1) ... 233s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 233s Setting up libtirpc-common (1.3.4+ds-1.1) ... 233s Setting up ubuntu-standard (1.536) ... 233s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 233s No schema files found: doing nothing. 233s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 233s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 233s Setting up openssl (3.0.13-0ubuntu1) ... 233s Setting up readline-common (8.2-3.1) ... 233s Processing triggers for man-db (2.12.0-3) ... 234s Processing triggers for install-info (7.1-3) ... 234s Processing triggers for libc-bin (2.39-0ubuntu2) ... 234s Reading package lists... 234s Building dependency tree... 234s Reading state information... 235s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 236s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 236s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 236s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 236s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 237s Reading package lists... 237s Reading package lists... 237s Building dependency tree... 237s Reading state information... 238s Calculating upgrade... 238s The following packages have been kept back: 238s curl 238s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 238s Reading package lists... 239s Building dependency tree... 239s Reading state information... 240s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 243s autopkgtest [19:36:49]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 243s autopkgtest [19:36:49]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-prabclus 245s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-prabclus 2.3-3-1 (dsc) [2190 B] 245s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-prabclus 2.3-3-1 (tar) [192 kB] 245s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-prabclus 2.3-3-1 (diff) [2544 B] 245s gpgv: Signature made Tue Nov 21 14:28:24 2023 UTC 245s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 245s gpgv: issuer "tille@debian.org" 245s gpgv: Can't check signature: No public key 245s dpkg-source: warning: cannot verify inline signature for ./r-cran-prabclus_2.3-3-1.dsc: no acceptable signature found 245s autopkgtest [19:36:51]: testing package r-cran-prabclus version 2.3-3-1 246s autopkgtest [19:36:52]: build not needed 247s autopkgtest [19:36:53]: test run-unit-test: preparing testbed 250s Reading package lists... 250s Building dependency tree... 250s Reading state information... 250s Starting pkgProblemResolver with broken count: 0 250s Starting 2 pkgProblemResolver with broken count: 0 250s Done 251s The following additional packages will be installed: 251s curl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 251s gdal-data gdal-plugins libaec0 libarmadillo12 libarpack2 libblas3 libblosc1 251s libcairo2 libcfitsio10 libcurl4t64 libdatrie1 libdav1d7 libde265-0 251s libdeflate0 libfontconfig1 libfreexl1 libfyba0 libgdal34 libgeos-c1v5 251s libgeos3.12.1 libgeotiff5 libgfortran5 libgif7 libgomp1 libgraphite2-3 251s libharfbuzz0b libhdf4-0-alt libhdf5-103-1 libhdf5-hl-100 251s libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libice6 libjbig0 251s libjpeg-turbo8 libjpeg8 libkmlbase1 libkmldom1 libkmlengine1 liblapack3 251s liblcms2-2 liblerc4 libltdl7 libminizip1 libmysqlclient21 libnetcdf19 251s libodbc2 libodbcinst2 libogdi4.1 libopenjp2-7 libpango-1.0-0 251s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 251s libpng16-16t64 libpoppler134 libpq5 libproj25 libpsl5t64 libqhull-r8.0 251s libreadline8t64 librttopo1 libsharpyuv0 libsm6 libsnappy1v5 libspatialite8 251s libsuperlu6 libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc3t64 251s libtk8.6 libudunits2-0 libudunits2-data liburiparser1 libwebp7 251s libxcb-render0 libxcb-shm0 libxerces-c3.2 libxft2 libxrender1 libxss1 251s libxt6t64 littler mysql-common proj-data r-base-core r-cran-boot 251s r-cran-class r-cran-classint r-cran-coda r-cran-codetools r-cran-dbi 251s r-cran-deldir r-cran-e1071 r-cran-foreign r-cran-kernsmooth r-cran-lattice 251s r-cran-learnbayes r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix 251s r-cran-mclust r-cran-multcomp r-cran-mvtnorm r-cran-nlme r-cran-pkgkitten 251s r-cran-prabclus r-cran-proxy r-cran-rcpp r-cran-s2 r-cran-sandwich r-cran-sf 251s r-cran-sp r-cran-spatialreg r-cran-spdata r-cran-spdep r-cran-survival 251s r-cran-th.data r-cran-units r-cran-wk r-cran-zoo unixodbc-common unzip 251s x11-common xdg-utils zip 251s Suggested packages: 251s geotiff-bin gdal-bin libgeotiff-epsg libhdf4-doc libhdf4-alt-dev hdf4-tools 251s libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc 251s libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-rav1e 251s libheif-plugin-svtenc liblcms2-utils odbc-postgresql tdsodbc ogdi-bin 251s proj-bin tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 251s r-cran-rmysql r-cran-polyclip r-cran-getopt r-cran-covr r-cran-knitr 251s r-cran-rlang r-cran-rmarkdown r-cran-geometry r-cran-inline 251s Recommended packages: 251s proj-bin libheif-plugin-aomenc libheif-plugin-x265 poppler-data 251s r-recommended r-base-dev r-doc-html r-cran-knitr r-cran-rmarkdown 251s r-cran-tinytest r-cran-testthat r-cran-crayon r-cran-cba r-cran-bit64 251s r-cran-vctrs r-cran-blob r-cran-covr r-cran-dplyr r-cran-ggplot2 251s r-cran-lwgeom r-cran-maps r-cran-pbapply r-cran-pillar r-cran-raster 251s r-cran-rlang r-cran-rpostgresql r-cran-rsqlite r-cran-spatstat 251s r-cran-spatstat.geom r-cran-spatstat.random r-cran-spatstat.linnet 251s r-cran-spatstat.utils r-cran-stars r-cran-terra r-cran-tibble r-cran-tidyr 251s r-cran-tidyselect r-cran-rcolorbrewer r-cran-gstat r-cran-rspectra 251s r-cran-spam r-cran-lmtest r-cran-expm r-cran-igraph r-cran-dbscan 251s r-cran-xtable r-cran-xml2 r-cran-vdiffr r-cran-readr libfile-mimeinfo-perl 251s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 251s The following packages will be REMOVED: 251s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 251s The following NEW packages will be installed: 251s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 251s fonts-dejavu-mono gdal-data gdal-plugins libaec0 libarmadillo12 libarpack2 251s libblas3 libblosc1 libcairo2 libcfitsio10 libcurl4t64 libdatrie1 libdav1d7 251s libde265-0 libdeflate0 libfontconfig1 libfreexl1 libfyba0 libgdal34 251s libgeos-c1v5 libgeos3.12.1 libgeotiff5 libgfortran5 libgif7 libgomp1 251s libgraphite2-3 libharfbuzz0b libhdf4-0-alt libhdf5-103-1 libhdf5-hl-100 251s libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libice6 libjbig0 251s libjpeg-turbo8 libjpeg8 libkmlbase1 libkmldom1 libkmlengine1 liblapack3 251s liblcms2-2 liblerc4 libltdl7 libminizip1 libmysqlclient21 libnetcdf19 251s libodbc2 libodbcinst2 libogdi4.1 libopenjp2-7 libpango-1.0-0 251s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 251s libpng16-16t64 libpoppler134 libpq5 libproj25 libpsl5t64 libqhull-r8.0 251s libreadline8t64 librttopo1 libsharpyuv0 libsm6 libsnappy1v5 libspatialite8 251s libsuperlu6 libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc3t64 251s libtk8.6 libudunits2-0 libudunits2-data liburiparser1 libwebp7 251s libxcb-render0 libxcb-shm0 libxerces-c3.2 libxft2 libxrender1 libxss1 251s libxt6t64 littler mysql-common proj-data r-base-core r-cran-boot 251s r-cran-class r-cran-classint r-cran-coda r-cran-codetools r-cran-dbi 251s r-cran-deldir r-cran-e1071 r-cran-foreign r-cran-kernsmooth r-cran-lattice 251s r-cran-learnbayes r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix 251s r-cran-mclust r-cran-multcomp r-cran-mvtnorm r-cran-nlme r-cran-pkgkitten 251s r-cran-prabclus r-cran-proxy r-cran-rcpp r-cran-s2 r-cran-sandwich r-cran-sf 251s r-cran-sp r-cran-spatialreg r-cran-spdata r-cran-spdep r-cran-survival 251s r-cran-th.data r-cran-units r-cran-wk r-cran-zoo unixodbc-common unzip 251s x11-common xdg-utils zip 251s The following packages will be upgraded: 251s curl 251s 1 upgraded, 137 newly installed, 5 to remove and 0 not upgraded. 251s Need to get 120 MB/120 MB of archives. 251s After this operation, 261 MB of additional disk space will be used. 251s Get:1 /tmp/autopkgtest.smI7Ml/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [736 B] 251s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 251s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 252s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 252s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 252s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 252s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 252s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 252s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 252s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 252s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 252s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 252s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 gdal-data all 3.8.4+dfsg-1 [261 kB] 252s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 gdal-plugins arm64 3.8.4+dfsg-1 [24.5 kB] 252s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 252s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 252s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 252s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 252s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 libarpack2 arm64 3.9.1-1 [90.2 kB] 252s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 libsuperlu6 arm64 6.0.1+dfsg1-1 [166 kB] 252s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 libarmadillo12 arm64 1:12.6.7+dfsg-1 [134 kB] 252s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libsnappy1v5 arm64 1.1.10-1 [28.2 kB] 252s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 libblosc1 arm64 1.21.5+ds-1 [25.5 kB] 252s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 252s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 252s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 252s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 252s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 252s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 libcfitsio10 arm64 4.3.1-1 [519 kB] 252s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 252s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 libdav1d7 arm64 1.4.0-1 [297 kB] 252s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 libde265-0 arm64 1.0.15-1 [167 kB] 252s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 252s Get:34 http://ftpmaster.internal/ubuntu noble/universe arm64 libfyba0 arm64 4.1.1-8 [119 kB] 252s Get:35 http://ftpmaster.internal/ubuntu noble/universe arm64 libminizip1 arm64 1:1.3.dfsg-3ubuntu1 [22.3 kB] 252s Get:36 http://ftpmaster.internal/ubuntu noble/universe arm64 libfreexl1 arm64 2.0.0-1 [41.1 kB] 252s Get:37 http://ftpmaster.internal/ubuntu noble/universe arm64 libgeos3.12.1 arm64 3.12.1-1 [825 kB] 252s Get:38 http://ftpmaster.internal/ubuntu noble/universe arm64 libgeos-c1v5 arm64 3.12.1-1 [88.8 kB] 252s Get:39 http://ftpmaster.internal/ubuntu noble/universe arm64 proj-data all 9.3.1-1 [7867 kB] 252s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 252s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 252s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 252s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 252s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 252s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 252s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 252s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 libproj25 arm64 9.3.1-1 [1261 kB] 252s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 libgeotiff5 arm64 1.7.1-5 [59.8 kB] 252s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libgif7 arm64 5.2.1-2.5 [34.2 kB] 253s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf4-0-alt arm64 4.2.16-3 [267 kB] 253s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 253s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 253s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 libheif-plugin-dav1d arm64 1.17.6-1ubuntu1 [10.9 kB] 253s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 libheif-plugin-libde265 arm64 1.17.6-1ubuntu1 [9062 B] 253s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 libheif1 arm64 1.17.6-1ubuntu1 [311 kB] 253s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 liburiparser1 arm64 0.9.7+dfsg-2 [34.0 kB] 253s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 libkmlbase1 arm64 1.3.0-10 [45.7 kB] 253s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 libkmldom1 arm64 1.3.0-10 [140 kB] 253s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 libkmlengine1 arm64 1.3.0-10 [64.9 kB] 253s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 mysql-common all 5.8+1.1.0 [6626 B] 253s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libmysqlclient21 arm64 8.0.36-1 [1271 kB] 253s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-hl-100 arm64 1.10.10+repack-3ubuntu1 [55.5 kB] 253s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 libnetcdf19 arm64 1:4.9.2-3ubuntu1 [470 kB] 253s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libltdl7 arm64 2.4.7-7 [40.3 kB] 253s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libodbc2 arm64 2.3.12-1 [144 kB] 253s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 unixodbc-common all 2.3.12-1 [8524 B] 253s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libodbcinst2 arm64 2.3.12-1 [29.3 kB] 253s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 libogdi4.1 arm64 4.1.1+ds-1 [204 kB] 253s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 253s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 253s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libpoppler134 arm64 24.02.0-1ubuntu2 [1072 kB] 253s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libpq5 arm64 16.2-1 [136 kB] 253s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 libqhull-r8.0 arm64 2020.2-6 [188 kB] 253s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 librttopo1 arm64 1.1.0-3 [184 kB] 253s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 libspatialite8 arm64 5.1.0-1 [1938 kB] 253s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 libxerces-c3.2 arm64 3.2.4+debian-1.1 [1065 kB] 253s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 libgdal34 arm64 3.8.4+dfsg-1 [7887 kB] 253s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 253s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 253s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 253s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 253s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 253s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 253s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 253s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 253s Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 253s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 253s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 253s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 253s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 253s Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 253s Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 253s Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 253s Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 253s Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 libudunits2-data all 2.2.28-7 [19.3 kB] 253s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 libudunits2-0 arm64 2.2.28-7 [52.5 kB] 254s Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 254s Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 254s Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 254s Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 254s Get:101 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 254s Get:102 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 255s Get:103 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 255s Get:104 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-boot all 1.3-30-1 [619 kB] 255s Get:105 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 255s Get:106 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-class arm64 7.3-22-2 [88.2 kB] 255s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-proxy arm64 0.4-27-1 [181 kB] 255s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-e1071 arm64 1.7-14-1 [556 kB] 255s Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-kernsmooth arm64 2.23-22-1 [91.1 kB] 255s Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-classint arm64 0.4-10+dfsg-1 [106 kB] 255s Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 255s Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-coda all 0.19-4.1-1 [321 kB] 255s Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-codetools all 0.2-19-1 [90.5 kB] 255s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dbi all 1.2.2-1 [823 kB] 255s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-deldir arm64 2.0-4-1 [270 kB] 255s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-foreign arm64 0.8.86-1 [240 kB] 255s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-learnbayes all 2.15.1-4build1 [963 kB] 255s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 255s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 255s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mclust arm64 6.0.1-1 [3898 kB] 256s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mvtnorm arm64 1.2-4-1 [723 kB] 256s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survival arm64 3.5-8-1 [6116 kB] 256s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-th.data all 1.1-2-2 [8794 kB] 256s Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-zoo arm64 1.8-12-2 [984 kB] 256s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sandwich all 3.1-0-1 [1484 kB] 256s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-multcomp all 1.4-25-1 [709 kB] 256s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 256s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 256s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-prabclus all 2.3-3-1 [521 kB] 256s Get:130 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 256s Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-wk arm64 0.9.1-1 [1785 kB] 256s Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-s2 arm64 1.1.6-1 [1947 kB] 257s Get:133 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-units arm64 0.8-5+dfsg-1 [270 kB] 257s Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sf arm64 1.0-15+dfsg-1 [2989 kB] 257s Get:135 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sp arm64 1:2.1-2+dfsg-1 [1448 kB] 257s Get:136 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spdata all 2.3.0-1 [3734 kB] 257s Get:137 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spdep arm64 1.3-1+dfsg-1 [2134 kB] 257s Get:138 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatialreg arm64 1.3-1+dfsg-1 [915 kB] 258s Preconfiguring packages ... 258s Fetched 120 MB in 6s (20.5 MB/s) 258s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 258s wget depends on libpsl5 (>= 0.16.0). 258s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 258s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 258s 258s (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.) 258s Removing libpsl5:arm64 (0.21.2-1build1) ... 258s Selecting previously unselected package libpsl5t64:arm64. 258s (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.) 258s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 258s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 258s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 258s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 258s (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.) 258s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 258s Selecting previously unselected package libcurl4t64:arm64. 258s (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.) 258s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 258s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 258s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 258s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 258s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 258s 258s (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.) 258s Removing libpng16-16:arm64 (1.6.43-1) ... 258s Selecting previously unselected package libpng16-16t64:arm64. 258s (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.) 258s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 258s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 259s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 259s parted depends on libreadline8 (>= 6.0). 259s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 259s gpgsm depends on libreadline8 (>= 6.0). 259s gpgconf depends on libreadline8 (>= 6.0). 259s gpg depends on libreadline8 (>= 6.0). 259s gawk depends on libreadline8 (>= 6.0). 259s fdisk depends on libreadline8 (>= 6.0). 259s 259s (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.) 259s Removing libreadline8:arm64 (8.2-3) ... 259s Selecting previously unselected package libreadline8t64:arm64. 259s (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.) 259s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 259s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 259s 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' 259s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 259s 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' 259s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 259s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 259s lsof depends on libtirpc3 (>= 1.0.2). 259s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 259s libnss-nisplus:arm64 depends on libtirpc3 (>= 1.0.2). 259s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 259s iproute2 depends on libtirpc3 (>= 1.0.2). 259s 259s (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.) 259s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 259s Selecting previously unselected package libtirpc3t64:arm64. 259s (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.) 259s Preparing to unpack .../000-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 259s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 259s 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' 259s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 259s Selecting previously unselected package fonts-dejavu-mono. 259s Preparing to unpack .../001-fonts-dejavu-mono_2.37-8_all.deb ... 259s Unpacking fonts-dejavu-mono (2.37-8) ... 259s Selecting previously unselected package fonts-dejavu-core. 259s Preparing to unpack .../002-fonts-dejavu-core_2.37-8_all.deb ... 259s Unpacking fonts-dejavu-core (2.37-8) ... 259s Selecting previously unselected package fontconfig-config. 259s Preparing to unpack .../003-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 260s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 260s Selecting previously unselected package libfontconfig1:arm64. 260s Preparing to unpack .../004-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 260s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 260s Selecting previously unselected package fontconfig. 260s Preparing to unpack .../005-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 260s Unpacking fontconfig (2.15.0-1ubuntu1) ... 260s Selecting previously unselected package gdal-data. 260s Preparing to unpack .../006-gdal-data_3.8.4+dfsg-1_all.deb ... 260s Unpacking gdal-data (3.8.4+dfsg-1) ... 260s Selecting previously unselected package gdal-plugins:arm64. 260s Preparing to unpack .../007-gdal-plugins_3.8.4+dfsg-1_arm64.deb ... 260s Unpacking gdal-plugins:arm64 (3.8.4+dfsg-1) ... 260s Selecting previously unselected package libaec0:arm64. 260s Preparing to unpack .../008-libaec0_1.1.2-1_arm64.deb ... 260s Unpacking libaec0:arm64 (1.1.2-1) ... 260s Selecting previously unselected package libblas3:arm64. 260s Preparing to unpack .../009-libblas3_3.12.0-3_arm64.deb ... 260s Unpacking libblas3:arm64 (3.12.0-3) ... 260s Selecting previously unselected package libgfortran5:arm64. 260s Preparing to unpack .../010-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 260s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 260s Selecting previously unselected package liblapack3:arm64. 260s Preparing to unpack .../011-liblapack3_3.12.0-3_arm64.deb ... 260s Unpacking liblapack3:arm64 (3.12.0-3) ... 260s Selecting previously unselected package libarpack2:arm64. 260s Preparing to unpack .../012-libarpack2_3.9.1-1_arm64.deb ... 260s Unpacking libarpack2:arm64 (3.9.1-1) ... 260s Selecting previously unselected package libsuperlu6:arm64. 260s Preparing to unpack .../013-libsuperlu6_6.0.1+dfsg1-1_arm64.deb ... 260s Unpacking libsuperlu6:arm64 (6.0.1+dfsg1-1) ... 260s Selecting previously unselected package libarmadillo12. 260s Preparing to unpack .../014-libarmadillo12_1%3a12.6.7+dfsg-1_arm64.deb ... 260s Unpacking libarmadillo12 (1:12.6.7+dfsg-1) ... 260s Selecting previously unselected package libsnappy1v5:arm64. 260s Preparing to unpack .../015-libsnappy1v5_1.1.10-1_arm64.deb ... 260s Unpacking libsnappy1v5:arm64 (1.1.10-1) ... 260s Selecting previously unselected package libblosc1:arm64. 260s Preparing to unpack .../016-libblosc1_1.21.5+ds-1_arm64.deb ... 260s Unpacking libblosc1:arm64 (1.21.5+ds-1) ... 260s Selecting previously unselected package libpixman-1-0:arm64. 260s Preparing to unpack .../017-libpixman-1-0_0.42.2-1_arm64.deb ... 260s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 260s Selecting previously unselected package libxcb-render0:arm64. 260s Preparing to unpack .../018-libxcb-render0_1.15-1_arm64.deb ... 260s Unpacking libxcb-render0:arm64 (1.15-1) ... 260s Selecting previously unselected package libxcb-shm0:arm64. 260s Preparing to unpack .../019-libxcb-shm0_1.15-1_arm64.deb ... 260s Unpacking libxcb-shm0:arm64 (1.15-1) ... 260s Selecting previously unselected package libxrender1:arm64. 260s Preparing to unpack .../020-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 260s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 260s Selecting previously unselected package libcairo2:arm64. 260s Preparing to unpack .../021-libcairo2_1.18.0-1_arm64.deb ... 260s Unpacking libcairo2:arm64 (1.18.0-1) ... 260s Selecting previously unselected package libcfitsio10:arm64. 260s Preparing to unpack .../022-libcfitsio10_4.3.1-1_arm64.deb ... 260s Unpacking libcfitsio10:arm64 (4.3.1-1) ... 260s Selecting previously unselected package libdatrie1:arm64. 260s Preparing to unpack .../023-libdatrie1_0.2.13-3_arm64.deb ... 260s Unpacking libdatrie1:arm64 (0.2.13-3) ... 260s Selecting previously unselected package libdav1d7:arm64. 260s Preparing to unpack .../024-libdav1d7_1.4.0-1_arm64.deb ... 260s Unpacking libdav1d7:arm64 (1.4.0-1) ... 260s Selecting previously unselected package libde265-0:arm64. 260s Preparing to unpack .../025-libde265-0_1.0.15-1_arm64.deb ... 260s Unpacking libde265-0:arm64 (1.0.15-1) ... 260s Selecting previously unselected package libdeflate0:arm64. 260s Preparing to unpack .../026-libdeflate0_1.19-1_arm64.deb ... 260s Unpacking libdeflate0:arm64 (1.19-1) ... 261s Selecting previously unselected package libfyba0:arm64. 261s Preparing to unpack .../027-libfyba0_4.1.1-8_arm64.deb ... 261s Unpacking libfyba0:arm64 (4.1.1-8) ... 261s Selecting previously unselected package libminizip1:arm64. 261s Preparing to unpack .../028-libminizip1_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 261s Unpacking libminizip1:arm64 (1:1.3.dfsg-3ubuntu1) ... 261s Selecting previously unselected package libfreexl1:arm64. 261s Preparing to unpack .../029-libfreexl1_2.0.0-1_arm64.deb ... 261s Unpacking libfreexl1:arm64 (2.0.0-1) ... 261s Selecting previously unselected package libgeos3.12.1:arm64. 261s Preparing to unpack .../030-libgeos3.12.1_3.12.1-1_arm64.deb ... 261s Unpacking libgeos3.12.1:arm64 (3.12.1-1) ... 261s Selecting previously unselected package libgeos-c1v5:arm64. 261s Preparing to unpack .../031-libgeos-c1v5_3.12.1-1_arm64.deb ... 261s Unpacking libgeos-c1v5:arm64 (3.12.1-1) ... 261s Selecting previously unselected package proj-data. 261s Preparing to unpack .../032-proj-data_9.3.1-1_all.deb ... 261s Unpacking proj-data (9.3.1-1) ... 261s Selecting previously unselected package libjbig0:arm64. 261s Preparing to unpack .../033-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 261s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 261s Selecting previously unselected package libjpeg-turbo8:arm64. 261s Preparing to unpack .../034-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 261s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 261s Selecting previously unselected package libjpeg8:arm64. 261s Preparing to unpack .../035-libjpeg8_8c-2ubuntu11_arm64.deb ... 261s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 261s Selecting previously unselected package liblerc4:arm64. 261s Preparing to unpack .../036-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 261s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 261s Selecting previously unselected package libsharpyuv0:arm64. 261s Preparing to unpack .../037-libsharpyuv0_1.3.2-0.4_arm64.deb ... 261s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 261s Selecting previously unselected package libwebp7:arm64. 261s Preparing to unpack .../038-libwebp7_1.3.2-0.4_arm64.deb ... 261s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 261s Selecting previously unselected package libtiff6:arm64. 261s Preparing to unpack .../039-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 261s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 261s Selecting previously unselected package libproj25:arm64. 261s Preparing to unpack .../040-libproj25_9.3.1-1_arm64.deb ... 261s Unpacking libproj25:arm64 (9.3.1-1) ... 261s Selecting previously unselected package libgeotiff5:arm64. 261s Preparing to unpack .../041-libgeotiff5_1.7.1-5_arm64.deb ... 261s Unpacking libgeotiff5:arm64 (1.7.1-5) ... 261s Selecting previously unselected package libgif7:arm64. 261s Preparing to unpack .../042-libgif7_5.2.1-2.5_arm64.deb ... 261s Unpacking libgif7:arm64 (5.2.1-2.5) ... 261s Selecting previously unselected package libhdf4-0-alt. 261s Preparing to unpack .../043-libhdf4-0-alt_4.2.16-3_arm64.deb ... 261s Unpacking libhdf4-0-alt (4.2.16-3) ... 261s Selecting previously unselected package libsz2:arm64. 261s Preparing to unpack .../044-libsz2_1.1.2-1_arm64.deb ... 261s Unpacking libsz2:arm64 (1.1.2-1) ... 261s Selecting previously unselected package libhdf5-103-1:arm64. 261s Preparing to unpack .../045-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 261s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 261s Selecting previously unselected package libheif-plugin-dav1d:arm64. 261s Preparing to unpack .../046-libheif-plugin-dav1d_1.17.6-1ubuntu1_arm64.deb ... 261s Unpacking libheif-plugin-dav1d:arm64 (1.17.6-1ubuntu1) ... 261s Selecting previously unselected package libheif-plugin-libde265:arm64. 261s Preparing to unpack .../047-libheif-plugin-libde265_1.17.6-1ubuntu1_arm64.deb ... 261s Unpacking libheif-plugin-libde265:arm64 (1.17.6-1ubuntu1) ... 261s Selecting previously unselected package libheif1:arm64. 261s Preparing to unpack .../048-libheif1_1.17.6-1ubuntu1_arm64.deb ... 261s Unpacking libheif1:arm64 (1.17.6-1ubuntu1) ... 261s Selecting previously unselected package liburiparser1:arm64. 261s Preparing to unpack .../049-liburiparser1_0.9.7+dfsg-2_arm64.deb ... 261s Unpacking liburiparser1:arm64 (0.9.7+dfsg-2) ... 262s Selecting previously unselected package libkmlbase1:arm64. 262s Preparing to unpack .../050-libkmlbase1_1.3.0-10_arm64.deb ... 262s Unpacking libkmlbase1:arm64 (1.3.0-10) ... 262s Selecting previously unselected package libkmldom1:arm64. 262s Preparing to unpack .../051-libkmldom1_1.3.0-10_arm64.deb ... 262s Unpacking libkmldom1:arm64 (1.3.0-10) ... 262s Selecting previously unselected package libkmlengine1:arm64. 262s Preparing to unpack .../052-libkmlengine1_1.3.0-10_arm64.deb ... 262s Unpacking libkmlengine1:arm64 (1.3.0-10) ... 262s Selecting previously unselected package mysql-common. 262s Preparing to unpack .../053-mysql-common_5.8+1.1.0_all.deb ... 262s Unpacking mysql-common (5.8+1.1.0) ... 262s Selecting previously unselected package libmysqlclient21:arm64. 262s Preparing to unpack .../054-libmysqlclient21_8.0.36-1_arm64.deb ... 262s Unpacking libmysqlclient21:arm64 (8.0.36-1) ... 262s Selecting previously unselected package libhdf5-hl-100:arm64. 262s Preparing to unpack .../055-libhdf5-hl-100_1.10.10+repack-3ubuntu1_arm64.deb ... 262s Unpacking libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 262s Selecting previously unselected package libnetcdf19:arm64. 262s Preparing to unpack .../056-libnetcdf19_1%3a4.9.2-3ubuntu1_arm64.deb ... 262s Unpacking libnetcdf19:arm64 (1:4.9.2-3ubuntu1) ... 262s Selecting previously unselected package libltdl7:arm64. 262s Preparing to unpack .../057-libltdl7_2.4.7-7_arm64.deb ... 262s Unpacking libltdl7:arm64 (2.4.7-7) ... 262s Selecting previously unselected package libodbc2:arm64. 262s Preparing to unpack .../058-libodbc2_2.3.12-1_arm64.deb ... 262s Unpacking libodbc2:arm64 (2.3.12-1) ... 262s Selecting previously unselected package unixodbc-common. 262s Preparing to unpack .../059-unixodbc-common_2.3.12-1_all.deb ... 262s Unpacking unixodbc-common (2.3.12-1) ... 262s Selecting previously unselected package libodbcinst2:arm64. 262s Preparing to unpack .../060-libodbcinst2_2.3.12-1_arm64.deb ... 262s Unpacking libodbcinst2:arm64 (2.3.12-1) ... 262s Selecting previously unselected package libogdi4.1. 262s Preparing to unpack .../061-libogdi4.1_4.1.1+ds-1_arm64.deb ... 262s Unpacking libogdi4.1 (4.1.1+ds-1) ... 262s Selecting previously unselected package libopenjp2-7:arm64. 262s Preparing to unpack .../062-libopenjp2-7_2.5.0-2_arm64.deb ... 262s Unpacking libopenjp2-7:arm64 (2.5.0-2) ... 262s Selecting previously unselected package liblcms2-2:arm64. 262s Preparing to unpack .../063-liblcms2-2_2.14-2_arm64.deb ... 262s Unpacking liblcms2-2:arm64 (2.14-2) ... 262s Selecting previously unselected package libpoppler134:arm64. 262s Preparing to unpack .../064-libpoppler134_24.02.0-1ubuntu2_arm64.deb ... 262s Unpacking libpoppler134:arm64 (24.02.0-1ubuntu2) ... 262s Selecting previously unselected package libpq5:arm64. 262s Preparing to unpack .../065-libpq5_16.2-1_arm64.deb ... 262s Unpacking libpq5:arm64 (16.2-1) ... 262s Selecting previously unselected package libqhull-r8.0:arm64. 262s Preparing to unpack .../066-libqhull-r8.0_2020.2-6_arm64.deb ... 262s Unpacking libqhull-r8.0:arm64 (2020.2-6) ... 262s Selecting previously unselected package librttopo1:arm64. 262s Preparing to unpack .../067-librttopo1_1.1.0-3_arm64.deb ... 262s Unpacking librttopo1:arm64 (1.1.0-3) ... 262s Selecting previously unselected package libspatialite8:arm64. 262s Preparing to unpack .../068-libspatialite8_5.1.0-1_arm64.deb ... 262s Unpacking libspatialite8:arm64 (5.1.0-1) ... 262s Selecting previously unselected package libxerces-c3.2:arm64. 262s Preparing to unpack .../069-libxerces-c3.2_3.2.4+debian-1.1_arm64.deb ... 262s Unpacking libxerces-c3.2:arm64 (3.2.4+debian-1.1) ... 262s Selecting previously unselected package libgdal34:arm64. 262s Preparing to unpack .../070-libgdal34_3.8.4+dfsg-1_arm64.deb ... 262s Unpacking libgdal34:arm64 (3.8.4+dfsg-1) ... 263s Selecting previously unselected package libgomp1:arm64. 263s Preparing to unpack .../071-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 263s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 263s Selecting previously unselected package libgraphite2-3:arm64. 263s Preparing to unpack .../072-libgraphite2-3_1.3.14-2_arm64.deb ... 263s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 263s Selecting previously unselected package libharfbuzz0b:arm64. 263s Preparing to unpack .../073-libharfbuzz0b_8.3.0-2_arm64.deb ... 263s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 263s Selecting previously unselected package x11-common. 263s Preparing to unpack .../074-x11-common_1%3a7.7+23ubuntu2_all.deb ... 263s Unpacking x11-common (1:7.7+23ubuntu2) ... 263s Selecting previously unselected package libice6:arm64. 263s Preparing to unpack .../075-libice6_2%3a1.0.10-1build2_arm64.deb ... 263s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 263s Selecting previously unselected package libthai-data. 263s Preparing to unpack .../076-libthai-data_0.1.29-2_all.deb ... 263s Unpacking libthai-data (0.1.29-2) ... 263s Selecting previously unselected package libthai0:arm64. 263s Preparing to unpack .../077-libthai0_0.1.29-2_arm64.deb ... 263s Unpacking libthai0:arm64 (0.1.29-2) ... 263s Selecting previously unselected package libpango-1.0-0:arm64. 263s Preparing to unpack .../078-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 263s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 263s Selecting previously unselected package libpangoft2-1.0-0:arm64. 263s Preparing to unpack .../079-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 263s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 263s Selecting previously unselected package libpangocairo-1.0-0:arm64. 263s Preparing to unpack .../080-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 263s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 263s Selecting previously unselected package libpaper1:arm64. 263s Preparing to unpack .../081-libpaper1_1.1.29_arm64.deb ... 263s 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(0.4-10+dfsg-1) ... 270s Setting up libheif-plugin-dav1d:arm64 (1.17.6-1ubuntu1) ... 270s Setting up libheif-plugin-libde265:arm64 (1.17.6-1ubuntu1) ... 270s Setting up libheif1:arm64 (1.17.6-1ubuntu1) ... 270s Setting up libgdal34:arm64 (3.8.4+dfsg-1) ... 270s Setting up r-cran-sf (1.0-15+dfsg-1) ... 270s Setting up r-cran-spdep (1.3-1+dfsg-1) ... 270s Setting up r-cran-spatialreg (1.3-1+dfsg-1) ... 270s Setting up autopkgtest-satdep (0) ... 270s Processing triggers for libc-bin (2.39-0ubuntu2) ... 270s Processing triggers for man-db (2.12.0-3) ... 271s Processing triggers for install-info (7.1-3) ... 279s (Reading database ... 80514 files and directories currently installed.) 279s Removing autopkgtest-satdep (0) ... 280s autopkgtest [19:37:26]: test run-unit-test: [----------------------- 280s BEGIN TEST donttestexamples.R 281s 281s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 281s Copyright (C) 2024 The R Foundation for Statistical Computing 281s Platform: aarch64-unknown-linux-gnu (64-bit) 281s 281s R is free software and comes with ABSOLUTELY NO WARRANTY. 281s You are welcome to redistribute it under certain conditions. 281s Type 'license()' or 'licence()' for distribution details. 281s 281s R is a collaborative project with many contributors. 281s Type 'contributors()' for more information and 281s 'citation()' on how to cite R or R packages in publications. 281s 281s Type 'demo()' for some demos, 'help()' for on-line help, or 281s 'help.start()' for an HTML browser interface to help. 281s Type 'q()' to quit R. 281s 281s > library(prabclus) 281s Loading required package: MASS 281s Loading required package: mclust 281s Package 'mclust' version 6.0.1 281s Type 'citation("mclust")' for citing this R package in publications. 281s > 281s > # example(prabclust) 281s > data(kykladspecreg) 281s > data(nb) 281s > set.seed(1234) 281s > x <- prabinit(prabmatrix=kykladspecreg, neighborhood=nb) 281s > # If you want to use your own ASCII data files, use 281s > # x <- prabinit(file="path/prabmatrixfile", 281s > # neighborhood="path/neighborhoodfile") 281s > print(prabclust(x)) 281s * Clustered presence-absence matrix * 281s 281s Clustered: 4 -dim. MDS result from method classical 281s 281s Noise-detector NNclean has been used with k= 2 281s NNclean is explained in S. Byers and A. E. Raftery, JASA 95 (1998), 781-794 281s A Normal mixture model with noise component (mclust) has been used. 281s Mixture component memberships: 281s [1] 0 1 2 3 3 2 7 0 8 0 3 0 0 5 1 7 7 2 5 0 0 2 5 1 5 6 7 6 4 1 4 6 0 7 1 0 0 1 281s [39] 0 2 1 3 4 4 6 0 1 4 3 1 8 0 0 5 6 4 8 5 0 2 5 1 6 8 0 4 3 0 3 4 0 1 8 5 2 2 281s [77] 3 6 0 7 281s 281s Clustering (N denotes noise or one-point components): 281s [1] "N" "1" "2" "3" "3" "2" "7" "N" "8" "N" "3" "N" "N" "5" "1" "7" "7" "2" "5" 281s [20] "N" "N" "2" "5" "1" "5" "6" "7" "6" "4" "1" "4" "6" "N" "7" "1" "N" "N" "1" 281s [39] "N" "2" "1" "3" "4" "4" "6" "N" "1" "4" "3" "1" "8" "N" "N" "5" "6" "4" "8" 281s [58] "5" "N" "2" "5" "1" "6" "8" "N" "4" "3" "N" "3" "4" "N" "1" "8" "5" "2" "2" 281s [77] "3" "6" "N" "7" 281s > 281s > # Here is an example for species delimitation with codominant markers; 281s > # only 50 individuals were used in order to have a fast example. 281s > data(tetragonula) 281s > ta <- alleleconvert(strmatrix=tetragonula[1:50,]) 281s > tai <- alleleinit(allelematrix=ta) 281s > print(prabclust(tai)) 281s * Clustered presence-absence matrix * 281s 281s Clustered: 4 -dim. MDS result from method classical 281s 281s Noise-detector NNclean has been used with k= 2 281s NNclean is explained in S. Byers and A. E. Raftery, JASA 95 (1998), 781-794 281s A Normal mixture model with noise component (mclust) has been used. 281s Mixture component memberships: 281s [1] 2 2 1 1 1 1 1 2 2 1 1 1 2 2 2 1 2 1 2 1 2 2 1 2 1 2 2 2 1 1 1 1 2 1 2 3 0 3 281s [39] 0 0 0 3 3 3 3 0 3 3 3 3 281s 281s Clustering (N denotes noise or one-point components): 281s [1] "2" "2" "1" "1" "1" "1" "1" "2" "2" "1" "1" "1" "2" "2" "2" "1" "2" "1" "2" 281s [20] "1" "2" "2" "1" "2" "1" "2" "2" "2" "1" "1" "1" "1" "2" "1" "2" "3" "N" "3" 281s [39] "N" "N" "N" "3" "3" "3" "3" "N" "3" "3" "3" "3" 281s > 281s > # Here is an example for species delimitation with dominant markers; 281s > # only 50 individuals were used in order to have a fast example. 281s > # You may want to use stressvals to choose mdsdim. 281s > data(veronica) 281s > vei <- prabinit(prabmatrix=veronica[1:50,],distance="jaccard") 281s > print(prabclust(vei,mdsmethod="kruskal",mdsdim=3)) 281s initial value 28.163173 281s iter 5 value 20.897590 281s iter 10 value 19.154545 281s iter 15 value 18.814679 281s iter 20 value 18.493361 281s iter 20 value 18.475223 281s final value 18.228921 281s converged 281s * Clustered presence-absence matrix * 281s 281s Clustered: 3 -dim. MDS result from method kruskal 281s 281s Noise-detector NNclean has been used with k= 2 281s NNclean is explained in S. Byers and A. E. Raftery, JASA 95 (1998), 781-794 281s A Normal mixture model with noise component (mclust) has been used. 281s Mixture component memberships: 281s [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 281s [39] 1 0 0 1 1 1 1 1 1 0 1 0 281s 281s Clustering (N denotes noise or one-point components): 281s [1] "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" 281s [20] "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "N" "1" "1" "1" "1" "1" "1" "1" "1" 281s [39] "1" "N" "N" "1" "1" "1" "1" "1" "1" "N" "1" "N" 281s > 281s > # example(crmatrix) 281s > options(digits=3) 281s > data(kykladspecreg) 281s > data(nb) 281s > set.seed(1234) 281s > x <- prabinit(prabmatrix=kykladspecreg, neighborhood=nb) 282s > xc <- prabclust(x) 282s > 282s > crmatrix(x,xc) 282s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 282s [1,] 0 0 0 1 0 0 0 0 0 0 0 0 0 282s [2,] 0 0 0 0 0 0 0 0 0 0 0 0 0 282s [3,] 0 0 0 0 0 0 0 1 0 1 0 0 0 282s [4,] 0 0 0 0 0 0 0 0 0 1 2 2 2 282s [5,] 1 0 0 0 2 7 3 0 1 2 0 0 1 282s [6,] 0 0 0 0 0 0 0 0 0 0 0 0 0 282s [7,] 0 0 0 0 0 0 0 0 0 0 0 0 0 282s [8,] 5 4 1 0 0 0 0 0 2 0 0 0 0 282s [9,] 9 10 3 3 4 4 4 9 7 9 3 1 4 282s [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] 282s [1,] 0 0 0 0 0 0 0 0 0 0 0 0 282s [2,] 0 0 0 0 0 0 0 0 0 0 0 0 282s [3,] 2 3 2 2 0 1 6 1 3 6 2 2 282s [4,] 1 1 0 1 0 0 0 0 0 0 2 0 282s [5,] 0 0 0 0 0 1 0 0 0 1 0 0 282s [6,] 0 0 0 0 0 0 0 0 0 0 0 0 282s [7,] 0 0 0 0 0 0 0 0 0 0 0 0 282s [8,] 0 0 0 0 0 0 0 0 0 0 0 0 282s [9,] 8 7 6 5 6 8 10 3 4 7 6 8 282s [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] 282s [1,] 0 0 7 8 3 0 0 0 0 282s [2,] 0 8 5 8 1 1 0 3 0 282s [3,] 2 0 0 0 0 0 0 0 0 282s [4,] 2 0 0 0 0 0 0 0 0 282s [5,] 0 0 0 0 0 0 0 0 0 282s [6,] 0 7 0 0 1 1 0 0 0 282s [7,] 0 0 0 0 3 4 2 6 0 282s [8,] 0 0 0 0 0 0 0 0 0 282s [9,] 5 4 4 5 3 4 2 4 4 282s > crmatrix(x,xc, percentages=TRUE) 282s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] 282s [1,] 0.000 0.000 0.000 0.0909 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.0000 282s [2,] 0.000 0.000 0.000 0.0000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.0000 282s [3,] 0.000 0.000 0.000 0.0000 0.000 0.000 0.000 0.125 0.000 0.125 0.000 0.0000 282s [4,] 0.000 0.000 0.000 0.0000 0.000 0.000 0.000 0.000 0.000 0.125 0.250 0.2500 282s [5,] 0.125 0.000 0.000 0.0000 0.250 0.875 0.375 0.000 0.125 0.250 0.000 0.0000 282s [6,] 0.000 0.000 0.000 0.0000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.0000 282s [7,] 0.000 0.000 0.000 0.0000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.0000 282s [8,] 1.000 0.800 0.200 0.0000 0.000 0.000 0.000 0.000 0.400 0.000 0.000 0.0000 282s [9,] 0.474 0.526 0.158 0.1579 0.211 0.211 0.211 0.474 0.368 0.474 0.158 0.0526 282s [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] 282s [1,] 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 282s [2,] 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 282s [3,] 0.000 0.250 0.375 0.250 0.250 0.000 0.125 0.750 0.125 0.375 0.750 0.250 282s [4,] 0.250 0.125 0.125 0.000 0.125 0.000 0.000 0.000 0.000 0.000 0.000 0.250 282s [5,] 0.125 0.000 0.000 0.000 0.000 0.000 0.125 0.000 0.000 0.000 0.125 0.000 282s [6,] 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 282s [7,] 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 282s [8,] 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 282s [9,] 0.211 0.421 0.368 0.316 0.263 0.316 0.421 0.526 0.158 0.211 0.368 0.316 282s [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] 282s [1,] 0.000 0.000 0.000 0.636 0.727 0.273 0.000 0.000 0.000 0.000 282s [2,] 0.000 0.000 1.000 0.625 1.000 0.125 0.125 0.000 0.375 0.000 282s [3,] 0.250 0.250 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 282s [4,] 0.000 0.250 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 282s [5,] 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 282s [6,] 0.000 0.000 1.000 0.000 0.000 0.143 0.143 0.000 0.000 0.000 282s [7,] 0.000 0.000 0.000 0.000 0.000 0.500 0.667 0.333 1.000 0.000 282s [8,] 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 282s [9,] 0.421 0.263 0.211 0.211 0.263 0.158 0.211 0.105 0.211 0.211 282s > 282s > 282s > # example(lociplots) 282s > options(digits=4) 282s > data(veronica) 282s > vei <- prabinit(prabmatrix=veronica[1:50,],distance="jaccard") 282s > ppv <- prabclust(vei) 282s > veloci <- prabinit(prabmatrix=veronica[1:50,],rows.are.species=FALSE) 282s > velociclust <- prabclust(veloci,nnk=0) 282s > lociplots(ppv,velociclust$clustering,veloci,lcluster=3) 282s $locfreq 282s [1] 0.13333 0.26667 0.13333 0.20000 0.13333 0.13333 0.40000 0.20000 0.13333 282s [10] 0.13333 0.06667 0.00000 0.00000 0.20000 0.00000 0.00000 0.06667 0.00000 282s [19] 0.00000 0.00000 0.06667 0.00000 0.06667 0.00000 0.00000 0.00000 0.13333 282s [28] 0.00000 0.00000 0.26667 0.26667 0.33333 0.06667 0.13333 0.13333 0.20000 282s [37] 0.13333 0.13333 0.20000 0.00000 0.00000 0.06667 0.00000 0.06667 0.06667 282s [46] 0.06667 0.06667 0.33333 0.20000 0.13333 282s 282s $locfreqmin 282s [1] 0 0 0 0 282s 282s $locfreqmax 282s [1] 0.33333 0.40000 0.26667 0.06667 282s 282s $locfreqmean 282s [1] 0.14167 0.14510 0.10769 0.02778 282s 282s > 282s > 282s > # Results: 282s > 282s > # R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" 282s > # Copyright (C) 2014 The R Foundation for Statistical Computing 282s > # Platform: x86_64-pc-linux-gnu (64-bit) 282s > # 282s > # R is free software and comes with ABSOLUTELY NO WARRANTY. 282s > # You are welcome to redistribute it under certain conditions. 282s > # Type 'license()' or 'licence()' for distribution details. 282s > # 282s > # R is a collaborative project with many contributors. 282s > # Type 'contributors()' for more information and 282s > # 'citation()' on how to cite R or R packages in publications. 282s > # 282s > # Type 'demo()' for some demos, 'help()' for on-line help, or 282s > # 'help.start()' for an HTML browser interface to help. 282s > # Type 'q()' to quit R. 282s > # 282s > # > library(prabclus) 282s > # Loading required package: MASS 282s > # Loading required package: mclust 282s > # Package 'mclust' version 4.4 282s > # Type 'citation("mclust")' for citing this R package in publications. 282s > # > 282s > # > # example(prabclust) 282s > # > data(kykladspecreg) 282s > # > data(nb) 282s > # > set.seed(1234) 282s > # > x <- prabinit(prabmatrix=kykladspecreg, neighborhood=nb) 282s > # > # If you want to use your own ASCII data files, use 282s > # > # x <- prabinit(file="path/prabmatrixfile", 282s > # > # neighborhood="path/neighborhoodfile") 282s > # > print(prabclust(x)) 282s > # * Clustered presence-absence matrix * 282s > # 282s > # Clustered: 4 -dim. MDS result from method classical 282s > # 282s > # Noise-detector NNclean has been used with k= 2 282s > # NNclean is explained in S. Byers and A. E. Raftery, JASA 95 (1998), 781-794 282s > # A Normal mixture model with noise component (mclust) has been used. 282s > # Mixture component memberships: 282s > # [1] 0 1 0 2 2 8 6 0 7 0 2 0 0 4 1 6 6 8 4 0 0 0 4 1 4 0 6 5 3 1 3 5 0 6 1 0 0 1 282s > # [39] 0 8 1 2 3 3 5 0 1 3 2 1 7 0 0 4 5 3 7 4 0 0 4 1 5 7 0 3 2 0 2 3 0 1 7 4 0 0 282s > # [77] 2 5 0 6 282s > # 282s > # Clustering (N denotes noise or one-point components): 282s > # [1] "N" "1" "N" "2" "2" "8" "6" "N" "7" "N" "2" "N" "N" "4" "1" "6" "6" "8" "4" 282s > # [20] "N" "N" "N" "4" "1" "4" "N" "6" "5" "3" "1" "3" "5" "N" "6" "1" "N" "N" "1" 282s > # [39] "N" "8" "1" "2" "3" "3" "5" "N" "1" "3" "2" "1" "7" "N" "N" "4" "5" "3" "7" 282s > # [58] "4" "N" "N" "4" "1" "5" "7" "N" "3" "2" "N" "2" "3" "N" "1" "7" "4" "N" "N" 282s > # [77] "2" "5" "N" "6" 282s > # > 282s > # > # Here is an example for species delimitation with codominant markers; 282s > # > # only 50 individuals were used in order to have a fast example. 282s > # > data(tetragonula) 282s > # > ta <- alleleconvert(strmatrix=tetragonula[1:50,]) 282s > # > tai <- alleleinit(allelematrix=ta) 282s > # > print(prabclust(tai)) 282s > # * Clustered presence-absence matrix * 282s > # 282s > # Clustered: 4 -dim. MDS result from method classical 282s > # 282s > # Noise-detector NNclean has been used with k= 2 282s > # NNclean is explained in S. Byers and A. E. Raftery, JASA 95 (1998), 781-794 282s > # A Normal mixture model with noise component (mclust) has been used. 282s > # Mixture component memberships: 282s > # [1] 2 2 1 1 1 1 1 2 2 1 1 1 2 2 2 1 2 1 2 1 2 2 1 2 1 2 2 2 1 1 1 1 2 1 2 3 0 3 282s > # [39] 0 0 0 3 3 3 3 0 3 3 3 3 282s > # 282s > # Clustering (N denotes noise or one-point components): 282s > # [1] "2" "2" "1" "1" "1" "1" "1" "2" "2" "1" "1" "1" "2" "2" "2" "1" "2" "1" "2" 282s > # [20] "1" "2" "2" "1" "2" "1" "2" "2" "2" "1" "1" "1" "1" "2" "1" "2" "3" "N" "3" 282s > # [39] "N" "N" "N" "3" "3" "3" "3" "N" "3" "3" "3" "3" 282s > # > 282s > # > # Here is an example for species delimitation with dominant markers; 282s > # > # only 50 individuals were used in order to have a fast example. 282s > # > # You may want to use stressvals to choose mdsdim. 282s > # > data(veronica) 282s > # > vei <- prabinit(prabmatrix=veronica[1:50,],distance="jaccard") 282s > # > print(prabclust(vei,mdsmethod="kruskal",mdsdim=3)) 282s > # initial value 28.163173 282s > # iter 5 value 20.897590 282s > # iter 10 value 19.154545 282s > # iter 15 value 18.814679 282s > # iter 20 value 18.493361 282s > # iter 20 value 18.475223 282s > # final value 18.228921 282s > # converged 282s > # * Clustered presence-absence matrix * 282s > # 282s > # Clustered: 3 -dim. MDS result from method kruskal 282s > # 282s > # Noise-detector NNclean has been used with k= 2 282s > # NNclean is explained in S. Byers and A. E. Raftery, JASA 95 (1998), 781-794 282s > # A Normal mixture model with noise component (mclust) has been used. 282s > # Mixture component memberships: 282s > # [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 282s > # [39] 1 0 0 1 1 1 1 1 1 0 1 0 282s > # 282s > # Clustering (N denotes noise or one-point components): 282s > # [1] "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" 282s > # [20] "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "N" "1" "1" "1" "1" "1" "1" "1" "1" 282s > # [39] "1" "N" "N" "1" "1" "1" "1" "1" "1" "N" "1" "N" 282s > # > 282s > # > # example(crmatrix) 282s > # > options(digits=3) 282s > # > data(kykladspecreg) 282s > # > data(nb) 282s > # > set.seed(1234) 282s > # > x <- prabinit(prabmatrix=kykladspecreg, neighborhood=nb) 282s > # > xc <- prabclust(x) 282s > # > 282s > # > crmatrix(x,xc) 282s > # [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 282s > # [1,] 0 0 0 1 0 0 0 0 0 0 0 0 0 282s > # [2,] 0 0 0 0 0 0 0 1 0 1 0 0 0 282s > # [3,] 0 0 0 0 0 0 0 0 0 1 2 2 2 282s > # [4,] 1 0 0 0 2 7 3 0 1 2 0 0 1 282s > # [5,] 0 0 0 0 0 0 0 0 0 0 0 0 0 282s > # [6,] 0 0 0 0 0 0 0 0 0 0 0 0 0 282s > # [7,] 5 4 1 0 0 0 0 0 2 0 0 0 0 282s > # [8,] 0 0 0 0 0 0 0 0 0 0 0 0 0 282s > # [9,] 9 10 3 3 4 4 4 9 7 9 3 1 4 282s > # [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] 282s > # [1,] 0 0 0 0 0 0 0 0 0 0 0 0 282s > # [2,] 2 3 2 2 0 1 6 1 3 6 2 2 282s > # [3,] 1 1 0 1 0 0 0 0 0 0 2 0 282s > # [4,] 0 0 0 0 0 1 0 0 0 1 0 0 282s > # [5,] 0 0 0 0 0 0 0 0 0 0 0 0 282s > # [6,] 0 0 0 0 0 0 0 0 0 0 0 0 282s > # [7,] 0 0 0 0 0 0 0 0 0 0 0 0 282s > # [8,] 0 0 0 0 0 0 0 0 0 0 0 0 282s > # [9,] 8 7 6 5 6 8 10 3 4 7 6 8 282s > # [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] 282s > # [1,] 0 0 7 8 3 0 0 0 0 282s > # [2,] 2 0 0 0 0 0 0 0 0 282s > # [3,] 2 0 0 0 0 0 0 0 0 282s > # [4,] 0 0 0 0 0 0 0 0 0 282s > # [5,] 0 6 0 0 0 0 0 0 0 282s > # [6,] 0 0 0 0 3 4 2 6 0 282s > # [7,] 0 0 0 0 0 0 0 0 0 282s > # [8,] 0 3 3 3 0 0 0 0 0 282s > # [9,] 5 10 6 10 5 6 2 7 4 282s > # > crmatrix(x,xc, percentages=TRUE) 282s > # [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] 282s > # [1,] 0.000 0.0 0.00 0.0909 0.00 0.000 0.000 0.000 0.000 0.000 0.00 0.00 282s > # [2,] 0.000 0.0 0.00 0.0000 0.00 0.000 0.000 0.125 0.000 0.125 0.00 0.00 282s > # [3,] 0.000 0.0 0.00 0.0000 0.00 0.000 0.000 0.000 0.000 0.125 0.25 0.25 282s > # [4,] 0.125 0.0 0.00 0.0000 0.25 0.875 0.375 0.000 0.125 0.250 0.00 0.00 282s > # [5,] 0.000 0.0 0.00 0.0000 0.00 0.000 0.000 0.000 0.000 0.000 0.00 0.00 282s > # [6,] 0.000 0.0 0.00 0.0000 0.00 0.000 0.000 0.000 0.000 0.000 0.00 0.00 282s > # [7,] 1.000 0.8 0.20 0.0000 0.00 0.000 0.000 0.000 0.400 0.000 0.00 0.00 282s > # [8,] 0.000 0.0 0.00 0.0000 0.00 0.000 0.000 0.000 0.000 0.000 0.00 0.00 282s > # [9,] 0.360 0.4 0.12 0.1200 0.16 0.160 0.160 0.360 0.280 0.360 0.12 0.04 282s > # [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] 282s > # [1,] 0.000 0.000 0.000 0.00 0.000 0.00 0.000 0.00 0.000 0.000 0.000 0.00 282s > # [2,] 0.000 0.250 0.375 0.25 0.250 0.00 0.125 0.75 0.125 0.375 0.750 0.25 282s > # [3,] 0.250 0.125 0.125 0.00 0.125 0.00 0.000 0.00 0.000 0.000 0.000 0.25 282s > # [4,] 0.125 0.000 0.000 0.00 0.000 0.00 0.125 0.00 0.000 0.000 0.125 0.00 282s > # [5,] 0.000 0.000 0.000 0.00 0.000 0.00 0.000 0.00 0.000 0.000 0.000 0.00 282s > # [6,] 0.000 0.000 0.000 0.00 0.000 0.00 0.000 0.00 0.000 0.000 0.000 0.00 282s > # [7,] 0.000 0.000 0.000 0.00 0.000 0.00 0.000 0.00 0.000 0.000 0.000 0.00 282s > # [8,] 0.000 0.000 0.000 0.00 0.000 0.00 0.000 0.00 0.000 0.000 0.000 0.00 282s > # [9,] 0.160 0.320 0.280 0.24 0.200 0.24 0.320 0.40 0.120 0.160 0.280 0.24 282s > # [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] 282s > # [1,] 0.00 0.00 0.0 0.636 0.727 0.273 0.000 0.000 0.00 0.00 282s > # [2,] 0.25 0.25 0.0 0.000 0.000 0.000 0.000 0.000 0.00 0.00 282s > # [3,] 0.00 0.25 0.0 0.000 0.000 0.000 0.000 0.000 0.00 0.00 282s > # [4,] 0.00 0.00 0.0 0.000 0.000 0.000 0.000 0.000 0.00 0.00 282s > # [5,] 0.00 0.00 1.0 0.000 0.000 0.000 0.000 0.000 0.00 0.00 282s > # [6,] 0.00 0.00 0.0 0.000 0.000 0.500 0.667 0.333 1.00 0.00 282s > # [7,] 0.00 0.00 0.0 0.000 0.000 0.000 0.000 0.000 0.00 0.00 282s > # [8,] 0.00 0.00 1.0 1.000 1.000 0.000 0.000 0.000 0.00 0.00 282s > # [9,] 0.32 0.20 0.4 0.240 0.400 0.200 0.240 0.080 0.28 0.16 282s > # > 282s > # > 282s > # > # example(lociplots) 282s > # > options(digits=4) 282s > # > data(veronica) 282s > # > vei <- prabinit(prabmatrix=veronica[1:50,],distance="jaccard") 282s > # > ppv <- prabclust(vei) 282s > # > veloci <- prabinit(prabmatrix=veronica[1:50,],rows.are.species=FALSE) 282s > # > velociclust <- prabclust(veloci,nnk=0) 282s > # > lociplots(ppv,velociclust$clustering,veloci,lcluster=3) 282s > # $locfreq 282s > # [1] 0.4737 0.3684 0.4737 0.5263 0.3684 0.4211 0.3684 0.5263 0.5263 0.5263 282s > # [11] 0.6842 0.4211 0.4211 0.5263 0.4211 0.2632 0.4211 0.4737 0.5263 0.4211 282s > # [21] 0.4737 0.4211 0.5263 0.4211 0.6316 0.5263 0.4211 0.4737 0.4211 0.3684 282s > # [31] 0.5263 0.4737 0.4737 0.4211 0.4737 0.5789 0.5263 0.5263 0.4211 0.3684 282s > # [41] 0.2632 0.4211 0.3684 0.4737 0.5263 0.4211 0.4211 0.2632 0.5263 0.5263 282s > # 282s > # $locfreqmin 282s > # [1] 0.2632 0.3684 0.2632 0.4211 282s > # 282s > # $locfreqmax 282s > # [1] 0.5263 0.5263 0.5789 0.6842 282s > # 282s > # $locfreqmean 282s > # [1] 0.3947 0.4520 0.4575 0.5044 282s > # 282s > # > 282s > # > proc.time() 282s > # user system elapsed 282s > # 1.708 0.020 1.729 282s > 282s BEGIN TEST prabclustests.R 282s 282s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 282s Copyright (C) 2024 The R Foundation for Statistical Computing 282s Platform: aarch64-unknown-linux-gnu (64-bit) 282s 282s R is free software and comes with ABSOLUTELY NO WARRANTY. 282s You are welcome to redistribute it under certain conditions. 282s Type 'license()' or 'licence()' for distribution details. 282s 282s R is a collaborative project with many contributors. 282s Type 'contributors()' for more information and 282s 'citation()' on how to cite R or R packages in publications. 282s 282s Type 'demo()' for some demos, 'help()' for on-line help, or 282s 'help.start()' for an HTML browser interface to help. 282s Type 'q()' to quit R. 282s 282s > library(prabclus) 282s Loading required package: MASS 282s Loading required package: mclust 282s Package 'mclust' version 6.0.1 282s Type 'citation("mclust")' for citing this R package in publications. 282s > options(digits=4) 282s > 282s > data(kykladspecreg) 282s > data(nb) 282s > set.seed(1234) 282s > x <- prabinit(prabmatrix=kykladspecreg, neighborhood=nb) 282s > 282s > p1 <- prabtest(x, times=3, pd=0.35, ignore.richness=TRUE) 282s Simulation run 1 statistics value= 0.5811 282s Simulation run 2 statistics value= 0.4761 282s Simulation run 3 statistics value= 0.5022 282s Data value: 0.408 282s > p2 <- prabtest(x, times=3, pd=0.35, teststat="lcomponent") 282s Simulation run 1 statistics value= 9 282s Simulation run 2 statistics value= 19 282s Simulation run 3 statistics value= 43 282s Data value: 8 282s > p3 <- prabtest(x, times=3, pd=0.35, teststat="isovertice") 283s Simulation run 1 statistics value= 9 283s Simulation run 2 statistics value= 9 283s Simulation run 3 statistics value= 23 283s Data value: 15 283s > p4 <- prabtest(x, times=3, pd=0.35, teststat="nn", sf.sim=TRUE) 283s Simulation run 1 statistics value= 0.3598 283s Simulation run 2 statistics value= 0.3635 283s Simulation run 3 statistics value= 0.3441 283s Data value: 0.3192 283s > p5 <- prabtest(x, times=3, pd=0.35, teststat="inclusions") 283s Simulation run 1 statistics value= 470 283s Simulation run 2 statistics value= 547 283s Simulation run 3 statistics value= 365 283s Data value: 602 283s > summary(p1) 283s * Parametric bootstrap test for presence-absence data * 283s 283s Test statistics: distratio , Tuning constant= 0.25 283s Distance: kulczynski 283s Simulation runs: 3 283s Disjunction parameter for presence-absence pattern: 0.35 283s Rows (regions) richness has been ignored by the null model. 283s Statistics value for original data: 0.408 283s Mean for null data: 0.5198 , range: 0.4761 0.5811 283s p= 0.25 283s > summary(p2) 283s * Parametric bootstrap test for presence-absence data * 283s 283s Test statistics: lcomponent , Tuning constant= 60 283s Distance: kulczynski 283s Simulation runs: 3 283s Disjunction parameter for presence-absence pattern: 0.35 283s Statistics value for original data: 8 283s Mean for null data: 23.67 , range: 9 43 283s p= 0.25 283s > summary(p3) 283s * Parametric bootstrap test for presence-absence data * 283s 283s Test statistics: isovertice , Tuning constant= 80 283s Distance: kulczynski 283s Simulation runs: 3 283s Disjunction parameter for presence-absence pattern: 0.35 283s Statistics value for original data: 15 283s Mean for null data: 13.67 , range: 9 23 283s p= 1 283s > summary(p4) 283s * Parametric bootstrap test for presence-absence data * 283s 283s Test statistics: nn , Tuning constant= 4 283s Distance: kulczynski 283s Simulation runs: 3 283s Disjunction parameter for presence-absence pattern: 0.35 283s Statistics value for original data: 0.3192 283s Mean for null data: 0.3558 , range: 0.3441 0.3635 283s p= 0.25 283s > summary(p5) 283s * Parametric bootstrap test for presence-absence data * 283s 283s Test statistics: inclusions , Tuning constant= NA 283s Distance: kulczynski 283s Simulation runs: 3 283s Disjunction parameter for presence-absence pattern: 0.35 283s Statistics value for original data: 602 283s Mean for null data: 460.7 , range: 365 547 283s p= 0.25 283s > 283s > data(veronica) 283s > vnb <- coord2dist(coordmatrix=veronica.coord[1:50,], cut=20, 283s + file.format="decimal2",neighbors=TRUE) 283s > vei <- prabinit(prabmatrix=veronica[1:50,], 283s + neighborhood=vnb$nblist,nbbetweenregions=FALSE, 283s + distance="jaccard") 283s > print(vei) 283s Presence-absence matrix object with 283s 50 species and 583 regions, 283s including species/individuals neighborhoods and 283s between-species distance matrix of type jaccard . 283s > 283s > library(spdep) 283s Loading required package: spData 283s To access larger datasets in this package, install the spDataLarge 283s package with: `install.packages('spDataLarge', 283s repos='https://nowosad.github.io/drat/', type='source')` 283s Loading required package: sf 284s Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.3.1; sf_use_s2() is TRUE 284s > data(siskiyou) 284s > x <- prabinit(prabmatrix=siskiyou, neighborhood=siskiyou.nb, 284s + distance="logkulczynski") 284s > build.nblist(x) 284s > a1 <- abundtest(x, times=5, p.nb=0.0465) 286s Simulation run 1 statistics value= 0.2931 286s Simulation run 2 statistics value= 0.3109 287s Simulation run 3 statistics value= 0.2936 287s Simulation run 4 statistics value= 0.3119 287s Simulation run 5 statistics value= 0.3048 287s Data value: 0.2789 287s > a2 <- abundtest(x, times=5, p.nb=0.0465, teststat="groups", 287s + groupvector=siskiyou.groups) 288s Simulation run 1 statistics value= 0.4916 288s Simulation run 2 statistics value= 0.5779 288s Simulation run 3 statistics value= 0.5337 288s Simulation run 4 statistics value= 0.5873 289s Simulation run 5 statistics value= 0.617 289s Data value: 0.5864 289s > # These settings are chosen to make the example execution 289s > # faster; usually you will use abundtest(x). 289s > summary(a1) 289s * Parametric bootstrap test for spatial abundance data * 289s 289s Test statistics: distratio , Tuning constant= 0.25 289s Distance: logkulczynski 289s Simulation runs: 5 289s Disjunction parameter for presence-absence pattern: 0.0465 289s Neighborhood parameter lambda for SAR-model: -0.05515 289s Statistics value for original data: 0.2789 289s Mean for null data: 0.3029 , range: 0.2931 0.3119 289s p= 0.1667 289s > summary(a2) 289s * Parametric bootstrap test for spatial abundance data * 289s 289s Test statistics: groups , Tuning constant= NA 289s Distance: logkulczynski 289s Simulation runs: 5 289s Disjunction parameter for presence-absence pattern: 0.0465 289s Neighborhood parameter lambda for SAR-model: -0.05515 289s Mean within group distances for original data: 0.5864 289s Mean of mean within group distances for null data: 0.5615 , range: 0.4916 0.617 289s p= 0.5 289s Group 7 statistics value for original data: 0.7897 289s Group 7 mean for null data: 0.4531 , range: 0.4156 0.4727 289s p= 0.1667 289s Group 16 statistics value for original data: 0.2778 289s Group 16 mean for null data: 0.3438 , range: 0.2231 0.4107 289s p= 0.8333 289s Group 21 statistics value for original data: 1 289s Group 21 mean for null data: 0.6664 , range: 0.3384 1 289s p= 0.5 289s Group 24 statistics value for original data: 0.4815 289s Group 24 mean for null data: 0.3202 , range: 0.2768 0.3746 289s p= 0.1667 289s Group 27 statistics value for original data: 0.353 289s Group 27 mean for null data: 0.6447 , range: 0.3722 1 289s p= 1 289s Group 30 statistics value for original data: 0.2257 289s Group 30 mean for null data: 0.1347 , range: 0.06729 0.1949 289s p= 0.1667 289s Group 33 statistics value for original data: 0.7591 289s Group 33 mean for null data: 0.5463 , range: 0.4448 0.6791 289s p= 0.1667 289s Group 41 statistics value for original data: 0.5354 289s Group 41 mean for null data: 0.4502 , range: 0.3351 0.5298 289s p= 0.1667 289s Group 51 statistics value for original data: 0.7529 289s Group 51 mean for null data: 0.7072 , range: 0.6229 0.859 289s p= 0.5 289s Group 61 statistics value for original data: 0.4842 289s Group 61 mean for null data: 0.6812 , range: 0.4593 1 289s p= 0.5 289s Group 66 statistics value for original data: 0.9123 289s Group 66 mean for null data: 0.9564 , range: 0.8345 1 289s p= 0.8333 289s Group 74 statistics value for original data: 0.8442 289s Group 74 mean for null data: 0.546 , range: 0.3173 1 289s p= 0.3333 289s Group 80 statistics value for original data: 0.2595 289s Group 80 mean for null data: 0.3406 , range: 0.2541 0.3817 289s p= 0.8333 289s Group 88 statistics value for original data: 0.7163 289s Group 88 mean for null data: 0.6213 , range: 0.3689 0.7709 289s p= 0.5 289s Group 96 statistics value for original data: 0.4578 289s Group 96 mean for null data: 0.4455 , range: 0.417 0.4682 289s p= 0.5 289s Group 99 statistics value for original data: 0.4293 289s Group 99 mean for null data: 0.7328 , range: 0.5584 0.8119 289s p= 1 289s Group 103 statistics value for original data: 0.4432 289s Group 103 mean for null data: 0.6986 , range: 0.4646 1 289s p= 1 289s Group 107 statistics value for original data: 0.5259 289s Group 107 mean for null data: 0.808 , range: 0.5826 1 289s p= 1 289s Group 114 statistics value for original data: 0.4325 289s Group 114 mean for null data: 0.4392 , range: 0.3879 0.4892 289s p= 0.6667 289s Group 125 statistics value for original data: 0.6856 289s Group 125 mean for null data: 0.3745 , range: 0.268 0.4779 289s p= 0.1667 289s Group 127 statistics value for original data: 0.2832 289s Group 127 mean for null data: 0.1782 , range: 0.1558 0.2164 289s p= 0.1667 289s Group 140 statistics value for original data: 0.5829 289s Group 140 mean for null data: 0.5161 , range: 0.3774 0.6366 289s p= 0.3333 289s > 289s > options(digits=2) 289s > prab.sarestimate(x) 289s $sar 289s [1] TRUE 289s 289s $intercept 289s (Intercept) 289s 1.1 289s 289s $sigma 289s [1] 1 289s 289s $regeffects 289s region2 region3 region4 region5 region6 289s 0.000 -0.056 0.517 0.682 0.597 0.834 289s 289s $speffects 289s species2 species3 species4 species5 species6 species7 289s 0.0000 -1.0986 -0.4055 -0.4055 -0.1746 -0.1746 0.5186 289s species8 species9 species10 species11 species12 species13 species14 289s 0.1720 -0.3773 2.4585 2.4632 2.3148 0.7966 -0.5523 289s species15 species16 species17 species18 species19 species20 species21 289s -0.9997 2.8542 3.1175 -0.1624 -1.2164 0.8256 0.0025 289s species22 species23 species24 species25 species26 species27 species28 289s -2.0213 -0.6407 2.6430 4.3446 3.3794 2.7244 2.6713 289s species29 species30 species31 species32 species33 species34 species35 289s 2.7303 1.5682 1.8833 2.9410 1.7488 2.9594 2.5965 289s species36 species37 species38 species39 species40 species41 species42 289s 2.7883 1.0393 0.9960 1.4137 1.9796 -1.8561 1.6207 289s species43 species44 species45 species46 species47 species48 species49 289s 1.7423 2.2793 2.0573 2.3259 1.0857 3.3730 3.2701 289s species50 species51 species52 species53 species54 species55 species56 289s 2.7610 2.6443 -0.1027 1.9857 2.3219 -0.3492 -1.0423 289s species57 species58 species59 species60 species61 species62 species63 289s -1.0423 -1.0423 -0.3492 2.1940 -0.6358 -0.4330 -1.3289 289s species64 species65 species66 species67 species68 species69 species70 289s -2.2767 -2.3501 -1.7023 1.3365 1.9931 1.3771 0.7127 289s species71 species72 species73 species74 species75 species76 species77 289s 2.1431 -1.6155 -0.9223 -1.6155 0.4640 -1.6155 1.0236 289s species78 species79 species80 species81 species82 species83 species84 289s -0.5168 -1.6979 -1.6979 -1.0047 -2.5026 1.7620 0.6432 289s species85 species86 species87 species88 species89 species90 species91 289s -2.1138 1.5735 1.3492 1.8530 0.3853 2.6159 -0.2037 289s species92 species93 species94 species95 species96 species97 species98 289s -0.4353 0.1952 -1.5037 0.5223 -0.3940 -1.7803 -1.0871 289s species99 species100 species101 species102 species103 species104 species105 289s -1.7803 -1.8497 0.5645 -0.0720 -0.1926 -0.3926 1.5433 289s species106 species107 species108 species109 species110 species111 species112 289s -0.5872 0.3140 3.4881 1.3971 0.4806 3.2341 -0.4859 289s species113 species114 species115 species116 species117 species118 species119 289s 1.8359 0.2072 -0.7822 1.0575 1.9314 2.2148 -0.5973 289s species120 species121 species122 species123 species124 species125 species126 289s 0.0959 0.7020 -1.6959 -1.0028 -0.4950 0.0299 0.3509 289s species127 species128 species129 species130 species131 species132 species133 289s -0.1855 -0.8416 0.5266 -0.6632 -0.4950 -1.4679 -0.8416 289s species134 species135 species136 species137 species138 species139 species140 289s 0.9045 3.1571 1.6834 -0.3166 -1.2400 -1.2400 -1.2400 289s species141 species142 species143 species144 289s 0.7749 1.2858 -0.3237 -1.2400 289s 289s $lambda 289s lambda 289s -0.078 289s 289s $size 289s [1] 421 289s 289s $nbweight 289s [1] 0.7 289s 289s $lmobject 289s 289s Call: 289s spatialreg::errorsarlm(formula = logabund ~ region + species, 289s data = abundreg, listw = nblistw, method = sarmethod, quiet = quiet, 289s zero.policy = TRUE) 289s Type: error 289s 289s Coefficients: 289s lambda (Intercept) region2 region3 region4 region5 289s -0.0784 1.0986 -0.0563 0.5168 0.6817 0.5973 289s region6 species2 species3 species4 species5 species6 289s 0.8345 -1.0986 -0.4055 -0.4055 -0.1746 -0.1746 289s species7 species8 species9 species10 species11 species12 289s 0.5186 0.1720 -0.3773 2.4585 2.4632 2.3148 289s species13 species14 species15 species16 species17 species18 289s 0.7966 -0.5523 -0.9997 2.8542 3.1175 -0.1624 289s species19 species20 species21 species22 species23 species24 289s -1.2164 0.8256 0.0025 -2.0213 -0.6407 2.6430 289s species25 species26 species27 species28 species29 species30 289s 4.3446 3.3794 2.7244 2.6713 2.7303 1.5682 289s species31 species32 species33 species34 species35 species36 289s 1.8833 2.9410 1.7488 2.9594 2.5965 2.7883 289s species37 species38 species39 species40 species41 species42 289s 1.0393 0.9960 1.4137 1.9796 -1.8561 1.6207 289s species43 species44 species45 species46 species47 species48 289s 1.7423 2.2793 2.0573 2.3259 1.0857 3.3730 289s species49 species50 species51 species52 species53 species54 289s 3.2701 2.7610 2.6443 -0.1027 1.9857 2.3219 289s species55 species56 species57 species58 species59 species60 289s -0.3492 -1.0423 -1.0423 -1.0423 -0.3492 2.1940 289s species61 species62 species63 species64 species65 species66 289s -0.6358 -0.4330 -1.3289 -2.2767 -2.3501 -1.7023 289s species67 species68 species69 species70 species71 species72 289s 1.3365 1.9931 1.3771 0.7127 2.1431 -1.6155 289s species73 species74 species75 species76 species77 species78 289s -0.9223 -1.6155 0.4640 -1.6155 1.0236 -0.5168 289s species79 species80 species81 species82 species83 species84 289s -1.6979 -1.6979 -1.0047 -2.5026 1.7620 0.6432 289s species85 species86 species87 species88 species89 species90 289s -2.1138 1.5735 1.3492 1.8530 0.3853 2.6159 289s species91 species92 species93 species94 species95 species96 289s -0.2037 -0.4353 0.1952 -1.5037 0.5223 -0.3940 289s species97 species98 species99 species100 species101 species102 289s -1.7803 -1.0871 -1.7803 -1.8497 0.5645 -0.0720 289s species103 species104 species105 species106 species107 species108 289s -0.1926 -0.3926 1.5433 -0.5872 0.3140 3.4881 289s species109 species110 species111 species112 species113 species114 289s 1.3971 0.4806 3.2341 -0.4859 1.8359 0.2072 289s species115 species116 species117 species118 species119 species120 289s -0.7822 1.0575 1.9314 2.2148 -0.5973 0.0959 289s species121 species122 species123 species124 species125 species126 289s 0.7020 -1.6959 -1.0028 -0.4950 0.0299 0.3509 289s species127 species128 species129 species130 species131 species132 289s -0.1855 -0.8416 0.5266 -0.6632 -0.4950 -1.4679 289s species133 species134 species135 species136 species137 species138 289s -0.8416 0.9045 3.1571 1.6834 -0.3166 -1.2400 289s species139 species140 species141 species142 species143 species144 289s -1.2400 -1.2400 0.7749 1.2858 -0.3237 -1.2400 289s 289s Log likelihood: -597 289s 289s > regpop.sar(x, p.nb=0.046) 290s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 290s [1,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00 0 0 0 0.0 290s [2,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.87 0 0 0 0.0 290s [3,] 0.0 0.0 0.0 0.0 0.0 5.5 0.0 1.5 20.79 25 12 34 0.0 290s [4,] 0.0 1.7 0.0 0.0 2.7 18.2 0.0 2.1 0.00 23 0 155 42.2 290s [5,] 4.5 0.0 4.1 0.0 5.7 0.0 3.7 0.0 0.00 0 29 99 9.1 290s [6,] 0.0 0.0 0.0 3.5 0.0 0.0 78.4 0.0 0.00 0 0 0 13.1 290s [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] 290s [1,] 0.0 0.00 46 0 1.6 4.3 0.00 4.4 0.028 0.74 76 0 290s [2,] 17.3 0.00 79 66 0.9 2.0 0.00 1.4 0.187 2.97 44 75 290s [3,] 2.1 0.00 79 16 7.5 52.3 3.37 10.6 0.258 4.15 96 5493 290s [4,] 16.0 6.72 76 256 4.3 0.0 8.84 1.5 0.308 7.90 81 54 290s [5,] 0.0 5.52 0 237 0.0 0.0 0.71 0.0 0.000 0.00 19 414 290s [6,] 0.0 0.39 0 0 0.0 0.0 102.84 0.0 0.000 0.00 0 246 290s [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] 290s [1,] 0 0 11 10.0 14.1 0.0 0.0 59.2 230 84 90 0.0 290s [2,] 126 63 94 9.4 20.1 54.3 120.7 6.3 107 70 34 6.8 290s [3,] 232 509 26 210.3 3.2 173.4 8.6 39.3 303 225 23 11.6 290s [4,] 89 20 32 23.8 32.9 64.1 80.0 29.1 486 111 71 15.8 290s [5,] 51 13 25 81.2 42.1 33.3 84.2 13.1 19 18 206 9.5 290s [6,] 1378 265 0 0.0 0.0 4.7 72.7 0.0 0 0 0 17.0 290s [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49] 290s [1,] 0.0 0 42 0.00 24.2 0 19 62 26 53.3 201 34 290s [2,] 8.6 33 16 0.00 3.6 23 55 18 128 3.9 34 214 290s [3,] 1.7 20 39 0.00 45.9 55 41 24 125 17.7 1103 63 290s [4,] 3.7 21 28 0.37 111.8 72 123 42 118 5.3 489 66 290s [5,] 47.7 22 86 1.40 3.5 17 135 232 60 11.7 51 16 290s [6,] 0.0 22 0 0.43 38.1 44 26 21 104 7.1 473 236 290s [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61] 290s [1,] 68 0 2.45 5.3 47.2 0.0 0.0 0.0 0 0 0 0.0 290s [2,] 22 62 5.73 83.3 7.4 0.0 0.0 0.0 0 0 0 0.0 290s [3,] 1120 61 3.87 38.7 58.9 0.0 0.0 4.2 0 10 0 0.0 290s [4,] 69 443 3.29 49.2 32.5 0.0 0.0 0.0 0 0 0 0.0 290s [5,] 99 91 0.91 46.9 251.6 0.0 6.5 0.0 0 0 13 1.6 290s [6,] 260 136 3.70 57.1 113.2 1.8 0.0 0.0 4 0 32 2.3 290s [,62] [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72] [,73] 290s [1,] 0.0 0.00 0.16 0.00 0.00 0 0 0.0 0.0 41 0 0.0 290s [2,] 0.0 0.00 1.18 0.00 0.00 0 24 5.4 4.2 17 0 3.4 290s [3,] 0.0 0.00 6.63 0.50 0.40 47 30 41.4 21.7 119 0 0.0 290s [4,] 3.1 0.00 0.00 0.10 3.74 22 126 83.3 6.7 54 0 0.0 290s [5,] 4.7 0.61 0.00 0.38 0.44 57 20 43.7 69.3 16 3 0.0 290s [6,] 0.0 1.69 0.00 0.00 0.00 53 0 19.5 32.3 0 0 0.0 290s [,74] [,75] [,76] [,77] [,78] [,79] [,80] [,81] [,82] [,83] [,84] [,85] 290s [1,] 0.00 0 0 0 0.0 0.0 0.00 0.0 0.00 10.6 0.0 0.00 290s [2,] 0.00 0 0 0 0.0 1.2 0.00 0.0 0.00 9.7 13.4 0.00 290s [3,] 0.00 13 11 0 3.2 1.0 0.00 2.0 0.00 0.0 6.9 0.00 290s [4,] 0.87 0 0 0 0.0 0.0 0.99 3.5 0.26 0.0 0.0 0.51 290s [5,] 0.00 0 0 0 0.0 0.0 0.73 0.0 1.47 0.0 0.0 0.61 290s [6,] 0.00 0 0 41 0.0 0.0 0.00 0.0 0.00 0.0 0.0 0.00 290s [,86] [,87] [,88] [,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96] [,97] 290s [1,] 12.6 0 0 0.0 0 2.6 0.0 1.2 3.62 0.0 0.47 0.00 290s [2,] 3.2 0 25 0.0 0 0.9 0.0 3.6 0.39 0.0 0.00 0.00 290s [3,] 9.6 0 11 2.2 0 9.9 1.0 12.3 1.84 0.0 0.00 0.00 290s [4,] 0.0 22 18 19.1 230 10.4 7.7 18.8 1.42 0.0 0.00 0.93 290s [5,] 0.0 39 51 4.2 52 0.0 12.8 0.0 0.00 0.0 0.00 0.00 290s [6,] 0.0 26 0 4.4 98 0.0 1.5 0.0 0.00 3.9 0.00 0.00 290s [,98] [,99] [,100] [,101] [,102] [,103] [,104] [,105] [,106] [,107] [,108] 290s [1,] 0.0 0.00 0.00 0.0 0.0 18.4 1.1 0 0.0 0.0 0 290s [2,] 0.0 0.00 0.00 0.0 9.8 3.3 5.4 0 1.5 0.0 0 290s [3,] 0.0 0.00 0.00 36.2 25.5 0.0 2.8 0 2.9 12.2 0 290s [4,] 3.8 0.00 0.82 8.2 0.0 0.0 0.0 41 14.6 25.8 432 290s [5,] 0.0 0.98 0.84 0.0 0.0 0.0 0.0 28 0.0 5.4 3135 290s [6,] 0.0 0.00 0.00 0.0 0.0 0.0 0.0 80 0.0 0.0 524 290s [,109] [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117] [,118] 290s [1,] 0.0 0.0 0 0.0 0 0.0 0.0 8.8 11.6 39 290s [2,] 7.8 0.0 0 2.1 0 0.0 0.0 8.6 0.0 90 290s [3,] 10.0 0.0 0 0.8 0 7.1 5.6 8.0 31.6 27 290s [4,] 30.3 22.9 30 3.7 184 3.5 14.9 0.0 5.3 0 290s [5,] 0.0 2.4 116 0.0 16 13.0 1.4 0.0 0.0 0 290s [6,] 0.0 3.8 76 0.0 65 0.0 0.0 0.0 0.0 0 290s [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126] [,127] [,128] 290s [1,] 0.00 0.0 0 0.0 0.0 0.0 0.0 0.0 0.0 0.7 290s [2,] 0.46 0.0 0 0.0 5.8 0.0 0.0 0.0 8.5 1.7 290s [3,] 0.00 0.0 0 0.0 0.0 0.0 0.0 3.2 0.0 0.0 290s [4,] 0.00 0.0 0 0.0 0.0 0.0 0.0 5.2 0.0 0.0 290s [5,] 0.00 8.6 0 1.1 0.0 6.8 9.6 0.0 2.1 0.0 290s [6,] 0.00 0.0 19 0.0 0.0 2.9 6.9 0.0 0.0 0.0 290s [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137] [,138] 290s [1,] 0.0 0.00 0.00 0.00 0.00 0.0 0 0 0.77 0.0 290s [2,] 3.2 0.55 2.30 1.33 0.00 0.0 0 0 1.48 0.0 290s [3,] 1.7 2.04 0.52 0.64 0.00 0.0 0 27 0.00 0.0 290s [4,] 0.0 0.00 0.00 0.00 0.96 4.0 0 26 0.00 2.4 290s [5,] 0.0 0.00 0.00 0.00 0.93 1.7 43 0 0.00 0.0 290s [6,] 0.0 0.00 0.00 0.00 0.00 0.0 45 0 0.00 0.0 290s [,139] [,140] [,141] [,142] [,143] [,144] 290s [1,] 0 0.0 0.0 0 1.8 0.00 290s [2,] 0 0.0 0.0 11 0.0 0.00 290s [3,] 4 0.0 0.0 0 0.0 0.55 290s [4,] 0 0.0 5.9 0 0.0 0.00 290s [5,] 0 3.6 0.0 0 0.0 0.00 290s [6,] 0 0.0 0.0 0 0.0 0.00 290s > options(digits=4) 290s > 290s > x <- prabinit(prabmatrix=siskiyou, neighborhood=siskiyou.nb, distance="none",toprab=TRUE,toprabp=0.5) 290s > x2 <- prabinit(prabmatrix=siskiyou, neighborhood=siskiyou.nb, distance="none",toprab=TRUE,toprabp=0) 290s > x$prab 290s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] 290s [1,] FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [2,] FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [3,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE 290s [4,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [5,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [6,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] 290s [1,] TRUE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [2,] TRUE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE 290s [3,] TRUE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [4,] FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [5,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE 290s [6,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] 290s [1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [2,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [3,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [4,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [5,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE 290s [6,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] 290s [1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE 290s [2,] TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE 290s [3,] TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [4,] TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [5,] TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE 290s [6,] FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE 290s [,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] [,60] 290s [1,] TRUE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] TRUE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE 290s [3,] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE 290s [4,] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE 290s [5,] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE 290s [6,] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE 290s [,61] [,62] [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE 290s [3,] TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE 290s [4,] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE FALSE 290s [5,] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE 290s [6,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE 290s [,73] [,74] [,75] [,76] [,77] [,78] [,79] [,80] [,81] [,82] [,83] [,84] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [3,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE TRUE 290s [4,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE TRUE 290s [5,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [6,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [,85] [,86] [,87] [,88] [,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [3,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE 290s [4,] FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE 290s [5,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE 290s [6,] FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE 290s [,97] [,98] [,99] [,100] [,101] [,102] [,103] [,104] [,105] [,106] [,107] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [3,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [4,] FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE 290s [5,] FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [6,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE 290s [,108] [,109] [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [3,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [4,] TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE FALSE 290s [5,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [6,] TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE 290s [,118] [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126] [,127] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [3,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [4,] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [5,] TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE 290s [6,] TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE 290s [,128] [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [3,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [4,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [5,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [6,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [,138] [,139] [,140] [,141] [,142] [,143] [,144] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [3,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [4,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [5,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [6,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s > x2$prab 290s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] 290s [1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [2,] FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [3,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE 290s [4,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [5,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [6,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] 290s [1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [2,] TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE 290s [3,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [4,] FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [5,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE 290s [6,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] 290s [1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [2,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [3,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [4,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [5,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [6,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] 290s [1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [2,] TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [3,] TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [4,] TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [5,] TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE 290s [6,] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] [,60] 290s [1,] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [3,] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE 290s [4,] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE 290s [5,] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE 290s [6,] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE 290s [,61] [,62] [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE 290s [3,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [4,] FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE FALSE 290s [5,] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE 290s [6,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE 290s [,73] [,74] [,75] [,76] [,77] [,78] [,79] [,80] [,81] [,82] [,83] [,84] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [3,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [4,] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE 290s [5,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [6,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [,85] [,86] [,87] [,88] [,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [3,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE 290s [4,] FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [5,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE 290s [6,] FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE 290s [,97] [,98] [,99] [,100] [,101] [,102] [,103] [,104] [,105] [,106] [,107] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [3,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [4,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [5,] FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [6,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE 290s [,108] [,109] [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [3,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [4,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [5,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [6,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [,118] [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126] [,127] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [3,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [4,] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [5,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [6,] TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE 290s [,128] [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [3,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [4,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [5,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [6,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s [,138] [,139] [,140] [,141] [,142] [,143] [,144] 290s [1,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [2,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [3,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [4,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [5,] FALSE FALSE FALSE FALSE FALSE FALSE FALSE 290s [6,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE 290s > 290s > 290s > 291s autopkgtest [19:37:37]: test run-unit-test: -----------------------] 291s autopkgtest [19:37:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 291s run-unit-test PASS 292s autopkgtest [19:37:38]: test pkg-r-autopkgtest: preparing testbed 293s Reading package lists... 293s Building dependency tree... 293s Reading state information... 294s Starting pkgProblemResolver with broken count: 0 294s Starting 2 pkgProblemResolver with broken count: 0 294s Done 294s The following additional packages will be installed: 294s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 294s dctrl-tools g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 294s gcc-13 gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-13 294s gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 294s libasan8 libatomic1 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 294s libcrypt-dev libgcc-13-dev libgfortran-13-dev libhwasan0 libicu-dev libisl23 294s libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 294s liblzma-dev libmpc3 libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 294s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev 294s libstdc++-13-dev libtirpc-dev libtsan2 libubsan1 linux-libc-dev pkg-config 294s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev rpcsvc-proto zlib1g-dev 294s Suggested packages: 294s cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib 294s manpages-dev autoconf automake libtool flex bison gdb gcc-doc 294s gdb-aarch64-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev 294s liblapack-doc glibc-doc icu-doc liblzma-doc ncurses-doc readline-doc 294s libstdc++-13-doc texlive-base texlive-latex-base texlive-plain-generic 294s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils 294s texlive-latex-recommended texlive-latex-extra texinfo 294s Recommended packages: 294s bzip2-doc manpages manpages-dev libc-devtools libpng-tools 294s The following NEW packages will be installed: 294s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu 294s cpp-aarch64-linux-gnu dctrl-tools g++ g++-13 g++-13-aarch64-linux-gnu 294s g++-aarch64-linux-gnu gcc gcc-13 gcc-13-aarch64-linux-gnu 294s gcc-aarch64-linux-gnu gfortran gfortran-13 gfortran-13-aarch64-linux-gnu 294s gfortran-aarch64-linux-gnu icu-devtools libasan8 libatomic1 libblas-dev 294s libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libgcc-13-dev 294s libgfortran-13-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 294s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 294s libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev 294s libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev libstdc++-13-dev 294s libtirpc-dev libtsan2 libubsan1 linux-libc-dev pkg-config pkg-r-autopkgtest 294s pkgconf pkgconf-bin r-base-dev rpcsvc-proto zlib1g-dev 295s 0 upgraded, 62 newly installed, 0 to remove and 0 not upgraded. 295s Need to get 92.8 MB/92.8 MB of archives. 295s After this operation, 343 MB of additional disk space will be used. 295s Get:1 /tmp/autopkgtest.smI7Ml/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [748 B] 295s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 295s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 295s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 295s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1 [201 kB] 295s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 295s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 295s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 295s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 295s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 295s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 296s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 296s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 296s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 296s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 296s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 296s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 296s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 296s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 296s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 296s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 296s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 296s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 296s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 296s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 296s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 296s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 296s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 297s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 297s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 297s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 297s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 297s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 297s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 dctrl-tools arm64 2.24-3build2 [65.2 kB] 297s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-17ubuntu2 [478 kB] 297s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.8 MB] 297s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-17ubuntu2 [10.3 kB] 297s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1022 B] 297s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B] 297s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB] 297s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB] 297s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 297s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB] 297s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu1 [304 kB] 297s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 297s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 297s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB] 297s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses-dev arm64 6.4+20240113-1ubuntu1 [385 kB] 297s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu1 [195 kB] 297s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu1 [183 kB] 297s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-posix3 arm64 10.42-4ubuntu1 [6654 B] 297s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-dev arm64 10.42-4ubuntu1 [679 kB] 297s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB] 297s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 297s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng-dev arm64 1.6.43-3 [267 kB] 297s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline-dev arm64 8.2-3.1 [177 kB] 298s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB] 298s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] 298s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B] 298s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB] 298s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-dev all 4.3.3-2build1 [4334 B] 298s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 299s Fetched 92.8 MB in 3s (29.9 MB/s) 299s Selecting previously unselected package libc-dev-bin. 299s (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 ... 80514 files and directories currently installed.) 299s Preparing to unpack .../00-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 299s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 299s Selecting previously unselected package linux-libc-dev:arm64. 299s Preparing to unpack .../01-linux-libc-dev_6.8.0-11.11_arm64.deb ... 299s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 299s Selecting previously unselected package libcrypt-dev:arm64. 299s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 299s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 299s Selecting previously unselected package libtirpc-dev:arm64. 299s Preparing to unpack .../03-libtirpc-dev_1.3.4+ds-1.1_arm64.deb ... 299s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 299s Selecting previously unselected package libnsl-dev:arm64. 299s Preparing to unpack .../04-libnsl-dev_1.3.0-3_arm64.deb ... 299s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 299s Selecting previously unselected package rpcsvc-proto. 299s Preparing to unpack .../05-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 299s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 299s Selecting previously unselected package libc6-dev:arm64. 299s Preparing to unpack .../06-libc6-dev_2.39-0ubuntu2_arm64.deb ... 299s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 299s Selecting previously unselected package libisl23:arm64. 299s Preparing to unpack .../07-libisl23_0.26-3_arm64.deb ... 299s Unpacking libisl23:arm64 (0.26-3) ... 300s Selecting previously unselected package libmpc3:arm64. 300s Preparing to unpack .../08-libmpc3_1.3.1-1_arm64.deb ... 300s Unpacking libmpc3:arm64 (1.3.1-1) ... 300s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 300s Preparing to unpack .../09-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 300s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 300s Selecting previously unselected package cpp-13. 300s Preparing to unpack .../10-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 300s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 300s Selecting previously unselected package cpp-aarch64-linux-gnu. 300s Preparing to unpack .../11-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 300s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 300s Selecting previously unselected package cpp. 300s Preparing to unpack .../12-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 300s Unpacking cpp (4:13.2.0-7ubuntu1) ... 300s Selecting previously unselected package libcc1-0:arm64. 300s Preparing to unpack .../13-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 300s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 300s Selecting previously unselected package libitm1:arm64. 300s Preparing to unpack .../14-libitm1_14-20240303-1ubuntu1_arm64.deb ... 300s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 300s Selecting previously unselected package libatomic1:arm64. 300s Preparing to unpack .../15-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 300s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 300s Selecting previously unselected package libasan8:arm64. 300s Preparing to unpack .../16-libasan8_14-20240303-1ubuntu1_arm64.deb ... 300s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 301s Selecting previously unselected package liblsan0:arm64. 301s Preparing to unpack .../17-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 301s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 301s Selecting previously unselected package libtsan2:arm64. 301s Preparing to unpack .../18-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 301s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 301s Selecting previously unselected package libubsan1:arm64. 301s Preparing to unpack .../19-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 301s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 301s Selecting previously unselected package libhwasan0:arm64. 301s Preparing to unpack .../20-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 301s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 301s Selecting previously unselected package libgcc-13-dev:arm64. 301s Preparing to unpack .../21-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 301s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 301s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 301s Preparing to unpack .../22-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 301s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 301s Selecting previously unselected package gcc-13. 301s Preparing to unpack .../23-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 301s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 301s Selecting previously unselected package gcc-aarch64-linux-gnu. 301s Preparing to unpack .../24-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 301s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 301s Selecting previously unselected package gcc. 301s Preparing to unpack .../25-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 301s Unpacking gcc (4:13.2.0-7ubuntu1) ... 301s Selecting previously unselected package libstdc++-13-dev:arm64. 301s Preparing to unpack .../26-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 301s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 302s Selecting previously unselected package g++-13-aarch64-linux-gnu. 302s Preparing to unpack .../27-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 302s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 302s Selecting previously unselected package g++-13. 302s Preparing to unpack .../28-g++-13_13.2.0-17ubuntu2_arm64.deb ... 302s Unpacking g++-13 (13.2.0-17ubuntu2) ... 302s Selecting previously unselected package g++-aarch64-linux-gnu. 302s Preparing to unpack .../29-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 302s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 302s Selecting previously unselected package g++. 302s Preparing to unpack .../30-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 302s Unpacking g++ (4:13.2.0-7ubuntu1) ... 302s Selecting previously unselected package build-essential. 302s Preparing to unpack .../31-build-essential_12.10ubuntu1_arm64.deb ... 302s Unpacking build-essential (12.10ubuntu1) ... 302s Selecting previously unselected package dctrl-tools. 302s Preparing to unpack .../32-dctrl-tools_2.24-3build2_arm64.deb ... 302s Unpacking dctrl-tools (2.24-3build2) ... 302s Selecting previously unselected package libgfortran-13-dev:arm64. 302s Preparing to unpack .../33-libgfortran-13-dev_13.2.0-17ubuntu2_arm64.deb ... 302s Unpacking libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 302s Selecting previously unselected package gfortran-13-aarch64-linux-gnu. 302s Preparing to unpack .../34-gfortran-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 302s Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 302s Selecting previously unselected package gfortran-13. 302s Preparing to unpack .../35-gfortran-13_13.2.0-17ubuntu2_arm64.deb ... 302s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 302s Selecting previously unselected package gfortran-aarch64-linux-gnu. 302s Preparing to unpack .../36-gfortran-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 302s Unpacking gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 302s Selecting previously unselected package gfortran. 302s Preparing to unpack .../37-gfortran_4%3a13.2.0-7ubuntu1_arm64.deb ... 302s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 302s Selecting previously unselected package icu-devtools. 302s Preparing to unpack .../38-icu-devtools_74.2-1ubuntu1_arm64.deb ... 302s Unpacking icu-devtools (74.2-1ubuntu1) ... 302s Selecting previously unselected package libblas-dev:arm64. 302s Preparing to unpack .../39-libblas-dev_3.12.0-3_arm64.deb ... 302s Unpacking libblas-dev:arm64 (3.12.0-3) ... 302s Selecting previously unselected package libbz2-dev:arm64. 303s Preparing to unpack .../40-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 303s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 303s Selecting previously unselected package libicu-dev:arm64. 303s Preparing to unpack .../41-libicu-dev_74.2-1ubuntu1_arm64.deb ... 303s Unpacking libicu-dev:arm64 (74.2-1ubuntu1) ... 303s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 303s Preparing to unpack .../42-libjpeg-turbo8-dev_2.1.5-2ubuntu1_arm64.deb ... 303s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 303s Selecting previously unselected package libjpeg8-dev:arm64. 303s Preparing to unpack .../43-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 303s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 303s Selecting previously unselected package libjpeg-dev:arm64. 303s Preparing to unpack .../44-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 303s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 303s Selecting previously unselected package liblapack-dev:arm64. 303s Preparing to unpack .../45-liblapack-dev_3.12.0-3_arm64.deb ... 303s Unpacking liblapack-dev:arm64 (3.12.0-3) ... 303s Selecting previously unselected package libncurses-dev:arm64. 303s Preparing to unpack .../46-libncurses-dev_6.4+20240113-1ubuntu1_arm64.deb ... 303s Unpacking libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 303s Selecting previously unselected package libpcre2-16-0:arm64. 303s Preparing to unpack .../47-libpcre2-16-0_10.42-4ubuntu1_arm64.deb ... 303s Unpacking libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 303s Selecting previously unselected package libpcre2-32-0:arm64. 303s Preparing to unpack .../48-libpcre2-32-0_10.42-4ubuntu1_arm64.deb ... 303s Unpacking libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 303s Selecting previously unselected package libpcre2-posix3:arm64. 303s Preparing to unpack .../49-libpcre2-posix3_10.42-4ubuntu1_arm64.deb ... 303s Unpacking libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 303s Selecting previously unselected package libpcre2-dev:arm64. 303s Preparing to unpack .../50-libpcre2-dev_10.42-4ubuntu1_arm64.deb ... 303s Unpacking libpcre2-dev:arm64 (10.42-4ubuntu1) ... 303s Selecting previously unselected package libpkgconf3:arm64. 303s Preparing to unpack .../51-libpkgconf3_1.8.1-2_arm64.deb ... 303s Unpacking libpkgconf3:arm64 (1.8.1-2) ... 303s Selecting previously unselected package zlib1g-dev:arm64. 303s Preparing to unpack .../52-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 303s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 303s Selecting previously unselected package libpng-dev:arm64. 303s Preparing to unpack .../53-libpng-dev_1.6.43-3_arm64.deb ... 303s Unpacking libpng-dev:arm64 (1.6.43-3) ... 303s 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libubsan1:arm64 (14-20240303-1ubuntu1) ... 304s Setting up libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 304s Setting up libnsl-dev:arm64 (1.3.0-3) ... 304s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 304s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 304s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 304s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 304s Setting up libisl23:arm64 (0.26-3) ... 304s Setting up libc-dev-bin (2.39-0ubuntu2) ... 304s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 304s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 304s Setting up libblas-dev:arm64 (3.12.0-3) ... 304s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 304s Setting up dctrl-tools (2.24-3build2) ... 304s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ... 304s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 304s Setting up pkgconf:arm64 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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 304s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 304s 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 304s Setting up g++ (4:13.2.0-7ubuntu1) ... 304s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 304s Setting up build-essential (12.10ubuntu1) ... 304s Setting up r-base-dev (4.3.3-2build1) ... 304s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 304s Setting up autopkgtest-satdep (0) ... 304s Processing triggers for man-db (2.12.0-3) ... 304s Processing triggers for install-info (7.1-3) ... 305s Processing triggers for libc-bin (2.39-0ubuntu2) ... 308s (Reading database ... 84073 files and directories currently installed.) 308s Removing autopkgtest-satdep (0) ... 309s autopkgtest [19:37:55]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 309s autopkgtest [19:37:55]: test pkg-r-autopkgtest: [----------------------- 309s Test: Try to load the R library prabclus 309s 309s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 309s Copyright (C) 2024 The R Foundation for Statistical Computing 309s Platform: aarch64-unknown-linux-gnu (64-bit) 309s 309s R is free software and comes with ABSOLUTELY NO WARRANTY. 309s You are welcome to redistribute it under certain conditions. 309s Type 'license()' or 'licence()' for distribution details. 309s 309s R is a collaborative project with many contributors. 309s Type 'contributors()' for more information and 309s 'citation()' on how to cite R or R packages in publications. 309s 309s Type 'demo()' for some demos, 'help()' for on-line help, or 309s 'help.start()' for an HTML browser interface to help. 309s Type 'q()' to quit R. 309s 309s > library('prabclus') 309s Loading required package: MASS 309s Loading required package: mclust 309s Package 'mclust' version 6.0.1 309s Type 'citation("mclust")' for citing this R package in publications. 309s > 309s > 309s Other tests are currently unsupported! 309s They will be progressively added. 310s autopkgtest [19:37:55]: test pkg-r-autopkgtest: -----------------------] 310s autopkgtest [19:37:56]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 310s pkg-r-autopkgtest PASS 310s autopkgtest [19:37:56]: @@@@@@@@@@@@@@@@@@@@ summary 310s run-unit-test PASS 310s pkg-r-autopkgtest PASS 321s Creating nova instance adt-noble-arm64-r-cran-prabclus-20240316-193246-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...