0s autopkgtest [20:15:12]: starting date and time: 2024-03-16 20:15:12+0000 0s autopkgtest [20:15:12]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [20:15:12]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1geg36v9/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --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.explore --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-3@bos03-arm64-16.secgroup --name adt-noble-arm64-r-cran-spatstat.explore-20240316-201512-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 81s autopkgtest [20:16:33]: testbed dpkg architecture: arm64 81s autopkgtest [20:16:33]: testbed apt version: 2.7.12 81s autopkgtest [20:16:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 81s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 82s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3704 kB] 82s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 82s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 82s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 82s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 82s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 82s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 82s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 82s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4012 kB] 82s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 82s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 82s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 84s Fetched 9112 kB in 2s (5678 kB/s) 84s Reading package lists... 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Calculating upgrade... 88s The following packages will be REMOVED: 88s libglib2.0-0 libssl3 88s The following NEW packages will be installed: 88s libglib2.0-0t64 libssl3t64 xdg-user-dirs 88s The following packages have been kept back: 88s curl 88s The following packages will be upgraded: 88s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 88s ubuntu-minimal ubuntu-standard 88s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 88s Need to get 4613 kB of archives. 88s After this operation, 211 kB of additional disk space will be used. 88s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 88s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 89s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 89s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 89s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 89s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 89s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 89s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 89s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 89s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 89s Fetched 4613 kB in 1s (6280 kB/s) 90s (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.) 90s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 90s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 90s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 90s udisks2 depends on libglib2.0-0 (>= 2.77.0). 90s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 90s python3-gi depends on libglib2.0-0 (>= 2.77.0). 90s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 90s netplan.io depends on libglib2.0-0 (>= 2.70.0). 90s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 90s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 90s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 90s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 90s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 90s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 90s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 90s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 90s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 90s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 90s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 90s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 90s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 90s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 90s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 90s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 90s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 90s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 90s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 90s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 90s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 90s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 90s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 90s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 90s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 90s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 90s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 90s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 90s fwupd depends on libglib2.0-0 (>= 2.79.0). 90s bolt depends on libglib2.0-0 (>= 2.56.0). 90s 90s (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.) 90s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 90s Selecting previously unselected package libglib2.0-0t64:arm64. 90s (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.) 90s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 90s 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... 90s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 90s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 90s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 90s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 90s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 90s wget depends on libssl3 (>= 3.0.0). 90s u-boot-tools depends on libssl3 (>= 3.0.0). 90s tnftp depends on libssl3 (>= 3.0.0). 90s tcpdump depends on libssl3 (>= 3.0.0). 90s systemd-resolved depends on libssl3 (>= 3.0.0). 90s systemd depends on libssl3 (>= 3.0.0). 90s sudo depends on libssl3 (>= 3.0.0). 90s sbsigntool depends on libssl3 (>= 3.0.0). 90s rsync depends on libssl3 (>= 3.0.0). 90s python3-cryptography depends on libssl3 (>= 3.0.0). 90s openssh-server depends on libssl3 (>= 3.0.10). 90s openssh-client depends on libssl3 (>= 3.0.10). 90s mtd-utils depends on libssl3 (>= 3.0.0). 90s mokutil depends on libssl3 (>= 3.0.0). 90s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 90s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 90s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 90s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 90s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 90s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 90s libnvme1 depends on libssl3 (>= 3.0.0). 90s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 90s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 90s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 90s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 90s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 90s kmod depends on libssl3 (>= 3.0.0). 90s dhcpcd-base depends on libssl3 (>= 3.0.0). 90s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 90s 90s (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.) 90s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 90s Selecting previously unselected package libssl3t64:arm64. 90s (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.) 90s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 90s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 90s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 90s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 90s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ... 90s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 90s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ... 90s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 90s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ... 90s Unpacking ubuntu-minimal (1.536) over (1.535) ... 90s Selecting previously unselected package xdg-user-dirs. 90s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ... 90s Unpacking xdg-user-dirs (0.18-1) ... 90s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ... 90s Unpacking ubuntu-standard (1.536) over (1.535) ... 90s Setting up ubuntu-minimal (1.536) ... 90s Setting up xdg-user-dirs (0.18-1) ... 90s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 90s Setting up libtirpc-common (1.3.4+ds-1.1) ... 90s Setting up ubuntu-standard (1.536) ... 90s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 91s No schema files found: doing nothing. 91s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 91s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 91s Setting up openssl (3.0.13-0ubuntu1) ... 91s Setting up readline-common (8.2-3.1) ... 91s Processing triggers for man-db (2.12.0-3) ... 91s Processing triggers for install-info (7.1-3) ... 91s Processing triggers for libc-bin (2.39-0ubuntu2) ... 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 93s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 94s sh: Attempting to set up Debian/Ubuntu apt sources automatically 94s sh: Distribution appears to be Ubuntu 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 95s eatmydata is already the newest version (131-1). 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Reading package lists... 96s Building dependency tree... 96s Reading state information... 96s dbus is already the newest version (1.14.10-4ubuntu1). 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 96s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s rng-tools-debian is already the newest version (2.4). 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 98s The following packages will be REMOVED: 98s cloud-init* python3-configobj* python3-debconf* 98s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 98s After this operation, 3252 kB disk space will be freed. 98s (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.) 98s Removing cloud-init (24.1.1-0ubuntu1) ... 99s Removing python3-configobj (5.0.8-3) ... 99s Removing python3-debconf (1.5.86) ... 99s Processing triggers for man-db (2.12.0-3) ... 99s (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 ... 74385 files and directories currently installed.) 99s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 100s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 100s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 100s invoke-rc.d: policy-rc.d denied execution of try-restart. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 101s linux-generic is already the newest version (6.8.0-11.11+1). 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 102s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 102s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 104s Reading package lists... 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 105s Calculating upgrade... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s autopkgtest [20:16:59]: rebooting testbed after setup commands that affected boot 290s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 297s autopkgtest [20:20:09]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 300s autopkgtest [20:20:12]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-spatstat.explore 303s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-spatstat.explore 3.2-5-1 (dsc) [2539 B] 303s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-spatstat.explore 3.2-5-1 (tar) [765 kB] 303s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-spatstat.explore 3.2-5-1 (diff) [3312 B] 304s gpgv: Signature made Tue Oct 24 08:19:13 2023 UTC 304s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 304s gpgv: issuer "tille@debian.org" 304s gpgv: Can't check signature: No public key 304s dpkg-source: warning: cannot verify inline signature for ./r-cran-spatstat.explore_3.2-5-1.dsc: no acceptable signature found 305s autopkgtest [20:20:17]: testing package r-cran-spatstat.explore version 3.2-5-1 305s autopkgtest [20:20:17]: build not needed 306s autopkgtest [20:20:18]: test run-unit-test: preparing testbed 308s Reading package lists... 309s Building dependency tree... 309s Reading state information... 310s Starting pkgProblemResolver with broken count: 0 310s Starting 2 pkgProblemResolver with broken count: 0 310s Done 311s The following additional packages will be installed: 311s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 311s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 311s libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libice6 libjbig0 311s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 311s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 311s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 311s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 311s r-base-core r-cran-abind r-cran-deldir r-cran-goftest r-cran-gsl 311s r-cran-lattice r-cran-locfit r-cran-matrix r-cran-mgcv r-cran-nlme 311s r-cran-polyclip r-cran-rpart r-cran-sm r-cran-spatial r-cran-spatstat 311s r-cran-spatstat.data r-cran-spatstat.explore r-cran-spatstat.geom 311s r-cran-spatstat.linnet r-cran-spatstat.model r-cran-spatstat.random 311s r-cran-spatstat.sparse r-cran-spatstat.utils r-cran-survival r-cran-tensor 311s unzip x11-common xdg-utils zip 311s Suggested packages: 311s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html tcl8.6 tk8.6 311s elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-interp 311s r-cran-gam 311s Recommended packages: 311s r-recommended r-base-dev r-doc-html r-cran-nleqslv r-cran-glmnet 311s libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils 311s x11-xserver-utils 311s The following NEW packages will be installed: 311s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 311s fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 311s libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b 311s libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 311s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 311s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 311s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 311s r-base-core r-cran-abind r-cran-deldir r-cran-goftest r-cran-gsl 311s r-cran-lattice r-cran-locfit r-cran-matrix r-cran-mgcv r-cran-nlme 311s r-cran-polyclip r-cran-rpart r-cran-sm r-cran-spatial r-cran-spatstat 311s r-cran-spatstat.data r-cran-spatstat.explore r-cran-spatstat.geom 311s r-cran-spatstat.linnet r-cran-spatstat.model r-cran-spatstat.random 311s r-cran-spatstat.sparse r-cran-spatstat.utils r-cran-survival r-cran-tensor 311s unzip x11-common xdg-utils zip 311s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 311s Need to get 78.8 MB/78.8 MB of archives. 311s After this operation, 132 MB of additional disk space will be used. 311s Get:1 /tmp/autopkgtest.BrJapW/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [772 B] 311s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 312s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 312s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 312s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 312s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 312s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 312s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 312s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 312s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 312s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 312s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 312s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 312s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 312s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 312s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 312s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 312s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu1 [72.5 kB] 312s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu1 [912 kB] 312s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 312s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 312s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 312s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 312s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 312s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 312s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 312s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 312s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 312s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 312s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 312s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 312s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 312s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 312s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 312s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 312s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 312s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 312s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 312s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 312s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 312s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 312s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 312s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB] 312s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 312s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 312s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 312s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB] 313s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-abind all 1.4-5-2 [63.6 kB] 313s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-deldir arm64 2.0-4-1 [270 kB] 313s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-goftest arm64 1.2-3-1 [60.2 kB] 313s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gsl arm64 2.1-8-1 [489 kB] 313s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 313s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-locfit arm64 1.5-9.8-1 [507 kB] 313s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 313s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 313s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 313s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-polyclip arm64 1.10-6-1 [110 kB] 313s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survival arm64 3.5-8-1 [6116 kB] 314s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rpart arm64 4.1.23-1 [660 kB] 314s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sm arm64 2.2-6.0-1 [787 kB] 314s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatial arm64 7.3-17-1 [130 kB] 314s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.utils arm64 3.0-4-1 [360 kB] 314s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.data all 3.0-4-1 [4090 kB] 314s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.geom arm64 3.2-8-1 [3805 kB] 314s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.random arm64 3.2-2-1 [1127 kB] 314s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tensor all 1.5-4 [15.7 kB] 314s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.sparse arm64 3.0-3-1 [214 kB] 314s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.explore arm64 3.2-5-1 [3264 kB] 314s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.model arm64 3.2-8-1 [3289 kB] 314s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.linnet arm64 3.1-3-1 [1404 kB] 314s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat arm64 3.0-7-1 [3817 kB] 316s Preconfiguring packages ... 317s Fetched 78.8 MB in 3s (24.4 MB/s) 317s Selecting previously unselected package fonts-dejavu-mono. 317s (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 ... 74330 files and directories currently installed.) 317s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 317s Unpacking fonts-dejavu-mono (2.37-8) ... 317s Selecting previously unselected package fonts-dejavu-core. 318s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 318s Unpacking fonts-dejavu-core (2.37-8) ... 318s Selecting previously unselected package fontconfig-config. 318s Preparing to unpack .../02-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 319s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 319s Selecting previously unselected package libfontconfig1:arm64. 319s Preparing to unpack .../03-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 319s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 319s Selecting previously unselected package fontconfig. 319s Preparing to unpack .../04-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 319s Unpacking fontconfig (2.15.0-1ubuntu1) ... 319s Selecting previously unselected package libblas3:arm64. 319s Preparing to unpack .../05-libblas3_3.12.0-3_arm64.deb ... 319s Unpacking libblas3:arm64 (3.12.0-3) ... 320s Selecting previously unselected package libpixman-1-0:arm64. 320s Preparing to unpack .../06-libpixman-1-0_0.42.2-1_arm64.deb ... 320s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 320s Selecting previously unselected package libxcb-render0:arm64. 320s Preparing to unpack .../07-libxcb-render0_1.15-1_arm64.deb ... 320s Unpacking libxcb-render0:arm64 (1.15-1) ... 321s Selecting previously unselected package libxcb-shm0:arm64. 321s Preparing to unpack .../08-libxcb-shm0_1.15-1_arm64.deb ... 321s Unpacking libxcb-shm0:arm64 (1.15-1) ... 321s Selecting previously unselected package libxrender1:arm64. 321s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 321s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 321s Selecting previously unselected package libcairo2:arm64. 321s Preparing to unpack .../10-libcairo2_1.18.0-1_arm64.deb ... 321s Unpacking libcairo2:arm64 (1.18.0-1) ... 322s Selecting previously unselected package libdatrie1:arm64. 322s Preparing to unpack .../11-libdatrie1_0.2.13-3_arm64.deb ... 322s Unpacking libdatrie1:arm64 (0.2.13-3) ... 322s Selecting previously unselected package libdeflate0:arm64. 322s Preparing to unpack .../12-libdeflate0_1.19-1_arm64.deb ... 322s Unpacking libdeflate0:arm64 (1.19-1) ... 322s Selecting previously unselected package libgfortran5:arm64. 323s Preparing to unpack .../13-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 323s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 323s Selecting previously unselected package libgomp1:arm64. 323s Preparing to unpack .../14-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 323s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 323s Selecting previously unselected package libgraphite2-3:arm64. 324s Preparing to unpack .../15-libgraphite2-3_1.3.14-2_arm64.deb ... 324s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 324s Selecting previously unselected package libgslcblas0:arm64. 324s Preparing to unpack .../16-libgslcblas0_2.7.1+dfsg-6ubuntu1_arm64.deb ... 324s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 324s Selecting previously unselected package libgsl27:arm64. 324s Preparing to unpack .../17-libgsl27_2.7.1+dfsg-6ubuntu1_arm64.deb ... 324s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 324s Selecting previously unselected package libharfbuzz0b:arm64. 326s Preparing to unpack .../18-libharfbuzz0b_8.3.0-2_arm64.deb ... 326s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 326s Selecting previously unselected package x11-common. 328s Preparing to unpack .../19-x11-common_1%3a7.7+23ubuntu2_all.deb ... 328s Unpacking x11-common (1:7.7+23ubuntu2) ... 329s Selecting previously unselected package libice6:arm64. 329s Preparing to unpack .../20-libice6_2%3a1.0.10-1build2_arm64.deb ... 329s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 330s Selecting previously unselected package libjpeg-turbo8:arm64. 330s Preparing to unpack .../21-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 330s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 330s Selecting previously unselected package libjpeg8:arm64. 330s Preparing to unpack .../22-libjpeg8_8c-2ubuntu11_arm64.deb ... 330s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 330s Selecting previously unselected package liblapack3:arm64. 330s Preparing to unpack .../23-liblapack3_3.12.0-3_arm64.deb ... 330s Unpacking liblapack3:arm64 (3.12.0-3) ... 330s Selecting previously unselected package liblerc4:arm64. 330s Preparing to unpack .../24-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 330s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 330s Selecting previously unselected package libthai-data. 330s Preparing to unpack .../25-libthai-data_0.1.29-2_all.deb ... 330s Unpacking libthai-data (0.1.29-2) ... 330s Selecting previously unselected package libthai0:arm64. 330s Preparing to unpack .../26-libthai0_0.1.29-2_arm64.deb ... 330s Unpacking libthai0:arm64 (0.1.29-2) ... 330s Selecting previously unselected package libpango-1.0-0:arm64. 330s Preparing to unpack .../27-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 330s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 330s Selecting previously unselected package libpangoft2-1.0-0:arm64. 330s Preparing to unpack .../28-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 330s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 330s Selecting previously unselected package libpangocairo-1.0-0:arm64. 331s Preparing to unpack .../29-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 331s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 331s Selecting previously unselected package libpaper1:arm64. 331s Preparing to unpack .../30-libpaper1_1.1.29_arm64.deb ... 331s Unpacking libpaper1:arm64 (1.1.29) ... 331s Selecting previously unselected package libpaper-utils. 331s Preparing to unpack .../31-libpaper-utils_1.1.29_arm64.deb ... 331s Unpacking libpaper-utils (1.1.29) ... 331s Selecting previously unselected package libsharpyuv0:arm64. 331s Preparing to unpack .../32-libsharpyuv0_1.3.2-0.4_arm64.deb ... 331s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 331s Selecting previously unselected package libsm6:arm64. 331s Preparing to unpack .../33-libsm6_2%3a1.2.3-1build2_arm64.deb ... 331s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 331s Selecting previously unselected package libtcl8.6:arm64. 331s Preparing to unpack .../34-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 331s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 331s Selecting previously unselected package libjbig0:arm64. 331s Preparing to unpack .../35-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 331s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 331s Selecting previously unselected package libwebp7:arm64. 331s Preparing to unpack .../36-libwebp7_1.3.2-0.4_arm64.deb ... 331s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 331s Selecting previously unselected package libtiff6:arm64. 331s Preparing to unpack .../37-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 331s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 331s Selecting previously unselected package libxft2:arm64. 331s Preparing to unpack .../38-libxft2_2.3.6-1_arm64.deb ... 331s Unpacking libxft2:arm64 (2.3.6-1) ... 331s Selecting previously unselected package libxss1:arm64. 332s Preparing to unpack .../39-libxss1_1%3a1.2.3-1build2_arm64.deb ... 332s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 332s Selecting previously unselected package libtk8.6:arm64. 332s Preparing to unpack .../40-libtk8.6_8.6.13-2_arm64.deb ... 332s Unpacking libtk8.6:arm64 (8.6.13-2) ... 332s Selecting previously unselected package libxt6:arm64. 332s Preparing to unpack .../41-libxt6_1%3a1.2.1-1.1_arm64.deb ... 332s Unpacking libxt6:arm64 (1:1.2.1-1.1) ... 332s Selecting previously unselected package zip. 332s Preparing to unpack .../42-zip_3.0-13_arm64.deb ... 332s Unpacking zip (3.0-13) ... 332s Selecting previously unselected package unzip. 332s Preparing to unpack .../43-unzip_6.0-28ubuntu3_arm64.deb ... 332s Unpacking unzip (6.0-28ubuntu3) ... 332s Selecting previously unselected package xdg-utils. 332s Preparing to unpack .../44-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 332s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 332s Selecting previously unselected package r-base-core. 332s Preparing to unpack .../45-r-base-core_4.3.2-1build1_arm64.deb ... 332s Unpacking r-base-core (4.3.2-1build1) ... 333s Selecting previously unselected package r-cran-abind. 333s Preparing to unpack .../46-r-cran-abind_1.4-5-2_all.deb ... 333s Unpacking r-cran-abind (1.4-5-2) ... 333s Selecting previously unselected package r-cran-deldir. 333s Preparing to unpack .../47-r-cran-deldir_2.0-4-1_arm64.deb ... 333s Unpacking r-cran-deldir (2.0-4-1) ... 333s Selecting previously unselected package r-cran-goftest. 333s Preparing to unpack .../48-r-cran-goftest_1.2-3-1_arm64.deb ... 333s Unpacking r-cran-goftest (1.2-3-1) ... 333s Selecting previously unselected package r-cran-gsl. 333s Preparing to unpack .../49-r-cran-gsl_2.1-8-1_arm64.deb ... 333s Unpacking r-cran-gsl (2.1-8-1) ... 333s Selecting previously unselected package r-cran-lattice. 333s Preparing to unpack .../50-r-cran-lattice_0.22-5-1_arm64.deb ... 333s Unpacking r-cran-lattice (0.22-5-1) ... 333s Selecting previously unselected package r-cran-locfit. 333s Preparing to unpack .../51-r-cran-locfit_1.5-9.8-1_arm64.deb ... 333s Unpacking r-cran-locfit (1.5-9.8-1) ... 333s Selecting previously unselected package r-cran-matrix. 333s Preparing to unpack .../52-r-cran-matrix_1.6-5-1_arm64.deb ... 333s Unpacking r-cran-matrix (1.6-5-1) ... 333s Selecting previously unselected package r-cran-nlme. 333s Preparing to unpack .../53-r-cran-nlme_3.1.164-1_arm64.deb ... 333s Unpacking r-cran-nlme (3.1.164-1) ... 333s Selecting previously unselected package r-cran-mgcv. 333s Preparing to unpack .../54-r-cran-mgcv_1.9-1-1_arm64.deb ... 333s Unpacking r-cran-mgcv (1.9-1-1) ... 334s Selecting previously unselected package r-cran-polyclip. 334s Preparing to unpack .../55-r-cran-polyclip_1.10-6-1_arm64.deb ... 334s Unpacking r-cran-polyclip (1.10-6-1) ... 334s Selecting previously unselected package r-cran-survival. 334s Preparing to unpack .../56-r-cran-survival_3.5-8-1_arm64.deb ... 334s Unpacking r-cran-survival (3.5-8-1) ... 334s Selecting previously unselected package r-cran-rpart. 334s Preparing to unpack .../57-r-cran-rpart_4.1.23-1_arm64.deb ... 334s Unpacking r-cran-rpart 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(2023-10-31) -- "Eye Holes" 349s Copyright (C) 2023 The R Foundation for Statistical Computing 349s Platform: aarch64-unknown-linux-gnu (64-bit) 349s 349s R is free software and comes with ABSOLUTELY NO WARRANTY. 349s You are welcome to redistribute it under certain conditions. 349s Type 'license()' or 'licence()' for distribution details. 349s 349s R is a collaborative project with many contributors. 349s Type 'contributors()' for more information and 349s 'citation()' on how to cite R or R packages in publications. 349s 349s Type 'demo()' for some demos, 'help()' for on-line help, or 349s 'help.start()' for an HTML browser interface to help. 349s Type 'q()' to quit R. 349s 349s > #' 349s > #' Header for all (concatenated) test files 349s > #' 349s > #' Require spatstat.explore 349s > #' Obtain environment variable controlling tests. 349s > #' 349s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 349s > 349s > require(spatstat.explore) 349s Loading required package: spatstat.explore 349s Loading required package: spatstat.data 350s Loading required package: spatstat.geom 350s spatstat.geom 3.2-8 350s Loading required package: spatstat.random 350s spatstat.random 3.2-2 350s Loading required package: nlme 350s spatstat.explore 3.2-5 350s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 350s > ALWAYS <- TRUE 350s > cat(paste("--------- Executing", 350s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 350s + "test code -----------\n")) 350s --------- Executing **RESTRICTED** subset of test code ----------- 350s > ## tests/cdf.test.R 350s > 350s > 350s > local({ 350s + NSIM <- 9 350s + op <- spatstat.options(ndummy.min=16, npixel=32) 350s + AA <- split(ants, un=FALSE) 350s + AC <- AA[["Cataglyphis"]] 350s + AM <- AA[["Messor"]] 350s + DM <- distmap(AM) 350s + if(ALWAYS) { 350s + ## Check cdf.test with strange data 350s + ## Marked point patterns with some marks not represented 350s + ## should produce a warning, rather than a crash: 350s + cdf.test(AC, DM) 350s + } 350s + if(FULLTEST) { 350s + ## should be OK: 350s + cdf.test(unmark(AC), DM) 350s + cdf.test(unmark(AC), DM, "cvm") 350s + cdf.test(unmark(AC), DM, "ad") 350s + ## other code blocks 350s + cdf.test(finpines, "x") 350s + } 350s + }) 350s > 350s > 350s > #' tests/circular.R 350s > #' 350s > #' Circular data and periodic distributions 350s > #' 350s > #' $Revision: 1.4 $ $Date: 2020/04/28 12:58:26 $ 350s > 350s > 350s > local({ 350s + if(ALWAYS) { 350s + a <- pairorient(redwood, 0.05, 0.15, correction="none") 350s + rose(a) 350s + } 350s + if(FULLTEST) { 350s + b <- pairorient(redwood, 0.05, 0.15, correction="best") 350s + rose(b, start="N", clockwise=TRUE) 350s + } 350s + if(ALWAYS) { 350s + #' arcs on the circle 350s + #' (depends on numerical behaviour) 350s + set.seed(19171025) 350s + aa <- replicate(7, runif(1, 0, 2*pi) + c(0, runif(1, 0, pi)), 350s + simplify=FALSE) 350s + bb <- circunion(aa) 350s + 350s + assertsingle <- function(x, a, id) { 350s + y <- circunion(x) 350s + if(length(y) != 1 || max(abs(y[[1]] - a)) > .Machine$double.eps) 350s + stop(paste("Incorrect result from circunion in case", id), 350s + call.=FALSE) 350s + invisible(NULL) 350s + } 350s + 350s + assertsingle(list(c(pi/3, pi), c(pi/2, 3*pi/2)), 350s + c(pi/3, 3*pi/2), 350s + 1) 350s + assertsingle(list(c(0, pi/2), c(pi/4, pi)), 350s + c(0,pi), 350s + 2) 350s + assertsingle(list(c(-pi/4, pi/2), c(pi/4, pi)), 350s + c((2-1/4)*pi, pi), 350s + 3) 350s + } 350s + }) 350s Warning message: 350s In cdf.test.ppp(AC, DM) : 350s Ignoring marks, because some mark values have zero frequency 350s > 350s > 350s > #' 350s > #' tests/closecore.R 350s > #' 350s > #' check 'closepairs/crosspairs' code 350s > #' invoked in core package 350s > #' 350s > #' $Revision: 1.4 $ $Date: 2021/04/17 04:16:43 $ 350s > #' 350s > #' ------- All this code must be run on every hardware ------- 350s > #' 350s > 350s > local({ 350s + #' weightedclosepairs is in wtdclosepair.R 350s + wi <- weightedclosepairs(redwood, 0.05, "isotropic") 350s + if(FULLTEST) { 350s + wt <- weightedclosepairs(redwood, 0.05, "translate") 350s + wp <- weightedclosepairs(redwood, 0.05, "periodic") 350s + } 350s + #' markmarkscatter uses closepairs.pp3 350s + X <- runifpoint3(100) 350s + marks(X) <- runif(100) 350s + markmarkscatter(X, 0.2) 350s + if(FULLTEST) { 350s + markmarkscatter(X[FALSE], 0.2) 350s + } 350s + }) 350s > 350s > #' 350s > #' contact.R 350s > #' 350s > #' Check machinery for first contact distributions 350s > #' 350s > #' $Revision: 1.8 $ $Date: 2021/04/17 02:25:55 $ 350s > 350s > local({ 350s + if(ALWAYS) { 350s + #' reduce complexity 350s + Y <- as.mask(heather$coarse, dimyx=c(50, 25)) 350s + 350s + X <- runifpoint(100, win = complement.owin(Y)) 350s + if(FULLTEST) G <- Gfox(X, Y) 350s + J <- Jfox(X, Y) 350s + 350s + Y <- as.polygonal(Y) 350s + X <- runifpoint(100, win = complement.owin(Y)) 350s + if(FULLTEST) G <- Gfox(X, Y) 350s + J <- Jfox(X, Y) 350s + 350s + op <- spatstat.options(exactdt.checks.data=TRUE) 350s + U <- exactdt(X) 350s + spatstat.options(op) 350s + } 350s + }) 351s > 351s > reset.spatstat.options() 351s > 351s BEGIN TEST testsD.R 351s 351s R version 4.3.2 (2023-10-31) -- "Eye Holes" 351s Copyright (C) 2023 The R Foundation for Statistical Computing 351s Platform: aarch64-unknown-linux-gnu (64-bit) 351s 351s R is free software and comes with ABSOLUTELY NO WARRANTY. 351s You are welcome to redistribute it under certain conditions. 351s Type 'license()' or 'licence()' for distribution details. 351s 351s R is a collaborative project with many contributors. 351s Type 'contributors()' for more information and 351s 'citation()' on how to cite R or R packages in publications. 351s 351s Type 'demo()' for some demos, 'help()' for on-line help, or 351s 'help.start()' for an HTML browser interface to help. 351s Type 'q()' to quit R. 351s 351s > #' 351s > #' Header for all (concatenated) test files 351s > #' 351s > #' Require spatstat.explore 351s > #' Obtain environment variable controlling tests. 351s > #' 351s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 351s > 351s > require(spatstat.explore) 351s Loading required package: spatstat.explore 351s Loading required package: spatstat.data 352s Loading required package: spatstat.geom 352s spatstat.geom 3.2-8 352s Loading required package: spatstat.random 352s spatstat.random 3.2-2 352s Loading required package: nlme 352s spatstat.explore 3.2-5 352s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 352s > ALWAYS <- TRUE 352s > cat(paste("--------- Executing", 352s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 352s + "test code -----------\n")) 352s --------- Executing **RESTRICTED** subset of test code ----------- 352s > #' 352s > #' tests/density.R 352s > #' 352s > #' Test behaviour of density() methods, 352s > #' relrisk(), Smooth() 352s > #' and inhomogeneous summary functions 352s > #' and idw, adaptive.density, intensity 352s > #' 352s > #' $Revision: 1.62 $ $Date: 2022/05/22 11:14:51 $ 352s > #' 352s > 352s > if(!FULLTEST) 352s + spatstat.options(npixel=32, ndummy.min=16) 352s > 352s > 352s > local({ 352s + 352s + # test all cases of density.ppp and densityfun.ppp 352s + 352s + tryit <- function(..., do.fun=TRUE, badones=FALSE) { 352s + Z <- density(cells, ..., at="pixels") 352s + Z <- density(cells, ..., at="points") 352s + if(do.fun) { 352s + f <- densityfun(cells, ...) 352s + U <- f(0.1, 0.3) 352s + if(badones) { 352s + U2 <- f(1.1, 0.3) 352s + U3 <- f(1.1, 0.3, drop=FALSE) 352s + } 352s + } 352s + return(invisible(NULL)) 352s + } 353s + 353s + if(ALWAYS) { 353s + tryit(0.05) 353s + tryit(0.05, diggle=TRUE) 353s + tryit(0.05, se=TRUE) 353s + tryit(0.05, weights=expression(x)) 353s + tryit(0.07, kernel="epa") 353s + tryit(sigma=Inf) 353s + tryit(0.05, badones=TRUE) 353s + } 353s + if(FULLTEST) { 353s + tryit(0.07, kernel="quartic") 353s + tryit(0.07, kernel="disc") 353s + tryit(0.07, kernel="epa", weights=expression(x)) 353s + tryit(sigma=Inf, weights=expression(x)) 353s + } 353s + 353s + V <- diag(c(0.05^2, 0.07^2)) 353s + 353s + if(ALWAYS) { 353s + tryit(varcov=V) 353s + } 353s + if(FULLTEST) { 353s + tryit(varcov=V, diggle=TRUE) 353s + tryit(varcov=V, weights=expression(x)) 353s + tryit(varcov=V, weights=expression(x), diggle=TRUE) 353s + Z <- distmap(runifpoint(5, Window(cells))) 353s + tryit(0.05, weights=Z) 353s + tryit(0.05, weights=Z, diggle=TRUE) 353s + } 353s + 353s + trymost <- function(...) tryit(..., do.fun=FALSE) 353s + wdf <- data.frame(a=1:42,b=42:1) 353s + if(ALWAYS) { 353s + trymost(0.05, weights=wdf) 353s + trymost(sigma=Inf, weights=wdf) 353s + } 353s + if(FULLTEST) { 353s + trymost(0.05, weights=wdf, diggle=TRUE) 353s + trymost(varcov=V, weights=wdf) 353s + trymost(varcov=V, weights=expression(cbind(x,y))) 353s + } 353s + 353s + ## check conservation of mass 353s + checkconserve <- function(X, xname, sigma, toler=0.01) { 353s + veritas <- npoints(X) 353s + vino <- integral(density(X, sigma, diggle=TRUE)) 353s + relerr <- abs(vino - veritas)/veritas 353s + if(relerr > toler) 353s + stop(paste("density.ppp(diggle=TRUE) fails to conserve mass:", 353s + vino, "!=", veritas, 353s + "for", sQuote(xname)), 353s + call.=FALSE) 353s + return(relerr) 353s + } 353s + if(FULLTEST) { 353s + checkconserve(cells, "cells", 0.15) 353s + } 353s + if(ALWAYS) { 353s + checkconserve(split(chorley)[["lung"]], "lung", 2) 353s + } 353s + 353s + ## run C algorithm 'denspt' 353s + opa <- spatstat.options(densityC=TRUE, densityTransform=FALSE) 353s + if(ALWAYS) { 353s + tryit(varcov=V) 353s + } 353s + if(FULLTEST) { 353s + tryit(varcov=V, weights=expression(x)) 353s + trymost(varcov=V, weights=wdf) 353s + } 353s + spatstat.options(opa) 353s + 353s + crossit <- function(..., sigma=NULL) { 353s + U <- runifpoint(20, Window(cells)) 353s + a <- densitycrossEngine(cells, U, ..., sigma=sigma) 353s + a <- densitycrossEngine(cells, U, ..., sigma=sigma, diggle=TRUE) 353s + invisible(NULL) 353s + } 353s + if(ALWAYS) { 353s + crossit(varcov=V, weights=cells$x) 353s + crossit(sigma=Inf) 353s + } 353s + if(FULLTEST) { 353s + crossit(varcov=V, weights=wdf) 353s + crossit(sigma=0.1, weights=wdf) 353s + crossit(sigma=0.1, kernel="epa", weights=wdf) 353s + } 353s + 353s + ## apply different discretisation rules 353s + if(ALWAYS) { 353s + Z <- density(cells, 0.05, fractional=TRUE) 353s + } 353s + if(FULLTEST) { 353s + Z <- density(cells, 0.05, preserve=TRUE) 353s + Z <- density(cells, 0.05, fractional=TRUE, preserve=TRUE) 353s + } 353s + 353s + ## compare results with different algorithms 353s + crosscheque <- function(expr) { 353s + e <- as.expression(substitute(expr)) 353s + ename <- sQuote(deparse(substitute(expr))) 353s + ## interpreted R 353s + opa <- spatstat.options(densityC=FALSE, densityTransform=FALSE) 353s + val.interpreted <- eval(e) 353s + ## established C algorithm 'denspt' 353s + spatstat.options(densityC=TRUE, densityTransform=FALSE) 353s + val.C <- eval(e) 353s + ## new C algorithm 'Gdenspt' using transformed coordinates 353s + spatstat.options(densityC=TRUE, densityTransform=TRUE) 353s + val.Transform <- eval(e) 353s + spatstat.options(opa) 353s + if(max(abs(val.interpreted - val.C)) > 0.001) 353s + stop(paste("Numerical discrepancy between R and C algorithms in", 353s + ename)) 353s + if(max(abs(val.C - val.Transform)) > 0.001) 353s + stop(paste("Numerical discrepancy between C algorithms", 353s + "using transformed and untransformed coordinates in", 353s + ename)) 353s + invisible(NULL) 353s + } 353s + 353s + ## execute & compare results of density(at="points") with different algorithms 353s + wdfr <- cbind(1:npoints(redwood), 2) 353s + if(ALWAYS) { 353s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE)) 353s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE, 353s + weights=wdfr[,1])) 353s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE, 353s + weights=wdfr)) 353s + } 353s + 353s + ## correctness of non-Gaussian kernel calculation 353s + leavein <- function(ker, maxd=0.025) { 353s + ZI <- density(redwood, 0.12, kernel=ker, edge=FALSE, 353s + dimyx=256)[redwood] 353s + ZP <- density(redwood, 0.12, kernel=ker, edge=FALSE, 353s + at="points", leaveoneout=FALSE) 353s + discrep <- max(abs(ZP - ZI))/npoints(redwood) 353s + if(discrep > maxd) 353s + stop(paste("Discrepancy", 353s + signif(discrep, 3), 353s + "in calculation for", ker, "kernel")) 353s + return(invisible(NULL)) 353s + } 353s + if(ALWAYS) { 353s + leavein("epanechnikov", 0.015) 353s + } 353s + if(FULLTEST) { 353s + leavein("quartic", 0.010) 353s + leavein("disc", 0.100) 353s + } 353s + 353s + ## bandwidth selection code blocks 353s + sigvec <- 0.01 * 2:15 353s + sigran <- range(sigvec) 353s + if(ALWAYS) { 353s + bw.ppl(redwood, sigma=sigvec) 353s + bw.CvL(redwood, sigma=sigvec) 353s + } 353s + if(FULLTEST) { 353s + bw.ppl(redwood, srange=sigran, ns=5) 353s + bw.CvL(redwood, srange=sigran, ns=5) 353s + } 353s + ## adaptive bandwidth 353s + if(ALWAYS) { 353s + a <- bw.abram(redwood) 353s + } 353s + if(FULLTEST) { 353s + a <- bw.abram(redwood, pilot=density(redwood, 0.2)) 353s + a <- bw.abram(redwood, smoother="densityVoronoi", at="pixels") 353s + } 353s + 353s + ## Kinhom 353s + if(ALWAYS) { 353s + lam <- density(redwood) 353s + K <- Kinhom(redwood, lam) 353s + 353s + lamX <- density(redwood, at="points") 353s + KX <- Kinhom(redwood, lamX) 353s + } 353s + 353s + ## test all code cases of new 'relrisk.ppp' algorithm 353s + pants <- function(..., X=ants, sigma=100, se=TRUE) { 353s + a <- relrisk(X, sigma=sigma, se=se, ...) 353s + return(TRUE) 353s + } 353s + if(ALWAYS) { 353s + pants() 353s + pants(diggle=TRUE) 353s + pants(edge=FALSE) 353s + pants(at="points") 353s + pants(casecontrol=FALSE) 353s + pants(relative=TRUE) 353s + pants(sigma=Inf) 353s + pants(sigma=NULL, varcov=diag(c(100,100)^2)) 353s + f <- 1/area(Window(ants)) 353s + pants(fudge=f) 353s + } 353s + if(FULLTEST) { 353s + pants(diggle=TRUE, at="points") 353s + pants(edge=FALSE, at="points", fudge=f) 353s + pants(casecontrol=FALSE, relative=TRUE) 353s + pants(casecontrol=FALSE,at="points") 353s + pants(relative=TRUE,at="points", fudge=f) 353s + pants(casecontrol=FALSE, relative=TRUE,at="points") 353s + pants(relative=TRUE, control="Cataglyphis", case="Messor", fudge=f) 353s + pants(relative=TRUE, control="Cataglyphis", case="Messor", at="points") 353s + pants(casecontrol=FALSE, case="Messor", se=FALSE) 353s + pants(case=2, at="pixels", relative=TRUE) 353s + pants(case=2, at="points", relative=TRUE) 353s + pants(case=2, at="pixels", relative=FALSE) 353s + pants(case=2, at="points", relative=FALSE) 353s + } 353s + if(ALWAYS) { 353s + ## underflow example from stackoverflow! 353s + funky <- scanpp("funky.tab", owin(c(4, 38), c(0.3, 17))) 353s + P <- relrisk(funky, 0.5) 353s + R <- relrisk(funky, 0.5, relative=TRUE) 353s + } 353s + ## more than 2 types 353s + if(ALWAYS) { 353s + pants(X=sporophores) 353s + pants(X=sporophores, sigma=20, at="points") 353s + pants(X=sporophores, sigma=20, at="points", fudge=f) 353s + bw.relrisk(sporophores, method="leastsquares") 353s + } 353s + if(FULLTEST) { 353s + pants(X=sporophores, sigma=20, relative=TRUE, at="points", fudge=f) 353s + pants(X=sporophores, sigma=20, at="pixels", se=FALSE) 353s + pants(X=sporophores, sigma=20, relative=TRUE, at="pixels", se=FALSE) 353s + bw.relrisk(sporophores, method="weightedleastsquares") 353s + } 353s + 353s + ## execute Smooth.ppp and Smoothfun.ppp in all cases 353s + stroke <- function(..., Y = longleaf, FUN=TRUE) { 353s + Z <- Smooth(Y, ..., at="pixels") 353s + Z <- Smooth(Y, ..., at="points", leaveoneout=TRUE) 353s + Z <- Smooth(Y, ..., at="points", leaveoneout=FALSE) 353s + if(FUN) { 353s + f <- Smoothfun(Y, ...) 353s + f(120, 80) 353s + f(Y[1:2]) 353s + f(Y[FALSE]) 353s + U <- as.im(f) 353s + } 353s + return(invisible(NULL)) 353s + } 353s + if(ALWAYS) { 353s + stroke() 353s + stroke(5, diggle=TRUE) 353s + stroke(5, geometric=TRUE) 353s + stroke(1e-6) # generates warning about small bandwidth 353s + stroke(5, weights=expression(x)) 353s + stroke(5, kernel="epa") 353s + stroke(sigma=Inf) 353s + } 353s + if(FULLTEST) { 353s + Z <- as.im(function(x,y){abs(x)+1}, Window(longleaf)) 353s + stroke(5, weights=Z) 353s + stroke(5, weights=runif(npoints(longleaf))) 353s + stroke(varcov=diag(c(25, 36))) 353s + stroke(varcov=diag(c(25, 36)), weights=runif(npoints(longleaf))) 353s + stroke(5, Y=longleaf %mark% 1) 353s + stroke(5, Y=cut(longleaf,breaks=3)) 353s + stroke(5, weights=Z, geometric=TRUE) 353s + g <- function(x,y) { dnorm(x, sd=10) * dnorm(y, sd=10) } 353s + stroke(kernel=g, cutoff=30, FUN=FALSE) 353s + stroke(kernel=g, cutoff=30, scalekernel=TRUE, sigma=1, FUN=FALSE) 353s + } 353s + if(FULLTEST) { 353s + ## standard errors - single column of marks 353s + stroke(sigma=5, se=TRUE) 353s + stroke(sigma=5, se=TRUE, loctype="f") 353s + w <- runif(npoints(longleaf)) 353s + stroke(sigma=5, se=TRUE, weights=w, loctype="r", wtype="i") 353s + stroke(sigma=5, se=TRUE, weights=w, loctype="r", wtype="m") 353s + stroke(sigma=5, se=TRUE, weights=w, loctype="f", wtype="i") 353s + stroke(sigma=5, se=TRUE, weights=w, loctype="f", wtype="m") 353s + } 353s + 353s + niets <- markmean(longleaf, 9) 353s + 353s + strike <- function(..., Y=finpines) { 353s + Z <- Smooth(Y, ..., at="pixels") 353s + Z <- Smooth(Y, ..., at="points", leaveoneout=TRUE) 353s + Z <- Smooth(Y, ..., at="points", leaveoneout=FALSE) 353s + f <- Smoothfun(Y, ...) 353s + f(4, 1) 353s + f(Y[1:2]) 353s + f(Y[FALSE]) 353s + U <- as.im(f) 353s + return(invisible(NULL)) 353s + } 353s + if(ALWAYS) { 353s + strike() 353s + strike(sigma=1.5, kernel="epa") 353s + strike(varcov=diag(c(1.2, 2.1))) 353s + strike(sigma=1e-6) 353s + strike(sigma=Inf) 353s + } 353s + if(FULLTEST) { 353s + strike(sigma=1e-6, kernel="epa") 353s + strike(1.5, weights=runif(npoints(finpines))) 353s + strike(1.5, weights=expression(y)) 353s + strike(1.5, geometric=TRUE) 353s + strike(1.5, Y=finpines[FALSE]) 353s + flatfin <- finpines %mark% data.frame(a=rep(1, npoints(finpines)), b=2) 353s + strike(1.5, Y=flatfin) 353s + strike(1.5, Y=flatfin, geometric=TRUE) 353s + } 353s + if(FULLTEST) { 353s + ## standard errors - multivariate marks 353s + strike(sigma=1.5, se=TRUE) 353s + strike(sigma=1.5, se=TRUE, loctype="f") 353s + w <- runif(npoints(finpines)) 353s + strike(sigma=1.5, se=TRUE, weights=w, loctype="r", wtype="i") 353s + strike(sigma=1.5, se=TRUE, weights=w, loctype="r", wtype="m") 353s + strike(sigma=1.5, se=TRUE, weights=w, loctype="f", wtype="i") 353s + strike(sigma=1.5, se=TRUE, weights=w, loctype="f", wtype="m") 353s + } 353s + opx <- spatstat.options(densityTransform=FALSE) 353s + if(ALWAYS) { 353s + stroke(5, Y=longleaf[order(longleaf$x)], sorted=TRUE) 353s + } 353s + if(FULLTEST) { 353s + strike(1.5, Y=finpines[order(finpines$x)], sorted=TRUE) 353s + } 353s + spatstat.options(opx) 353s + 353s + ## detect special cases 353s + if(ALWAYS) { 353s + Smooth(longleaf[FALSE]) 353s + Smooth(longleaf, minnndist(longleaf)) 353s + Xconst <- cells %mark% 1 353s + Smooth(Xconst, 0.1) 353s + Smooth(Xconst, 0.1, at="points") 353s + Smooth(cells %mark% runif(42), sigma=Inf) 353s + Smooth(cells %mark% runif(42), sigma=Inf, at="points") 353s + Smooth(cells %mark% runif(42), sigma=Inf, at="points", leaveoneout=FALSE) 353s + Smooth(cut(longleaf, breaks=4)) 353s + } 353s + 353s + ## code not otherwise reached 353s + if(ALWAYS) { 353s + smoothpointsEngine(cells, values=rep(1, npoints(cells)), sigma=0.2) 353s + } 353s + if(FULLTEST) { 353s + smoothpointsEngine(cells, values=runif(npoints(cells)), sigma=Inf) 353s + smoothpointsEngine(cells, values=runif(npoints(cells)), sigma=1e-16) 353s + } 353s + 353s + ## validity of Smooth.ppp(at='points') 353s + Y <- longleaf %mark% runif(npoints(longleaf), min=41, max=43) 353s + Z <- Smooth(Y, 5, at="points", leaveoneout=TRUE) 353s + rZ <- range(Z) 353s + if(rZ[1] < 40 || rZ[2] > 44) 353s + stop("Implausible results from Smooth.ppp(at=points, leaveoneout=TRUE)") 353s + 353s + Z <- Smooth(Y, 5, at="points", leaveoneout=FALSE) 353s + rZ <- range(Z) 353s + if(rZ[1] < 40 || rZ[2] > 44) 353s + stop("Implausible results from Smooth.ppp(at=points, leaveoneout=FALSE)") 353s + 353s + ## compare Smooth.ppp results with different algorithms 353s + if(ALWAYS) { 353s + crosscheque(Smooth(longleaf, at="points", sigma=6)) 353s + wt <- runif(npoints(longleaf)) 353s + crosscheque(Smooth(longleaf, at="points", sigma=6, weights=wt)) 353s + } 353s + if(FULLTEST) { 353s + vc <- diag(c(25,36)) 353s + crosscheque(Smooth(longleaf, at="points", varcov=vc)) 353s + crosscheque(Smooth(longleaf, at="points", varcov=vc, weights=wt)) 353s + } 353s + ## drop-dimension coding errors 353s + if(FULLTEST) { 353s + X <- longleaf 353s + marks(X) <- cbind(marks(X), 1) 353s + Z <- Smooth(X, 5) 353s + 353s + ZZ <- bw.smoothppp(finpines, hmin=0.01, hmax=0.012, nh=2) # reshaping problem 353s + } 353s + 353s + ## geometric-mean smoothing 353s + if(ALWAYS) { 353s + U <- Smooth(longleaf, 5, geometric=TRUE) 353s + } 353s + if(FULLTEST) { 353s + UU <- Smooth(X, 5, geometric=TRUE) 353s + V <- Smooth(longleaf, 5, geometric=TRUE, at="points") 353s + VV <- Smooth(X, 5, geometric=TRUE, at="points") 353s + } 353s + }) 356s > 356s > reset.spatstat.options() 356s > 356s > local({ 356s + There were 22 warnings (use warnings() to see them) 356s if(ALWAYS) { 356s + #' Kmeasure, second.moment.engine 356s + #' Expansion of window 356s + Zno <- Kmeasure(redwood, sigma=0.2, expand=FALSE) 356s + Zyes <- Kmeasure(redwood, sigma=0.2, expand=TRUE) 356s + #' All code blocks 356s + sigmadouble <- rep(0.1, 2) 356s + diagmat <- diag(sigmadouble^2) 356s + generalmat <- matrix(c(1, 0.5, 0.5, 1)/100, 2, 2) 356s + Z <- Kmeasure(redwood, sigma=sigmadouble) 356s + Z <- Kmeasure(redwood, varcov=diagmat) 356s + Z <- Kmeasure(redwood, varcov=generalmat) 356s + A <- second.moment.calc(redwood, 0.1, what="all", debug=TRUE) 356s + B <- second.moment.calc(redwood, varcov=diagmat, what="all") 356s + B <- second.moment.calc(redwood, varcov=diagmat, what="all") 356s + D <- second.moment.calc(redwood, varcov=generalmat, what="all") 356s + PR <- pixellate(redwood) 356s + DRno <- second.moment.calc(PR, 0.2, debug=TRUE, expand=FALSE, 356s + npts=npoints(redwood), obswin=Window(redwood)) 356s + DRyes <- second.moment.calc(PR, 0.2, debug=TRUE, expand=TRUE, 356s + npts=npoints(redwood), obswin=Window(redwood)) 356s + DR2 <- second.moment.calc(solist(PR, PR), 0.2, debug=TRUE, expand=TRUE, 356s + npts=npoints(redwood), obswin=Window(redwood)) 356s + Gmat <- generalmat * 100 356s + isoGauss <- function(x,y) {dnorm(x) * dnorm(y)} 356s + ee <- evaluate2Dkernel(isoGauss, runif(10), runif(10), 356s + varcov=Gmat, scalekernel=TRUE) 356s + isoGaussIm <- as.im(isoGauss, square(c(-3,3))) 356s + gg <- evaluate2Dkernel(isoGaussIm, runif(10), runif(10), 356s + varcov=Gmat, scalekernel=TRUE) 356s + ## experimental code 356s + op <- spatstat.options(developer=TRUE) 356s + DR <- density(redwood, 0.1) 356s + spatstat.options(op) 356s + } 356s + }) 356s smooth: maximum imaginary part= 4.59e-18 356s smooth: mass error= 0 356s 2nd moment measure: maximum imaginary part= 1.06e-16 356s 2nd moment measure: mass error= 0 356s smooth: maximum imaginary part= 2.27e-18 356s smooth: mass error= 0 356s 2nd moment measure: maximum imaginary part= 7.68e-17 356s 2nd moment measure: mass error= 0 356s smooth: maximum imaginary part= 6.13e-18 356s smooth: mass error= -4.97e-14 356s 2nd moment measure: maximum imaginary part= 3.87e-16 356s 2nd moment measure: mass error= 4.55e-13 356s smooth component 1 : maximum imaginary part= 6.13e-18 356s smooth component 1 : mass error= -4.97e-14 356s smooth component 2 : maximum imaginary part= 6.13e-18 356s smooth component 2 : mass error= -4.97e-14 356s 2nd moment measure: maximum imaginary part= 3.87e-16 356s 2nd moment measure: mass error= 4.55e-13 356s 2nd moment measure: maximum imaginary part= 3.87e-16 356s 2nd moment measure: mass error= 4.55e-13 357s > 357s > local({ 357s + if(FULLTEST) { 357s + #' bandwidth selection 357s + op <- spatstat.options(n.bandwidth=8) 357s + bw.diggle(cells) 357s + bw.diggle(cells, method="interpreted") # undocumented test 357s + ## bw.relrisk(urkiola, hmax=20) is tested in man/bw.relrisk.Rd 357s + bw.relrisk(urkiola, hmax=20, method="leastsquares") 357s + bw.relrisk(urkiola, hmax=20, method="weightedleastsquares") 357s + ZX <- density(swedishpines, at="points") 357s + bw.pcf(swedishpines, lambda=ZX) 357s + bw.pcf(swedishpines, lambda=ZX, 357s + bias.correct=FALSE, simple=FALSE, cv.method="leastSQ") 357s + spatstat.options(op) 357s + } 357s + }) 357s > 357s > local({ 357s + if(FULLTEST) { 357s + ## FOR EXCISION 357s + #' code in kernels.R 357s + kernames <- c("gaussian", "rectangular", "triangular", 357s + "epanechnikov", "biweight", "cosine", "optcosine") 357s + X <- rnorm(20) 357s + U <- runif(20) 357s + for(ker in kernames) { 357s + dX <- dkernel(X, ker) 357s + fX <- pkernel(X, ker) 357s + qU <- qkernel(U, ker) 357s + m0 <- kernel.moment(0, 0, ker) 357s + m1 <- kernel.moment(1, 0, ker) 357s + m2 <- kernel.moment(2, 0, ker) 357s + m3 <- kernel.moment(3, 0, ker) 357s + } 357s + } 357s + }) 357s > 357s > local({ 357s + if(FULLTEST) { 357s + ## idw 357s + Z <- idw(longleaf, power=4) 357s + Z <- idw(longleaf, power=4, se=TRUE) 357s + ZX <- idw(longleaf, power=4, at="points") 357s + ZX <- idw(longleaf, power=4, at="points", se=TRUE) 357s + } 357s + if(ALWAYS) { 357s + ## former bug in densityVoronoi.ppp 357s + X <- redwood[1:2] 357s + A <- densityVoronoi(X, f=0.51, counting=FALSE, fixed=FALSE, nrep=50, verbose=FALSE) 357s + ## dodgy code blocks in densityVoronoi.R 357s + A <- adaptive.density(nztrees, nrep=2, f=0.5, counting=TRUE) 357s + B <- adaptive.density(nztrees, nrep=2, f=0.5, counting=TRUE, fixed=TRUE) 357s + D <- adaptive.density(nztrees, nrep=2, f=0.5, counting=FALSE) 357s + E <- adaptive.density(nztrees, nrep=2, f=0.5, counting=FALSE, fixed=TRUE) 357s + } 357s + if(FULLTEST) { 357s + #' adaptive kernel estimation 357s + d10 <- nndist(nztrees, k=10) 357s + d10fun <- distfun(nztrees, k=10) 357s + d10im <- as.im(d10fun) 357s + uN <- 2 * runif(npoints(nztrees)) 357s + AA <- densityAdaptiveKernel(nztrees, bw=d10) 357s + BB <- densityAdaptiveKernel(nztrees, bw=d10, weights=uN) 357s + DD <- densityAdaptiveKernel(nztrees, bw=d10fun, weights=uN) 357s + EE <- densityAdaptiveKernel(nztrees, bw=d10im, weights=uN) 357s + } 357s + }) 357s Computing 2 intensity estimates...1, 357s 2. 357s Done. 357s Computing 2 intensity estimates...1, 357s 2. 357s Done. 357s Computing 2 intensity estimates...1, 357s 2. 357s Done. 357s Computing 2 intensity estimates...1, 357s 2. 357s Done. 357s > 357s > local({ 357s + if(ALWAYS) { 357s + ## FOR EXCISION 357s + ## unnormdensity 357s + x <- rnorm(20) 357s + d0 <- unnormdensity(x, weights=rep(0, 20)) 357s + dneg <- unnormdensity(x, weights=c(-runif(19), 0)) 357s + } 357s + if(FULLTEST) { 357s + ## cases of 'intensity' etc 357s + a <- intensity(amacrine, weights=expression(x)) 357s + SA <- split(amacrine) 357s + a <- intensity(SA, weights=expression(x)) 357s + a <- intensity(SA, weights=amacrine$x) 357s + 357s + ## check infrastructure for 'densityfun' 357s + f <- densityfun(cells, 0.05) 357s + Z <- as.im(f) 357s + Z <- as.im(f, W=square(0.5)) 357s + } 357s + }) 357s > 357s > 357s > reset.spatstat.options() 357s > 357s > 357s BEGIN TEST testsEtoF.R 358s 358s R version 4.3.2 (2023-10-31) -- "Eye Holes" 358s Copyright (C) 2023 The R Foundation for Statistical Computing 358s Platform: aarch64-unknown-linux-gnu (64-bit) 358s 358s R is free software and comes with ABSOLUTELY NO WARRANTY. 358s You are welcome to redistribute it under certain conditions. 358s Type 'license()' or 'licence()' for distribution details. 358s 358s R is a collaborative project with many contributors. 358s Type 'contributors()' for more information and 358s 'citation()' on how to cite R or R packages in publications. 358s 358s Type 'demo()' for some demos, 'help()' for on-line help, or 358s 'help.start()' for an HTML browser interface to help. 358s Type 'q()' to quit R. 358s 358s > #' 358s > #' Header for all (concatenated) test files 358s > #' 358s > #' Require spatstat.explore 358s > #' Obtain environment variable controlling tests. 358s > #' 358s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 358s > 358s > require(spatstat.explore) 358s Loading required package: spatstat.explore 358s Loading required package: spatstat.data 359s Loading required package: spatstat.geom 359s spatstat.geom 3.2-8 359s Loading required package: spatstat.random 359s spatstat.random 3.2-2 359s Loading required package: nlme 359s spatstat.explore 3.2-5 359s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 359s > ALWAYS <- TRUE 359s > cat(paste("--------- Executing", 359s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 359s + "test code -----------\n")) 359s --------- Executing **RESTRICTED** subset of test code ----------- 359s > # 359s > # tests/envelopes.R 359s > # 359s > # Test validity of envelope data 359s > # 359s > # $Revision: 1.28 $ $Date: 2022/11/24 01:35:26 $ 359s > # 359s > 359s > local({ 359s + 359s + 359s + 359s + ## check envelope calls from 'alltypes' 359s + if(ALWAYS) a <- alltypes(demopat, Kcross, nsim=4, envelope=TRUE) 359s + if(FULLTEST) b <- alltypes(demopat, Kcross, nsim=4, envelope=TRUE, global=TRUE) 359s + ## check 'transform' idioms 359s + if(ALWAYS) A <- envelope(cells, Kest, nsim=4, transform=expression(. - .x)) 359s + if(FULLTEST) B <- envelope(cells, Kest, nsim=4, transform=expression(sqrt(./pi) - .x)) 359s + 359s + 359s + # check conditional simulation 359s + if(FULLTEST) { 359s + e1 <- envelope(cells, Kest, nsim=4, fix.n=TRUE) 359s + e2 <- envelope(amacrine, Kest, nsim=4, fix.n=TRUE) 359s + e3 <- envelope(amacrine, Kcross, nsim=4, fix.marks=TRUE) 359s + e4 <- envelope(finpines, Kest, nsim=4, fix.n=TRUE) # multiple columns of marks 359s + e5 <- envelope(finpines, Kest, nsim=4, fix.marks=TRUE) 359s + } 359s + 359s + 359s + ## check pooling of envelopes in global case 359s + E1 <- envelope(cells, Kest, nsim=5, savefuns=TRUE, global=TRUE) 359s + E2 <- envelope(cells, Kest, nsim=12, savefuns=TRUE, global=TRUE) 359s + p12 <- pool(E1, E2) 359s + p12 <- pool(E1, E2, savefuns=TRUE) 359s + if(FULLTEST) { 359s + F1 <- envelope(cells, Kest, nsim=5, 359s + savefuns=TRUE, savepatterns=TRUE, global=TRUE) 359s + F2 <- envelope(cells, Kest, nsim=12, 359s + savefuns=TRUE, savepatterns=TRUE, global=TRUE) 359s + p12 <- pool(F1, F2) 359s + p12 <- pool(F1, F2, savefuns=TRUE, savepatterns=TRUE) 359s + E1r <- envelope(cells, Kest, nsim=5, savefuns=TRUE, global=TRUE, 359s + ginterval=c(0.05, 0.15)) 359s + E2r <- envelope(cells, Kest, nsim=12, savefuns=TRUE, global=TRUE, 359s + ginterval=c(0.05, 0.15)) 359s + p12r <- pool(E1r, E2r) 359s + } 359s + 359s + if(FULLTEST) { 359s + #' as.data.frame.envelope 359s + Nsim <- 5 359s + E <- envelope(cells, nsim=Nsim, savefuns=TRUE) 359s + A <- as.data.frame(E) 359s + B <- as.data.frame(E, simfuns=TRUE) 359s + stopifnot(ncol(B) - ncol(A) == Nsim) 359s + } 359s + 359s + if(FULLTEST) { 359s + #' cases not covered elsewhere 359s + A <- envelope(cells, nsim=5, alternative="less", 359s + do.pwrong=TRUE, use.theory=FALSE, 359s + savepatterns=TRUE, savefuns=TRUE) 359s + print(A) 359s + B <- envelope(A, nsim=5, savefuns=TRUE) 359s + D <- envelope(cells, "Lest", nsim=5) 359s + 359s + UU <- envelope(cells, nsim=5, foreignclass="ppp", clipdata=TRUE) 359s + 359s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", global=TRUE) 359s + AA <- envelope(cells, nsim=5, jsim=5, alternative="less", global=TRUE) 359s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", VARIANCE=TRUE) 359s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", VARIANCE=TRUE) 359s + 359s + #' spotted by Art Stock - bugs in ratfv class support 359s + BB <- envelope(redwood, Kinhom, nsim=5, sigma=bw.scott, ratio=TRUE, correction="border") 359s + CC <- envelope(redwood, Kinhom, nsim=5, sigma=bw.scott, global=TRUE, ratio=TRUE, correction="border") 359s + DD <- envelope(redwood, Finhom, nsim=5, sigma=bw.scott, ratio=TRUE, correction="trans") 359s + EE <- envelope(redwood, Finhom, nsim=5, sigma=bw.scott, global=TRUE, ratio=TRUE, correction="trans") 359s + 359s + #' envelopes based on sample variance 359s + E <- envelope(cells, nsim=8, VARIANCE=TRUE) 359s + G <- envelope(cells, nsim=8, VARIANCE=TRUE, 359s + use.theory=FALSE, do.pwrong=TRUE) 359s + print(G) 359s + #' summary method 359s + summary(E) 359s + summary(envelope(cells, nsim=5, simulate=expression(runifpoint(42)))) 359s + #' weights argument 359s + H1 <- envelope(cells, nsim=4, weights=npoints, savefuns=TRUE) 359s + H2 <- envelope(cells, nsim=4, weights=npoints, savefuns=TRUE) 359s + J1 <- envelope(cells, nsim=4, weights=npoints, VARIANCE=TRUE) 359s + J2 <- envelope(cells, nsim=4, weights=npoints, VARIANCE=TRUE) 359s + #' pooling with weights 359s + H <- pool(H1, H2) 359s + J <- pool(J1, J2) 359s + #' pooling envelopes with non-identical attributes 359s + H0 <- envelope(cells, nsim=4, savefuns=TRUE) 359s + HH <- pool(H0, H1) 359s + #' malformed argument 'simulate' 359s + A <- replicate(3, list(list(runifpoint(ex=cells)))) # list(list(ppp), list(ppp), list(ppp)) 359s + E <- envelope(cells, simulate=A, nsim=3) 359s + #' undocumented/secret 359s + K <- envelope(cells, nsim=4, saveresultof=npoints, collectrubbish=TRUE) 359s + #' so secret I've even forgotten how to do it 359s + M <- envelope(cells, nsim=4, internal=list(eject="patterns")) 359s + } 359s + 359s + 359s + if(ALWAYS) { 359s + #' Test robustness of envelope() sorting procedure when NA's are present 359s + #' Fails with spatstat.utils 1.12-0 359s + set.seed(42) 359s + EP <- envelope(longleaf, pcf, nsim=10, nrank=2) 359s + 359s + #' Test case when the maximum permitted number of failures is exceeded 359s + X <- amacrine[1:153] # contains exactly one point with mark='off' 359s + #' High probability of generating a pattern with no marks = 'off' 359s + E <- envelope(X, Kcross, nsim=39, maxnerr=2, maxerr.action="warn") 359s + A <- alltypes(X, Kcross, envelope=TRUE, nsim=39, maxnerr=2) 359s + } 359s + 359s + if(ALWAYS) { 359s + #' Internals: envelope.matrix 359s + Y <- matrix(rnorm(200), 10, 20) 359s + rr <- 1:10 359s + oo <- rnorm(10) 359s + zz <- numeric(10) 359s + E <- envelope(Y, rvals=rr, observed=oo, nsim=10) 359s + E <- envelope(Y, rvals=rr, observed=oo, jsim=1:10) 359s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 359s + type="global", use.theory=TRUE) 359s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 359s + type="global", use.theory=TRUE, nsim=10) 359s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 359s + type="global", use.theory=FALSE, nsim=10) 359s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 359s + nsim=10, nsim2=10) 359s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 359s + jsim=1:10, jsim.mean=11:20) 359s + if(FULLTEST) print(E) 359s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 359s + nsim=10, jsim.mean=11:20) 359s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 359s + jsim=1:10, nsim2=10) 359s + } 359s + 359s + if(ALWAYS) { 359s + #' quirk with handmade summary functions ('conserve' attribute) 359s + Kdif <- function(X, r=NULL) { # note no ellipsis 359s + Y <- split(X) 359s + K1 <- Kest(Y[[1]], r=r) 359s + K2 <- Kest(Y[[2]], r=r) 359s + D <- eval.fv(K1-K2) 359s + return(D) 359s + } 359s + envelope(amacrine, Kdif, nsim=3) 359s + } 359s + 359s + 359s + ## close 'local' 359s + }) 359s Generating 4 simulations of CSR ... 359s 1, 2, 3, 359s 4. 359s 359s Done. 359s Generating 5 simulations of CSR ... 360s 1, 2, 3, 4, 360s 5. 360s 360s Done. 360s Generating 12 simulations of CSR ... 360s 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 360s 12. 360s 360s Done. 360s Generating 10 simulations of CSR ... 360s 1, 2, 3, 4, 5, 6, 7, 8, 9, 360s 10. 360s 360s Done. 360s Generating 39 simulations of CSR ... 360s [retrying] 360s 1, 2, Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 360s No points have mark i = off 360s 3, 4, [retrying] 360s 5, 6, 360s Done. 360s Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 360s No points have mark i = off 360s Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 360s No points have mark i = off 360s Generating 3 simulations of CSR ... 360s 1, 2, 360s 3. 360s 360s Done. 360s Pointwise critical envelopes for K1(r)-K2(r) 360s and observed value for ‘amacrine’ 360s Edge correction: “iso” 360s Obtained from 3 simulations of CSR 360s Alternative: two.sided 360s Significance level of pointwise Monte Carlo test: 2/4 = 0.5 360s ................................................................................ 360s Math.label 360s r r 360s obs hat((K1-K2))[obs](r) 360s theo (K1-K2)[theo](r) 360s lo hat((K1-K2))[lo](r) 360s hi hat((K1-K2))[hi](r) 360s Description 360s r distance argument r 360s obs observed value of K1(r)-K2(r) for data pattern 360s theo theoretical value of K1(r)-K2(r) for CSR 360s lo lower pointwise envelope of K1(r)-K2(r) from simulations 360s hi upper pointwise envelope of K1(r)-K2(r) from simulations 360s ................................................................................ 360s Default plot formula: .~r 360s where “.” stands for ‘obs’, ‘theo’, ‘hi’, ‘lo’ 360s Columns ‘lo’ and ‘hi’ will be plotted as shading (by default) 360s Recommended range of argument r: [0, 0.25] 360s Available range of argument r: [0, 0.25] 360s Unit of length: 662 microns 360s > # 360s > # tests/fastK.R 360s > # 360s > # check fast and slow code for Kest 360s > # and options not tested elsewhere 360s > # 360s > # $Revision: 1.5 $ $Date: 2020/04/28 12:58:26 $ 360s > # 360s > if(ALWAYS) { 360s + local({ 360s + ## fast code 360s + Kb <- Kest(cells, nlarge=0) 360s + Ku <- Kest(cells, correction="none") 360s + Kbu <- Kest(cells, correction=c("none", "border")) 360s + ## slow code, full set of corrections, sqrt transformation, ratios 360s + Ldd <- Lest(unmark(demopat), correction="all", var.approx=TRUE, ratio=TRUE) 360s + ## Lotwick-Silverman var approx (rectangular window) 360s + Loo <- Lest(cells, correction="all", var.approx=TRUE, ratio=TRUE) 360s + ## Code for large dataset 360s + nbig <- .Machine$integer.max 360s + if(!is.null(nbig)) { 360s + nn <- ceiling(sqrt(nbig)) 360s + if(nn < 1e6) Kbig <- Kest(runifpoint(nn), 360s + correction=c("border", "bord.modif", "none"), 360s + ratio=TRUE) 360s + } 360s + 360s + ## Kinhom 360s + lam <- density(cells, at="points", leaveoneout=TRUE) 360s + ## fast code 360s + Kib <- Kinhom(cells, lam, nlarge=0) 360s + Kiu <- Kest(cells, lam, correction="none") 360s + Kibu <- Kest(cells, lam, correction=c("none", "border")) 360s + ## slow code 360s + Lidd <- Linhom(unmark(demopat), sigma=bw.scott) 360s + }) 360s + 360s + } 360s Warning messages: 360s 1: Exceeded maximum permissible number of (maxnerr = 2) when evaluating summary function for simulated point patterns 360s 2: In alltypes(X, Kcross, envelope = TRUE, nsim = 39, maxnerr = 2) : 360s 3 out of 4 envelopes were not computed, due to errors in evaluating the summary functions for simulated patterns 360s number of data points exceeds 0 - computing border correction estimate only 362s number of data points exceeds 0 - computing border correction estimate only 363s > Warning message: 363s Periodic correction is not defined for non-rectangular windows 363s ## 363s > ## tests/fvproblems.R 363s > ## 363s > ## problems with fv, ratfv and fasp code 363s > ## 363s > ## $Revision: 1.15 $ $Date: 2020/04/28 12:58:26 $ 363s > 363s > #' This appears in the workshop notes 363s > #' Problem detected by Martin Bratschi 363s > 363s > if(FULLTEST) { 363s + local({ 363s + Jdif <- function(X, ..., i) { 363s + Jidot <- Jdot(X, ..., i=i) 363s + J <- Jest(X, ...) 363s + dif <- eval.fv(Jidot - J) 363s + return(dif) 363s + } 363s + Z <- Jdif(amacrine, i="on") 363s + }) 363s + } 363s > #' 363s > #' Test mathlegend code 363s > #' 363s > local({ 363s + K <- Kest(cells) 363s + if(FULLTEST) { 363s + plot(K) 363s + plot(K, . ~ r) 363s + plot(K, . - theo ~ r) 363s + } 363s + if(ALWAYS) { 363s + plot(K, sqrt(./pi) ~ r) 363s + } 363s + if(FULLTEST) { 363s + plot(K, cbind(iso, theo) ~ r) 363s + plot(K, cbind(iso, theo) - theo ~ r) 363s + plot(K, sqrt(cbind(iso, theo)/pi) ~ r) 363s + plot(K, cbind(iso/2, -theo) ~ r) 363s + plot(K, cbind(iso/2, trans/2) - theo ~ r) 363s + } 363s + if(FULLTEST) { 363s + ## test expansion of .x and .y 363s + plot(K, . ~ .x) 363s + plot(K, . - theo ~ .x) 363s + plot(K, .y - theo ~ .x) 363s + } 363s + if(ALWAYS) { 363s + plot(K, sqrt(.y) - sqrt(theo) ~ .x) 363s + } 363s + 363s + # problems with parsing weird strings in levels(marks(X)) 363s + # noted by Ulf Mehlig 363s + if(ALWAYS) { 363s + levels(marks(amacrine)) <- c("Nasticreechia krorluppia", "Homo habilis") 363s + plot(Kcross(amacrine)) 363s + plot(alltypes(amacrine, "K")) 363s + } 363s + if(FULLTEST) { 363s + plot(alltypes(amacrine, "J")) 363s + plot(alltypes(amacrine, pcfcross)) 363s + } 363s + }) 363s > 363s > #' 363s > #' Test quirks related to 'alim' attribute 363s > 363s > if(FULLTEST) { 363s + local({ 363s + K <- Kest(cells) 363s + attr(K, "alim") <- NULL 363s + plot(K) 363s + attr(K, "alim") <- c(0, 0.1) 363s + plot(tail(K)) 363s + }) 363s + } 363s > 363s > #' 363s > #' Check that default 'r' vector passes the test for fine spacing 363s > 363s > if(ALWAYS) { 363s + local({ 363s + a <- Fest(cells) 363s + A <- Fest(cells, r=a$r) 363s + b <- Hest(heather$coarse) 363s + B <- Hest(heather$coarse, r=b$r) 363s + # from Cenk Icos 363s + X <- runifpoint(100, owin(c(0,3), c(0,10))) 363s + FX <- Fest(X) 363s + FXr <- Fest(X, r=FX$r) 363s + JX <- Jest(X) 363s + }) 363s + } 363s > 363s > ##' various functionality in fv.R 363s > 363s > if(ALWAYS) { 363s + local({ 363s + M <- cbind(1:20, matrix(runif(100), 20, 5)) 363s + A <- as.fv(M) 363s + fvlabels(A) <- c("r","%s(r)", "%s[A](r)", "%s[B](r)", "%s[C](r)", "%s[D](r)") 363s + A <- rename.fv(A, "M", quote(M(r))) 363s + A <- tweak.fv.entry(A, "V1", new.tag="r") 363s + A[,3] <- NULL 363s + A$hogwash <- runif(nrow(A)) 363s + fvnames(A, ".") <- NULL 363s + #' bind.fv with qualitatively different functions 363s + GK <- harmonise(G=Gest(cells), K=Kest(cells)) 363s + G <- GK$G 363s + K <- GK$K 363s + ss <- c(rep(TRUE, nrow(K)-10), rep(FALSE, 10)) 363s + U <- bind.fv(G, K[ss, ], clip=TRUE) 363s + #' 363s + H <- rebadge.as.crossfun(K, "H", "inhom", 1, 2) 363s + H <- rebadge.as.dotfun(K, "H", "inhom", 3) 363s + #' text layout 363s + op <- options(width=27) 363s + print(K) 363s + options(width=18) 363s + print(K) 363s + options(op) 363s + #' collapse.fv 363s + Kb <- Kest(cells, correction="border") 363s + Ki <- Kest(cells, correction="isotropic") 363s + collapse.fv(Kb, Ki, same="theo") 363s + collapse.fv(anylist(B=Kb, I=Ki), same="theo") 363s + collapse.fv(anylist(B=Kb), I=Ki, same="theo") 363s + Xlist <- replicate(3, runifpoint(30), simplify=FALSE) 363s + Klist <- anylapply(Xlist, Kest) 363s + collapse.fv(Klist, same="theo", different=c("iso", "border")) 363s + names(Klist) <- LETTERS[24:26] 363s + collapse.fv(Klist, same="theo", different=c("iso", "border")) 363s + }) 363s + } 363s Function value object 363s (class ‘fv’) 363s for the function r -> K(r) 363s ........................... 363s Math.label 363s r r 363s theo K[pois](r) 363s border hat(K)[bord](r) 363s trans hat(K)[trans](r) 363s iso hat(K)[iso](r) 363s Description 363s r distance argument r 363s theo theoretical [..] 363s border [..] 363s trans [..] 363s iso [..] 363s ........................... 363s Default plot formula: .~r 363s where “.” stands for 363s ‘iso’, ‘trans’, 363s ‘border’, ‘theo’ 363s Recommended range of 363s argument r: [0, 0.25] 363s Available range of 363s argument r: [0, 0.25] 363s Function value 363s object (class 363s ‘fv’) 363s for the function 363s r -> K(r) 363s .................. 363s Math.label 363s r r 363s theo K[pois](r) 363s border hat(K)[bord](r) 363s trans hat(K)[trans](r) 363s iso hat(K)[iso](r) 363s Description 363s r [..] 363s theo [..] 363s border [..] 363s trans [..] 363s iso [..] 363s .................. 363s Default plot 363s formula: .~r 363s where “.” 363s stands for 363s ‘iso’, 363s ‘trans’, 363s ‘border’, 363s ‘theo’ 363s Recommended range 363s of argument r: 363s [0, 0.25] 363s Available range 363s of argument r: 363s [0, 0.25] 363s Function value object (class ‘fv’) 363s for the function r -> K(r) 363s ................................................................ 363s Math.label Description 363s r r distance argument r 363s theo K[pois](r) theoretical Poisson K(r) 363s Xborder X~hat(K)[bord](r) X border-corrected estimate of K(r) 363s Xiso X~hat(K)[iso](r) X isotropic-corrected estimate of K(r) 363s Yborder Y~hat(K)[bord](r) Y border-corrected estimate of K(r) 363s Yiso Y~hat(K)[iso](r) Y isotropic-corrected estimate of K(r) 363s Zborder Z~hat(K)[bord](r) Z border-corrected estimate of K(r) 363s Ziso Z~hat(K)[iso](r) Z isotropic-corrected estimate of K(r) 363s ................................................................ 363s Default plot formula: .~.x 363s where “.” stands for ‘theo’, ‘Xborder’, ‘Xiso’, ‘Yborder’, 363s ‘Yiso’, ‘Zborder’, ‘Ziso’ 363s Recommended range of argument r: [0, 0.25] 363s Available range of argument r: [0, 0.25] 363s > 363s > if(FULLTEST) { 363s + local({ 363s + ## rat 363s + K <- Kest(cells, ratio=TRUE) 363s + G <- Gest(cells, ratio=TRUE) 363s + print(K) 363s + compatible(K, K) 363s + compatible(K, G) 363s + H <- rat(K, attr(K, "numerator"), attr(K, "denominator"), check=TRUE) 363s + }) 363s + } 363s > 363s > if(FULLTEST) { 363s + local({ 363s + ## bug in Jmulti.R colliding with breakpts.R 363s + B <- owin(c(0,3), c(0,10)) 363s + Y <- superimpose(A=runifpoint(1212, B), B=runifpoint(496, B)) 363s + JDX <- Jdot(Y) 363s + JCX <- Jcross(Y) 363s + Jdif <- function(X, ..., i) { 363s + Jidot <- Jdot(X, ..., i=i) 363s + J <- Jest(X, ...) 363s + dif <- eval.fv(Jidot - J) 363s + return(dif) 363s + } 363s + E <- envelope(Y, Jdif, nsim=19, i="A", simulate=expression(rlabel(Y))) 363s + }) 363s + } 363s Warning message: 363s In bind.fv(G, K[ss, ], clip = TRUE) : 363s The column name ‘theo’ was duplicated. Unique names were generated 363s > 363s > if(FULLTEST) { 363s + local({ 363s + #' fasp axes, title, dimnames 363s + a <- alltypes(amacrine) 363s + a$title <- NULL 363s + plot(a, samex=TRUE, samey=TRUE) 363s + dimnames(a) <- lapply(dimnames(a), toupper) 363s + 363s + b <- as.fv(a) 363s + }) 363s + } 363s > 363s > if(FULLTEST) { 363s + local({ 363s + ## plot.anylist (fv) 363s + b <- anylist(A=Kcross(amacrine), B=Kest(amacrine)) 363s + plot(b, equal.scales=TRUE, main=expression(sqrt(pi))) 363s + plot(b, arrange=FALSE) 363s + }) 363s + } 363s > 363s BEGIN TEST testsGtoJ.R 363s 363s R version 4.3.2 (2023-10-31) -- "Eye Holes" 363s Copyright (C) 2023 The R Foundation for Statistical Computing 363s Platform: aarch64-unknown-linux-gnu (64-bit) 363s 363s R is free software and comes with ABSOLUTELY NO WARRANTY. 363s You are welcome to redistribute it under certain conditions. 363s Type 'license()' or 'licence()' for distribution details. 363s 363s R is a collaborative project with many contributors. 363s Type 'contributors()' for more information and 363s 'citation()' on how to cite R or R packages in publications. 363s 363s Type 'demo()' for some demos, 'help()' for on-line help, or 363s 'help.start()' for an HTML browser interface to help. 363s Type 'q()' to quit R. 363s 364s > #' 364s > #' Header for all (concatenated) test files 364s > #' 364s > #' Require spatstat.explore 364s > #' Obtain environment variable controlling tests. 364s > #' 364s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 364s > 364s > require(spatstat.explore) 364s Loading required package: spatstat.explore 364s Loading required package: spatstat.data 364s Loading required package: spatstat.geom 364s spatstat.geom 3.2-8 364s Loading required package: spatstat.random 365s spatstat.random 3.2-2 365s Loading required package: nlme 365s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 365s > ALWAYS <- TRUE 365s > cat(paste("--------- Executing", 365s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 365s + "test code -----------\n")) 365s spatstat.explore 3.2-5 365s --------- Executing **RESTRICTED** subset of test code ----------- 365s > ## 365s > ## tests/gcc323.R 365s > ## 365s > ## $Revision: 1.3 $ $Date: 2020/04/28 12:58:26 $ 365s > ## 365s > if(ALWAYS) { # depends on hardware 365s + local({ 365s + # critical R values that provoke GCC bug #323 365s + a <- marktable(lansing, R=0.25) 365s + a <- marktable(lansing, R=0.21) 365s + a <- marktable(lansing, R=0.20) 365s + a <- marktable(lansing, R=0.10) 365s + }) 365s + } 365s > #' tests/hypotests.R 365s > #' Hypothesis tests 365s > #' 365s > #' $Revision: 1.10 $ $Date: 2023/07/17 07:30:48 $ 365s > 365s > if(FULLTEST) { 365s + local({ 365s + 365s + hopskel.test(redwood, method="MonteCarlo", nsim=5) 365s + 365s + #' quadrat test - spatial methods 365s + a <- quadrat.test(redwood, 3) 365s + domain(a) 365s + shift(a, c(1,1)) 365s + 365s + #' quadrat test - correctness of mapping from table to quadrats 365s + Q2 <- quadratcount(humberside, 2, 3) 365s + T2 <- suppressWarnings(quadrat.test(Q2)) 365s + R2 <- cbind(as.numeric(t(Q2)), round(10 * residuals(T2))) 365s + R2correct <- cbind(c(2, 20, 13, 11, 34, 123), 365s + c(-46, -12, -62, -41, 50, 134)) 365s + if(!all(R2 == R2correct)) 365s + stop("Incorrect count-residual map for quadrat.test(2,3)") 365s + 365s + Q5 <- quadratcount(humberside, 5, 3) 365s + T5 <- suppressWarnings(quadrat.test(Q5)) 365s + R5 <- cbind(as.numeric(t(Q5)), round(10 * residuals(T5))) 365s + R5correct <- cbind( 365s + c( 0, 0, 3, 19, 3, 2, 14, 5, 0, 2, 117, 35, 3), 365s + c(-19, -33, -42, 16, -37, -49, -28, -35, -5, -21, 295, 40, -32)) 365s + if(!all(R5 == R5correct)) 365s + stop("Incorrect count-residual map for quadrat.test(5,3)") 365s + 365s + #' cases of studpermu.test 365s + #' X is a hyperframe 365s + b <- studpermu.test(pyramidal, nperm=9) 365s + b <- studpermu.test(pyramidal, nperm=9, use.Tbar=TRUE) 365s + #' X is a list of lists of ppp 365s + ZZ <- split(pyramidal$Neurons, pyramidal$group) 365s + bb <- studpermu.test(ZZ, nperm=9) 365s + 365s + #' Issue #115 365s + X <- runifpoint(50, nsim = 3) 365s + Y <- runifpoint(3000, nsim = 3) 365s + h <- hyperframe(ppp = c(X, Y), group = rep(1:2, 3)) 365s + studpermu.test(h, ppp ~ group) 365s + 365s + #' scan test 365s + Z <- scanmeasure(cells, 0.1, method="fft") 365s + rr <- c(0.05, 1) 365s + scan.test(amacrine, rr, nsim=5, 365s + method="binomial", alternative="less") 365s + }) 365s + } 365s > # 365s > # tests/imageops.R 365s > # 365s > # $Revision: 1.43 $ $Date: 2023/08/29 01:03:59 $ 365s > # 365s > 365s > 365s > if(FULLTEST) { 365s + local({ 365s + #' case of "[.im" and "[<-.im" where index is an ssf 365s + d <- distmap(cells, dimyx=32) 365s + Empty <- cells[FALSE] 365s + EmptyFun <- ssf(Empty, numeric(0)) 365s + ff <- d[EmptyFun] 365s + d[EmptyFun] <- 42 365s + 365s + #' Smooth.im -> blur.im with sigma=NULL 365s + Z <- as.im(function(x,y) { x - y }, letterR, dimyx=32) 365s + ZS <- Smooth(Z) 365s + 365s + #' deprecated -> im.apply(DA, which.max) 365s + Z <- which.max.im(bei.extra) 365s + 365s + #' rotmean 365s + U <- rotmean(Z, origin="midpoint", result="im", padzero=FALSE) 365s + 365s + #' cases of distcdf 365s + distcdf(cells[1:5]) 365s + distcdf(W=cells[1:5], dW=1:5) 365s + distcdf(W=Window(cells), V=cells[1:5]) 365s + distcdf(W=Window(cells), V=cells[1:5], dV=1:5) 365s + }) 365s + } 365s > 365s > 365s BEGIN TEST testsK.R 365s 365s R version 4.3.2 (2023-10-31) -- "Eye Holes" 365s Copyright (C) 2023 The R Foundation for Statistical Computing 365s Platform: aarch64-unknown-linux-gnu (64-bit) 365s 365s R is free software and comes with ABSOLUTELY NO WARRANTY. 365s You are welcome to redistribute it under certain conditions. 365s Type 'license()' or 'licence()' for distribution details. 365s 365s R is a collaborative project with many contributors. 365s Type 'contributors()' for more information and 365s 'citation()' on how to cite R or R packages in publications. 365s 365s Type 'demo()' for some demos, 'help()' for on-line help, or 365s 'help.start()' for an HTML browser interface to help. 365s Type 'q()' to quit R. 365s 365s > #' 365s > #' Header for all (concatenated) test files 365s > #' 365s > #' Require spatstat.explore 365s > #' Obtain environment variable controlling tests. 365s > #' 365s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 365s > 365s > require(spatstat.explore) 365s Loading required package: spatstat.explore 365s Loading required package: spatstat.data 366s Loading required package: spatstat.geom 366s spatstat.geom 3.2-8 366s Loading required package: spatstat.random 366s spatstat.random 3.2-2 366s Loading required package: nlme 366s spatstat.explore 3.2-5 366s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 366s > ALWAYS <- TRUE 366s > cat(paste("--------- Executing", 366s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 366s + "test code -----------\n")) 366s --------- Executing **RESTRICTED** subset of test code ----------- 366s > #' 367s > #' tests/Kfuns.R 367s > #' 367s > #' Various K and L functions and pcf 367s > #' 367s > #' $Revision: 1.43 $ $Date: 2022/06/17 01:47:08 $ 367s > #' 367s > #' Assumes 'EveryStart.R' was run 367s > 367s > if(FULLTEST) { 367s + Cells <- cells 367s + Amacrine <- amacrine 367s + Redwood <- redwood 367s + } else { 367s + ## reduce numbers of data + dummy points 367s + spatstat.options(npixel=32, ndummy.min=16) 367s + Cells <- cells[c(FALSE, TRUE)] 367s + Amacrine <- amacrine[c(FALSE, TRUE)] 367s + Redwood <- redwood[c(FALSE, TRUE)] 367s + } 367s > 367s > 367s > myfun <- function(x,y){(x+1) * y } # must be outside 367s > 367s > local({ 367s + if(FULLTEST) { 367s + #' supporting code 367s + rmax.rule("Kscaled", owin(), 42) 367s + implemented.for.K(c("border", "bord.modif", "translate", "good", "best"), 367s + "polygonal", TRUE) 367s + implemented.for.K(c("border", "bord.modif", "translate", "good", "best"), 367s + "mask", TRUE) 367s + implemented.for.K(c("border", "isotropic"), "mask", TRUE) 367s + implemented.for.K(c("border", "isotropic"), "mask", FALSE) 367s + #' shortcuts 367s + D <- density(Cells) 367s + K <- Kborder.engine(Cells, rmax=0.4, weights=D, ratio=TRUE) 367s + K <- Knone.engine(Cells, rmax=0.4, weights=D, ratio=TRUE) 367s + allcor <- c("none", "border", "bord.modif","isotropic", "translate") 367s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor) 367s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor, 367s + weights=D) 367s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor, 367s + use.integers=FALSE) 367s + #' Kest special code blocks 367s + K <- Kest(Cells, var.approx=TRUE, ratio=FALSE) 367s + Z <- distmap(Cells) + 1 367s + Kb <- Kest(Cells, correction=c("border","bord.modif"), 367s + weights=Z, ratio=TRUE) 367s + Kn <- Kest(Cells, correction="none", 367s + weights=Z, ratio=TRUE) 367s + Knb <- Kest(Cells, correction=c("border","bord.modif","none"), 367s + weights=Z, ratio=TRUE) 367s + } 367s + if(ALWAYS) { 367s + bigint <- 50000 # This is only "big" on a 32-bit system where 367s + # sqrt(.Machine$integer.max) = 46340.9 367s + X <- runifpoint(bigint) 367s + Z <- as.im(1/bigint, owin()) 367s + Kb <- Kest(X, correction=c("border","bord.modif"), 367s + rmax=0.02, weights=Z, ratio=TRUE) 367s + } 367s + if(FULLTEST) { 367s + Kn <- Kest(X, correction="none", 367s + rmax=0.02, weights=Z, ratio=TRUE) 367s + Knb <- Kest(X, correction=c("border","bord.modif","none"), 367s + rmax=0.02, weights=Z, ratio=TRUE) 367s + #' pcf.ppp special code blocks 367s + pr <- pcf(Cells, ratio=TRUE, var.approx=TRUE) 367s + pc <- pcf(Cells, domain=square(0.5)) 367s + pcr <- pcf(Cells, domain=square(0.5), ratio=TRUE) 367s + pw <- pcf(Redwood, correction="none") 367s + pwr <- pcf(Redwood, correction="none", ratio=TRUE) 367s + pv <- pcf(Redwood, kernel="rectangular") 367s + p1 <- pcf(Redwood[1]) 367s + #' pcf.fv 367s + K <- Kest(Redwood) 367s + g <- pcf(K, method="a") 367s + g <- pcf(K, method="c") 367s + g <- pcf(K, method="d") 367s + #' Kinhom code blocks 367s + X <- rpoispp(function(x,y) { 100 * x }, 100, square(1)) 367s + lambda <- 100 * X$x 367s + Kin <- Kinhom(X, lambda, correction=c("none", "border")) 367s + lambda2 <- outer(lambda, lambda, "*") 367s + Ki2 <- Kinhom(X, lambda2=lambda2, diagonal=FALSE, 367s + correction=c("translate", "isotropic")) 367s + } 367s + if(ALWAYS) { 367s + #' edge corrections 367s + rr <- rep(0.1, npoints(Cells)) 367s + eC <- edge.Ripley(Cells, rr) 367s + eI <- edge.Ripley(Cells, rr, method="interpreted") 367s + if(max(abs(eC-eI)) > 0.1) 367s + stop("Ripley edge correction results do not match") 367s + } 367s + if(FULLTEST) { 367s + a <- rmax.Ripley(square(1)) 367s + a <- rmax.Rigid(square(1)) 367s + a <- rmax.Ripley(as.polygonal(square(1))) 367s + a <- rmax.Rigid(as.polygonal(square(1))) 367s + a <- rmax.Ripley(letterR) 367s + a <- rmax.Rigid(letterR) 367s + } 367s + if(ALWAYS) { 367s + #' run slow code for edge correction and compare results 367s + op <- spatstat.options(npixel=128) 367s + X <- Redwood[c(TRUE, FALSE, FALSE, FALSE)] 367s + Window(X) <- as.polygonal(Window(X)) 367s + Eapprox <- edge.Trans(X) 367s + Eexact <- edge.Trans(X, exact=TRUE) 367s + maxrelerr <- max(abs(1 - range(Eapprox/Eexact))) 367s + if(maxrelerr > 0.1) 367s + stop(paste("Exact and approximate algorithms for edge.Trans disagree by", 367s + paste0(round(100*maxrelerr), "%")), 367s + call.=FALSE) 367s + spatstat.options(op) 367s + } 367s + }) 367s > 367s > local({ 367s + if(FULLTEST) { 367s + #' ---- multitype ------ 367s + K <- Kcross(Amacrine, correction=c("none", "bord.modif")) 367s + K <- Kcross(Amacrine, correction=c("none", "bord", "bord.modif"), 367s + ratio=TRUE) 367s + #' inhomogeneous multitype 367s + K2 <- Kcross.inhom(Amacrine, lambdaX=densityfun(Amacrine)) 367s + K3 <- Kcross.inhom(Amacrine, lambdaX=density(Amacrine, at="points")) 367s + K5 <- Kcross.inhom(Amacrine, correction="bord.modif") 367s + #' markconnect, markcorr 367s + M <- markconnect(Amacrine, "on", "off", normalise=TRUE) 367s + M <- markcorr(longleaf, normalise=TRUE, 367s + correction=c("isotropic", "translate", "border", "none")) 367s + M <- markcorr(longleaf, normalise=TRUE, fargs=list()) 367s + #' Kmark (=markcorrint) 367s + X <- runifpoint(100) %mark% runif(100) 367s + km <- Kmark(X, f=atan2) 367s + km <- Kmark(X, f1=sin) 367s + km <- Kmark(X, f="myfun") 367s + aa <- Kmark(X, normalise=FALSE, returnL=FALSE) 367s + aa <- Kmark(X, normalise=FALSE, returnL=TRUE) 367s + aa <- Kmark(X, normalise=TRUE, returnL=FALSE) 367s + aa <- Kmark(X, normalise=TRUE, returnL=TRUE) 367s + } 367s + }) 367s > 367s > local({ 367s + if(FULLTEST) { 367s + #' various modified K functions 367s + #' 367s + #' directional K functions 367s + #' 367s + a <- Ksector(swedishpines, 367s + -pi/2, pi/2, units="radians", 367s + correction=c("none", "border", "bord.modif", 367s + "Ripley", "translate"), 367s + ratio=TRUE) 367s + plot(a) 367s + #' 367s + #' local K functions 367s + #' 367s + Z <- as.im(intensity(swedishpines), W=Window(swedishpines)) 367s + ZX <- Z[swedishpines] 367s + a <- localLinhom(swedishpines, lambda=Z) 367s + a <- localLinhom(swedishpines, lambda=ZX) 367s + a <- localLinhom(swedishpines, lambda=Z, correction="none") 367s + a <- localLinhom(swedishpines, lambda=Z, correction="translate") 367s + a <- localLcross(Amacrine) 367s + a <- localLcross(Amacrine, from="off", to="off") 367s + a <- localKdot(Amacrine) 367s + a <- localLdot(Amacrine) 367s + a <- localKcross.inhom(Amacrine) 367s + a <- localLcross.inhom(Amacrine) 367s + Zed <- solapply(intensity(amacrine), as.im, W=Window(amacrine)) 367s + Lum <- evaluateCovariateAtPoints(Zed, Amacrine) 367s + moff <- (marks(Amacrine) == "off") 367s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed) 367s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Lum) 367s + a <- localLcross.inhom(Amacrine, from="off", to="on", 367s + lambdaFrom=Lum[moff], lambdaTo=Lum[!moff]) 367s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 367s + correction="none") 367s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 367s + correction="translate") 367s + #' 367s + #' cases of resolve.lambdacross 367s + #' 367s + h <- resolve.lambdacross(Amacrine, moff, !moff) 367s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=Zed) 367s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=Lum) 367s + h <- resolve.lambdacross(Amacrine, moff, !moff, 367s + lambdaI=Zed[["off"]], lambdaJ=Zed[["on"]]) 367s + h <- resolve.lambdacross(Amacrine, moff, !moff, 367s + lambdaI=Lum[moff], lambdaJ=Lum[!moff]) 367s + d <- densityfun(unmark(Amacrine), sigma=0.1) 367s + dm <- lapply(split(Amacrine), densityfun, sigma=0.1) 367s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=d) 367s + h <- resolve.lambdacross(Amacrine, moff, !moff, 367s + lambdaI=dm[["off"]], lambdaJ=dm[["on"]]) 367s + h <- resolve.lambdacross(Amacrine, moff, !moff, 367s + lambdaX=function(x,y,m){ d(x,y) }) 367s + #' 367s + #' multitype inhomogeneous pcf 367s + #' 367s + g <- pcfcross.inhom(Amacrine, 367s + lambdaI=dm[["off"]], lambdaJ=dm[["on"]]) 367s + 367s + #' 367s + #' lohboot code blocks 367s + #' 367s + Ared <- lohboot(Redwood, fun="Kest", block=TRUE, 367s + Vcorrection=TRUE, global=FALSE, correction="none") 367s + Bred <- lohboot(Redwood, block=TRUE, basicboot=TRUE, global=FALSE) 367s + Cred <- lohboot(Redwood, fun=Kest, block=TRUE, global=TRUE, 367s + correction="translate") 367s + Dred <- lohboot(Redwood, Lest) 367s + Kred <- lohboot(Redwood, Kinhom) 367s + Lred <- lohboot(Redwood, Linhom) 367s + gred <- lohboot(Redwood, pcfinhom, sigma=0.1) 367s + #' 367s + X <- runifpoint(100, letterR) 367s + AX <- lohboot(X, block=TRUE, nx=7, ny=10) 367s + #' multitype 367s + b <- lohboot(Amacrine, Kcross) 367s + b <- lohboot(Amacrine, Lcross) 367s + b <- lohboot(Amacrine, Kdot) 367s + b <- lohboot(Amacrine, Ldot) 367s + b <- lohboot(Amacrine, Kcross.inhom) 367s + b <- lohboot(Amacrine, Lcross.inhom) 367s + 367s + ## Kscaled 367s + A <- Lscaled(japanesepines, renormalise=TRUE, correction="all") 367s + } 367s + }) 367s > 367s > local({ 367s + if(ALWAYS) { 367s + #' From Ege, in response to a stackoverflow question. 367s + #' The following example has two points separated by r = 1 with 1/4 of the 367s + #' circumference outside the 10x10 window (i.e. area 100). 367s + #' Thus the value of K^(r) should jump from 0 to 367s + #' 100/(2\cdot 1)\cdot ((3/4)^{-1} + (3/4)^{-1}) = 100 \cdot 4/3 = 133.333. 367s + x <- c(4.5,5.5) 367s + y <- c(10,10)-sqrt(2)/2 367s + W <- square(10) 367s + X <- ppp(x, y, W) 367s + compere <- function(a, b, where, tol=1e-6) { 367s + descrip <- paste("discrepancy in isotropic edge correction", where) 367s + err <- as.numeric(a) - as.numeric(b) 367s + maxerr <- max(abs(err)) 367s + blurb <- paste(descrip, "is", paste0(signif(maxerr, 4), ","), 367s + if(maxerr > tol) "exceeding" else "within", 367s + "tolerance of", tol) 367s + message(blurb) 367s + if(maxerr > tol) { 367s + message(paste("Discrepancies:", paste(err, collapse=", "))) 367s + stop(paste("excessive", descrip), call.=FALSE) 367s + } 367s + invisible(TRUE) 367s + } 367s + ## Testing: 367s + eX <- edge.Ripley(X, c(1,1)) 367s + compere(eX, c(4/3,4/3), "at interior point of rectangle") 367s + ## Corner case: 367s + Y <- X 367s + Y$x <- X$x-4.5+sqrt(2)/2 367s + eY <- edge.Ripley(Y, c(1,1)) 367s + compere(eY, c(2,4/3), "near corner of rectangle") 367s + ## Invoke polygonal code 367s + Z <- rotate(Y, pi/4) 367s + eZdebug <- edge.Ripley(Z, c(1,1), internal=list(debug=TRUE)) 367s + compere(eZdebug, c(2,4/3), "at interior point of polygon (debug on)") 367s + ## test validity without debugger,in case of quirks of compiler optimisation 367s + eZ <- edge.Ripley(Z, c(1,1)) 367s + compere(eZ, c(2,4/3), "at interior point of polygon (debug off)") 367s + } 367s + }) 367s /// Debug level 3 /// 367s ------- centre[0] = (-6.071068, 7.071068) ------ 367s boundary distance 0.707107 367s radius[0] = 1.000000 367s ... Edge[0] = (0.000000,0.000000) to (7.071068,7.071068) 367s Left: det = -35.857864 367s Right: det = -171.715729 367s Top: det = -34143.145751 367s Finished cutting; ncut = 0 367s contrib = -0.000000 367s ... Edge[1] = (7.071068,7.071068) to (0.000000,14.142136) 367s Left: det = -171.715729 367s Right: det = -35.857864 367s Top: det = -34143.145751 367s Finished cutting; ncut = 0 367s contrib = 0.000000 367s ... Edge[2] = (0.000000,14.142136) to (-7.071068,7.071068) 367s Left: det = -35.857864 367s Right: det = 0.000000 367s det = 0 367s Top: det = 200.000000 367s det > 0 367s hits + segment: t = 1.000000, theta = 3.141593 367s hits - segment: t = 0.858579, theta = 1.570796 367s Finished cutting; ncut = 2 367s theta[0] = 1.570796 367s theta[1] = 3.141593 367s Interval 0, width 1.570796:inside 367s Interval 1, width 1.570796:outside 367s Interval 2, width 3.141593:inside 367s contrib = 4.712389 367s ... Edge[3] = (-7.071068,7.071068) to (0.000000,0.000000) 367s Left: det = 0.000000 367s det = 0 367s Right: det = -35.857864 367s Top: det = 200.000000 367s det > 0 367s hits + segment: t = 0.141421, theta = -1.570796 367s hits - segment: t = 0.000000, theta = 3.141593 367s Finished cutting; ncut = 2 367s theta[0] = 3.141593 367s theta[1] = 4.712389 367s Interval 0, width 3.141593:outside 367s Interval 1, width 1.570796:inside 367s Interval 2, width 1.570796:outside 367s contrib = -1.570796 367s 367s Total = 3.141593 = 0.500000 * (2 * pi) 367s ------- centre[1] = (-5.363961, 7.778175) ------ 367s boundary distance 0.707107 367s radius[0] = 1.000000 367s ... Edge[0] = (0.000000,0.000000) to (7.071068,7.071068) 367s Left: det = -27.772078 367s Right: det = -153.629942 367s Top: det = -34143.145751 367s Finished cutting; ncut = 0 367s contrib = -0.000000 367s ... Edge[1] = (7.071068,7.071068) to (0.000000,14.142136) 367s Left: det = -153.629942 367s Right: det = -27.772078 367s Top: det = -27108.831175 367s Finished cutting; ncut = 0 367s contrib = 0.000000 367s ... Edge[2] = (0.000000,14.142136) to (-7.071068,7.071068) 367s Left: det = -27.772078 367s Right: det = -1.914214 367s Top: det = 200.000000 367s det > 0 367s hits + segment: t = 0.900000, theta = 3.141593 367s hits - segment: t = 0.758579, theta = 1.570796 367s Finished cutting; ncut = 2 367s theta[0] = 1.570796 367s theta[1] = 3.141593 367s Interval 0, width 1.570796:inside 367s Interval 1, width 1.570796:outside 367s Interval 2, width 3.141593:inside 367s contrib = 4.712389 367s ... Edge[3] = (-7.071068,7.071068) to (0.000000,0.000000) 367s Left: det = -1.914214 367s Right: det = -27.772078 367s Top: det = -765.685425 367s Finished cutting; ncut = 0 367s contrib = -0.000000 367s 367s Total = 4.712389 = 0.750000 * (2 * pi) 367s > 367s > 367s > 367s > reset.spatstat.options() 367s > 367s BEGIN TEST testsL.R 367s discrepancy in isotropic edge correction at interior point of rectangle is 2.22e-16, within tolerance of 1e-06 367s discrepancy in isotropic edge correction near corner of rectangle is 8.882e-16, within tolerance of 1e-06 367s discrepancy in isotropic edge correction at interior point of polygon (debug on) is 6.439e-15, within tolerance of 1e-06 367s discrepancy in isotropic edge correction at interior point of polygon (debug off) is 6.439e-15, within tolerance of 1e-06 367s 367s R version 4.3.2 (2023-10-31) -- "Eye Holes" 367s Copyright (C) 2023 The R Foundation for Statistical Computing 367s Platform: aarch64-unknown-linux-gnu (64-bit) 367s 367s R is free software and comes with ABSOLUTELY NO WARRANTY. 367s You are welcome to redistribute it under certain conditions. 367s Type 'license()' or 'licence()' for distribution details. 367s 367s R is a collaborative project with many contributors. 367s Type 'contributors()' for more information and 367s 'citation()' on how to cite R or R packages in publications. 367s 367s Type 'demo()' for some demos, 'help()' for on-line help, or 367s 'help.start()' for an HTML browser interface to help. 367s Type 'q()' to quit R. 367s 367s > #' 367s > #' Header for all (concatenated) test files 367s > #' 367s > #' Require spatstat.explore 367s > #' Obtain environment variable controlling tests. 367s > #' 367s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 367s > 367s > require(spatstat.explore) 367s Loading required package: spatstat.explore 367s Loading required package: spatstat.data 368s Loading required package: spatstat.geom 368s spatstat.geom 3.2-8 368s Loading required package: spatstat.random 368s spatstat.random 3.2-2 368s Loading required package: nlme 368s spatstat.explore 3.2-5 368s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 368s > ALWAYS <- TRUE 368s > cat(paste("--------- Executing", 368s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 368s + "test code -----------\n")) 368s --------- Executing **RESTRICTED** subset of test code ----------- 368s > ## 368s > ## tests/localpcf.R 368s > ## 368s > ## temporary test file for localpcfmatrix 368s > ## $Revision: 1.2 $ $Date: 2015/12/29 08:54:49 $ 368s > 368s > local({ 368s + a <- localpcfmatrix(redwood) 368s + if(FULLTEST) { 368s + a 368s + plot(a) 368s + a[, 3:5] 368s + } 368s + }) 368s > 368s BEGIN TEST testsM.R 368s 368s R version 4.3.2 (2023-10-31) -- "Eye Holes" 368s Copyright (C) 2023 The R Foundation for Statistical Computing 368s Platform: aarch64-unknown-linux-gnu (64-bit) 368s 368s R is free software and comes with ABSOLUTELY NO WARRANTY. 368s You are welcome to redistribute it under certain conditions. 368s Type 'license()' or 'licence()' for distribution details. 368s 368s R is a collaborative project with many contributors. 368s Type 'contributors()' for more information and 368s 'citation()' on how to cite R or R packages in publications. 368s 368s Type 'demo()' for some demos, 'help()' for on-line help, or 368s 'help.start()' for an HTML browser interface to help. 368s Type 'q()' to quit R. 368s 368s > #' 368s > #' Header for all (concatenated) test files 368s > #' 368s > #' Require spatstat.explore 368s > #' Obtain environment variable controlling tests. 368s > #' 368s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 368s > 368s > require(spatstat.explore) 368s Loading required package: spatstat.explore 368s Loading required package: spatstat.data 369s Loading required package: spatstat.geom 369s spatstat.geom 3.2-8 369s Loading required package: spatstat.random 369s spatstat.random 3.2-2 369s Loading required package: nlme 369s spatstat.explore 3.2-5 369s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 369s > ALWAYS <- TRUE 369s > cat(paste("--------- Executing", 369s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 369s + "test code -----------\n")) 369s --------- Executing **RESTRICTED** subset of test code ----------- 369s > ## 369s > ## tests/markcor.R 369s > ## 369s > ## Tests of mark correlation code (etc) 369s > ## 369s > ## $Revision: 1.7 $ $Date: 2020/11/25 01:23:32 $ 369s > 369s > local({ 369s + if(ALWAYS) { 369s + ## check.testfun checks equality of functions 369s + ## and is liable to break if the behaviour of all.equal is changed 369s + fe <- function(m1, m2) {m1 == m2} 369s + fm <- function(m1, m2) {m1 * m2} 369s + fs <- function(m1, m2) {sqrt(m1)} 369s + if(check.testfun(fe, X=amacrine)$ftype != "equ") 369s + warning("check.testfun fails to recognise mark equality function") 369s + if(check.testfun(fm, X=longleaf)$ftype != "mul") 369s + warning("check.testfun fails to recognise mark product function") 369s + check.testfun(fs, X=longleaf) 369s + check.testfun("mul") 369s + check.testfun("equ") 369s + } 369s + 369s + if(FULLTEST) { 369s + ## test all is well in Kmark -> Kinhom 369s + MA <- Kmark(amacrine,function(m1,m2){m1==m2}) 369s + set.seed(42) 369s + AR <- rlabel(amacrine) 369s + MR <- Kmark(AR,function(m1,m2){m1==m2}) 369s + if(isTRUE(all.equal(MA,MR))) 369s + stop("Kmark unexpectedly ignores marks") 369s + 369s + ## cover code blocks in markcorr() 369s + X <- runifpoint(100) %mark% runif(100) 369s + Y <- X %mark% data.frame(u=runif(100), v=runif(100)) 369s + ww <- runif(100) 369s + fone <- function(x) { x/2 } 369s + ffff <- function(x,y) { fone(x) * fone(y) } 369s + aa <- markcorr(Y) 369s + bb <- markcorr(Y, ffff, weights=ww, normalise=TRUE) 369s + bb <- markcorr(Y, ffff, weights=ww, normalise=FALSE) 369s + bb <- markcorr(Y, f1=fone, weights=ww, normalise=TRUE) 369s + bb <- markcorr(Y, f1=fone, weights=ww, normalise=FALSE) 369s + 369s + ## markcrosscorr 369s + a <- markcrosscorr(betacells, normalise=FALSE) 369s + if(require(sm)) { 369s + b <- markcrosscorr(betacells, method="sm") 369s + } 369s + 369s + ## Vmark with normalisation 369s + v <- Vmark(spruces, normalise=TRUE) 369s + v <- Vmark(finpines, normalise=TRUE) 369s + } 369s + }) 369s Warning messages: 369s 1: In eval(quote({ : 369s check.testfun fails to recognise mark equality function 369s 2: In eval(quote({ :> #' tests/mctests.R 369s > #' Monte Carlo tests 369s > #' (mad.test, dclf.test, envelopeTest, hasenvelope) 369s > #' $Revision: 1.5 $ $Date: 2022/05/23 04:09:49 $ 369s > 369s > local({ 369s + if(FULLTEST) { 369s + envelopeTest(cells, Lest, exponent=1, nsim=9, savepatterns=TRUE) 369s + (a3 <- envelopeTest(cells, Lest, exponent=3, nsim=9, savepatterns=TRUE)) 369s + 369s + envelopeTest(a3, Lest, exponent=3, nsim=9, alternative="less") 369s + 369s + envelopeTest(redwood, Lest, exponent=1, nsim=19, 369s + rinterval=c(0, 0.1), alternative="greater", clamp=TRUE) 369s + envelopeTest(redwood, pcf, exponent=Inf, nsim=19, 369s + rinterval=c(0, 0.1), alternative="greater", clamp=TRUE) 369s + } 369s + }) 369s > 369s > 369s > 369s BEGIN TEST testsNtoO.R 369s 369s check.testfun fails to recognise mark product function 369s 369s R version 4.3.2 (2023-10-31) -- "Eye Holes" 369s Copyright (C) 2023 The R Foundation for Statistical Computing 369s Platform: aarch64-unknown-linux-gnu (64-bit) 369s 369s R is free software and comes with ABSOLUTELY NO WARRANTY. 369s You are welcome to redistribute it under certain conditions. 369s Type 'license()' or 'licence()' for distribution details. 369s 369s R is a collaborative project with many contributors. 369s Type 'contributors()' for more information and 369s 'citation()' on how to cite R or R packages in publications. 369s 369s Type 'demo()' for some demos, 'help()' for on-line help, or 369s 'help.start()' for an HTML browser interface to help. 369s Type 'q()' to quit R. 369s 370s > #' 370s > #' Header for all (concatenated) test files 370s > #' 370s > #' Require spatstat.explore 370s > #' Obtain environment variable controlling tests. 370s > #' 370s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 370s > 370s > require(spatstat.explore) 370s Loading required package: spatstat.explore 370s Loading required package: spatstat.data 370s Loading required package: spatstat.geom 370s spatstat.geom 3.2-8 370s Loading required package: spatstat.random 370s spatstat.random 3.2-2 370s Loading required package: nlme 371s spatstat.explore 3.2-5 371s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 371s > ALWAYS <- TRUE 371s > cat(paste("--------- Executing", 371s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 371s + "test code -----------\n")) 371s --------- Executing **RESTRICTED** subset of test code ----------- 371s > # 371s > # tests/NAinCov.R 371s > # 371s > # Testing the response to the presence of NA's in covariates 371s > # 371s > # $Revision: 1.8 $ $Date: 2022/05/22 08:37:38 $ 371s > 371s > if(FULLTEST) { 371s + local({ 371s + #' quantile.ewcdf 371s + f <- ewcdf(runif(100), runif(100)) 371s + qf <- quantile(f, probs=c(0.1, NA, 0.8)) 371s + #' quantile.density 371s + f <- density(runif(100)) 371s + qf <- quantile(f, probs=c(0.1, NA, 0.8)) 371s + }) 371s + } 371s > # 371s > # tests/nnstat.R 371s > # 371s > # Check code that uses nndist/nnwhich 371s > # 371s > # nnorient() 371s > # stienen() 371s > # 371s > # $Revision: 1.1 $ $Date: 2020/12/04 03:45:44 $ 371s > # 371s > 371s > 371s > local({ 371s + if(FULLTEST) { 371s + #' test nnorient 371s + nnorient(cells, domain=erosion(Window(cells), 0.1)) 371s + #' degenerate case 371s + X <- cells[nndist(cells) > bdist.points(cells)] 371s + f <- nnorient(X) 371s + #' nnclean 371s + A <- nnclean(shapley, k=17, edge.correct=TRUE) 371s + B <- nnclean(runifpoint3(300), 3) 371s + #' stienen set 371s + #' bug when disc radius is zero 371s + Y <- unmark(humberside)[40:100] # contains duplicated points 371s + stienen(Y) 371s + Z <- stienenSet(Y) 371s + #' other cases 371s + U <- stienen(cells[1]) 371s + V <- stienenSet(cells, edge=FALSE) 371s + } 371s + }) 371s > 371s > 371s > 371s > 371s BEGIN TEST testsP1.R 371s 371s R version 4.3.2 (2023-10-31) -- "Eye Holes" 371s Copyright (C) 2023 The R Foundation for Statistical Computing 371s Platform: aarch64-unknown-linux-gnu (64-bit) 371s 371s R is free software and comes with ABSOLUTELY NO WARRANTY. 371s You are welcome to redistribute it under certain conditions. 371s Type 'license()' or 'licence()' for distribution details. 371s 371s R is a collaborative project with many contributors. 371s Type 'contributors()' for more information and 371s 'citation()' on how to cite R or R packages in publications. 371s 371s Type 'demo()' for some demos, 'help()' for on-line help, or 371s 'help.start()' for an HTML browser interface to help. 371s Type 'q()' to quit R. 371s 371s Loading required package: spatstat.explore 371s Loading required package: spatstat.data 371s > #' 371s > #' Header for all (concatenated) test files 371s > #' 371s > #' Require spatstat.explore 371s > #' Obtain environment variable controlling tests. 371s > #' 371s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 371s > 371s > require(spatstat.explore) 372s Loading required package: spatstat.geom 372s spatstat.geom 3.2-8 372s Loading required package: spatstat.random 372s spatstat.random 3.2-2 372s Loading required package: nlme 372s spatstat.explore 3.2-5 372s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 372s > ALWAYS <- TRUE 372s > cat(paste("--------- Executing", 372s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 372s + "test code -----------\n")) 372s --------- Executing **RESTRICTED** subset of test code ----------- 372s > ## 372s > ## tests/pixelgripes.R 372s > ## Problems related to pixellation of windows 372s > ## 372s > ## $Revision: 1.8 $ $Date: 2022/10/23 06:21:10 $ 372s > 372s > if(FULLTEST) { 372s + local({ 372s + 372s + 372s + }) 372s + } 372s > 372s BEGIN TEST testsP2.R 372s 372s R version 4.3.2 (2023-10-31) -- "Eye Holes" 372s Copyright (C) 2023 The R Foundation for Statistical Computing 372s Platform: aarch64-unknown-linux-gnu (64-bit) 372s 372s R is free software and comes with ABSOLUTELY NO WARRANTY. 372s You are welcome to redistribute it under certain conditions. 372s Type 'license()' or 'licence()' for distribution details. 372s 372s R is a collaborative project with many contributors. 372s Type 'contributors()' for more information and 372s 'citation()' on how to cite R or R packages in publications. 372s 372s Type 'demo()' for some demos, 'help()' for on-line help, or 372s 'help.start()' for an HTML browser interface to help. 372s Type 'q()' to quit R. 372s 372s > #' 372s > #' Header for all (concatenated) test files 372s > #' 372s > #' Require spatstat.explore 372s > #' Obtain environment variable controlling tests. 372s > #' 372s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 372s > 372s > require(spatstat.explore) 372s Loading required package: spatstat.explore 372s Loading required package: spatstat.data 373s Loading required package: spatstat.geom 373s spatstat.geom 3.2-8 373s Loading required package: spatstat.random 373s spatstat.random 3.2-2 373s Loading required package: nlme 373s spatstat.explore 3.2-5 373s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 373s > ALWAYS <- TRUE 373s > cat(paste("--------- Executing", 373s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 373s + "test code -----------\n")) 373s --------- Executing **RESTRICTED** subset of test code ----------- 373s > 373s BEGIN TEST testsQ.R 373s 373s R version 4.3.2 (2023-10-31) -- "Eye Holes" 373s Copyright (C) 2023 The R Foundation for Statistical Computing 373s Platform: aarch64-unknown-linux-gnu (64-bit) 373s 373s R is free software and comes with ABSOLUTELY NO WARRANTY. 373s You are welcome to redistribute it under certain conditions. 373s Type 'license()' or 'licence()' for distribution details. 373s 373s R is a collaborative project with many contributors. 373s Type 'contributors()' for more information and 373s 'citation()' on how to cite R or R packages in publications. 373s 373s Type 'demo()' for some demos, 'help()' for on-line help, or 373s 'help.start()' for an HTML browser interface to help. 373s Type 'q()' to quit R. 373s 373s > #' 373s > #' Header for all (concatenated) test files 373s > #' 373s > #' Require spatstat.explore 373s > #' Obtain environment variable controlling tests. 373s > #' 373s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 373s > 373s > require(spatstat.explore) 373s Loading required package: spatstat.explore 373s Loading required package: spatstat.data 374s Loading required package: spatstat.geom 374s spatstat.geom 3.2-8 374s Loading required package: spatstat.random 374s spatstat.random 3.2-2 374s Loading required package: nlme 374s spatstat.explore 3.2-5 374s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 374s > ALWAYS <- TRUE 374s > cat(paste("--------- Executing", 374s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 374s + "test code -----------\n")) 374s --------- Executing **RESTRICTED** subset of test code ----------- 374s > 375s BEGIN TEST testsR1.R 375s 375s R version 4.3.2 (2023-10-31) -- "Eye Holes" 375s Copyright (C) 2023 The R Foundation for Statistical Computing 375s Platform: aarch64-unknown-linux-gnu (64-bit) 375s 375s R is free software and comes with ABSOLUTELY NO WARRANTY. 375s You are welcome to redistribute it under certain conditions. 375s Type 'license()' or 'licence()' for distribution details. 375s 375s R is a collaborative project with many contributors. 375s Type 'contributors()' for more information and 375s 'citation()' on how to cite R or R packages in publications. 375s 375s Type 'demo()' for some demos, 'help()' for on-line help, or 375s 'help.start()' for an HTML browser interface to help. 375s Type 'q()' to quit R. 375s 375s > #' 375s > #' Header for all (concatenated) test files 375s > #' 375s > #' Require spatstat.explore 375s > #' Obtain environment variable controlling tests. 375s > #' 375s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 375s > 375s > require(spatstat.explore) 375s Loading required package: spatstat.explore 375s Loading required package: spatstat.data 376s Loading required package: spatstat.geom 376s spatstat.geom 3.2-8 376s Loading required package: spatstat.random 376s spatstat.random 3.2-2 376s Loading required package: nlme 376s spatstat.explore 3.2-5 376s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 376s > ALWAYS <- TRUE 376s > cat(paste("--------- Executing", 376s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 376s + "test code -----------\n")) 376s --------- Executing **RESTRICTED** subset of test code ----------- 376s > ## 376s > ## tests/rhohat.R 376s > ## 376s > ## Test all combinations of options for rhohatCalc 376s > ## 376s > ## $Revision: 1.6 $ $Date: 2022/05/22 08:03:48 $ 376s > 376s > local({ 376s + if(FULLTEST) { 376s + X <- rpoispp(function(x,y){exp(3+3*x)}) 376s + Z <- as.im(function(x,y) { x }, Window(X)) 376s + f <- funxy(function(x,y) { y + 1 }, Window(X)) 376s + 376s + ## rhohat.ppp 376s + ## done in example(rhohat): 376s + ## rhoA <- rhohat(X, "x") 376s + ## rhoB <- rhohat(X, "x", method="reweight") 376s + ## rhoC <- rhohat(X, "x", method="transform") 376s + ## alternative smoother (if package locfit available) 376s + rhoA <- rhohat(X, "x", smoother="local") 376s + rhoB <- rhohat(X, "x", smoother="local", method="reweight") 376s + rhoC <- rhohat(X, "x", smoother="local", method="transform") 376s + 376s + #' code blocks 376s + rhoD <- rhohat(X, "y", positiveCI=TRUE) 376s + rhoE <- rhohat(X, Z, positiveCI=TRUE) 376s + #' weights 376s + rhoF <- rhohat(X, Z, weights=f(X)) 376s + rhoG <- rhohat(X, Z, weights=f) 376s + rhoH <- rhohat(X, Z, weights=as.im(f)) 376s + 376s + lam <- as.im(function(x,y) {exp(3+2*x)}, W=Window(Z)) 376s + 376s + ## Baseline 376s + rhoAb <- rhohat(X, "x", baseline=lam) 376s + rhoBb <- rhohat(X, "x", method="reweight", baseline=lam) 376s + rhoCb <- rhohat(X, "x", method="transform", baseline=lam) 376s + 376s + ## Horvitz-Thompson 376s + rhoAH <- rhohat(X, "x", horvitz=TRUE) 376s + rhoBH <- rhohat(X, "x", method="reweight", horvitz=TRUE) 376s + rhoCH <- rhohat(X, "x", method="transform", horvitz=TRUE) 376s + 376s + ## class support 376s + plot(rhoA) 376s + plot(rhoA, rho ~ x, shade=NULL) 376s + plot(rhoA, log(rho) ~ x, shade=NULL) 376s + plot(rhoA, log(.) ~ x) 376s + 376s + ## rho2hat 376s + r2xy <- rho2hat(X, "x", "y") 376s + r2xyw <- rho2hat(X, "x", "y", method="reweight") 376s + print(r2xyw) 376s + plot(r2xy, do.points=TRUE) 376s + xcoord <- function(x,y) x 376s + ycoord <- function(x,y) y 376s + xim <- as.im(xcoord, W=Window(X)) 376s + r2fi <- rho2hat(X, ycoord, xim) 376s + r2if <- rho2hat(X, xim, ycoord) 376s + } 376s + }) 376s > 376s BEGIN TEST testsR2.R 376s 376s R version 4.3.2 (2023-10-31) -- "Eye Holes" 376s Copyright (C) 2023 The R Foundation for Statistical Computing 376s Platform: aarch64-unknown-linux-gnu (64-bit) 376s 376s R is free software and comes with ABSOLUTELY NO WARRANTY. 376s You are welcome to redistribute it under certain conditions. 376s Type 'license()' or 'licence()' for distribution details. 376s 376s R is a collaborative project with many contributors. 376s Type 'contributors()' for more information and 376s 'citation()' on how to cite R or R packages in publications. 376s 376s Type 'demo()' for some demos, 'help()' for on-line help, or 376s 'help.start()' for an HTML browser interface to help. 376s Type 'q()' to quit R. 376s 376s > #' 376s > #' Header for all (concatenated) test files 376s > #' 376s > #' Require spatstat.explore 376s > #' Obtain environment variable controlling tests. 376s > #' 376s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 376s > 376s > require(spatstat.explore) 376s Loading required package: spatstat.explore 376s Loading required package: spatstat.data 377s Loading required package: spatstat.geom 377s spatstat.geom 3.2-8 377s Loading required package: spatstat.random 377s spatstat.random 3.2-2 377s Loading required package: nlme 377s spatstat.explore 3.2-5 377s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 377s > ALWAYS <- TRUE 377s > cat(paste("--------- Executing", 377s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 377s + "test code -----------\n")) 377s --------- Executing **RESTRICTED** subset of test code ----------- 377s > 377s BEGIN TEST testsS.R 377s 377s R version 4.3.2 (2023-10-31) -- "Eye Holes" 377s Copyright (C) 2023 The R Foundation for Statistical Computing 377s Platform: aarch64-unknown-linux-gnu (64-bit) 377s 377s R is free software and comes with ABSOLUTELY NO WARRANTY. 377s You are welcome to redistribute it under certain conditions. 377s Type 'license()' or 'licence()' for distribution details. 377s 377s R is a collaborative project with many contributors. 377s Type 'contributors()' for more information and 377s 'citation()' on how to cite R or R packages in publications. 377s 377s Type 'demo()' for some demos, 'help()' for on-line help, or 377s 'help.start()' for an HTML browser interface to help. 377s Type 'q()' to quit R. 377s 377s > #' 377s > #' Header for all (concatenated) test files 377s > #' 377s > #' Require spatstat.explore 377s > #' Obtain environment variable controlling tests. 377s > #' 377s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 377s > 377s > require(spatstat.explore) 377s Loading required package: spatstat.explore 377s Loading required package: spatstat.data 378s Loading required package: spatstat.geom 378s spatstat.geom 3.2-8 378s Loading required package: spatstat.random 378s spatstat.random 3.2-2 378s Loading required package: nlme 378s spatstat.explore 3.2-5 378s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 378s > ALWAYS <- TRUE 378s > cat(paste("--------- Executing", 378s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 378s + "test code -----------\n")) 378s --------- Executing **RESTRICTED** subset of test code ----------- 378s > #' tests/sdr.R 378s > #' 378s > #' $Revision: 1.2 $ $Date: 2020/05/01 09:59:59 $ 379s > 379s > if(FULLTEST) { 379s + local({ 379s + AN <- sdr(bei, bei.extra, method="NNIR") 379s + AV <- sdr(bei, bei.extra, method="SAVE") 379s + AI <- sdr(bei, bei.extra, method="SIR") 379s + AT <- sdr(bei, bei.extra, method="TSE") 379s + subspaceDistance(AN$B, AV$B) 379s + dimhat(AN$M) 379s + }) 379s + } 379s > ## 379s > ## tests/segments.R 379s > ## Tests of psp class and related code 379s > ## [SEE ALSO: tests/xysegment.R] 379s > ## 379s > ## $Revision: 1.33 $ $Date: 2022/05/22 08:39:47 $ 379s > 379s > 379s > local({ 379s + if(ALWAYS) { # C code 379s + #' tests of density.psp 379s + Y <- edges(letterR) 379s + Window(Y) <- grow.rectangle(Frame(Y), 0.4) 379s + YC <- density(Y, 0.2, method="C", edge=FALSE, dimyx=64) 379s + YI <- density(Y, 0.2, method="interpreted", edge=FALSE, dimyx=64) 379s + YF <- density(Y, 0.2, method="FFT", edge=FALSE, dimyx=64) 379s + xCI <- max(abs(YC/YI - 1)) 379s + xFI <- max(abs(YF/YI - 1)) 379s + cat(paste("xCI =", xCI, "\txFI =", signif(xFI, 5)), fill=TRUE) 379s + if(xCI > 0.01) stop(paste("density.psp C algorithm relative error =", xCI)) 379s + if(xFI > 0.1) stop(paste("density.psp FFT algorithm relative error =", xFI)) 379s + 379s + B <- square(0.3) 379s + density(Y, 0.2, at=B) 379s + density(Y, 0.2, at=B, edge=TRUE, method="C") 379s + Z <- runifrect(3, B) 379s + density(Y, 0.2, at=Z) 379s + density(Y, 0.2, at=Z, edge=TRUE, method="C") 379s + } 379s + 379s + if(FULLTEST) { 379s + #' segment clipping in window (bug found by Rolf) 379s + set.seed(42) 379s + X <- runifpoint(50, letterR) 379s + SP <- dirichletEdges(X) #' clip to polygonal window 379s + Window(X) <- as.mask(Window(X)) 379s + SM <- dirichletEdges(X) #' clip to mask window 379s + } 379s + 379s + if(FULLTEST) { 379s + #' test rshift.psp and append.psp with marks (Ute Hahn) 379s + m <- data.frame(A=1:10, B=letters[1:10]) 379s + g <- gl(3, 3, length=10) 379s + X <- psp(runif(10), runif(10), runif(10), runif(10), window=owin(), marks=m) 379s + Y <- rshift(X, radius = 0.1) 379s + Y <- rshift(X, radius = 0.1, group=g) 379s + #' mark management 379s + b <- data.frame(A=1:10) 379s + X <- psp(runif(10), runif(10), runif(10), runif(10), window=owin(), marks=b) 379s + stopifnot(is.data.frame(marks(X))) 379s + Y <- rshift(X, radius = 0.1) 379s + Y <- rshift(X, radius = 0.1, group=g) 379s + } 379s + 379s + }) 379s xCI = 2.55351295663786e-15 xFI = 0.073128 380s > 380s > 380s > 380s > # 380s > ## tests/sigtraceprogress.R 380s > # 380s > ## Tests of *.sigtrace and *.progress 380s > # 380s > ## $Revision: 1.5 $ $Date: 2020/05/01 09:59:59 $ 380s > 380s > if(FULLTEST) { 380s + local({ 380s + plot(dclf.sigtrace(redwood, nsim=19, alternative="greater", rmin=0.02, 380s + verbose=FALSE)) 380s + plot(dclf.progress(redwood, nsim=19, alternative="greater", rmin=0.02, 380s Warning message: 380s the images ‘dens’ and ‘edg’ were not compatible 380s + verbose=FALSE)) 380s + plot(dg.sigtrace(redwood, nsim=5, alternative="greater", rmin=0.02, 380s + verbose=FALSE)) 380s + plot(dg.progress(redwood, nsim=5, alternative="greater", rmin=0.02, 380s + verbose=FALSE)) 380s + ## test 'leave-two-out' algorithm 380s + a <- dclf.sigtrace(redwood, Lest, nsim=9, use.theory=FALSE, leaveout=2, 380s + verbose=FALSE) 380s + aa <- dclf.progress(redwood, Lest, nsim=9, use.theory=FALSE, leaveout=2, 380s + verbose=FALSE) 380s + b <- dg.sigtrace(redwood, Lest, nsim=5, use.theory=FALSE, leaveout=2) 380s + bb <- dg.progress(redwood, Lest, nsim=5, use.theory=FALSE, leaveout=2, 380s + verbose=FALSE) 380s + ## other code blocks 380s + e <- mad.progress(redwood, nsim=5) 380s + e <- mad.progress(redwood, nsim=19, alpha=0.05) 380s + f <- dclf.progress(redwood, nsim=5, scale=function(x) x^2) 380s + f <- dclf.progress(redwood, nsim=5, normalize=TRUE, deflate=TRUE) 380s + g <- dg.progress(redwood, nsim=5, scale=function(x) x^2) 380s + g <- dg.progress(redwood, nsim=5, normalize=TRUE, deflate=TRUE) 380s + }) 380s + } 380s > #' 380s > #' tests/ssf.R 380s > #' 380s > #' Tests of 'ssf' class 380s > #' 380s > #' $Revision: 1.5 $ $Date: 2020/12/04 08:02:25 $ 380s > #' 380s > 380s > if(FULLTEST) { 380s + local({ 380s + Y <- cells[1:5] 380s + X <- rsyst(Window(Y), 5) 380s + Z <- runifpoint(3, Window(Y)) 380s + f1 <- ssf(X, nncross(X,Y,what="dist")) 380s + f2 <- ssf(X, nncross(X,Y,what="dist", k=1:2)) 380s + image(f1) 380s + g1 <- as.function(f1) 380s + g1(Z) 380s + g2 <- as.function(f2) 380s + g2(Z) 380s + plot(f1, style="contour") 380s + plot(f1, style="imagecontour") 380s + contour(f1) 380s + apply.ssf(f2, 1, sum) 380s + range(f1) 380s + min(f1) 380s + max(f1) 380s + integral(f1, weights=tile.areas(dirichlet(X))) 380s + }) 380s + } 380s > #' 380s > #' tests/sumfun.R 380s > #' 380s > #' Tests of code for summary functions 380s > #' 380s > #' $Revision: 1.9 $ $Date: 2022/05/22 08:45:23 $ 380s > 380s > if(ALWAYS) { # involves C code 380s + local({ 380s + W <- owin(c(0,1), c(-1/2, 0)) 380s + Gr <- Gest(redwood, correction="all",domain=W) 380s + Fr <- Fest(redwood, correction="all",domain=W) 380s + Jr <- Jest(redwood, correction="all",domain=W) 380s + 380s + F0 <- Fest(redwood[FALSE], correction="all") 380s + Fh <- Fest(humberside, domain=erosion(Window(humberside), 100)) 380s + 380s + FIr <- Finhom(redwood, savelambda=TRUE, ratio=TRUE) 380s + JIr <- Jinhom(redwood, savelambda=TRUE, ratio=TRUE) 380s + 380s + Ga <- Gcross(amacrine, correction="all") 380s + Ia <- Iest(amacrine, correction="all") 380s + lam <- intensity(amacrine) 380s + lmin <- 0.9 * min(lam) 380s + nJ <- sum(marks(amacrine) == "off") 380s + FM <- FmultiInhom(amacrine, marks(amacrine) == "off", 380s + lambdaJ=rep(lam["off"], nJ), 380s + lambdamin = lmin) 380s + GM <- GmultiInhom(amacrine, marks(amacrine) == "on", 380s + marks(amacrine) == "off", 380s + lambda=lam[marks(amacrine)], 380s + lambdamin=lmin, 380s + ReferenceMeasureMarkSetI=42) 380s + 380s + a <- compileCDF(D=nndist(redwood), 380s + B=bdist.points(redwood), 380s + r=seq(0, 1, length=256)) 380s + 380s + #' Tstat (triplet) function, all code blocks 380s + a <- Tstat(redwood, ratio=TRUE, 380s + correction=c("none", "border", "bord.modif", "translate")) 380s + 380s + ## distance argument spacing and breakpoints 380s + e <- check.finespacing(c(0,1,2), eps=0.1, action="silent") 380s + b <- as.breakpts(pi, 20) 380s + b <- as.breakpts(42, max=pi, npos=20) 380s + b <- even.breaks.owin(letterR) 380s + }) 380s + } 382s Searching 59340 potential triangles; estimated time 0.000426 sec 382s > 382s BEGIN TEST testsT.R 382s 382s R version 4.3.2 (2023-10-31) -- "Eye Holes" 382s Copyright (C) 2023 The R Foundation for Statistical Computing 382s Platform: aarch64-unknown-linux-gnu (64-bit) 382s 382s R is free software and comes with ABSOLUTELY NO WARRANTY. 382s You are welcome to redistribute it under certain conditions. 382s Type 'license()' or 'licence()' for distribution details. 382s 382s R is a collaborative project with many contributors. 382s Type 'contributors()' for more information and 382s 'citation()' on how to cite R or R packages in publications. 382s 382s Type 'demo()' for some demos, 'help()' for on-line help, or 382s 'help.start()' for an HTML browser interface to help. 382s Type 'q()' to quit R. 382s 383s > #' 383s > #' Header for all (concatenated) test files 383s > #' 383s > #' Require spatstat.explore 383s > #' Obtain environment variable controlling tests. 383s > #' 383s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 383s > 383s > require(spatstat.explore) 383s Loading required package: spatstat.explore 383s Loading required package: spatstat.data 383s Loading required package: spatstat.geom 383s spatstat.geom 3.2-8 384s Loading required package: spatstat.random 384s spatstat.random 3.2-2 384s Loading required package: nlme 384s spatstat.explore 3.2-5 384s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 384s > ALWAYS <- TRUE 384s > cat(paste("--------- Executing", 384s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 384s + "test code -----------\n")) 384s --------- Executing **RESTRICTED** subset of test code ----------- 384s > #' 384s > #' tests/threedee.R 384s > #' 384s > #' Tests of 3D code 384s > #' 384s > #' $Revision: 1.8 $ $Date: 2020/05/02 01:32:58 $ 384s > #' 384s > 384s > local({ 384s + X <- runifpoint3(30) 384s + Y <- runifpoint3(20) 384s + if(FULLTEST) { 384s + A <- runifpoint3(10, nsim=2) 384s + Z <- ppsubset(X, 2:4) 384s + } 384s + ## 384s + if(ALWAYS) { # includes C code 384s + d <- pairdist(X, periodic=TRUE, squared=TRUE) 384s + d <- crossdist(X, Y, squared=TRUE) 384s + d <- crossdist(X, Y, squared=TRUE, periodic=TRUE) 384s + #' 384s + h <- has.close(X, 0.2) 384s + h <- has.close(X, 0.2, periodic=TRUE) 384s + h <- has.close(X, 0.2, Y=Y) 384s + h <- has.close(X, 0.2, Y=Y, periodic=TRUE) 384s + #' code blocks not otherwise reached 384s + rmax <- 0.6 * max(nndist(X)) 384s + g <- G3est(X, rmax=rmax, correction="rs") 384s + g <- G3est(X, rmax=rmax, correction="km") 384s + g <- G3est(X, rmax=rmax, correction="Hanisch") 384s + g <- G3est(X, rmax=rmax, sphere="ideal") 384s + g <- G3est(X, rmax=rmax, sphere="digital") 384s + v <- sphere.volume() 384s + v <- digital.volume() 384s + #' older code 384s + co <- coords(X) 384s + xx <- co$x 384s + yy <- co$y 384s + zz <- co$z 384s + gg1 <- g3engine(xx, yy, zz, correction="Hanisch G3") 384s + gg2 <- g3engine(xx, yy, zz, correction="minus sampling") 384s + ff1 <- f3engine(xx, yy, zz, correction="no") 384s + ff2 <- f3engine(xx, yy, zz, correction="minus sampling") 384s + } 384s + ## 384s + if(ALWAYS) { 384s + #'class support 384s + X <- runifpoint3(10) 384s + print(X) 384s + print(X %mark% runif(10)) 384s + print(X %mark% factor(letters[c(1:5,5:1)])) 384s + print(X %mark% data.frame(a=1:10, b=runif(10))) 384s + da <- as.Date(paste0("2020-01-0", c(1:5,5:1))) 384s + print(X %mark% da) 384s + print(X %mark% data.frame(a=1:10, b=da)) 384s + } 384s + }) 384s Three-dimensional point pattern: 10 points 384s Box: [0, 1] x [0, 1] x [0, 1] units 384s Marked three-dimensional point pattern: 10 points 384s marks are numeric, of storage type ‘double’ 384s Box: [0, 1] x [0, 1] x [0, 1] units 384s Marked three-dimensional point pattern: 10 points 384s Multitype, with levels = a, b, c, d, e 384s Box: [0, 1] x [0, 1] x [0, 1] units 384s Marked three-dimensional point pattern: 10 points 384s Mark variables: a, b 384s Box: [0, 1] x [0, 1] x [0, 1] units 384s Marked three-dimensional point pattern: 10 points 384s marks are dates, of class ‘Date’ 384s Box: [0, 1] x [0, 1] x [0, 1] units 384s Marked three-dimensional point pattern: 10 points 384s Mark variables: a, b 384s Box: [0, 1] x [0, 1] x [0, 1] units 384s > 384s Warning messages: 384s 1: In G3est: unrecognised argument ‘sphere’ was ignored 384s 2: In G3est: unrecognised argument ‘sphere’ was ignored 384s BEGIN TEST testsUtoZ.R 384s 384s R version 4.3.2 (2023-10-31) -- "Eye Holes" 384s Copyright (C) 2023 The R Foundation for Statistical Computing 384s Platform: aarch64-unknown-linux-gnu (64-bit) 384s 384s R is free software and comes with ABSOLUTELY NO WARRANTY. 384s You are welcome to redistribute it under certain conditions. 384s Type 'license()' or 'licence()' for distribution details. 384s 384s R is a collaborative project with many contributors. 384s Type 'contributors()' for more information and 384s 'citation()' on how to cite R or R packages in publications. 384s 384s Type 'demo()' for some demos, 'help()' for on-line help, or 384s 'help.start()' for an HTML browser interface to help. 384s Type 'q()' to quit R. 384s 384s > #' 384s > #' Header for all (concatenated) test files 384s > #' 384s > #' Require spatstat.explore 384s > #' Obtain environment variable controlling tests. 384s > #' 384s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 384s > 384s > require(spatstat.explore) 384s Loading required package: spatstat.explore 384s Loading required package: spatstat.data 385s Loading required package: spatstat.geom 385s spatstat.geom 3.2-8 385s Loading required package: spatstat.random 385s spatstat.random 3.2-2 385s Loading required package: nlme 385s spatstat.explore 3.2-5 385s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 385s > ALWAYS <- TRUE 385s > cat(paste("--------- Executing", 385s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 385s + "test code -----------\n")) 385s --------- Executing **RESTRICTED** subset of test code ----------- 385s > 386s autopkgtest [20:21:38]: test run-unit-test: -----------------------] 386s autopkgtest [20:21:38]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 386s run-unit-test PASS 387s autopkgtest [20:21:39]: test pkg-r-autopkgtest: preparing testbed 466s autopkgtest [20:22:58]: testbed dpkg architecture: arm64 466s autopkgtest [20:22:58]: testbed apt version: 2.7.12 466s autopkgtest [20:22:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 467s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 467s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 467s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 467s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3704 kB] 468s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 468s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 468s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 468s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 468s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 468s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4012 kB] 468s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 468s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 468s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 470s Fetched 9112 kB in 2s (4587 kB/s) 470s Reading package lists... 473s Reading package lists... 473s Building dependency tree... 473s Reading state information... 474s Calculating upgrade... 475s The following packages will be REMOVED: 475s libglib2.0-0 libssl3 475s The following NEW packages will be installed: 475s libglib2.0-0t64 libssl3t64 xdg-user-dirs 475s The following packages have been kept back: 475s curl 475s The following packages will be upgraded: 475s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 475s ubuntu-minimal ubuntu-standard 475s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 475s Need to get 4613 kB of archives. 475s After this operation, 211 kB of additional disk space will be used. 475s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 476s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 476s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 476s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 477s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 477s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 477s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 477s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 477s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 477s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 477s Fetched 4613 kB in 2s (2532 kB/s) 478s (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 ... 74758 files and directories currently installed.) 478s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 478s Selecting previously unselected package libglib2.0-0t64:arm64. 478s (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.) 478s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 478s 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... 478s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 478s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 478s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 478s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 478s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 478s wget depends on libssl3 (>= 3.0.0). 478s u-boot-tools depends on libssl3 (>= 3.0.0). 478s tnftp depends on libssl3 (>= 3.0.0). 478s tcpdump depends on libssl3 (>= 3.0.0). 478s systemd-resolved depends on libssl3 (>= 3.0.0). 478s systemd depends on libssl3 (>= 3.0.0). 478s sudo depends on libssl3 (>= 3.0.0). 478s sbsigntool depends on libssl3 (>= 3.0.0). 478s rsync depends on libssl3 (>= 3.0.0). 478s python3-cryptography depends on libssl3 (>= 3.0.0). 478s openssh-server depends on libssl3 (>= 3.0.10). 478s openssh-client depends on libssl3 (>= 3.0.10). 478s mtd-utils depends on libssl3 (>= 3.0.0). 478s mokutil depends on libssl3 (>= 3.0.0). 478s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 478s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 478s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 478s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 478s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 478s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 478s libnvme1 depends on libssl3 (>= 3.0.0). 478s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 478s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 478s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 478s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 478s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 478s kmod depends on libssl3 (>= 3.0.0). 478s dhcpcd-base depends on libssl3 (>= 3.0.0). 478s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 478s 478s (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.) 478s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 478s Selecting previously unselected package libssl3t64:arm64. 478s (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.) 478s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 478s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 478s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 478s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 479s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ... 479s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 479s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ... 479s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 479s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ... 479s Unpacking ubuntu-minimal (1.536) over (1.535) ... 479s Selecting previously unselected package xdg-user-dirs. 479s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ... 479s Unpacking xdg-user-dirs (0.18-1) ... 479s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ... 479s Unpacking ubuntu-standard (1.536) over (1.535) ... 479s Setting up ubuntu-minimal (1.536) ... 479s Setting up xdg-user-dirs (0.18-1) ... 479s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 479s Setting up libtirpc-common (1.3.4+ds-1.1) ... 479s Setting up ubuntu-standard (1.536) ... 479s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 479s No schema files found: doing nothing. 479s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 479s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 479s Setting up openssl (3.0.13-0ubuntu1) ... 479s Setting up readline-common (8.2-3.1) ... 479s Processing triggers for man-db (2.12.0-3) ... 480s Processing triggers for install-info (7.1-3) ... 480s Processing triggers for libc-bin (2.39-0ubuntu2) ... 480s Reading package lists... 481s Building dependency tree... 481s Reading state information... 482s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 483s sh: Attempting to set up Debian/Ubuntu apt sources automatically 483s sh: Distribution appears to be Ubuntu 484s Reading package lists... 484s Building dependency tree... 484s Reading state information... 485s eatmydata is already the newest version (131-1). 485s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 485s Reading package lists... 485s Building dependency tree... 485s Reading state information... 486s dbus is already the newest version (1.14.10-4ubuntu1). 486s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 486s Reading package lists... 486s Building dependency tree... 486s Reading state information... 487s rng-tools-debian is already the newest version (2.4). 487s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 487s Reading package lists... 487s Building dependency tree... 487s Reading state information... 488s The following packages will be REMOVED: 488s cloud-init* python3-configobj* python3-debconf* 488s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 488s After this operation, 3252 kB disk space will be freed. 488s (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.) 488s Removing cloud-init (24.1.1-0ubuntu1) ... 489s Removing python3-configobj (5.0.8-3) ... 489s Removing python3-debconf (1.5.86) ... 489s Processing triggers for man-db (2.12.0-3) ... 490s (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 ... 74385 files and directories currently installed.) 490s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 491s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 491s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 491s invoke-rc.d: policy-rc.d denied execution of try-restart. 491s Reading package lists... 491s Building dependency tree... 491s Reading state information... 492s linux-generic is already the newest version (6.8.0-11.11+1). 492s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 493s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 493s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 493s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 495s Reading package lists... 495s Reading package lists... 495s Building dependency tree... 495s Reading state information... 496s Calculating upgrade... 496s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 496s Reading package lists... 496s Building dependency tree... 496s Reading state information... 497s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 497s autopkgtest [20:23:29]: rebooting testbed after setup commands that affected boot 756s Reading package lists... 756s Building dependency tree... 756s Reading state information... 757s Starting pkgProblemResolver with broken count: 0 757s Starting 2 pkgProblemResolver with broken count: 0 757s Done 758s The following additional packages will be installed: 758s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 758s dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 758s g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 758s gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-13 758s gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 758s libasan8 libatomic1 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev 758s libcairo2 libcc1-0 libcrypt-dev libdatrie1 libdeflate0 libfontconfig1 758s libgcc-13-dev libgfortran-13-dev libgfortran5 libgomp1 libgraphite2-3 758s libgsl27 libgslcblas0 libharfbuzz0b libhwasan0 libice6 libicu-dev libisl23 758s libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 758s libjpeg8-dev liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 758s libncurses-dev libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 758s libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0 758s libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev 758s libreadline-dev libsharpyuv0 libsm6 libstdc++-13-dev libtcl8.6 libthai-data 758s libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 libwebp7 758s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 linux-libc-dev 758s pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev 758s r-cran-abind r-cran-deldir r-cran-goftest r-cran-gsl r-cran-lattice 758s r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-polyclip r-cran-rpart r-cran-sm 758s r-cran-spatial r-cran-spatstat r-cran-spatstat.data r-cran-spatstat.explore 758s r-cran-spatstat.geom r-cran-spatstat.linnet r-cran-spatstat.model 758s r-cran-spatstat.random r-cran-spatstat.sparse r-cran-spatstat.utils 758s r-cran-survival r-cran-tensor rpcsvc-proto unzip x11-common xdg-utils zip 758s zlib1g-dev 758s Suggested packages: 758s cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib 758s manpages-dev autoconf automake libtool flex bison gdb gcc-doc 758s gdb-aarch64-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev 758s liblapack-doc glibc-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info 758s | gsl-ref-html icu-doc liblzma-doc ncurses-doc readline-doc libstdc++-13-doc 758s tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 758s texlive-base texlive-latex-base texlive-plain-generic 758s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils 758s texlive-latex-recommended texlive-latex-extra texinfo 758s Recommended packages: 758s bzip2-doc manpages manpages-dev libc-devtools libpng-tools r-recommended 758s r-doc-html r-cran-locfit r-cran-nleqslv r-cran-glmnet libfile-mimeinfo-perl 758s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 758s The following NEW packages will be installed: 758s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu 758s cpp-aarch64-linux-gnu dctrl-tools fontconfig fontconfig-config 758s fonts-dejavu-core fonts-dejavu-mono g++ g++-13 g++-13-aarch64-linux-gnu 758s g++-aarch64-linux-gnu gcc gcc-13 gcc-13-aarch64-linux-gnu 758s gcc-aarch64-linux-gnu gfortran gfortran-13 gfortran-13-aarch64-linux-gnu 758s gfortran-aarch64-linux-gnu icu-devtools libasan8 libatomic1 libblas-dev 758s libblas3 libbz2-dev libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev 758s libdatrie1 libdeflate0 libfontconfig1 libgcc-13-dev libgfortran-13-dev 758s libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b 758s libhwasan0 libice6 libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev 758s libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev 758s liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 libncurses-dev libnsl-dev 758s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 758s libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 758s libpixman-1-0 libpkgconf3 libpng-dev libreadline-dev libsharpyuv0 libsm6 758s libstdc++-13-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-dev 758s libtk8.6 libtsan2 libubsan1 libwebp7 libxcb-render0 libxcb-shm0 libxft2 758s libxrender1 libxss1 libxt6 linux-libc-dev pkg-config pkg-r-autopkgtest 758s pkgconf pkgconf-bin r-base-core r-base-dev r-cran-abind r-cran-deldir 758s r-cran-goftest r-cran-gsl r-cran-lattice r-cran-matrix r-cran-mgcv 758s r-cran-nlme r-cran-polyclip r-cran-rpart r-cran-sm r-cran-spatial 758s r-cran-spatstat r-cran-spatstat.data r-cran-spatstat.explore 758s r-cran-spatstat.geom r-cran-spatstat.linnet r-cran-spatstat.model 758s r-cran-spatstat.random r-cran-spatstat.sparse r-cran-spatstat.utils 758s r-cran-survival r-cran-tensor rpcsvc-proto unzip x11-common xdg-utils zip 758s zlib1g-dev 758s 0 upgraded, 131 newly installed, 0 to remove and 0 not upgraded. 758s Need to get 171 MB/171 MB of archives. 758s After this operation, 474 MB of additional disk space will be used. 758s Get:1 /tmp/autopkgtest.BrJapW/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [756 B] 758s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 758s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 759s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 759s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-dev arm64 1.3.4+ds-1build1 [232 kB] 759s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 759s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 759s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 760s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 760s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 760s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 761s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 761s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 761s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 761s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 761s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 761s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 761s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 761s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 761s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 761s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 761s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 761s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 761s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 762s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 762s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 762s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 762s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 762s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 762s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 763s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 763s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 763s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 763s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 763s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 dctrl-tools arm64 2.24-3build2 [65.2 kB] 763s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 763s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 763s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 763s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 763s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 763s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 763s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-17ubuntu2 [478 kB] 763s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.8 MB] 763s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-17ubuntu2 [10.3 kB] 763s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1022 B] 763s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B] 763s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB] 763s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 763s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB] 763s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 763s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 763s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 763s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 763s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 763s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 763s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 763s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 763s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 763s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu1 [72.5 kB] 763s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu1 [912 kB] 763s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 763s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 763s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 763s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB] 763s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 763s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu1 [304 kB] 763s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 763s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 763s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 763s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 763s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB] 764s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 764s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses-dev arm64 6.4+20240113-1ubuntu1 [385 kB] 764s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 764s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 764s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 764s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 764s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 764s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 764s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 764s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu1 [195 kB] 764s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu1 [183 kB] 764s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-posix3 arm64 10.42-4ubuntu1 [6654 B] 764s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-dev arm64 10.42-4ubuntu1 [679 kB] 764s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB] 764s Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 764s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libpng-dev arm64 1.6.43-1 [266 kB] 764s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libreadline-dev arm64 8.2-3 [177 kB] 764s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 764s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 764s Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 764s Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 764s Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 764s Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 764s Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 764s Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 764s Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 764s Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB] 764s Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB] 764s Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] 764s Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B] 764s Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 764s Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 764s Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 764s Get:105 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB] 765s Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB] 765s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-dev all 4.3.2-1build1 [4336 B] 765s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 765s Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-abind all 1.4-5-2 [63.6 kB] 765s Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-deldir arm64 2.0-4-1 [270 kB] 765s Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-goftest arm64 1.2-3-1 [60.2 kB] 765s Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gsl arm64 2.1-8-1 [489 kB] 765s Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 765s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 766s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 766s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 766s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-polyclip arm64 1.10-6-1 [110 kB] 766s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survival arm64 3.5-8-1 [6116 kB] 766s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rpart arm64 4.1.23-1 [660 kB] 766s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sm arm64 2.2-6.0-1 [787 kB] 766s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatial arm64 7.3-17-1 [130 kB] 766s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.utils arm64 3.0-4-1 [360 kB] 766s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.data all 3.0-4-1 [4090 kB] 766s Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.geom arm64 3.2-8-1 [3805 kB] 766s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.random arm64 3.2-2-1 [1127 kB] 766s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tensor all 1.5-4 [15.7 kB] 766s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.sparse arm64 3.0-3-1 [214 kB] 766s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.explore arm64 3.2-5-1 [3264 kB] 766s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.model arm64 3.2-8-1 [3289 kB] 767s Get:130 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat.linnet arm64 3.1-3-1 [1404 kB] 767s Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-spatstat arm64 3.0-7-1 [3817 kB] 768s Preconfiguring packages ... 769s Fetched 171 MB in 9s (19.4 MB/s) 769s Selecting previously unselected package libc-dev-bin. 769s (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 ... 74330 files and directories currently installed.) 769s Preparing to unpack .../000-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 769s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 769s Selecting previously unselected package linux-libc-dev:arm64. 769s Preparing to unpack .../001-linux-libc-dev_6.8.0-11.11_arm64.deb ... 769s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 769s Selecting previously unselected package libcrypt-dev:arm64. 769s Preparing to unpack .../002-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 769s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 769s Selecting previously unselected package libtirpc-dev:arm64. 769s Preparing to unpack .../003-libtirpc-dev_1.3.4+ds-1build1_arm64.deb ... 769s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1build1) ... 769s Selecting previously unselected package libnsl-dev:arm64. 769s Preparing to unpack .../004-libnsl-dev_1.3.0-3_arm64.deb ... 769s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 769s Selecting previously unselected package rpcsvc-proto. 769s Preparing to unpack .../005-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 769s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 769s Selecting previously unselected package libc6-dev:arm64. 769s Preparing to unpack .../006-libc6-dev_2.39-0ubuntu2_arm64.deb ... 769s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 770s Selecting previously unselected package libisl23:arm64. 770s Preparing to unpack .../007-libisl23_0.26-3_arm64.deb ... 770s Unpacking libisl23:arm64 (0.26-3) ... 770s Selecting previously unselected package libmpc3:arm64. 770s Preparing to unpack .../008-libmpc3_1.3.1-1_arm64.deb ... 770s Unpacking libmpc3:arm64 (1.3.1-1) ... 770s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 770s Preparing to unpack .../009-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 770s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 770s Selecting previously unselected package cpp-13. 770s Preparing to unpack .../010-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 770s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 770s Selecting previously unselected package cpp-aarch64-linux-gnu. 770s Preparing to unpack .../011-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 770s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 770s Selecting previously unselected package cpp. 770s Preparing to unpack .../012-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 770s Unpacking cpp (4:13.2.0-7ubuntu1) ... 770s Selecting previously unselected package libcc1-0:arm64. 770s Preparing to unpack .../013-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 770s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 770s Selecting previously unselected package libgomp1:arm64. 770s Preparing to unpack .../014-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 770s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 770s Selecting previously unselected package libitm1:arm64. 770s Preparing to unpack .../015-libitm1_14-20240303-1ubuntu1_arm64.deb ... 770s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 770s Selecting previously unselected package libatomic1:arm64. 770s Preparing to unpack .../016-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 770s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 770s Selecting previously unselected package libasan8:arm64. 770s Preparing to unpack .../017-libasan8_14-20240303-1ubuntu1_arm64.deb ... 770s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 770s Selecting previously unselected package liblsan0:arm64. 770s Preparing to unpack .../018-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 770s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 770s Selecting previously unselected package libtsan2:arm64. 770s Preparing to unpack .../019-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 770s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 770s Selecting previously unselected package libubsan1:arm64. 771s Preparing to unpack .../020-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 771s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 771s Selecting previously unselected package libhwasan0:arm64. 771s Preparing to unpack .../021-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 771s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 771s Selecting previously unselected package libgcc-13-dev:arm64. 771s Preparing to unpack .../022-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 771s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 771s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 771s Preparing to unpack .../023-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 771s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 771s Selecting previously unselected package gcc-13. 771s Preparing to unpack .../024-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 771s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 771s Selecting previously unselected package gcc-aarch64-linux-gnu. 771s Preparing to unpack .../025-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 771s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 771s Selecting previously unselected package gcc. 771s Preparing to unpack .../026-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 771s Unpacking gcc (4:13.2.0-7ubuntu1) ... 771s Selecting previously unselected package libstdc++-13-dev:arm64. 771s Preparing to unpack .../027-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 771s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 772s Selecting previously unselected package g++-13-aarch64-linux-gnu. 772s Preparing to unpack .../028-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 772s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 772s Selecting previously unselected package g++-13. 772s Preparing to unpack .../029-g++-13_13.2.0-17ubuntu2_arm64.deb ... 772s Unpacking g++-13 (13.2.0-17ubuntu2) ... 772s Selecting previously unselected package g++-aarch64-linux-gnu. 772s Preparing to unpack .../030-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 772s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 772s Selecting previously unselected package g++. 772s Preparing to unpack .../031-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 772s Unpacking g++ (4:13.2.0-7ubuntu1) ... 772s Selecting previously unselected package build-essential. 772s Preparing to unpack .../032-build-essential_12.10ubuntu1_arm64.deb ... 772s Unpacking build-essential (12.10ubuntu1) ... 772s Selecting previously unselected package dctrl-tools. 772s Preparing to unpack .../033-dctrl-tools_2.24-3build2_arm64.deb ... 772s Unpacking dctrl-tools (2.24-3build2) ... 772s Selecting previously unselected package fonts-dejavu-mono. 772s Preparing to unpack .../034-fonts-dejavu-mono_2.37-8_all.deb ... 772s Unpacking fonts-dejavu-mono (2.37-8) ... 772s Selecting previously unselected package fonts-dejavu-core. 772s Preparing to unpack .../035-fonts-dejavu-core_2.37-8_all.deb ... 772s Unpacking fonts-dejavu-core (2.37-8) ... 772s Selecting previously unselected package fontconfig-config. 772s Preparing to unpack .../036-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 773s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 773s Selecting previously unselected package libfontconfig1:arm64. 773s Preparing to unpack .../037-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 773s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 773s Selecting previously unselected package fontconfig. 773s Preparing to unpack .../038-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 773s Unpacking fontconfig (2.15.0-1ubuntu1) ... 773s Selecting previously unselected package libgfortran5:arm64. 773s Preparing to unpack .../039-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 773s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 773s Selecting previously unselected package libgfortran-13-dev:arm64. 773s Preparing to unpack .../040-libgfortran-13-dev_13.2.0-17ubuntu2_arm64.deb ... 773s Unpacking libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 773s Selecting previously unselected package gfortran-13-aarch64-linux-gnu. 773s Preparing to unpack .../041-gfortran-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 773s Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 773s Selecting previously unselected package gfortran-13. 773s Preparing to unpack .../042-gfortran-13_13.2.0-17ubuntu2_arm64.deb ... 773s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 773s Selecting previously unselected package gfortran-aarch64-linux-gnu. 773s Preparing to unpack .../043-gfortran-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 773s Unpacking gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 773s Selecting previously unselected package gfortran. 773s Preparing to unpack .../044-gfortran_4%3a13.2.0-7ubuntu1_arm64.deb ... 773s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 773s Selecting previously unselected package icu-devtools. 773s Preparing to unpack .../045-icu-devtools_74.2-1ubuntu1_arm64.deb ... 773s Unpacking icu-devtools (74.2-1ubuntu1) ... 773s Selecting previously unselected package libblas3:arm64. 773s Preparing to unpack .../046-libblas3_3.12.0-3_arm64.deb ... 773s Unpacking libblas3:arm64 (3.12.0-3) ... 773s Selecting previously unselected package libblas-dev:arm64. 773s Preparing to unpack .../047-libblas-dev_3.12.0-3_arm64.deb ... 773s Unpacking libblas-dev:arm64 (3.12.0-3) ... 773s Selecting previously unselected package libbz2-dev:arm64. 773s Preparing to unpack .../048-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 773s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 774s Selecting previously unselected package libpixman-1-0:arm64. 774s Preparing to unpack .../049-libpixman-1-0_0.42.2-1_arm64.deb ... 774s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 774s Selecting previously unselected package libxcb-render0:arm64. 774s Preparing to unpack .../050-libxcb-render0_1.15-1_arm64.deb ... 774s Unpacking libxcb-render0:arm64 (1.15-1) ... 774s Selecting previously unselected package libxcb-shm0:arm64. 774s Preparing to unpack .../051-libxcb-shm0_1.15-1_arm64.deb ... 774s Unpacking libxcb-shm0:arm64 (1.15-1) ... 774s Selecting previously unselected package libxrender1:arm64. 774s Preparing to unpack .../052-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 774s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 774s Selecting previously unselected package libcairo2:arm64. 774s Preparing to unpack .../053-libcairo2_1.18.0-1_arm64.deb ... 774s Unpacking libcairo2:arm64 (1.18.0-1) ... 774s Selecting previously unselected package libdatrie1:arm64. 774s Preparing to unpack .../054-libdatrie1_0.2.13-3_arm64.deb ... 774s Unpacking libdatrie1:arm64 (0.2.13-3) ... 774s Selecting previously unselected package libdeflate0:arm64. 774s Preparing to unpack .../055-libdeflate0_1.19-1_arm64.deb ... 774s Unpacking libdeflate0:arm64 (1.19-1) ... 774s Selecting previously unselected package libgraphite2-3:arm64. 774s Preparing to unpack .../056-libgraphite2-3_1.3.14-2_arm64.deb ... 774s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 774s Selecting previously unselected package libgslcblas0:arm64. 774s Preparing to unpack .../057-libgslcblas0_2.7.1+dfsg-6ubuntu1_arm64.deb ... 774s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 774s Selecting previously unselected package libgsl27:arm64. 774s Preparing to unpack .../058-libgsl27_2.7.1+dfsg-6ubuntu1_arm64.deb ... 774s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 774s Selecting previously unselected package libharfbuzz0b:arm64. 774s Preparing to unpack .../059-libharfbuzz0b_8.3.0-2_arm64.deb ... 774s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 774s Selecting previously unselected package x11-common. 774s Preparing to unpack .../060-x11-common_1%3a7.7+23ubuntu2_all.deb ... 774s Unpacking x11-common (1:7.7+23ubuntu2) ... 774s Selecting previously unselected package libice6:arm64. 774s Preparing to unpack .../061-libice6_2%3a1.0.10-1build2_arm64.deb ... 774s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 774s Selecting previously unselected package libicu-dev:arm64. 774s Preparing to unpack .../062-libicu-dev_74.2-1ubuntu1_arm64.deb ... 774s Unpacking libicu-dev:arm64 (74.2-1ubuntu1) ... 775s Selecting previously unselected package libjpeg-turbo8:arm64. 775s Preparing to unpack .../063-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 775s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 775s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 775s Preparing to unpack .../064-libjpeg-turbo8-dev_2.1.5-2ubuntu1_arm64.deb ... 775s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 775s Selecting previously unselected package libjpeg8:arm64. 775s Preparing to unpack .../065-libjpeg8_8c-2ubuntu11_arm64.deb ... 775s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 775s Selecting previously unselected package libjpeg8-dev:arm64. 775s Preparing to unpack .../066-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 775s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 775s Selecting previously unselected package libjpeg-dev:arm64. 775s Preparing to unpack .../067-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 775s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 775s Selecting previously unselected package liblapack3:arm64. 775s Preparing to unpack .../068-liblapack3_3.12.0-3_arm64.deb ... 775s Unpacking liblapack3:arm64 (3.12.0-3) ... 775s Selecting previously unselected package liblapack-dev:arm64. 775s Preparing to unpack .../069-liblapack-dev_3.12.0-3_arm64.deb ... 775s Unpacking liblapack-dev:arm64 (3.12.0-3) ... 776s Selecting previously unselected package liblerc4:arm64. 776s Preparing to unpack .../070-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 776s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 776s Selecting previously unselected package libncurses-dev:arm64. 776s Preparing to unpack .../071-libncurses-dev_6.4+20240113-1ubuntu1_arm64.deb ... 776s Unpacking libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 776s Selecting previously unselected package libthai-data. 776s Preparing to unpack .../072-libthai-data_0.1.29-2_all.deb ... 776s Unpacking libthai-data (0.1.29-2) ... 776s Selecting previously unselected package libthai0:arm64. 776s Preparing to unpack .../073-libthai0_0.1.29-2_arm64.deb ... 776s Unpacking libthai0:arm64 (0.1.29-2) ... 776s Selecting previously unselected package libpango-1.0-0:arm64. 776s Preparing to unpack .../074-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 776s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 776s Selecting previously unselected package libpangoft2-1.0-0:arm64. 776s Preparing to unpack .../075-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 776s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 776s Selecting previously unselected package libpangocairo-1.0-0:arm64. 776s Preparing to unpack .../076-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 776s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 776s Selecting previously unselected package libpaper1:arm64. 776s Preparing to unpack .../077-libpaper1_1.1.29_arm64.deb ... 776s Unpacking libpaper1:arm64 (1.1.29) ... 776s Selecting previously unselected package libpaper-utils. 776s Preparing to unpack .../078-libpaper-utils_1.1.29_arm64.deb ... 776s Unpacking libpaper-utils (1.1.29) ... 776s Selecting previously unselected package libpcre2-16-0:arm64. 776s Preparing to unpack .../079-libpcre2-16-0_10.42-4ubuntu1_arm64.deb ... 776s Unpacking libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 776s Selecting previously unselected package libpcre2-32-0:arm64. 776s Preparing to unpack .../080-libpcre2-32-0_10.42-4ubuntu1_arm64.deb ... 776s Unpacking libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 776s Selecting previously unselected package libpcre2-posix3:arm64. 776s Preparing to unpack .../081-libpcre2-posix3_10.42-4ubuntu1_arm64.deb ... 776s Unpacking libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 776s Selecting previously unselected package libpcre2-dev:arm64. 776s Preparing to unpack .../082-libpcre2-dev_10.42-4ubuntu1_arm64.deb ... 776s Unpacking libpcre2-dev:arm64 (10.42-4ubuntu1) ... 776s Selecting previously unselected package libpkgconf3:arm64. 776s Preparing to unpack .../083-libpkgconf3_1.8.1-2_arm64.deb ... 776s Unpacking libpkgconf3:arm64 (1.8.1-2) ... 776s Selecting previously unselected package zlib1g-dev:arm64. 776s Preparing to unpack .../084-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 776s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 776s Selecting previously unselected package libpng-dev:arm64. 776s Preparing to unpack .../085-libpng-dev_1.6.43-1_arm64.deb ... 776s Unpacking libpng-dev:arm64 (1.6.43-1) ... 776s Selecting previously unselected package libreadline-dev:arm64. 776s Preparing to unpack .../086-libreadline-dev_8.2-3_arm64.deb ... 776s Unpacking libreadline-dev:arm64 (8.2-3) ... 776s Selecting previously unselected package libsharpyuv0:arm64. 776s Preparing to unpack .../087-libsharpyuv0_1.3.2-0.4_arm64.deb ... 776s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 776s Selecting previously unselected package libsm6:arm64. 777s Preparing to unpack .../088-libsm6_2%3a1.2.3-1build2_arm64.deb ... 777s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 777s Selecting previously unselected package libtcl8.6:arm64. 777s Preparing to unpack .../089-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 777s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 777s Selecting previously unselected package libjbig0:arm64. 777s Preparing to unpack .../090-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 777s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 777s Selecting previously unselected package libwebp7:arm64. 777s Preparing to unpack .../091-libwebp7_1.3.2-0.4_arm64.deb ... 777s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 777s Selecting previously unselected package libtiff6:arm64. 777s Preparing to unpack .../092-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 777s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 777s Selecting previously unselected package libxft2:arm64. 777s Preparing to unpack .../093-libxft2_2.3.6-1_arm64.deb ... 777s Unpacking libxft2:arm64 (2.3.6-1) ... 777s Selecting previously unselected package libxss1:arm64. 777s Preparing to unpack .../094-libxss1_1%3a1.2.3-1build2_arm64.deb ... 777s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 777s Selecting previously unselected package libtk8.6:arm64. 777s Preparing to unpack .../095-libtk8.6_8.6.13-2_arm64.deb ... 777s Unpacking libtk8.6:arm64 (8.6.13-2) ... 777s Selecting previously unselected package libxt6:arm64. 777s Preparing to unpack .../096-libxt6_1%3a1.2.1-1.1_arm64.deb ... 777s Unpacking libxt6:arm64 (1:1.2.1-1.1) ... 777s Selecting previously unselected package pkgconf-bin. 777s Preparing to unpack .../097-pkgconf-bin_1.8.1-2_arm64.deb ... 777s Unpacking pkgconf-bin (1.8.1-2) ... 777s Selecting previously unselected package pkgconf:arm64. 777s Preparing to unpack .../098-pkgconf_1.8.1-2_arm64.deb ... 777s Unpacking pkgconf:arm64 (1.8.1-2) ... 777s Selecting previously unselected package pkg-config:arm64. 777s Preparing to unpack .../099-pkg-config_1.8.1-2_arm64.deb ... 777s Unpacking pkg-config:arm64 (1.8.1-2) ... 777s Selecting previously unselected package zip. 777s Preparing to unpack .../100-zip_3.0-13_arm64.deb ... 777s Unpacking zip (3.0-13) ... 777s Selecting previously unselected package unzip. 777s Preparing to unpack .../101-unzip_6.0-28ubuntu3_arm64.deb ... 777s Unpacking unzip (6.0-28ubuntu3) ... 777s Selecting previously unselected package xdg-utils. 777s Preparing to unpack .../102-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 777s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 777s Selecting previously unselected package r-base-core. 777s Preparing to unpack .../103-r-base-core_4.3.2-1build1_arm64.deb ... 777s Unpacking r-base-core (4.3.2-1build1) ... 778s Selecting previously unselected package liblzma-dev:arm64. 778s Preparing to unpack .../104-liblzma-dev_5.4.5-0.3_arm64.deb ... 778s Unpacking liblzma-dev:arm64 (5.4.5-0.3) ... 778s Selecting previously unselected package r-base-dev. 778s Preparing to unpack .../105-r-base-dev_4.3.2-1build1_all.deb ... 778s Unpacking r-base-dev (4.3.2-1build1) ... 778s Selecting previously unselected package pkg-r-autopkgtest. 778s Preparing to unpack .../106-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 778s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 778s Selecting previously unselected package r-cran-abind. 778s Preparing to unpack .../107-r-cran-abind_1.4-5-2_all.deb ... 778s Unpacking r-cran-abind (1.4-5-2) ... 778s Selecting previously unselected package r-cran-deldir. 778s Preparing to unpack .../108-r-cran-deldir_2.0-4-1_arm64.deb ... 778s Unpacking r-cran-deldir (2.0-4-1) ... 778s Selecting previously unselected package r-cran-goftest. 778s Preparing to unpack .../109-r-cran-goftest_1.2-3-1_arm64.deb ... 778s Unpacking r-cran-goftest (1.2-3-1) ... 778s Selecting previously unselected package r-cran-gsl. 778s Preparing to unpack .../110-r-cran-gsl_2.1-8-1_arm64.deb ... 778s Unpacking r-cran-gsl (2.1-8-1) ... 778s Selecting previously unselected package r-cran-lattice. 778s Preparing to unpack .../111-r-cran-lattice_0.22-5-1_arm64.deb ... 778s Unpacking r-cran-lattice (0.22-5-1) ... 778s Selecting previously unselected package r-cran-matrix. 778s Preparing to unpack .../112-r-cran-matrix_1.6-5-1_arm64.deb ... 778s Unpacking r-cran-matrix (1.6-5-1) ... 778s Selecting previously unselected package r-cran-nlme. 778s Preparing to unpack .../113-r-cran-nlme_3.1.164-1_arm64.deb ... 778s Unpacking r-cran-nlme (3.1.164-1) ... 778s Selecting previously unselected package r-cran-mgcv. 779s Preparing to unpack .../114-r-cran-mgcv_1.9-1-1_arm64.deb ... 779s Unpacking r-cran-mgcv (1.9-1-1) ... 779s Selecting previously unselected package r-cran-polyclip. 779s Preparing to unpack .../115-r-cran-polyclip_1.10-6-1_arm64.deb ... 779s Unpacking r-cran-polyclip (1.10-6-1) ... 779s Selecting previously unselected package r-cran-survival. 779s Preparing to unpack .../116-r-cran-survival_3.5-8-1_arm64.deb ... 779s Unpacking r-cran-survival (3.5-8-1) ... 779s Selecting previously unselected package r-cran-rpart. 779s Preparing to unpack .../117-r-cran-rpart_4.1.23-1_arm64.deb ... 779s Unpacking r-cran-rpart (4.1.23-1) ... 779s Selecting previously unselected package r-cran-sm. 779s Preparing to unpack .../118-r-cran-sm_2.2-6.0-1_arm64.deb ... 779s Unpacking r-cran-sm (2.2-6.0-1) ... 779s Selecting previously unselected package r-cran-spatial. 779s Preparing to unpack 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Unpacking r-cran-tensor (1.5-4) ... 779s Selecting previously unselected package r-cran-spatstat.sparse. 779s Preparing to unpack .../125-r-cran-spatstat.sparse_3.0-3-1_arm64.deb ... 779s Unpacking r-cran-spatstat.sparse (3.0-3-1) ... 779s Selecting previously unselected package r-cran-spatstat.explore. 779s Preparing to unpack .../126-r-cran-spatstat.explore_3.2-5-1_arm64.deb ... 779s Unpacking r-cran-spatstat.explore (3.2-5-1) ... 780s Selecting previously unselected package r-cran-spatstat.model. 780s Preparing to unpack .../127-r-cran-spatstat.model_3.2-8-1_arm64.deb ... 780s Unpacking r-cran-spatstat.model (3.2-8-1) ... 780s Selecting previously unselected package r-cran-spatstat.linnet. 780s Preparing to unpack .../128-r-cran-spatstat.linnet_3.1-3-1_arm64.deb ... 780s Unpacking r-cran-spatstat.linnet (3.1-3-1) ... 780s Selecting previously unselected package r-cran-spatstat. 780s Preparing to unpack .../129-r-cran-spatstat_3.0-7-1_arm64.deb ... 780s Unpacking r-cran-spatstat (3.0-7-1) ... 780s Selecting previously unselected package autopkgtest-satdep. 780s Preparing to unpack .../130-2-autopkgtest-satdep.deb ... 780s Unpacking autopkgtest-satdep (0) ... 780s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 780s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 780s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 780s Setting up libpaper1:arm64 (1.1.29) ... 780s 780s Creating config file /etc/papersize with new version 781s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 781s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 781s Setting up libdatrie1:arm64 (0.2.13-3) ... 781s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ... 781s Setting up libxcb-render0:arm64 (1.15-1) ... 781s Setting up unzip (6.0-28ubuntu3) ... 781s Setting up x11-common (1:7.7+23ubuntu2) ... 781s Setting up libdeflate0:arm64 (1.19-1) ... 781s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 781s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ... 781s Setting up libxcb-shm0:arm64 (1.15-1) ... 781s Setting up libpaper-utils (1.1.29) ... 781s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 781s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 781s Setting up libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 781s Setting up zip (3.0-13) ... 781s Setting up libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 781s Setting up libblas3:arm64 (3.12.0-3) ... 781s 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 781s Setting up libtirpc-dev:arm64 (1.3.4+ds-1build1) ... 781s Setting up libpkgconf3:arm64 (1.8.1-2) ... 781s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 781s Setting up fonts-dejavu-mono (2.37-8) ... 781s Setting up libmpc3:arm64 (1.3.1-1) ... 781s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 781s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 781s Setting up icu-devtools (74.2-1ubuntu1) ... 781s Setting up fonts-dejavu-core (2.37-8) ... 781s Setting up pkgconf-bin (1.8.1-2) ... 781s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 781s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 781s Setting up libwebp7:arm64 (1.3.2-0.4) ... 781s Setting up liblzma-dev:arm64 (5.4.5-0.3) ... 781s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 781s Setting up libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 781s Setting up libnsl-dev:arm64 (1.3.0-3) ... 781s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 781s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 781s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 781s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 781s Setting up libthai-data (0.1.29-2) ... 781s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 781s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 781s Setting up libisl23:arm64 (0.26-3) ... 781s Setting up libc-dev-bin (2.39-0ubuntu2) ... 781s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 781s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 781s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 781s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 781s Setting up libblas-dev:arm64 (3.12.0-3) ... 781s 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 781s Setting up dctrl-tools (2.24-3build2) ... 781s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ... 781s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 781s Setting up libice6:arm64 (2:1.0.10-1build2) ... 781s Setting up liblapack3:arm64 (3.12.0-3) ... 781s 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 781s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 781s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 782s Setting up pkgconf:arm64 (1.8.1-2) ... 782s Setting up libthai0:arm64 (0.1.29-2) ... 782s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 782s Setting up liblapack-dev:arm64 (3.12.0-3) ... 782s 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 782s Setting up pkg-config:arm64 (1.8.1-2) ... 782s Setting up libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 782s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 782s Setting up libc6-dev:arm64 (2.39-0ubuntu2) ... 782s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 782s Setting up libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 782s Setting up libsm6:arm64 (2:1.2.3-1build2) ... 782s Setting up libicu-dev:arm64 (74.2-1ubuntu1) ... 782s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 782s Setting up libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 782s Setting up fontconfig (2.15.0-1ubuntu1) ... 784s Regenerating fonts cache... done. 784s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 784s Setting up libxft2:arm64 (2.3.6-1) ... 784s Setting up libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 784s Setting up libpcre2-dev:arm64 (10.42-4ubuntu1) ... 784s Setting up cpp-13 (13.2.0-17ubuntu2) ... 784s Setting up libtk8.6:arm64 (8.6.13-2) ... 784s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 784s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 784s Setting up libreadline-dev:arm64 (8.2-3) ... 784s Setting up libcairo2:arm64 (1.18.0-1) ... 784s Setting up gcc-13 (13.2.0-17ubuntu2) ... 784s Setting up libxt6:arm64 (1:1.2.1-1.1) ... 784s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 784s Setting up cpp (4:13.2.0-7ubuntu1) ... 784s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 784s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 784s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 784s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 784s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 784s Setting up g++-13 (13.2.0-17ubuntu2) ... 784s Setting up libpng-dev:arm64 (1.6.43-1) ... 784s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 784s Setting up gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 784s Setting up gcc (4:13.2.0-7ubuntu1) ... 784s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 784s Setting up r-base-core (4.3.2-1build1) ... 785s 785s Creating config file /etc/R/Renviron with new version 785s Setting up r-cran-lattice (0.22-5-1) ... 785s Setting up r-cran-nlme (3.1.164-1) ... 785s Setting up r-cran-spatstat.utils (3.0-4-1) ... 785s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 785s Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 785s Setting up r-cran-tensor (1.5-4) ... 785s Setting up r-cran-gsl (2.1-8-1) ... 785s Setting up r-cran-spatial (7.3-17-1) ... 785s Setting up r-cran-abind (1.4-5-2) ... 785s Setting up r-cran-sm (2.2-6.0-1) ... 785s Setting up r-cran-polyclip (1.10-6-1) ... 785s Setting up gfortran (4:13.2.0-7ubuntu1) ... 785s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 785s 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 785s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 785s 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 785s Setting up r-cran-deldir (2.0-4-1) ... 785s Setting up r-cran-goftest (1.2-3-1) ... 785s Setting up r-cran-matrix (1.6-5-1) ... 785s Setting up r-cran-spatstat.sparse (3.0-3-1) ... 785s Setting up r-cran-mgcv (1.9-1-1) ... 785s Setting up g++ (4:13.2.0-7ubuntu1) ... 785s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 785s Setting up build-essential (12.10ubuntu1) ... 785s Setting up r-base-dev (4.3.2-1build1) ... 785s Setting up r-cran-survival (3.5-8-1) ... 785s Setting up r-cran-spatstat.data (3.0-4-1) ... 785s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 785s Setting up r-cran-spatstat.geom (3.2-8-1) ... 785s Setting up r-cran-rpart (4.1.23-1) ... 785s Setting up r-cran-spatstat.random (3.2-2-1) ... 785s Setting up r-cran-spatstat.explore (3.2-5-1) ... 785s Setting up r-cran-spatstat.model (3.2-8-1) ... 785s Setting up r-cran-spatstat.linnet (3.1-3-1) ... 785s Setting up r-cran-spatstat (3.0-7-1) ... 785s Setting up autopkgtest-satdep (0) ... 785s Processing triggers for man-db (2.12.0-3) ... 786s Processing triggers for install-info (7.1-3) ... 786s Processing triggers for libc-bin (2.39-0ubuntu2) ... 793s (Reading database ... 81284 files and directories currently installed.) 793s Removing autopkgtest-satdep (0) ... 794s autopkgtest [20:28:26]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 794s autopkgtest [20:28:26]: test pkg-r-autopkgtest: [----------------------- 795s Test: Try to load the R library spatstat.explore 795s 795s R version 4.3.2 (2023-10-31) -- "Eye Holes" 795s Copyright (C) 2023 The R Foundation for Statistical Computing 795s Platform: aarch64-unknown-linux-gnu (64-bit) 795s 795s R is free software and comes with ABSOLUTELY NO WARRANTY. 795s You are welcome to redistribute it under certain conditions. 795s Type 'license()' or 'licence()' for distribution details. 795s 795s R is a collaborative project with many contributors. 795s Type 'contributors()' for more information and 795s 'citation()' on how to cite R or R packages in publications. 795s 795s Type 'demo()' for some demos, 'help()' for on-line help, or 795s 'help.start()' for an HTML browser interface to help. 795s Type 'q()' to quit R. 795s 795s > library('spatstat.explore') 795s Loading required package: spatstat.data 796s Loading required package: spatstat.geom 796s spatstat.geom 3.2-8 796s Loading required package: spatstat.random 796s spatstat.random 3.2-2 796s Loading required package: nlme 797s > 797s > 797s spatstat.explore 3.2-5 797s Other tests are currently unsupported! 797s They will be progressively added. 797s autopkgtest [20:28:29]: test pkg-r-autopkgtest: -----------------------] 798s pkg-r-autopkgtest PASS 798s autopkgtest [20:28:30]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 798s autopkgtest [20:28:30]: @@@@@@@@@@@@@@@@@@@@ summary 798s run-unit-test PASS 798s pkg-r-autopkgtest PASS 802s Creating nova instance adt-noble-arm64-r-cran-spatstat.explore-20240316-201512-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)... 802s Creating nova instance adt-noble-arm64-r-cran-spatstat.explore-20240316-201512-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...