0s autopkgtest [20:15:45]: starting date and time: 2024-03-16 20:15:45+0000 0s autopkgtest [20:15:45]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [20:15:45]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.iulx9vmm/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-spatstat.model --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-arm64-18.secgroup --name adt-noble-arm64-r-cran-spatstat.model-20240316-201545-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/ 167s autopkgtest [20:18:32]: testbed dpkg architecture: arm64 167s autopkgtest [20:18:32]: testbed apt version: 2.7.12 167s autopkgtest [20:18:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 168s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 169s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 169s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 169s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 169s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3704 kB] 170s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 170s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 170s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 170s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 170s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4012 kB] 170s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 170s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 170s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 172s Fetched 9112 kB in 2s (3930 kB/s) 172s Reading package lists... 176s Reading package lists... 177s Building dependency tree... 177s Reading state information... 177s Calculating upgrade... 178s The following packages will be REMOVED: 178s libglib2.0-0 libssl3 178s The following NEW packages will be installed: 178s libglib2.0-0t64 libssl3t64 xdg-user-dirs 178s The following packages have been kept back: 178s curl 178s The following packages will be upgraded: 178s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 178s ubuntu-minimal ubuntu-standard 178s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 178s Need to get 4613 kB of archives. 178s After this operation, 211 kB of additional disk space will be used. 178s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 178s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 178s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 178s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 178s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 178s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 178s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 178s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 178s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 178s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 179s Fetched 4613 kB in 1s (5539 kB/s) 179s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74758 files and directories currently installed.) 179s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 179s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 179s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 179s udisks2 depends on libglib2.0-0 (>= 2.77.0). 179s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 179s python3-gi depends on libglib2.0-0 (>= 2.77.0). 179s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 179s netplan.io depends on libglib2.0-0 (>= 2.70.0). 179s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 179s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 179s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 179s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 179s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 179s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 179s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 179s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 179s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 179s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 179s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 179s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 179s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 179s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 179s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 179s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 179s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 179s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 179s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 179s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 179s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 179s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 179s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 179s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 179s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 179s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 179s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 179s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 179s fwupd depends on libglib2.0-0 (>= 2.79.0). 179s bolt depends on libglib2.0-0 (>= 2.56.0). 179s 179s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74758 files and directories currently installed.) 179s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 180s Selecting previously unselected package libglib2.0-0t64:arm64. 180s (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.) 180s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 180s 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... 180s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 180s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 180s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 180s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 180s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 180s wget depends on libssl3 (>= 3.0.0). 180s u-boot-tools depends on libssl3 (>= 3.0.0). 180s tnftp depends on libssl3 (>= 3.0.0). 180s tcpdump depends on libssl3 (>= 3.0.0). 180s systemd-resolved depends on libssl3 (>= 3.0.0). 180s systemd depends on libssl3 (>= 3.0.0). 180s sudo depends on libssl3 (>= 3.0.0). 180s sbsigntool depends on libssl3 (>= 3.0.0). 180s rsync depends on libssl3 (>= 3.0.0). 180s python3-cryptography depends on libssl3 (>= 3.0.0). 180s openssh-server depends on libssl3 (>= 3.0.10). 180s openssh-client depends on libssl3 (>= 3.0.10). 180s mtd-utils depends on libssl3 (>= 3.0.0). 180s mokutil depends on libssl3 (>= 3.0.0). 180s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 180s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 180s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 180s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 180s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 180s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 180s libnvme1 depends on libssl3 (>= 3.0.0). 180s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 180s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 180s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 180s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 180s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 180s kmod depends on libssl3 (>= 3.0.0). 180s dhcpcd-base depends on libssl3 (>= 3.0.0). 180s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 180s 180s (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.) 180s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 180s Selecting previously unselected package libssl3t64:arm64. 180s (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.) 180s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 180s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 180s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 180s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 180s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ... 180s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 180s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ... 180s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 181s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ... 181s Unpacking ubuntu-minimal (1.536) over (1.535) ... 181s Selecting previously unselected package xdg-user-dirs. 181s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ... 181s Unpacking xdg-user-dirs (0.18-1) ... 181s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ... 181s Unpacking ubuntu-standard (1.536) over (1.535) ... 181s Setting up ubuntu-minimal (1.536) ... 181s Setting up xdg-user-dirs (0.18-1) ... 181s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 181s Setting up libtirpc-common (1.3.4+ds-1.1) ... 181s Setting up ubuntu-standard (1.536) ... 181s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 181s No schema files found: doing nothing. 181s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 181s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 181s Setting up openssl (3.0.13-0ubuntu1) ... 181s Setting up readline-common (8.2-3.1) ... 181s Processing triggers for man-db (2.12.0-3) ... 182s Processing triggers for install-info (7.1-3) ... 182s Processing triggers for libc-bin (2.39-0ubuntu2) ... 183s Reading package lists... 183s Building dependency tree... 183s Reading state information... 183s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 184s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 184s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 184s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 184s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 187s Reading package lists... 187s Reading package lists... 187s Building dependency tree... 187s Reading state information... 188s Calculating upgrade... 188s The following packages have been kept back: 188s curl 188s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 188s Reading package lists... 188s Building dependency tree... 188s Reading state information... 189s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 192s autopkgtest [20:18:57]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 192s autopkgtest [20:18:57]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-spatstat.model 194s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-spatstat.model 3.2-8-1 (dsc) [2597 B] 194s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-spatstat.model 3.2-8-1 (tar) [804 kB] 194s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-spatstat.model 3.2-8-1 (diff) [3384 B] 194s gpgv: Signature made Tue Oct 24 08:22:10 2023 UTC 194s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 194s gpgv: issuer "tille@debian.org" 194s gpgv: Can't check signature: No public key 195s dpkg-source: warning: cannot verify inline signature for ./r-cran-spatstat.model_3.2-8-1.dsc: no acceptable signature found 195s autopkgtest [20:19:00]: testing package r-cran-spatstat.model version 3.2-8-1 195s autopkgtest [20:19:00]: build not needed 196s autopkgtest [20:19:01]: test run-unit-test: preparing testbed 198s Reading package lists... 198s Building dependency tree... 198s Reading state information... 199s Starting pkgProblemResolver with broken count: 0 199s Starting 2 pkgProblemResolver with broken count: 0 199s Done 199s The following additional packages will be installed: 199s curl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 199s fonts-mathjax libblas3 libcairo2 libcurl4t64 libdatrie1 libdeflate0 199s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 199s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-mathjax 199s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 199s libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 libpsl5t64 199s libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 199s libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 199s libxrender1 libxss1 libxt6t64 littler r-base-core r-cran-abind 199s r-cran-codetools r-cran-deldir r-cran-foreach r-cran-glmnet r-cran-goftest 199s r-cran-gsl r-cran-iterators r-cran-lattice r-cran-littler r-cran-locfit 199s r-cran-matrix r-cran-mgcv r-cran-nleqslv r-cran-nlme r-cran-pkgkitten 199s r-cran-polyclip r-cran-rcpp r-cran-rcppeigen r-cran-rpart r-cran-shape 199s r-cran-sm r-cran-spatial r-cran-spatstat r-cran-spatstat.data 199s r-cran-spatstat.explore r-cran-spatstat.geom r-cran-spatstat.linnet 199s r-cran-spatstat.model r-cran-spatstat.random r-cran-spatstat.sparse 199s r-cran-spatstat.utils r-cran-survival r-cran-tensor unzip x11-common 199s xdg-utils zip 200s Suggested packages: 200s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 200s fonts-mathjax-extras fonts-stix libjs-mathjax-doc tcl8.6 tk8.6 elpa-ess 200s r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-knitr r-cran-testthat 200s r-cran-xfun r-cran-rmarkdown r-cran-getopt r-cran-interp r-cran-gam 200s r-cran-inline 200s Recommended packages: 200s r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl 200s libx11-protocol-perl x11-utils x11-xserver-utils 200s The following packages will be REMOVED: 200s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 200s The following NEW packages will be installed: 200s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 200s fonts-dejavu-mono fonts-mathjax libblas3 libcairo2 libcurl4t64 libdatrie1 200s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 200s libgslcblas0 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 200s libjs-mathjax liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 200s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 200s libpsl5t64 libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 libthai-data 200s libthai0 libtiff6 libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 200s libxft2 libxrender1 libxss1 libxt6t64 littler r-base-core r-cran-abind 200s r-cran-codetools r-cran-deldir r-cran-foreach r-cran-glmnet r-cran-goftest 200s r-cran-gsl r-cran-iterators r-cran-lattice r-cran-littler r-cran-locfit 200s r-cran-matrix r-cran-mgcv r-cran-nleqslv r-cran-nlme r-cran-pkgkitten 200s r-cran-polyclip r-cran-rcpp r-cran-rcppeigen r-cran-rpart r-cran-shape 200s r-cran-sm r-cran-spatial r-cran-spatstat r-cran-spatstat.data 200s r-cran-spatstat.explore r-cran-spatstat.geom r-cran-spatstat.linnet 200s r-cran-spatstat.model r-cran-spatstat.random r-cran-spatstat.sparse 200s r-cran-spatstat.utils r-cran-survival r-cran-tensor unzip x11-common 200s xdg-utils zip 200s The following packages will be upgraded: 200s curl 200s 1 upgraded, 89 newly installed, 5 to remove and 0 not upgraded. 200s Need to get 94.3 MB/94.3 MB of archives. 200s After this operation, 201 MB of additional disk space will be used. 200s Get:1 /tmp/autopkgtest.Ey2R3T/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [772 B] 200s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 200s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 200s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 200s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 200s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 200s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 200s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 200s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 200s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 200s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 200s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 200s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 200s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 200s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 200s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 200s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 200s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 201s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 201s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 201s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 201s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 201s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 201s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 201s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu1 [72.5 kB] 201s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu1 [912 kB] 201s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 201s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 201s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 201s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 201s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 201s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 201s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 201s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 201s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 201s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 201s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 201s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 201s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 201s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 201s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 201s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 201s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 201s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 201s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 201s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 201s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 201s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 201s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 201s Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 201s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 201s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 201s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 201s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 202s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 202s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 202s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-abind all 1.4-5-2 [63.6 kB] 202s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-codetools all 0.2-19-1 [90.5 kB] 202s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-deldir arm64 2.0-4-1 [270 kB] 202s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-iterators all 1.0.14-1 [336 kB] 202s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-foreach all 1.5.2-1 [124 kB] 202s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 202s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 203s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-shape all 1.4.6-1 [770 kB] 203s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survival arm64 3.5-8-1 [6116 kB] 203s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 203s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 203s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcppeigen arm64 0.3.3.9.4-1 [1180 kB] 203s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 203s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glmnet arm64 4.1-8-1 [1898 kB] 203s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-goftest arm64 1.2-3-1 [60.2 kB] 203s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gsl arm64 2.1-8-1 [489 kB] 203s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-locfit arm64 1.5-9.8-1 [507 kB] 203s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 203s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 204s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nleqslv arm64 3.3.5-1 [101 kB] 204s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-polyclip arm64 1.10-6-1 [110 kB] 204s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rpart arm64 4.1.23-1 [660 kB] 204s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sm arm64 2.2-6.0-1 [787 kB] 204s Get:80 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatial arm64 7.3-17-1 [130 kB] 204s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.utils arm64 3.0-4-1 [360 kB] 204s Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.data all 3.0-4-1 [4090 kB] 204s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.geom arm64 3.2-8-1 [3805 kB] 204s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.random arm64 3.2-2-1 [1127 kB] 204s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tensor all 1.5-4 [15.7 kB] 204s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.sparse arm64 3.0-3-1 [214 kB] 204s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.explore arm64 3.2-5-1 [3264 kB] 204s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.model arm64 3.2-8-1 [3289 kB] 204s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.linnet arm64 3.1-3-1 [1404 kB] 204s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat arm64 3.0-7-1 [3817 kB] 206s Preconfiguring packages ... 206s Fetched 94.3 MB in 5s (19.0 MB/s) 206s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 206s wget depends on libpsl5 (>= 0.16.0). 206s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 206s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 206s 206s (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.) 206s Removing libpsl5:arm64 (0.21.2-1build1) ... 207s Selecting previously unselected package libpsl5t64:arm64. 207s (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.) 207s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 207s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 207s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 207s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 207s (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.) 207s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 207s Selecting previously unselected package libcurl4t64:arm64. 207s (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.) 207s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 207s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 207s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 207s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 207s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 207s 207s (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.) 207s Removing libpng16-16:arm64 (1.6.43-1) ... 207s Selecting previously unselected package libpng16-16t64:arm64. 207s (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.) 207s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 207s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 207s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 207s parted depends on libreadline8 (>= 6.0). 207s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 207s gpgsm depends on libreadline8 (>= 6.0). 207s gpgconf depends on libreadline8 (>= 6.0). 207s gpg depends on libreadline8 (>= 6.0). 207s gawk depends on libreadline8 (>= 6.0). 207s fdisk depends on libreadline8 (>= 6.0). 207s 207s (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.) 207s Removing libreadline8:arm64 (8.2-3) ... 207s Selecting previously unselected package libreadline8t64:arm64. 207s (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.) 207s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 207s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 207s 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' 207s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 207s 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' 207s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 207s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 207s lsof depends on libtirpc3 (>= 1.0.2). 207s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 207s libnss-nisplus:arm64 depends on libtirpc3 (>= 1.0.2). 207s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 207s iproute2 depends on libtirpc3 (>= 1.0.2). 207s 207s (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.) 207s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 207s Selecting previously unselected package libtirpc3t64:arm64. 207s (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.) 207s Preparing to unpack .../00-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 207s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 207s 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' 207s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 207s Selecting previously unselected package fonts-dejavu-mono. 207s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 207s Unpacking fonts-dejavu-mono (2.37-8) ... 207s Selecting previously unselected package fonts-dejavu-core. 208s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 208s Unpacking fonts-dejavu-core (2.37-8) ... 208s Selecting previously unselected package fontconfig-config. 208s Preparing to unpack .../03-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 208s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 208s Selecting previously unselected package libfontconfig1:arm64. 208s Preparing to unpack .../04-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 208s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 208s Selecting previously unselected package fontconfig. 208s Preparing to unpack .../05-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 208s Unpacking fontconfig (2.15.0-1ubuntu1) ... 208s Selecting previously unselected package fonts-mathjax. 208s Preparing to unpack .../06-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 208s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 208s Selecting previously unselected package libblas3:arm64. 208s Preparing to unpack .../07-libblas3_3.12.0-3_arm64.deb ... 208s Unpacking libblas3:arm64 (3.12.0-3) ... 208s Selecting previously unselected package libpixman-1-0:arm64. 208s Preparing to unpack .../08-libpixman-1-0_0.42.2-1_arm64.deb ... 208s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 208s Selecting previously unselected package libxcb-render0:arm64. 208s Preparing to unpack .../09-libxcb-render0_1.15-1_arm64.deb ... 208s Unpacking libxcb-render0:arm64 (1.15-1) ... 208s Selecting previously unselected package libxcb-shm0:arm64. 208s Preparing to unpack .../10-libxcb-shm0_1.15-1_arm64.deb ... 208s Unpacking libxcb-shm0:arm64 (1.15-1) ... 208s Selecting previously unselected package libxrender1:arm64. 208s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 208s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 209s Selecting previously unselected package libcairo2:arm64. 209s Preparing to unpack .../12-libcairo2_1.18.0-1_arm64.deb ... 209s Unpacking libcairo2:arm64 (1.18.0-1) ... 209s Selecting previously unselected package libdatrie1:arm64. 209s Preparing to unpack .../13-libdatrie1_0.2.13-3_arm64.deb ... 209s Unpacking libdatrie1:arm64 (0.2.13-3) ... 209s Selecting previously unselected package libdeflate0:arm64. 209s Preparing to unpack .../14-libdeflate0_1.19-1_arm64.deb ... 209s Unpacking libdeflate0:arm64 (1.19-1) ... 209s Selecting previously unselected package libgfortran5:arm64. 209s Preparing to unpack .../15-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 209s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 209s Selecting previously unselected package libgomp1:arm64. 209s Preparing to unpack .../16-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 209s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 209s Selecting previously unselected package libgraphite2-3:arm64. 209s Preparing to unpack .../17-libgraphite2-3_1.3.14-2_arm64.deb ... 209s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 209s Selecting previously unselected package libgslcblas0:arm64. 209s Preparing to unpack .../18-libgslcblas0_2.7.1+dfsg-6ubuntu1_arm64.deb ... 209s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 209s Selecting previously unselected package libgsl27:arm64. 209s Preparing to unpack .../19-libgsl27_2.7.1+dfsg-6ubuntu1_arm64.deb ... 209s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 209s Selecting previously unselected package libharfbuzz0b:arm64. 209s Preparing to unpack .../20-libharfbuzz0b_8.3.0-2_arm64.deb ... 209s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 209s Selecting previously unselected package x11-common. 209s Preparing to unpack .../21-x11-common_1%3a7.7+23ubuntu2_all.deb ... 209s Unpacking x11-common (1:7.7+23ubuntu2) ... 209s Selecting previously unselected package libice6:arm64. 209s Preparing to unpack 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package libpaper-utils. 210s Preparing to unpack .../33-libpaper-utils_1.1.29_arm64.deb ... 210s Unpacking libpaper-utils (1.1.29) ... 210s Selecting previously unselected package libsharpyuv0:arm64. 210s Preparing to unpack .../34-libsharpyuv0_1.3.2-0.4_arm64.deb ... 210s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 210s Selecting previously unselected package libsm6:arm64. 210s Preparing to unpack .../35-libsm6_2%3a1.2.3-1build2_arm64.deb ... 210s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 210s Selecting previously unselected package libtcl8.6:arm64. 210s Preparing to unpack .../36-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 210s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 210s Selecting previously unselected package libjbig0:arm64. 210s Preparing to unpack .../37-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 210s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 210s Selecting previously unselected package libwebp7:arm64. 210s Preparing to unpack .../38-libwebp7_1.3.2-0.4_arm64.deb ... 210s 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Preparing to unpack .../44-zip_3.0-13_arm64.deb ... 211s Unpacking zip (3.0-13) ... 211s Selecting previously unselected package unzip. 211s Preparing to unpack .../45-unzip_6.0-28ubuntu3_arm64.deb ... 211s Unpacking unzip (6.0-28ubuntu3) ... 211s Selecting previously unselected package xdg-utils. 211s Preparing to unpack .../46-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 211s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 211s Selecting previously unselected package r-base-core. 211s Preparing to unpack .../47-r-base-core_4.3.3-2build1_arm64.deb ... 211s Unpacking r-base-core (4.3.3-2build1) ... 211s Selecting previously unselected package r-cran-littler. 211s Preparing to unpack .../48-r-cran-littler_0.3.19-1_arm64.deb ... 211s Unpacking r-cran-littler (0.3.19-1) ... 211s Selecting previously unselected package littler. 211s Preparing to unpack .../49-littler_0.3.19-1_all.deb ... 211s Unpacking littler (0.3.19-1) ... 211s Selecting previously unselected package r-cran-abind. 211s Preparing to unpack .../50-r-cran-abind_1.4-5-2_all.deb ... 211s Unpacking r-cran-abind (1.4-5-2) ... 211s Selecting previously unselected package r-cran-codetools. 211s Preparing to unpack .../51-r-cran-codetools_0.2-19-1_all.deb ... 211s Unpacking r-cran-codetools (0.2-19-1) ... 211s Selecting previously unselected package r-cran-deldir. 211s Preparing to unpack .../52-r-cran-deldir_2.0-4-1_arm64.deb ... 211s Unpacking r-cran-deldir (2.0-4-1) ... 211s Selecting previously unselected package r-cran-iterators. 211s Preparing to unpack .../53-r-cran-iterators_1.0.14-1_all.deb ... 211s Unpacking r-cran-iterators (1.0.14-1) ... 211s Selecting previously unselected package r-cran-foreach. 211s Preparing to unpack .../54-r-cran-foreach_1.5.2-1_all.deb ... 211s Unpacking r-cran-foreach (1.5.2-1) ... 211s Selecting previously unselected package r-cran-lattice. 211s Preparing to unpack .../55-r-cran-lattice_0.22-5-1_arm64.deb ... 211s Unpacking r-cran-lattice (0.22-5-1) ... 211s Selecting previously unselected package r-cran-matrix. 212s Preparing to unpack .../56-r-cran-matrix_1.6-5-1_arm64.deb ... 212s Unpacking r-cran-matrix (1.6-5-1) ... 212s Selecting previously unselected package r-cran-shape. 212s Preparing to unpack .../57-r-cran-shape_1.4.6-1_all.deb ... 212s Unpacking r-cran-shape (1.4.6-1) ... 212s Selecting previously unselected package r-cran-survival. 212s Preparing to unpack .../58-r-cran-survival_3.5-8-1_arm64.deb ... 212s Unpacking r-cran-survival (3.5-8-1) ... 212s Selecting previously unselected package r-cran-pkgkitten. 212s Preparing to unpack .../59-r-cran-pkgkitten_0.2.3-1_all.deb ... 212s Unpacking r-cran-pkgkitten (0.2.3-1) ... 212s Selecting previously unselected package r-cran-rcpp. 212s Preparing to unpack .../60-r-cran-rcpp_1.0.12-1_arm64.deb ... 212s Unpacking r-cran-rcpp (1.0.12-1) ... 212s Selecting previously unselected package r-cran-rcppeigen. 212s Preparing to unpack .../61-r-cran-rcppeigen_0.3.3.9.4-1_arm64.deb ... 212s Unpacking r-cran-rcppeigen (0.3.3.9.4-1) ... 212s Selecting previously unselected package libjs-mathjax. 212s Preparing to unpack .../62-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 212s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 213s Selecting previously unselected package r-cran-glmnet. 213s Preparing to unpack .../63-r-cran-glmnet_4.1-8-1_arm64.deb ... 213s Unpacking r-cran-glmnet (4.1-8-1) ... 213s Selecting previously unselected package r-cran-goftest. 213s Preparing to unpack .../64-r-cran-goftest_1.2-3-1_arm64.deb ... 213s Unpacking r-cran-goftest (1.2-3-1) ... 213s Selecting previously unselected package r-cran-gsl. 213s Preparing to unpack .../65-r-cran-gsl_2.1-8-1_arm64.deb ... 213s Unpacking r-cran-gsl (2.1-8-1) ... 213s Selecting previously unselected package r-cran-locfit. 213s Preparing to unpack .../66-r-cran-locfit_1.5-9.8-1_arm64.deb ... 213s Unpacking r-cran-locfit (1.5-9.8-1) ... 213s Selecting previously unselected package r-cran-nlme. 213s Preparing to unpack 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... 217s Unpacking r-cran-spatstat (3.0-7-1) ... 218s Selecting previously unselected package autopkgtest-satdep. 218s Preparing to unpack .../84-1-autopkgtest-satdep.deb ... 218s Unpacking autopkgtest-satdep (0) ... 218s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 218s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 218s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 218s Setting up libpaper1:arm64 (1.1.29) ... 218s 218s Creating config file /etc/papersize with new version 218s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 218s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 218s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 218s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 218s Setting up libdatrie1:arm64 (0.2.13-3) ... 218s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 218s Setting up libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 218s Setting up libxcb-render0:arm64 (1.15-1) ... 218s Setting up unzip (6.0-28ubuntu3) ... 218s Setting up x11-common (1:7.7+23ubuntu2) ... 219s Setting up libpsl5t64:arm64 (0.21.2-1.1) ... 219s Setting up libdeflate0:arm64 (1.19-1) ... 219s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 219s Setting up libxcb-shm0:arm64 (1.15-1) ... 219s Setting up libpaper-utils (1.1.29) ... 219s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 219s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 219s Setting up zip (3.0-13) ... 219s Setting up libblas3:arm64 (3.12.0-3) ... 219s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 219s Setting up fonts-dejavu-mono (2.37-8) ... 219s Setting up libpng16-16t64:arm64 (1.6.43-3) ... 219s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 219s Setting up fonts-dejavu-core (2.37-8) ... 219s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 219s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 219s Setting up libwebp7:arm64 (1.3.2-0.4) ... 219s Setting up libreadline8t64:arm64 (8.2-3.1) ... 219s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 219s Setting up libthai-data (0.1.29-2) ... 219s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 219s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 219s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 219s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 219s Setting up libice6:arm64 (2:1.0.10-1build2) ... 219s Setting up liblapack3:arm64 (3.12.0-3) ... 219s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 219s Setting up libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 219s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 219s Setting up libthai0:arm64 (0.1.29-2) ... 219s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 219s Setting up curl (8.5.0-2ubuntu7) ... 219s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 219s Setting up 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(1.0.12-1) ... 221s Setting up r-cran-codetools (0.2-19-1) ... 221s Setting up littler (0.3.19-1) ... 221s Setting up r-cran-gsl (2.1-8-1) ... 221s Setting up r-cran-spatial (7.3-17-1) ... 221s Setting up r-cran-iterators (1.0.14-1) ... 221s Setting up r-cran-abind (1.4-5-2) ... 221s Setting up r-cran-foreach (1.5.2-1) ... 221s Setting up r-cran-sm (2.2-6.0-1) ... 221s Setting up r-cran-polyclip (1.10-6-1) ... 221s Setting up r-cran-deldir (2.0-4-1) ... 221s Setting up r-cran-goftest (1.2-3-1) ... 221s Setting up r-cran-shape (1.4.6-1) ... 221s Setting up r-cran-matrix (1.6-5-1) ... 221s Setting up r-cran-spatstat.sparse (3.0-3-1) ... 221s Setting up r-cran-mgcv (1.9-1-1) ... 221s Setting up r-cran-rcppeigen (0.3.3.9.4-1) ... 221s Setting up r-cran-survival (3.5-8-1) ... 221s Setting up r-cran-spatstat.data (3.0-4-1) ... 221s Setting up r-cran-spatstat.geom (3.2-8-1) ... 221s Setting up r-cran-glmnet (4.1-8-1) ... 221s Setting up r-cran-rpart (4.1.23-1) ... 221s Setting up r-cran-spatstat.random (3.2-2-1) ... 221s Setting up r-cran-spatstat.explore (3.2-5-1) ... 221s Setting up r-cran-spatstat.model (3.2-8-1) ... 221s Setting up r-cran-spatstat.linnet (3.1-3-1) ... 221s Setting up r-cran-spatstat (3.0-7-1) ... 221s Setting up autopkgtest-satdep (0) ... 221s Processing triggers for man-db (2.12.0-3) ... 222s Processing triggers for install-info (7.1-3) ... 222s Processing triggers for libc-bin (2.39-0ubuntu2) ... 231s (Reading database ... 84399 files and directories currently installed.) 231s Removing autopkgtest-satdep (0) ... 231s autopkgtest [20:19:36]: test run-unit-test: [----------------------- 232s BEGIN TEST testsAtoC.R 232s 232s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 232s Copyright (C) 2024 The R Foundation for Statistical Computing 232s Platform: aarch64-unknown-linux-gnu (64-bit) 232s 232s R is free software and comes with ABSOLUTELY NO WARRANTY. 232s You are welcome to redistribute it under certain conditions. 232s Type 'license()' or 'licence()' for distribution details. 232s 232s R is a collaborative project with many contributors. 232s Type 'contributors()' for more information and 232s 'citation()' on how to cite R or R packages in publications. 232s 232s Type 'demo()' for some demos, 'help()' for on-line help, or 232s 'help.start()' for an HTML browser interface to help. 232s Type 'q()' to quit R. 232s 232s > #' 232s > #' Header for all (concatenated) test files 232s > #' 232s > #' Require spatstat.model 232s > #' Obtain environment variable controlling tests. 232s > #' 232s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 232s > 232s > require(spatstat.model) 232s Loading required package: spatstat.model 232s Loading required package: spatstat.data 233s Loading required package: spatstat.geom 233s spatstat.geom 3.2-8 233s Loading required package: spatstat.random 233s spatstat.random 3.2-2 233s Loading required package: spatstat.explore 233s Loading required package: nlme 233s spatstat.explore 3.2-5 233s Loading required package: rpart 233s spatstat.model 3.2-8 233s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 233s > ALWAYS <- TRUE 233s > cat(paste("--------- Executing", 233s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 233s + "test code -----------\n")) 233s --------- Executing **RESTRICTED** subset of test code ----------- 233s > #' tests/aucroc.R 233s > #' 233s > #' AUC and ROC code 233s > #' 233s > #' $Revision: 1.6 $ $Date: 2020/11/02 06:26:45 $ 233s > 233s > local({ 233s + if(FULLTEST) { 233s + fit <- kppm(redwood ~ I(y-x)) 233s + a <- roc(fit) 233s + b <- auc(fit) 233s + fet <- ppm(amacrine~x+y+marks) 233s + d <- roc(fet) 233s + e <- auc(fet) 233s + } 233s + }) 233s > ## tests/cdf.test.R 233s > 233s > 233s > local({ 233s + NSIM <- 9 233s + op <- spatstat.options(ndummy.min=16, npixel=32) 233s + if(FULLTEST) { 233s + ## Monte Carlo test for Gibbs model 233s + fit <- ppm(cells ~ 1, Strauss(0.07)) 233s + cdf.test(fit, "x", nsim=NSIM) 233s + 233s + ## cdf.test.slrm 233s + fut <- slrm(japanesepines ~ x + y) 233s + Z <- distmap(japanesepines) 233s + cdf.test(fut, Z) 233s + } 233s + reset.spatstat.options() 233s + }) 233s > 233s > 233s > #' 233s > #' tests/contrib.R 233s > #' 233s > #' Tests for user-contributed code in spatstat 233s > #' 233s > #' $Revision: 1.4 $ $Date: 2021/04/17 02:32:24 $ 233s > 233s > local({ 233s + #' Jinhom 233s + #' Marie-Colette van Lieshout and Ottmar Cronie 233s + X <- redwood3 233s + if(FULLTEST) { 233s + fit <- ppm(X ~ polynom(x,y,2)) 233s + } else { 233s + X <- X[c(TRUE,FALSE)] 233s + spatstat.options(npixel=32, ndummy.min=16) 233s + fit <- ppm(X ~ x) 233s + } 233s + lam <- predict(fit) 233s + lamX <- fitted(fit, dataonly=TRUE) 233s + lmin <- 0.9 * min(lam) 233s + g1 <- Ginhom(X, lambda=fit, update=TRUE) 233s + if(FULLTEST) { 233s + g2 <- Ginhom(X, lambda=fit, update=FALSE, lmin = lmin) 233s + g3 <- Ginhom(X, lambda=lam, lmin=lmin) 233s + g4 <- Ginhom(X, lambda=lamX, lmin=lmin) 233s + } 233s + if(ALWAYS) { 233s + f2 <- Finhom(X, lambda=fit, update=FALSE) 233s + } 233s + if(FULLTEST) { 233s + f1 <- Finhom(X, lambda=fit, update=TRUE) 233s + f3 <- Finhom(X, lambda=lam, lmin=lmin) 233s + } 233s + if(!FULLTEST) reset.spatstat.options() 233s + }) 234s > 234s BEGIN TEST testsD.R 234s 234s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 234s Copyright (C) 2024 The R Foundation for Statistical Computing 234s Platform: aarch64-unknown-linux-gnu (64-bit) 234s 234s R is free software and comes with ABSOLUTELY NO WARRANTY. 234s You are welcome to redistribute it under certain conditions. 234s Type 'license()' or 'licence()' for distribution details. 234s 234s R is a collaborative project with many contributors. 234s Type 'contributors()' for more information and 234s 'citation()' on how to cite R or R packages in publications. 234s 234s Type 'demo()' for some demos, 'help()' for on-line help, or 234s 'help.start()' for an HTML browser interface to help. 234s Type 'q()' to quit R. 234s 234s > #' 234s > #' Header for all (concatenated) test files 234s > #' 234s > #' Require spatstat.model 234s > #' Obtain environment variable controlling tests. 234s > #' 234s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 234s > 234s > require(spatstat.model) 234s Loading required package: spatstat.model 234s Loading required package: spatstat.data 235s Loading required package: spatstat.geom 235s spatstat.geom 3.2-8 235s Loading required package: spatstat.random 235s spatstat.random 3.2-2 235s Loading required package: spatstat.explore 235s Loading required package: nlme 235s spatstat.explore 3.2-5 235s Loading required package: rpart 235s spatstat.model 3.2-8 235s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 235s > ALWAYS <- TRUE 235s > cat(paste("--------- Executing", 235s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 235s + "test code -----------\n")) 235s --------- Executing **RESTRICTED** subset of test code ----------- 235s > #' 235s > #' tests/deltasuffstat.R 235s > #' 235s > #' Explicit tests of 'deltasuffstat' 235s > #' 235s > #' $Revision: 1.4 $ $Date: 2021/01/22 08:08:48 $ 235s > 235s > if(!FULLTEST) 235s + spatstat.options(npixel=32, ndummy.min=16) 235s > 235s > if(ALWAYS) { # depends on C code 235s + local({ 235s + 235s + disagree <- function(x, y, tol=1e-7) { !is.null(x) && !is.null(y) && max(abs(x-y)) > tol } 235s + 235s + flydelta <- function(model, modelname="") { 235s + ## Check execution of different algorithms for 'deltasuffstat' 235s + dSS <- deltasuffstat(model, sparseOK=TRUE) 235s + dBS <- deltasuffstat(model, sparseOK=TRUE, use.special=FALSE, force=TRUE) 235s + dBF <- deltasuffstat(model, sparseOK=FALSE, use.special=FALSE, force=TRUE) 235s + ## Compare results 235s + if(disagree(dBS, dSS)) 235s + stop(paste(modelname, "model: Brute force algorithm disagrees with special algorithm")) 235s + if(disagree(dBF, dBS)) 235s + stop(paste(modelname, "model: Sparse and full versions of brute force algorithm disagree")) 235s + return(invisible(NULL)) 235s + } 235s + 235s + modelS <- ppm(cells ~ x, Strauss(0.13), nd=10) 235s + flydelta(modelS, "Strauss") 235s + 235s + antsub <- ants[c(FALSE,TRUE,FALSE)] 235s + rmat <- matrix(c(130, 90, 90, 60), 2, 2) 235s + 235s + modelM <- ppm(antsub ~ 1, MultiStrauss(rmat), nd=16) 235s + flydelta(modelM, "MultiStrauss") 235s + 235s + modelA <- ppm(antsub ~ 1, HierStrauss(rmat, archy=c(2,1)), nd=16) 235s + flydelta(modelA, "HierStrauss") 235s + }) 235s + 235s + } 241s > 241s > reset.spatstat.options() 241s > #' 241s > #' tests/density.R 241s > #' 241s > #' Test behaviour of density() methods, 241s > #' relrisk(), Smooth() 241s > #' and inhomogeneous summary functions 241s > #' and idw, adaptive.density, intensity 241s > #' 241s > #' $Revision: 1.62 $ $Date: 2022/05/22 11:14:51 $ 241s > #' 241s > 241s > if(!FULLTEST) 241s + spatstat.options(npixel=32, ndummy.min=16) 241s > 241s > 241s > local({ 241s + ## likewise 'relrisk.ppm' 241s + fit <- ppm(ants ~ x) 241s + rants <- function(..., model=fit) { 241s + a <- relrisk(model, sigma=100, se=TRUE, ...) 241s + return(TRUE) 241s + } 241s + if(ALWAYS) { 241s + rants() 241s + rants(diggle=TRUE) 241s + rants(edge=FALSE) 241s + rants(at="points") 241s + rants(casecontrol=FALSE) 241s + rants(relative=TRUE) 241s + } 241s + if(FULLTEST) { 241s + rants(diggle=TRUE, at="points") 241s + rants(edge=FALSE, at="points") 241s + rants(casecontrol=FALSE, relative=TRUE) 241s + rants(casecontrol=FALSE,at="points") 241s + rants(relative=TRUE,at="points") 241s + rants(casecontrol=FALSE, relative=TRUE,at="points") 241s + rants(relative=TRUE, control="Cataglyphis", case="Messor") 241s + rants(relative=TRUE, control="Cataglyphis", case="Messor", at="points") 241s + } 241s + ## more than 2 types 241s + fut <- ppm(sporophores ~ x) 241s + if(ALWAYS) { 241s + rants(model=fut) 241s + } 241s + if(FULLTEST) { 241s + rants(model=fut, at="points") 241s + rants(model=fut, relative=TRUE, at="points") 241s + } 241s + if(FULLTEST) { 241s + ## cases of 'intensity' etc 241s + a <- intensity(ppm(amacrine ~ 1)) 241s + } 241s + }) 242s > 242s > reset.spatstat.options() 242s > 242s > #' 242s > #' tests/diagnostique.R 242s > #' 242s > #' Diagnostic tools such as diagnose.ppm, qqplot.ppm 242s > #' 242s > #' $Revision: 1.6 $ $Date: 2020/04/28 12:58:26 $ 242s > #' 242s > 242s > if(FULLTEST) { 242s + local({ 242s + fit <- ppm(cells ~ x) 242s + diagE <- diagnose.ppm(fit, type="eem") 242s + diagI <- diagnose.ppm(fit, type="inverse") 242s + diagP <- diagnose.ppm(fit, type="Pearson") 242s + plot(diagE, which="all") 242s + plot(diagI, which="smooth") 242s + plot(diagP, which="x") 242s + plot(diagP, which="marks", plot.neg="discrete") 242s + plot(diagP, which="marks", plot.neg="contour") 242s + plot(diagP, which="smooth", srange=c(-5,5)) 242s + plot(diagP, which="smooth", plot.smooth="contour") 242s + plot(diagP, which="smooth", plot.smooth="image") 242s + 242s + fitS <- ppm(cells ~ x, Strauss(0.08)) 242s + diagES <- diagnose.ppm(fitS, type="eem", clip=FALSE) 242s + diagIS <- diagnose.ppm(fitS, type="inverse", clip=FALSE) 242s + diagPS <- diagnose.ppm(fitS, type="Pearson", clip=FALSE) 242s + plot(diagES, which="marks", plot.neg="imagecontour") 242s + plot(diagPS, which="marks", plot.neg="discrete") 242s + plot(diagPS, which="marks", plot.neg="contour") 242s + plot(diagPS, which="smooth", plot.smooth="image") 242s + plot(diagPS, which="smooth", plot.smooth="contour") 242s + plot(diagPS, which="smooth", plot.smooth="persp") 242s + 242s + #' infinite reach, not border-corrected 242s + fut <- ppm(cells ~ x, Softcore(0.5), correction="isotropic") 242s + diagnose.ppm(fut) 242s + 242s + #' 242s + diagPX <- diagnose.ppm(fit, type="Pearson", cumulative=FALSE) 242s + plot(diagPX, which="y") 242s + 242s + #' simulation based 242s + e <- envelope(cells, nsim=4, savepatterns=TRUE, savefuns=TRUE) 242s + Plist <- rpoispp(40, nsim=5) 242s + 242s + qf <- qqplot.ppm(fit, nsim=4, expr=e, plot.it=FALSE) 242s + print(qf) 242s + qp <- qqplot.ppm(fit, nsim=5, expr=Plist, fast=FALSE) 242s + print(qp) 242s + qp <- qqplot.ppm(fit, nsim=5, expr=expression(rpoispp(40)), plot.it=FALSE) 242s + print(qp) 242s + qg <- qqplot.ppm(fit, nsim=5, style="classical", plot.it=FALSE) 242s + print(qg) 242s + 242s + #' lurking.ppm 242s + #' covariate is numeric vector 242s + fitx <- ppm(cells ~ x) 242s + yvals <- coords(as.ppp(quad.ppm(fitx)))[,"y"] 242s + lurking(fitx, yvals) 242s + #' covariate is stored but is not used in model 242s + Z <- as.im(function(x,y){ x+y }, Window(cells)) 242s + fitxx <- ppm(cells ~ x, data=solist(Zed=Z), allcovar=TRUE) 242s + lurking(fitxx, expression(Zed)) 242s + #' envelope is a ppplist; length < nsim; glmdata=NULL 242s + fit <- ppm(cells ~ 1) 242s + stuff <- lurking(fit, expression(x), envelope=Plist, plot.sd=FALSE) 242s + #' plot.lurk 242s + plot(stuff, shade=NULL) 242s + }) 242s + } 242s > 242s > #' 242s > #' tests/deepeepee.R 242s > #' 242s > #' Tests for determinantal point process models 242s > #' 242s > #' $Revision: 1.9 $ $Date: 2022/04/24 09:14:46 $ 242s > 242s > local({ 242s + if(ALWAYS) { 242s + #' simulate.dppm 242s + jpines <- residualspaper$Fig1 242s + fit <- dppm(jpines ~ 1, dppGauss) 242s + set.seed(10981) 242s + simulate(fit, W=square(5)) 242s + } 242s + if(FULLTEST) { 242s + #' simulate.detpointprocfamily - code blocks 242s + model <- dppGauss(lambda=100, alpha=.05, d=2) 242s + simulate(model, seed=1999, correction="border") 242s + u <- is.stationary(model) 242s + #' other methods for dppm 242s + kay <- Kmodel(fit) 242s + gee <- pcfmodel(fit) 242s + lam <- intensity(fit) 242s + arr <- reach(fit) 242s + pah <- parameters(fit) 242s + #' a user bug report - matrix dimension error 242s + set.seed(256) 242s + dat <- simulate( dppGauss(lambda = 8.5, alpha = 0.1, d = 2), nsim = 1) 242s + } 242s + if(FULLTEST) { 242s + ## cover print.summary.dppm 242s + jpines <- japanesepines[c(TRUE,FALSE,FALSE,FALSE)] 242s + print(summary(dppm(jpines ~ 1, dppGauss))) 242s + print(summary(dppm(jpines ~ 1, dppGauss, method="c"))) 242s + print(summary(dppm(jpines ~ 1, dppGauss, method="p"))) 242s + print(summary(dppm(jpines ~ 1, dppGauss, method="a"))) 242s + } 242s + #' dppeigen code blocks 242s + if(ALWAYS) { 242s + mod <- dppMatern(lambda=2, alpha=0.01, nu=1, d=2) 242s + uT <- dppeigen(mod, trunc=1.1, Wscale=c(1,1), stationary=TRUE) 242s + } 242s + if(FULLTEST) { 242s + uF <- dppeigen(mod, trunc=1.1, Wscale=c(1,1), stationary=FALSE) 242s + vT <- dppeigen(mod, trunc=0.98, Wscale=c(1,1), stationary=TRUE) 242s + vF <- dppeigen(mod, trunc=0.98, Wscale=c(1,1), stationary=FALSE) 242s + } 242s + }) 243s > 243s BEGIN TEST testsEtoF.R 245s 245s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 245s Copyright (C) 2024 The R Foundation for Statistical Computing 245s Platform: aarch64-unknown-linux-gnu (64-bit) 245s 245s R is free software and comes with ABSOLUTELY NO WARRANTY. 245s You are welcome to redistribute it under certain conditions. 245s Type 'license()' or 'licence()' for distribution details. 245s 245s R is a collaborative project with many contributors. 245s Type 'contributors()' for more information and 245s 'citation()' on how to cite R or R packages in publications. 245s 245s Type 'demo()' for some demos, 'help()' for on-line help, or 245s 'help.start()' for an HTML browser interface to help. 245s Type 'q()' to quit R. 245s 245s > #' 245s > #' Header for all (concatenated) test files 245s > #' 245s > #' Require spatstat.model 245s > #' Obtain environment variable controlling tests. 245s > #' 245s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 245s > 245s > require(spatstat.model) 245s Loading required package: spatstat.model 245s Loading required package: spatstat.data 246s Loading required package: spatstat.geom 246s spatstat.geom 3.2-8 246s Loading required package: spatstat.random 246s spatstat.random 3.2-2 246s Loading required package: spatstat.explore 246s Loading required package: nlme 246s spatstat.explore 3.2-5 246s Loading required package: rpart 246s spatstat.model 3.2-8 246s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 246s > ALWAYS <- TRUE 246s > cat(paste("--------- Executing", 246s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 246s + "test code -----------\n")) 246s --------- Executing **RESTRICTED** subset of test code ----------- 246s > # 246s > # tests/envelopes.R 246s > # 246s > # Test validity of envelope data 246s > # 246s > # $Revision: 1.28 $ $Date: 2022/11/24 01:35:26 $ 246s > # 246s > 246s > local({ 246s + 246s + 246s + checktheo <- function(fit) { 246s + fitname <- deparse(substitute(fit)) 246s + en <- envelope(fit, nsim=4, verbose=FALSE, nrep=1e3) 246s + nama <- names(en) 246s + expecttheo <- is.poisson(fit) && is.stationary(fit) 246s + context <- paste("Envelope of", fitname) 246s + if(expecttheo) { 246s + if(!("theo" %in% nama)) 246s + stop(paste(context, "did not contain", sQuote("theo"))) 246s + if("mmean" %in% nama) 246s + stop(paste(context, "unexpectedly contained", sQuote("mmean"))) 246s + } else { 246s + if("theo" %in% nama) 246s + stop(paste(context, "unexpectedly contained", sQuote("theo"))) 246s + if(!("mmean" %in% nama)) 246s + stop(paste(context, "did not contain", sQuote("mmean"))) 246s + } 246s + cat(paste(context, "has correct format\n")) 246s + } 246s + 246s + if(ALWAYS) { 246s + checktheo(ppm(cells ~x)) 246s + } 246s + if(FULLTEST) { 246s + checktheo(ppm(cells)) 246s + checktheo(ppm(cells ~1, Strauss(0.1))) 246s + } 246s + 246s + 246s + #' check savefuns/savepatterns with global 246s + fit <- ppm(cells~x) 246s + if(ALWAYS) Ef <- envelope(fit, Kest, nsim=4, savefuns=TRUE, global=TRUE) 246s + if(FULLTEST) Ep <- envelope(fit, Kest, nsim=4, savepatterns=TRUE, global=TRUE) 246s + #' check handling of 'dangerous' cases 246s + if(FULLTEST) { 246s + fut <- ppm(redwood ~ x) 246s + Ek <- envelope(fut, Kinhom, update=FALSE, nsim=4) 246s + kfut <- kppm(redwood3 ~ x) 246s + Ekk <- envelope(kfut, Kinhom, lambda=density(redwood3), nsim=7) 246s + } 246s + 246s + 246s + if(ALWAYS) { # invokes C code 246s + fit <- ppm(japanesepines ~ 1, Strauss(0.04)) 246s + e6 <- envelope(fit, Kest, nsim=4, fix.n=TRUE) 246s + fit2 <- ppm(amacrine ~ 1, Strauss(0.03)) 246s + e7 <- envelope(fit2, Gcross, nsim=4, fix.marks=TRUE) 246s + } 246s + 246s + 246s + if(FULLTEST) { 246s + fit <- ppm(cells ~ 1, Strauss(0.07)) 246s + U <- envelope(fit, nsim=3, simulate=expression(runifpoint(20))) 246s + kfit <- kppm(redwood3 ~ x) 246s + UU <- envelope(kfit, nsim=7, simulate=expression(simulate(kfit, drop=TRUE))) 246s + VV <- envelope(kfit, nsim=7, weights=1:7) 246s + MM <- envelope(kfit, nsim=7, Kinhom, lambda=density(redwood3)) 246s + } 246s + 246s + if(FULLTEST) { 246s + #' envelope computations in other functions 246s + P <- lurking(cells, expression(x), envelope=TRUE, nsim=9) 246s + print(P) 246s + #' re-using envelope objects in other functions 246s + A <- envelope(cells, nsim=9, savepatterns=TRUE, savefuns=TRUE) 246s + S <- lurking(cells, expression(x), envelope=A, nsim=9) 246s + #' envelope.envelope 246s + B <- envelope(cells, nsim=5, savepatterns=TRUE, savefuns=FALSE) 246s + envelope(B) 246s + } 246s + 246s + 246s + 246s + ## close 'local' 246s + }) 246s Envelope of ppm(cells ~ x) has correct format 246s Generating 8 simulated realisations of fitted Poisson model (4 to estimate the 247s mean and 4 to calculate envelopes) ... 247s 1, 2, 3, 4, 5, 6, 7, 247s 8. 247s 247s Done. 247s Generating 4 simulated realisations of fitted Gibbs model with fixed number of 247s points ... 247s 1, 2, 3, 247s 4. 247s 247s Done. 247s Generating 4 simulated realisations of fitted Gibbs model with fixed number of 247s points of each type ... 247s 1, 2, 3, 247s 4. 247s 247s Done. 247s > #' tests/enveltest.R 247s > #' Envelope tests (dclf.test, mad.test) 247s > #' and two-stage tests (bits.test, dg.test, bits.envelope, dg.envelope) 247s > #' 247s > #' $Revision: 1.3 $ $Date: 2020/04/28 12:58:26 $ 247s > #' 247s > if(FULLTEST) { 247s + local({ 247s + #' handling of NA function values (due to empty point patterns) 247s + set.seed(1234) 247s + X <- rThomas(5, 0.05, 10) 247s + fit <- kppm(X ~ 1, "Thomas") 247s + set.seed(100000) 247s + dclf.test(fit) 247s + set.seed(909) 247s + dg.test(fit, nsim=9) 247s + #' other code blocks 247s + dclf.test(fit, rinterval=c(0, 3), nsim=9) 247s + envelopeTest(X, exponent=3, clamp=TRUE, nsim=9) 247s + }) 247s + } 247s > # 247s > # tests/fastgeyer.R 247s > # 247s > # checks validity of fast C implementation of Geyer interaction 247s > # 247s > # $Revision: 1.4 $ $Date: 2020/04/28 12:58:26 $ 247s > # 247s > if(FULLTEST) { # depends on hardware 247s + local({ 247s + X <- redwood 247s + Q <- quadscheme(X) 247s + U <- union.quad(Q) 247s + EP <- equalpairs.quad(Q) 247s + G <- Geyer(0.11, 2) 247s + # The value r=0.11 is chosen to avoid hardware numerical effects (gcc bug 323). 247s + # It avoids being close any value of pairdist(redwood). 247s + # The nearest such values are 0.1077.. and 0.1131.. 247s + # By contrast if r = 0.1 there are values differing from 0.1 by 3e-17 247s + a <- pairsat.family$eval(X,U,EP,G$pot,G$par,"border") 247s + b <- G$fasteval(X,U,EP,G$pot,G$par,"border") 247s + if(!all(a==b)) 247s + stop("Results of Geyer()$fasteval and pairsat.family$eval do not match") 247s + # ... 247s + # and again for a non-integer value of 'sat' 247s + # (spotted by Thordis Linda Thorarinsdottir) 247s + G <- Geyer(0.11, 2.5) 247s + a <- pairsat.family$eval(X,U,EP,G$pot,G$par,"border") 247s + b <- G$fasteval(X,U,EP,G$pot,G$par,"border") 247s + if(!all(a==b)) 247s + stop("Results of Geyer()$fasteval and pairsat.family$eval do not match when sat is not an integer") 247s + # and again for sat < 1 247s + # (spotted by Rolf) 247s + G <- Geyer(0.11, 0.5) 247s + a <- pairsat.family$eval(X,U,EP,G$pot,G$par,"border") 247s + b <- G$fasteval(X,U,EP,G$pot,G$par,"border") 247s + if(!all(a==b)) 247s + stop("Results of Geyer()$fasteval and pairsat.family$eval do not match when sat < 1") 247s + }) 247s + } 247s > 247s > #' tests/formuli.R 247s > #' 247s > #' Test machinery for manipulating formulae 247s > #' 247s > #' $Revision: 1.7 $ $Date: 2020/04/28 12:58:26 $ 247s > 247s > local({ 247s + 247s + ff <- function(A, deletevar, B) { 247s + D <- reduceformula(A, deletevar) 247s + if(!spatstat.utils::identical.formulae(D, B)) { 247s + AD <- as.expression(substitute(reduceformula(A,d), 247s + list(A=A, d=deletevar))) 247s + stop(paste(AD, "\n\tyields ", spatstat.utils::pasteFormula(D), 247s + " instead of ", spatstat.utils::pasteFormula(B)), 247s + call.=FALSE) 247s + } 247s + invisible(NULL) 247s + } 247s + 247s + ff(~ x + z, "x", ~z) 247s + 247s + ff(y ~ x + z, "x", y~z) 247s + 247s + ff(~ I(x^2) + z, "x", ~z) 247s + 247s + ff(y ~ poly(x,2) + poly(z,3), "x", y ~poly(z,3)) 247s + 247s + ff(y ~ x + z, "g", y ~ x + z) 247s + 247s + reduceformula(y ~ x+z, "g", verbose=TRUE) 247s + reduceformula(y ~ sin(x-z), "z", verbose=TRUE) 247s + 247s + illegal.iformula(~str*g, itags="str", dfvarnames=c("marks", "g", "x", "y")) 247s + }) 247s NULL 247s > 247s > 247s > 247s > ## 247s > ## tests/funnymarks.R 247s > ## 247s > ## tests involving strange mark values 247s > ## $Revision: 1.7 $ $Date: 2020/04/28 12:58:26 $ 247s > 247s > if(ALWAYS) { # depends on locale 247s + local({ 247s + ## ppm() where mark levels contain illegal characters 247s + hyphenated <- c("a", "not-a") 247s + spaced <- c("U", "non U") 247s + suffixed <- c("a+", "a*") 247s + charred <- c("+", "*") 247s + 247s + irad <- matrix(0.1, 2,2) 247s + hrad <- matrix(0.005, 2, 2) 247s + 247s + tryit <- function(types, X, irad, hrad) { 247s + levels(marks(X)) <- types 247s + fit <- ppm(X ~marks + polynom(x,y,2), 247s + MultiStraussHard(types=types,iradii=irad,hradii=hrad)) 247s + print(fit) 247s + print(coef(fit)) 247s + val <- fitted(fit) 247s + pred <- predict(fit) 247s + return(invisible(NULL)) 247s + The formula does not involve “g” and is therefore unchanged 247s Don't know how to reduce the term “sin(x - z)” 247s } 247s + 247s + tryit(hyphenated, amacrine, irad, hrad) 247s + tryit(spaced, amacrine, irad, hrad) 247s + tryit(suffixed, amacrine, irad, hrad) 247s + tryit(charred, amacrine, irad, hrad) 247s + 247s + ## marks which are dates 247s + X <- cells 247s + n <- npoints(X) 247s + endoftime <- rep(ISOdate(2001,1,1), n) 247s + eotDate <- rep(as.Date("2001-01-01"), n) 247s + markformat(endoftime) 247s + markformat(eotDate) 247s + marks(X) <- endoftime 247s + print(X) 247s + Y <- X %mark% data.frame(id=1:42, date=endoftime, dd=eotDate) 247s + print(Y) 247s + md <- markformat(endoftime) 247s + 247s + ## mark formats 247s + Z <- Y 247s + marks(Z) <- marks(Z)[1,,drop=FALSE] 247s + ms <- markformat(solist(cells, redwood)) 247s + marks(Z) <- factor(1:npoints(Z)) 247s + marks(Z)[12] <- NA 247s + mz <- is.multitype(Z) 247s + cZ <- coerce.marks.numeric(Z) 247s + marks(Z) <- data.frame(n=1:npoints(Z), 247s + a=factor(sample(letters, npoints(Z), replace=TRUE))) 247s + cZ <- coerce.marks.numeric(Z) 247s + stopifnot(is.multitype(cells %mark% data.frame(a=factor(1:npoints(cells))))) 247s + 247s + a <- numeric.columns(finpines) 247s + b1 <- numeric.columns(amacrine) 247s + b2 <- coerce.marks.numeric(amacrine) 247s + d <- numeric.columns(cells) 247s + f <- numeric.columns(longleaf) 247s + ff <- data.frame(a=factor(letters[1:10]), y=factor(sample(letters, 10))) 247s + numeric.columns(ff) 247s + 247s + ## mark operations 247s + df <- data.frame(x=1:2, y=sample(letters, 2)) 247s + h <- hyperframe(z=1:2, p=solist(cells, cells)) 247s + a <- NULL %mrep% 3 247s + a <- 1:4 %mrep% 3 247s + a <- df %mrep% 3 247s + a <- h %mrep% 3 247s + b <- markcbind(df, h) 247s + b <- markcbind(h, df) 247s + }) 247s + } 248s Nonstationary Multitype Strauss Hardcore process 248s Fitted to point pattern dataset ‘X’ 248s 248s Possible marks: ‘a’ and ‘not-a’ 248s 248s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 248s 248s Fitted trend coefficients: 248s (Intercept) marksnot-a x y I(x^2) I(x * y) 248s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 248s I(y^2) 248s -0.5425654 248s 248s 2 types of points 248s Possible types: 248s [1] a not-a 248s Interaction radii: 248s a not-a 248s a 0.1 0.1 248s not-a 0.1 0.1 248s Hardcore radii: 248s a not-a 248s a 0.005 0.005 248s not-a 0.005 0.005 248s Fitted interaction parameters gamma_ij 248s a not-a 248s a 0.2699920 0.8920719 248s not-a 0.8920719 0.2694374 248s 248s Relevant coefficients: 248s markaxa markaxnot.a marknot.axnot.a 248s -1.3093629 -0.1142086 -1.3114192 248s 248s For standard errors, type coef(summary(x)) 248s (Intercept) marksnot-a x y I(x^2) 248s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 248s I(x * y) I(y^2) markaxa markaxnot.a marknot.axnot.a 248s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 248s Nonstationary Multitype Strauss Hardcore process 248s Fitted to point pattern dataset ‘X’ 248s 248s Possible marks: ‘U’ and ‘non U’ 248s 248s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 248s 248s Fitted trend coefficients: 248s (Intercept) marksnon U x y I(x^2) I(x * y) 248s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 248s I(y^2) 248s -0.5425654 248s 248s 2 types of points 248s Possible types: 248s [1] U non U 248s Interaction radii: 248s U non U 248s U 0.1 0.1 248s non U 0.1 0.1 248s Hardcore radii: 248s U non U 248s U 0.005 0.005 248s non U 0.005 0.005 248s Fitted interaction parameters gamma_ij 248s U non U 248s U 0.2699920 0.8920719 248s non U 0.8920719 0.2694374 248s 248s Relevant coefficients: 248s markUxU markUxnon.U marknon.Uxnon.U 248s -1.3093629 -0.1142086 -1.3114192 248s 248s For standard errors, type coef(summary(x)) 248s (Intercept) marksnon U x y I(x^2) 248s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 248s I(x * y) I(y^2) markUxU markUxnon.U marknon.Uxnon.U 248s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 248s Nonstationary Multitype Strauss Hardcore process 248s Fitted to point pattern dataset ‘X’ 248s 248s Possible marks: ‘a+’ and ‘a*’ 248s 248s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 248s 248s Fitted trend coefficients: 248s (Intercept) marksa* x y I(x^2) I(x * y) 248s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 248s I(y^2) 248s -0.5425654 248s 248s 2 types of points 248s Possible types: 248s [1] a+ a* 248s Interaction radii: 248s a+ a* 248s a+ 0.1 0.1 248s a* 0.1 0.1 248s Hardcore radii: 248s a+ a* 248s a+ 0.005 0.005 248s a* 0.005 0.005 248s Fitted interaction parameters gamma_ij 248s a+ a* 248s a+ 0.2699920 0.8920719 248s a* 0.8920719 0.2694374 248s 248s Relevant coefficients: 248s marka.xa. marka.xa..1 marka..1xa..1 248s -1.3093629 -0.1142086 -1.3114192 248s 248s For standard errors, type coef(summary(x)) 248s (Intercept) marksa* x y I(x^2) 248s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 248s I(x * y) I(y^2) marka.xa. marka.xa..1 marka..1xa..1 248s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 248s Nonstationary Multitype Strauss Hardcore process 248s Fitted to point pattern dataset ‘X’ 248s 248s Possible marks: ‘+’ and ‘*’ 248s 248s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 248s 248s Fitted trend coefficients: 248s (Intercept) marks* x y I(x^2) I(x * y) 248s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 248s I(y^2) 248s -0.5425654 248s 248s 2 types of points 248s Possible types: 248s [1] + * 248s Interaction radii: 248s + * 248s + 0.1 0.1 248s * 0.1 0.1 248s Hardcore radii: 248s + * 248s + 0.005 0.005 248s * 0.005 0.005 248s Fitted interaction parameters gamma_ij 248s + * 248s + 0.2699920 0.8920719 248s * 0.8920719 0.2694374 248s 248s Relevant coefficients: 248s markX.xX. markX.xX..1 markX..1xX..1 248s -1.3093629 -0.1142086 -1.3114192 248s 248s For standard errors, type coef(summary(x)) 248s (Intercept) marks* x y I(x^2) 248s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 248s I(x * y) I(y^2) markX.xX. markX.xX..1 markX..1xX..1 248s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 248s Marked planar point pattern: 42 points 248s marks are dates, of class ‘POSIXt’ 248s window: rectangle = [0, 1] x [0, 1] units 248s Marked planar point pattern: 42 points 248s Mark variables: id, date, dd 248s window: rectangle = [0, 1] x [0, 1] units 248s Warning messages: 249s > 249s 1: In is.multitype.ppp(Z) : some mark values are NA in the point pattern Z 249s 2: Factor-valued marks were converted to integer codes 249s 3: Factor-valued mark variable ‘a’ was converted to integer codes 249s 4: Factor-valued marks were converted to integer codes 249s BEGIN TEST testsGtoJ.R 249s 249s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 249s Copyright (C) 2024 The R Foundation for Statistical Computing 249s Platform: aarch64-unknown-linux-gnu (64-bit) 249s 249s R is free software and comes with ABSOLUTELY NO WARRANTY. 249s You are welcome to redistribute it under certain conditions. 249s Type 'license()' or 'licence()' for distribution details. 249s 249s R is a collaborative project with many contributors. 249s Type 'contributors()' for more information and 249s 'citation()' on how to cite R or R packages in publications. 249s 249s Type 'demo()' for some demos, 'help()' for on-line help, or 249s 'help.start()' for an HTML browser interface to help. 249s Type 'q()' to quit R. 249s 249s > #' 249s > #' Header for all (concatenated) test files 249s > #' 249s > #' Require spatstat.model 249s > #' Obtain environment variable controlling tests. 249s > #' 249s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 249s > 249s > require(spatstat.model) 249s Loading required package: spatstat.model 249s Loading required package: spatstat.data 250s Loading required package: spatstat.geom 250s spatstat.geom 3.2-8 250s Loading required package: spatstat.random 250s spatstat.random 3.2-2 250s Loading required package: spatstat.explore 250s Loading required package: nlme 251s spatstat.explore 3.2-5 251s Loading required package: rpart 251s spatstat.model 3.2-8 251s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 251s > ALWAYS <- TRUE 251s > cat(paste("--------- Executing", 251s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 251s + "test code -----------\n")) 251s --------- Executing **RESTRICTED** subset of test code ----------- 251s > #' 251s > #' tests/hobjects.R 251s > #' 251s > #' Validity of methods for ppm(... method="ho") 251s > #' 251s > #' $Revision: 1.4 $ $Date: 2022/06/18 10:14:44 $ 251s > 251s > 251s > if(FULLTEST) { 251s + local({ 251s + set.seed(42) 251s + fit <- ppm(cells ~1, Strauss(0.1), improve.type="ho", nsim=10) 251s + fitx <- ppm(cells ~offset(x), Strauss(0.1), improve.type="ho", nsim=10) 251s + 251s + a <- AIC(fit) 251s + ax <- AIC(fitx) 251s + 251s + f <- fitted(fit) 251s + fx <- fitted(fitx) 251s + 251s + p <- predict(fit) 251s + px <- predict(fitx) 251s + }) 251s + } 251s > 251s > 251s > #' tests/hypotests.R 251s > #' Hypothesis tests 251s > #' 251s > #' $Revision: 1.10 $ $Date: 2023/07/17 07:30:48 $ 251s > 251s > if(FULLTEST) { 251s + local({ 251s + 251s + #' scan test with baseline 251s + fit <- ppm(cells ~ x) 251s + lam <- predict(fit) 251s + rr <- c(0.05, 1) 251s + scan.test(cells, rr, nsim=5, 251s + method="poisson", baseline=fit, alternative="less") 251s + scan.test(cells, rr, nsim=5, 251s + method="poisson", baseline=lam, alternative="less") 251s + }) 251s + } 251s > #' 251s > #' tests/interact.R 251s > #' 251s > #' Support for interaction objects 251s > #' 251s > #' $Revision: 1.2 $ $Date: 2020/04/28 12:58:26 $ 251s > 251s > if(FULLTEST) { 251s + local({ 251s + #' print.intermaker 251s + Strauss 251s + Geyer 251s + Ord 251s + #' intermaker 251s + BS <- get("BlankStrauss", envir=environment(Strauss)) 251s + BD <- function(r) { instantiate.interact(BS, list(r=r)) } 251s + BlueDanube <- intermaker(BD, BS) 251s + }) 251s + } 251s > 251s > #' tests/ippm.R 251s > #' Tests of 'ippm' class 251s > #' $Revision: 1.6 $ $Date: 2020/04/28 12:58:26 $ 251s > 251s > if(FULLTEST) { 251s + local({ 251s + # .......... set up example from help file ................. 251s + nd <- 10 251s + gamma0 <- 3 251s + delta0 <- 5 251s + POW <- 3 251s + # Terms in intensity 251s + Z <- function(x,y) { -2*y } 251s + f <- function(x,y,gamma,delta) { 1 + exp(gamma - delta * x^POW) } 251s + # True intensity 251s + lamb <- function(x,y,gamma,delta) { 200 * exp(Z(x,y)) * f(x,y,gamma,delta) } 251s + # Simulate realisation 251s + lmax <- max(lamb(0,0,gamma0,delta0), lamb(1,1,gamma0,delta0)) 251s + set.seed(42) 251s + X <- rpoispp(lamb, lmax=lmax, win=owin(), gamma=gamma0, delta=delta0) 251s + # Partial derivatives of log f 251s + DlogfDgamma <- function(x,y, gamma, delta) { 251s + topbit <- exp(gamma - delta * x^POW) 251s + topbit/(1 + topbit) 251s + } 251s + DlogfDdelta <- function(x,y, gamma, delta) { 251s + topbit <- exp(gamma - delta * x^POW) 251s + - (x^POW) * topbit/(1 + topbit) 251s + } 251s + # irregular score 251s + Dlogf <- list(gamma=DlogfDgamma, delta=DlogfDdelta) 251s + # fit model 251s + fit <- ippm(X ~Z + offset(log(f)), 251s + covariates=list(Z=Z, f=f), 251s + iScore=Dlogf, 251s + start=list(gamma=1, delta=1), 251s + nd=nd) 251s + # fit model with logistic likelihood but without iScore 251s + fitlo <- ippm(X ~Z + offset(log(f)), 251s + method="logi", 251s + covariates=list(Z=Z, f=f), 251s + start=list(gamma=1, delta=1), 251s + nd=nd) 251s + 251s + ## ............. test ippm class support ...................... 251s + Ar <- model.matrix(fit) 251s + Ai <- model.matrix(fit, irregular=TRUE) 251s + An <- model.matrix(fit, irregular=TRUE, keepNA=FALSE) 251s + AS <- model.matrix(fit, irregular=TRUE, subset=(abs(Z) < 0.5)) 251s + 251s + Zr <- model.images(fit) 251s + Zi <- model.images(fit, irregular=TRUE) 251s + ## update.ippm 251s + fit2 <- update(fit, . ~ . + I(Z^2)) 251s + fit0 <- update(fit, 251s + . ~ . - Z, 251s + start=list(gamma=2, delta=4)) 251s + oldfit <- ippm(X, 251s + ~Z + offset(log(f)), 251s + covariates=list(Z=Z, f=f), 251s + iScore=Dlogf, 251s + start=list(gamma=1, delta=1), 251s + nd=nd) 251s + oldfit2 <- update(oldfit, . ~ . + I(Z^2)) 251s + oldfit0 <- update(oldfit, 251s + . ~ . - Z, 251s + start=list(gamma=2, delta=4)) 251s + ## again with logistic 251s + fitlo2 <- update(fitlo, . ~ . + I(Z^2)) 251s + fitlo0 <- update(fitlo, 251s + . ~ . - Z, 251s + start=list(gamma=2, delta=4)) 251s + oldfitlo <- ippm(X, 251s + ~Z + offset(log(f)), 251s + method="logi", 251s + covariates=list(Z=Z, f=f), 251s + start=list(gamma=1, delta=1), 251s + nd=nd) 251s + oldfitlo2 <- update(oldfitlo, . ~ . + I(Z^2)) 251s + oldfitlo0 <- update(oldfitlo, 251s + . ~ . - Z, 251s + start=list(gamma=2, delta=4)) 251s + ## anova.ppm including ippm objects 251s + fit0 <- update(fit, . ~ Z) 251s + fit0lo <- update(fitlo, . ~ Z) 251s + A <- anova(fit0, fit) 251s + Alo <- anova(fit0lo, fitlo) 251s + }) 251s + } 251s > 251s BEGIN TEST testsK.R 251s 251s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 251s Copyright (C) 2024 The R Foundation for Statistical Computing 251s Platform: aarch64-unknown-linux-gnu (64-bit) 251s 251s R is free software and comes with ABSOLUTELY NO WARRANTY. 251s You are welcome to redistribute it under certain conditions. 251s Type 'license()' or 'licence()' for distribution details. 251s 251s R is a collaborative project with many contributors. 251s Type 'contributors()' for more information and 251s 'citation()' on how to cite R or R packages in publications. 251s 251s Type 'demo()' for some demos, 'help()' for on-line help, or 251s 'help.start()' for an HTML browser interface to help. 251s Type 'q()' to quit R. 251s 251s > #' 251s > #' Header for all (concatenated) test files 251s > #' 251s > #' Require spatstat.model 251s > #' Obtain environment variable controlling tests. 251s > #' 251s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 251s > 251s > require(spatstat.model) 251s Loading required package: spatstat.model 251s Loading required package: spatstat.data 252s Loading required package: spatstat.geom 252s spatstat.geom 3.2-8 252s Loading required package: spatstat.random 252s spatstat.random 3.2-2 252s Loading required package: spatstat.explore 252s Loading required package: nlme 253s spatstat.explore 3.2-5 253s Loading required package: rpart 253s spatstat.model 3.2-8 253s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 253s > ALWAYS <- TRUE 253s > cat(paste("--------- Executing", 253s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 253s + "test code -----------\n")) 253s --------- Executing **RESTRICTED** subset of test code ----------- 253s > # 253s > # tests/kppm.R 253s > # 253s > # $Revision: 1.39 $ $Date: 2023/10/21 04:25:51 $ 253s > # 253s > # Test functionality of kppm that once depended on RandomFields 253s > # Test update.kppm for old style kppm objects 253s > 253s > if(!FULLTEST) 253s + spatstat.options(npixel=32, ndummy.min=16) 253s > 253s > local({ 253s + 253s + fit <- kppm(redwood ~1, "Thomas") # sic 253s + fitx <- kppm(redwood ~x, "Thomas", verbose=TRUE) 253s + if(FULLTEST) { 253s + fitx <- update(fit, ~ . + x) 253s + fitM <- update(fit, clusters="MatClust") 253s + fitC <- update(fit, cells) 253s + fitCx <- update(fit, cells ~ x) 253s + #' 253s + Wsub <- owin(c(0, 0.5), c(-0.5, 0)) 253s + Zsub <- (bdist.pixels(Window(redwood)) > 0.1) 253s + fitWsub <- kppm(redwood ~1, "Thomas", subset=Wsub) 253s + fitZsub <- kppm(redwood ~1, "Thomas", subset=Zsub) 253s + fitWsub 253s + 253s + #' various methods 253s + ff <- as.fv(fitx) 253s + uu <- unitname(fitx) 253s + unitname(fitCx) <- "furlong" 253s + mo <- model.images(fitCx) 253s + p <- psib(fit) 253s + px <- psib(fitx) 253s + } 253s + if(ALWAYS) { 253s + Y <- simulate(fitx, seed=42, saveLambda=TRUE)[[1]] 253s + } 253s + 253s + if(FULLTEST) { 253s + #' vcov.kppm different algorithms 253s + vc <- vcov(fitx) 253s + vc2 <- vcov(fitx, fast=TRUE) 253s + vc3 <- vcov(fitx, fast=TRUE, splitup=TRUE) 253s + vc4 <- vcov(fitx, splitup=TRUE) 253s + 253s + ## other code blocks 253s + a <- varcount(fitx, function(x,y){x+1}) # always positive 253s + a <- varcount(fitx, function(x,y){y-1}) # always negative 253s + a <- varcount(fitx, function(x,y){x+y}) # positive or negative 253s + 253s + #' improve.kppm 253s + fitI <- update(fit, improve.type="quasi") 253s + fitxI <- update(fitx, improve.type="quasi") 253s + fitxIs <- update(fitx, improve.type="quasi", fast=FALSE) 253s + #' vcov.kppm 253s + vcI <- vcov(fitxI) 253s + } 253s + 253s + ## plot.kppm including predict.kppm 253s + if(ALWAYS) { 253s + fitMC <- kppm(redwood ~ x, "Thomas") 253s + plot(fitMC) 253s + } 253s + if(FULLTEST) { 253s + fitCL <- kppm(redwood ~ x, "Thomas", method="c") 253s + fitPA <- kppm(redwood ~ x, "Thomas", method="p") 253s + plot(fitCL) 253s + plot(fitPA) 253s + 253s + ## fit with composite likelihood method [thanks to Abdollah Jalilian] 253s + fut <- kppm(redwood ~ x, "VarGamma", method="clik2", nu.ker=-3/8) 253s + kfut <- as.fv(fut) 253s + } 253s + 253s + if(ALWAYS) { 253s + fit0 <- kppm(redwood ~1, "LGCP") 253s + is.poisson(fit0) 253s + Y0 <- simulate(fit0, saveLambda=TRUE)[[1]] 253s + stopifnot(is.ppp(Y0)) 253s + p0 <- psib(fit0) # issues a warning 253s + 253s + if(FULLTEST) { 253s + ## fit LGCP using K function: slow 253s + fit1 <- kppm(redwood ~x, "LGCP", 253s + covmodel=list(model="matern", nu=0.3), 253s + control=list(maxit=3)) 253s + Y1 <- simulate(fit1, saveLambda=TRUE)[[1]] 253s + stopifnot(is.ppp(Y1)) 253s + } 253s + 253s + ## fit LGCP using pcf 253s + fit1p <- kppm(redwood ~x, "LGCP", 253s + covmodel=list(model="matern", nu=0.3), 253s + statistic="pcf") 253s + Y1p <- simulate(fit1p, saveLambda=TRUE)[[1]] 253s + stopifnot(is.ppp(Y1p)) 253s + 253s + ## .. and using different fitting methods 253s + if(FULLTEST) { 253s + fit1pClik <- update(fit1p, method="clik") 253s + fit1pPalm <- update(fit1p, method="palm") 253s + } 253s + 253s + ## shortcut evaluation of pcf 253s + ## (the code being tested is in spatstat.random::clusterinfo.R) 253s + if(FULLTEST) { 253s + putSpatstatVariable("RFshortcut", TRUE) 253s + fitGshort <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="gauss")) 253s + fitSshort <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="stable", alpha=1)) 253s + putSpatstatVariable("RFshortcut", FALSE) 253s + fitGlong <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="gauss")) 253s + fitSlong <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="stable", alpha=1)) 253s + discrepG <- unlist(parameters(fitGshort)) - unlist(parameters(fitGlong)) 253s + discrepS <- unlist(parameters(fitSshort)) - unlist(parameters(fitSlong)) 253s + print(discrepG) 253s + print(discrepS) 253s + if(max(abs(discrepG) > 0.01)) 253s + stop("Discrepancy in short-cut fitting of Gaussian LGCP") 253s + if(max(abs(discrepS) > 0.01)) 253s + stop("Discrepancy in short-cut fitting of stable LGCP") 253s + } 253s + 253s + ## image covariate (a different code block) 253s + xx <- as.im(function(x,y) x, Window(redwood)) 253s + fit1xx <- update(fit1p, . ~ xx, data=solist(xx=xx)) 253s + Y1xx <- simulate(fit1xx, saveLambda=TRUE)[[1]] 253s + stopifnot(is.ppp(Y1xx)) 253s + if(FULLTEST) { 253s + fit1xxVG <- update(fit1xx, clusters="VarGamma", nu=-1/4) 253s + Y1xxVG <- simulate(fit1xxVG, saveLambda=TRUE)[[1]] 253s + stopifnot(is.ppp(Y1xxVG)) 253s + } 253s + fit1xxLG <- update(fit1xx, clusters="LGCP", 253s + covmodel=list(model="matern", nu=0.3), 253s + statistic="pcf") 253s + Y1xxLG <- simulate(fit1xxLG, saveLambda=TRUE, drop=TRUE) 253s + stopifnot(is.ppp(Y1xxLG)) 253s + 253s + # ... and Abdollah's code 253s + if(FULLTEST) { 253s + fit2 <- kppm(redwood ~x, cluster="Cauchy", statistic="K") 253s + Y2 <- simulate(fit2, saveLambda=TRUE)[[1]] 253s + stopifnot(is.ppp(Y2)) 253s + } 253s + } 253s + 253s + }) 253s Fitting cluster model 253s Retrieved cluster model information 253s Algorithm parameters: 253s $rmax 253s NULL 253s 253s $q 253s [1] 0.25 253s 253s $p 253s [1] 2 253s 253s $rmin 253s NULL 253s 253s Using point pattern data 253s Starting parameters: 253s kappa sigma2 253s 62.000000000 0.006173033 253s Calculating summary function...Done. 253s Starting minimum contrast fit 253s Returned from minimum contrast fit 253s Returning from clusterfit 254s Warning messages: 254s > 254s > if(FULLTEST) { 254s + local({ 254s + #' various code blocks 254s + fut <- kppm(redwood, ~x) 254s + fet <- update(fut, redwood3) 254s + fot <- update(fut, trend=~y) 254s + fit <- kppm(redwoodfull ~ x) 254s + Y <- simulate(fit, window=redwoodfull.extra$regionII, saveLambda=TRUE) 254s + gut <- improve.kppm(fit, type="wclik1") 254s + 1: Internal error: fvlabels truncated the function name 254s 2: Internal error: fvlabels truncated the function name 254s 3: Internal error: fvlabels truncated the function name 254s 4: In psib.kppm(fit0) : The model is not a cluster process 254s 5: The value of the empirical function ‘pcf’ for r= 0 was Inf. Range of r values was reset to [0.00048828125, 0.25] 254s 6: The value of the empirical function ‘pcf’ for r= 0 was Inf. Range of r values was reset to [0.00048828125, 0.25] 254s 7: The value of the empirical function ‘pcf’ for r= 0 was Inf. Range of r values was reset to [0.00048828125, 0.25] 254s gut <- improve.kppm(fit, vcov=TRUE, fast.vcov=TRUE, save.internals=TRUE) 254s + hut <- kppm(redwood ~ x, method="clik", weightfun=NULL) 254s + hut <- kppm(redwood ~ x, method="palm", weightfun=NULL) 254s + mut <- kppm(redwood) 254s + nut <- update(mut, Y) 254s + if(TRUE) { 254s + #' Bug in rLGCP spotted by Tilman Davies 254s + X <- rLGCP("matern", function(x,y) { 1 - 0.4* y }, 254s + var=2, scale=0.7, nu=0.5, win = square(10), 254s + dimyx=c(32,64)) 254s + } 254s + }) 254s + } 254s > 254s > if(FULLTEST) { 254s + local({ 254s + #' minimum contrast code 254s + K <- Kest(redwood) 254s + a <- matclust.estK(K) 254s + a <- thomas.estK(K) 254s + a <- cauchy.estK(K) 254s + a <- vargamma.estK(K) 254s + a <- lgcp.estK(K) 254s + 254s + print(a) 254s + u <- unitname(a) 254s + 254s + g <- pcf(redwood) 254s + a <- matclust.estpcf(g) 254s + a <- thomas.estpcf(g) 254s + a <- cauchy.estpcf(g) 254s + a <- vargamma.estpcf(g) 254s + a <- lgcp.estpcf(g) 254s + 254s + #' auxiliary functions 254s + b <- resolve.vargamma.shape(nu.pcf=1.5) 254s + Z <- clusterfield("Thomas", kappa=1, scale=0.2) 254s + 254s + aa <- NULL 254s + aa <- accumulateStatus(simpleMessage("Woof"), aa) 254s + aa <- accumulateStatus(simpleMessage("Sit"), aa) 254s + aa <- accumulateStatus(simpleMessage("Woof"), aa) 254s + printStatusList(aa) 254s + 254s + RMIN <- 0.01 254s + fit <- kppm(redwood ~ 1, ctrl=list(rmin=RMIN,q=1/2)) 254s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 254s + stop("kppm did not handle parameter 'rmin' in argument 'ctrl' ") 254s + fit <- kppm(redwood ~ 1, ctrl=list(rmin=0,q=1/2), rmin=RMIN) 254s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 254s + stop("kppm did not handle parameter 'rmin' in argument 'ctrl'") 254s + 254s + RMIN <- 2 254s + fit <- dppm(swedishpines~1, dppGauss(), ctrl=list(rmin=RMIN,q=1)) 254s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 254s + stop("dppm did not handle parameter 'rmin' in argument 'ctrl'") 254s + fit <- dppm(swedishpines~1, dppGauss(), ctrl=list(rmin=0,q=1), rmin=RMIN) 254s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 254s + stop("dppm did not handle argument 'rmin'") 254s + }) 254s + } 254s > 254s > 254s > 254s > if(FULLTEST) { 254s + local({ 254s + #' cover a few code blocks 254s + fut <- kppm(redwood ~ x, method="clik") 254s + print(summary(fut)) 254s + a <- residuals(fut) 254s + fut2 <- kppm(redwood ~ x, "LGCP", method="palm") 254s + print(summary(fut2)) 254s + b <- residuals(fut2) 254s + #' 254s + po <- ppm(redwood ~ 1) 254s + A <- kppmComLik(redwood, Xname="redwood", po=po, clusters="Thomas", 254s + statistic="pcf", statargs=list(), control=list(), 254s + weightfun=NULL, rmax=0.1) 254s + A <- kppmPalmLik(redwood, Xname="redwood", po=po, clusters="Thomas", 254s + statistic="pcf", statargs=list(), control=list(), 254s + weightfun=NULL, rmax=0.1) 254s + }) 254s + } 254s > 254s > reset.spatstat.options() 254s > 254s > #' 254s > #' tests/Kfuns.R 254s > #' 254s > #' Various K and L functions and pcf 254s > #' 254s > #' $Revision: 1.43 $ $Date: 2022/06/17 01:47:08 $ 254s > #' 254s > #' Assumes 'EveryStart.R' was run 254s > 254s > if(FULLTEST) { 254s + Cells <- cells 254s + Amacrine <- amacrine 254s + Redwood <- redwood 254s + } else { 254s + ## reduce numbers of data + dummy points 254s + spatstat.options(npixel=32, ndummy.min=16) 254s + Cells <- cells[c(FALSE, TRUE)] 254s + Amacrine <- amacrine[c(FALSE, TRUE)] 254s + Redwood <- redwood[c(FALSE, TRUE)] 254s + } 254s > 254s > 254s > if(FULLTEST) { 254s + local({ 254s + #' code blocks using fitted model to determine intensity 254s + #' Kinhom 254s + X <- rpoispp(function(x,y) { 100 * x }, 100, square(1)) 254s + fut <- ppm(X ~ x) 254s + Kio <- Kinhom(X, fut, update=FALSE) 254s + Kiu <- Kinhom(X, fut, update=TRUE, diagonal=FALSE) 254s + fit <- ppm(Amacrine ~ marks) 254s + #' lohboot Linhom 254s + Zred <- predict(ppm(Redwood ~ x+y)) 254s + Lred <- lohboot(Redwood, Linhom, lambda=Zred) 254s + #' Kmulti.inhom 254s + K1 <- Kcross.inhom(Amacrine, lambdaX=fit) 254s + On <- split(Amacrine)$on 254s + Off <- split(Amacrine)$off 254s + K4 <- Kcross.inhom(Amacrine, lambdaI=ppm(On), lambdaJ=ppm(Off)) 254s + #' local K functions 254s + fut <- ppm(swedishpines ~ polynom(x,y,2)) 254s + Z <- predict(fut) 254s + Lam <- fitted(fut, dataonly=TRUE) 254s + a <- localLinhom(swedishpines, lambda=fut) 254s + a <- localLinhom(swedishpines, lambda=Z) 254s + a <- localLinhom(swedishpines, lambda=Lam) 254s + a <- localLinhom(swedishpines, lambda=Z, correction="none") 254s + a <- localLinhom(swedishpines, lambda=Z, correction="translate") 254s + #' local cross K functions 254s + fat <- ppm(Amacrine ~ x * marks) 254s + Zed <- predict(fat) 254s + Lum <- fitted(fat, dataonly=TRUE) 254s + moff <- (marks(Amacrine) == "off") 254s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed) 254s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Lum) 254s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=fat) 254s + a <- localLcross.inhom(Amacrine, from="off", to="on", 254s + lambdaFrom=Lum[moff], lambdaTo=Lum[!moff]) 254s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 254s + correction="none") 254s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 254s + correction="translate") 254s + #' cases of resolve.lambdacross 254s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=fat) 254s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=fat, update=FALSE) 254s + h <- resolve.lambdacross(Amacrine, moff, !moff, 254s + lambdaI=fat, lambdaJ=fat) 254s + h <- resolve.lambdacross(Amacrine, moff, !moff, 254s + lambdaI=fat, lambdaJ=fat, 254s + update=FALSE) 254s + #' lohboot 254s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", lambdaX=Zed) 254s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", lambdaX=Lum) 254s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", lambdaX=fat) 254s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", 254s + lambdaFrom=Lum[moff], lambdaTo=Lum[!moff]) 254s + #' 254s + #' residual K functions etc 254s + #' 254s + rco <- compareFit(Cells, Kcom, 254s + interaction=anylist(P=Poisson(), S=Strauss(0.08)), 254s + same="trans", different="tcom") 254s + fit <- ppm(Cells ~ x, Strauss(0.07)) 254s + K <- Kcom(Cells, model=fit, restrict=TRUE) 254s + }) 254s + } 254s > 254s > reset.spatstat.options() 254s > 254s BEGIN TEST testsL.R 255s 255s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 255s Copyright (C) 2024 The R Foundation for Statistical Computing 255s Platform: aarch64-unknown-linux-gnu (64-bit) 255s 255s R is free software and comes with ABSOLUTELY NO WARRANTY. 255s You are welcome to redistribute it under certain conditions. 255s Type 'license()' or 'licence()' for distribution details. 255s 255s R is a collaborative project with many contributors. 255s Type 'contributors()' for more information and 255s 'citation()' on how to cite R or R packages in publications. 255s 255s Type 'demo()' for some demos, 'help()' for on-line help, or 255s 'help.start()' for an HTML browser interface to help. 255s Type 'q()' to quit R. 255s 255s > #' 255s > #' Header for all (concatenated) test files 255s > #' 255s > #' Require spatstat.model 255s > #' Obtain environment variable controlling tests. 255s > #' 255s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 255s > 255s > require(spatstat.model) 255s Loading required package: spatstat.model 255s Loading required package: spatstat.data 256s Loading required package: spatstat.geom 256s spatstat.geom 3.2-8 256s Loading required package: spatstat.random 256s spatstat.random 3.2-2 256s Loading required package: spatstat.explore 256s Loading required package: nlme 256s spatstat.explore 3.2-5 256s Loading required package: rpart 256s spatstat.model 3.2-8 256s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 256s > ALWAYS <- TRUE 256s > cat(paste("--------- Executing", 256s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 256s + "test code -----------\n")) 256s --------- Executing **RESTRICTED** subset of test code ----------- 256s > ## 256s > ## tests/legacy.R 256s > ## 256s > ## Test that current version of spatstat is compatible with outmoded usage 256s > ## $Revision: 1.3 $ $Date: 2020/04/29 08:55:17 $ 256s > 256s > if(FULLTEST) { 256s + local({ 256s + 256s + ## (1) Old syntax of ppm 256s + ppm(cells, ~x) 256s + 256s + ## (2) Old syntax of MultiStrauss etc. 256s + r <- matrix(3, 2, 2) 256s + a <- MultiStrauss( , r) 256s + a <- MultiStrauss(NULL, r) 256s + a <- MultiHard(, r) 256s + 256s + h <- r/2 256s + a <- MultiStraussHard( , r, h) 256s + 256s + NULL 256s + }) 256s + } 256s > #' 256s > #' tests/leverinf.R 256s > #' 256s > #' leverage and influence for Gibbs models 256s > #' 256s > #' $Revision: 1.35 $ $Date: 2022/06/18 10:15:17 $ 256s > #' 256s > 256s > if(FULLTEST) { 256s + Cells <- cells 256s + Amacrine <- amacrine 256s + Redwood <- redwood 256s + } else { 256s + ## reduce number of data + dummy points 256s + spatstat.options(npixel=32, ndummy.min=16) 256s + Cells <- cells[c(FALSE,TRUE)] 256s + Redwood <- redwood[c(FALSE, TRUE)] 256s + Amacrine <- amacrine[c(FALSE, TRUE)] 256s + } 256s > 256s > local({ 256s + cat("Running non-sparse algorithm...", fill=TRUE) 256s + # original non-sparse algorithm 256s + Leverage <- function(...) leverage(..., sparseOK=FALSE) 256s + Influence <- function(...) influence(..., sparseOK=FALSE) 256s + Dfbetas <- function(...) dfbetas(..., sparseOK=FALSE) 256s + if(ALWAYS) { 256s + ## Strauss()$delta2 256s + fitS <- ppm(Cells ~ x, Strauss(0.12), rbord=0) 256s + levS <- Leverage(fitS) 256s + infS <- Influence(fitS) 256s + dfbS <- Dfbetas(fitS) 256s + ## Geyer()$delta2 256s + fitG <- ppm(Redwood ~ 1, Geyer(0.1, 2), rbord=0) 256s + levG <- Leverage(fitG) 256s + infG <- Influence(fitG) 256s + ## AreaInter()$delta2 256s + fitA <- ppm(Cells ~ 1, AreaInter(0.06), rbord=0, nd=11) 256s + levA <- Leverage(fitA) 256s + infA <- Influence(fitA) 256s + ## pairwise.family$delta2 256s + fitD <- ppm(Cells ~ 1, DiggleGatesStibbard(0.12), rbord=0) 256s + levD <- Leverage(fitD) 256s + infD <- Influence(fitD) 256s + ## DiggleGratton() special code 256s + fitDG <- ppm(Cells ~ 1, DiggleGratton(0.05, 0.12), rbord=0) 256s + levDG <- Leverage(fitDG) 256s + infDG <- Influence(fitDG) 256s + ## ppmInfluence; offset is present; coefficient vector has length 0 256s + fitH <- ppm(Cells ~ 1, Hardcore(0.07)) 256s + levH <- Leverage(fitH) 256s + infH <- Influence(fitH) 256s + ## ppmInfluence; hard core 256s + fitSH <- ppm(Cells ~ 1, StraussHard(0.07, 0.01)) 256s + levSH <- Leverage(fitSH) 256s + infSH <- Influence(fitSH) 256s + ## ppmInfluence; offset is present; coefficient vector has length 1 256s + fitHx <- ppm(Cells ~ x, Hardcore(0.07), rbord=0) 256s + levHx <- Leverage(fitHx) 256s + infHx <- Influence(fitHx) 256s + ## multitype 256s + futAm <- ppm(Amacrine ~ x + marks, Strauss(0.07)) 256s + levAm <- leverage(futAm) 256s + } 256s + 256s + if(FULLTEST) { 256s + ## ......... class support ............................. 256s + ## other methods for classes leverage.ppm and influence.ppm 256s + ## not elsewhere tested 256s + cat("Testing class support...", fill=TRUE) 256s + w <- domain(levS) 256s + w <- Window(infS) 256s + vv <- shift(levS, c(1.2, 1.3)) 256s + vv <- shift(infS, c(1.2, 1.3)) 256s + A <- quadrats(Window(Cells), 2) 256s + a <- integral(levS,domain=A) 256s + b <- integral(infS,domain=A) 256s + u <- Smooth(levS, sigma=0.07) 256s + v <- Smooth(infS, sigma=0.1) 256s + ## plot options 256s + plot(levS, what="exact") 256s + plot(levS, what="nearest") 256s + contour(levS, what="nearest") 256s + persp(levS, what="nearest") 256s + ## plotting for multitype models 256s + plot(levAm) 256s + contour(levAm) 256s + persp(levAm) 256s + plot(levAm, multiplot=FALSE) 256s + contour(levAm, multiplot=FALSE) 256s + } 256s + 256s + if(ALWAYS) { 256s + ## .......... compare algorithms ......................... 256s + ## divide and recombine algorithm 256s + cat("Reduce maximum block side to 50,000 ...", fill=TRUE) 256s + op <- spatstat.options(maxmatrix=50000) 256s + ## non-sparse 256s + levSB <- Leverage(fitS) 256s + infSB <- Influence(fitS) 256s + dfbSB <- Dfbetas(fitS) 256s + } 256s + 256s + chk <- function(x, y, what, 256s + from="single-block and multi-block", 256s + thresh=1e-12) { 256s + if(max(abs(x-y)) > thresh) 256s + stop(paste("Different results for", what, "obtained from", 256s + from, "algorithms"), 256s + call.=FALSE) 256s + invisible(NULL) 256s + } 256s + 256s + if(ALWAYS) { 256s + cat("Compare single-block to multi-block...", fill=TRUE) 256s + chk(marks(as.ppp(infS)), marks(as.ppp(infSB)), "influence") 256s + chk(as.im(levS), as.im(levSB), "leverage") 256s + chk(dfbS$val, dfbSB$val, "dfbetas$value") 256s + chk(dfbS$density, dfbSB$density, "dfbetas$density") 256s + } 256s + 256s + if(FULLTEST) { 256s + ## also check case of zero cif 256s + cat("Check zero cif cases...", fill=TRUE) 256s + levHB <- Leverage(fitH) 256s + infHB <- Influence(fitH) 256s + dfbHB <- Dfbetas(fitH) 256s + levHxB <- Leverage(fitHx) 256s + infHxB <- Influence(fitHx) 256s + dfbHxB <- Dfbetas(fitHx) 256s + } 256s + 256s + ## run all code segments 256s + Everything <- function(model, ...) { ppmInfluence(model, ..., what="all") } 256s + 256s + if(FULLTEST) { 256s + cat("Run full code on AreaInteraction model...", fill=TRUE) 256s + pmiA <- Everything(fitA) 256s + 256s + ## sparse algorithm, with blocks 256s + cat("Run sparse algorithm with blocks...", fill=TRUE) 256s + pmiSSB <- Everything(fitS, sparseOK=TRUE) 256s + ## also check case of zero cif 256s + pmiHSB <- Everything(fitH, sparseOK=TRUE) 256s + pmiSHSB <- Everything(fitSH, sparseOK=TRUE) 256s + pmiHxSB <- Everything(fitHx, sparseOK=TRUE) 256s + 256s + cat("Reinstate maxmatrix...", fill=TRUE) 256s + spatstat.options(op) 256s + } 256s + 256s + if(ALWAYS) { 256s + ## sparse algorithm, no blocks 256s + cat("Compare sparse and non-sparse results...", fill=TRUE) 256s + pmi <- Everything(fitS, sparseOK=TRUE) 256s + levSp <- pmi$leverage 256s + infSp <- pmi$influence 256s + dfbSp <- pmi$dfbetas 256s + chks <- function(...) chk(..., from="sparse and non-sparse") 256s + 256s + chks(marks(as.ppp(infS)), marks(as.ppp(infSp)), "influence") 256s + chks(as.im(levS), as.im(levSp), "leverage") 256s + chks(dfbS$val, dfbSp$val, "dfbetas$value") 256s + chks(dfbS$density, dfbSp$density, "dfbetas$density") 256s + } 256s + 256s + if(ALWAYS) { 256s + #' case of zero cif 256s + cat("zero cif...", fill=TRUE) 256s + pmiH <- Everything(fitH, sparseOK=TRUE) 256s + pmiSH <- Everything(fitSH, sparseOK=TRUE) 256s + pmiHx <- Everything(fitHx, sparseOK=TRUE) 256s + } 256s + if(FULLTEST) { 256s + #' other code blocks - check execution only 256s + cat("other code blocks...", fill=TRUE) 256s + a <- Everything(fitS) 256s + a <- Everything(fitS, method="interpreted") 256s + a <- Everything(fitS, method="interpreted", entrywise=FALSE) 256s + a <- Everything(fitS, entrywise=FALSE) 256s + #' zero cif 256s + b <- Everything(fitSH) 256s + b <- Everything(fitSH, method="interpreted") 256s + b <- Everything(fitSH, method="interpreted", entrywise=FALSE) 256s + b <- Everything(fitSH, entrywise=FALSE) 256s + } 256s + #' NOTE: code for irregular parameters is tested below, and in 'make bookcheck' 256s + 256s + ## ........... logistic fits ....................... 256s + cat("Logistic fits...", fill=TRUE) 256s + #' special algorithm for delta2 256s + fitSlogi <- ppm(Cells ~ x, Strauss(0.12), rbord=0, method="logi") 256s + 256s + if(FULLTEST) { 256s + pmiSlogi <- Everything(fitSlogi) 256s + #' special algorithm for delta2 256s + fitGlogi <- ppm(Redwood ~ 1, Geyer(0.1, 2), rbord=0, method="logi") 256s + pmiGlogi <- Everything(fitGlogi) 256s + #' generic algorithm for delta2 256s + fitDlogi <- ppm(Cells ~ 1, DiggleGatesStibbard(0.12), 256s + rbord=0, method="logi") 256s + pmiDlogi <- Everything(fitDlogi) 256s + #' generic algorithm for delta2 : offset; zero-dimensional 256s + fitHlogi <- ppm(Cells ~ 1, Hardcore(0.07), method="logi") 256s + pmiHlogi <- Everything(fitHlogi) 256s + #' generic algorithm for delta2 : offset; 1-dimensional 256s + fitHxlogi <- ppm(Cells ~ x, Hardcore(0.07), rbord=0, method="logi") 256s + pmiHxlogi <- Everything(fitHxlogi) 256s + #' plotting 256s + plot(leverage(fitSlogi)) 256s + plot(influence(fitSlogi)) 256s + plot(dfbetas(fitSlogi)) 256s + } 256s + 256s + if(ALWAYS) { 256s + #' other code blocks - check execution only 256s + cat("Other code blocks...", fill=TRUE) 256s + b <- Everything(fitSlogi) # i.e. full set of results 256s + b <- Everything(fitSlogi, method="interpreted") 256s + b <- Everything(fitSlogi, method="interpreted", entrywise=FALSE) 256s + b <- Everything(fitSlogi, entrywise=FALSE) 256s + } 256s + 256s + #' irregular parameters 256s + cat("Irregular parameters...", fill=TRUE) 256s + ytoa <- function(x,y, alpha=1) { y^alpha } 256s + lam <- function(x,y,alpha=1) { exp(4 + y^alpha) } 256s + set.seed(90210) 256s + X <- rpoispp(lam, alpha=2) 256s + iScor <- list(alpha=function(x,y,alpha) { alpha * y^(alpha-1) } ) 256s + iHess <- list(alpha=function(x,y,alpha) { alpha * (alpha-1) * y^(alpha-2) } ) 256s + gogo <- function(tag, ..., iS=iScor, iH=iHess) { 256s + cat(tag, fill=TRUE) 256s + #' compute all leverage+influence terms 256s + ppmInfluence(..., what="all", iScore=iS, iHessian=iH) 256s + } 256s + gogogo <- function(hdr, fit) { 256s + cat(hdr, fill=TRUE) 256s + force(fit) 256s + #' try all code options 256s + d <- gogo("a", fit) 256s + d <- gogo("b", fit, method="interpreted") 256s + d <- gogo("c", fit, method="interpreted", entrywise=FALSE) 256s + d <- gogo("d", fit, entrywise=FALSE) 256s + invisible(NULL) 256s + } 256s + gogogo("Offset model...", 256s + ippm(X ~ offset(ytoa), start=list(alpha=1), iterlim=40)) 256s + gogogo("Offset model (logistic) ...", 256s + ippm(X ~ offset(ytoa), start=list(alpha=1), 256s + method="logi", iterlim=40)) 256s + gogogo("Offset+x model...", 256s + ippm(X ~ x + offset(ytoa), start=list(alpha=1), iterlim=40)) 256s + gogogo("Offset+x model (logistic) ...", 256s + ippm(X ~ x + offset(ytoa), start=list(alpha=1), 256s + method="logi", iterlim=40)) 256s + gogogo("Offset model Strauss ...", 256s + ippm(X ~ offset(ytoa), Strauss(0.07), start=list(alpha=1), iterlim=40)) 256s + gogogo("Offset model Strauss (logistic) ...", 256s + ippm(X ~ offset(ytoa), Strauss(0.07), start=list(alpha=1), 256s + method="logi", iterlim=40)) 256s + if(FULLTEST) { 256s + gogogo("Offset+x model Strauss ...", 256s + ippm(X ~ x + offset(ytoa), Strauss(0.07), start=list(alpha=1), 256s + iterlim=40)) 256s + gogogo("Offset+x model Strauss (logistic)...", 256s + ippm(X ~ x + offset(ytoa), Strauss(0.07), start=list(alpha=1), 256s + method="logi", iterlim=40)) 256s + } 256s + #' 256s + if(FULLTEST) { 256s + set.seed(452) 256s + foo <- ppm(Cells ~ 1, Strauss(0.15), improve.type="ho", nsim=5) 256s + aa <- Everything(foo) 256s + 256s + #' Gradient and Hessian obtained by symbolic differentiation 256s + f <- deriv(expression((1+x)^a), 256s + "a", function.arg=c("x", "y", "a"), 256s + hessian=TRUE) 256s + #' check they can be extracted 256s + fit <- ippm(Cells ~offset(f), start=list(a=0.7)) 256s + Everything(fit) 256s + } 256s + }) 256s Running non-sparse algorithm... 265s Reduce maximum block side to 50,000 ... 266s Compare single-block to multi-block... 266s Compare sparse and non-sparse results... 266s zero cif... 269s Logistic fits... 269s Other code blocks... 272s Irregular parameters... 272s Offset model... 272s a 273s b 273s c 273s d 274s Offset model (logistic) ... 274s a 275s b 275s c 276s d 276s Offset+x model... 276s a 277s b 277s c 278s d 278s Offset+x model (logistic) ... 279s a 279s b 280s c 281s d 281s Offset model Strauss ... 281s a 281s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points 282s b 282s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points 283s c 283s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points 284s d 284s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points 285s Offset model Strauss (logistic) ... 285s a 285s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points 286s b 286s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points 286s c 286s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points 287s d 287s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points 288s > 288s > reset.spatstat.options() 288s > 288s There were 11 warnings (use warnings() to see them) 288s BEGIN TEST testsM.R 289s 289s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 289s Copyright (C) 2024 The R Foundation for Statistical Computing 289s Platform: aarch64-unknown-linux-gnu (64-bit) 289s 289s R is free software and comes with ABSOLUTELY NO WARRANTY. 289s You are welcome to redistribute it under certain conditions. 289s Type 'license()' or 'licence()' for distribution details. 289s 289s R is a collaborative project with many contributors. 289s Type 'contributors()' for more information and 289s 'citation()' on how to cite R or R packages in publications. 289s 289s Type 'demo()' for some demos, 'help()' for on-line help, or 289s 'help.start()' for an HTML browser interface to help. 289s Type 'q()' to quit R. 289s 289s Loading required package: spatstat.model 289s > #' 289s > #' Header for all (concatenated) test files 289s > #' 289s > #' Require spatstat.model 289s > #' Obtain environment variable controlling tests. 289s > #' 289s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 289s > 289s > require(spatstat.model) 289s Loading required package: spatstat.data 290s Loading required package: spatstat.geom 290s spatstat.geom 3.2-8 290s Loading required package: spatstat.random 290s spatstat.random 3.2-2 290s Loading required package: spatstat.explore 290s Loading required package: nlme 290s spatstat.explore 3.2-5 290s Loading required package: rpart 290s spatstat.model 3.2-8 290s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 290s > ALWAYS <- TRUE 290s > cat(paste("--------- Executing", 290s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 290s + "test code -----------\n")) 290s --------- Executing **RESTRICTED** subset of test code ----------- 290s > ## 290s > ## tests/marcelino.R 290s > ## 290s > ## $Revision: 1.4 $ $Date: 2020/04/30 02:18:23 $ 290s > ## 290s > 290s > local({ 290s + if(FULLTEST) { 290s + Y <- split(urkiola) 290s + B <- Y$birch 290s + O <- Y$oak 290s + B.lam <- predict (ppm(B ~polynom(x,y,2)), type="trend") 290s + O.lam <- predict (ppm(O ~polynom(x,y,2)), type="trend") 290s + 290s + Kinhom(B, lambda=B.lam, correction="iso") 290s + Kinhom(B, lambda=B.lam, correction="border") 290s + 290s + Kcross.inhom(urkiola, i="birch", j="oak", B.lam, O.lam) 290s + Kcross.inhom(urkiola, i="birch", j="oak", B.lam, O.lam, correction = "iso") 290s + Kcross.inhom(urkiola, i="birch", j="oak", B.lam, O.lam, correction = "border") 290s + } 290s + }) 290s > 290s > 290s > #' tests/mctests.R 290s > #' Monte Carlo tests 290s > #' (mad.test, dclf.test, envelopeTest, hasenvelope) 290s > #' $Revision: 1.5 $ $Date: 2022/05/23 04:09:49 $ 290s > 290s > 290s > local({ 290s + if(FULLTEST) { 290s + fitx <- ppm(redwood~x) 290s + ax <- envelopeTest(fitx, exponent=2, nsim=9, savefuns=TRUE) 290s + print(ax) 290s + } 290s + }) 290s > 290s > 290s > # 290s > # tests/mppm.R 290s > # 290s > # Basic tests of mppm 290s > # 290s > # $Revision: 1.23 $ $Date: 2022/07/08 04:55:13 $ 290s > # 290s > 290s > if(!FULLTEST) 290s + spatstat.options(npixel=32, ndummy.min=16) 290s > 290s > local({ 290s + ## test interaction formulae and subfits 290s + fit1 <- mppm(Points ~ group, simba, 290s + hyperframe(po=Poisson(), str=Strauss(0.1)), 290s + iformula=~ifelse(group=="control", po, str)) 290s + fit2 <- mppm(Points ~ group, simba, 290s + hyperframe(po=Poisson(), str=Strauss(0.1)), 290s + iformula=~str/id) 290s + fit2w <- mppm(Points ~ group, simba, 290s + hyperframe(po=Poisson(), str=Strauss(0.1)), 290s + iformula=~str/id, weights=runif(nrow(simba))) 290s + # currently invalid 290s + # fit3 <- mppm(Points ~ group, simba, 290s + # hyperframe(po=Poisson(), pie=PairPiece(c(0.05,0.1))), 290s + # iformula=~I((group=="control") * po) + I((group=="treatment") * pie)) 290s + 290s + fit1 290s + fit2 290s + fit2w 290s + # fit3 290s + 290s + if(FULLTEST) { 290s + ## run summary.mppm which currently sits in spatstat-internal.Rd 290s + summary(fit1) 290s + summary(fit2) 290s + summary(fit2w) 290s + # summary(fit3) 290s + } 290s + 290s + ## test vcov algorithm 290s + vcov(fit1) 290s + vcov(fit2) 290s + # vcov(fit3) 290s + 290s + if(FULLTEST) { 290s + fit4 <- mppm(Points ~ group, simba, hyperframe(str=Strauss(0.1)), iformula=~str/group) 290s + fit4 290s + summary(fit4) 290s + vcov(fit4) 290s + fit0 <- mppm(Points ~ group, simba) 290s + anova(fit0, fit4, test="Chi") 290s + ## [bug from Fernando Milesi] 290s + fit5 <- mppm(Wat ~ id, 290s + data=hyperframe(Wat=waterstriders), 290s + interaction=StraussHard(4.5, 1.5), 290s + iformula=~Interaction:id) 290s + fit5 290s + summary(fit5) 290s + vcov(fit5) 290s + } 290s + 290s + ## test subfits algorithm 290s + if(FULLTEST) { 290s + s1 <- subfits(fit1) 290s + s2 <- subfits(fit2) 290s + # s3 <- subfits(fit3) 290s + s4 <- subfits(fit4) 290s + s5 <- subfits(fit5) 290s + 290s + ## validity of results of subfits() 290s + p1 <- solapply(s1, predict) 290s + p2 <- solapply(s2, predict) 290s + # p3 <- solapply(s3, predict) 290s + p4 <- solapply(s4, predict) 290s + p5 <- solapply(s5, predict) 290s + } 290s + }) 292s > 292s > local({ 292s + if(FULLTEST) { 292s + ## cases of predict.mppm 292s + W <- solapply(waterstriders, Window) 292s + Fakes <- solapply(W, runifpoint, n=30) 292s + FakeDist <- solapply(Fakes, distfun) 292s + H <- hyperframe(Bugs=waterstriders, 292s + D=FakeDist) 292s + fit <- mppm(Bugs ~ D, data=H) 292s + p1 <- predict(fit) 292s + p2 <- predict(fit, locations=Fakes) 292s + p3 <- predict(fit, locations=solapply(W, erosion, r=4)) 292s + locn <- as.data.frame(do.call(cbind, lapply(Fakes, coords))) 292s + df <- data.frame(id=sample(1:3, nrow(locn), replace=TRUE), 292s + D=runif(nrow(locn))) 292s + p4 <- predict(fit, locations=locn, newdata=df) 292s + 292s + fitG <- mppm(Bugs ~ D, data=H, use.gam=TRUE) 292s + p1G <- predict(fitG) 292s + p2G <- predict(fitG, locations=Fakes) 292s + p3G <- predict(fitG, locations=solapply(W, erosion, r=4)) 292s + p4G <- predict(fitG, locations=locn, newdata=df) 292s + } 292s + }) 292s > 292s > local({ 292s + ## [thanks to Sven Wagner] 292s + ## factor covariate, with some levels unused in some rows 292s + if(FULLTEST) { 292s + set.seed(14921788) 292s + H <- hyperframe(X=replicate(3, runifpoint(20), simplify=FALSE), 292s + Z=solist(as.im(function(x,y){x}, owin()), 292s + as.im(function(x,y){y}, owin()), 292s + as.im(function(x,y){x+y}, owin()))) 292s + H$Z <- solapply(H$Z, cut, breaks=(0:4)/2) 292s + 292s + fit6 <- mppm(X ~ Z, H) 292s + v6 <- vcov(fit6) 292s + s6 <- subfits(fit6) 292s + p6 <- solapply(s6, predict) 292s + 292s + ## random effects 292s + fit7 <- mppm(X ~ Z, H, random=~1|id) 292s + v7 <- vcov(fit7) 292s + s7 <- subfits(fit7) 292s + p7 <- solapply(s7, predict) 292s + 292s + fit7a <- mppm(X ~ Z, H, random=~x|id) 292s + v7a <- vcov(fit7a) 292s + s7a <- subfits(fit7a) 292s + p7a <- solapply(s7a, predict) 292s + 292s + ## multitype: collisions in vcov.ppm, predict.ppm 292s + H$X <- lapply(H$X, rlabel, labels=factor(c("a","b")), permute=FALSE) 292s + M <- MultiStrauss(matrix(0.1, 2, 2), c("a","b")) 292s + fit8 <- mppm(X ~ Z, H, M) 292s + v8 <- vcov(fit8, fine=TRUE) 292s + s8 <- subfits(fit8) 292s + p8 <- lapply(s8, predict) 292s + c8 <- lapply(s8, predict, type="cif") 292s + 292s + fit9 <- mppm(X ~ Z, H, M, iformula=~Interaction * id) 292s + v9 <- vcov(fit9, fine=TRUE) 292s + s9 <- subfits(fit9) 292s + p9 <- lapply(s9, predict) 292s + c9 <- lapply(s9, predict, type="cif") 292s + 292s + ## and a simple error in recognising 'marks' 292s + fit10 <- mppm(X ~ marks, H) 292s + } 292s + }) 292s > 292s > local({ 292s + if(FULLTEST) { 292s + ## test handling of offsets and zero cif values in mppm 292s + H <- hyperframe(Y = waterstriders) 292s + (fit1 <- mppm(Y ~ 1, data=H, Hardcore(1.5))) 292s + (fit2 <- mppm(Y ~ 1, data=H, StraussHard(7, 1.5))) 292s + (fit3 <- mppm(Y ~ 1, data=H, Hybrid(S=Strauss(7), H=Hardcore(1.5)))) 292s + s1 <- subfits(fit1) 292s + s2 <- subfits(fit2) 292s + s3 <- subfits(fit3) 292s + 292s + ## prediction, in training/testing context 292s + ## (example from Markus Herrmann and Ege Rubak) 292s + X <- waterstriders 292s + dist <- solapply(waterstriders, 292s + function(z) distfun(runifpoint(1, Window(z)))) 292s + i <- 3 292s + train <- hyperframe(pattern = X[-i], dist = dist[-i]) 292s + test <- hyperframe(pattern = X[i], dist = dist[i]) 292s + fit <- mppm(pattern ~ dist, data = train) 292s + pred <- predict(fit, type="cif", newdata=test, verbose=TRUE) 292s + 292s + ## examples from Robert Aue 292s + GH <- Hybrid(G=Geyer(r=0.1, sat=3), H=Hardcore(0.01)) 292s + res <- mppm(Points ~ 1, interaction = GH, data=demohyper) 292s + print(summary(res)) 292s + sub <- subfits(res, verbose=TRUE) 292s + print(sub) 292s + } 292s + }) 292s > 292s > local({ 292s + if(FULLTEST) { 292s + ## test handling of interaction coefficients in multitype case 292s + set.seed(42) 292s + XX <- as.solist(replicate(3, rthin(amacrine, 0.8), simplify=FALSE)) 292s + H <- hyperframe(X=XX) 292s + M <- MultiStrauss(matrix(0.1, 2, 2), levels(marks(amacrine))) 292s + fit <- mppm(X ~ 1, H, M) 292s + co <- coef(fit) 292s + subco <- sapply(subfits(fit), coef) 292s + if(max(abs(subco - co)) > 0.001) 292s + stop("Wrong coefficient values in subfits, for multitype interaction") 292s + } 292s + }) 292s > 292s > local({ 292s + if(FULLTEST) { 292s + ## test lurking.mppm 292s + ## example from 'mppm' 292s + n <- 7 292s + H <- hyperframe(V=1:n, 292s + U=runif(n, min=-1, max=1)) 292s + H$Z <- setcov(square(1)) 292s + H$U <- with(H, as.im(U, as.rectangle(Z))) 292s + H$Y <- with(H, rpoispp(eval.im(exp(2+3*Z)))) 292s + fit <- mppm(Y ~ Z + U + V, data=H) 292s + 292s + lurking(fit, expression(Z), type="P") 292s + lurking(fit, expression(V), type="raw") # design covariate 292s + lurking(fit, expression(U), type="raw") # image, constant in each row 292s + lurking(fit, H$Z, type="P") # list of images 292s + } 292s + }) 292s > 292s > local({ 292s + if(FULLTEST) { 292s + ## test anova.mppm code blocks and scoping problem 292s + H <- hyperframe(X=waterstriders) 292s + mod0 <- mppm(X~1, data=H, Poisson()) 292s + modxy <- mppm(X~x+y, data=H, Poisson()) 292s + mod0S <- mppm(X~1, data=H, Strauss(2)) 292s + modxyS <- mppm(X~x+y, data=H, Strauss(2)) 292s + anova(mod0, modxy, test="Chi") 292s + anova(mod0S, modxyS, test="Chi") 292s + anova(modxy, test="Chi") 292s + anova(modxyS, test="Chi") 292s + #' models with random effects (example from Marcelino de la Cruz) 292s + mod0r <- mppm(X~1, data=H, Poisson(), random = ~1|id) 292s + modxr <- mppm(X~x, data=H, Poisson(), random = ~1|id) 292s + anova(mod0r, modxr, test="Chi") 292s + } 292s + }) 292s > 292s > local({ 292s + if(FULLTEST) { 292s + ## test multitype stuff 292s + foo <- flu[1:3,] 292s + msh <- MultiStraussHard(iradii=matrix(100, 2, 2), 292s + hradii=matrix(10,2,2), 292s + types=levels(marks(foo$pattern[[1]]))) 292s + msh0 <- MultiStraussHard(iradii=matrix(100, 2, 2), 292s + hradii=matrix(10,2,2)) 292s + fit <- mppm(pattern ~ 1, data=foo, interaction=msh0) 292s + print(fit) 292s + print(summary(fit)) 292s + v <- vcov(fit) 292s + } 292s + }) 292s > 292s > reset.spatstat.options() 292s > #' 292s > #' tests/msr.R 292s > #' 292s > #' $Revision: 1.5 $ $Date: 2020/11/30 07:27:44 $ 292s > #' 292s > #' Tests of code for measures 292s > #' 292s > 292s > if(FULLTEST) { 292s + local({ 292s + 292s + ## cases of 'msr' 292s + Q <- quadscheme(cells) 292s + nQ <- n.quad(Q) 292s + nX <- npoints(cells) 292s + A <- matrix(nX * 3, nX, 3) 292s + B <- matrix(nQ * 3, nQ, 3) 292s + 292s + m <- msr(Q, A, B) 292s + 292s + M <- msr(Q, A, 1) 292s + M <- msr(Q, 1, B) 292s + M <- msr(Q, A, B[,1]) 292s + M <- msr(Q, A[,1], B) 292s + M <- msr(Q, A, B[,1,drop=FALSE]) 292s + M <- msr(Q, A[,1,drop=FALSE], B) 292s + 292s + ## methods 292s + a <- summary(m) 292s + b <- is.marked(m) 292s + w <- as.owin(m) 292s + z <- domain(m) 292s + ss <- scalardilate(m, 2) 292s + tt <- rescale(m, 2) 292s + ee <- rotate(m, pi/4) 292s + aa <- affine(m, mat=diag(c(1,2)), vec=c(0,1)) 292s + ff <- flipxy(m) 292s + 292s + am <- augment.msr(m, sigma=0.08) 292s + ua <- update(am) 292s + 292s + rr <- residuals(ppm(cells ~ x)) 292s + mm <- residuals(ppm(amacrine ~ x)) 292s + ss <- residuals(ppm(amacrine ~ x), type="score") 292s + gg <- rescale(ss, 1/662, c("micron", "microns")) 292s + 292s + plot(mm) 292s + plot(mm, multiplot=FALSE) 292s + plot(mm, equal.markscale=TRUE, equal.ribbon=TRUE) 292s + plot(ss) 292s + plot(ss, multiplot=FALSE) 292s + }) 292s + } 292s > 292s BEGIN TEST testsNtoO.R 292s 292s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 292s Copyright (C) 2024 The R Foundation for Statistical Computing 292s Platform: aarch64-unknown-linux-gnu (64-bit) 292s 292s R is free software and comes with ABSOLUTELY NO WARRANTY. 292s You are welcome to redistribute it under certain conditions. 292s Type 'license()' or 'licence()' for distribution details. 292s 292s R is a collaborative project with many contributors. 292s Type 'contributors()' for more information and 292s 'citation()' on how to cite R or R packages in publications. 292s 292s Type 'demo()' for some demos, 'help()' for on-line help, or 292s 'help.start()' for an HTML browser interface to help. 292s Type 'q()' to quit R. 292s 293s > #' 293s > #' Header for all (concatenated) test files 293s > #' 293s > #' Require spatstat.model 293s > #' Obtain environment variable controlling tests. 293s > #' 293s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 293s > 293s > require(spatstat.model) 293s Loading required package: spatstat.model 293s Loading required package: spatstat.data 293s Loading required package: spatstat.geom 293s spatstat.geom 3.2-8 293s Loading required package: spatstat.random 293s spatstat.random 3.2-2 293s Loading required package: spatstat.explore 293s Loading required package: nlme 294s spatstat.explore 3.2-5 294s Loading required package: rpart 294s spatstat.model 3.2-8 294s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 294s > ALWAYS <- TRUE 294s > cat(paste("--------- Executing", 294s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 294s + "test code -----------\n")) 294s --------- Executing **RESTRICTED** subset of test code ----------- 294s > # 294s > # tests/NAinCov.R 294s > # 294s > # Testing the response to the presence of NA's in covariates 294s > # 294s > # $Revision: 1.8 $ $Date: 2022/05/22 08:37:38 $ 294s > 294s > if(FULLTEST) { 294s + local({ 294s + X <- runifpoint(42) 294s + Y <- as.im(function(x,y) { x+y }, owin()) 294s + Y[owin(c(0.2,0.4),c(0.2,0.4))] <- NA 294s + # fit model: should produce a warning but no failure 294s + misfit <- ppm(X ~Y, covariates=list(Y=Y)) 294s + # prediction 294s + Z <- predict(misfit, type="trend", se=TRUE) 294s + # covariance matrix: all should be silent 294s + v <- vcov(misfit) 294s + ss <- vcov(misfit, what="internals") 294s + }) 294s + } 294s > 294s BEGIN TEST testsP1.R 294s 294s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 294s Copyright (C) 2024 The R Foundation for Statistical Computing 294s Platform: aarch64-unknown-linux-gnu (64-bit) 294s 294s R is free software and comes with ABSOLUTELY NO WARRANTY. 294s You are welcome to redistribute it under certain conditions. 294s Type 'license()' or 'licence()' for distribution details. 294s 294s R is a collaborative project with many contributors. 294s Type 'contributors()' for more information and 294s 'citation()' on how to cite R or R packages in publications. 294s 294s Type 'demo()' for some demos, 'help()' for on-line help, or 294s 'help.start()' for an HTML browser interface to help. 294s Type 'q()' to quit R. 294s 294s > #' 294s > #' Header for all (concatenated) test files 294s > #' 294s > #' Require spatstat.model 294s > #' Obtain environment variable controlling tests. 294s > #' 294s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 294s > 294s > require(spatstat.model) 294s Loading required package: spatstat.model 294s Loading required package: spatstat.data 295s Loading required package: spatstat.geom 295s spatstat.geom 3.2-8 295s Loading required package: spatstat.random 295s spatstat.random 3.2-2 295s Loading required package: spatstat.explore 295s Loading required package: nlme 295s spatstat.explore 3.2-5 295s Loading required package: rpart 295s spatstat.model 3.2-8 295s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 295s > ALWAYS <- TRUE 295s > cat(paste("--------- Executing", 295s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 295s + "test code -----------\n")) 295s --------- Executing **RESTRICTED** subset of test code ----------- 295s > ## 295s > ## tests/percy.R 295s > ## 295s > ## Tests of Percus-Yevick approximations 295s > ## 295s > ## $Revision: 1.3 $ $Date: 2020/04/30 05:23:52 $ 295s > 295s > if(FULLTEST) { 295s + local({ 295s + fit <- ppm(swedishpines ~1, DiggleGatesStibbard(6)) 295s + K <- Kmodel(fit) 295s + }) 295s + } 295s > 295s > ## 295s > ## tests/pixelgripes.R 295s > ## Problems related to pixellation of windows 295s > ## 295s > ## $Revision: 1.8 $ $Date: 2022/10/23 06:21:10 $ 295s > 295s > if(FULLTEST) { 295s + local({ 295s + 295s + ## From Philipp Hunziker: bug in rNeymanScott (etc) 295s + ## Create an irregular window 295s + PM <- matrix(c(1,0,0.5,1,0,0), 3, 2, byrow=TRUE) 295s + P <- owin(poly=PM) 295s + ## Generate Matern points 295s + X <- rMatClust(50, 0.05, 5, win=P) 295s + ## Some distance function as a covariate 295s + distorigin <- function(x, y) { sqrt(x^2 + y^2) } 295s + ## No covariates: works fine 295s + fit0 <- kppm(X ~ 1, clusters="MatClust") 295s + Y0 <- simulate(fit0, retry=0) 295s + ## Covariates: Simulation fails 295s + fit1 <- kppm(X ~ distorigin, clusters="MatClust") 295s + Y1 <- simulate(fit1, retry=0) 295s + 295s + }) 295s + } 295s > 295s BEGIN TEST testsP2.R 296s 296s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 296s Copyright (C) 2024 The R Foundation for Statistical Computing 296s Platform: aarch64-unknown-linux-gnu (64-bit) 296s 296s R is free software and comes with ABSOLUTELY NO WARRANTY. 296s You are welcome to redistribute it under certain conditions. 296s Type 'license()' or 'licence()' for distribution details. 296s 296s R is a collaborative project with many contributors. 296s Type 'contributors()' for more information and 296s 'citation()' on how to cite R or R packages in publications. 296s 296s Type 'demo()' for some demos, 'help()' for on-line help, or 296s 'help.start()' for an HTML browser interface to help. 296s Type 'q()' to quit R. 296s 296s > #' 296s > #' Header for all (concatenated) test files 296s > #' 296s > #' Require spatstat.model 296s > #' Obtain environment variable controlling tests. 296s > #' 296s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 296s > 296s > require(spatstat.model) 296s Loading required package: spatstat.model 296s Loading required package: spatstat.data 297s Loading required package: spatstat.geom 297s spatstat.geom 3.2-8 297s Loading required package: spatstat.random 297s spatstat.random 3.2-2 297s Loading required package: spatstat.explore 297s Loading required package: nlme 297s spatstat.explore 3.2-5 297s Loading required package: rpart 297s spatstat.model 3.2-8 297s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 297s > ALWAYS <- TRUE 297s > cat(paste("--------- Executing", 297s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 297s + "test code -----------\n")) 297s --------- Executing **RESTRICTED** subset of test code ----------- 297s > # 297s > # tests/ppmBadData.R 297s > # 297s > # $Revision: 1.6 $ $Date: 2020/04/30 05:23:52 $ 297s > 297s > # Testing robustness of ppm and support functions 297s > # when data are rubbish 297s > 297s > local({ 297s + if(ALWAYS) { 297s + ## from Rolf: very large proportion of data is NA 297s + SEED <- 42 297s + K <- 101 297s + A <- 500 297s + X <- seq(0, A, length=K) 297s + G <- expand.grid(x=X, y=X) 297s + FOO <- function(x,y) { sin(x)^2 + cos(y)^2 } 297s + M1 <- im(matrix(FOO(G$x, G$y), K, K), xcol=X, yrow=X) 297s + M <- im(matrix(FOO(G$x, G$y), K, K)) 297s + BAR <- function(x) { exp(-6.618913 + 5.855337 * x - 8.432483 * x^2) } 297s + V <- im(BAR(M$v), xcol=X, yrow=X) 297s + # V <- eval.im(exp(-6.618913 + 5.855337 * M - 8.432483 * M^2)) 297s + set.seed(SEED) 297s + Y <- rpoispp(V) 297s + fY <- ppm(Y ~cv + I(cv^2), data=list(cv=M), correction="translate") 297s + diagnose.ppm(fY) 297s + lurking(fY, covariate=as.im(function(x,y){x}, square(A)), type="raw") 297s + } 297s + 297s + if(ALWAYS) { 297s + ## from Andrew Bevan: numerical overflow, ill-conditioned Fisher information 297s + SEED <- 42 297s + nongranite<- owin(poly = list(x = c(0, 8500, 7000, 6400, 6400, 6700, 7000, 7200, 7300, 8000, 8100, 8800, 9500, 10000, 10000, 0), y = c(0, 0, 2000, 3800, 4000, 5000, 6500, 7400, 7500, 8000, 8100, 9000, 9500, 9600, 10000, 10000))) 297s + ## Trend on raster grid 297s + rain <- as.im(X=function(x,y) { x^2 + y^2 }, W=nongranite, dimyx=100) 297s + ## Generate a point pattern via a Lennard-Jones process 297s + set.seed(SEED) 297s + mod4<- rmhmodel(cif="lennard", 297s + par=list(beta=1, sigma=250, epsilon=2.2), 297s + trend=rain, w=nongranite) 297s + ljtr<- rmh(mod4, start=list(n.start=80), control=list(p=1, nrep=1e5)) 297s + 297s + ## Fit a point process model to the pattern with rain as a covariate 297s + ## NOTE INCORRECT TREND FORMULA 297s + ljtrmod <- ppm(ljtr, trend= ~ Z, interaction=NULL, data=list(Z=rain)) 297s + ss <- summary(ljtrmod) 297s + } 297s + 297s + if(FULLTEST) { 297s + ## From Ege 297s + ## Degenerate but non-null argument 'covariates' 297s + xx <- list() 297s + names(xx) <- character(0) 297s + fit <- ppm(cells ~x, covariates = xx) 297s + st <- summary(fit) 297s + } 297s + 297s + }) 297s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 297s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 298s > 298s > 298s > 298s > #' tests/ppmclass.R 298s > #' 298s > #' Class support for ppm 298s > #' 298s > #' $Revision: 1.9 $ $Date: 2022/03/07 03:26:09 $ 298s Error in solve.default(M) : 298s system is computationally singular: reciprocal condition number = 5.72254e-18 298s In addition: Warning messages: 298s 1: Values of the covariate ‘cv’ were NA or undefined at 96% (1774 out of 1845) of the quadrature points. Occurred while executing: ppm.ppp(Q = Y, trend = ~cv + I(cv^2), data = list(list(c(1, 1.91953576453823, 298s 2: Some infinite, NA or NaN increments were removed 298s 3: Numerical underflow detected: sigma is probably too small 298s 4: Some infinite, NA or NaN increments were removed 298s Error in solve.default(M) : 298s system is computationally singular: reciprocal condition number = 5.72254e-18 298s In addition: Warning message: 298s Cannot compute variance: Fisher information matrix is singular 298s Warning message: 298s Cannot compute variance: Fisher information matrix is singular 298s > 298s > if(FULLTEST) { 298s + local({ 298s + #' (1) print.ppm, summary.ppm, print.summary.ppm 298s + Z <- as.im(function(x,y){x}, Window(cells)) 298s + fitZ <- ppm(cells ~ Z) 298s + print(fitZ) 298s + print(summary(fitZ)) 298s + #' logistic 298s + fitl <- ppm(swedishpines ~ x+y, method="logi") 298s + print(fitl) 298s + print(summary(fitl)) 298s + #' Model with covariate arguments 298s + f <- function(x,y,b) { x+b } 298s + fitf <- ppm(cells ~ f, covfunargs=list(b=1)) 298s + print(fitf) 298s + print(summary(fitf)) 298s + #' Invalid model 298s + fitN <- ppm(redwood ~ 1, Strauss(0.1)) 298s + print(fitN) 298s + print(summary(fitN)) 298s + #' standard errors in output 298s + fat <- ppm(cells ~ x, Strauss(0.12)) 298s + op <- spatstat.options(print.ppm.SE='always') 298s + print(fat) 298s + spatstat.options(print.ppm.SE='never') 298s + print(fat) 298s + print(fitZ) 298s + spatstat.options(op) 298s + 298s + ## (2) plot.ppm 298s + plot(fitZ) 298s + plot(fat, trend=FALSE, cif=FALSE, se=FALSE) 298s + 298s + ## (3) emend.ppm 298s + fitZe <- emend(fitZ, trace=TRUE) 298s + ZZ <- Z 298s + fitZZ <- ppm(cells ~ Z + ZZ) 298s + fitZZe <- emend(fitZZ, trace=TRUE) 298s + fitOK <- ppm(redwood ~1, Strauss(0.1), emend=TRUE) 298s + print(fitOK) 298s + fitNot <- ppm(redwood ~1, Strauss(0.1)) 298s + fitSlow <- emend(fitNot, trace=TRUE) 298s + print(fitSlow) 298s + op <- spatstat.options(project.fast=TRUE) 298s + fitFast <- emend(fitNot, trace=TRUE) 298s + print(fitFast) 298s + fitZZe <- emend(fitZZ, trace=TRUE) 298s + spatstat.options(op) 298s + 298s + #' (4) methods for other generics 298s + logLik(fitZ, absolute=TRUE) 298s + unitname(fitZ) 298s + unitname(fat) <- c("metre", "metres") 298s + is.expandable(fitf) 298s + fit0 <- update(fitZ, . ~ 1) 298s + anova(fit0, fitZ, override=TRUE) 298s + interactionfamilyname(fat) 298s + interactionorder(fat) 298s + hardcoredist(fat) 298s + 298s + #' (5) miscellaneous 298s + 298s + ## example from Robert Aue - handling offsets 298s + X <- demohyper$Points[[1]] 298s + GH <- Hybrid(G=Geyer(r=0.1, sat=3), H=Hardcore(0.01)) 298s + fit <- ppm(X ~ 1, GH) 298s + valid.ppm(fit) 298s + 298s + #' hard core distance of hybrid 298s + hardcoredist(fit) 298s + #' interaction order of hybrid 298s + interactionorder(fit) 298s + 298s + #' case of boundingbox 298s + boundingbox(cells, ppm(cells ~ 1)) 298s + }) 298s + 298s + reset.spatstat.options() 298s + } 298s > # 298s > # tests/ppmgam.R 298s > # 298s > # Test ppm with use.gam=TRUE 298s > # 298s > # $Revision: 1.4 $ $Date: 2020/04/30 05:23:52 $ 298s > # 298s > 298s > if(FULLTEST) { 298s + local({ 298s + fit <- ppm(nztrees ~s(x,y), use.gam=TRUE) 298s + mm <- model.matrix(fit) 298s + mf <- model.frame(fit) 298s + v <- vcov(fit) 298s + prd <- predict(fit) 298s + }) 298s + } 298s > #' 298s > #' tests/ppmlogi.R 298s > #' 298s > #' Tests of ppm(method='logi') 298s > #' and related code (predict, leverage etc) 298s > #' 298s > #' $Revision: 1.15 $ $Date: 2020/04/30 05:23:52 $ 298s > #' 298s > 298s > local({ 298s + if(FULLTEST) { 298s + fit <- ppm(cells ~x, method="logi") 298s + f <- fitted(fit) 298s + p <- predict(fit) 298s + u <- summary(fit) 298s + fitS <- ppm(cells ~x, Strauss(0.12), method="logi") 298s + fS <- fitted(fitS) 298s + pS <- predict(fitS) 298s + uS <- summary(fitS) 298s + print(uS) 298s + 298s + plot(leverage(fit)) 298s + plot(influence(fit)) 298s + plot(dfbetas(fit)) 298s + plot(leverage(fitS)) 298s + plot(influence(fitS)) 298s + plot(dfbetas(fitS)) 298s + } 298s + 298s + if(FULLTEST) { 298s + #' same with hard core - A1 is singular 298s + fitH <- ppm(cells ~x, Strauss(0.08), method="logi") 298s + print(fitH) 298s + fH <- fitted(fitH) 298s + pH <- predict(fitH) 298s + uH <- summary(fitH) 298s + print(uH) 298s + plot(leverage(fitH)) 298s + plot(influence(fitH)) 298s + plot(dfbetas(fitH)) 298s + } 298s + 298s + if(FULLTEST) { 298s + #' logistic fit to data frame of covariates 298s + z <- c(rep(TRUE, 5), rep(FALSE, 5)) 298s + df <- data.frame(A=z + 2* runif(10), 298s + B=runif(10)) 298s + Y <- quadscheme.logi(runifpoint(5), runifpoint(5)) 298s + fut <- ppm(Y ~ A+B, data=df, method="logi") 298s + sf <- summary(fut) 298s + print(sf) 298s + } 298s + 298s + if(FULLTEST) { 298s + #' vblogit code, just to check that it runs. 298s + fee <- ppm(cells ~ x, method="VBlogi", nd=21) 298s + print(fee) 298s + summary(fee) 298s + logLik(fee) 298s + AIC(fee) 298s + extractAIC(fee) 298s + Z <- predict(fee) 298s + summary(Z) 298s + print(fee$internal$glmfit) # print.vblogit 298s + } 298s + }) 298s > 298s > # 298s > # tests/ppmmarkorder.R 298s > # 298s > # $Revision: 1.4 $ $Date: 2020/04/30 05:23:52 $ 298s > # 298s > # Test that predict.ppm, plot.ppm and plot.fitin 298s > # tolerate marks with levels that are not in alpha order 298s > # 298s > if(ALWAYS) { # locale-dependent? 298s + local({ 298s + X <- amacrine 298s + levels(marks(X)) <- c("ZZZ", "AAA") 298s + fit <- ppm(X ~marks, MultiStrauss(c("ZZZ","AAA"), matrix(0.06, 2, 2))) 298s + aa <- predict(fit, type="trend") 298s + bb <- predict(fit, type="cif") 298s + plot(fit) 298s + plot(fitin(fit)) 298s + }) 298s + } 300s > 300s > 300s > # 300s > # tests/ppmscope.R 300s > # 300s > # Test things that might corrupt the internal format of ppm objects 300s > # 300s > # $Revision: 1.7 $ $Date: 2022/01/19 09:18:20 $ 300s > # 300s > 300s > if(ALWAYS) { # dependent on R version? 300s + local({ 300s + 300s + ## (1) Scoping problem that can arise when ppm splits the data 300s + fit <- ppm(bei ~elev, data=bei.extra) 300s + mm <- model.matrix(fit) 300s + 300s + ## (2) Fast update mechanism 300s + fit1 <- ppm(cells ~x+y, Strauss(0.07)) 300s + fit2 <- update(fit1, ~y) 300s + fit3 <- update(fit2, ~x) 300s + 300s + ## (3) New formula-based syntax 300s + attach(bei.extra) 300s + slfit <- ppm(bei ~ grad) 300s + sl2fit <- update(slfit, ~grad + I(grad^2)) 300s + slfitup <- update(slfit, use.internal=TRUE) 300s + sl2fitup <- update(sl2fit, use.internal=TRUE) 300s + 300s + ## (4) anova.ppm 300s + fut1 <- ppm(cells ~ 1, Strauss(0.1)) 300s + futx <- ppm(cells ~ x, Strauss(0.1)) 300s + anova(fut1, test="Chi") 300s + anova(futx, test="Chi") 300s + fut1a <- ppm(cells ~ 1, Strauss(0.1), rbord=0) 300s + anova(fut1a, futx, test="Chi") 300s + fut1d <- ppm(cells ~ 1, Strauss(0.1), nd=23) 300s + anova(fut1d, futx, test="Chi") 300s + ## This now works! 300s + futxyg <- ppm(cells ~ x + s(y), Strauss(0.1), use.gam=TRUE) 300s + anova(futx, futxyg) 300s + ## marked 300s + fatP <- ppm(amacrine ~ marks) 300s + fatM <- ppm(amacrine ~ marks, MultiStrauss(matrix(0.07, 2, 2))) 300s + anova(fatP, fatM, test="Chi") 300s + 300s + ## (5) expansion of "." in update.ppm 300s + fitb <- ppm(bei ~ . , data=bei.extra) 300s + step(fitb) 300s + }) 300s + } 302s Start: AIC=42295.11 302s ~elev + grad 302s 302s Df AIC 302s 42295 302s - elev 1 42383 302s - grad 1 42760 302s Nonstationary Poisson process 302s Fitted to point pattern dataset ‘bei’ 302s 302s Log intensity: ~elev + grad 302s 302s Fitted trend coefficients: 302s (Intercept) elev grad 302s -8.56355220 0.02143995 5.84646680 302s 302s Estimate S.E. CI95.lo CI95.hi Ztest Zval 302s (Intercept) -8.56355220 0.341113849 -9.23212306 -7.89498134 *** -25.104675 302s elev 0.02143995 0.002287866 0.01695581 0.02592408 *** 9.371155 302s grad 5.84646680 0.255781018 5.34514522 6.34778838 *** 22.857313 302s > grep# 302s function (pattern, x, ignore.case = FALSE, perl = FALSE, value = FALSE, 302s fixed = FALSE, useBytes = FALSE, invert = FALSE) 302s { 302s pattern <- as.character(pattern) 302s if (is.factor(x) && length(levx <- levels(x)) < length(x) && 302s !is.na(pattern[1L])) { 302s value <- is.character(idxna <- suppressWarnings(grep(pattern, 302s Warning messages: 302s 1: anova.ppm now computes the *adjusted* deviances when the models are not Poisson processes. 302s 2: Models were re-fitted using a common value of 'rbord' 302s 3: Models were re-fitted using a common quadrature scheme 302s 4: Models were re-fitted with use.gam=TRUE 302s 5: Deviance adjustment is not available for gam fits; unadjusted composite deviance calculated. 302s 6: Models were re-fitted using a common value of 'rbord' 302s NA_character_, ignore.case, perl, value, fixed, useBytes, 302s invert))) 302s idx <- logical(length(levx)) 302s idx[grep(pattern, levx, ignore.case, perl, FALSE, fixed, 302s useBytes, invert)] <- TRUE 302s idx <- idx[x] 302s if (length(idxna)) 302s idx[is.na(x)] <- TRUE 302s idx <- which(idx) 302s if (value) { 302s idx <- x[idx] 302s structure(as.character(idx), names = names(idx)) 302s } 302s else idx 302s } 302s else { 302s if (!is.character(x)) 302s x <- structure(as.character(x), names = names(x)) 302s .Internal(grep(pattern, x, ignore.case, value, perl, 302s fixed, useBytes, invert)) 302s } 302s } 302s 302s 302s > # tests/ppmtricks.R 302s > # 302s > # Test backdoor exits, hidden options, internals and tricks in ppm 302s > # 302s > # $Revision: 1.19 $ $Date: 2020/04/30 05:23:52 $ 302s > # 302s > local({ 302s + 302s + ## (1) skip.border 302s + if(ALWAYS) { # needed below 302s + fit <- ppm(cells, ~1, Strauss(0.1), skip.border=TRUE) 302s + } 302s + 302s + ## (2) subset arguments of different kinds 302s + if(FULLTEST) { 302s + fut <- ppm(cells ~ x, subset=(x > 0.5)) 302s + fot <- ppm(cells ~ x, subset=(x > 0.5), method="logi") 302s + W <- owin(c(0.4, 0.8), c(0.2, 0.7)) 302s + fut <- ppm(cells ~ x, subset=W) 302s + fot <- ppm(cells ~ x, subset=W, method="logi") 302s + V <- as.im(inside.owin, Window(cells), w=W) 302s + fet <- ppm(cells ~ x, subset=V) 302s + fet <- ppm(cells ~ x, subset=V, method="logi") 302s + } 302s + 302s + ## (3) profilepl -> ppm 302s + ## uses 'skip.border' and 'precomputed' 302s + ## also tests scoping for covariates 302s + if(FULLTEST) { 302s + splants <- split(ants) 302s + mess <- splants[["Messor"]] 302s + cats <- splants[["Cataglyphis"]] 302s + ss <- data.frame(r=seq(60,120,by=20),hc=29/6) 302s + dM <- distmap(mess,dimyx=256) 302s + mungf <- profilepl(ss, StraussHard, cats ~ dM) 302s + mungp <- profilepl(ss, StraussHard, trend=~dM, Q=cats) 302s + } 302s + 302s + ## (4) splitting large quadschemes into blocks 302s + if(FULLTEST) { 302s + mop <- spatstat.options(maxmatrix=5000) 302s + qr <- quadBlockSizes(quadscheme(cells)) 302s + pr <- predict(ppm(cells ~ x, AreaInter(0.05))) 302s + spatstat.options(mop) 302s + qr <- quadBlockSizes(quadscheme(cells)) 302s + } 302s + 302s + ## (5) shortcuts in summary.ppm 302s + ## and corresponding behaviour of print.summary.ppm 302s + if(FULLTEST) { 302s + print(summary(fit, quick=TRUE)) 302s + print(summary(fit, quick="entries")) 302s + print(summary(fit, quick="no prediction")) 302s + print(summary(fit, quick="no variances")) 302s + } 302s + 302s + ## (6) suffstat.R 302s + if(ALWAYS) { 302s + fitP <- update(fit, Poisson()) 302s + suffstat.poisson(fitP, cells) 302s + fit0 <- killinteraction(fit) 302s + suffstat.poisson(fit0, cells) 302s + } 302s + 302s + ## (7) various support for class ppm 302s + if(FULLTEST) { 302s + fut <- kppm(redwood ~ x) 302s + A <- quad.ppm(fut) 302s + Z <- as.im(function(x,y){x}, Window(cells)) 302s + fitZ <- ppm(cells ~ Z) 302s + U <- getppmOriginalCovariates(fitZ) 302s + } 302s + 302s + ## (8) support for class profilepl 302s + if(FULLTEST) { 302s + rr <- data.frame(r=seq(0.05, 0.15, by=0.02)) 302s + ps <- profilepl(rr, Strauss, cells) 302s + ## plot(ps) ## covered in plot.profilepl.Rd 302s + simulate(ps, nrep=1e4) 302s + parameters(ps) 302s + fitin(ps) 302s + predict(ps, type="cif") 302s + } 302s + 302s + ## (9) class 'plotppm' 302s + if(FULLTEST) { 302s + fut <- ppm(amacrine ~ marks + polynom(x,y,2), Strauss(0.07)) 302s + p <- plot(fut, plot.it=FALSE) 302s + print(p) 302s + plot(p, how="contour") 302s + plot(p, how="persp") 302s + } 302s + 302s + ## (10) ppm -> mpl.engine -> mpl.prepare 302s + if(ALWAYS) { # includes C code 302s + fit <- ppm(cells, NULL) 302s + fit <- ppm(cells ~ x, clipwin=square(0.7)) 302s + fit <- ppm(cells ~ x, subset=square(0.7)) 302s + DG <- as.im(function(x,y){x+y < 1}, square(1)) 302s + fit <- ppm(cells ~ x, subset=DG) 302s + fit <- ppm(cells ~ x, GLM=glm) 302s + fit <- ppm(cells ~ x, famille=quasi(link='log', variance='mu')) 302s + fit <- ppm(cells ~ x, Hardcore(0.07), skip.border=TRUE, splitInf=TRUE) 302s + } 302s + 302s + ## (11) unidentifiable model (triggers an error in ppm) 302s + if(FULLTEST) { 302s + Q <- quadscheme(cells) 302s + M <- mpl.prepare(Q, cells, as.ppp(Q), trend=~1, covariates=NULL, 302s + interaction=Hardcore(0.3), correction="none") 302s + } 302s + }) 302s > 302s > reset.spatstat.options() 302s > # 302s > # tests/prediction.R 302s > # 302s > # Things that might go wrong with predict() 302s > # 302s > # $Revision: 1.20 $ $Date: 2020/04/30 05:41:59 $ 302s > # 302s > 302s > local({ 302s + if(ALWAYS) { 302s + ## test of 'covfunargs' - platform dependent? 302s + f <- function(x,y,a){ y - a } 302s + fit <- ppm(cells ~x + f, covariates=list(f=f), covfunargs=list(a=1/2)) 302s + p <- predict(fit) 302s + 302s + ## prediction involving 0 * NA 302s + qc <- quadscheme(cells, nd=10) 302s + r <- minnndist(as.ppp(qc))/10 302s + fit <- ppm(qc ~ 1, Strauss(r)) # model has NA for interaction coefficient 302s + p1 <- predict(fit) 302s + p2 <- predict(fit, type="cif", ngrid=10) 302s + stopifnot(all(is.finite(as.matrix(p1)))) 302s + stopifnot(all(is.finite(as.matrix(p2)))) 302s + } 302s + 302s + if(FULLTEST) { 302s + ## test of 'new.coef' mechanism 302s + fut <- ppm(cells ~ x, Strauss(0.15), rbord=0) 302s + p0 <- predict(fut, type="cif") 302s + pe <- predict(fut, type="cif", new.coef=coef(fut)) 302s + pn <- predict(fut, type="cif", new.coef=unname(coef(fut))) 302s + if(max(abs(pe-p0)) > 0.01) 302s + stop("new.coef mechanism is broken!") 302s + if(max(abs(pn-p0)) > 0.01) 302s + stop("new.coef mechanism gives wrong answer, for unnamed vectors") 302s + #' adaptcoef 302s + a <- c(A=1,B=2,Z=42) 302s + b <- c(B=41,A=0) 302s + ab <- adaptcoef(a, b, drop=TRUE) 302s + } 302s + 302s + if(FULLTEST) { 302s + ## tests of relrisk.ppm 302s + fut <- ppm(amacrine ~ x * marks) 302s + a <- relrisk(fut, control=2, relative=TRUE) 302s + a <- relrisk(fut, se=TRUE) 302s + a <- relrisk(fut, relative=TRUE, se=TRUE) 302s + fut <- ppm(sporophores ~ marks + x) 302s + a <- relrisk(fut, control=2, relative=TRUE) 302s + a <- relrisk(fut, se=TRUE) 302s + a <- relrisk(fut, relative=TRUE, se=TRUE) 302s + 302s + ## untested cases of predict.ppm 302s + fit0 <- ppm(cells) 302s + a <- predict(fit0, interval="confidence") 302s + a <- predict(fit0, interval="confidence", type="count") 302s + fit <- ppm(cells ~ x) 302s + b <- predict(fit, se=TRUE, locations=cells) 302s + b <- predict(fit, se=TRUE, interval="confidence") 302s + b <- predict(fit, type="count", se=TRUE) 302s + b <- predict(fit, type="count", window=square(0.5), se=TRUE) 302s + b <- predict(fit, type="count", window=quadrats(cells, 3), se=TRUE) 302s + d <- predict(fit, type="count", interval="prediction", se=TRUE) 302s + d <- predict(fit, type="count", interval="confidence", se=TRUE) 302s + d <- predict(fit, interval="confidence", se=TRUE) 302s + foot <- ppm(cells ~ x, StraussHard(0.12)) 302s + d <- predict(foot, ignore.hardcore=TRUE) 302s + dX <- predict(foot, ignore.hardcore=TRUE, locations=cells) 302s + 302s + ## superseded usages 302s + b <- predict(fit, type="se", getoutofjail=TRUE) 302s + b <- predict(fit, type="se", locations=cells) # warning 302s + b <- predict(fit, total=TRUE) 302s + b <- predict(fit, total=square(0.5)) 302s + b <- predict(fit, total=quadrats(cells, 3)) 302s + 302s + ## supporting code 302s + u <- model.se.image(fit, square(0.5)) 302s + u <- model.se.image(fit, square(0.5), what="cv") 302s + u <- model.se.image(fit, square(0.5), what="ce") 302s + co <- c(Intercept=5, slope=3, kink=2) 302s + re <- c("Intercept", "slope") 302s + a <- fill.coefs(co, re) # warning 302s + b <- fill.coefs(co, rev(names(co))) 302s + d <- fill.coefs(co, letters[1:3]) 302s + ## model matrix etc 302s + v <- model.frame(ppm(cells)) 302s + fut <- ppm(cells ~ x, Strauss(0.1)) 302s + v <- model.matrix(fut, subset=(x<0.5), keepNA=FALSE) 302s + df <- data.frame(x=runif(10), y=runif(10), 302s + Interaction=sample(0:1, 10, TRUE)) 302s + m10 <- PPMmodelmatrix(fut, data=df) 302s + mmm <- PPMmodelmatrix(fut, Q=quad.ppm(fut)) 302s + #' effectfun for Gibbs 302s + effectfun(fut, "x") 303s + effectfun(fut, "x", se.fit=TRUE) 303s + #' implicit covariate when there is only one 303s + effectfun(fut) 303s + effectfun(fut, se.fit=TRUE) 303s + #' given covariate 303s + dlin <- distfun(copper$SouthLines) 303s + copfit <- ppm(copper$SouthPoints ~ dlin, Geyer(1,1)) 303s + effectfun(copfit, "dlin") 303s + effectfun(copfit) 303s + #' covariate that is not used in model 303s + effectfun(fut, "y", x=0) 303s + futS <- ppm(cells ~ 1, Strauss(0.1)) 303s + effectfun(futS, "x") 303s + effectfun(futS, "y") 303s + #' factor covariate 303s + fot <- ppm(amacrine~x+marks) 303s + effectfun(fot, "marks", x=0.5, se.fit=TRUE) 303s + #' covariate retained but not used 303s + W <- Window(swedishpines) 303s + a <- solist(A=funxy(function(x,y){x < 20}, W), 303s + B=funxy(function(x,y){factor(x < 20)}, W)) 303s + fvt <- ppm(swedishpines ~ A, data=a, allcovar=TRUE) 303s + effectfun(fvt, "A", se.fit=TRUE) 303s + effectfun(fvt, "B", A=TRUE, se.fit=TRUE) 303s + 303s + ## ppm with covariate values in data frame 303s + X <- rpoispp(42) 303s + Q <- quadscheme(X) 303s + weirdfunction <- function(x,y){ 10 * x^2 + 5 * sin(10 * y) } 303s + Zvalues <- weirdfunction(x.quad(Q), y.quad(Q)) 303s + fot <- ppm(Q ~ y + Z, data=data.frame(Z=Zvalues)) 303s + effectfun(fot, "y", Z=0) 303s + effectfun(fot, "Z", y=0) 303s + 303s + #' multitype 303s + modX <- ppm(amacrine ~ polynom(x,2)) 303s + effectfun(modX) 303s + effectfun(modX, "x") 303s + modXM <- ppm(amacrine ~ marks*polynom(x,2)) 303s + effectfun(modXM, "x", marks="on") 303s + modXYM <- ppm(amacrine ~ marks*polynom(x,y,2)) 303s + effectfun(modXYM, "x", y=0, marks="on") 303s + 303s + df <- as.data.frame(simulate(modXM, drop=TRUE)) 303s + df$marks <- as.character(df$marks) 303s + dfpr <- predict(modXM, locations=df) 303s + } 303s + }) 303s > 303s > # 303s > # tests/project.ppm.R 303s > # 303s > # $Revision: 1.7 $ $Date: 2020/04/30 05:41:59 $ 303s > # 303s > # Tests of projection mechanism 303s > # 303s > 303s > local({ 303s + chk <- function(m) { 303s + if(!valid.ppm(m)) stop("Projected model was still not valid") 303s + return(invisible(NULL)) 303s + } 303s + 303s + if(FULLTEST) { 303s + ## a very unidentifiable model 303s + fit <- ppm(cells ~Z, Strauss(1e-06), covariates=list(Z=0)) 303s + chk(emend(fit)) 303s + ## multitype 303s + r <- matrix(1e-06, 2, 2) 303s + fit2 <- ppm(amacrine ~1, MultiStrauss(types=c("off", "on"), radii=r)) 303s + chk(emend(fit2)) 303s + ## complicated multitype 303s + fit3 <- ppm(amacrine ~1, MultiStraussHard(types=c("off", "on"), 303s + iradii=r, hradii=r/5)) 303s + chk(emend(fit3)) 303s + 303s + #' code coverage 303s + op <- spatstat.options(project.fast=TRUE) 303s + fut <- emend(fit, trace=TRUE) 303s + chk(fut) 303s + spatstat.options(op) 303s + 303s + #' hierarchical 303s + ra <- r 303s + r[2,1] <- NA 303s + fit4 <- ppm(amacrine ~1, HierStrauss(types=c("off", "on"), radii=r)) 303s + chk(emend(fit4)) 303s + #' complicated hierarchical 303s + fit5 <- ppm(amacrine ~1, HierStraussHard(types=c("off", "on"), 303s + iradii=r, hradii=r/5)) 303s + chk(emend(fit5)) 303s + 303s + ## hybrids 303s + r0 <- min(nndist(redwood)) 303s + ra <- 1.25 * r0 303s + rb <- 0.8 * r0 303s + f1 <- ppm(redwood ~1, Hybrid(A=Strauss(ra), B=Geyer(0.1, 2)), project=TRUE) 303s + chk(f1) 303s + f2 <- ppm(redwood ~1, Hybrid(A=Strauss(rb), B=Geyer(0.1, 2)), project=TRUE) 303s + chk(f2) 303s + f3 <- ppm(redwood ~1, Hybrid(A=Strauss(ra), B=Strauss(0.1)), project=TRUE) 303s + chk(f3) 303s + f4 <- ppm(redwood ~1, Hybrid(A=Strauss(rb), B=Strauss(0.1)), project=TRUE) 303s + chk(f4) 303s + f5 <- ppm(redwood ~1, Hybrid(A=Hardcore(rb), B=Strauss(0.1)), project=TRUE) 303s + chk(f5) 303s + f6 <- ppm(redwood ~1, Hybrid(A=Hardcore(rb), B=Geyer(0.1, 2)), project=TRUE) 303s + chk(f6) 303s + f7 <- ppm(redwood ~1, Hybrid(A=Geyer(rb, 1), B=Strauss(0.1)), project=TRUE) 303s + chk(f7) 303s + } 303s + }) 303s > 303s > reset.spatstat.options() 303s > 303s BEGIN TEST testsQ.R 303s 303s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 303s Copyright (C) 2024 The R Foundation for Statistical Computing 303s Platform: aarch64-unknown-linux-gnu (64-bit) 303s 303s R is free software and comes with ABSOLUTELY NO WARRANTY. 303s You are welcome to redistribute it under certain conditions. 303s Type 'license()' or 'licence()' for distribution details. 303s 303s R is a collaborative project with many contributors. 303s Type 'contributors()' for more information and 303s 'citation()' on how to cite R or R packages in publications. 303s 303s Type 'demo()' for some demos, 'help()' for on-line help, or 303s 'help.start()' for an HTML browser interface to help. 303s Type 'q()' to quit R. 303s 303s > #' 303s > #' Header for all (concatenated) test files 303s > #' 303s > #' Require spatstat.model 303s > #' Obtain environment variable controlling tests. 303s > #' 303s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 303s > 303s > require(spatstat.model) 303s Loading required package: spatstat.model 303s Loading required package: spatstat.data 304s Loading required package: spatstat.geom 304s spatstat.geom 3.2-8 304s Loading required package: spatstat.random 304s spatstat.random 3.2-2 304s Loading required package: spatstat.explore 304s Loading required package: nlme 304s spatstat.explore 3.2-5 304s Loading required package: rpart 305s spatstat.model 3.2-8 305s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 305s > ALWAYS <- TRUE 305s > cat(paste("--------- Executing", 305s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 305s + "test code -----------\n")) 305s --------- Executing **RESTRICTED** subset of test code ----------- 305s > 305s BEGIN TEST testsR1.R 305s 305s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 305s Copyright (C) 2024 The R Foundation for Statistical Computing 305s Platform: aarch64-unknown-linux-gnu (64-bit) 305s 305s R is free software and comes with ABSOLUTELY NO WARRANTY. 305s You are welcome to redistribute it under certain conditions. 305s Type 'license()' or 'licence()' for distribution details. 305s 305s R is a collaborative project with many contributors. 305s Type 'contributors()' for more information and 305s 'citation()' on how to cite R or R packages in publications. 305s 305s Type 'demo()' for some demos, 'help()' for on-line help, or 305s 'help.start()' for an HTML browser interface to help. 305s Type 'q()' to quit R. 305s 305s > #' 305s > #' Header for all (concatenated) test files 305s > #' 305s > #' Require spatstat.model 305s > #' Obtain environment variable controlling tests. 305s > #' 305s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 305s > 305s > require(spatstat.model) 305s Loading required package: spatstat.model 305s Loading required package: spatstat.data 306s Loading required package: spatstat.geom 306s spatstat.geom 3.2-8 306s Loading required package: spatstat.random 306s spatstat.random 3.2-2 306s Loading required package: spatstat.explore 306s Loading required package: nlme 307s spatstat.explore 3.2-5 307s Loading required package: rpart 307s spatstat.model 3.2-8 307s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 307s > ALWAYS <- TRUE 307s > cat(paste("--------- Executing", 307s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 307s + "test code -----------\n")) 307s --------- Executing **RESTRICTED** subset of test code ----------- 307s > #' tests/resid.R 307s > #' 307s > #' Stuff related to residuals and residual diagnostics 307s > #' including residual summary functions 307s > #' 307s > #' $Revision: 1.7 $ $Date: 2022/05/22 08:43:31 $ 307s > #' 307s > 307s > local({ 307s + fit <- ppm(cells ~x, Strauss(r=0.15)) 307s + rr <- residuals(fit, quad=quadscheme(cells, nd=128)) 307s + diagnose.ppm(fit, cumulative=FALSE, type="pearson") 307s + 307s + if(FULLTEST) { 307s + diagnose.ppm(fit, cumulative=FALSE) 307s + 307s + fitoff <- ppm(cells ~ sin(x) + offset(y)) 307s + plot(a <- parres(fitoff, "x")) 307s + plot(b <- parres(fitoff, "y")) 307s + print(a) 307s + print(b) 307s + 307s + d <- diagnose.ppm(fit, which="marks") 307s + plot(d, plot.neg="discrete") 307s + plot(d, plot.neg="imagecontour") 307s + 307s + d <- diagnose.ppm(fit, type="pearson", which="smooth") 307s + plot(d, plot.smooth="image") 307s + plot(d, plot.smooth="contour") 307s + plot(d, plot.smooth="imagecontour") 307s + 307s + d <- diagnose.ppm(fit, type="pearson", which="x") 307s + plot(d) 307s + d <- diagnose.ppm(fit, type="pearson", which="y") 307s + plot(d) 307s + 307s + diagnose.ppm(fit, type="pearson", which="x", cumulative=FALSE) 307s + diagnose.ppm(fit, type="pearson", which="x", cumulative=FALSE) 307s + diagnose.ppm(fit, type="raw", plot.neg="discrete", plot.smooth="image") 307s + diagnose.ppm(fit, type="pearson", plot.neg="contour", plot.smooth="contour") 307s + 307s + diagnose.ppm(fitoff, type="raw", which="smooth", plot.smooth="persp") 307s + diagnose.ppm(fitoff, type="pearson", plot.neg="imagecontour") 307s + 307s + plot(Frame(letterR), main="") 307s + ploterodewin(letterR, erosion(letterR, 0.05), main="jeans") 307s + W <- as.mask(letterR) 307s + plot(Frame(W), main="") 307s + ploterodewin(W, erosion(W, 0.05), main="JeAnS") 307s + 307s + #' entangled terms in model 307s + U <- as.im(1, owin()) 307s + Z <- as.im(function(x,y) x, owin()) 307s + X <- runifpoint(40) 307s + fut <- ppm(X ~ Z:U) 307s + a <- parres(fut, "Z") 307s + futoff <- ppm(X ~ offset(Z*U)) 307s + a <- parres(futoff, "Z") 307s + 307s + #' residual summary functions 307s + pt <- psst(cells, interaction=Strauss(0.1), fun=nndcumfun) 307s + } 307s + }) 307s > 307s > 307s > 307s > ## 307s > ## tests/rhohat.R 307s > ## 307s > ## Test all combinations of options for rhohatCalc 307s > ## 307s > ## $Revision: 1.6 $ $Date: 2022/05/22 08:03:48 $ 307s > 307s > local({ 307s + if(FULLTEST) { 307s + X <- rpoispp(function(x,y){exp(3+3*x)}) 307s + Z <- as.im(function(x,y) { x }, Window(X)) 307s + f <- funxy(function(x,y) { y + 1 }, Window(X)) 307s + 307s + 307s + ## rhohat.ppm 307s + fit <- ppm(X ~x) 307s + rhofitA <- rhohat(fit, "x") 307s + rhofitB <- rhohat(fit, "x", method="reweight") 307s + rhofitC <- rhohat(fit, "x", method="transform") 307s + rhofitD <- rhohat(fit, Z) 307s + rhofitD <- rhohat(fit, Z, positiveCI=TRUE) 307s + lam <- predict(fit) 307s + 307s + 307s + ## Horvitz-Thompson 307s + rhofitAH <- rhohat(fit, "x", horvitz=TRUE) 307s + rhofitBH <- rhohat(fit, "x", method="reweight", horvitz=TRUE) 307s + rhofitCH <- rhohat(fit, "x", method="transform", horvitz=TRUE) 307s + 307s + r2myx <- rho2hat(fit, "y", "x") 307s + r2myxw <- rho2hat(fit, "y", "x", method="reweight") 307s + plot(r2myx) 307s + plot(r2myxw) 307s + print(r2myxw) 307s + predict(r2myxw) 307s + predict(r2myxw, relative=TRUE) 307s + } 307s + }) 307s > 307s BEGIN TEST testsR2.R 308s 308s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 308s Copyright (C) 2024 The R Foundation for Statistical Computing 308s Platform: aarch64-unknown-linux-gnu (64-bit) 308s 308s R is free software and comes with ABSOLUTELY NO WARRANTY. 308s You are welcome to redistribute it under certain conditions. 308s Type 'license()' or 'licence()' for distribution details. 308s 308s R is a collaborative project with many contributors. 308s Type 'contributors()' for more information and 308s 'citation()' on how to cite R or R packages in publications. 308s 308s Type 'demo()' for some demos, 'help()' for on-line help, or 308s 'help.start()' for an HTML browser interface to help. 308s Type 'q()' to quit R. 308s 308s > #' 308s > #' Header for all (concatenated) test files 308s > #' 308s > #' Require spatstat.model 308s > #' Obtain environment variable controlling tests. 308s > #' 308s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 308s > 308s > require(spatstat.model) 308s Loading required package: spatstat.model 308s Loading required package: spatstat.data 309s Loading required package: spatstat.geom 309s spatstat.geom 3.2-8 309s Loading required package: spatstat.random 309s spatstat.random 3.2-2 309s Loading required package: spatstat.explore 309s Loading required package: nlme 309s spatstat.explore 3.2-5 309s Loading required package: rpart 309s spatstat.model 3.2-8 309s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 309s > ALWAYS <- TRUE 309s > cat(paste("--------- Executing", 309s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 309s + "test code -----------\n")) 309s --------- Executing **RESTRICTED** subset of test code ----------- 309s > # 309s > # tests/rmhExpand.R 309s > # 309s > # test decisions about expansion of simulation window 309s > # 309s > # $Revision: 1.9 $ $Date: 2022/10/23 01:17:33 $ 309s > # 309s > 309s > local({ 309s + if(FULLTEST) { 309s + ## check expansion in rmhmodel.ppm 309s + fit <- ppm(cells ~x) 309s + mod <- rmhmodel(fit) 309s + is.expandable(mod) 309s + wsim <- as.rectangle(mod$trend) 309s + ## work around changes in 'unitname' 309s + wcel <- as.owin(cells) 309s + unitname(wcel) <- unitname(cells) 309s + ## test 309s + if(!identical(wsim, wcel)) 309s + stop("Expansion occurred improperly in rmhmodel.ppm") 309s + } 309s + }) 309s > 309s > 309s > 309s > # 309s > # tests/rmhTrend.R 309s > # 309s > # Problems with trend images (rmhmodel.ppm or rmhEngine) 309s > # 309s > 309s > if(ALWAYS) { 309s + local({ 309s + set.seed(42) 309s + 309s + # Bug folder 37 of 8 feb 2011 309s + # rmhmodel.ppm -> predict.ppm 309s + # + rmhResolveTypes -> is.subset.owin 309s + 309s + Z <- rescale(demopat, 7000) 309s + X <- unmark(Z) 309s + X1 <- split(Z)[[1]] 309s + Int <- density(X,dimyx=200) 309s + Lint <- eval.im(log(npoints(X1)*Int/npoints(X))) 309s + M <- as.owin(Int) 309s + MR <- intersect.owin(M,scalardilate(M,0.5,origin="midpoint")) 309s + X1 <- X1[MR] 309s + Fut <- ppm(X1~offset(Lint),covariates=list(Lint=Lint), 309s + inter=BadGey(r=c(0.03,0.05),sat=3)) 309s + Y <- rmh(Fut,control=list(expand=M,nrep=1e3), verbose=FALSE) 309s + 309s + }) 309s + } 309s > # 309s > # tests/rmhmodel.ppm.R 309s > # 309s > # $Revision: 1.10 $ $Date: 2020/05/01 05:29:42 $ 309s > # 309s > # Case-by-case tests of rmhmodel.ppm 309s > # 309s > 309s > if(FULLTEST) { 309s + local({ 309s + f <- ppm(cells) 309s + m <- rmhmodel(f) 309s + 309s + f <- ppm(cells ~x) 309s + m <- rmhmodel(f) 309s + 309s + f <- ppm(cells ~1, Strauss(0.1)) 309s + m <- rmhmodel(f) 309s + 309s + f <- ppm(cells ~1, StraussHard(r=0.1,hc=0.05)) 309s + m <- rmhmodel(f) 309s + print(m) 309s + 309s + f <- ppm(cells ~1, Hardcore(0.07)) 309s + m <- rmhmodel(f) 309s + 309s + f <- ppm(cells ~1, DiggleGratton(0.05,0.1)) 309s + m <- rmhmodel(f) 309s + 309s + f <- ppm(cells ~1, Softcore(0.5), correction="isotropic") 309s + m <- rmhmodel(f) 309s + 309s + f <- ppm(cells ~1, Geyer(0.07,2)) 309s + m <- rmhmodel(f) 309s + 309s + f <- ppm(cells ~1, BadGey(c(0.07,0.1,0.13),2)) 309s + m <- rmhmodel(f) 309s + 309s + f <- ppm(cells ~1, PairPiece(r = c(0.05, 0.1, 0.2))) 309s + m <- rmhmodel(f) 309s + 309s + f <- ppm(cells ~1, AreaInter(r=0.06)) 309s + m <- rmhmodel(f) 309s + print(m) 309s + 309s + # multitype 309s + 309s + r <- matrix(0.07, 2, 2) 309s + f <- ppm(amacrine ~1, MultiStrauss(c("off","on"),r)) 309s + m <- rmhmodel(f) 309s + print(m) 309s + 309s + h <- matrix(min(nndist(amacrine))/2, 2, 2) 309s + f <- ppm(amacrine ~1, MultiStraussHard(c("off","on"),r, h)) 309s + m <- rmhmodel(f) 309s + 309s + diag(r) <- NA 309s + diag(h) <- NA 309s + f <- ppm(amacrine ~1, MultiStrauss(c("off","on"),r)) 309s + m <- rmhmodel(f) 309s + 309s + f <- ppm(amacrine ~1, MultiStraussHard(c("off","on"),r, h)) 309s + m <- rmhmodel(f) 309s + 309s + # multitype data, interaction not dependent on type 309s + 309s + f <- ppm(amacrine ~marks, Strauss(0.05)) 309s + m <- rmhmodel(f) 309s + print(m) 309s + 309s + # trends 309s + 309s + f <- ppm(cells ~x, Strauss(0.1)) 309s + m <- rmhmodel(f) 309s + 309s + f <- ppm(cells ~y, StraussHard(r=0.1,hc=0.05)) 309s + m <- rmhmodel(f) 310s + 310s + f <- ppm(cells ~x+y, Hardcore(0.07)) 310s + m <- rmhmodel(f) 310s + print(m) 310s + 310s + f <- ppm(cells ~polynom(x,y,2), Softcore(0.5), correction="isotropic") 310s + m <- rmhmodel(f) 310s + 310s + # covariates 310s + 310s + Z <- as.im(function(x,y){ x^2+y^2 }, as.owin(cells)) 310s + f <- ppm(cells ~z, covariates=list(z=Z)) 310s + m <- rmhmodel(f) 310s + m <- rmhmodel(f, control=list(p=1)) 310s + print(m) 310s + 310s + Zim <- as.im(Z, as.owin(cells)) 310s + f <- ppm(cells ~z, covariates=list(z=Zim)) 310s + m <- rmhmodel(f) 310s + 310s + Z <- as.im(function(x,y){ x^2+y }, as.owin(amacrine)) 310s + f <- ppm(amacrine ~z + marks, covariates=list(z=Z)) 310s + m <- rmhmodel(f) 310s + print(m) 310s + m <- rmhmodel(f, control=list(p=1)) 310s + m <- rmhmodel(f, control=list(p=1,fixall=TRUE)) 310s + print(m) 310s + 310s + Zim <- as.im(Z, as.owin(amacrine)) 310s + f <- ppm(amacrine ~z + marks, covariates=list(z=Zim)) 310s + m <- rmhmodel(f) 310s + print(m) 310s + 310s + }) 310s + } 310s > # 310s > # tests/rmhmodelHybrids.R 310s > # 310s > # Test that rmhmodel.ppm and rmhmodel.default 310s > # work on Hybrid interaction models 310s > # 310s > # $Revision: 1.6 $ $Date: 2022/10/23 01:17:56 $ 310s > # 310s > 310s > if(ALWAYS) { # involves C code 310s + local({ 310s + 310s + ## ......... rmhmodel.ppm ....................... 310s + fit1 <- ppm(redwood ~1, 310s + Hybrid(A=Strauss(0.02), B=Geyer(0.1, 2), C=Geyer(0.15, 1))) 310s + m1 <- rmhmodel(fit1) 310s + m1 310s + reach(m1) 310s + 310s + ## Test of handling 'IsOffset' 310s + fit2 <- ppm(cells ~1, Hybrid(H=Hardcore(0.05), G=Geyer(0.15, 2))) 310s + m2 <- rmhmodel(fit2) 310s + ## also test C code for hybrid interaction with hard core 310s + fakecells <- rmh(fit2, nrep=1e4) 310s + 310s + ## Test of handling Poisson components 310s + fit3 <- ppm(cells ~1, Hybrid(P=Poisson(), S=Strauss(0.05))) 310s + X3 <- rmh(fit3, control=list(nrep=1e3,expand=1), verbose=FALSE) 310s + 310s + 310s + }) 310s + } 310s Extracting model information...Evaluating trend...done. 310s Extracting model information...Evaluating trend...done. 310s Extracting model information...Evaluating trend...done. 310s Checking arguments..determining simulation windows...Starting simulation. 310s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 310s > 310s > # 310s > # tests/rmh.ppm.R 310s > # 310s > # $Revision: 1.5 $ $Date: 2020/05/01 05:29:42 $ 310s > # 310s > # Examples removed from rmh.ppm.Rd 310s > # stripped down to minimal tests of validity 310s > # 310s > 310s > local({ 310s + op <- spatstat.options() 310s + spatstat.options(rmh.nrep=10, npixel=10, ndummy.min=10) 310s + spatstat.options(project.fast=TRUE) 310s + Nrep <- 10 310s + 310s + X <- swedishpines 310s + if(FULLTEST) { 310s + ## Poisson process 310s + fit <- ppm(X ~1, Poisson()) 310s + Xsim <- rmh(fit) 310s + } 310s + if(ALWAYS) { # Gibbs model => C code 310s + ## Strauss process 310s + fit <- ppm(X ~1, Strauss(r=7)) 310s + Xsim <- rmh(fit) 310s + 310s + ## Strauss process simulated on a larger window 310s + ## then clipped to original window 310s + Xsim <- rmh(fit, control=list(nrep=Nrep, expand=1.1, periodic=TRUE)) 310s + 310s + ## Extension of model to another window (thanks to Tuomas Rajala) 310s + Xsim <- rmh(fit, w=square(2)) 310s + Xsim <- simulate(fit, w=square(2)) 310s + 310s + ## Strauss - hard core process 310s + ## fit <- ppm(X ~1, StraussHard(r=7,hc=2)) 310s + ## Xsim <- rmh(fit, start=list(n.start=X$n)) 310s + 310s + ## Geyer saturation process 310s + ## fit <- ppm(X ~1, Geyer(r=7,sat=2)) 310s + ## Xsim <- rmh(fit, start=list(n.start=X$n)) 310s + 310s + ## Area-interaction process 310s + fit <- ppm(X ~1, AreaInter(r=7)) 310s + Xsim <- rmh(fit, start=list(n.start=X$n)) 310s + 310s + ## Penttinen process 310s + fit <- ppm(X ~1, Penttinen(r=7)) 310s + Xsim <- rmh(fit, start=list(n.start=X$n)) 310s + 310s + ## soft core interaction process 310s + ## X <- quadscheme(X, nd=50) 310s + ## fit <- ppm(X ~1, Softcore(kappa=0.1), correction="isotropic") 310s + ## Xsim <- rmh(fit, start=list(n.start=X$n)) 310s + 310s + ## Diggle-Gratton pairwise interaction model 310s + ## fit <- ppm(cells ~1, DiggleGratton(0.05, 0.1)) 310s + ## Xsim <- rmh(fit, start=list(n.start=cells$n)) 310s + ## plot(Xsim, main="simulation from fitted Diggle-Gratton model") 310s + 310s + 310s + ## piecewise-constant pairwise interaction function 310s + X <- rSSI(0.05, 100) 310s + fit <- ppm(X ~1, PairPiece(seq(0.02, 0.1, by=0.01))) 310s + Xsim <- rmh(fit) 310s + } 310s + 310s + ## marked point pattern 310s + Y <- amacrine 310s + 310s + if(FULLTEST) { 310s + #' marked Poisson models 310s + fit <- ppm(Y) 310s + Ysim <- rmh(fit) 310s + 310s + fit <- ppm(Y~marks) 310s + Ysim <- rmh(fit) 310s + 310s + fit <- ppm(Y~x) 310s + Ysim <- rmh(fit) 310s + 310s + fit <- ppm(Y~marks+x) 310s + Ysim <- rmh(fit) 310s + } 310s + 310s + if(ALWAYS) { 310s + #' multitype Strauss 310s + typ <- levels(Y$marks) 310s + MS <- MultiStrauss(types = typ, 310s + radii=matrix(0.07, ncol=2, nrow=2)) 310s + 310s + fit <- ppm(Y~marks*x, MS) 310s + Ysim <- rmh(fit) 310s + 310s + #' multitype Hardcore 310s + h0 <- minnndist(unmark(Y)) * 0.95 310s + MH <- MultiHard(types = typ, 310s + hradii=matrix(h0, ncol=2, nrow=2)) 310s + fit <- ppm(Y ~ marks+x, MH) 310s + Ysim <- rmh(fit) 310s + #' other code blocks 310s + Ysim <- rmh(fit, control=list(periodic=TRUE, expand=1)) 310s + Ysim <- rmh(fit, control=list(periodic=FALSE, expand=1)) 310s + #' multihard core with invalid initial state 310s + Ydouble <- superimpose(Y, rjitter(Y, h0/10)) 310s + Ysim <- rmh(fit, start=list(x.start=Ydouble)) 310s + 310s + #' Lennard-Jones 310s + fut <- ppm(unmark(longleaf) ~ 1, LennardJones(), rbord=1) 310s + Ysim <- rmh(fut) 310s + Ysim <- rmh(fut, control=list(periodic=TRUE, expand=1)) 310s + } 310s + 310s + spatstat.options(op) 310s + }) 310s Extracting model information...Evaluating trend...done. 310s Checking arguments..determining simulation windows...Starting simulation. 310s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 310s Extracting model information...Evaluating trend...done. 310s Checking arguments..determining simulation windows...Starting simulation. 310s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 310s Extracting model information...Evaluating trend...done. 310s Checking arguments..determining simulation windows...Starting simulation. 310s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 313s Extracting model information...Evaluating trend...done. 313s Checking arguments..determining simulation windows...Starting simulation. 313s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 313s Extracting model information...Evaluating trend...done. 313s Checking arguments..determining simulation windows...Starting simulation. 313s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 313s Model is invalid - projecting it 314s Extracting model information...Evaluating trend...done. 314s Checking arguments..determining simulation windows...Starting simulation. 314s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 314s Extracting model information...Evaluating trend...done. 314s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 314s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 314s Extracting model information...Evaluating trend...done. 314s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 314s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 314s Extracting model information...Evaluating trend...done. 314s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 314s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 314s Extracting model information...Evaluating trend...done. 314s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 314s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 314s Extracting model information...Evaluating trend...done. 315s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 315s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 315s Extracting model information...Evaluating trend...done. 315s Checking arguments..determining simulation windows...Starting simulation. 315s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 315s Extracting model information...Evaluating trend...done. 315s Checking arguments..determining simulation windows...Starting simulation. 315s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 315s > 315s > 315s > reset.spatstat.options() 315s > #' 315s > #' tests/rmhsnoopy.R 315s > #' 315s > #' Test the rmh interactive debugger 315s > #' 315s > #' $Revision: 1.11 $ $Date: 2022/10/23 01:19:00 $ 315s > 315s > if(ALWAYS) { # may depend on platform 315s + local({ 315s + R <- 0.1 315s + ## fit a model and prepare to simulate 315s + model <- ppm(amacrine ~ marks + x, Strauss(R)) 315s + siminfo <- rmh(model, preponly=TRUE) 315s + Wsim <- siminfo$control$internal$w.sim 315s + Wclip <- siminfo$control$internal$w.clip 315s + if(is.null(Wclip)) Wclip <- Window(cells) 315s + 315s + ## determine debugger interface panel geometry 315s + Xinit <- runifpoint(ex=amacrine)[1:40] 315s + P <- rmhsnoop(Wsim=Wsim, Wclip=Wclip, R=R, 315s + xcoords=Xinit$x, 315s + ycoords=Xinit$y, 315s + mlevels=levels(marks(Xinit)), 315s + mcodes=as.integer(marks(Xinit)) - 1L, 315s + irep=3L, itype=1L, 315s + proptype=1, proplocn=c(0.5, 0.5), propmark=0, propindx=0, 315s + numerator=42, denominator=24, 315s + panel.only=TRUE) 315s + boxes <- P$boxes 315s + clicknames <- names(P$clicks) 315s + boxcentres <- do.call(concatxy, lapply(boxes, centroid.owin)) 315s + 315s + ## design a sequence of clicks 315s + actionsequence <- c("Up", "Down", "Left", "Right", 315s + "At Proposal", "Zoom Out", "Zoom In", "Reset", 315s + "Accept", "Reject", "Print Info", 315s + "Next Iteration", "Next Shift", "Next Death", 315s + "Skip 10", "Skip 100", "Skip 1000", "Skip 10,000", 315s + "Skip 100,000", "Exit Debugger") 315s + actionsequence <- match(actionsequence, clicknames) 315s + actionsequence <- actionsequence[!is.na(actionsequence)] 315s + xy <- lapply(boxcentres, "[", actionsequence) 315s + 315s + ## queue the click sequence 315s + spatstat.utils::queueSpatstatLocator(xy$x,xy$y) 315s + 315s + ## go 315s + rmh(model, snoop=TRUE) 315s + }) 315s + } 315s Extracting model information...Evaluating trend...done. 315s Checking arguments..determining simulation windows...Evaluating trend integral...Extracting model information...Evaluating trend...done. 315s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 315s Initial state... 315s Creating debugger environment..Done. 316s Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 317s 317s 317s ------------------- 317s Iteration 0 317s Simulation window: 317s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 317s Clipping window: 317s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 317s Current state: 317s Marked planar point pattern: 72 points 317s Multitype, with levels = off, on 317s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 317s Proposal type: Shift 317s Shift data point 18 from current location (0.290108, 0.0160037, “off”) to 317s new location (0.620599, 0.378428, “off”) 317s Hastings ratio = 6831.92992943093 / 14545.6615344216 = 0.469688498750194 317s Fate of proposal: Rejected 318s Marked planar point pattern: 350 points 318s Multitype, with levels = off, on 318s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 318s Pattern was generated by Metropolis-Hastings simulation. 318s > 318s BEGIN TEST testsS.R 319s 319s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 319s Copyright (C) 2024 The R Foundation for Statistical Computing 319s Platform: aarch64-unknown-linux-gnu (64-bit) 319s 319s R is free software and comes with ABSOLUTELY NO WARRANTY. 319s You are welcome to redistribute it under certain conditions. 319s Type 'license()' or 'licence()' for distribution details. 319s 319s R is a collaborative project with many contributors. 319s Type 'contributors()' for more information and 319s 'citation()' on how to cite R or R packages in publications. 319s 319s Type 'demo()' for some demos, 'help()' for on-line help, or 319s 'help.start()' for an HTML browser interface to help. 319s Type 'q()' to quit R. 319s 319s > #' 319s > #' Header for all (concatenated) test files 319s > #' 319s > #' Require spatstat.model 319s > #' Obtain environment variable controlling tests. 319s > #' 319s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 319s > 319s > require(spatstat.model) 319s Loading required package: spatstat.model 319s Loading required package: spatstat.data 320s Loading required package: spatstat.geom 320s spatstat.geom 3.2-8 320s Loading required package: spatstat.random 320s spatstat.random 3.2-2 320s Loading required package: spatstat.explore 320s Loading required package: nlme 320s spatstat.explore 3.2-5 320s Loading required package: rpart 320s spatstat.model 3.2-8 320s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 320s > ALWAYS <- TRUE 320s > cat(paste("--------- Executing", 320s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 320s + "test code -----------\n")) 320s --------- Executing **RESTRICTED** subset of test code ----------- 320s > # 320s > # tests/slrm.R 320s > # 320s > # $Revision: 1.3 $ $Date: 2020/05/01 09:59:59 $ 320s > # 320s > # Test slrm fitting and prediction when there are NA's 320s > # 320s > 320s > if(ALWAYS) { 320s + local({ 320s + X <- copper$SouthPoints 320s + W <- owin(poly=list(x=c(0,35,35,1),y=c(1,1,150,150))) 320s + Y <- X[W] 320s + fit <- slrm(Y ~ x+y) 320s + pred <- predict(fit) 320s + extractAIC(fit) 320s + fitx <- update(fit, . ~ x) 320s + simulate(fitx, seed=42) 320s + if(FULLTEST) { 320s + unitname(fitx) 320s + unitname(fitx) <- "km" 320s + 320s + mur <- solapply(murchison,rescale, 1000, "km") 320s + mur$dfault <- distfun(mur$faults) 320s + fut <- slrm(gold ~ dfault, data=mur, splitby="greenstone") 320s + A <- model.images(fut) 320s + } 320s + }) 320s + } 320s > 320s > 320s > # 320s > # tests/step.R 320s > # 320s > # $Revision: 1.5 $ $Date: 2020/05/01 09:59:59 $ 320s > # 320s > # test for step() operation 320s > # 320s > if(FULLTEST) { 320s + local({ 320s + Z <- as.im(function(x,y){ x^3 - y^2 }, nztrees$window) 320s + fitP <- ppm(nztrees ~x+y+Z, covariates=list(Z=Z)) 320s + step(fitP) 320s + fitS <- update(fitP, Strauss(7)) 320s + step(fitS) 320s + fitM <- ppm(amacrine ~ marks*(x+y), 320s + MultiStrauss(types=levels(marks(amacrine)), radii=matrix(0.04, 2, 2))) 320s + step(fitM) 320s + }) 320s + } 320s > 320s > 320s > 320s > 320s BEGIN TEST testsT.R 320s 320s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 320s Copyright (C) 2024 The R Foundation for Statistical Computing 320s Platform: aarch64-unknown-linux-gnu (64-bit) 320s 320s R is free software and comes with ABSOLUTELY NO WARRANTY. 320s You are welcome to redistribute it under certain conditions. 320s Type 'license()' or 'licence()' for distribution details. 320s 320s R is a collaborative project with many contributors. 320s Type 'contributors()' for more information and 320s 'citation()' on how to cite R or R packages in publications. 320s 320s Type 'demo()' for some demos, 'help()' for on-line help, or 320s 'help.start()' for an HTML browser interface to help. 320s Type 'q()' to quit R. 320s 320s > #' 320s > #' Header for all (concatenated) test files 320s > #' 320s > #' Require spatstat.model 320s > #' Obtain environment variable controlling tests. 320s > #' 320s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 320s > 320s > require(spatstat.model) 320s Loading required package: spatstat.model 320s Loading required package: spatstat.data 321s Loading required package: spatstat.geom 321s spatstat.geom 3.2-8 321s Loading required package: spatstat.random 321s spatstat.random 3.2-2 321s Loading required package: spatstat.explore 321s Loading required package: nlme 321s spatstat.explore 3.2-5 321s Loading required package: rpart 322s spatstat.model 3.2-8 322s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 322s > ALWAYS <- TRUE 322s > cat(paste("--------- Executing", 322s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 322s + "test code -----------\n")) 322s --------- Executing **RESTRICTED** subset of test code ----------- 322s > # 322s > # tests/testaddvar.R 322s > # 322s > # test addvar options 322s > # 322s > # $Revision: 1.3 $ $Date: 2020/05/02 01:32:58 $ 322s > 322s > if(FULLTEST) { 322s + local({ 322s + X <- rpoispp(function(x,y){exp(3+3*x)}) 322s + model <- ppm(X ~y) 322s + addvar(model, "x", crosscheck=TRUE) 322s + addvar(model, "x", bw.input="quad") 322s + w <- square(0.5) 322s + addvar(model, "x", subregion=w) 322s + addvar(model, "x", subregion=w, bw.input="points") 322s + Z <- as.im(function(x,y) { x }, Window(X)) 322s + addvar(model, Z) 322s + }) 322s + } 322s > # 322s > # tests/testparres.R 322s > # 322s > # additional test of parres 322s > # 322s > # $Revision: 1.8 $ $Date: 2022/05/20 06:59:59 $ 322s > # 322s > 322s > if(FULLTEST) { 322s + local({ 322s + X <- rpoispp(function(x,y){exp(3+x+2*x^2)}) 322s + model <- ppm(X ~x+y) 322s + 322s + # options in parres (and code blocks in print.parres) 322s + parres(model, "x") 322s + parres(model, "x", smooth.effect=TRUE) 322s + parres(model, "x", bw.input="quad") 322s + w <- square(0.5) 322s + parres(model, "x", subregion=w) 322s + parres(model, "x", subregion=w, bw.input="quad") 322s + f <- function(x,y) { x + y } 322s + parres(model, f) 322s + 322s + # check whether 'update.ppm' has messed up internals 322s + mod2 <- update(model, ~x) 322s + parres(mod2, "x") 322s + 322s + #' other kinds of covariates 322s + mod3 <- ppm(X ~ x + offset(y)) 322s + parres(mod3, "offset(y)") 322s + Z <- distmap(runifpoint(3)) 322s + parres(mod3, Z) 322s + mod4 <- ppm(X ~ sin(x), data=solist(B=Z)) 322s + parres(mod4, "sin(x)") 322s + parres(mod4, "B") 322s + 322s + #' models with interaction 322s + mod5 <- ppm(cells ~ x, AreaInter(0.06)) 322s + parres(mod5, "x") 322s + dlin <- distfun(copper$SouthLines) 322s + copfit <- ppm(copper$SouthPoints ~ dlin, Geyer(1,1)) 322s + parres(copfit, "dlin") 322s + 322s + #' covariate need not be specified if there is only one. 322s + parres(mod5) 322s + parres(copfit) 322s + 322s + #' infrastructure 322s + ltuae <- evaluateCovariate(42, cells) 322s + LTUAE <- evaluateCovariate(ltuae, cells) 322s + 322s + fit <- ppm(amacrine ~ x * marks, nd=16) 322s + dmat <- model.depends(fit) 322s + check.separable(dmat, "x", c(x=FALSE, marks=FALSE), FALSE) 322s + check.separable(dmat, "x", c(FALSE, FALSE), FALSE) 322s + check.separable(dmat, "x", c(x=FALSE, marks=TRUE), FALSE) 322s + }) 322s + } 322s > #' 322s > #' tests/threedee.R 322s > #' 322s > #' Tests of 3D code 322s > #' 322s > #' $Revision: 1.8 $ $Date: 2020/05/02 01:32:58 $ 322s > #' 322s > 322s > local({ 322s + X <- runifpoint3(30) 322s + Y <- runifpoint3(20) 322s + if(FULLTEST) { 322s + A <- runifpoint3(10, nsim=2) 322s + Z <- ppsubset(X, 2:4) 322s + } 322s + ## 322s + if(ALWAYS) { # includes C code 322s + d <- pairdist(X, periodic=TRUE, squared=TRUE) 322s + d <- crossdist(X, Y, squared=TRUE) 322s + d <- crossdist(X, Y, squared=TRUE, periodic=TRUE) 322s + #' 322s + h <- has.close(X, 0.2) 322s + h <- has.close(X, 0.2, periodic=TRUE) 322s + h <- has.close(X, 0.2, Y=Y) 322s + h <- has.close(X, 0.2, Y=Y, periodic=TRUE) 322s + #' code blocks not otherwise reached 322s + rmax <- 0.6 * max(nndist(X)) 322s + g <- G3est(X, rmax=rmax, correction="rs") 322s + g <- G3est(X, rmax=rmax, correction="km") 322s + g <- G3est(X, rmax=rmax, correction="Hanisch") 322s + g <- G3est(X, rmax=rmax, sphere="ideal") 322s + g <- G3est(X, rmax=rmax, sphere="digital") 322s + v <- sphere.volume() 322s + v <- digital.volume() 322s + #' older code 322s + co <- coords(X) 322s + xx <- co$x 322s + yy <- co$y 322s + zz <- co$z 322s + gg1 <- g3engine(xx, yy, zz, correction="Hanisch G3") 322s + gg2 <- g3engine(xx, yy, zz, correction="minus sampling") 322s + ff1 <- f3engine(xx, yy, zz, correction="no") 322s + ff2 <- f3engine(xx, yy, zz, correction="minus sampling") 322s + } 322s + ## 322s + if(ALWAYS) { 322s + #'class support 322s + X <- runifpoint3(10) 322s + print(X) 322s + print(X %mark% runif(10)) 322s + print(X %mark% factor(letters[c(1:5,5:1)])) 322s + print(X %mark% data.frame(a=1:10, b=runif(10))) 322s + da <- as.Date(paste0("2020-01-0", c(1:5,5:1))) 322s + print(X %mark% da) 322s + print(X %mark% data.frame(a=1:10, b=da)) 322s + } 322s + }) 322s Three-dimensional point pattern: 10 points 322s Box: [0, 1] x [0, 1] x [0, 1] units 322s Marked three-dimensional point pattern: 10 points 322s marks are numeric, of storage type ‘double’ 322s Box: [0, 1] x [0, 1] x [0, 1] units 322s Marked three-dimensional point pattern: 10 points 322s Multitype, with levels = a, b, c, d, e 322s Box: [0, 1] x [0, 1] x [0, 1] units 322s Marked three-dimensional point pattern: 10 points 322s Mark variables: a, b 322s Box: [0, 1] x [0, 1] x [0, 1] units 322s Marked three-dimensional point pattern: 10 points 322s marks are dates, of class ‘Date’ 322s Box: [0, 1] x [0, 1] x [0, 1] units 322s Marked three-dimensional point pattern: 10 points 322s Mark variables: a, b 322s Box: [0, 1] x [0, 1] xWarning messages: 322s 1: In G3est: unrecognised argument ‘sphere’ was ignored 322s 2: In G3est: unrecognised argument ‘sphere’ was ignored 322s [0, 1] units 322s > # 322s > # tests/triplets.R 322s > # 322s > # test code for triplet interaction 322s > # 322s > # $Revision: 1.9 $ $Date: 2022/05/22 08:45:38 $ 322s > # 322s > if(ALWAYS) { # C code, platform dependence 322s + local({ 322s + #' valid model 322s + fit <- ppm(cells ~1, Triplets(0.1)) 322s + fit 322s + suffstat(fit) 322s + #' invalid model 322s + fitR <- ppm(redwood ~1, Triplets(0.1)) 322s + fitR 322s + suffstat(fitR) 322s + #' hard core (zero triangles, coefficient is NA) 322s + fit0 <- ppm(cells ~1, Triplets(0.05)) 322s + fit0 322s + suffstat(fit0) 322s + #' bug case (1 triangle in data) 322s + fit1 <- ppm(cells ~1, Triplets(0.15)) 322s + fit1 322s + suffstat(fit1) 322s + #' simulation 322s + X <- simulate(fit) 322s + mod <- list(cif="triplets",par=list(beta=50,gamma=0.2,r=0.07), w=square(1)) 322s + Xm <- rmh(model=mod,start=list(n.start=5), control=list(nrep=1e5)) 322s + #' hard core 322s + mod$par$gamma <- 0 322s + XmHard <- rmh(model=mod,start=list(n.start=5), control=list(nrep=1e5)) 322s + }) 322s + } 323s Checking arguments..determining simulation windows...Starting simulation. 323s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 323s Checking arguments..determining simulation windows...Starting simulation. 323s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 324s > 324s BEGIN TEST testsUtoZ.R 324s 324s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 324s Copyright (C) 2024 The R Foundation for Statistical Computing 324s Platform: aarch64-unknown-linux-gnu (64-bit) 324s 324s R is free software and comes with ABSOLUTELY NO WARRANTY. 324s You are welcome to redistribute it under certain conditions. 324s Type 'license()' or 'licence()' for distribution details. 324s 324s R is a collaborative project with many contributors. 324s Type 'contributors()' for more information and 324s 'citation()' on how to cite R or R packages in publications. 324s 324s Type 'demo()' for some demos, 'help()' for on-line help, or 324s 'help.start()' for an HTML browser interface to help. 324s Type 'q()' to quit R. 324s 324s > #' 324s > #' Header for all (concatenated) test files 324s > #' 324s > #' Require spatstat.model 324s > #' Obtain environment variable controlling tests. 324s > #' 324s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 324s > 324s > require(spatstat.model) 324s Loading required package: spatstat.model 324s Loading required package: spatstat.data 325s Loading required package: spatstat.geom 325s spatstat.geom 3.2-8 325s Loading required package: spatstat.random 325s spatstat.random 3.2-2 325s Loading required package: spatstat.explore 325s Loading required package: nlme 325s spatstat.explore 3.2-5 325s Loading required package: rpart 325s spatstat.model 3.2-8 325s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 325s > ALWAYS <- TRUE 325s > cat(paste("--------- Executing", 325s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 325s + "test code -----------\n")) 325s --------- Executing **RESTRICTED** subset of test code ----------- 325s > # 325s > # tests/undoc.R 325s > # 325s > # $Revision: 1.16 $ $Date: 2020/11/02 07:06:49 $ 325s > # 325s > # Test undocumented hacks, experimental code, etc 325s > 325s > 325s > local({ 325s + if(FULLTEST) { 325s + ## cases of 'pickoption' 325s + aliases <- c(Lenin="Ulyanov", Stalin="Djugashvili", Trotsky="Bronstein") 325s + surname <- "Trot" 325s + pickoption("leader", surname, aliases) 325s + pickoption("leader", surname, aliases, exact=TRUE, die=FALSE) 325s + } 325s + if(ALWAYS) { 325s + ## pixellate.ppp accepts a data frame of weights 325s + pixellate(cells, weights=data.frame(a=1:42, b=42:1)) 325s + ## test parts of 'rmhsnoop' that don't require interaction with user 325s + rmhSnoopEnv(cells, Window(cells), 0.1) 325s + } 325s + if(FULLTEST) { 325s + ## Berman-Turner frame 325s + A <- bt.frame(quadscheme(cells), ~x, Strauss(0.07), rbord=0.07) 325s + print(A) 325s + ## digestCovariates 325s + D <- distfun(cells) 325s + Z <- distmap(cells) 325s + U <- dirichlet(cells) 325s + stopifnot(is.scov(D)) 325s + stopifnot(is.scov(Z)) 325s + stopifnot(is.scov(U)) 325s + stopifnot(is.scov("x")) 325s + dg <- digestCovariates(D=D,Z=Z,U=U,"x",list(A="x", B=D)) 325s + ## 325s + a <- getfields(dg, c("A", "D", "niets"), fatal=FALSE) 325s + ## util.R 325s + gg <- pointgrid(owin(), 7) 325s + checkbigmatrix(1000000L, 1000000L, FALSE, TRUE) 325s + spatstatDiagnostic("whatever") 325s + M <- list(list(a=2, b=FALSE), 325s + list(a=2, b=TRUE)) 325s + stopifnot(!allElementsIdentical(M)) 325s + stopifnot(allElementsIdentical(M, "a")) 325s + ## 325s + A <- Strauss(0.1) 325s + A <- reincarnate.interact(A) 325s + ## 325s + ## special lists 325s + B <- solist(a=cells, b=redwood, c=japanesepines) 325s + BB <- as.ppplist(B) 325s + BL <- as.layered(B) 325s + DB <- as.imlist(lapply(B, density)) 325s + is.solist(B) 325s + is.ppplist(B) 325s + is.imlist(DB) 325s + ## case of density.ppplist 325s + DEB <- density(BB, se=TRUE) 325s + } 325s + 325s + if(ALWAYS) { 325s + ## fft 325s + z <- matrix(1:16, 4, 4) 325s + a <- fft2D(z, west=FALSE) 325s + if(fftwAvailable()) 325s + b <- fft2D(z, west=TRUE) 325s + } 325s + 325s + if(ALWAYS) { 325s + ## experimental interactions 325s + pot <- function(d, par) { d <= 0.1 } 325s + A <- Saturated(pot) 325s + print(A) 325s + A <- update(A, name="something") 325s + ppm(amacrine ~ x, A, rbord=0.1) 325s + } 325s + 325s + if(ALWAYS) { # platform dependent 325s + #' version-checking 325s + now <- Sys.Date() 325s + versioncurrency.spatstat(now + 80, FALSE) 325s + versioncurrency.spatstat(now + 140, FALSE) 325s + versioncurrency.spatstat(now + 400, FALSE) 325s + versioncurrency.spatstat(now + 1000) 325s + } 325s + 325s + if(FULLTEST) { 325s + #' general Ord interaction 325s + gradual <- function(d, pars) { 325s + y <- pmax(0, 0.005 - d)/0.005 325s + if(is.matrix(d)) y <- matrix(y, nrow(d), ncol(d)) 325s + return(y) 325s + } 325s + B <- Ord(gradual, "gradual Ord process") 325s + } 325s + }) 325s Saturated pairwise interaction family 325s Interaction:Saturated process with user-defined potential 325s Potential function: 325s function (d, par) 325s { 325s d <= 0.1 325s } 325s 326s > 326s > 326s > ## 326s > ## tests/updateppm.R 326s > ## 326s > ## Check validity of update.ppm 326s > ## 326s > ## $Revision: 1.8 $ $Date: 2022/10/23 01:19:19 $ 326s > 326s > local({ 326s + if(ALWAYS) { 326s + require(spatstat.utils) 326s + h <- function(m1, m2) { 326s + mc <- short.deparse(sys.call()) 326s + cat(paste(mc, "\t... ")) 326s + m1name <- short.deparse(substitute(m1)) 326s + m2name <- short.deparse(substitute(m2)) 326s + if(!identical(names(coef(m1)), names(coef(m2)))) 326s + stop(paste("Differing results for", m1name, "and", m2name, 326s + "in updateppm.R"), 326s + call.=FALSE) 326s + cat("OK\n") 326s + } 326s + 326s + X <- redwood[c(TRUE,FALSE)] 326s + Y <- redwood[c(FALSE,TRUE)] 326s + fit0f <- ppm(X ~ 1, nd=8) 326s + fit0p <- ppm(X, ~1, nd=8) 326s + fitxf <- ppm(X ~ x, nd=8) 326s + fitxp <- ppm(X, ~x, nd=8) 326s + 326s + cat("Basic consistency ...\n") 326s + h(fit0f, fit0p) 326s + h(fitxf, fitxp) 326s + 326s + cat("\nTest correct handling of model formulas ...\n") 326s + h(update(fitxf, Y), fitxf) 326s + h(update(fitxf, Q=Y), fitxf) 326s + h(update(fitxf, Y~x), fitxf) 326s + h(update(fitxf, Q=Y~x), fitxf) 326s + h(update(fitxf, ~x), fitxf) 326s + } 326s + 326s + if(FULLTEST) { 326s + h(update(fitxf, Y~1), fit0f) 326s + h(update(fitxf, ~1), fit0f) 326s + h(update(fit0f, Y~x), fitxf) 326s + h(update(fit0f, ~x), fitxf) 326s + 326s + h(update(fitxp, Y), fitxp) 326s + h(update(fitxp, Q=Y), fitxp) 326s + h(update(fitxp, Y~x), fitxp) 326s + h(update(fitxp, Q=Y~x), fitxp) 326s + h(update(fitxp, ~x), fitxp) 326s + 326s + h(update(fitxp, Y~1), fit0p) 326s + h(update(fitxp, ~1), fit0p) 326s + h(update(fit0p, Y~x), fitxp) 326s + h(update(fit0p, ~x), fitxp) 326s + } 326s + 326s + if(ALWAYS) { 326s + cat("\nTest scope handling for left hand side ...\n") 326s + X <- Y 326s + h(update(fitxf), fitxf) 326s + } 326s + 326s + if(ALWAYS) { 326s + cat("\nTest scope handling for right hand side ...\n") 326s + Z <- distmap(X) 326s + fitZf <- ppm(X ~ Z) 326s + fitZp <- ppm(X, ~ Z) 326s + h(update(fitxf, X ~ Z), fitZf) 326s + } 326s + if(FULLTEST) { 326s + h(update(fitxp, X ~ Z), fitZp) 326s + h(update(fitxf, . ~ Z), fitZf) 326s + h(update(fitZf, . ~ x), fitxf) 326s + h(update(fitZf, . ~ . - Z), fit0f) 326s + h(update(fitxp, . ~ Z), fitZp) 326s + h(update(fitZp, . ~ . - Z), fit0p) 326s + h(update(fit0p, . ~ . + Z), fitZp) 326s + h(update(fitZf, . ~ . ), fitZf) 326s + h(update(fitZp, . ~ . ), fitZp) 326s + } 326s + if(ALWAYS) { 326s + cat("\nTest use of internal data ...\n") 326s + h(update(fitZf, ~ x, use.internal=TRUE), fitxf) 326s + fitsin <- update(fitZf, X~sin(Z)) 326s + h(update(fitZf, ~ sin(Z), use.internal=TRUE), fitsin) 326s + } 326s + if(FULLTEST) { 326s + cat("\nTest step() ... ") 326s + fut <- ppm(X ~ Z + x + y, nd=8) 326s + fut0 <- step(fut, trace=0) 326s + cat("OK\n") 326s + } 326s + 326s + }) 326s Loading required package: spatstat.utils 326s Basic consistency ... 326s h(fit0f, fit0p) ... OK 326s h(fitxf, fitxp) ... OK 326s 326s Test correct handling of model formulas ... 326s h(update(fitxf, Y), fitxf) ... OK 326s h(update(fitxf, Q = Y), fitxf) ... OK 326s h(update(fitxf, Y ~ x), fitxf) ... OK 326s h(update(fitxf, Q = Y ~ x), fitxf) ... OK 326s h(update(fitxf, ~x), fitxf) ... OK 326s 326s Test scope handling for left hand side ... 326s h(update(fitxf), fitxf) ... OK 326s 326s Test scope handling for right hand side ... 326s h(update(fitxf, X ~ Z), fitZf) ... OK 326s 326s Test use of internal data ... 326s h(update(fitZf, ~x, use.internal = TRUE), fitxf) ... OK 326s h(update(fitZf, ~sin(Z), use.internal = TRUE), fitsin) ... OK 326s > # 326s > # tests/vcovppm.R 326s > # 326s > # Check validity of vcov.ppm algorithms 326s > # 326s > # Thanks to Ege Rubak 326s > # 326s > # $Revision: 1.12 $ $Date: 2020/05/02 01:32:58 $ 326s > # 326s > 326s > local({ 326s + 326s + set.seed(42) 326s + X <- rStrauss(200, .5, .05) 326s + model <- ppm(X, inter = Strauss(.05)) 326s + 326s + if(ALWAYS) { 326s + b <- vcov(model, generic = TRUE, algorithm = "basic") 326s + v <- vcov(model, generic = TRUE, algorithm = "vector") 326s + vc <- vcov(model, generic = TRUE, algorithm = "vectorclip") 326s + vn <- vcov(model, generic = FALSE) 326s + 326s + disagree <- function(x, y, tol=1e-7) { max(abs(x-y)) > tol } 326s + asymmetric <- function(x) { disagree(x, t(x)) } 326s + 326s + if(asymmetric(b)) 326s + stop("Non-symmetric matrix produced by vcov.ppm 'basic' algorithm") 326s + if(asymmetric(v)) 326s + stop("Non-symmetric matrix produced by vcov.ppm 'vector' algorithm") 326s + if(asymmetric(vc)) 326s + stop("Non-symmetric matrix produced by vcov.ppm 'vectorclip' algorithm") 326s + if(asymmetric(vn)) 326s + stop("Non-symmetric matrix produced by vcov.ppm Strauss algorithm") 326s + 326s + if(disagree(v, b)) 326s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'basic' ") 326s + if(disagree(v, vc)) 326s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'vectorclip' ") 326s + if(disagree(vn, vc)) 326s + stop("Disagreement between vcov.ppm generic and Strauss algorithms") 326s + } 326s + 326s + if(ALWAYS) { # C code 326s + ## Geyer code 326s + xx <- c(0.7375956, 0.6851697, 0.6399788, 0.6188382) 326s + yy <- c(0.5816040, 0.6456319, 0.5150633, 0.6191592) 326s + Y <- ppp(xx, yy, window=square(1)) 326s + modelY <- ppm(Y ~1, Geyer(0.1, 1)) 326s + 326s + b <- vcov(modelY, generic = TRUE, algorithm = "basic") 326s + v <- vcov(modelY, generic = TRUE, algorithm = "vector") 326s + vc <- vcov(modelY, generic = TRUE, algorithm = "vectorclip") 326s + 326s + if(asymmetric(b)) 326s + stop("Non-symmetric matrix produced by vcov.ppm 'basic' algorithm for Geyer model") 326s + if(asymmetric(v)) 326s + stop("Non-symmetric matrix produced by vcov.ppm 'vector' algorithm for Geyer model") 326s + if(asymmetric(vc)) 326s + stop("Non-symmetric matrix produced by vcov.ppm 'vectorclip' algorithm for Geyer model") 326s + 326s + if(disagree(v, b)) 326s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'basic' for Geyer model") 326s + if(disagree(v, vc)) 326s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'vectorclip' for Geyer model") 326s + } 326s + 326s + if(ALWAYS) { # C code 326s + ## tests of 'deltasuffstat' code 326s + ## Handling of offset terms 326s + modelH <- ppm(cells ~x, Hardcore(0.05)) 326s + a <- vcov(modelH, generic=TRUE) ## may fall over 326s + b <- vcov(modelH, generic=FALSE) 326s + if(disagree(a, b)) 326s + stop("Disagreement between vcov.ppm algorithms for Hardcore model") 326s + 326s + ## Correctness of pairwise.family$delta2 326s + modelZ <- ppm(amacrine ~1, MultiStrauss(radii=matrix(0.1, 2, 2))) 326s + b <- vcov(modelZ, generic=FALSE) 326s + g <- vcov(modelZ, generic=TRUE) 326s + if(disagree(b, g)) 326s + stop("Disagreement between vcov.ppm algorithms for MultiStrauss model") 326s + 326s + ## Test that 'deltasuffstat' works for Hybrids 326s + modelHyb <- ppm(japanesepines ~ 1, Hybrid(Strauss(0.05), Strauss(0.1))) 326s + vHyb <- vcov(modelHyb) 326s + } 326s + 326s + if(FULLTEST) { 326s + ## Code blocks for other choices of 'what' 326s + model <- ppm(X ~ 1, Strauss(.05)) 326s + cG <- vcov(model, what="corr") 326s + cP <- vcov(update(model, Poisson()), what="corr") 326s + ## outdated usage 326s + cX <- vcov(model, A1dummy=TRUE) 326s + 326s + ## Model with zero-length coefficient vector 326s + lam <- intensity(X) 326s + f <- function(x,y) { rep(lam, length(x)) } 326s + model0 <- ppm(X ~ offset(log(f)) - 1) 326s + dd <- vcov(model0) 326s + cc <- vcov(model0, what="corr") 326s + 326s + ## Model with NA coefficients 326s + fit <- ppm(X ~ log(f)) 326s + vcov(fit) 326s + fitE <- emend(fit, trace=TRUE) 326s + 326s + ## Other weird stuff 326s + su <- suffloc(ppm(X ~ x)) 326s + } 326s + }) 328s > 330s autopkgtest [20:21:15]: test run-unit-test: -----------------------] 331s run-unit-test PASS 331s autopkgtest [20:21:16]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 331s autopkgtest [20:21:16]: test pkg-r-autopkgtest: preparing testbed 469s autopkgtest [20:23:34]: testbed dpkg architecture: arm64 469s autopkgtest [20:23:34]: testbed apt version: 2.7.12 469s autopkgtest [20:23:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 470s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 470s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 470s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 470s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3704 kB] 471s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 471s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 471s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 471s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 471s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 471s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4012 kB] 471s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 471s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 471s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 472s Fetched 9112 kB in 2s (5070 kB/s) 473s Reading package lists... 476s Reading package lists... 476s Building dependency tree... 476s Reading state information... 477s Calculating upgrade... 477s The following packages will be REMOVED: 477s libglib2.0-0 libssl3 477s The following NEW packages will be installed: 477s libglib2.0-0t64 libssl3t64 xdg-user-dirs 477s The following packages have been kept back: 477s curl 477s The following packages will be upgraded: 477s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 477s ubuntu-minimal ubuntu-standard 477s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 477s Need to get 4613 kB of archives. 477s After this operation, 211 kB of additional disk space will be used. 477s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 478s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 478s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 478s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 478s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 478s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 478s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 478s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 478s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 478s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 479s Fetched 4613 kB in 1s (6468 kB/s) 479s (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.) 479s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 479s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 479s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 479s udisks2 depends on libglib2.0-0 (>= 2.77.0). 479s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 479s python3-gi depends on libglib2.0-0 (>= 2.77.0). 479s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 479s netplan.io depends on libglib2.0-0 (>= 2.70.0). 479s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 479s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 479s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 479s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 479s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 479s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 479s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 479s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 479s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 479s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 479s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 479s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 479s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 479s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 479s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 479s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 479s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 479s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 479s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 479s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 479s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 479s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 479s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 479s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 479s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 479s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 479s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 479s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 479s fwupd depends on libglib2.0-0 (>= 2.79.0). 479s bolt depends on libglib2.0-0 (>= 2.56.0). 479s 479s (Reading database ... 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(1.3.4+ds-1build1) ... 480s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ... 480s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 480s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ... 480s Unpacking ubuntu-minimal (1.536) over (1.535) ... 480s Selecting previously unselected package xdg-user-dirs. 480s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ... 480s Unpacking xdg-user-dirs (0.18-1) ... 480s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ... 480s Unpacking ubuntu-standard (1.536) over (1.535) ... 480s Setting up ubuntu-minimal (1.536) ... 480s Setting up xdg-user-dirs (0.18-1) ... 480s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 480s Setting up libtirpc-common (1.3.4+ds-1.1) ... 480s Setting up ubuntu-standard (1.536) ... 480s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 480s No schema files found: doing nothing. 480s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 480s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 480s Setting up openssl (3.0.13-0ubuntu1) ... 480s Setting up readline-common (8.2-3.1) ... 480s Processing triggers for man-db (2.12.0-3) ... 481s Processing triggers for install-info (7.1-3) ... 481s Processing triggers for libc-bin (2.39-0ubuntu2) ... 482s Reading package lists... 482s Building dependency tree... 482s Reading state information... 484s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 485s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 485s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 485s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 485s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 487s Reading package lists... 487s Reading package lists... 488s Building dependency tree... 488s Reading state information... 489s Calculating upgrade... 490s The following packages have been kept back: 490s curl 490s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 490s Reading package lists... 490s Building dependency tree... 490s Reading state information... 491s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 497s Reading package lists... 497s Building dependency tree... 497s Reading state information... 498s Starting pkgProblemResolver with broken count: 0 498s Starting 2 pkgProblemResolver with broken count: 0 498s Done 499s The following additional packages will be installed: 499s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 499s curl dctrl-tools fontconfig fontconfig-config fonts-dejavu-core 499s fonts-dejavu-mono fonts-mathjax g++ g++-13 g++-13-aarch64-linux-gnu 499s g++-aarch64-linux-gnu gcc gcc-13 gcc-13-aarch64-linux-gnu 499s gcc-aarch64-linux-gnu gfortran gfortran-13 gfortran-13-aarch64-linux-gnu 499s gfortran-aarch64-linux-gnu icu-devtools libasan8 libatomic1 libblas-dev 499s libblas3 libbz2-dev libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev 499s libcurl4t64 libdatrie1 libdeflate0 libfontconfig1 libgcc-13-dev 499s libgfortran-13-dev libgfortran5 libgomp1 libgraphite2-3 libgsl27 499s libgslcblas0 libharfbuzz0b libhwasan0 libice6 libicu-dev libisl23 libitm1 499s libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev 499s libjs-mathjax liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 499s libncurses-dev libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 499s libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0 499s libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev 499s libpng16-16t64 libpsl5t64 libreadline-dev libreadline8t64 libsharpyuv0 499s libsm6 libstdc++-13-dev libtcl8.6 libthai-data libthai0 libtiff6 499s libtirpc-dev libtirpc3t64 libtk8.6 libtsan2 libubsan1 libwebp7 499s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 499s linux-libc-dev littler pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin 499s r-base-core r-base-dev r-cran-abind r-cran-codetools r-cran-deldir 499s r-cran-foreach r-cran-glmnet r-cran-goftest r-cran-gsl r-cran-iterators 499s r-cran-lattice r-cran-littler r-cran-matrix r-cran-mgcv r-cran-nleqslv 499s r-cran-nlme r-cran-pkgkitten r-cran-polyclip r-cran-rcpp r-cran-rcppeigen 499s r-cran-rpart r-cran-shape r-cran-sm r-cran-spatial r-cran-spatstat 499s r-cran-spatstat.data r-cran-spatstat.explore r-cran-spatstat.geom 499s r-cran-spatstat.linnet r-cran-spatstat.model r-cran-spatstat.random 499s r-cran-spatstat.sparse r-cran-spatstat.utils r-cran-survival r-cran-tensor 499s rpcsvc-proto unzip x11-common xdg-utils zip zlib1g-dev 499s Suggested packages: 499s cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib 499s manpages-dev autoconf automake libtool flex bison gdb gcc-doc 499s gdb-aarch64-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev 499s liblapack-doc glibc-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info 499s | gsl-ref-html icu-doc fonts-mathjax-extras fonts-stix libjs-mathjax-doc 499s liblzma-doc ncurses-doc readline-doc libstdc++-13-doc tcl8.6 tk8.6 elpa-ess 499s r-doc-info | r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base 499s texlive-plain-generic texlive-fonts-recommended texlive-fonts-extra 499s texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo 499s r-cran-knitr r-cran-testthat r-cran-xfun r-cran-rmarkdown r-cran-getopt 499s r-cran-inline 499s Recommended packages: 499s bzip2-doc manpages manpages-dev libc-devtools libpng-tools r-recommended 499s r-doc-html r-cran-locfit libfile-mimeinfo-perl libnet-dbus-perl 499s libx11-protocol-perl x11-utils x11-xserver-utils 500s The following packages will be REMOVED: 500s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 500s The following NEW packages will be installed: 500s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu 500s cpp-aarch64-linux-gnu dctrl-tools fontconfig fontconfig-config 500s fonts-dejavu-core fonts-dejavu-mono fonts-mathjax g++ g++-13 500s g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 500s gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-13 500s gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 500s libasan8 libatomic1 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev 500s libcairo2 libcc1-0 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 500s libfontconfig1 libgcc-13-dev libgfortran-13-dev libgfortran5 libgomp1 500s libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libhwasan0 libice6 500s libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 500s libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-mathjax liblapack-dev 500s liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 libncurses-dev libnsl-dev 500s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 500s libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 500s libpixman-1-0 libpkgconf3 libpng-dev libpng16-16t64 libpsl5t64 500s libreadline-dev libreadline8t64 libsharpyuv0 libsm6 libstdc++-13-dev 500s libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-dev libtirpc3t64 libtk8.6 500s libtsan2 libubsan1 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 500s libxss1 libxt6t64 linux-libc-dev littler pkg-config pkg-r-autopkgtest 500s pkgconf pkgconf-bin r-base-core r-base-dev r-cran-abind r-cran-codetools 500s r-cran-deldir r-cran-foreach r-cran-glmnet r-cran-goftest r-cran-gsl 500s r-cran-iterators r-cran-lattice r-cran-littler r-cran-matrix r-cran-mgcv 500s r-cran-nleqslv r-cran-nlme r-cran-pkgkitten r-cran-polyclip r-cran-rcpp 500s r-cran-rcppeigen r-cran-rpart r-cran-shape r-cran-sm r-cran-spatial 500s r-cran-spatstat r-cran-spatstat.data r-cran-spatstat.explore 500s r-cran-spatstat.geom r-cran-spatstat.linnet r-cran-spatstat.model 500s r-cran-spatstat.random r-cran-spatstat.sparse r-cran-spatstat.utils 500s r-cran-survival r-cran-tensor rpcsvc-proto unzip x11-common xdg-utils zip 500s zlib1g-dev 500s The following packages will be upgraded: 500s curl 500s 1 upgraded, 149 newly installed, 5 to remove and 0 not upgraded. 500s Need to get 187 MB/187 MB of archives. 500s After this operation, 543 MB of additional disk space will be used. 500s Get:1 /tmp/autopkgtest.Ey2R3T/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [764 B] 500s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 500s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 500s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 500s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 500s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 500s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 500s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 500s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 501s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 501s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1 [201 kB] 501s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 501s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 501s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 501s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 501s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 501s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 501s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 501s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 501s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 501s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 501s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 501s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 501s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 501s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 501s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 501s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 501s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 501s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 501s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 501s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 502s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 502s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 502s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 502s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 502s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 502s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 502s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 502s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 502s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 502s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 dctrl-tools arm64 2.24-3build2 [65.2 kB] 502s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 502s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 502s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 502s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 502s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 502s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 502s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 502s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-17ubuntu2 [478 kB] 502s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.8 MB] 503s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-17ubuntu2 [10.3 kB] 503s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1022 B] 503s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B] 503s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB] 503s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 503s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB] 503s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 503s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 503s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 503s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 503s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 503s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 503s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 503s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 503s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 503s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu1 [72.5 kB] 503s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu1 [912 kB] 503s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 503s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 503s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 503s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB] 503s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 503s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu1 [304 kB] 503s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 503s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 503s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 503s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 503s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB] 503s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 503s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses-dev arm64 6.4+20240113-1ubuntu1 [385 kB] 503s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 503s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 503s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 503s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 503s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 503s Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 503s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 503s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu1 [195 kB] 503s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu1 [183 kB] 503s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-posix3 arm64 10.42-4ubuntu1 [6654 B] 503s Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-dev arm64 10.42-4ubuntu1 [679 kB] 503s Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB] 503s Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 503s Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng-dev arm64 1.6.43-3 [267 kB] 503s Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline-dev arm64 8.2-3.1 [177 kB] 503s Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 503s Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 503s Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 503s Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 503s Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 503s Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 503s Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 504s Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 504s Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 504s Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 504s Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 504s Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 504s Get:108 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 504s Get:109 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 505s Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 505s Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 505s Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB] 505s Get:113 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] 505s Get:114 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B] 505s Get:115 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB] 505s Get:116 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-dev all 4.3.3-2build1 [4334 B] 505s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 505s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-abind all 1.4-5-2 [63.6 kB] 505s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-codetools all 0.2-19-1 [90.5 kB] 505s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-deldir arm64 2.0-4-1 [270 kB] 505s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-iterators all 1.0.14-1 [336 kB] 505s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-foreach all 1.5.2-1 [124 kB] 505s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 505s Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 506s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-shape all 1.4.6-1 [770 kB] 506s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survival arm64 3.5-8-1 [6116 kB] 506s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 506s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 506s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcppeigen arm64 0.3.3.9.4-1 [1180 kB] 506s Get:130 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 506s Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glmnet arm64 4.1-8-1 [1898 kB] 506s Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-goftest arm64 1.2-3-1 [60.2 kB] 506s Get:133 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gsl arm64 2.1-8-1 [489 kB] 506s Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 506s Get:135 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 506s Get:136 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nleqslv arm64 3.3.5-1 [101 kB] 506s Get:137 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-polyclip arm64 1.10-6-1 [110 kB] 506s Get:138 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rpart arm64 4.1.23-1 [660 kB] 506s Get:139 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sm arm64 2.2-6.0-1 [787 kB] 506s Get:140 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatial arm64 7.3-17-1 [130 kB] 506s Get:141 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.utils arm64 3.0-4-1 [360 kB] 506s Get:142 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.data all 3.0-4-1 [4090 kB] 506s Get:143 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.geom arm64 3.2-8-1 [3805 kB] 507s Get:144 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.random arm64 3.2-2-1 [1127 kB] 507s Get:145 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tensor all 1.5-4 [15.7 kB] 507s Get:146 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.sparse arm64 3.0-3-1 [214 kB] 507s Get:147 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.explore arm64 3.2-5-1 [3264 kB] 507s Get:148 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.model arm64 3.2-8-1 [3289 kB] 507s Get:149 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.linnet arm64 3.1-3-1 [1404 kB] 507s Get:150 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat arm64 3.0-7-1 [3817 kB] 509s Preconfiguring packages ... 510s Fetched 187 MB in 7s (25.0 MB/s) 510s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 510s wget depends on libpsl5 (>= 0.16.0). 510s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 510s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 510s 510s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74770 files and directories currently installed.) 511s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 511s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 513s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 513s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 513s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 513s 513s (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.) 513s Removing libpng16-16:arm64 (1.6.43-1) ... 513s Selecting previously unselected package libpng16-16t64:arm64. 513s (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.) 513s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 513s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 513s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 513s parted depends on libreadline8 (>= 6.0). 513s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 513s gpgsm depends on libreadline8 (>= 6.0). 513s gpgconf depends on libreadline8 (>= 6.0). 513s gpg depends on libreadline8 (>= 6.0). 513s gawk depends on libreadline8 (>= 6.0). 513s fdisk depends on libreadline8 (>= 6.0). 513s 513s (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.) 513s Removing libreadline8:arm64 (8.2-3) ... 513s Selecting previously unselected package libreadline8t64:arm64. 513s (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.) 513s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 513s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 513s 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' 513s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 513s 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' 513s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 513s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 513s lsof depends on libtirpc3 (>= 1.0.2). 513s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 513s libnss-nisplus:arm64 depends on libtirpc3 (>= 1.0.2). 513s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 513s iproute2 depends on libtirpc3 (>= 1.0.2). 513s 513s (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.) 513s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 513s Selecting previously unselected package libtirpc3t64:arm64. 513s (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.) 513s Preparing to unpack .../000-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 513s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 513s 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' 513s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 513s Selecting previously unselected package libc-dev-bin. 513s Preparing to unpack .../001-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 513s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 513s Selecting previously unselected package linux-libc-dev:arm64. 513s Preparing to unpack .../002-linux-libc-dev_6.8.0-11.11_arm64.deb ... 513s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 514s Selecting previously unselected package libcrypt-dev:arm64. 514s Preparing to unpack .../003-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 514s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 514s Selecting previously unselected package libtirpc-dev:arm64. 514s Preparing to unpack .../004-libtirpc-dev_1.3.4+ds-1.1_arm64.deb ... 514s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 514s Selecting previously unselected package libnsl-dev:arm64. 514s Preparing to unpack .../005-libnsl-dev_1.3.0-3_arm64.deb ... 514s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 514s Selecting previously unselected package rpcsvc-proto. 514s Preparing to unpack .../006-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 514s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 514s Selecting previously unselected package libc6-dev:arm64. 514s Preparing to unpack .../007-libc6-dev_2.39-0ubuntu2_arm64.deb ... 514s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 514s Selecting previously unselected package libisl23:arm64. 514s Preparing to unpack .../008-libisl23_0.26-3_arm64.deb ... 514s Unpacking libisl23:arm64 (0.26-3) ... 514s Selecting previously unselected package libmpc3:arm64. 514s Preparing to unpack .../009-libmpc3_1.3.1-1_arm64.deb ... 514s Unpacking libmpc3:arm64 (1.3.1-1) ... 514s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 514s Preparing to unpack .../010-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 514s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 514s Selecting previously unselected package cpp-13. 514s Preparing to unpack .../011-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 514s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 514s Selecting previously unselected package cpp-aarch64-linux-gnu. 514s Preparing to unpack .../012-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 514s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 514s Selecting previously unselected package cpp. 514s Preparing to unpack .../013-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 514s Unpacking cpp (4:13.2.0-7ubuntu1) ... 514s Selecting previously unselected package libcc1-0:arm64. 514s Preparing to unpack .../014-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 514s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 514s Selecting previously unselected package libgomp1:arm64. 514s Preparing to unpack .../015-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 514s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 514s Selecting previously unselected package libitm1:arm64. 514s Preparing to unpack .../016-libitm1_14-20240303-1ubuntu1_arm64.deb ... 514s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 514s Selecting previously unselected package libatomic1:arm64. 514s Preparing to unpack .../017-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 514s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 514s Selecting previously unselected package libasan8:arm64. 514s Preparing to unpack .../018-libasan8_14-20240303-1ubuntu1_arm64.deb ... 514s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 515s Selecting previously unselected package liblsan0:arm64. 515s Preparing to unpack .../019-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 515s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 515s Selecting previously unselected package libtsan2:arm64. 515s Preparing to unpack .../020-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 515s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 515s Selecting previously unselected package libubsan1:arm64. 515s Preparing to unpack .../021-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 515s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 515s Selecting previously unselected package libhwasan0:arm64. 515s Preparing to unpack .../022-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 515s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 515s Selecting previously unselected package libgcc-13-dev:arm64. 515s Preparing to unpack .../023-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 515s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 515s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 515s Preparing to unpack .../024-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 515s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 515s Selecting previously unselected package gcc-13. 515s Preparing to unpack .../025-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 515s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 515s Selecting previously unselected package gcc-aarch64-linux-gnu. 515s Preparing to unpack .../026-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 515s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 515s Selecting previously unselected package gcc. 515s Preparing to unpack .../027-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 515s Unpacking gcc (4:13.2.0-7ubuntu1) ... 515s Selecting previously unselected package libstdc++-13-dev:arm64. 515s Preparing to unpack .../028-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 515s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 516s Selecting previously unselected package g++-13-aarch64-linux-gnu. 516s Preparing to unpack .../029-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 516s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 516s Selecting previously unselected package g++-13. 516s Preparing to unpack .../030-g++-13_13.2.0-17ubuntu2_arm64.deb ... 516s Unpacking g++-13 (13.2.0-17ubuntu2) ... 516s Selecting previously unselected package g++-aarch64-linux-gnu. 516s Preparing to unpack .../031-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 516s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 516s Selecting previously unselected package g++. 516s Preparing to unpack .../032-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 516s Unpacking g++ (4:13.2.0-7ubuntu1) ... 516s Selecting previously unselected package build-essential. 516s Preparing to unpack .../033-build-essential_12.10ubuntu1_arm64.deb ... 516s Unpacking build-essential (12.10ubuntu1) ... 516s Selecting previously unselected package dctrl-tools. 516s Preparing to unpack .../034-dctrl-tools_2.24-3build2_arm64.deb ... 516s Unpacking dctrl-tools (2.24-3build2) ... 516s Selecting previously unselected package fonts-dejavu-mono. 516s Preparing to unpack .../035-fonts-dejavu-mono_2.37-8_all.deb ... 516s Unpacking fonts-dejavu-mono (2.37-8) ... 516s Selecting previously unselected package fonts-dejavu-core. 516s Preparing to unpack .../036-fonts-dejavu-core_2.37-8_all.deb ... 516s Unpacking fonts-dejavu-core (2.37-8) ... 516s Selecting previously unselected package fontconfig-config. 517s Preparing to unpack .../037-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 517s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 517s Selecting previously unselected package libfontconfig1:arm64. 517s Preparing to unpack .../038-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 517s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 517s Selecting previously unselected package fontconfig. 517s Preparing to unpack .../039-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 517s Unpacking fontconfig (2.15.0-1ubuntu1) ... 518s Selecting previously unselected package fonts-mathjax. 518s Preparing to unpack .../040-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 518s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 518s Selecting previously unselected package libgfortran5:arm64. 518s Preparing to unpack .../041-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 518s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 518s Selecting previously unselected package libgfortran-13-dev:arm64. 518s Preparing to unpack .../042-libgfortran-13-dev_13.2.0-17ubuntu2_arm64.deb ... 518s Unpacking libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 518s Selecting previously unselected package gfortran-13-aarch64-linux-gnu. 518s Preparing to unpack .../043-gfortran-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 518s Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 518s Selecting previously unselected package gfortran-13. 518s Preparing to unpack .../044-gfortran-13_13.2.0-17ubuntu2_arm64.deb ... 518s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 518s Selecting previously unselected package gfortran-aarch64-linux-gnu. 518s Preparing to unpack .../045-gfortran-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 518s Unpacking gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 518s Selecting previously unselected package gfortran. 518s Preparing to unpack .../046-gfortran_4%3a13.2.0-7ubuntu1_arm64.deb ... 518s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 518s Selecting previously unselected package icu-devtools. 518s Preparing to unpack .../047-icu-devtools_74.2-1ubuntu1_arm64.deb ... 518s Unpacking icu-devtools (74.2-1ubuntu1) ... 518s Selecting previously unselected package libblas3:arm64. 519s Preparing to unpack .../048-libblas3_3.12.0-3_arm64.deb ... 519s Unpacking libblas3:arm64 (3.12.0-3) ... 519s Selecting previously unselected package libblas-dev:arm64. 519s Preparing to unpack .../049-libblas-dev_3.12.0-3_arm64.deb ... 519s Unpacking libblas-dev:arm64 (3.12.0-3) ... 519s Selecting previously unselected package libbz2-dev:arm64. 519s Preparing to unpack .../050-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 519s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 519s Selecting previously unselected package libpixman-1-0:arm64. 519s Preparing to unpack .../051-libpixman-1-0_0.42.2-1_arm64.deb ... 519s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 519s Selecting previously unselected package libxcb-render0:arm64. 519s Preparing to unpack .../052-libxcb-render0_1.15-1_arm64.deb ... 519s Unpacking libxcb-render0:arm64 (1.15-1) ... 519s Selecting previously unselected package libxcb-shm0:arm64. 519s Preparing to unpack .../053-libxcb-shm0_1.15-1_arm64.deb ... 519s Unpacking libxcb-shm0:arm64 (1.15-1) ... 519s Selecting previously unselected package libxrender1:arm64. 519s Preparing to unpack .../054-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 519s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 519s Selecting previously unselected package libcairo2:arm64. 519s Preparing to unpack .../055-libcairo2_1.18.0-1_arm64.deb ... 519s Unpacking libcairo2:arm64 (1.18.0-1) ... 519s Selecting previously unselected package libdatrie1:arm64. 519s Preparing to unpack .../056-libdatrie1_0.2.13-3_arm64.deb ... 519s Unpacking libdatrie1:arm64 (0.2.13-3) ... 519s Selecting previously unselected package libdeflate0:arm64. 519s Preparing to unpack .../057-libdeflate0_1.19-1_arm64.deb ... 519s Unpacking libdeflate0:arm64 (1.19-1) ... 519s Selecting previously unselected package libgraphite2-3:arm64. 519s Preparing to unpack .../058-libgraphite2-3_1.3.14-2_arm64.deb ... 519s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 519s Selecting previously unselected package libgslcblas0:arm64. 519s Preparing to unpack .../059-libgslcblas0_2.7.1+dfsg-6ubuntu1_arm64.deb ... 519s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 519s Selecting previously unselected package libgsl27:arm64. 519s Preparing to unpack .../060-libgsl27_2.7.1+dfsg-6ubuntu1_arm64.deb ... 519s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 519s Selecting previously unselected package libharfbuzz0b:arm64. 519s Preparing to unpack .../061-libharfbuzz0b_8.3.0-2_arm64.deb ... 519s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 519s Selecting previously unselected package x11-common. 519s Preparing to unpack .../062-x11-common_1%3a7.7+23ubuntu2_all.deb ... 519s Unpacking x11-common (1:7.7+23ubuntu2) ... 519s Selecting previously unselected package libice6:arm64. 519s Preparing to unpack .../063-libice6_2%3a1.0.10-1build2_arm64.deb ... 519s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 519s Selecting previously unselected package libicu-dev:arm64. 519s Preparing to unpack .../064-libicu-dev_74.2-1ubuntu1_arm64.deb ... 519s Unpacking libicu-dev:arm64 (74.2-1ubuntu1) ... 519s Selecting previously unselected package libjpeg-turbo8:arm64. 520s Preparing to unpack .../065-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 520s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 520s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 520s Preparing to unpack .../066-libjpeg-turbo8-dev_2.1.5-2ubuntu1_arm64.deb ... 520s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 520s Selecting previously unselected package libjpeg8:arm64. 520s Preparing to unpack .../067-libjpeg8_8c-2ubuntu11_arm64.deb ... 520s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 520s Selecting previously unselected package libjpeg8-dev:arm64. 520s Preparing to unpack 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Unpacking libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 520s Selecting previously unselected package libthai-data. 520s Preparing to unpack .../074-libthai-data_0.1.29-2_all.deb ... 520s Unpacking libthai-data (0.1.29-2) ... 520s Selecting previously unselected package libthai0:arm64. 520s Preparing to unpack .../075-libthai0_0.1.29-2_arm64.deb ... 520s Unpacking libthai0:arm64 (0.1.29-2) ... 520s Selecting previously unselected package libpango-1.0-0:arm64. 520s Preparing to unpack .../076-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 520s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 520s Selecting previously unselected package libpangoft2-1.0-0:arm64. 520s Preparing to unpack .../077-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 520s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 520s Selecting previously unselected package libpangocairo-1.0-0:arm64. 520s Preparing to unpack .../078-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 520s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 520s Selecting previously unselected package libpaper1:arm64. 520s Preparing to unpack .../079-libpaper1_1.1.29_arm64.deb ... 520s Unpacking libpaper1:arm64 (1.1.29) ... 520s Selecting previously unselected package libpaper-utils. 520s Preparing to unpack .../080-libpaper-utils_1.1.29_arm64.deb ... 520s Unpacking libpaper-utils (1.1.29) ... 520s Selecting previously unselected package libpcre2-16-0:arm64. 520s Preparing to unpack .../081-libpcre2-16-0_10.42-4ubuntu1_arm64.deb ... 520s Unpacking libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 520s Selecting previously unselected package libpcre2-32-0:arm64. 520s Preparing to unpack .../082-libpcre2-32-0_10.42-4ubuntu1_arm64.deb ... 520s Unpacking libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 520s Selecting previously unselected package libpcre2-posix3:arm64. 521s Preparing to unpack .../083-libpcre2-posix3_10.42-4ubuntu1_arm64.deb ... 521s Unpacking libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 521s Selecting previously unselected package libpcre2-dev:arm64. 521s Preparing to unpack .../084-libpcre2-dev_10.42-4ubuntu1_arm64.deb ... 521s Unpacking libpcre2-dev:arm64 (10.42-4ubuntu1) ... 521s Selecting previously unselected package libpkgconf3:arm64. 521s Preparing to unpack .../085-libpkgconf3_1.8.1-2_arm64.deb ... 521s Unpacking libpkgconf3:arm64 (1.8.1-2) ... 521s Selecting previously unselected package zlib1g-dev:arm64. 521s Preparing to unpack .../086-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 521s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 521s Selecting previously unselected package libpng-dev:arm64. 521s Preparing to unpack .../087-libpng-dev_1.6.43-3_arm64.deb ... 521s Unpacking libpng-dev:arm64 (1.6.43-3) ... 521s Selecting previously unselected package libreadline-dev:arm64. 521s Preparing to unpack .../088-libreadline-dev_8.2-3.1_arm64.deb ... 521s Unpacking libreadline-dev:arm64 (8.2-3.1) ... 521s Selecting previously unselected package libsharpyuv0:arm64. 521s Preparing to unpack .../089-libsharpyuv0_1.3.2-0.4_arm64.deb ... 521s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 521s Selecting previously unselected package libsm6:arm64. 521s Preparing to unpack .../090-libsm6_2%3a1.2.3-1build2_arm64.deb ... 521s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 521s Selecting previously unselected package libtcl8.6:arm64. 521s Preparing to unpack .../091-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 521s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 521s Selecting previously unselected package libjbig0:arm64. 521s Preparing to unpack .../092-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 521s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 521s Selecting previously unselected package libwebp7:arm64. 521s Preparing to unpack .../093-libwebp7_1.3.2-0.4_arm64.deb ... 521s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 521s Selecting previously unselected package libtiff6:arm64. 521s Preparing to unpack .../094-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 521s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 521s Selecting previously unselected package libxft2:arm64. 521s Preparing to unpack .../095-libxft2_2.3.6-1_arm64.deb ... 521s Unpacking libxft2:arm64 (2.3.6-1) ... 521s Selecting previously unselected package libxss1:arm64. 521s Preparing to unpack .../096-libxss1_1%3a1.2.3-1build2_arm64.deb ... 521s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 521s Selecting previously unselected package libtk8.6:arm64. 521s Preparing to unpack .../097-libtk8.6_8.6.13-2_arm64.deb ... 521s Unpacking libtk8.6:arm64 (8.6.13-2) ... 521s Selecting previously unselected package libxt6t64:arm64. 521s Preparing to unpack .../098-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... 521s Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... 521s Selecting previously unselected package zip. 521s Preparing to unpack .../099-zip_3.0-13_arm64.deb ... 521s Unpacking zip (3.0-13) ... 521s Selecting previously unselected package unzip. 521s Preparing to unpack .../100-unzip_6.0-28ubuntu3_arm64.deb ... 521s Unpacking unzip (6.0-28ubuntu3) ... 521s Selecting previously unselected package xdg-utils. 521s Preparing to unpack .../101-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 521s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 521s Selecting previously unselected package r-base-core. 521s Preparing to unpack .../102-r-base-core_4.3.3-2build1_arm64.deb ... 521s Unpacking r-base-core (4.3.3-2build1) ... 522s Selecting previously unselected package r-cran-littler. 523s Preparing to unpack .../103-r-cran-littler_0.3.19-1_arm64.deb ... 523s Unpacking r-cran-littler (0.3.19-1) ... 523s Selecting previously unselected package littler. 523s Preparing to unpack .../104-littler_0.3.19-1_all.deb ... 523s Unpacking littler (0.3.19-1) ... 523s Selecting previously unselected package pkgconf-bin. 523s Preparing to unpack .../105-pkgconf-bin_1.8.1-2_arm64.deb ... 523s Unpacking pkgconf-bin (1.8.1-2) ... 523s Selecting previously unselected package pkgconf:arm64. 523s Preparing to unpack .../106-pkgconf_1.8.1-2_arm64.deb ... 523s Unpacking pkgconf:arm64 (1.8.1-2) ... 523s Selecting previously unselected package pkg-config:arm64. 523s Preparing to unpack .../107-pkg-config_1.8.1-2_arm64.deb ... 523s Unpacking pkg-config:arm64 (1.8.1-2) ... 523s Selecting previously unselected package liblzma-dev:arm64. 523s Preparing to unpack .../108-liblzma-dev_5.4.5-0.3_arm64.deb ... 523s Unpacking liblzma-dev:arm64 (5.4.5-0.3) ... 523s Selecting previously unselected package r-base-dev. 523s Preparing to unpack .../109-r-base-dev_4.3.3-2build1_all.deb ... 523s Unpacking r-base-dev (4.3.3-2build1) ... 523s Selecting previously unselected package pkg-r-autopkgtest. 523s Preparing to unpack .../110-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 523s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 523s Selecting previously unselected package r-cran-abind. 523s Preparing to unpack .../111-r-cran-abind_1.4-5-2_all.deb ... 523s Unpacking r-cran-abind (1.4-5-2) ... 523s Selecting previously unselected package r-cran-codetools. 523s Preparing to unpack .../112-r-cran-codetools_0.2-19-1_all.deb ... 523s Unpacking r-cran-codetools (0.2-19-1) ... 523s Selecting previously unselected package r-cran-deldir. 523s Preparing to unpack .../113-r-cran-deldir_2.0-4-1_arm64.deb ... 523s Unpacking r-cran-deldir (2.0-4-1) ... 523s Selecting previously unselected package r-cran-iterators. 523s Preparing to unpack .../114-r-cran-iterators_1.0.14-1_all.deb ... 523s Unpacking r-cran-iterators (1.0.14-1) ... 523s Selecting previously unselected package r-cran-foreach. 523s Preparing to unpack .../115-r-cran-foreach_1.5.2-1_all.deb ... 523s Unpacking r-cran-foreach (1.5.2-1) ... 523s Selecting previously unselected package r-cran-lattice. 523s Preparing to unpack .../116-r-cran-lattice_0.22-5-1_arm64.deb ... 523s Unpacking r-cran-lattice (0.22-5-1) ... 523s Selecting previously unselected package r-cran-matrix. 523s Preparing to unpack .../117-r-cran-matrix_1.6-5-1_arm64.deb ... 523s Unpacking r-cran-matrix (1.6-5-1) ... 523s Selecting previously unselected package r-cran-shape. 523s Preparing to unpack .../118-r-cran-shape_1.4.6-1_all.deb ... 523s Unpacking r-cran-shape (1.4.6-1) ... 523s Selecting previously unselected package r-cran-survival. 523s Preparing to unpack .../119-r-cran-survival_3.5-8-1_arm64.deb ... 523s Unpacking r-cran-survival (3.5-8-1) ... 523s Selecting previously unselected package r-cran-pkgkitten. 523s Preparing to unpack .../120-r-cran-pkgkitten_0.2.3-1_all.deb ... 523s Unpacking r-cran-pkgkitten (0.2.3-1) ... 523s Selecting previously unselected package r-cran-rcpp. 523s Preparing to unpack .../121-r-cran-rcpp_1.0.12-1_arm64.deb ... 523s Unpacking r-cran-rcpp (1.0.12-1) ... 523s Selecting previously unselected package r-cran-rcppeigen. 523s Preparing to unpack .../122-r-cran-rcppeigen_0.3.3.9.4-1_arm64.deb ... 523s Unpacking r-cran-rcppeigen (0.3.3.9.4-1) ... 523s Selecting previously unselected package libjs-mathjax. 523s Preparing to unpack .../123-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 523s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 524s Selecting previously unselected package r-cran-glmnet. 525s Preparing to unpack .../124-r-cran-glmnet_4.1-8-1_arm64.deb ... 525s Unpacking r-cran-glmnet (4.1-8-1) ... 525s Selecting previously unselected package r-cran-goftest. 525s Preparing to unpack .../125-r-cran-goftest_1.2-3-1_arm64.deb ... 525s Unpacking r-cran-goftest (1.2-3-1) ... 525s Selecting previously unselected package r-cran-gsl. 526s Preparing to unpack .../126-r-cran-gsl_2.1-8-1_arm64.deb ... 526s Unpacking r-cran-gsl (2.1-8-1) ... 527s Selecting previously unselected package r-cran-nlme. 527s Preparing to unpack .../127-r-cran-nlme_3.1.164-1_arm64.deb ... 527s Unpacking r-cran-nlme (3.1.164-1) ... 527s Selecting previously unselected package r-cran-mgcv. 527s Preparing to unpack .../128-r-cran-mgcv_1.9-1-1_arm64.deb ... 527s Unpacking r-cran-mgcv (1.9-1-1) ... 527s Selecting previously unselected package r-cran-nleqslv. 527s Preparing to unpack .../129-r-cran-nleqslv_3.3.5-1_arm64.deb ... 527s Unpacking r-cran-nleqslv (3.3.5-1) ... 527s Selecting previously unselected package r-cran-polyclip. 527s Preparing to unpack .../130-r-cran-polyclip_1.10-6-1_arm64.deb ... 527s Unpacking r-cran-polyclip (1.10-6-1) ... 528s Selecting previously unselected package r-cran-rpart. 528s Preparing to unpack .../131-r-cran-rpart_4.1.23-1_arm64.deb ... 528s Unpacking r-cran-rpart (4.1.23-1) ... 528s Selecting previously unselected package r-cran-sm. 528s Preparing to unpack .../132-r-cran-sm_2.2-6.0-1_arm64.deb ... 528s Unpacking r-cran-sm (2.2-6.0-1) ... 528s Selecting previously unselected package r-cran-spatial. 528s Preparing to unpack .../133-r-cran-spatial_7.3-17-1_arm64.deb ... 528s Unpacking r-cran-spatial (7.3-17-1) ... 528s Selecting previously unselected package r-cran-spatstat.utils. 528s Preparing to unpack .../134-r-cran-spatstat.utils_3.0-4-1_arm64.deb ... 528s Unpacking 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previously unselected package r-cran-spatstat.explore. 530s Preparing to unpack .../140-r-cran-spatstat.explore_3.2-5-1_arm64.deb ... 530s Unpacking r-cran-spatstat.explore (3.2-5-1) ... 530s Selecting previously unselected package r-cran-spatstat.model. 530s Preparing to unpack .../141-r-cran-spatstat.model_3.2-8-1_arm64.deb ... 530s Unpacking r-cran-spatstat.model (3.2-8-1) ... 530s Selecting previously unselected package r-cran-spatstat.linnet. 530s Preparing to unpack .../142-r-cran-spatstat.linnet_3.1-3-1_arm64.deb ... 530s Unpacking r-cran-spatstat.linnet (3.1-3-1) ... 530s Selecting previously unselected package r-cran-spatstat. 530s Preparing to unpack .../143-r-cran-spatstat_3.0-7-1_arm64.deb ... 530s Unpacking r-cran-spatstat (3.0-7-1) ... 530s Selecting previously unselected package autopkgtest-satdep. 530s Preparing to unpack .../144-2-autopkgtest-satdep.deb ... 530s Unpacking autopkgtest-satdep (0) ... 530s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 530s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 530s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 530s Setting up libpaper1:arm64 (1.1.29) ... 531s 531s Creating config file /etc/papersize with new version 531s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 531s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 531s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 531s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 531s Setting up libdatrie1:arm64 (0.2.13-3) ... 531s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 531s Setting up libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 531s Setting up libxcb-render0:arm64 (1.15-1) ... 531s Setting up unzip (6.0-28ubuntu3) ... 531s Setting up x11-common (1:7.7+23ubuntu2) ... 532s Setting up libpsl5t64:arm64 (0.21.2-1.1) ... 532s Setting up libdeflate0:arm64 (1.19-1) ... 532s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 532s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 532s Setting up libxcb-shm0:arm64 (1.15-1) ... 532s Setting up libpaper-utils (1.1.29) ... 532s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 532s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 532s Setting up libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 532s Setting up zip (3.0-13) ... 532s Setting up libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 532s Setting up libblas3:arm64 (3.12.0-3) ... 532s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 532s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 532s Setting up libpkgconf3:arm64 (1.8.1-2) ... 532s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 532s Setting up fonts-dejavu-mono (2.37-8) ... 532s Setting up libpng16-16t64:arm64 (1.6.43-3) ... 532s Setting up libmpc3:arm64 (1.3.1-1) ... 532s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 532s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 532s Setting up icu-devtools (74.2-1ubuntu1) ... 532s Setting up fonts-dejavu-core (2.37-8) ... 532s Setting up pkgconf-bin (1.8.1-2) ... 532s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 532s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 532s Setting up libwebp7:arm64 (1.3.2-0.4) ... 532s Setting up libreadline8t64:arm64 (8.2-3.1) ... 532s Setting up liblzma-dev:arm64 (5.4.5-0.3) ... 532s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 532s Setting up libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 532s Setting up libnsl-dev:arm64 (1.3.0-3) ... 532s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 532s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 532s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 532s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 532s Setting up libthai-data (0.1.29-2) ... 532s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 532s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 532s Setting up libisl23:arm64 (0.26-3) ... 532s Setting up libc-dev-bin (2.39-0ubuntu2) ... 532s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 532s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 532s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 532s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 532s Setting up libblas-dev:arm64 (3.12.0-3) ... 532s 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 532s Setting up dctrl-tools (2.24-3build2) ... 532s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ... 532s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 532s Setting up libice6:arm64 (2:1.0.10-1build2) ... 532s Setting up liblapack3:arm64 (3.12.0-3) ... 532s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 532s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 532s Setting up libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 532s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 532s Setting up pkgconf:arm64 (1.8.1-2) ... 532s Setting up libthai0:arm64 (0.1.29-2) ... 532s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 532s Setting up liblapack-dev:arm64 (3.12.0-3) ... 532s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode 532s Setting up pkg-config:arm64 (1.8.1-2) ... 532s Setting up libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 532s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 532s Setting up libc6-dev:arm64 (2.39-0ubuntu2) ... 532s Setting up curl (8.5.0-2ubuntu7) ... 532s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 532s Setting up libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 532s Setting up libsm6:arm64 (2:1.2.3-1build2) ... 532s Setting up libicu-dev:arm64 (74.2-1ubuntu1) ... 532s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 532s Setting up libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 532s Setting up fontconfig (2.15.0-1ubuntu1) ... 534s Regenerating fonts cache... done. 534s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 534s Setting up libxft2:arm64 (2.3.6-1) ... 534s Setting up libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 534s Setting up libpcre2-dev:arm64 (10.42-4ubuntu1) ... 534s Setting up cpp-13 (13.2.0-17ubuntu2) ... 534s Setting up libtk8.6:arm64 (8.6.13-2) ... 534s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 534s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 534s Setting up libreadline-dev:arm64 (8.2-3.1) ... 534s Setting up libcairo2:arm64 (1.18.0-1) ... 534s Setting up libxt6t64:arm64 (1:1.2.1-1.2) ... 534s Setting up gcc-13 (13.2.0-17ubuntu2) ... 534s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 534s Setting up cpp (4:13.2.0-7ubuntu1) ... 534s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 534s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 534s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 534s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 534s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 534s Setting up g++-13 (13.2.0-17ubuntu2) ... 534s Setting up libpng-dev:arm64 (1.6.43-3) ... 534s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 534s Setting up gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 534s Setting up gcc (4:13.2.0-7ubuntu1) ... 534s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 534s Setting up r-base-core (4.3.3-2build1) ... 534s 534s Creating config file /etc/R/Renviron with new version 534s Setting up r-cran-lattice (0.22-5-1) ... 534s Setting up r-cran-nlme (3.1.164-1) ... 534s Setting up r-cran-spatstat.utils (3.0-4-1) ... 534s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 534s Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 534s Setting up r-cran-tensor (1.5-4) ... 534s Setting up r-cran-pkgkitten (0.2.3-1) ... 534s Setting up r-cran-littler (0.3.19-1) ... 534s Setting up r-cran-nleqslv (3.3.5-1) ... 534s Setting up r-cran-rcpp (1.0.12-1) ... 534s Setting up r-cran-codetools (0.2-19-1) ... 534s Setting up littler (0.3.19-1) ... 534s Setting up r-cran-gsl (2.1-8-1) ... 534s Setting up r-cran-spatial (7.3-17-1) ... 534s Setting up r-cran-iterators (1.0.14-1) ... 534s Setting up r-cran-abind (1.4-5-2) ... 534s Setting up r-cran-foreach (1.5.2-1) ... 534s Setting up r-cran-sm (2.2-6.0-1) ... 534s Setting up r-cran-polyclip (1.10-6-1) ... 534s Setting up gfortran (4:13.2.0-7ubuntu1) ... 534s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 534s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 534s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 534s 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 534s Setting up r-cran-deldir (2.0-4-1) ... 534s Setting up r-cran-goftest (1.2-3-1) ... 534s Setting up r-cran-shape (1.4.6-1) ... 534s Setting up r-cran-matrix (1.6-5-1) ... 534s Setting up r-cran-spatstat.sparse (3.0-3-1) ... 534s Setting up r-cran-mgcv (1.9-1-1) ... 534s Setting up g++ (4:13.2.0-7ubuntu1) ... 534s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 534s Setting up build-essential (12.10ubuntu1) ... 534s Setting up r-cran-rcppeigen (0.3.3.9.4-1) ... 534s Setting up r-base-dev (4.3.3-2build1) ... 534s Setting up r-cran-survival (3.5-8-1) ... 534s Setting up r-cran-spatstat.data (3.0-4-1) ... 534s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 534s Setting up r-cran-spatstat.geom (3.2-8-1) ... 534s Setting up r-cran-glmnet (4.1-8-1) ... 534s Setting up r-cran-rpart (4.1.23-1) ... 534s Setting up r-cran-spatstat.random (3.2-2-1) ... 534s Setting up r-cran-spatstat.explore (3.2-5-1) ... 534s Setting up r-cran-spatstat.model (3.2-8-1) ... 534s Setting up r-cran-spatstat.linnet (3.1-3-1) ... 534s Setting up r-cran-spatstat (3.0-7-1) ... 534s Setting up autopkgtest-satdep (0) ... 534s Processing triggers for man-db (2.12.0-3) ... 535s Processing triggers for install-info (7.1-3) ... 535s Processing triggers for libc-bin (2.39-0ubuntu2) ... 543s (Reading database ... 87900 files and directories currently installed.) 543s Removing autopkgtest-satdep (0) ... 545s autopkgtest [20:24:50]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 545s autopkgtest [20:24:50]: test pkg-r-autopkgtest: [----------------------- 545s Test: Try to load the R library spatstat.model 545s 545s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 545s Copyright (C) 2024 The R Foundation for Statistical Computing 545s Platform: aarch64-unknown-linux-gnu (64-bit) 545s 545s R is free software and comes with ABSOLUTELY NO WARRANTY. 545s You are welcome to redistribute it under certain conditions. 545s Type 'license()' or 'licence()' for distribution details. 545s 545s R is a collaborative project with many contributors. 545s Type 'contributors()' for more information and 545s 'citation()' on how to cite R or R packages in publications. 545s 545s Type 'demo()' for some demos, 'help()' for on-line help, or 545s 'help.start()' for an HTML browser interface to help. 545s Type 'q()' to quit R. 545s 546s > library('spatstat.model') 546s Loading required package: spatstat.data 547s Loading required package: spatstat.geom 547s spatstat.geom 3.2-8 547s Loading required package: spatstat.random 547s spatstat.random 3.2-2 547s Loading required package: spatstat.explore 547s Loading required package: nlme 547s spatstat.explore 3.2-5 547s Loading required package: rpart 547s > 547s > 547s spatstat.model 3.2-8 547s Other tests are currently unsupported! 547s They will be progressively added. 548s autopkgtest [20:24:53]: test pkg-r-autopkgtest: -----------------------] 548s pkg-r-autopkgtest PASS 548s autopkgtest [20:24:53]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 549s autopkgtest [20:24:54]: @@@@@@@@@@@@@@@@@@@@ summary 549s run-unit-test PASS 549s pkg-r-autopkgtest PASS 560s Creating nova instance adt-noble-arm64-r-cran-spatstat.model-20240316-201545-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)... 560s Creating nova instance adt-noble-arm64-r-cran-spatstat.model-20240316-201545-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...