0s autopkgtest [16:10:15]: starting date and time: 2024-03-23 16:10:15+0000 0s autopkgtest [16:10:15]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [16:10:15]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fq8_27o8/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 --apt-upgrade r-cran-spatstat.model --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-spatstat.explore/3.2-6-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-s390x-3.secgroup --name adt-noble-s390x-r-cran-spatstat.model-20240323-161015-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 92s autopkgtest [16:11:47]: testbed dpkg architecture: s390x 92s autopkgtest [16:11:47]: testbed apt version: 2.7.12 92s autopkgtest [16:11:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 93s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 93s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 93s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 93s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 93s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 93s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [652 kB] 93s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 93s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 93s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 93s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4143 kB] 94s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 94s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [46.8 kB] 94s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 97s Fetched 9495 kB in 3s (3459 kB/s) 97s Reading package lists... 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s Calculating upgrade... 99s The following packages will be upgraded: 99s cloud-init debianutils fonts-ubuntu-console libbsd0 libc-bin libc6 locales 99s python3-markupsafe 100s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Need to get 8499 kB of archives. 100s After this operation, 9216 B disk space will be freed. 100s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.17 [90.1 kB] 100s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libc6 s390x 2.39-0ubuntu6 [2847 kB] 100s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libc-bin s390x 2.39-0ubuntu6 [654 kB] 100s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libbsd0 s390x 0.12.1-1 [46.7 kB] 100s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x locales all 2.39-0ubuntu6 [4232 kB] 100s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 100s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x python3-markupsafe s390x 2.1.5-1build1 [12.8 kB] 100s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x cloud-init all 24.1.2-0ubuntu1 [597 kB] 101s Preconfiguring packages ... 101s Fetched 8499 kB in 1s (9730 kB/s) 101s (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 ... 51778 files and directories currently installed.) 101s Preparing to unpack .../debianutils_5.17_s390x.deb ... 101s Unpacking debianutils (5.17) over (5.16) ... 101s Setting up debianutils (5.17) ... 101s (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 ... 51778 files and directories currently installed.) 101s Preparing to unpack .../libc6_2.39-0ubuntu6_s390x.deb ... 101s Unpacking libc6:s390x (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 102s Setting up libc6:s390x (2.39-0ubuntu6) ... 102s (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 ... 51778 files and directories currently installed.) 102s Preparing to unpack .../libc-bin_2.39-0ubuntu6_s390x.deb ... 102s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 102s Setting up libc-bin (2.39-0ubuntu6) ... 102s (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 ... 51778 files and directories currently installed.) 102s Preparing to unpack .../libbsd0_0.12.1-1_s390x.deb ... 102s Unpacking libbsd0:s390x (0.12.1-1) over (0.11.8-1) ... 102s Preparing to unpack .../locales_2.39-0ubuntu6_all.deb ... 102s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 103s Preparing to unpack .../fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 103s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 103s Preparing to unpack .../python3-markupsafe_2.1.5-1build1_s390x.deb ... 103s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 103s Preparing to unpack .../cloud-init_24.1.2-0ubuntu1_all.deb ... 103s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 103s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 103s Setting up cloud-init (24.1.2-0ubuntu1) ... 105s Setting up locales (2.39-0ubuntu6) ... 105s Generating locales (this might take a while)... 108s en_US.UTF-8... done 108s Generation complete. 108s Setting up python3-markupsafe (2.1.5-1build1) ... 108s Setting up libbsd0:s390x (0.12.1-1) ... 108s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 108s Processing triggers for man-db (2.12.0-3) ... 109s Processing triggers for libc-bin (2.39-0ubuntu6) ... 109s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s 0 upgraded, 0 newly installed, 0 to remove and 234 not upgraded. 110s Unknown architecture, assuming PC-style ttyS0 110s sh: Attempting to set up Debian/Ubuntu apt sources automatically 110s sh: Distribution appears to be Ubuntu 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s eatmydata is already the newest version (131-1). 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s dbus is already the newest version (1.14.10-4ubuntu1). 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s rng-tools-debian is already the newest version (2.4). 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s The following packages will be REMOVED: 114s cloud-init* python3-configobj* python3-debconf* 114s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 114s After this operation, 3256 kB disk space will be freed. 114s (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 ... 51777 files and directories currently installed.) 114s Removing cloud-init (24.1.2-0ubuntu1) ... 115s Removing python3-configobj (5.0.8-3) ... 115s Removing python3-debconf (1.5.86) ... 115s Processing triggers for man-db (2.12.0-3) ... 115s (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 ... 51388 files and directories currently installed.) 115s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 116s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 116s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 116s invoke-rc.d: policy-rc.d denied execution of try-restart. 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 117s linux-generic is already the newest version (6.8.0-11.11+1). 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 117s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 117s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 119s Reading package lists... 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 120s Calculating upgrade... 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s autopkgtest [16:12:16]: rebooting testbed after setup commands that affected boot 261s autopkgtest [16:14:36]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 272s autopkgtest [16:14:47]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-spatstat.model 276s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-spatstat.model 3.2-8-1 (dsc) [2597 B] 276s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-spatstat.model 3.2-8-1 (tar) [804 kB] 276s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-spatstat.model 3.2-8-1 (diff) [3384 B] 276s gpgv: Signature made Tue Oct 24 08:22:10 2023 UTC 276s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 276s gpgv: issuer "tille@debian.org" 276s gpgv: Can't check signature: No public key 276s dpkg-source: warning: cannot verify inline signature for ./r-cran-spatstat.model_3.2-8-1.dsc: no acceptable signature found 276s autopkgtest [16:14:50]: testing package r-cran-spatstat.model version 3.2-8-1 277s autopkgtest [16:14:52]: build not needed 279s autopkgtest [16:14:54]: test run-unit-test: preparing testbed 291s Reading package lists... 291s Building dependency tree... 291s Reading state information... 291s Starting pkgProblemResolver with broken count: 0 291s Starting 2 pkgProblemResolver with broken count: 0 291s Done 292s The following additional packages will be installed: 292s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 292s fonts-mathjax libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 292s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 292s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-mathjax 292s liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 292s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 292s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 292s libxft2 libxrender1 libxss1 libxt6 littler r-base-core r-cran-abind 292s r-cran-codetools r-cran-deldir r-cran-foreach r-cran-glmnet r-cran-goftest 292s r-cran-gsl r-cran-iterators r-cran-lattice r-cran-littler r-cran-locfit 292s r-cran-matrix r-cran-mgcv r-cran-nleqslv r-cran-nlme r-cran-pkgkitten 292s r-cran-polyclip r-cran-rcpp r-cran-rcppeigen r-cran-rpart r-cran-shape 292s r-cran-sm r-cran-spatial r-cran-spatstat r-cran-spatstat.data 292s r-cran-spatstat.explore r-cran-spatstat.geom r-cran-spatstat.linnet 292s r-cran-spatstat.model r-cran-spatstat.random r-cran-spatstat.sparse 292s r-cran-spatstat.utils r-cran-survival r-cran-tensor unzip x11-common 292s xdg-utils zip 292s Suggested packages: 292s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 292s fonts-mathjax-extras fonts-stix libjs-mathjax-doc tcl8.6 tk8.6 elpa-ess 292s r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-knitr r-cran-testthat 292s r-cran-xfun r-cran-rmarkdown r-cran-getopt r-cran-interp r-cran-gam 292s r-cran-inline 292s Recommended packages: 292s r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl 292s libx11-protocol-perl x11-utils x11-xserver-utils 292s The following NEW packages will be installed: 292s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 292s fonts-dejavu-mono fonts-mathjax libblas3 libcairo2 libdatrie1 libdeflate0 292s libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libgsl27 292s libgslcblas0 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 292s libjs-mathjax liblapack3 libpango-1.0-0 libpangocairo-1.0-0 292s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 292s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 292s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 littler r-base-core 292s r-cran-abind r-cran-codetools r-cran-deldir r-cran-foreach r-cran-glmnet 292s r-cran-goftest r-cran-gsl r-cran-iterators r-cran-lattice r-cran-littler 292s r-cran-locfit r-cran-matrix r-cran-mgcv r-cran-nleqslv r-cran-nlme 292s r-cran-pkgkitten r-cran-polyclip r-cran-rcpp r-cran-rcppeigen r-cran-rpart 292s r-cran-shape r-cran-sm r-cran-spatial r-cran-spatstat r-cran-spatstat.data 292s r-cran-spatstat.explore r-cran-spatstat.geom r-cran-spatstat.linnet 292s r-cran-spatstat.model r-cran-spatstat.random r-cran-spatstat.sparse 292s r-cran-spatstat.utils r-cran-survival r-cran-tensor unzip x11-common 292s xdg-utils zip 292s 0 upgraded, 84 newly installed, 0 to remove and 0 not upgraded. 292s Need to get 95.7 MB/95.7 MB of archives. 292s After this operation, 204 MB of additional disk space will be used. 292s Get:1 /tmp/autopkgtest.qd1hMn/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [764 B] 292s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 292s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 293s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 293s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 293s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 293s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig s390x 2.15.0-1ubuntu1 [191 kB] 293s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 294s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 294s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB] 294s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB] 294s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B] 294s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB] 294s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libcairo2 s390x 1.18.0-1 [578 kB] 294s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libdatrie1 s390x 0.2.13-3 [22.6 kB] 294s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 294s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 294s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 294s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] 294s Get:20 http://ftpmaster.internal/ubuntu noble/universe s390x libgslcblas0 s390x 2.7.1+dfsg-6ubuntu1 [147 kB] 294s Get:21 http://ftpmaster.internal/ubuntu noble/universe s390x libgsl27 s390x 2.7.1+dfsg-6ubuntu1 [1069 kB] 294s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2 [515 kB] 294s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x x11-common all 1:7.7+23ubuntu2 [23.4 kB] 294s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libice6 s390x 2:1.0.10-1build2 [40.8 kB] 294s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 294s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 294s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 295s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x libthai-data all 0.1.29-2 [158 kB] 295s Get:29 http://ftpmaster.internal/ubuntu noble/main s390x libthai0 s390x 0.1.29-2 [20.6 kB] 295s Get:30 http://ftpmaster.internal/ubuntu noble/main s390x libpango-1.0-0 s390x 1.51.0+ds-4 [240 kB] 295s Get:31 http://ftpmaster.internal/ubuntu noble/main s390x libpangoft2-1.0-0 s390x 1.51.0+ds-4 [43.6 kB] 295s Get:32 http://ftpmaster.internal/ubuntu noble/main s390x libpangocairo-1.0-0 s390x 1.51.0+ds-4 [28.9 kB] 295s Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libpaper1 s390x 1.1.29 [13.3 kB] 295s Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libpaper-utils s390x 1.1.29 [8452 B] 295s Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libsharpyuv0 s390x 1.3.2-0.4 [14.8 kB] 295s Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libsm6 s390x 2:1.2.3-1build2 [16.9 kB] 295s Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libtcl8.6 s390x 8.6.13+dfsg-2 [948 kB] 295s Get:38 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu1 [29.8 kB] 295s Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libwebp7 s390x 1.3.2-0.4 [207 kB] 295s Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libtiff6 s390x 4.5.1+git230720-3ubuntu1 [253 kB] 295s Get:41 http://ftpmaster.internal/ubuntu noble/main s390x libxft2 s390x 2.3.6-1 [44.3 kB] 295s Get:42 http://ftpmaster.internal/ubuntu noble/main s390x libxss1 s390x 1:1.2.3-1build2 [8192 B] 295s Get:43 http://ftpmaster.internal/ubuntu noble/main s390x libtk8.6 s390x 8.6.14-1 [833 kB] 295s Get:44 http://ftpmaster.internal/ubuntu noble/main s390x libxt6 s390x 1:1.2.1-1.1 [166 kB] 295s Get:45 http://ftpmaster.internal/ubuntu noble/main s390x zip s390x 3.0-13 [175 kB] 295s Get:46 http://ftpmaster.internal/ubuntu noble/main s390x unzip s390x 6.0-28ubuntu3 [180 kB] 295s Get:47 http://ftpmaster.internal/ubuntu noble/main s390x xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 295s Get:48 http://ftpmaster.internal/ubuntu noble/universe s390x r-base-core s390x 4.3.2-1build1 [27.1 MB] 296s Get:49 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-littler s390x 0.3.19-1 [93.0 kB] 296s Get:50 http://ftpmaster.internal/ubuntu noble/universe s390x littler all 0.3.19-1 [2472 B] 296s Get:51 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-abind all 1.4-5-2 [63.6 kB] 296s Get:52 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-codetools all 0.2-19-1 [90.5 kB] 296s Get:53 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-deldir s390x 2.0-4-1 [271 kB] 296s Get:54 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-iterators all 1.0.14-1 [336 kB] 296s Get:55 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-foreach all 1.5.2-1 [124 kB] 296s Get:56 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-lattice s390x 0.22-5-1 [1341 kB] 296s Get:57 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-matrix s390x 1.6-5-1 [3983 kB] 297s Get:58 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-shape all 1.4.6-1 [770 kB] 297s Get:59 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-survival s390x 3.5-8-1 [6161 kB] 297s Get:60 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 297s Get:61 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rcpp s390x 1.0.12-1 [1985 kB] 297s Get:62 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rcppeigen s390x 0.3.3.9.4-1 [1187 kB] 297s Get:63 http://ftpmaster.internal/ubuntu noble/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 297s Get:64 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-glmnet s390x 4.1-8-1 [1942 kB] 297s Get:65 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-goftest s390x 1.2-3-1 [59.2 kB] 297s Get:66 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-gsl s390x 2.1-8-1 [490 kB] 297s Get:67 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-locfit s390x 1.5-9.8-1 [511 kB] 297s Get:68 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-nlme s390x 3.1.164-1 [2268 kB] 297s Get:69 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-mgcv s390x 1.9-1-1 [3348 kB] 297s Get:70 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-nleqslv s390x 3.3.5-1 [104 kB] 297s Get:71 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-polyclip s390x 1.10-6-1 [119 kB] 297s Get:72 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rpart s390x 4.1.23-1 [667 kB] 297s Get:73 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-sm s390x 2.2-6.0-1 [792 kB] 297s Get:74 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatial s390x 7.3-17-1 [134 kB] 297s Get:75 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.utils s390x 3.0-4-1 [361 kB] 297s Get:76 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.data all 3.0-4-1 [4090 kB] 297s Get:77 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.geom s390x 3.2-8-1 [3829 kB] 297s Get:78 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.random s390x 3.2-2-1 [1146 kB] 297s Get:79 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-tensor all 1.5-4 [15.7 kB] 297s Get:80 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.sparse s390x 3.0-3-1 [217 kB] 297s Get:81 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.explore s390x 3.2-5-1 [3289 kB] 298s Get:82 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.model s390x 3.2-8-1 [3290 kB] 298s Get:83 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.linnet s390x 3.1-3-1 [1411 kB] 298s Get:84 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat s390x 3.0-7-1 [3817 kB] 299s Preconfiguring packages ... 299s Fetched 95.7 MB in 6s (15.8 MB/s) 299s Selecting previously unselected package libfreetype6:s390x. 299s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 51331 files and directories currently installed.) 299s Preparing to unpack .../00-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 299s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 299s Selecting previously unselected package fonts-dejavu-mono. 299s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 299s Unpacking fonts-dejavu-mono (2.37-8) ... 299s Selecting previously unselected package fonts-dejavu-core. 299s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 299s Unpacking fonts-dejavu-core (2.37-8) ... 299s Selecting previously unselected package fontconfig-config. 299s Preparing to unpack .../03-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 299s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 299s Selecting previously unselected package libfontconfig1:s390x. 299s Preparing to unpack .../04-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 299s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 299s Selecting previously unselected package fontconfig. 299s Preparing to unpack .../05-fontconfig_2.15.0-1ubuntu1_s390x.deb ... 299s Unpacking fontconfig (2.15.0-1ubuntu1) ... 299s Selecting previously unselected package fonts-mathjax. 299s Preparing to unpack .../06-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 299s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 299s Selecting previously unselected package libblas3:s390x. 300s Preparing to unpack .../07-libblas3_3.12.0-3_s390x.deb ... 300s Unpacking libblas3:s390x (3.12.0-3) ... 300s Selecting previously unselected package libpixman-1-0:s390x. 300s Preparing to unpack .../08-libpixman-1-0_0.42.2-1_s390x.deb ... 300s Unpacking libpixman-1-0:s390x (0.42.2-1) ... 300s Selecting previously unselected package libxcb-render0:s390x. 300s Preparing to unpack .../09-libxcb-render0_1.15-1_s390x.deb ... 300s Unpacking libxcb-render0:s390x (1.15-1) ... 300s Selecting previously unselected package libxcb-shm0:s390x. 300s Preparing to unpack .../10-libxcb-shm0_1.15-1_s390x.deb ... 300s Unpacking libxcb-shm0:s390x (1.15-1) ... 300s Selecting previously unselected package libxrender1:s390x. 300s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1_s390x.deb ... 300s Unpacking libxrender1:s390x (1:0.9.10-1.1) ... 300s Selecting previously unselected package libcairo2:s390x. 300s Preparing to unpack .../12-libcairo2_1.18.0-1_s390x.deb ... 300s Unpacking libcairo2:s390x (1.18.0-1) ... 300s Selecting previously unselected package libdatrie1:s390x. 300s Preparing to unpack .../13-libdatrie1_0.2.13-3_s390x.deb ... 300s Unpacking libdatrie1:s390x (0.2.13-3) ... 300s Selecting previously unselected package libdeflate0:s390x. 300s Preparing to unpack .../14-libdeflate0_1.19-1_s390x.deb ... 300s Unpacking libdeflate0:s390x (1.19-1) ... 300s Selecting previously unselected package libgfortran5:s390x. 300s Preparing to unpack .../15-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 300s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 300s Selecting previously unselected package libgomp1:s390x. 300s Preparing to unpack .../16-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 300s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 300s Selecting previously unselected package libgraphite2-3:s390x. 300s Preparing to unpack .../17-libgraphite2-3_1.3.14-2_s390x.deb ... 300s Unpacking libgraphite2-3:s390x (1.3.14-2) ... 300s Selecting previously unselected package libgslcblas0:s390x. 300s Preparing to unpack .../18-libgslcblas0_2.7.1+dfsg-6ubuntu1_s390x.deb ... 300s Unpacking libgslcblas0:s390x (2.7.1+dfsg-6ubuntu1) ... 300s Selecting previously unselected package libgsl27:s390x. 300s Preparing to unpack .../19-libgsl27_2.7.1+dfsg-6ubuntu1_s390x.deb ... 300s Unpacking libgsl27:s390x (2.7.1+dfsg-6ubuntu1) ... 300s Selecting previously unselected package libharfbuzz0b:s390x. 300s Preparing to unpack .../20-libharfbuzz0b_8.3.0-2_s390x.deb ... 300s Unpacking libharfbuzz0b:s390x (8.3.0-2) ... 300s Selecting previously unselected package x11-common. 300s Preparing to unpack .../21-x11-common_1%3a7.7+23ubuntu2_all.deb ... 300s Unpacking x11-common (1:7.7+23ubuntu2) ... 300s Selecting previously unselected package libice6:s390x. 300s Preparing to unpack .../22-libice6_2%3a1.0.10-1build2_s390x.deb ... 300s Unpacking libice6:s390x (2:1.0.10-1build2) ... 300s Selecting previously unselected package libjpeg-turbo8:s390x. 300s Preparing to unpack .../23-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 300s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 300s Selecting previously unselected package libjpeg8:s390x. 300s Preparing to unpack .../24-libjpeg8_8c-2ubuntu11_s390x.deb ... 300s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 300s Selecting previously unselected package liblapack3:s390x. 300s Preparing to unpack .../25-liblapack3_3.12.0-3_s390x.deb ... 300s Unpacking liblapack3:s390x (3.12.0-3) ... 300s Selecting previously unselected package libthai-data. 300s Preparing to unpack .../26-libthai-data_0.1.29-2_all.deb ... 300s Unpacking libthai-data (0.1.29-2) ... 300s Selecting previously unselected package libthai0:s390x. 300s Preparing to unpack .../27-libthai0_0.1.29-2_s390x.deb ... 300s Unpacking libthai0:s390x (0.1.29-2) ... 300s Selecting previously unselected package libpango-1.0-0:s390x. 300s Preparing to unpack .../28-libpango-1.0-0_1.51.0+ds-4_s390x.deb ... 300s Unpacking libpango-1.0-0:s390x (1.51.0+ds-4) ... 300s Selecting previously unselected package libpangoft2-1.0-0:s390x. 300s Preparing to unpack .../29-libpangoft2-1.0-0_1.51.0+ds-4_s390x.deb ... 300s Unpacking libpangoft2-1.0-0:s390x (1.51.0+ds-4) ... 300s Selecting previously unselected package libpangocairo-1.0-0:s390x. 300s Preparing to unpack .../30-libpangocairo-1.0-0_1.51.0+ds-4_s390x.deb ... 300s Unpacking libpangocairo-1.0-0:s390x (1.51.0+ds-4) ... 300s Selecting previously unselected package libpaper1:s390x. 300s Preparing to unpack .../31-libpaper1_1.1.29_s390x.deb ... 300s Unpacking libpaper1:s390x (1.1.29) ... 300s Selecting previously unselected package libpaper-utils. 300s Preparing to unpack .../32-libpaper-utils_1.1.29_s390x.deb ... 300s Unpacking libpaper-utils (1.1.29) ... 300s Selecting previously unselected package libsharpyuv0:s390x. 300s Preparing to unpack .../33-libsharpyuv0_1.3.2-0.4_s390x.deb ... 300s Unpacking libsharpyuv0:s390x (1.3.2-0.4) ... 300s Selecting previously unselected package libsm6:s390x. 300s Preparing to unpack .../34-libsm6_2%3a1.2.3-1build2_s390x.deb ... 300s Unpacking libsm6:s390x (2:1.2.3-1build2) ... 300s Selecting previously unselected package libtcl8.6:s390x. 300s Preparing to unpack .../35-libtcl8.6_8.6.13+dfsg-2_s390x.deb ... 300s Unpacking libtcl8.6:s390x (8.6.13+dfsg-2) ... 300s Selecting previously unselected package libjbig0:s390x. 300s Preparing to unpack .../36-libjbig0_2.1-6.1ubuntu1_s390x.deb ... 300s Unpacking libjbig0:s390x (2.1-6.1ubuntu1) ... 300s Selecting previously unselected package libwebp7:s390x. 300s Preparing to unpack .../37-libwebp7_1.3.2-0.4_s390x.deb ... 300s Unpacking libwebp7:s390x (1.3.2-0.4) ... 300s Selecting previously unselected package libtiff6:s390x. 300s Preparing to unpack .../38-libtiff6_4.5.1+git230720-3ubuntu1_s390x.deb ... 300s Unpacking libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 300s Selecting previously unselected package libxft2:s390x. 300s Preparing to unpack .../39-libxft2_2.3.6-1_s390x.deb ... 300s Unpacking libxft2:s390x (2.3.6-1) ... 300s Selecting previously unselected package libxss1:s390x. 300s Preparing to unpack .../40-libxss1_1%3a1.2.3-1build2_s390x.deb ... 300s Unpacking libxss1:s390x (1:1.2.3-1build2) ... 300s Selecting previously unselected package libtk8.6:s390x. 300s Preparing to unpack .../41-libtk8.6_8.6.14-1_s390x.deb ... 300s Unpacking libtk8.6:s390x (8.6.14-1) ... 301s Selecting previously unselected package libxt6:s390x. 301s Preparing to unpack .../42-libxt6_1%3a1.2.1-1.1_s390x.deb ... 301s Unpacking libxt6:s390x (1:1.2.1-1.1) ... 301s Selecting previously unselected package zip. 301s Preparing to unpack .../43-zip_3.0-13_s390x.deb ... 301s Unpacking zip (3.0-13) ... 301s Selecting previously unselected package unzip. 301s Preparing to unpack .../44-unzip_6.0-28ubuntu3_s390x.deb ... 301s Unpacking unzip (6.0-28ubuntu3) ... 301s Selecting previously unselected package xdg-utils. 301s Preparing to unpack .../45-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 301s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 301s Selecting previously unselected package r-base-core. 301s Preparing to unpack .../46-r-base-core_4.3.2-1build1_s390x.deb ... 301s Unpacking r-base-core (4.3.2-1build1) ... 301s Selecting previously unselected package r-cran-littler. 301s Preparing to unpack .../47-r-cran-littler_0.3.19-1_s390x.deb ... 301s Unpacking r-cran-littler (0.3.19-1) ... 301s Selecting previously unselected package littler. 301s Preparing to unpack .../48-littler_0.3.19-1_all.deb ... 301s Unpacking littler (0.3.19-1) ... 301s Selecting previously unselected package r-cran-abind. 301s Preparing to unpack .../49-r-cran-abind_1.4-5-2_all.deb ... 301s Unpacking r-cran-abind (1.4-5-2) ... 301s Selecting previously unselected package r-cran-codetools. 301s Preparing to unpack .../50-r-cran-codetools_0.2-19-1_all.deb ... 301s Unpacking r-cran-codetools (0.2-19-1) ... 301s Selecting previously unselected package r-cran-deldir. 301s Preparing to unpack .../51-r-cran-deldir_2.0-4-1_s390x.deb ... 301s Unpacking r-cran-deldir (2.0-4-1) ... 301s Selecting previously unselected package r-cran-iterators. 301s Preparing to unpack .../52-r-cran-iterators_1.0.14-1_all.deb ... 301s Unpacking r-cran-iterators (1.0.14-1) ... 301s Selecting previously unselected package r-cran-foreach. 301s Preparing to unpack .../53-r-cran-foreach_1.5.2-1_all.deb ... 301s Unpacking r-cran-foreach (1.5.2-1) ... 301s Selecting previously unselected package r-cran-lattice. 301s Preparing to unpack .../54-r-cran-lattice_0.22-5-1_s390x.deb ... 301s Unpacking r-cran-lattice (0.22-5-1) ... 301s Selecting previously unselected package r-cran-matrix. 301s Preparing to unpack .../55-r-cran-matrix_1.6-5-1_s390x.deb ... 301s Unpacking r-cran-matrix (1.6-5-1) ... 301s Selecting previously unselected package r-cran-shape. 301s Preparing to unpack .../56-r-cran-shape_1.4.6-1_all.deb ... 301s Unpacking r-cran-shape (1.4.6-1) ... 301s Selecting previously unselected package r-cran-survival. 301s Preparing to unpack .../57-r-cran-survival_3.5-8-1_s390x.deb ... 301s Unpacking r-cran-survival (3.5-8-1) ... 302s Selecting previously unselected package r-cran-pkgkitten. 302s Preparing to unpack .../58-r-cran-pkgkitten_0.2.3-1_all.deb ... 302s Unpacking r-cran-pkgkitten (0.2.3-1) ... 302s Selecting previously unselected package r-cran-rcpp. 302s Preparing to unpack .../59-r-cran-rcpp_1.0.12-1_s390x.deb ... 302s Unpacking r-cran-rcpp (1.0.12-1) ... 302s Selecting previously unselected package r-cran-rcppeigen. 302s Preparing to unpack .../60-r-cran-rcppeigen_0.3.3.9.4-1_s390x.deb ... 302s Unpacking r-cran-rcppeigen (0.3.3.9.4-1) ... 302s Selecting previously unselected package libjs-mathjax. 302s Preparing to unpack .../61-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 302s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 303s Selecting previously unselected package r-cran-glmnet. 303s Preparing to unpack .../62-r-cran-glmnet_4.1-8-1_s390x.deb ... 303s Unpacking r-cran-glmnet (4.1-8-1) ... 303s Selecting previously unselected package r-cran-goftest. 303s Preparing to unpack .../63-r-cran-goftest_1.2-3-1_s390x.deb ... 303s Unpacking r-cran-goftest (1.2-3-1) ... 303s Selecting previously unselected package r-cran-gsl. 303s Preparing to unpack .../64-r-cran-gsl_2.1-8-1_s390x.deb ... 303s Unpacking r-cran-gsl (2.1-8-1) ... 303s Selecting previously unselected package r-cran-locfit. 303s Preparing to unpack .../65-r-cran-locfit_1.5-9.8-1_s390x.deb ... 303s Unpacking r-cran-locfit (1.5-9.8-1) ... 303s Selecting previously unselected package r-cran-nlme. 303s Preparing to unpack .../66-r-cran-nlme_3.1.164-1_s390x.deb ... 303s Unpacking r-cran-nlme (3.1.164-1) ... 303s Selecting previously unselected package r-cran-mgcv. 303s Preparing to unpack .../67-r-cran-mgcv_1.9-1-1_s390x.deb ... 303s Unpacking r-cran-mgcv (1.9-1-1) ... 303s Selecting previously unselected package r-cran-nleqslv. 303s Preparing to unpack .../68-r-cran-nleqslv_3.3.5-1_s390x.deb ... 303s Unpacking r-cran-nleqslv (3.3.5-1) ... 303s Selecting previously unselected package r-cran-polyclip. 303s Preparing to unpack .../69-r-cran-polyclip_1.10-6-1_s390x.deb ... 303s Unpacking r-cran-polyclip (1.10-6-1) ... 303s Selecting previously unselected package r-cran-rpart. 303s Preparing to unpack .../70-r-cran-rpart_4.1.23-1_s390x.deb ... 303s Unpacking r-cran-rpart (4.1.23-1) ... 303s Selecting previously unselected package r-cran-sm. 303s Preparing to unpack .../71-r-cran-sm_2.2-6.0-1_s390x.deb ... 303s Unpacking r-cran-sm (2.2-6.0-1) ... 303s Selecting previously unselected package r-cran-spatial. 303s Preparing to unpack .../72-r-cran-spatial_7.3-17-1_s390x.deb ... 303s Unpacking r-cran-spatial (7.3-17-1) ... 304s Selecting previously unselected package r-cran-spatstat.utils. 304s Preparing to unpack .../73-r-cran-spatstat.utils_3.0-4-1_s390x.deb ... 304s Unpacking r-cran-spatstat.utils (3.0-4-1) ... 304s Selecting previously unselected package r-cran-spatstat.data. 304s Preparing to unpack .../74-r-cran-spatstat.data_3.0-4-1_all.deb ... 304s Unpacking r-cran-spatstat.data (3.0-4-1) ... 304s Selecting previously unselected package r-cran-spatstat.geom. 304s Preparing to unpack .../75-r-cran-spatstat.geom_3.2-8-1_s390x.deb ... 304s Unpacking r-cran-spatstat.geom (3.2-8-1) ... 304s Selecting previously unselected package r-cran-spatstat.random. 304s Preparing to unpack .../76-r-cran-spatstat.random_3.2-2-1_s390x.deb ... 304s Unpacking r-cran-spatstat.random (3.2-2-1) ... 304s Selecting previously unselected package r-cran-tensor. 304s Preparing to unpack .../77-r-cran-tensor_1.5-4_all.deb ... 304s Unpacking r-cran-tensor (1.5-4) ... 304s Selecting previously unselected package r-cran-spatstat.sparse. 304s Preparing to unpack .../78-r-cran-spatstat.sparse_3.0-3-1_s390x.deb ... 304s Unpacking r-cran-spatstat.sparse (3.0-3-1) ... 304s Selecting previously unselected package r-cran-spatstat.explore. 304s Preparing to unpack .../79-r-cran-spatstat.explore_3.2-5-1_s390x.deb ... 304s Unpacking r-cran-spatstat.explore (3.2-5-1) ... 304s Selecting previously unselected package r-cran-spatstat.model. 304s Preparing to unpack .../80-r-cran-spatstat.model_3.2-8-1_s390x.deb ... 304s Unpacking r-cran-spatstat.model (3.2-8-1) ... 304s Selecting previously unselected package r-cran-spatstat.linnet. 304s Preparing to unpack .../81-r-cran-spatstat.linnet_3.1-3-1_s390x.deb ... 304s Unpacking r-cran-spatstat.linnet (3.1-3-1) ... 304s Selecting previously unselected package r-cran-spatstat. 304s Preparing to unpack .../82-r-cran-spatstat_3.0-7-1_s390x.deb ... 304s Unpacking r-cran-spatstat (3.0-7-1) ... 304s Selecting previously unselected package autopkgtest-satdep. 304s Preparing to unpack .../83-1-autopkgtest-satdep.deb ... 304s Unpacking autopkgtest-satdep (0) ... 304s Setting up libgraphite2-3:s390x (1.3.14-2) ... 304s Setting up libpixman-1-0:s390x (0.42.2-1) ... 304s Setting up libsharpyuv0:s390x (1.3.2-0.4) ... 304s Setting up libpaper1:s390x (1.1.29) ... 304s 304s Creating config file /etc/papersize with new version 304s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 304s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 304s Setting up libxrender1:s390x (1:0.9.10-1.1) ... 304s Setting up libdatrie1:s390x (0.2.13-3) ... 304s Setting up libgslcblas0:s390x (2.7.1+dfsg-6ubuntu1) ... 304s Setting up libxcb-render0:s390x (1.15-1) ... 304s Setting up unzip (6.0-28ubuntu3) ... 304s Setting up x11-common (1:7.7+23ubuntu2) ... 305s Setting up libdeflate0:s390x (1.19-1) ... 305s Setting up libgsl27:s390x (2.7.1+dfsg-6ubuntu1) ... 305s Setting up libxcb-shm0:s390x (1.15-1) ... 305s Setting up libpaper-utils (1.1.29) ... 305s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 305s Setting up libjbig0:s390x (2.1-6.1ubuntu1) ... 305s Setting up zip (3.0-13) ... 305s Setting up libblas3:s390x (3.12.0-3) ... 305s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 305s Setting up libfreetype6:s390x (2.13.2+dfsg-1) ... 305s Setting up fonts-dejavu-mono (2.37-8) ... 305s Setting up libtcl8.6:s390x (8.6.13+dfsg-2) ... 305s Setting up fonts-dejavu-core (2.37-8) ... 305s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 305s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 305s Setting up libwebp7:s390x (1.3.2-0.4) ... 305s Setting up libharfbuzz0b:s390x (8.3.0-2) ... 305s Setting up libthai-data (0.1.29-2) ... 305s Setting up libxss1:s390x (1:1.2.3-1build2) ... 305s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 305s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 305s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 305s Setting up libice6:s390x (2:1.0.10-1build2) ... 305s Setting up liblapack3:s390x (3.12.0-3) ... 305s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 305s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 305s Setting up libthai0:s390x (0.1.29-2) ... 305s Setting up libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 305s Setting up libfontconfig1:s390x (2.15.0-1ubuntu1) ... 305s Setting up libsm6:s390x (2:1.2.3-1build2) ... 305s Setting up fontconfig (2.15.0-1ubuntu1) ... 307s Regenerating fonts cache... done. 307s Setting up libxft2:s390x (2.3.6-1) ... 307s Setting up libtk8.6:s390x (8.6.14-1) ... 307s Setting up libpango-1.0-0:s390x (1.51.0+ds-4) ... 307s Setting up libcairo2:s390x (1.18.0-1) ... 307s Setting up libxt6:s390x (1:1.2.1-1.1) ... 307s Setting up libpangoft2-1.0-0:s390x (1.51.0+ds-4) ... 307s Setting up libpangocairo-1.0-0:s390x (1.51.0+ds-4) ... 307s Setting up r-base-core (4.3.2-1build1) ... 307s 307s Creating config file /etc/R/Renviron with new version 307s Setting up r-cran-lattice (0.22-5-1) ... 307s Setting up r-cran-nlme (3.1.164-1) ... 307s Setting up r-cran-spatstat.utils (3.0-4-1) ... 307s Setting up r-cran-locfit (1.5-9.8-1) ... 307s Setting up r-cran-tensor (1.5-4) ... 307s Setting up r-cran-pkgkitten (0.2.3-1) ... 307s Setting up r-cran-littler (0.3.19-1) ... 307s Setting up r-cran-nleqslv (3.3.5-1) ... 307s Setting up r-cran-rcpp (1.0.12-1) ... 307s Setting up r-cran-codetools (0.2-19-1) ... 307s Setting up littler (0.3.19-1) ... 307s Setting up r-cran-gsl (2.1-8-1) ... 307s Setting up r-cran-spatial (7.3-17-1) ... 307s Setting up r-cran-iterators (1.0.14-1) ... 307s Setting up r-cran-abind (1.4-5-2) ... 307s Setting up r-cran-foreach (1.5.2-1) ... 307s Setting up r-cran-sm (2.2-6.0-1) ... 307s Setting up r-cran-polyclip (1.10-6-1) ... 307s Setting up r-cran-deldir (2.0-4-1) ... 307s Setting up r-cran-goftest (1.2-3-1) ... 307s Setting up r-cran-shape (1.4.6-1) ... 307s Setting up r-cran-matrix (1.6-5-1) ... 307s Setting up r-cran-spatstat.sparse (3.0-3-1) ... 307s Setting up r-cran-mgcv (1.9-1-1) ... 307s Setting up r-cran-rcppeigen (0.3.3.9.4-1) ... 307s Setting up r-cran-survival (3.5-8-1) ... 307s Setting up r-cran-spatstat.data (3.0-4-1) ... 307s Setting up r-cran-spatstat.geom (3.2-8-1) ... 307s Setting up r-cran-glmnet (4.1-8-1) ... 307s Setting up r-cran-rpart (4.1.23-1) ... 307s Setting up r-cran-spatstat.random (3.2-2-1) ... 307s Setting up r-cran-spatstat.explore (3.2-5-1) ... 307s Setting up r-cran-spatstat.model (3.2-8-1) ... 307s Setting up r-cran-spatstat.linnet (3.1-3-1) ... 307s Setting up r-cran-spatstat (3.0-7-1) ... 307s Setting up autopkgtest-satdep (0) ... 307s Processing triggers for man-db (2.12.0-3) ... 308s Processing triggers for install-info (7.1-3) ... 308s Processing triggers for libc-bin (2.39-0ubuntu6) ... 314s (Reading database ... 60940 files and directories currently installed.) 314s Removing autopkgtest-satdep (0) ... 314s autopkgtest [16:15:29]: test run-unit-test: [----------------------- 314s BEGIN TEST testsAtoC.R 315s 315s R version 4.3.2 (2023-10-31) -- "Eye Holes" 315s Copyright (C) 2023 The R Foundation for Statistical Computing 315s Platform: s390x-ibm-linux-gnu (64-bit) 315s 315s R is free software and comes with ABSOLUTELY NO WARRANTY. 315s You are welcome to redistribute it under certain conditions. 315s Type 'license()' or 'licence()' for distribution details. 315s 315s R is a collaborative project with many contributors. 315s Type 'contributors()' for more information and 315s 'citation()' on how to cite R or R packages in publications. 315s 315s Type 'demo()' for some demos, 'help()' for on-line help, or 315s 'help.start()' for an HTML browser interface to help. 315s Type 'q()' to quit R. 315s 315s > #' 315s > #' Header for all (concatenated) test files 315s Loading required package: spatstat.model 315s > #' 315s > #' Require spatstat.model 315s > #' Obtain environment variable controlling tests. 315s > #' 315s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 315s > 315s > require(spatstat.model) 315s Loading required package: spatstat.data 316s Loading required package: spatstat.geom 316s spatstat.geom 3.2-8 316s Loading required package: spatstat.random 316s spatstat.random 3.2-2 316s Loading required package: spatstat.explore 316s Loading required package: nlme 316s spatstat.explore 3.2-5 316s Loading required package: rpart 317s spatstat.model 3.2-8 317s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 317s > ALWAYS <- TRUE 317s > cat(paste("--------- Executing", 317s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 317s + "test code -----------\n")) 317s --------- Executing **RESTRICTED** subset of test code ----------- 317s > #' tests/aucroc.R 317s > #' 317s > #' AUC and ROC code 317s > #' 317s > #' $Revision: 1.6 $ $Date: 2020/11/02 06:26:45 $ 317s > 317s > local({ 317s + if(FULLTEST) { 317s + fit <- kppm(redwood ~ I(y-x)) 317s + a <- roc(fit) 317s + b <- auc(fit) 317s + fet <- ppm(amacrine~x+y+marks) 317s + d <- roc(fet) 317s + e <- auc(fet) 317s + } 317s + }) 317s > ## tests/cdf.test.R 317s > 317s > 317s > local({ 317s + NSIM <- 9 317s + op <- spatstat.options(ndummy.min=16, npixel=32) 317s + if(FULLTEST) { 317s + ## Monte Carlo test for Gibbs model 317s + fit <- ppm(cells ~ 1, Strauss(0.07)) 317s + cdf.test(fit, "x", nsim=NSIM) 317s + 317s + ## cdf.test.slrm 317s + fut <- slrm(japanesepines ~ x + y) 317s + Z <- distmap(japanesepines) 317s + cdf.test(fut, Z) 317s + } 317s + reset.spatstat.options() 317s + }) 317s > 317s > 317s > #' 317s > #' tests/contrib.R 317s > #' 317s > #' Tests for user-contributed code in spatstat 317s > #' 317s > #' $Revision: 1.4 $ $Date: 2021/04/17 02:32:24 $ 317s > 317s > local({ 317s + #' Jinhom 317s + #' Marie-Colette van Lieshout and Ottmar Cronie 317s + X <- redwood3 317s + if(FULLTEST) { 317s + fit <- ppm(X ~ polynom(x,y,2)) 317s + } else { 317s + X <- X[c(TRUE,FALSE)] 317s + spatstat.options(npixel=32, ndummy.min=16) 317s + fit <- ppm(X ~ x) 317s + } 317s + lam <- predict(fit) 317s + lamX <- fitted(fit, dataonly=TRUE) 317s + lmin <- 0.9 * min(lam) 317s + g1 <- Ginhom(X, lambda=fit, update=TRUE) 317s + if(FULLTEST) { 317s + g2 <- Ginhom(X, lambda=fit, update=FALSE, lmin = lmin) 317s + g3 <- Ginhom(X, lambda=lam, lmin=lmin) 317s + g4 <- Ginhom(X, lambda=lamX, lmin=lmin) 317s + } 317s + if(ALWAYS) { 317s + f2 <- Finhom(X, lambda=fit, update=FALSE) 317s + } 317s + if(FULLTEST) { 317s + f1 <- Finhom(X, lambda=fit, update=TRUE) 317s + f3 <- Finhom(X, lambda=lam, lmin=lmin) 317s + } 317s + if(!FULLTEST) reset.spatstat.options() 317s + }) 317s > 317s BEGIN TEST testsD.R 317s 317s R version 4.3.2 (2023-10-31) -- "Eye Holes" 317s Copyright (C) 2023 The R Foundation for Statistical Computing 317s Platform: s390x-ibm-linux-gnu (64-bit) 317s 317s R is free software and comes with ABSOLUTELY NO WARRANTY. 317s You are welcome to redistribute it under certain conditions. 317s Type 'license()' or 'licence()' for distribution details. 317s 317s R is a collaborative project with many contributors. 317s Type 'contributors()' for more information and 317s 'citation()' on how to cite R or R packages in publications. 317s 317s Type 'demo()' for some demos, 'help()' for on-line help, or 317s 'help.start()' for an HTML browser interface to help. 317s Type 'q()' to quit R. 317s 317s > #' 317s > #' Header for all (concatenated) test files 317s > #' 317s > #' Require spatstat.model 317s > #' Obtain environment variable controlling tests. 317s > #' 317s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 317s > 317s > require(spatstat.model) 317s Loading required package: spatstat.model 317s Loading required package: spatstat.data 318s Loading required package: spatstat.geom 318s spatstat.geom 3.2-8 318s Loading required package: spatstat.random 318s spatstat.random 3.2-2 318s Loading required package: spatstat.explore 318s Loading required package: nlme 319s spatstat.explore 3.2-5 319s Loading required package: rpart 319s spatstat.model 3.2-8 319s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 319s > ALWAYS <- TRUE 319s > cat(paste("--------- Executing", 319s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 319s + "test code -----------\n")) 319s --------- Executing **RESTRICTED** subset of test code ----------- 319s > #' 319s > #' tests/deltasuffstat.R 319s > #' 319s > #' Explicit tests of 'deltasuffstat' 319s > #' 319s > #' $Revision: 1.4 $ $Date: 2021/01/22 08:08:48 $ 319s > 319s > if(!FULLTEST) 319s + spatstat.options(npixel=32, ndummy.min=16) 319s > 319s > if(ALWAYS) { # depends on C code 319s + local({ 319s + 319s + disagree <- function(x, y, tol=1e-7) { !is.null(x) && !is.null(y) && max(abs(x-y)) > tol } 319s + 319s + flydelta <- function(model, modelname="") { 319s + ## Check execution of different algorithms for 'deltasuffstat' 319s + dSS <- deltasuffstat(model, sparseOK=TRUE) 319s + dBS <- deltasuffstat(model, sparseOK=TRUE, use.special=FALSE, force=TRUE) 319s + dBF <- deltasuffstat(model, sparseOK=FALSE, use.special=FALSE, force=TRUE) 319s + ## Compare results 319s + if(disagree(dBS, dSS)) 319s + stop(paste(modelname, "model: Brute force algorithm disagrees with special algorithm")) 319s + if(disagree(dBF, dBS)) 319s + stop(paste(modelname, "model: Sparse and full versions of brute force algorithm disagree")) 319s + return(invisible(NULL)) 319s + } 319s + 319s + modelS <- ppm(cells ~ x, Strauss(0.13), nd=10) 319s + flydelta(modelS, "Strauss") 319s + 319s + antsub <- ants[c(FALSE,TRUE,FALSE)] 319s + rmat <- matrix(c(130, 90, 90, 60), 2, 2) 319s + 319s + modelM <- ppm(antsub ~ 1, MultiStrauss(rmat), nd=16) 319s + flydelta(modelM, "MultiStrauss") 319s + 319s + modelA <- ppm(antsub ~ 1, HierStrauss(rmat, archy=c(2,1)), nd=16) 319s + flydelta(modelA, "HierStrauss") 319s + }) 319s + 319s + } 324s > 324s > reset.spatstat.options() 324s > #' 324s > #' tests/density.R 324s > #' 324s > #' Test behaviour of density() methods, 324s > #' relrisk(), Smooth() 324s > #' and inhomogeneous summary functions 324s > #' and idw, adaptive.density, intensity 324s > #' 324s > #' $Revision: 1.62 $ $Date: 2022/05/22 11:14:51 $ 324s > #' 324s > 324s > if(!FULLTEST) 324s + spatstat.options(npixel=32, ndummy.min=16) 324s > 324s > 324s > local({ 324s + ## likewise 'relrisk.ppm' 324s + fit <- ppm(ants ~ x) 324s + rants <- function(..., model=fit) { 324s + a <- relrisk(model, sigma=100, se=TRUE, ...) 324s + return(TRUE) 324s + } 324s + if(ALWAYS) { 324s + rants() 324s + rants(diggle=TRUE) 324s + rants(edge=FALSE) 324s + rants(at="points") 324s + rants(casecontrol=FALSE) 324s + rants(relative=TRUE) 324s + } 324s + if(FULLTEST) { 324s + rants(diggle=TRUE, at="points") 324s + rants(edge=FALSE, at="points") 324s + rants(casecontrol=FALSE, relative=TRUE) 324s + rants(casecontrol=FALSE,at="points") 324s + rants(relative=TRUE,at="points") 324s + rants(casecontrol=FALSE, relative=TRUE,at="points") 324s + rants(relative=TRUE, control="Cataglyphis", case="Messor") 324s + rants(relative=TRUE, control="Cataglyphis", case="Messor", at="points") 324s + } 324s + ## more than 2 types 324s + fut <- ppm(sporophores ~ x) 324s + if(ALWAYS) { 324s + rants(model=fut) 324s + } 324s + if(FULLTEST) { 324s + rants(model=fut, at="points") 324s + rants(model=fut, relative=TRUE, at="points") 324s + } 324s + if(FULLTEST) { 324s + ## cases of 'intensity' etc 324s + a <- intensity(ppm(amacrine ~ 1)) 324s + } 324s + }) 325s > 325s > reset.spatstat.options() 325s > 325s > #' 325s > #' tests/diagnostique.R 325s > #' 325s > #' Diagnostic tools such as diagnose.ppm, qqplot.ppm 325s > #' 325s > #' $Revision: 1.6 $ $Date: 2020/04/28 12:58:26 $ 325s > #' 325s > 325s > if(FULLTEST) { 325s + local({ 325s + fit <- ppm(cells ~ x) 325s + diagE <- diagnose.ppm(fit, type="eem") 325s + diagI <- diagnose.ppm(fit, type="inverse") 325s + diagP <- diagnose.ppm(fit, type="Pearson") 325s + plot(diagE, which="all") 325s + plot(diagI, which="smooth") 325s + plot(diagP, which="x") 325s + plot(diagP, which="marks", plot.neg="discrete") 325s + plot(diagP, which="marks", plot.neg="contour") 325s + plot(diagP, which="smooth", srange=c(-5,5)) 325s + plot(diagP, which="smooth", plot.smooth="contour") 325s + plot(diagP, which="smooth", plot.smooth="image") 325s + 325s + fitS <- ppm(cells ~ x, Strauss(0.08)) 325s + diagES <- diagnose.ppm(fitS, type="eem", clip=FALSE) 325s + diagIS <- diagnose.ppm(fitS, type="inverse", clip=FALSE) 325s + diagPS <- diagnose.ppm(fitS, type="Pearson", clip=FALSE) 325s + plot(diagES, which="marks", plot.neg="imagecontour") 325s + plot(diagPS, which="marks", plot.neg="discrete") 325s + plot(diagPS, which="marks", plot.neg="contour") 325s + plot(diagPS, which="smooth", plot.smooth="image") 325s + plot(diagPS, which="smooth", plot.smooth="contour") 325s + plot(diagPS, which="smooth", plot.smooth="persp") 325s + 325s + #' infinite reach, not border-corrected 325s + fut <- ppm(cells ~ x, Softcore(0.5), correction="isotropic") 325s + diagnose.ppm(fut) 325s + 325s + #' 325s + diagPX <- diagnose.ppm(fit, type="Pearson", cumulative=FALSE) 325s + plot(diagPX, which="y") 325s + 325s + #' simulation based 325s + e <- envelope(cells, nsim=4, savepatterns=TRUE, savefuns=TRUE) 325s + Plist <- rpoispp(40, nsim=5) 325s + 325s + qf <- qqplot.ppm(fit, nsim=4, expr=e, plot.it=FALSE) 325s + print(qf) 325s + qp <- qqplot.ppm(fit, nsim=5, expr=Plist, fast=FALSE) 325s + print(qp) 325s + qp <- qqplot.ppm(fit, nsim=5, expr=expression(rpoispp(40)), plot.it=FALSE) 325s + print(qp) 325s + qg <- qqplot.ppm(fit, nsim=5, style="classical", plot.it=FALSE) 325s + print(qg) 325s + 325s + #' lurking.ppm 325s + #' covariate is numeric vector 325s + fitx <- ppm(cells ~ x) 325s + yvals <- coords(as.ppp(quad.ppm(fitx)))[,"y"] 325s + lurking(fitx, yvals) 325s + #' covariate is stored but is not used in model 325s + Z <- as.im(function(x,y){ x+y }, Window(cells)) 325s + fitxx <- ppm(cells ~ x, data=solist(Zed=Z), allcovar=TRUE) 325s + lurking(fitxx, expression(Zed)) 325s + #' envelope is a ppplist; length < nsim; glmdata=NULL 325s + fit <- ppm(cells ~ 1) 325s + stuff <- lurking(fit, expression(x), envelope=Plist, plot.sd=FALSE) 325s + #' plot.lurk 325s + plot(stuff, shade=NULL) 325s + }) 325s + } 325s > 325s > #' 325s > #' tests/deepeepee.R 325s > #' 325s > #' Tests for determinantal point process models 325s > #' 325s > #' $Revision: 1.9 $ $Date: 2022/04/24 09:14:46 $ 325s > 325s > local({ 325s + if(ALWAYS) { 325s + #' simulate.dppm 325s + jpines <- residualspaper$Fig1 325s + fit <- dppm(jpines ~ 1, dppGauss) 325s + set.seed(10981) 325s + simulate(fit, W=square(5)) 325s + } 325s + if(FULLTEST) { 325s + #' simulate.detpointprocfamily - code blocks 325s + model <- dppGauss(lambda=100, alpha=.05, d=2) 325s + simulate(model, seed=1999, correction="border") 325s + u <- is.stationary(model) 325s + #' other methods for dppm 325s + kay <- Kmodel(fit) 325s + gee <- pcfmodel(fit) 325s + lam <- intensity(fit) 325s + arr <- reach(fit) 325s + pah <- parameters(fit) 325s + #' a user bug report - matrix dimension error 325s + set.seed(256) 325s + dat <- simulate( dppGauss(lambda = 8.5, alpha = 0.1, d = 2), nsim = 1) 325s + } 325s + if(FULLTEST) { 325s + ## cover print.summary.dppm 325s + jpines <- japanesepines[c(TRUE,FALSE,FALSE,FALSE)] 325s + print(summary(dppm(jpines ~ 1, dppGauss))) 325s + print(summary(dppm(jpines ~ 1, dppGauss, method="c"))) 325s + print(summary(dppm(jpines ~ 1, dppGauss, method="p"))) 325s + print(summary(dppm(jpines ~ 1, dppGauss, method="a"))) 325s + } 325s + #' dppeigen code blocks 325s + if(ALWAYS) { 325s + mod <- dppMatern(lambda=2, alpha=0.01, nu=1, d=2) 325s + uT <- dppeigen(mod, trunc=1.1, Wscale=c(1,1), stationary=TRUE) 325s + } 325s + if(FULLTEST) { 325s + uF <- dppeigen(mod, trunc=1.1, Wscale=c(1,1), stationary=FALSE) 325s + vT <- dppeigen(mod, trunc=0.98, Wscale=c(1,1), stationary=TRUE) 325s + vF <- dppeigen(mod, trunc=0.98, Wscale=c(1,1), stationary=FALSE) 325s + } 325s + }) 327s > 327s BEGIN TEST testsEtoF.R 327s 327s R version 4.3.2 (2023-10-31) -- "Eye Holes" 327s Copyright (C) 2023 The R Foundation for Statistical Computing 327s Platform: s390x-ibm-linux-gnu (64-bit) 327s 327s R is free software and comes with ABSOLUTELY NO WARRANTY. 327s You are welcome to redistribute it under certain conditions. 327s Type 'license()' or 'licence()' for distribution details. 327s 327s R is a collaborative project with many contributors. 327s Type 'contributors()' for more information and 327s 'citation()' on how to cite R or R packages in publications. 327s 327s Type 'demo()' for some demos, 'help()' for on-line help, or 327s 'help.start()' for an HTML browser interface to help. 327s Type 'q()' to quit R. 327s 327s > #' 327s > Loading required package: spatstat.model 327s #' Header for all (concatenated) test files 327s > #' 327s > #' Require spatstat.model 327s > #' Obtain environment variable controlling tests. 327s > #' 327s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 327s > 327s > require(spatstat.model) 327s Loading required package: spatstat.data 328s Loading required package: spatstat.geom 328s spatstat.geom 3.2-8 328s Loading required package: spatstat.random 328s spatstat.random 3.2-2 328s Loading required package: spatstat.explore 328s Loading required package: nlme 328s spatstat.explore 3.2-5 328s Loading required package: rpart 329s spatstat.model 3.2-8 329s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 329s > ALWAYS <- TRUE 329s > cat(paste("--------- Executing", 329s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 329s + "test code -----------\n")) 329s --------- Executing **RESTRICTED** subset of test code ----------- 329s > # 329s > # tests/envelopes.R 329s > # 329s > # Test validity of envelope data 329s > # 329s > # $Revision: 1.28 $ $Date: 2022/11/24 01:35:26 $ 329s > # 329s > 329s > local({ 329s + 329s + 329s + checktheo <- function(fit) { 329s + fitname <- deparse(substitute(fit)) 329s + en <- envelope(fit, nsim=4, verbose=FALSE, nrep=1e3) 329s + nama <- names(en) 329s + expecttheo <- is.poisson(fit) && is.stationary(fit) 329s + context <- paste("Envelope of", fitname) 329s + if(expecttheo) { 329s + if(!("theo" %in% nama)) 329s + stop(paste(context, "did not contain", sQuote("theo"))) 329s + if("mmean" %in% nama) 329s + stop(paste(context, "unexpectedly contained", sQuote("mmean"))) 329s + } else { 329s + if("theo" %in% nama) 329s + stop(paste(context, "unexpectedly contained", sQuote("theo"))) 329s + if(!("mmean" %in% nama)) 329s + stop(paste(context, "did not contain", sQuote("mmean"))) 329s + } 329s + cat(paste(context, "has correct format\n")) 329s + } 329s + 329s + if(ALWAYS) { 329s + checktheo(ppm(cells ~x)) 329s + } 329s + if(FULLTEST) { 329s + checktheo(ppm(cells)) 329s + checktheo(ppm(cells ~1, Strauss(0.1))) 329s + } 329s + 329s + 329s + #' check savefuns/savepatterns with global 329s + fit <- ppm(cells~x) 329s + if(ALWAYS) Ef <- envelope(fit, Kest, nsim=4, savefuns=TRUE, global=TRUE) 329s + if(FULLTEST) Ep <- envelope(fit, Kest, nsim=4, savepatterns=TRUE, global=TRUE) 329s + #' check handling of 'dangerous' cases 329s + if(FULLTEST) { 329s + fut <- ppm(redwood ~ x) 329s + Ek <- envelope(fut, Kinhom, update=FALSE, nsim=4) 329s + kfut <- kppm(redwood3 ~ x) 329s + Ekk <- envelope(kfut, Kinhom, lambda=density(redwood3), nsim=7) 329s + } 329s + 329s + 329s + if(ALWAYS) { # invokes C code 329s + fit <- ppm(japanesepines ~ 1, Strauss(0.04)) 329s + e6 <- envelope(fit, Kest, nsim=4, fix.n=TRUE) 329s + fit2 <- ppm(amacrine ~ 1, Strauss(0.03)) 329s + e7 <- envelope(fit2, Gcross, nsim=4, fix.marks=TRUE) 329s + } 329s + 329s + 329s + if(FULLTEST) { 329s + fit <- ppm(cells ~ 1, Strauss(0.07)) 329s + U <- envelope(fit, nsim=3, simulate=expression(runifpoint(20))) 329s + kfit <- kppm(redwood3 ~ x) 329s + UU <- envelope(kfit, nsim=7, simulate=expression(simulate(kfit, drop=TRUE))) 329s + VV <- envelope(kfit, nsim=7, weights=1:7) 329s + MM <- envelope(kfit, nsim=7, Kinhom, lambda=density(redwood3)) 329s + } 329s + 329s + if(FULLTEST) { 329s + #' envelope computations in other functions 329s + P <- lurking(cells, expression(x), envelope=TRUE, nsim=9) 329s + print(P) 329s + #' re-using envelope objects in other functions 329s + A <- envelope(cells, nsim=9, savepatterns=TRUE, savefuns=TRUE) 329s + S <- lurking(cells, expression(x), envelope=A, nsim=9) 329s + #' envelope.envelope 329s + B <- envelope(cells, nsim=5, savepatterns=TRUE, savefuns=FALSE) 329s + envelope(B) 329s + } 329s + 329s + 329s + 329s + ## close 'local' 329s + }) 329s Envelope of ppm(cells ~ x) has correct format 329s Generating 8 simulated realisations of fitted Poisson model (4 to estimate the 329s mean and 4 to calculate envelopes) ... 329s 1, 2, 3, 4, 5, 6, 7, 329s 8. 329s 329s Done. 329s Generating 4 simulated realisations of fitted Gibbs model with fixed number of 329s points ... 329s 1, 2, 3, 329s 4. 329s 329s Done. 329s Generating 4 simulated realisations of fitted Gibbs model with fixed number of 329s points of each type ... 330s 1, 2, 3, 330s 4. 330s 330s Done. 330s > #' tests/enveltest.R 330s > #' Envelope tests (dclf.test, mad.test) 330s > #' and two-stage tests (bits.test, dg.test, bits.envelope, dg.envelope) 330s > #' 330s > #' $Revision: 1.3 $ $Date: 2020/04/28 12:58:26 $ 330s > #' 330s > if(FULLTEST) { 330s + local({ 330s + #' handling of NA function values (due to empty point patterns) 330s + set.seed(1234) 330s + X <- rThomas(5, 0.05, 10) 330s + fit <- kppm(X ~ 1, "Thomas") 330s + set.seed(100000) 330s + dclf.test(fit) 330s + set.seed(909) 330s + dg.test(fit, nsim=9) 330s + #' other code blocks 330s + dclf.test(fit, rinterval=c(0, 3), nsim=9) 330s + envelopeTest(X, exponent=3, clamp=TRUE, nsim=9) 330s + }) 330s + } 330s > # 330s > # tests/fastgeyer.R 330s > # 330s > # checks validity of fast C implementation of Geyer interaction 330s > # 330s > # $Revision: 1.4 $ $Date: 2020/04/28 12:58:26 $ 330s > # 330s > if(FULLTEST) { # depends on hardware 330s + local({ 330s + X <- redwood 330s + Q <- quadscheme(X) 330s + U <- union.quad(Q) 330s + EP <- equalpairs.quad(Q) 330s + G <- Geyer(0.11, 2) 330s + # The value r=0.11 is chosen to avoid hardware numerical effects (gcc bug 323). 330s + # It avoids being close any value of pairdist(redwood). 330s + # The nearest such values are 0.1077.. and 0.1131.. 330s + # By contrast if r = 0.1 there are values differing from 0.1 by 3e-17 330s + a <- pairsat.family$eval(X,U,EP,G$pot,G$par,"border") 330s + b <- G$fasteval(X,U,EP,G$pot,G$par,"border") 330s + if(!all(a==b)) 330s + stop("Results of Geyer()$fasteval and pairsat.family$eval do not match") 330s + # ... 330s + # and again for a non-integer value of 'sat' 330s + # (spotted by Thordis Linda Thorarinsdottir) 330s + G <- Geyer(0.11, 2.5) 330s + a <- pairsat.family$eval(X,U,EP,G$pot,G$par,"border") 330s + b <- G$fasteval(X,U,EP,G$pot,G$par,"border") 330s + if(!all(a==b)) 330s + stop("Results of Geyer()$fasteval and pairsat.family$eval do not match when sat is not an integer") 330s + # and again for sat < 1 330s + # (spotted by Rolf) 330s + G <- Geyer(0.11, 0.5) 330s + a <- pairsat.family$eval(X,U,EP,G$pot,G$par,"border") 330s + b <- G$fasteval(X,U,EP,G$pot,G$par,"border") 330s + if(!all(a==b)) 330s + stop("Results of Geyer()$fasteval and pairsat.family$eval do not match when sat < 1") 330s + }) 330s + } 330s > 330s > #' tests/formuli.R 330s > #' 330s > #' Test machinery for manipulating formulae 330s > #' 330s > #' $Revision: 1.7 $ $Date: 2020/04/28 12:58:26 $ 330s > 330s > local({ 330s + 330s + ff <- function(A, deletevar, B) { 330s + D <- reduceformula(A, deletevar) 330s + if(!spatstat.utils::identical.formulae(D, B)) { 330s + AD <- as.expression(substitute(reduceformula(A,d), 330s + list(A=A, d=deletevar))) 330s + stop(paste(AD, "\n\tyields ", spatstat.utils::pasteFormula(D), 330s + " instead of ", spatstat.utils::pasteFormula(B)), 330s + call.=FALSE) 330s + } 330s + invisible(NULL) 330s + } 330s + 330s + ff(~ x + z, "x", ~z) 330s + 330s + ff(y ~ x + z, "x", y~z) 330s + 330s + ff(~ I(x^2) + z, "x", ~z) 330s + 330s + ff(y ~ poly(x,2) + poly(z,3), "x", y ~poly(z,3)) 330s + 330s + ff(y ~ x + z, "g", y ~ x + z) 330s + 330s + reduceformula(y ~ x+z, "g", verbose=TRUE) 330s + reduceformula(y ~ sin(x-z), "z", verbose=TRUE) 330s + 330s + illegal.iformula(~str*g, itags="str", dfvarnames=c("marks", "g", "x", "y")) 330s + }) 330s NULL 330s > 330s > 330s > 330s > ## 330s > ## tests/funnymarks.R 330s > ## 330s > ## tests involving strange mark values 330s > ## $Revision: 1.7 $ $Date: 2020/04/28 12:58:26 $ 330s > 330s > if(ALWAYS) { # depends on locale 330s + local({ 330s + ## ppm() where mark levels contain illegal characters 330s + hyphenated <- c("a", "not-a") 330s + spaced <- c("U", "non U") 330s + suffixed <- c("a+", "a*") 330s + charred <- c("+", "*") 330s + 330s + irad <- matrix(0.1, 2,2) 330s + hrad <- matrix(0.005, 2, 2) 330s + 330s + tryit <- function(types, X, irad, hrad) { 330s + levels(marks(X)) <- types 330s + fit <- ppm(X ~marks + polynom(x,y,2), 330s + MultiStraussHard(types=types,iradii=irad,hradii=hrad)) 330s + print(fit) 330s + print(coef(fit)) 330s + val <- fitted(fit) 330s + pred <- predict(fit) 330s + return(invisible(NULL)) 330s + } 330s + 330s + tryit(hyphenated, amacrine, irad, hrad) 330s + tryit(spaced, amacrine, irad, hrad) 330s + tryit(suffixed, amacrine, irad, hrad) 330s + tryit(charred, amacrine, irad, hrad) 330s + 330s + ## marks which are dates 330s + X <- cells 330s + n <- npoints(X) 330s + endoftime <- rep(ISOdate(2001,1,1), n) 330s + eotDate <- rep(as.Date("2001-01-01"), n) 330s + markformat(endoftime) 330s + markformat(eotDate) 330s + marks(X) <- endoftime 330s + print(X) 330s + Y <- X %mark% data.frame(id=1:42, date=endoftime, dd=eotDate) 330s + print(Y) 330s + md <- markformat(endoftime) 330s + 330s + ## mark formats 330s + Z <- Y 330s + marks(Z) <- marks(Z)[1,,drop=FALSE] 330s + ms <- markformat(solist(cells, redwood)) 330s + marks(Z) <- factor(1:npoints(Z)) 330s + marks(Z)[12] <- NA 330s + mz <- is.multitype(Z) 330s + cZ <- coerce.marks.numeric(Z) 330s + marks(Z) <- data.frame(n=1:npoints(Z), 330s + a=factor(sample(letters, npoints(Z), replace=TRUE))) 330s + cZ <- coerce.marks.numeric(Z) 330s + stopifnot(is.multitype(cells %mark% data.frame(a=factor(1:npoints(cells))))) 330s + 330s + a <- numeric.columns(finpines) 330s + b1 <- numeric.columns(amacrine) 330s + b2 <- coerce.marks.numeric(amacrine) 330s + d <- numeric.columns(cells) 330s + f <- numeric.columns(longleaf) 330s + ff <- data.frame(a=factor(letters[1:10]), y=factor(sample(letters, 10))) 330s + numeric.columns(ff) 330s The formula does not involve “g” and is therefore unchanged 330s Don't know how to reduce the term “sin(x - z)” 330s + 330s + ## mark operations 330s + df <- data.frame(x=1:2, y=sample(letters, 2)) 330s + h <- hyperframe(z=1:2, p=solist(cells, cells)) 330s + a <- NULL %mrep% 3 330s + a <- 1:4 %mrep% 3 330s + a <- df %mrep% 3 330s + a <- h %mrep% 3 330s + b <- markcbind(df, h) 330s + b <- markcbind(h, df) 330s + }) 330s + } 330s Nonstationary Multitype Strauss Hardcore process 330s Fitted to point pattern dataset ‘X’ 330s 330s Possible marks: ‘a’ and ‘not-a’ 330s 330s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 330s 330s Fitted trend coefficients: 330s (Intercept) marksnot-a x y I(x^2) I(x * y) 330s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 330s I(y^2) 330s -0.5425654 330s 330s 2 types of points 330s Possible types: 330s [1] a not-a 330s Interaction radii: 330s a not-a 330s a 0.1 0.1 330s not-a 0.1 0.1 330s Hardcore radii: 330s a not-a 330s a 0.005 0.005 330s not-a 0.005 0.005 330s Fitted interaction parameters gamma_ij 330s a not-a 330s a 0.2699920 0.8920719 330s not-a 0.8920719 0.2694374 330s 330s Relevant coefficients: 330s markaxa markaxnot.a marknot.axnot.a 330s -1.3093629 -0.1142086 -1.3114192 330s 330s For standard errors, type coef(summary(x)) 330s (Intercept) marksnot-a x y I(x^2) 330s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 330s I(x * y) I(y^2) markaxa markaxnot.a marknot.axnot.a 330s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 331s Nonstationary Multitype Strauss Hardcore process 331s Fitted to point pattern dataset ‘X’ 331s 331s Possible marks: ‘U’ and ‘non U’ 331s 331s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 331s 331s Fitted trend coefficients: 331s (Intercept) marksnon U x y I(x^2) I(x * y) 331s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 331s I(y^2) 331s -0.5425654 331s 331s 2 types of points 331s Possible types: 331s [1] U non U 331s Interaction radii: 331s U non U 331s U 0.1 0.1 331s non U 0.1 0.1 331s Hardcore radii: 331s U non U 331s U 0.005 0.005 331s non U 0.005 0.005 331s Fitted interaction parameters gamma_ij 331s U non U 331s U 0.2699920 0.8920719 331s non U 0.8920719 0.2694374 331s 331s Relevant coefficients: 331s markUxU markUxnon.U marknon.Uxnon.U 331s -1.3093629 -0.1142086 -1.3114192 331s 331s For standard errors, type coef(summary(x)) 331s (Intercept) marksnon U x y I(x^2) 331s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 331s I(x * y) I(y^2) markUxU markUxnon.U marknon.Uxnon.U 331s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 331s Nonstationary Multitype Strauss Hardcore process 331s Fitted to point pattern dataset ‘X’ 331s 331s Possible marks: ‘a+’ and ‘a*’ 331s 331s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 331s 331s Fitted trend coefficients: 331s (Intercept) marksa* x y I(x^2) I(x * y) 331s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 331s I(y^2) 331s -0.5425654 331s 331s 2 types of points 331s Possible types: 331s [1] a+ a* 331s Interaction radii: 331s a+ a* 331s a+ 0.1 0.1 331s a* 0.1 0.1 331s Hardcore radii: 331s a+ a* 331s a+ 0.005 0.005 331s a* 0.005 0.005 331s Fitted interaction parameters gamma_ij 331s a+ a* 331s a+ 0.2699920 0.8920719 331s a* 0.8920719 0.2694374 331s 331s Relevant coefficients: 331s marka.xa. marka.xa..1 marka..1xa..1 331s -1.3093629 -0.1142086 -1.3114192 331s 331s For standard errors, type coef(summary(x)) 331s (Intercept) marksa* x y I(x^2) 331s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 331s I(x * y) I(y^2) marka.xa. marka.xa..1 marka..1xa..1 331s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 331s Nonstationary Multitype Strauss Hardcore process 332s Fitted to point pattern dataset ‘X’ 332s 332s Possible marks: ‘+’ and ‘*’ 332s 332s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 332s 332s Fitted trend coefficients: 332s (Intercept) marks* x y I(x^2) I(x * y) 332s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 332s I(y^2) 332s -0.5425654 332s 332s 2 types of points 332s Possible types: 332s [1] + * 332s Interaction radii: 332s + * 332s + 0.1 0.1 332s * 0.1 0.1 332s Hardcore radii: 332s + * 332s + 0.005 0.005 332s * 0.005 0.005 332s Fitted interaction parameters gamma_ij 332s + * 332s + 0.2699920 0.8920719 332s * 0.8920719 0.2694374 332s 332s Relevant coefficients: 332s markX.xX. markX.xX..1 markX..1xX..1 332s -1.3093629 -0.1142086 -1.3114192 332s 332s For standard errors, type coef(summary(x)) 332s (Intercept) marks* x y I(x^2) 332s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 332s I(x * y) I(y^2) markX.xX. markX.xX..1 markX..1xX..1 332s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 332s Marked planar point pattern: 42Warning messages: 332s 1: In is.multitype.ppp(Z) : some mark values are NA in the point pattern Z 332s 2: Factor-valued marks were converted to integer codes 332s 3: Factor-valued mark variable ‘a’ was converted to integer codes 332s 4: Factor-valued marks were converted to integer codes 332s points 332s marks are dates, of class ‘POSIXt’ 332s window: rectangle = [0, 1] x [0, 1] units 332s Marked planar point pattern: 42 points 332s Mark variables: id, date, dd 332s window: rectangle = [0, 1] x [0, 1] units 332s > 332s BEGIN TEST testsGtoJ.R 332s 332s R version 4.3.2 (2023-10-31) -- "Eye Holes" 332s Copyright (C) 2023 The R Foundation for Statistical Computing 332s Platform: s390x-ibm-linux-gnu (64-bit) 332s 332s R is free software and comes with ABSOLUTELY NO WARRANTY. 332s You are welcome to redistribute it under certain conditions. 332s Type 'license()' or 'licence()' for distribution details. 332s 332s R is a collaborative project with many contributors. 332s Type 'contributors()' for more information and 332s 'citation()' on how to cite R or R packages in publications. 332s 332s Type 'demo()' for some demos, 'help()' for on-line help, or 332s 'help.start()' for an HTML browser interface to help. 332s Type 'q()' to quit R. 332s 332s > #' 332s > #' Header for all (concatenated) test files 332s > #' 332s > #' Require spatstat.model 332s > #' Obtain environment variable controlling tests. 332s > #' 332s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 332s > 332s > require(spatstat.model) 332s Loading required package: spatstat.model 332s Loading required package: spatstat.data 333s Loading required package: spatstat.geom 333s spatstat.geom 3.2-8 333s Loading required package: spatstat.random 333s spatstat.random 3.2-2 333s Loading required package: spatstat.explore 333s Loading required package: nlme 333s spatstat.explore 3.2-5 333s Loading required package: rpart 333s spatstat.model 3.2-8 333s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 333s > ALWAYS <- TRUE 333s > cat(paste("--------- Executing", 333s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 333s + "test code -----------\n")) 333s --------- Executing **RESTRICTED** subset of test code ----------- 333s > #' 333s > #' tests/hobjects.R 333s > #' 333s > #' Validity of methods for ppm(... method="ho") 333s > #' 333s > #' $Revision: 1.4 $ $Date: 2022/06/18 10:14:44 $ 333s > 333s > 333s > if(FULLTEST) { 333s + local({ 333s + set.seed(42) 333s + fit <- ppm(cells ~1, Strauss(0.1), improve.type="ho", nsim=10) 333s + fitx <- ppm(cells ~offset(x), Strauss(0.1), improve.type="ho", nsim=10) 333s + 333s + a <- AIC(fit) 333s + ax <- AIC(fitx) 333s + 333s + f <- fitted(fit) 333s + fx <- fitted(fitx) 333s + 333s + p <- predict(fit) 333s + px <- predict(fitx) 333s + }) 333s + } 333s > 333s > 333s > #' tests/hypotests.R 333s > #' Hypothesis tests 333s > #' 333s > #' $Revision: 1.10 $ $Date: 2023/07/17 07:30:48 $ 333s > 333s > if(FULLTEST) { 333s + local({ 333s + 333s + #' scan test with baseline 333s + fit <- ppm(cells ~ x) 333s + lam <- predict(fit) 333s + rr <- c(0.05, 1) 333s + scan.test(cells, rr, nsim=5, 333s + method="poisson", baseline=fit, alternative="less") 333s + scan.test(cells, rr, nsim=5, 333s + method="poisson", baseline=lam, alternative="less") 333s + }) 333s + } 333s > #' 333s > #' tests/interact.R 333s > #' 333s > #' Support for interaction objects 333s > #' 333s > #' $Revision: 1.2 $ $Date: 2020/04/28 12:58:26 $ 333s > 333s > if(FULLTEST) { 333s + local({ 333s + #' print.intermaker 333s + Strauss 333s + Geyer 333s + Ord 333s + #' intermaker 333s + BS <- get("BlankStrauss", envir=environment(Strauss)) 333s + BD <- function(r) { instantiate.interact(BS, list(r=r)) } 333s + BlueDanube <- intermaker(BD, BS) 333s + }) 333s + } 333s > 333s > #' tests/ippm.R 333s > #' Tests of 'ippm' class 333s > #' $Revision: 1.6 $ $Date: 2020/04/28 12:58:26 $ 333s > 333s > if(FULLTEST) { 333s + local({ 333s + # .......... set up example from help file ................. 333s + nd <- 10 333s + gamma0 <- 3 333s + delta0 <- 5 333s + POW <- 3 333s + # Terms in intensity 333s + Z <- function(x,y) { -2*y } 333s + f <- function(x,y,gamma,delta) { 1 + exp(gamma - delta * x^POW) } 333s + # True intensity 333s + lamb <- function(x,y,gamma,delta) { 200 * exp(Z(x,y)) * f(x,y,gamma,delta) } 333s + # Simulate realisation 333s + lmax <- max(lamb(0,0,gamma0,delta0), lamb(1,1,gamma0,delta0)) 333s + set.seed(42) 333s + X <- rpoispp(lamb, lmax=lmax, win=owin(), gamma=gamma0, delta=delta0) 333s + # Partial derivatives of log f 333s + DlogfDgamma <- function(x,y, gamma, delta) { 333s + topbit <- exp(gamma - delta * x^POW) 333s + topbit/(1 + topbit) 333s + } 333s + DlogfDdelta <- function(x,y, gamma, delta) { 333s + topbit <- exp(gamma - delta * x^POW) 333s + - (x^POW) * topbit/(1 + topbit) 333s + } 333s + # irregular score 333s + Dlogf <- list(gamma=DlogfDgamma, delta=DlogfDdelta) 333s + # fit model 333s + fit <- ippm(X ~Z + offset(log(f)), 333s + covariates=list(Z=Z, f=f), 333s + iScore=Dlogf, 333s + start=list(gamma=1, delta=1), 333s + nd=nd) 333s + # fit model with logistic likelihood but without iScore 333s + fitlo <- ippm(X ~Z + offset(log(f)), 333s + method="logi", 333s + covariates=list(Z=Z, f=f), 333s + start=list(gamma=1, delta=1), 333s + nd=nd) 333s + 333s + ## ............. test ippm class support ...................... 333s + Ar <- model.matrix(fit) 333s + Ai <- model.matrix(fit, irregular=TRUE) 333s + An <- model.matrix(fit, irregular=TRUE, keepNA=FALSE) 333s + AS <- model.matrix(fit, irregular=TRUE, subset=(abs(Z) < 0.5)) 333s + 333s + Zr <- model.images(fit) 333s + Zi <- model.images(fit, irregular=TRUE) 333s + ## update.ippm 333s + fit2 <- update(fit, . ~ . + I(Z^2)) 333s + fit0 <- update(fit, 333s + . ~ . - Z, 333s + start=list(gamma=2, delta=4)) 333s + oldfit <- ippm(X, 333s + ~Z + offset(log(f)), 333s + covariates=list(Z=Z, f=f), 333s + iScore=Dlogf, 333s + start=list(gamma=1, delta=1), 333s + nd=nd) 333s + oldfit2 <- update(oldfit, . ~ . + I(Z^2)) 333s + oldfit0 <- update(oldfit, 333s + . ~ . - Z, 333s + start=list(gamma=2, delta=4)) 333s + ## again with logistic 333s + fitlo2 <- update(fitlo, . ~ . + I(Z^2)) 333s + fitlo0 <- update(fitlo, 333s + . ~ . - Z, 333s + start=list(gamma=2, delta=4)) 333s + oldfitlo <- ippm(X, 333s + ~Z + offset(log(f)), 333s + method="logi", 333s + covariates=list(Z=Z, f=f), 333s + start=list(gamma=1, delta=1), 333s + nd=nd) 333s + oldfitlo2 <- update(oldfitlo, . ~ . + I(Z^2)) 333s + oldfitlo0 <- update(oldfitlo, 333s + . ~ . - Z, 333s + start=list(gamma=2, delta=4)) 333s + ## anova.ppm including ippm objects 333s + fit0 <- update(fit, . ~ Z) 333s + fit0lo <- update(fitlo, . ~ Z) 333s + A <- anova(fit0, fit) 333s + Alo <- anova(fit0lo, fitlo) 333s + }) 333s + } 333s > 333s BEGIN TEST testsK.R 333s 333s R version 4.3.2 (2023-10-31) -- "Eye Holes" 333s Copyright (C) 2023 The R Foundation for Statistical Computing 333s Platform: s390x-ibm-linux-gnu (64-bit) 333s 333s R is free software and comes with ABSOLUTELY NO WARRANTY. 333s You are welcome to redistribute it under certain conditions. 333s Type 'license()' or 'licence()' for distribution details. 333s 333s R is a collaborative project with many contributors. 333s Type 'contributors()' for more information and 333s 'citation()' on how to cite R or R packages in publications. 333s 333s Type 'demo()' for some demos, 'help()' for on-line help, or 333s 'help.start()' for an HTML browser interface to help. 333s Type 'q()' to quit R. 333s 334s > #' 334s > #' Header for all (concatenated) test files 334s > #' 334s > #' Require spatstat.model 334s > #' Obtain environment variable controlling tests. 334s > #' 334s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 334s > 334s > require(spatstat.model) 334s Loading required package: spatstat.model 334s Loading required package: spatstat.data 335s Loading required package: spatstat.geom 335s spatstat.geom 3.2-8 335s Loading required package: spatstat.random 335s spatstat.random 3.2-2 335s Loading required package: spatstat.explore 335s Loading required package: nlme 335s spatstat.explore 3.2-5 335s Loading required package: rpart 335s spatstat.model 3.2-8 335s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 335s > ALWAYS <- TRUE 335s > cat(paste("--------- Executing", 335s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 335s + "test code -----------\n")) 335s --------- Executing **RESTRICTED** subset of test code ----------- 335s > # 335s > # tests/kppm.R 335s > # 335s > # $Revision: 1.39 $ $Date: 2023/10/21 04:25:51 $ 335s > # 335s > # Test functionality of kppm that once depended on RandomFields 335s > # Test update.kppm for old style kppm objects 335s > 335s > if(!FULLTEST) 335s + spatstat.options(npixel=32, ndummy.min=16) 335s > 335s > local({ 335s + 335s + fit <- kppm(redwood ~1, "Thomas") # sic 335s + fitx <- kppm(redwood ~x, "Thomas", verbose=TRUE) 335s + if(FULLTEST) { 335s + fitx <- update(fit, ~ . + x) 335s + fitM <- update(fit, clusters="MatClust") 335s + fitC <- update(fit, cells) 335s + fitCx <- update(fit, cells ~ x) 335s + #' 335s + Wsub <- owin(c(0, 0.5), c(-0.5, 0)) 335s + Zsub <- (bdist.pixels(Window(redwood)) > 0.1) 335s + fitWsub <- kppm(redwood ~1, "Thomas", subset=Wsub) 335s + fitZsub <- kppm(redwood ~1, "Thomas", subset=Zsub) 335s + fitWsub 335s + 335s + #' various methods 335s + ff <- as.fv(fitx) 335s + uu <- unitname(fitx) 335s + unitname(fitCx) <- "furlong" 335s + mo <- model.images(fitCx) 335s + p <- psib(fit) 335s + px <- psib(fitx) 335s + } 335s + if(ALWAYS) { 335s + Y <- simulate(fitx, seed=42, saveLambda=TRUE)[[1]] 335s + } 335s + 335s + if(FULLTEST) { 335s + #' vcov.kppm different algorithms 335s + vc <- vcov(fitx) 335s + vc2 <- vcov(fitx, fast=TRUE) 335s + vc3 <- vcov(fitx, fast=TRUE, splitup=TRUE) 335s + vc4 <- vcov(fitx, splitup=TRUE) 335s + 335s + ## other code blocks 335s + a <- varcount(fitx, function(x,y){x+1}) # always positive 335s + a <- varcount(fitx, function(x,y){y-1}) # always negative 335s + a <- varcount(fitx, function(x,y){x+y}) # positive or negative 335s + 335s + #' improve.kppm 335s + fitI <- update(fit, improve.type="quasi") 335s + fitxI <- update(fitx, improve.type="quasi") 335s + fitxIs <- update(fitx, improve.type="quasi", fast=FALSE) 335s + #' vcov.kppm 335s + vcI <- vcov(fitxI) 335s + } 335s + 335s + ## plot.kppm including predict.kppm 335s + if(ALWAYS) { 335s + fitMC <- kppm(redwood ~ x, "Thomas") 335s + plot(fitMC) 335s + } 335s + if(FULLTEST) { 335s + fitCL <- kppm(redwood ~ x, "Thomas", method="c") 335s + fitPA <- kppm(redwood ~ x, "Thomas", method="p") 335s + plot(fitCL) 335s + plot(fitPA) 335s + 335s + ## fit with composite likelihood method [thanks to Abdollah Jalilian] 335s + fut <- kppm(redwood ~ x, "VarGamma", method="clik2", nu.ker=-3/8) 335s + kfut <- as.fv(fut) 335s + } 335s + 335s + if(ALWAYS) { 335s + fit0 <- kppm(redwood ~1, "LGCP") 335s + is.poisson(fit0) 335s + Y0 <- simulate(fit0, saveLambda=TRUE)[[1]] 335s + stopifnot(is.ppp(Y0)) 335s + p0 <- psib(fit0) # issues a warning 335s + 335s + if(FULLTEST) { 335s + ## fit LGCP using K function: slow 335s + fit1 <- kppm(redwood ~x, "LGCP", 335s + covmodel=list(model="matern", nu=0.3), 335s + control=list(maxit=3)) 335s + Y1 <- simulate(fit1, saveLambda=TRUE)[[1]] 335s + stopifnot(is.ppp(Y1)) 335s + } 335s + 335s + ## fit LGCP using pcf 335s + fit1p <- kppm(redwood ~x, "LGCP", 335s + covmodel=list(model="matern", nu=0.3), 335s + statistic="pcf") 335s + Y1p <- simulate(fit1p, saveLambda=TRUE)[[1]] 335s + stopifnot(is.ppp(Y1p)) 335s + 335s + ## .. and using different fitting methods 335s + if(FULLTEST) { 335s + fit1pClik <- update(fit1p, method="clik") 335s + fit1pPalm <- update(fit1p, method="palm") 335s + } 335s + 335s + ## shortcut evaluation of pcf 335s + ## (the code being tested is in spatstat.random::clusterinfo.R) 335s + if(FULLTEST) { 335s + putSpatstatVariable("RFshortcut", TRUE) 335s + fitGshort <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="gauss")) 335s + fitSshort <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="stable", alpha=1)) 335s + putSpatstatVariable("RFshortcut", FALSE) 335s + fitGlong <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="gauss")) 335s + fitSlong <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="stable", alpha=1)) 335s + discrepG <- unlist(parameters(fitGshort)) - unlist(parameters(fitGlong)) 335s + discrepS <- unlist(parameters(fitSshort)) - unlist(parameters(fitSlong)) 335s + print(discrepG) 335s + print(discrepS) 335s + if(max(abs(discrepG) > 0.01)) 335s + stop("Discrepancy in short-cut fitting of Gaussian LGCP") 335s + if(max(abs(discrepS) > 0.01)) 335s + stop("Discrepancy in short-cut fitting of stable LGCP") 335s + } 335s + 335s + ## image covariate (a different code block) 335s + xx <- as.im(function(x,y) x, Window(redwood)) 335s + fit1xx <- update(fit1p, . ~ xx, data=solist(xx=xx)) 335s + Y1xx <- simulate(fit1xx, saveLambda=TRUE)[[1]] 335s + stopifnot(is.ppp(Y1xx)) 335s + if(FULLTEST) { 335s + fit1xxVG <- update(fit1xx, clusters="VarGamma", nu=-1/4) 335s + Y1xxVG <- simulate(fit1xxVG, saveLambda=TRUE)[[1]] 335s + stopifnot(is.ppp(Y1xxVG)) 335s + } 335s + fit1xxLG <- update(fit1xx, clusters="LGCP", 335s + covmodel=list(model="matern", nu=0.3), 335s + statistic="pcf") 335s + Y1xxLG <- simulate(fit1xxLG, saveLambda=TRUE, drop=TRUE) 335s + stopifnot(is.ppp(Y1xxLG)) 335s + 335s + # ... and Abdollah's code 335s + if(FULLTEST) { 335s + fit2 <- kppm(redwood ~x, cluster="Cauchy", statistic="K") 335s + Y2 <- simulate(fit2, saveLambda=TRUE)[[1]] 335s + stopifnot(is.ppp(Y2)) 335s + } 335s + } 335s + 335s + }) 336s Fitting cluster model 336s Retrieved cluster model information 336s Algorithm parameters: 336s $rmax 336s NULL 336s 336s $q 336s [1] 0.25 336s 336s $p 336s [1] 2 336s 336s $rmin 336s NULL 336s 336s Using point pattern data 336s Starting parameters: 336s kappa sigma2 336s 62.000000000 0.006173033 336s Calculating summary function...Done. 336s Starting minimum contrast fit 336s Returned from minimum contrast fit 336s Returning from clusterfit 338s > 338s > Warning messages: 338s 1: Internal error: fvlabels truncated the function name 338s 2: Internal error: fvlabels truncated the function name 338s 3: Internal error: fvlabels truncated the function name 338s 4: In psib.kppm(fit0) : The model is not a cluster process 338s if(FULLTEST) { 338s 5: The value of the empirical function ‘pcf’ for r= 0 was Inf. Range of r values was reset to [0.00048828125, 0.25] 338s 6: The value of the empirical function ‘pcf’ for r= 0 was Inf. Range of r values was reset to [0.00048828125, 0.25] 338s 7: The value of the empirical function ‘pcf’ for r= 0 was Inf. Range of r values was reset to [0.00048828125, 0.25] 338s + local({ 338s + #' various code blocks 338s + fut <- kppm(redwood, ~x) 338s + fet <- update(fut, redwood3) 338s + fot <- update(fut, trend=~y) 338s + fit <- kppm(redwoodfull ~ x) 338s + Y <- simulate(fit, window=redwoodfull.extra$regionII, saveLambda=TRUE) 338s + gut <- improve.kppm(fit, type="wclik1") 338s + gut <- improve.kppm(fit, vcov=TRUE, fast.vcov=TRUE, save.internals=TRUE) 338s + hut <- kppm(redwood ~ x, method="clik", weightfun=NULL) 338s + hut <- kppm(redwood ~ x, method="palm", weightfun=NULL) 338s + mut <- kppm(redwood) 338s + nut <- update(mut, Y) 338s + if(TRUE) { 338s + #' Bug in rLGCP spotted by Tilman Davies 338s + X <- rLGCP("matern", function(x,y) { 1 - 0.4* y }, 338s + var=2, scale=0.7, nu=0.5, win = square(10), 338s + dimyx=c(32,64)) 338s + } 338s + }) 338s + } 338s > 338s > if(FULLTEST) { 338s + local({ 338s + #' minimum contrast code 338s + K <- Kest(redwood) 338s + a <- matclust.estK(K) 338s + a <- thomas.estK(K) 338s + a <- cauchy.estK(K) 338s + a <- vargamma.estK(K) 338s + a <- lgcp.estK(K) 338s + 338s + print(a) 338s + u <- unitname(a) 338s + 338s + g <- pcf(redwood) 338s + a <- matclust.estpcf(g) 338s + a <- thomas.estpcf(g) 338s + a <- cauchy.estpcf(g) 338s + a <- vargamma.estpcf(g) 338s + a <- lgcp.estpcf(g) 338s + 338s + #' auxiliary functions 338s + b <- resolve.vargamma.shape(nu.pcf=1.5) 338s + Z <- clusterfield("Thomas", kappa=1, scale=0.2) 338s + 338s + aa <- NULL 338s + aa <- accumulateStatus(simpleMessage("Woof"), aa) 338s + aa <- accumulateStatus(simpleMessage("Sit"), aa) 338s + aa <- accumulateStatus(simpleMessage("Woof"), aa) 338s + printStatusList(aa) 338s + 338s + RMIN <- 0.01 338s + fit <- kppm(redwood ~ 1, ctrl=list(rmin=RMIN,q=1/2)) 338s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 338s + stop("kppm did not handle parameter 'rmin' in argument 'ctrl' ") 338s + fit <- kppm(redwood ~ 1, ctrl=list(rmin=0,q=1/2), rmin=RMIN) 338s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 338s + stop("kppm did not handle parameter 'rmin' in argument 'ctrl'") 338s + 338s + RMIN <- 2 338s + fit <- dppm(swedishpines~1, dppGauss(), ctrl=list(rmin=RMIN,q=1)) 338s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 338s + stop("dppm did not handle parameter 'rmin' in argument 'ctrl'") 338s + fit <- dppm(swedishpines~1, dppGauss(), ctrl=list(rmin=0,q=1), rmin=RMIN) 338s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 338s + stop("dppm did not handle argument 'rmin'") 338s + }) 338s + } 338s > 338s > 338s > 338s > if(FULLTEST) { 338s + local({ 338s + #' cover a few code blocks 338s + fut <- kppm(redwood ~ x, method="clik") 338s + print(summary(fut)) 338s + a <- residuals(fut) 338s + fut2 <- kppm(redwood ~ x, "LGCP", method="palm") 338s + print(summary(fut2)) 338s + b <- residuals(fut2) 338s + #' 338s + po <- ppm(redwood ~ 1) 338s + A <- kppmComLik(redwood, Xname="redwood", po=po, clusters="Thomas", 338s + statistic="pcf", statargs=list(), control=list(), 338s + weightfun=NULL, rmax=0.1) 338s + A <- kppmPalmLik(redwood, Xname="redwood", po=po, clusters="Thomas", 338s + statistic="pcf", statargs=list(), control=list(), 338s + weightfun=NULL, rmax=0.1) 338s + }) 338s + } 338s > 338s > reset.spatstat.options() 338s > 338s > #' 338s > #' tests/Kfuns.R 338s > #' 338s > #' Various K and L functions and pcf 338s > #' 338s > #' $Revision: 1.43 $ $Date: 2022/06/17 01:47:08 $ 338s > #' 338s > #' Assumes 'EveryStart.R' was run 338s > 338s > if(FULLTEST) { 338s + Cells <- cells 338s + Amacrine <- amacrine 338s + Redwood <- redwood 338s + } else { 338s + ## reduce numbers of data + dummy points 338s + spatstat.options(npixel=32, ndummy.min=16) 338s + Cells <- cells[c(FALSE, TRUE)] 338s + Amacrine <- amacrine[c(FALSE, TRUE)] 338s + Redwood <- redwood[c(FALSE, TRUE)] 338s + } 338s > 338s > 338s > if(FULLTEST) { 338s + local({ 338s + #' code blocks using fitted model to determine intensity 338s + #' Kinhom 338s + X <- rpoispp(function(x,y) { 100 * x }, 100, square(1)) 338s + fut <- ppm(X ~ x) 338s + Kio <- Kinhom(X, fut, update=FALSE) 338s + Kiu <- Kinhom(X, fut, update=TRUE, diagonal=FALSE) 338s + fit <- ppm(Amacrine ~ marks) 338s + #' lohboot Linhom 338s + Zred <- predict(ppm(Redwood ~ x+y)) 338s + Lred <- lohboot(Redwood, Linhom, lambda=Zred) 338s + #' Kmulti.inhom 338s + K1 <- Kcross.inhom(Amacrine, lambdaX=fit) 338s + On <- split(Amacrine)$on 338s + Off <- split(Amacrine)$off 338s + K4 <- Kcross.inhom(Amacrine, lambdaI=ppm(On), lambdaJ=ppm(Off)) 338s + #' local K functions 338s + fut <- ppm(swedishpines ~ polynom(x,y,2)) 338s + Z <- predict(fut) 338s + Lam <- fitted(fut, dataonly=TRUE) 338s + a <- localLinhom(swedishpines, lambda=fut) 338s + a <- localLinhom(swedishpines, lambda=Z) 338s + a <- localLinhom(swedishpines, lambda=Lam) 338s + a <- localLinhom(swedishpines, lambda=Z, correction="none") 338s + a <- localLinhom(swedishpines, lambda=Z, correction="translate") 338s + #' local cross K functions 338s + fat <- ppm(Amacrine ~ x * marks) 338s + Zed <- predict(fat) 338s + Lum <- fitted(fat, dataonly=TRUE) 338s + moff <- (marks(Amacrine) == "off") 338s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed) 338s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Lum) 338s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=fat) 338s + a <- localLcross.inhom(Amacrine, from="off", to="on", 338s + lambdaFrom=Lum[moff], lambdaTo=Lum[!moff]) 338s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 338s + correction="none") 338s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 338s + correction="translate") 338s + #' cases of resolve.lambdacross 338s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=fat) 338s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=fat, update=FALSE) 338s + h <- resolve.lambdacross(Amacrine, moff, !moff, 338s + lambdaI=fat, lambdaJ=fat) 338s + h <- resolve.lambdacross(Amacrine, moff, !moff, 338s + lambdaI=fat, lambdaJ=fat, 338s + update=FALSE) 338s + #' lohboot 338s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", lambdaX=Zed) 338s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", lambdaX=Lum) 338s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", lambdaX=fat) 338s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", 338s + lambdaFrom=Lum[moff], lambdaTo=Lum[!moff]) 338s + #' 338s + #' residual K functions etc 338s + #' 338s + rco <- compareFit(Cells, Kcom, 338s + interaction=anylist(P=Poisson(), S=Strauss(0.08)), 338s + same="trans", different="tcom") 338s + fit <- ppm(Cells ~ x, Strauss(0.07)) 338s + K <- Kcom(Cells, model=fit, restrict=TRUE) 338s + }) 338s + } 338s > 338s > reset.spatstat.options() 338s > 338s BEGIN TEST testsL.R 338s 338s R version 4.3.2 (2023-10-31) -- "Eye Holes" 338s Copyright (C) 2023 The R Foundation for Statistical Computing 338s Platform: s390x-ibm-linux-gnu (64-bit) 338s 338s R is free software and comes with ABSOLUTELY NO WARRANTY. 338s You are welcome to redistribute it under certain conditions. 338s Type 'license()' or 'licence()' for distribution details. 338s 338s R is a collaborative project with many contributors. 338s Type 'contributors()' for more information and 338s 'citation()' on how to cite R or R packages in publications. 338s 338s Type 'demo()' for some demos, 'help()' for on-line help, or 338s 'help.start()' for an HTML browser interface to help. 338s Type 'q()' to quit R. 338s 338s > #' 338s > #' Header for all (concatenated) test files 338s > #' 338s > #' Require spatstat.model 338s > #' Obtain environment variable controlling tests. 338s > #' 338s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 338s > 338s > require(spatstat.model) 338s Loading required package: spatstat.model 338s Loading required package: spatstat.data 340s Loading required package: spatstat.geom 340s spatstat.geom 3.2-8 340s Loading required package: spatstat.random 340s spatstat.random 3.2-2 340s Loading required package: spatstat.explore 340s Loading required package: nlme 344s spatstat.explore 3.2-5 344s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 344s > ALWAYS <- TRUE 344s > cat(paste("--------- Executing", 344s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 344s + "test code -----------\n")) 344s --------- Executing **RESTRICTED** subset of test code ----------- 344s > ## 344s > ## tests/legacy.R 344s > ## 344s > ## Test that current version of spatstat is compatible with outmoded usage 344s > ## $Revision: 1.3 $ $Date: 2020/04/29 08:55:17 $ 344s > 344s > if(FULLTEST) { 344s + local({ 344s + 344s + ## (1) Old syntax of ppm 344s + ppm(cells, ~x) 344s + 344s + ## (2) Old syntax of MultiStrauss etc. 344s + r <- matrix(3, 2, 2) 344s + a <- MultiStrauss( , r) 344s + a <- MultiStrauss(NULL, r) 344s + a <- MultiHard(, r) 344s + 344s + h <- r/2 344s + a <- MultiStraussHard( , r, h) 344s + 344s + NULL 344s + }) 344s + } 344s > #' 344s > #' tests/leverinf.R 344s > #' 344s > #' leverage and influence for Gibbs models 344s > #' 344s > #' $Revision: 1.35 $ $Date: 2022/06/18 10:15:17 $ 344s > #' 344s > 344s > if(FULLTEST) { 344s + Cells <- cells 344s + Amacrine <- amacrine 344s + Redwood <- redwood 344s + } else { 344s + ## reduce number of data + dummy points 344s + spatstat.options(npixel=32, ndummy.min=16) 344s + Cells <- cells[c(FALSE,TRUE)] 344s + Redwood <- redwood[c(FALSE, TRUE)] 344s + Amacrine <- amacrine[c(FALSE, TRUE)] 344s + } 344s > 344s > local({ 344s + cat("Running non-sparse algorithm...", fill=TRUE) 344s + # original non-sparse algorithm 344s + Leverage <- function(...) leverage(..., sparseOK=FALSE) 344s + Influence <- function(...) influence(..., sparseOK=FALSE) 344s + Dfbetas <- function(...) dfbetas(..., sparseOK=FALSE) 344s + if(ALWAYS) { 344s + ## Strauss()$delta2 344s + fitS <- ppm(Cells ~ x, Strauss(0.12), rbord=0) 344s + levS <- Leverage(fitS) 344s + infS <- Influence(fitS) 344s + dfbS <- Dfbetas(fitS) 344s + ## Geyer()$delta2 344s + fitG <- ppm(Redwood ~ 1, Geyer(0.1, 2), rbord=0) 344s + levG <- Leverage(fitG) 344s + infG <- Influence(fitG) 344s + ## AreaInter()$delta2 344s + fitA <- ppm(Cells ~ 1, AreaInter(0.06), rbord=0, nd=11) 344s + levA <- Leverage(fitA) 344s + infA <- Influence(fitA) 344s + ## pairwise.family$delta2 344s + fitD <- ppm(Cells ~ 1, DiggleGatesStibbard(0.12), rbord=0) 344s + levD <- Leverage(fitD) 344s + infD <- Influence(fitD) 344s + ## DiggleGratton() special code 344s + fitDG <- ppm(Cells ~ 1, DiggleGratton(0.05, 0.12), rbord=0) 344s + levDG <- Leverage(fitDG) 344s + infDG <- Influence(fitDG) 344s + ## ppmInfluence; offset is present; coefficient vector has length 0 344s + fitH <- ppm(Cells ~ 1, Hardcore(0.07)) 344s + levH <- Leverage(fitH) 344s + infH <- Influence(fitH) 344s + ## ppmInfluence; hard core 344s + fitSH <- ppm(Cells ~ 1, StraussHard(0.07, 0.01)) 344s + levSH <- Leverage(fitSH) 344s + infSH <- Influence(fitSH) 344s + ## ppmInfluence; offset is present; coefficient vector has length 1 344s + fitHx <- ppm(Cells ~ x, Hardcore(0.07), rbord=0) 344s + levHx <- Leverage(fitHx) 344s + infHx <- Influence(fitHx) 344s + ## multitype 344s + futAm <- ppm(Amacrine ~ x + marks, Strauss(0.07)) 344s + levAm <- leverage(futAm) 344s + } 344s + 344s + if(FULLTEST) { 344s + ## ......... class support ............................. 344s + ## other methods for classes leverage.ppm and influence.ppm 344s + ## not elsewhere tested 344s + cat("Testing class support...", fill=TRUE) 344s + w <- domain(levS) 344s + w <- Window(infS) 344s + vv <- shift(levS, c(1.2, 1.3)) 344s + vv <- shift(infS, c(1.2, 1.3)) 344s + A <- quadrats(Window(Cells), 2) 344s + a <- integral(levS,domain=A) 344s + b <- integral(infS,domain=A) 344s + u <- Smooth(levS, sigma=0.07) 344s + v <- Smooth(infS, sigma=0.1) 344s + ## plot options 344s + plot(levS, what="exact") 344s + plot(levS, what="nearest") 344s + contour(levS, what="nearest") 344s + persp(levS, what="nearest") 344s + ## plotting for multitype models 344s + plot(levAm) 344s + contour(levAm) 344s + persp(levAm) 344s + plot(levAm, multiplot=FALSE) 344s + contour(levAm, multiplot=FALSE) 344s + } 344s + 344s + if(ALWAYS) { 344s + ## .......... compare algorithms ......................... 344s + ## divide and recombine algorithm 344s + cat("Reduce maximum block side to 50,000 ...", fill=TRUE) 344s + op <- spatstat.options(maxmatrix=50000) 344s + ## non-sparse 344s + levSB <- Leverage(fitS) 344s + infSB <- Influence(fitS) 344s + dfbSB <- Dfbetas(fitS) 344s + } 344s + 344s + chk <- function(x, y, what, 344s + from="single-block and multi-block", 344s + thresh=1e-12) { 344s + if(max(abs(x-y)) > thresh) 344s + stop(paste("Different results for", what, "obtained from", 344s + from, "algorithms"), 344s + call.=FALSE) 344s + invisible(NULL) 344s + } 344s + 344s + if(ALWAYS) { 344s + cat("Compare single-block to multi-block...", fill=TRUE) 344s + chk(marks(as.ppp(infS)), marks(as.ppp(infSB)), "influence") 344s + chk(as.im(levS), as.im(levSB), "leverage") 344s + chk(dfbS$val, dfbSB$val, "dfbetas$value") 344s + chk(dfbS$density, dfbSB$density, "dfbetas$density") 344s + } 344s + 344s + if(FULLTEST) { 344s + ## also check case of zero cif 344s + cat("Check zero cif cases...", fill=TRUE) 344s + levHB <- Leverage(fitH) 344s + infHB <- Influence(fitH) 344s + dfbHB <- Dfbetas(fitH) 344s + levHxB <- Leverage(fitHx) 344s + infHxB <- Influence(fitHx) 344s + dfbHxB <- Dfbetas(fitHx) 344s + } 344s + 344s + ## run all code segments 344s + Everything <- function(model, ...) { ppmInfluence(model, ..., what="all") } 344s + 344s + if(FULLTEST) { 344s + cat("Run full code on AreaInteraction model...", fill=TRUE) 344s + pmiA <- Everything(fitA) 344s + 344s + ## sparse algorithm, with blocks 344s + cat("Run sparse algorithm with blocks...", fill=TRUE) 344s + pmiSSB <- Everything(fitS, sparseOK=TRUE) 344s + ## also check case of zero cif 344s + pmiHSB <- Everything(fitH, sparseOK=TRUE) 344s + pmiSHSB <- Everything(fitSH, sparseOK=TRUE) 344s + pmiHxSB <- Everything(fitHx, sparseOK=TRUE) 344s + 344s + cat("Reinstate maxmatrix...", fill=TRUE) 344s + spatstat.options(op) 344s + } 344s + 344s + if(ALWAYS) { 344s + ## sparse algorithm, no blocks 344s + cat("Compare sparse and non-sparse results...", fill=TRUE) 344s + pmi <- Everything(fitS, sparseOK=TRUE) 344s + levSp <- pmi$leverage 344s + infSp <- pmi$influence 344s + dfbSp <- pmi$dfbetas 344s + chks <- function(...) chk(..., from="sparse and non-sparse") 344s + 344s + chks(marks(as.ppp(infS)), marks(as.ppp(infSp)), "influence") 344s + chks(as.im(levS), as.im(levSp), "leverage") 344s + chks(dfbS$val, dfbSp$val, "dfbetas$value") 344s + chks(dfbS$density, dfbSp$density, "dfbetas$density") 344s + } 344s + 344s + if(ALWAYS) { 344s + #' case of zero cif 344s + cat("zero cif...", fill=TRUE) 344s + pmiH <- Everything(fitH, sparseOK=TRUE) 344s + pmiSH <- Everything(fitSH, sparseOK=TRUE) 344s + pmiHx <- Everything(fitHx, sparseOK=TRUE) 344s + } 344s + if(FULLTEST) { 344s + #' other code blocks - check execution only 344s + cat("other code blocks...", fill=TRUE) 344s + a <- Everything(fitS) 344s + a <- Everything(fitS, method="interpreted") 344s + a <- Everything(fitS, method="interpreted", entrywise=FALSE) 344s + a <- Everything(fitS, entrywise=FALSE) 344s + #' zero cif 344s + b <- Everything(fitSH) 344s + b <- Everything(fitSH, method="interpreted") 344s + b <- Everything(fitSH, method="interpreted", entrywise=FALSE) 344s + b <- Everything(fitSH, entrywise=FALSE) 344s + } 344s + #' NOTE: code for irregular parameters is tested below, and in 'make bookcheck' 344s + 344s + ## ........... logistic fits ....................... 344s + cat("Logistic fits...", fill=TRUE) 344s + #' special algorithm for delta2 344s + fitSlogi <- ppm(Cells ~ x, Strauss(0.12), rbord=0, method="logi") 344s + 344s + if(FULLTEST) { 344s + pmiSlogi <- Everything(fitSlogi) 344s + #' special algorithm for delta2 344s + fitGlogi <- ppm(Redwood ~ 1, Geyer(0.1, 2), rbord=0, method="logi") 344s + pmiGlogi <- Everything(fitGlogi) 344s + #' generic algorithm for delta2 344s + fitDlogi <- ppm(Cells ~ 1, DiggleGatesStibbard(0.12), 344s + rbord=0, method="logi") 344s + pmiDlogi <- Everything(fitDlogi) 344s + #' generic algorithm for delta2 : offset; zero-dimensional 344s + fitHlogi <- ppm(Cells ~ 1, Hardcore(0.07), method="logi") 344s + pmiHlogi <- Everything(fitHlogi) 344s + #' generic algorithm for delta2 : offset; 1-dimensional 344s + fitHxlogi <- ppm(Cells ~ x, Hardcore(0.07), rbord=0, method="logi") 344s + pmiHxlogi <- Everything(fitHxlogi) 344s + #' plotting 344s + plot(leverage(fitSlogi)) 344s + plot(influence(fitSlogi)) 344s + plot(dfbetas(fitSlogi)) 344s + } 344s + 344s + if(ALWAYS) { 344s + #' other code blocks - check execution only 344s + cat("Other code blocks...", fill=TRUE) 344s + b <- Everything(fitSlogi) # i.e. full set of results 344s + b <- Everything(fitSlogi, method="interpreted") 344s + b <- Everything(fitSlogi, method="interpreted", entrywise=FALSE) 344s + b <- Everything(fitSlogi, entrywise=FALSE) 344s + } 344s + 344s + #' irregular parameters 344s + cat("Irregular parameters...", fill=TRUE) 344s + ytoa <- function(x,y, alpha=1) { y^alpha } 344s + lam <- function(x,y,alpha=1) { exp(4 + y^alpha) } 344s + set.seed(90210) 344s + X <- rpoispp(lam, alpha=2) 344s + iScor <- list(alpha=function(x,y,alpha) { alpha * y^(alpha-1) } ) 344s + iHess <- list(alpha=function(x,y,alpha) { alpha * (alpha-1) * y^(alpha-2) } ) 344s + gogo <- function(tag, ..., iS=iScor, iH=iHess) { 344s + cat(tag, fill=TRUE) 344s + #' compute all leverage+influence terms 344s + ppmInfluence(..., what="all", iScore=iS, iHessian=iH) 344s + } 344s + gogogo <- function(hdr, fit) { 344s + cat(hdr, fill=TRUE) 344s + force(fit) 344s + #' try all code options 344s + d <- gogo("a", fit) 344s + d <- gogo("b", fit, method="interpreted") 344s + d <- gogo("c", fit, method="interpreted", entrywise=FALSE) 344s + d <- gogo("d", fit, entrywise=FALSE) 344s + invisible(NULL) 344s + } 344s + gogogo("Offset model...", 344s + ippm(X ~ offset(ytoa), start=list(alpha=1), iterlim=40)) 344s + gogogo("Offset model (logistic) ...", 344s + ippm(X ~ offset(ytoa), start=list(alpha=1), 344s + method="logi", iterlim=40)) 344s + gogogo("Offset+x model...", 344s + ippm(X ~ x + offset(ytoa), start=list(alpha=1), iterlim=40)) 344s + gogogo("Offset+x model (logistic) ...", 344s + ippm(X ~ x + offset(ytoa), start=list(alpha=1), 344s + method="logi", iterlim=40)) 344s + gogogo("Offset model Strauss ...", 344s + ippm(X ~ offset(ytoa), Strauss(0.07), start=list(alpha=1), iterlim=40)) 344s + gogogo("Offset model Strauss (logistic) ...", 344s + ippm(X ~ offset(ytoa), Strauss(0.07), start=list(alpha=1), 344s + method="logi", iterlim=40)) 344s + if(FULLTEST) { 344s + gogogo("Offset+x model Strauss ...", 344s + ippm(X ~ x + offset(ytoa), Strauss(0.07), start=list(alpha=1), 344s + iterlim=40)) 344s + gogogo("Offset+x model Strauss (logistic)...", 344s + ippm(X ~ x + offset(ytoa), Strauss(0.07), start=list(alpha=1), 344s + method="logi", iterlim=40)) 344s + } 344s + #' 344s + if(FULLTEST) { 344s + set.seed(452) 344s + foo <- ppm(Cells ~ 1, Strauss(0.15), improve.type="ho", nsim=5) 344s + aa <- Everything(foo) 344s + 344s + #' Gradient and Hessian obtained by symbolic differentiation 344s + f <- deriv(expression((1+x)^a), 344s + "a", function.arg=c("x", "y", "a"), 344s + hessian=TRUE) 344s + #' check they can be extracted 344s + fit <- ippm(Cells ~offset(f), start=list(a=0.7)) 344s + Everything(fit) 344s + } 344s + }) 344s Running non-sparse algorithm... 344s Loading required package: rpart 344s spatstat.model 3.2-8 351s Reduce maximum block side to 50,000 ... 353s Compare single-block to multi-block... 353s Compare sparse and non-sparse results... 354s zero cif... 361s Logistic fits... 361s Other code blocks... 362s Irregular parameters... 362s Offset model... 362s a 363s b 364s c 365s d 368s Offset model (logistic) ... 368s a 368s b 369s c 370s d 373s Offset+x model... 373s a 373s b 373s c 375s d 376s Offset+x model (logistic) ... 376s a 377s b 378s c 394s d 394s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points 394s Offset model Strauss ... 394s a 394s b 394s c 394s d 394s Offset model Strauss (logistic) ... 394s a 394s b 394s c 394s d 394s > 394s > reset.spatstat.options() 394s > 394s BEGIN TEST testsM.R 394s 394s R version 4.3.2 (2023-10-31) -- "Eye Holes" 394s Copyright (C) 2023 The R Foundation for Statistical Computing 394s Platform: s390x-ibm-linux-gnu (64-bit) 394s 394s R is free software and comes with ABSOLUTELY NO WARRANTY. 394s You are welcome to redistribute it under certain conditions. 394s Type 'license()' or 'licence()' for distribution details. 394s 394s R is a collaborative project with many contributors. 394s Type 'contributors()' for more information and 394s 'citation()' on how to cite R or R packages in publications. 394s 394s Type 'demo()' for some demos, 'help()' for on-line help, or 394s 'help.start()' for an HTML browser interface to help. 394s Type 'q()' to quit R. 394s 394s > #' 394s > #' Header for all (concatenated) test files 394s > #' 394s > #' Require spatstat.model 394s > #' Obtain environment variable controlling tests. 394s > #' 394s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 394s > 394s > require(spatstat.model) 394s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points 394s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points 394s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points 394s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points 394s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points 394s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points 394s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points 394s There were 11 warnings (use warnings() to see them) 394s Loading required package: spatstat.model 394s Loading required package: spatstat.data 394s Loading required package: spatstat.geom 394s spatstat.geom 3.2-8 394s Loading required package: spatstat.random 394s spatstat.random 3.2-2 394s Loading required package: spatstat.explore 394s Loading required package: nlme 395s spatstat.explore 3.2-5 395s Loading required package: rpart 395s spatstat.model 3.2-8 395s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 395s > ALWAYS <- TRUE 395s > cat(paste("--------- Executing", 395s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 395s + "test code -----------\n")) 395s --------- Executing **RESTRICTED** subset of test code ----------- 395s > ## 395s > ## tests/marcelino.R 395s > ## 395s > ## $Revision: 1.4 $ $Date: 2020/04/30 02:18:23 $ 395s > ## 395s > 395s > local({ 395s + if(FULLTEST) { 395s + Y <- split(urkiola) 395s + B <- Y$birch 395s + O <- Y$oak 395s + B.lam <- predict (ppm(B ~polynom(x,y,2)), type="trend") 395s + O.lam <- predict (ppm(O ~polynom(x,y,2)), type="trend") 395s + 395s + Kinhom(B, lambda=B.lam, correction="iso") 395s + Kinhom(B, lambda=B.lam, correction="border") 395s + 395s + Kcross.inhom(urkiola, i="birch", j="oak", B.lam, O.lam) 395s + Kcross.inhom(urkiola, i="birch", j="oak", B.lam, O.lam, correction = "iso") 395s + Kcross.inhom(urkiola, i="birch", j="oak", B.lam, O.lam, correction = "border") 395s + } 395s + }) 395s > 395s > 395s > #' tests/mctests.R 395s > #' Monte Carlo tests 395s > #' (mad.test, dclf.test, envelopeTest, hasenvelope) 395s > #' $Revision: 1.5 $ $Date: 2022/05/23 04:09:49 $ 395s > 395s > 395s > local({ 395s + if(FULLTEST) { 395s + fitx <- ppm(redwood~x) 395s + ax <- envelopeTest(fitx, exponent=2, nsim=9, savefuns=TRUE) 395s + print(ax) 395s + } 395s + }) 395s > 395s > 395s > # 395s > # tests/mppm.R 395s > # 395s > # Basic tests of mppm 395s > # 395s > # $Revision: 1.23 $ $Date: 2022/07/08 04:55:13 $ 395s > # 395s > 395s > if(!FULLTEST) 395s + spatstat.options(npixel=32, ndummy.min=16) 395s > 395s > local({ 395s + ## test interaction formulae and subfits 395s + fit1 <- mppm(Points ~ group, simba, 395s + hyperframe(po=Poisson(), str=Strauss(0.1)), 395s + iformula=~ifelse(group=="control", po, str)) 395s + fit2 <- mppm(Points ~ group, simba, 395s + hyperframe(po=Poisson(), str=Strauss(0.1)), 395s + iformula=~str/id) 395s + fit2w <- mppm(Points ~ group, simba, 395s + hyperframe(po=Poisson(), str=Strauss(0.1)), 395s + iformula=~str/id, weights=runif(nrow(simba))) 395s + # currently invalid 395s + # fit3 <- mppm(Points ~ group, simba, 395s + # hyperframe(po=Poisson(), pie=PairPiece(c(0.05,0.1))), 395s + # iformula=~I((group=="control") * po) + I((group=="treatment") * pie)) 395s + 395s + fit1 395s + fit2 395s + fit2w 395s + # fit3 395s + 395s + if(FULLTEST) { 395s + ## run summary.mppm which currently sits in spatstat-internal.Rd 395s + summary(fit1) 395s + summary(fit2) 395s + summary(fit2w) 395s + # summary(fit3) 395s + } 395s + 395s + ## test vcov algorithm 395s + vcov(fit1) 395s + vcov(fit2) 395s + # vcov(fit3) 395s + 395s + if(FULLTEST) { 395s + fit4 <- mppm(Points ~ group, simba, hyperframe(str=Strauss(0.1)), iformula=~str/group) 395s + fit4 395s + summary(fit4) 395s + vcov(fit4) 395s + fit0 <- mppm(Points ~ group, simba) 395s + anova(fit0, fit4, test="Chi") 395s + ## [bug from Fernando Milesi] 395s + fit5 <- mppm(Wat ~ id, 395s + data=hyperframe(Wat=waterstriders), 395s + interaction=StraussHard(4.5, 1.5), 395s + iformula=~Interaction:id) 395s + fit5 395s + summary(fit5) 395s + vcov(fit5) 395s + } 395s + 395s + ## test subfits algorithm 395s + if(FULLTEST) { 395s + s1 <- subfits(fit1) 395s + s2 <- subfits(fit2) 395s + # s3 <- subfits(fit3) 395s + s4 <- subfits(fit4) 395s + s5 <- subfits(fit5) 395s + 395s + ## validity of results of subfits() 395s + p1 <- solapply(s1, predict) 395s + p2 <- solapply(s2, predict) 395s + # p3 <- solapply(s3, predict) 395s + p4 <- solapply(s4, predict) 395s + p5 <- solapply(s5, predict) 395s + } 395s + }) 398s > 398s > local({ 398s + if(FULLTEST) { 398s + ## cases of predict.mppm 398s + W <- solapply(waterstriders, Window) 398s + Fakes <- solapply(W, runifpoint, n=30) 398s + FakeDist <- solapply(Fakes, distfun) 398s + H <- hyperframe(Bugs=waterstriders, 398s + D=FakeDist) 398s + fit <- mppm(Bugs ~ D, data=H) 398s + p1 <- predict(fit) 398s + p2 <- predict(fit, locations=Fakes) 398s + p3 <- predict(fit, locations=solapply(W, erosion, r=4)) 398s + locn <- as.data.frame(do.call(cbind, lapply(Fakes, coords))) 398s + df <- data.frame(id=sample(1:3, nrow(locn), replace=TRUE), 398s + D=runif(nrow(locn))) 398s + p4 <- predict(fit, locations=locn, newdata=df) 398s + 398s + fitG <- mppm(Bugs ~ D, data=H, use.gam=TRUE) 398s + p1G <- predict(fitG) 398s + p2G <- predict(fitG, locations=Fakes) 398s + p3G <- predict(fitG, locations=solapply(W, erosion, r=4)) 398s + p4G <- predict(fitG, locations=locn, newdata=df) 398s + } 398s + }) 398s > 398s > local({ 398s + ## [thanks to Sven Wagner] 398s + ## factor covariate, with some levels unused in some rows 398s + if(FULLTEST) { 398s + set.seed(14921788) 398s + H <- hyperframe(X=replicate(3, runifpoint(20), simplify=FALSE), 398s + Z=solist(as.im(function(x,y){x}, owin()), 398s + as.im(function(x,y){y}, owin()), 398s + as.im(function(x,y){x+y}, owin()))) 398s + H$Z <- solapply(H$Z, cut, breaks=(0:4)/2) 398s + 398s + fit6 <- mppm(X ~ Z, H) 398s + v6 <- vcov(fit6) 398s + s6 <- subfits(fit6) 398s + p6 <- solapply(s6, predict) 398s + 398s + ## random effects 398s + fit7 <- mppm(X ~ Z, H, random=~1|id) 398s + v7 <- vcov(fit7) 398s + s7 <- subfits(fit7) 398s + p7 <- solapply(s7, predict) 398s + 398s + fit7a <- mppm(X ~ Z, H, random=~x|id) 398s + v7a <- vcov(fit7a) 398s + s7a <- subfits(fit7a) 398s + p7a <- solapply(s7a, predict) 398s + 398s + ## multitype: collisions in vcov.ppm, predict.ppm 398s + H$X <- lapply(H$X, rlabel, labels=factor(c("a","b")), permute=FALSE) 398s + M <- MultiStrauss(matrix(0.1, 2, 2), c("a","b")) 398s + fit8 <- mppm(X ~ Z, H, M) 398s + v8 <- vcov(fit8, fine=TRUE) 398s + s8 <- subfits(fit8) 398s + p8 <- lapply(s8, predict) 398s + c8 <- lapply(s8, predict, type="cif") 398s + 398s + fit9 <- mppm(X ~ Z, H, M, iformula=~Interaction * id) 398s + v9 <- vcov(fit9, fine=TRUE) 398s + s9 <- subfits(fit9) 398s + p9 <- lapply(s9, predict) 398s + c9 <- lapply(s9, predict, type="cif") 398s + 398s + ## and a simple error in recognising 'marks' 398s + fit10 <- mppm(X ~ marks, H) 398s + } 398s + }) 398s > 398s > local({ 398s + if(FULLTEST) { 398s + ## test handling of offsets and zero cif values in mppm 398s + H <- hyperframe(Y = waterstriders) 398s + (fit1 <- mppm(Y ~ 1, data=H, Hardcore(1.5))) 398s + (fit2 <- mppm(Y ~ 1, data=H, StraussHard(7, 1.5))) 398s + (fit3 <- mppm(Y ~ 1, data=H, Hybrid(S=Strauss(7), H=Hardcore(1.5)))) 398s + s1 <- subfits(fit1) 398s + s2 <- subfits(fit2) 398s + s3 <- subfits(fit3) 398s + 398s + ## prediction, in training/testing context 398s + ## (example from Markus Herrmann and Ege Rubak) 398s + X <- waterstriders 398s + dist <- solapply(waterstriders, 398s + function(z) distfun(runifpoint(1, Window(z)))) 398s + i <- 3 398s + train <- hyperframe(pattern = X[-i], dist = dist[-i]) 398s + test <- hyperframe(pattern = X[i], dist = dist[i]) 398s + fit <- mppm(pattern ~ dist, data = train) 398s + pred <- predict(fit, type="cif", newdata=test, verbose=TRUE) 398s + 398s + ## examples from Robert Aue 398s + GH <- Hybrid(G=Geyer(r=0.1, sat=3), H=Hardcore(0.01)) 398s + res <- mppm(Points ~ 1, interaction = GH, data=demohyper) 398s + print(summary(res)) 398s + sub <- subfits(res, verbose=TRUE) 398s + print(sub) 398s + } 398s + }) 398s > 398s > local({ 398s + if(FULLTEST) { 398s + ## test handling of interaction coefficients in multitype case 398s + set.seed(42) 398s + XX <- as.solist(replicate(3, rthin(amacrine, 0.8), simplify=FALSE)) 398s + H <- hyperframe(X=XX) 398s + M <- MultiStrauss(matrix(0.1, 2, 2), levels(marks(amacrine))) 398s + fit <- mppm(X ~ 1, H, M) 398s + co <- coef(fit) 398s + subco <- sapply(subfits(fit), coef) 398s + if(max(abs(subco - co)) > 0.001) 398s + stop("Wrong coefficient values in subfits, for multitype interaction") 398s + } 398s + }) 398s > 398s > local({ 398s + if(FULLTEST) { 398s + ## test lurking.mppm 398s + ## example from 'mppm' 398s + n <- 7 398s + H <- hyperframe(V=1:n, 398s + U=runif(n, min=-1, max=1)) 398s + H$Z <- setcov(square(1)) 398s + H$U <- with(H, as.im(U, as.rectangle(Z))) 398s + H$Y <- with(H, rpoispp(eval.im(exp(2+3*Z)))) 398s + fit <- mppm(Y ~ Z + U + V, data=H) 398s + 398s + lurking(fit, expression(Z), type="P") 398s + lurking(fit, expression(V), type="raw") # design covariate 398s + lurking(fit, expression(U), type="raw") # image, constant in each row 398s + lurking(fit, H$Z, type="P") # list of images 398s + } 398s + }) 398s > 398s > local({ 398s + if(FULLTEST) { 398s + ## test anova.mppm code blocks and scoping problem 398s + H <- hyperframe(X=waterstriders) 398s + mod0 <- mppm(X~1, data=H, Poisson()) 398s + modxy <- mppm(X~x+y, data=H, Poisson()) 398s + mod0S <- mppm(X~1, data=H, Strauss(2)) 398s + modxyS <- mppm(X~x+y, data=H, Strauss(2)) 398s + anova(mod0, modxy, test="Chi") 398s + anova(mod0S, modxyS, test="Chi") 398s + anova(modxy, test="Chi") 398s + anova(modxyS, test="Chi") 398s + #' models with random effects (example from Marcelino de la Cruz) 398s + mod0r <- mppm(X~1, data=H, Poisson(), random = ~1|id) 398s + modxr <- mppm(X~x, data=H, Poisson(), random = ~1|id) 398s + anova(mod0r, modxr, test="Chi") 398s + } 398s + }) 398s > 398s > local({ 398s + if(FULLTEST) { 398s + ## test multitype stuff 398s + foo <- flu[1:3,] 398s + msh <- MultiStraussHard(iradii=matrix(100, 2, 2), 398s + hradii=matrix(10,2,2), 398s + types=levels(marks(foo$pattern[[1]]))) 398s + msh0 <- MultiStraussHard(iradii=matrix(100, 2, 2), 398s + hradii=matrix(10,2,2)) 398s + fit <- mppm(pattern ~ 1, data=foo, interaction=msh0) 398s + print(fit) 398s + print(summary(fit)) 398s + v <- vcov(fit) 398s + } 398s + }) 398s > 398s > reset.spatstat.options() 398s > #' 398s > #' tests/msr.R 398s > #' 398s > #' $Revision: 1.5 $ $Date: 2020/11/30 07:27:44 $ 398s > #' 398s > #' Tests of code for measures 398s > #' 398s > 398s > if(FULLTEST) { 398s + local({ 398s + 398s + ## cases of 'msr' 398s + Q <- quadscheme(cells) 398s + nQ <- n.quad(Q) 398s + nX <- npoints(cells) 398s + A <- matrix(nX * 3, nX, 3) 398s + B <- matrix(nQ * 3, nQ, 3) 398s + 398s + m <- msr(Q, A, B) 398s + 398s + M <- msr(Q, A, 1) 398s + M <- msr(Q, 1, B) 398s + M <- msr(Q, A, B[,1]) 398s + M <- msr(Q, A[,1], B) 398s + M <- msr(Q, A, B[,1,drop=FALSE]) 398s + M <- msr(Q, A[,1,drop=FALSE], B) 398s + 398s + ## methods 398s + a <- summary(m) 398s + b <- is.marked(m) 398s + w <- as.owin(m) 398s + z <- domain(m) 398s + ss <- scalardilate(m, 2) 398s + tt <- rescale(m, 2) 398s + ee <- rotate(m, pi/4) 398s + aa <- affine(m, mat=diag(c(1,2)), vec=c(0,1)) 398s + ff <- flipxy(m) 398s + 398s + am <- augment.msr(m, sigma=0.08) 398s + ua <- update(am) 398s + 398s + rr <- residuals(ppm(cells ~ x)) 398s + mm <- residuals(ppm(amacrine ~ x)) 398s + ss <- residuals(ppm(amacrine ~ x), type="score") 398s + gg <- rescale(ss, 1/662, c("micron", "microns")) 398s + 398s + plot(mm) 398s + plot(mm, multiplot=FALSE) 398s + plot(mm, equal.markscale=TRUE, equal.ribbon=TRUE) 398s + plot(ss) 398s + plot(ss, multiplot=FALSE) 398s + }) 398s + } 398s > 398s BEGIN TEST testsNtoO.R 398s 398s R version 4.3.2 (2023-10-31) -- "Eye Holes" 398s Copyright (C) 2023 The R Foundation for Statistical Computing 398s Platform: s390x-ibm-linux-gnu (64-bit) 398s 398s R is free software and comes with ABSOLUTELY NO WARRANTY. 398s You are welcome to redistribute it under certain conditions. 398s Type 'license()' or 'licence()' for distribution details. 398s 398s R is a collaborative project with many contributors. 398s Type 'contributors()' for more information and 398s 'citation()' on how to cite R or R packages in publications. 398s 398s Type 'demo()' for some demos, 'help()' for on-line help, or 398s 'help.start()' for an HTML browser interface to help. 398s Type 'q()' to quit R. 398s 398s > #' 398s > #' Header for all (concatenated) test files 398s > #' 398s > #' Require spatstat.model 398s > #' Obtain environment variable controlling tests. 398s > #' 398s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 398s > 398s > require(spatstat.model) 398s Loading required package: spatstat.model 398s Loading required package: spatstat.data 399s Loading required package: spatstat.geom 399s spatstat.geom 3.2-8 399s Loading required package: spatstat.random 399s spatstat.random 3.2-2 399s Loading required package: spatstat.explore 399s Loading required package: nlme 399s spatstat.explore 3.2-5 399s Loading required package: rpart 400s spatstat.model 3.2-8 400s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 400s > ALWAYS <- TRUE 400s > cat(paste("--------- Executing", 400s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 400s + "test code -----------\n")) 400s --------- Executing **RESTRICTED** subset of test code ----------- 400s > # 400s > # tests/NAinCov.R 400s > # 400s > # Testing the response to the presence of NA's in covariates 400s > # 400s > # $Revision: 1.8 $ $Date: 2022/05/22 08:37:38 $ 400s > 400s > if(FULLTEST) { 400s + local({ 400s + X <- runifpoint(42) 400s + Y <- as.im(function(x,y) { x+y }, owin()) 400s + Y[owin(c(0.2,0.4),c(0.2,0.4))] <- NA 400s + # fit model: should produce a warning but no failure 400s + misfit <- ppm(X ~Y, covariates=list(Y=Y)) 400s + # prediction 400s + Z <- predict(misfit, type="trend", se=TRUE) 400s + # covariance matrix: all should be silent 400s + v <- vcov(misfit) 400s + ss <- vcov(misfit, what="internals") 400s + }) 400s + } 400s > 400s BEGIN TEST testsP1.R 400s 400s R version 4.3.2 (2023-10-31) -- "Eye Holes" 400s Copyright (C) 2023 The R Foundation for Statistical Computing 400s Platform: s390x-ibm-linux-gnu (64-bit) 400s 400s R is free software and comes with ABSOLUTELY NO WARRANTY. 400s You are welcome to redistribute it under certain conditions. 400s Type 'license()' or 'licence()' for distribution details. 400s 400s R is a collaborative project with many contributors. 400s Type 'contributors()' for more information and 400s 'citation()' on how to cite R or R packages in publications. 400s 400s Type 'demo()' for some demos, 'help()' for on-line help, or 400s 'help.start()' for an HTML browser interface to help. 400s Type 'q()' to quit R. 400s 400s > #' 400s > #' Header for all (concatenated) test files 400s > #' 400s > #' Require spatstat.model 400s > #' Obtain environment variable controlling tests. 400s > #' 400s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 400s > 400s > require(spatstat.model) 400s Loading required package: spatstat.model 400s Loading required package: spatstat.data 401s Loading required package: spatstat.geom 401s spatstat.geom 3.2-8 401s Loading required package: spatstat.random 401s spatstat.random 3.2-2 401s Loading required package: spatstat.explore 401s Loading required package: nlme 402s spatstat.explore 3.2-5 402s Loading required package: rpart 402s spatstat.model 3.2-8 402s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 402s > ALWAYS <- TRUE 402s > cat(paste("--------- Executing", 402s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 402s + "test code -----------\n")) 402s --------- Executing **RESTRICTED** subset of test code ----------- 402s > ## 402s > ## tests/percy.R 402s > ## 402s > ## Tests of Percus-Yevick approximations 402s > ## 402s > ## $Revision: 1.3 $ $Date: 2020/04/30 05:23:52 $ 402s > 402s > if(FULLTEST) { 402s + local({ 402s + fit <- ppm(swedishpines ~1, DiggleGatesStibbard(6)) 402s + K <- Kmodel(fit) 402s + }) 402s + } 402s > 402s > ## 402s > ## tests/pixelgripes.R 402s > ## Problems related to pixellation of windows 402s > ## 402s > ## $Revision: 1.8 $ $Date: 2022/10/23 06:21:10 $ 402s > 402s > if(FULLTEST) { 402s + local({ 402s + 402s + ## From Philipp Hunziker: bug in rNeymanScott (etc) 402s + ## Create an irregular window 402s + PM <- matrix(c(1,0,0.5,1,0,0), 3, 2, byrow=TRUE) 402s + P <- owin(poly=PM) 402s + ## Generate Matern points 402s + X <- rMatClust(50, 0.05, 5, win=P) 402s + ## Some distance function as a covariate 402s + distorigin <- function(x, y) { sqrt(x^2 + y^2) } 402s + ## No covariates: works fine 402s + fit0 <- kppm(X ~ 1, clusters="MatClust") 402s + Y0 <- simulate(fit0, retry=0) 402s + ## Covariates: Simulation fails 402s + fit1 <- kppm(X ~ distorigin, clusters="MatClust") 402s + Y1 <- simulate(fit1, retry=0) 402s + 402s + }) 402s + } 402s > 402s BEGIN TEST testsP2.R 402s 402s R version 4.3.2 (2023-10-31) -- "Eye Holes" 402s Copyright (C) 2023 The R Foundation for Statistical Computing 402s Platform: s390x-ibm-linux-gnu (64-bit) 402s 402s R is free software and comes with ABSOLUTELY NO WARRANTY. 402s You are welcome to redistribute it under certain conditions. 402s Type 'license()' or 'licence()' for distribution details. 402s 402s R is a collaborative project with many contributors. 402s Type 'contributors()' for more information and 402s 'citation()' on how to cite R or R packages in publications. 402s 402s Type 'demo()' for some demos, 'help()' for on-line help, or 402s 'help.start()' for an HTML browser interface to help. 402s Type 'q()' to quit R. 402s 402s > Loading required package: spatstat.model 402s Loading required package: spatstat.data 402s #' 402s > #' Header for all (concatenated) test files 402s > #' 402s > #' Require spatstat.model 402s > #' Obtain environment variable controlling tests. 402s > #' 402s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 402s > 402s > require(spatstat.model) 403s Loading required package: spatstat.geom 404s spatstat.geom 3.2-8 404s Loading required package: spatstat.random 404s spatstat.random 3.2-2 404s Loading required package: spatstat.explore 404s Loading required package: nlme 404s spatstat.explore 3.2-5 404s Loading required package: rpart 404s spatstat.model 3.2-8 404s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 404s > ALWAYS <- TRUE 404s > cat(paste("--------- Executing", 404s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 404s + "test code -----------\n")) 404s --------- Executing **RESTRICTED** subset of test code ----------- 404s > # 404s > # tests/ppmBadData.R 404s > # 404s > # $Revision: 1.6 $ $Date: 2020/04/30 05:23:52 $ 404s > 404s > # Testing robustness of ppm and support functions 404s > # when data are rubbish 404s > 404s > local({ 404s + if(ALWAYS) { 404s + ## from Rolf: very large proportion of data is NA 404s + SEED <- 42 404s + K <- 101 404s + A <- 500 404s + X <- seq(0, A, length=K) 404s + G <- expand.grid(x=X, y=X) 404s + FOO <- function(x,y) { sin(x)^2 + cos(y)^2 } 404s + M1 <- im(matrix(FOO(G$x, G$y), K, K), xcol=X, yrow=X) 404s + M <- im(matrix(FOO(G$x, G$y), K, K)) 404s + BAR <- function(x) { exp(-6.618913 + 5.855337 * x - 8.432483 * x^2) } 404s + V <- im(BAR(M$v), xcol=X, yrow=X) 404s + # V <- eval.im(exp(-6.618913 + 5.855337 * M - 8.432483 * M^2)) 404s + set.seed(SEED) 404s + Y <- rpoispp(V) 404s + fY <- ppm(Y ~cv + I(cv^2), data=list(cv=M), correction="translate") 404s + diagnose.ppm(fY) 404s + lurking(fY, covariate=as.im(function(x,y){x}, square(A)), type="raw") 404s + } 404s + 404s + if(ALWAYS) { 404s + ## from Andrew Bevan: numerical overflow, ill-conditioned Fisher information 404s + SEED <- 42 404s + nongranite<- owin(poly = list(x = c(0, 8500, 7000, 6400, 6400, 6700, 7000, 7200, 7300, 8000, 8100, 8800, 9500, 10000, 10000, 0), y = c(0, 0, 2000, 3800, 4000, 5000, 6500, 7400, 7500, 8000, 8100, 9000, 9500, 9600, 10000, 10000))) 404s + ## Trend on raster grid 404s + rain <- as.im(X=function(x,y) { x^2 + y^2 }, W=nongranite, dimyx=100) 404s + ## Generate a point pattern via a Lennard-Jones process 404s + set.seed(SEED) 404s + mod4<- rmhmodel(cif="lennard", 404s + par=list(beta=1, sigma=250, epsilon=2.2), 404s + trend=rain, w=nongranite) 404s + ljtr<- rmh(mod4, start=list(n.start=80), control=list(p=1, nrep=1e5)) 404s + 404s + ## Fit a point process model to the pattern with rain as a covariate 404s + ## NOTE INCORRECT TREND FORMULA 404s + ljtrmod <- ppm(ljtr, trend= ~ Z, interaction=NULL, data=list(Z=rain)) 404s + ss <- summary(ljtrmod) 404s + } 404s + 404s + if(FULLTEST) { 404s + ## From Ege 404s + ## Degenerate but non-null argument 'covariates' 404s + xx <- list() 404s + names(xx) <- character(0) 404s + fit <- ppm(cells ~x, covariates = xx) 404s + st <- summary(fit) 404s + } 404s + 404s + }) 404s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 405s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 405s > Error in solve.default(M) : 405s system is computationally singular: reciprocal condition number = 5.72254e-18 405s In addition: Warning messages: 405s 1: Values of the covariate ‘cv’ were NA or undefined at 96% (1774 out of 1845) of the quadrature points. Occurred while executing: ppm.ppp(Q = Y, trend = ~cv + I(cv^2), data = list(list(c(1, 1.91953576453823, 405s 2: Some infinite, NA or NaN increments were removed 405s 3: Numerical underflow detected: sigma is probably too small 405s 4: Some infinite, NA or NaN increments were removed 405s Error in solve.default(M) : 405s system is computationally singular: reciprocal condition number = 5.72254e-18 405s In addition: Warning message: 405s Cannot compute variance: Fisher information matrix is singular 405s Warning message: 405s Cannot compute variance: Fisher information matrix is singular 405s 405s > 405s > 405s > #' tests/ppmclass.R 405s > #' 405s > #' Class support for ppm 405s > #' 405s > #' $Revision: 1.9 $ $Date: 2022/03/07 03:26:09 $ 405s > 405s > if(FULLTEST) { 405s + local({ 405s + #' (1) print.ppm, summary.ppm, print.summary.ppm 405s + Z <- as.im(function(x,y){x}, Window(cells)) 405s + fitZ <- ppm(cells ~ Z) 405s + print(fitZ) 405s + print(summary(fitZ)) 405s + #' logistic 405s + fitl <- ppm(swedishpines ~ x+y, method="logi") 405s + print(fitl) 405s + print(summary(fitl)) 405s + #' Model with covariate arguments 405s + f <- function(x,y,b) { x+b } 405s + fitf <- ppm(cells ~ f, covfunargs=list(b=1)) 405s + print(fitf) 405s + print(summary(fitf)) 405s + #' Invalid model 405s + fitN <- ppm(redwood ~ 1, Strauss(0.1)) 405s + print(fitN) 405s + print(summary(fitN)) 405s + #' standard errors in output 405s + fat <- ppm(cells ~ x, Strauss(0.12)) 405s + op <- spatstat.options(print.ppm.SE='always') 405s + print(fat) 405s + spatstat.options(print.ppm.SE='never') 405s + print(fat) 405s + print(fitZ) 405s + spatstat.options(op) 405s + 405s + ## (2) plot.ppm 405s + plot(fitZ) 405s + plot(fat, trend=FALSE, cif=FALSE, se=FALSE) 405s + 405s + ## (3) emend.ppm 405s + fitZe <- emend(fitZ, trace=TRUE) 405s + ZZ <- Z 405s + fitZZ <- ppm(cells ~ Z + ZZ) 405s + fitZZe <- emend(fitZZ, trace=TRUE) 405s + fitOK <- ppm(redwood ~1, Strauss(0.1), emend=TRUE) 405s + print(fitOK) 405s + fitNot <- ppm(redwood ~1, Strauss(0.1)) 405s + fitSlow <- emend(fitNot, trace=TRUE) 405s + print(fitSlow) 405s + op <- spatstat.options(project.fast=TRUE) 405s + fitFast <- emend(fitNot, trace=TRUE) 405s + print(fitFast) 405s + fitZZe <- emend(fitZZ, trace=TRUE) 405s + spatstat.options(op) 405s + 405s + #' (4) methods for other generics 405s + logLik(fitZ, absolute=TRUE) 405s + unitname(fitZ) 405s + unitname(fat) <- c("metre", "metres") 405s + is.expandable(fitf) 405s + fit0 <- update(fitZ, . ~ 1) 405s + anova(fit0, fitZ, override=TRUE) 405s + interactionfamilyname(fat) 405s + interactionorder(fat) 405s + hardcoredist(fat) 405s + 405s + #' (5) miscellaneous 405s + 405s + ## example from Robert Aue - handling offsets 405s + X <- demohyper$Points[[1]] 405s + GH <- Hybrid(G=Geyer(r=0.1, sat=3), H=Hardcore(0.01)) 405s + fit <- ppm(X ~ 1, GH) 405s + valid.ppm(fit) 405s + 405s + #' hard core distance of hybrid 405s + hardcoredist(fit) 405s + #' interaction order of hybrid 405s + interactionorder(fit) 405s + 405s + #' case of boundingbox 405s + boundingbox(cells, ppm(cells ~ 1)) 405s + }) 405s + 405s + reset.spatstat.options() 405s + } 405s > # 405s > # tests/ppmgam.R 405s > # 405s > # Test ppm with use.gam=TRUE 405s > # 405s > # $Revision: 1.4 $ $Date: 2020/04/30 05:23:52 $ 405s > # 405s > 405s > if(FULLTEST) { 405s + local({ 405s + fit <- ppm(nztrees ~s(x,y), use.gam=TRUE) 405s + mm <- model.matrix(fit) 405s + mf <- model.frame(fit) 405s + v <- vcov(fit) 405s + prd <- predict(fit) 405s + }) 405s + } 405s > #' 405s > #' tests/ppmlogi.R 405s > #' 405s > #' Tests of ppm(method='logi') 405s > #' and related code (predict, leverage etc) 405s > #' 405s > #' $Revision: 1.15 $ $Date: 2020/04/30 05:23:52 $ 405s > #' 405s > 405s > local({ 405s + if(FULLTEST) { 405s + fit <- ppm(cells ~x, method="logi") 405s + f <- fitted(fit) 405s + p <- predict(fit) 405s + u <- summary(fit) 405s + fitS <- ppm(cells ~x, Strauss(0.12), method="logi") 405s + fS <- fitted(fitS) 405s + pS <- predict(fitS) 405s + uS <- summary(fitS) 405s + print(uS) 405s + 405s + plot(leverage(fit)) 405s + plot(influence(fit)) 405s + plot(dfbetas(fit)) 405s + plot(leverage(fitS)) 405s + plot(influence(fitS)) 405s + plot(dfbetas(fitS)) 405s + } 405s + 405s + if(FULLTEST) { 405s + #' same with hard core - A1 is singular 405s + fitH <- ppm(cells ~x, Strauss(0.08), method="logi") 405s + print(fitH) 405s + fH <- fitted(fitH) 405s + pH <- predict(fitH) 405s + uH <- summary(fitH) 405s + print(uH) 405s + plot(leverage(fitH)) 405s + plot(influence(fitH)) 405s + plot(dfbetas(fitH)) 405s + } 405s + 405s + if(FULLTEST) { 405s + #' logistic fit to data frame of covariates 405s + z <- c(rep(TRUE, 5), rep(FALSE, 5)) 405s + df <- data.frame(A=z + 2* runif(10), 405s + B=runif(10)) 405s + Y <- quadscheme.logi(runifpoint(5), runifpoint(5)) 405s + fut <- ppm(Y ~ A+B, data=df, method="logi") 405s + sf <- summary(fut) 405s + print(sf) 405s + } 405s + 405s + if(FULLTEST) { 405s + #' vblogit code, just to check that it runs. 405s + fee <- ppm(cells ~ x, method="VBlogi", nd=21) 405s + print(fee) 405s + summary(fee) 405s + logLik(fee) 405s + AIC(fee) 405s + extractAIC(fee) 405s + Z <- predict(fee) 405s + summary(Z) 405s + print(fee$internal$glmfit) # print.vblogit 405s + } 405s + }) 405s > 405s > # 405s > # tests/ppmmarkorder.R 405s > # 405s > # $Revision: 1.4 $ $Date: 2020/04/30 05:23:52 $ 405s > # 405s > # Test that predict.ppm, plot.ppm and plot.fitin 405s > # tolerate marks with levels that are not in alpha order 405s > # 405s > if(ALWAYS) { # locale-dependent? 405s + local({ 405s + X <- amacrine 405s + levels(marks(X)) <- c("ZZZ", "AAA") 405s + fit <- ppm(X ~marks, MultiStrauss(c("ZZZ","AAA"), matrix(0.06, 2, 2))) 405s + aa <- predict(fit, type="trend") 405s + bb <- predict(fit, type="cif") 405s + plot(fit) 405s + plot(fitin(fit)) 405s + }) 405s + } 409s > 409s > 409s > # 409s > # tests/ppmscope.R 409s > # 409s > # Test things that might corrupt the internal format of ppm objects 409s > # 409s > # $Revision: 1.7 $ $Date: 2022/01/19 09:18:20 $ 409s > # 409s > 409s > if(ALWAYS) { # dependent on R version? 409s + local({ 409s + 409s + ## (1) Scoping problem that can arise when ppm splits the data 409s + fit <- ppm(bei ~elev, data=bei.extra) 409s + mm <- model.matrix(fit) 409s + 409s + ## (2) Fast update mechanism 409s + fit1 <- ppm(cells ~x+y, Strauss(0.07)) 409s + fit2 <- update(fit1, ~y) 409s + fit3 <- update(fit2, ~x) 409s + 409s + ## (3) New formula-based syntax 409s + attach(bei.extra) 409s + slfit <- ppm(bei ~ grad) 409s + sl2fit <- update(slfit, ~grad + I(grad^2)) 409s + slfitup <- update(slfit, use.internal=TRUE) 409s + sl2fitup <- update(sl2fit, use.internal=TRUE) 409s + 409s + ## (4) anova.ppm 409s + fut1 <- ppm(cells ~ 1, Strauss(0.1)) 409s + futx <- ppm(cells ~ x, Strauss(0.1)) 409s + anova(fut1, test="Chi") 409s + anova(futx, test="Chi") 409s + fut1a <- ppm(cells ~ 1, Strauss(0.1), rbord=0) 409s + anova(fut1a, futx, test="Chi") 409s + fut1d <- ppm(cells ~ 1, Strauss(0.1), nd=23) 409s + anova(fut1d, futx, test="Chi") 409s + ## This now works! 409s + futxyg <- ppm(cells ~ x + s(y), Strauss(0.1), use.gam=TRUE) 409s + anova(futx, futxyg) 409s + ## marked 409s + fatP <- ppm(amacrine ~ marks) 409s + fatM <- ppm(amacrine ~ marks, MultiStrauss(matrix(0.07, 2, 2))) 409s + anova(fatP, fatM, test="Chi") 409s + 409s + ## (5) expansion of "." in update.ppm 409s + fitb <- ppm(bei ~ . , data=bei.extra) 409s + step(fitb) 409s + }) 409s + } 412s Start: AIC=42295.11 412s ~elev + grad 412s 413s Df AIC 413s 42295 413s - elev 1 42383 413s - grad 1 42760 413s Nonstationary Poisson process 413s Fitted to point pattern dataset ‘bei’ 413s 413s Log intensity: ~elev + grad 413s 413s Fitted trend coefficients: 413s (Intercept) elev grad 413s -8.56355220 0.02143995 5.84646680 413s 413s Estimate S.E.Warning messages: 413s 1: anova.ppm now computes the *adjusted* deviances when the models are not Poisson processes. 413s 2: Models were re-fitted using a common value of 'rbord' 413s 3: Models were re-fitted using a common quadrature scheme 413s 4: Models were re-fitted with use.gam=TRUE 413s 5: Deviance adjustment is not available for gam fits; unadjusted composite deviance calculated. 413s 6: Models were re-fitted using a common value of 'rbord' 413s CI95.lo CI95.hi Ztest Zval 413s (Intercept) -8.56355220 0.341113849 -9.23212306 -7.89498134 *** -25.104675 413s elev 0.02143995 0.002287866 0.01695581 0.02592408 *** 9.371155 413s grad 5.84646680 0.255781018 5.34514522 6.34778838 *** 22.857313 413s > grep# 413s function (pattern, x, ignore.case = FALSE, perl = FALSE, value = FALSE, 413s fixed = FALSE, useBytes = FALSE, invert = FALSE) 413s { 413s pattern <- as.character(pattern) 413s if (is.factor(x) && length(levx <- levels(x)) < length(x) && 413s !is.na(pattern[1L])) { 413s value <- is.character(idxna <- suppressWarnings(grep(pattern, 413s NA_character_, ignore.case, perl, value, fixed, useBytes, 413s invert))) 413s idx <- logical(length(levx)) 413s idx[grep(pattern, levx, ignore.case, perl, FALSE, fixed, 413s useBytes, invert)] <- TRUE 413s idx <- idx[x] 413s if (length(idxna)) 413s idx[is.na(x)] <- TRUE 413s idx <- which(idx) 413s if (value) { 413s idx <- x[idx] 413s structure(as.character(idx), names = names(idx)) 413s } 413s else idx 413s } 413s else { 413s if (!is.character(x)) 413s x <- structure(as.character(x), names = names(x)) 413s .Internal(grep(pattern, x, ignore.case, value, perl, 413s fixed, useBytes, invert)) 413s } 413s } 413s 413s 413s > # tests/ppmtricks.R 413s > # 413s > # Test backdoor exits, hidden options, internals and tricks in ppm 413s > # 413s > # $Revision: 1.19 $ $Date: 2020/04/30 05:23:52 $ 413s > # 413s > local({ 413s + 413s + ## (1) skip.border 413s + if(ALWAYS) { # needed below 413s + fit <- ppm(cells, ~1, Strauss(0.1), skip.border=TRUE) 413s + } 413s + 413s + ## (2) subset arguments of different kinds 413s + if(FULLTEST) { 413s + fut <- ppm(cells ~ x, subset=(x > 0.5)) 413s + fot <- ppm(cells ~ x, subset=(x > 0.5), method="logi") 413s + W <- owin(c(0.4, 0.8), c(0.2, 0.7)) 413s + fut <- ppm(cells ~ x, subset=W) 413s + fot <- ppm(cells ~ x, subset=W, method="logi") 413s + V <- as.im(inside.owin, Window(cells), w=W) 413s + fet <- ppm(cells ~ x, subset=V) 413s + fet <- ppm(cells ~ x, subset=V, method="logi") 413s + } 413s + 413s + ## (3) profilepl -> ppm 413s + ## uses 'skip.border' and 'precomputed' 413s + ## also tests scoping for covariates 413s + if(FULLTEST) { 413s + splants <- split(ants) 413s + mess <- splants[["Messor"]] 413s + cats <- splants[["Cataglyphis"]] 413s + ss <- data.frame(r=seq(60,120,by=20),hc=29/6) 413s + dM <- distmap(mess,dimyx=256) 413s + mungf <- profilepl(ss, StraussHard, cats ~ dM) 413s + mungp <- profilepl(ss, StraussHard, trend=~dM, Q=cats) 413s + } 413s + 413s + ## (4) splitting large quadschemes into blocks 413s + if(FULLTEST) { 413s + mop <- spatstat.options(maxmatrix=5000) 413s + qr <- quadBlockSizes(quadscheme(cells)) 413s + pr <- predict(ppm(cells ~ x, AreaInter(0.05))) 413s + spatstat.options(mop) 413s + qr <- quadBlockSizes(quadscheme(cells)) 413s + } 413s + 413s + ## (5) shortcuts in summary.ppm 413s + ## and corresponding behaviour of print.summary.ppm 413s + if(FULLTEST) { 413s + print(summary(fit, quick=TRUE)) 413s + print(summary(fit, quick="entries")) 413s + print(summary(fit, quick="no prediction")) 413s + print(summary(fit, quick="no variances")) 413s + } 413s + 413s + ## (6) suffstat.R 413s + if(ALWAYS) { 413s + fitP <- update(fit, Poisson()) 413s + suffstat.poisson(fitP, cells) 413s + fit0 <- killinteraction(fit) 413s + suffstat.poisson(fit0, cells) 413s + } 413s + 413s + ## (7) various support for class ppm 413s + if(FULLTEST) { 413s + fut <- kppm(redwood ~ x) 413s + A <- quad.ppm(fut) 413s + Z <- as.im(function(x,y){x}, Window(cells)) 413s + fitZ <- ppm(cells ~ Z) 413s + U <- getppmOriginalCovariates(fitZ) 413s + } 413s + 413s + ## (8) support for class profilepl 413s + if(FULLTEST) { 413s + rr <- data.frame(r=seq(0.05, 0.15, by=0.02)) 413s + ps <- profilepl(rr, Strauss, cells) 413s + ## plot(ps) ## covered in plot.profilepl.Rd 413s + simulate(ps, nrep=1e4) 413s + parameters(ps) 413s + fitin(ps) 413s + predict(ps, type="cif") 413s + } 413s + 413s + ## (9) class 'plotppm' 413s + if(FULLTEST) { 413s + fut <- ppm(amacrine ~ marks + polynom(x,y,2), Strauss(0.07)) 413s + p <- plot(fut, plot.it=FALSE) 413s + print(p) 413s + plot(p, how="contour") 413s + plot(p, how="persp") 413s + } 413s + 413s + ## (10) ppm -> mpl.engine -> mpl.prepare 413s + if(ALWAYS) { # includes C code 413s + fit <- ppm(cells, NULL) 413s + fit <- ppm(cells ~ x, clipwin=square(0.7)) 413s + fit <- ppm(cells ~ x, subset=square(0.7)) 413s + DG <- as.im(function(x,y){x+y < 1}, square(1)) 413s + fit <- ppm(cells ~ x, subset=DG) 413s + fit <- ppm(cells ~ x, GLM=glm) 413s + fit <- ppm(cells ~ x, famille=quasi(link='log', variance='mu')) 413s + fit <- ppm(cells ~ x, Hardcore(0.07), skip.border=TRUE, splitInf=TRUE) 413s + } 413s + 413s + ## (11) unidentifiable model (triggers an error in ppm) 413s + if(FULLTEST) { 413s + Q <- quadscheme(cells) 413s + M <- mpl.prepare(Q, cells, as.ppp(Q), trend=~1, covariates=NULL, 413s + interaction=Hardcore(0.3), correction="none") 413s + } 413s + }) 413s > 413s > reset.spatstat.options() 413s > # 413s > # tests/prediction.R 413s > # 413s > # Things that might go wrong with predict() 413s > # 413s > # $Revision: 1.20 $ $Date: 2020/04/30 05:41:59 $ 413s > # 413s > 413s > local({ 413s + if(ALWAYS) { 413s + ## test of 'covfunargs' - platform dependent? 413s + f <- function(x,y,a){ y - a } 413s + fit <- ppm(cells ~x + f, covariates=list(f=f), covfunargs=list(a=1/2)) 413s + p <- predict(fit) 413s + 413s + ## prediction involving 0 * NA 413s + qc <- quadscheme(cells, nd=10) 413s + r <- minnndist(as.ppp(qc))/10 413s + fit <- ppm(qc ~ 1, Strauss(r)) # model has NA for interaction coefficient 413s + p1 <- predict(fit) 413s + p2 <- predict(fit, type="cif", ngrid=10) 413s + stopifnot(all(is.finite(as.matrix(p1)))) 413s + stopifnot(all(is.finite(as.matrix(p2)))) 413s + } 413s + 413s + if(FULLTEST) { 413s + ## test of 'new.coef' mechanism 413s + fut <- ppm(cells ~ x, Strauss(0.15), rbord=0) 413s + p0 <- predict(fut, type="cif") 413s + pe <- predict(fut, type="cif", new.coef=coef(fut)) 413s + pn <- predict(fut, type="cif", new.coef=unname(coef(fut))) 413s + if(max(abs(pe-p0)) > 0.01) 413s + stop("new.coef mechanism is broken!") 413s + if(max(abs(pn-p0)) > 0.01) 413s + stop("new.coef mechanism gives wrong answer, for unnamed vectors") 413s + #' adaptcoef 413s + a <- c(A=1,B=2,Z=42) 413s + b <- c(B=41,A=0) 413s + ab <- adaptcoef(a, b, drop=TRUE) 413s + } 413s + 413s + if(FULLTEST) { 413s + ## tests of relrisk.ppm 413s + fut <- ppm(amacrine ~ x * marks) 413s + a <- relrisk(fut, control=2, relative=TRUE) 413s + a <- relrisk(fut, se=TRUE) 413s + a <- relrisk(fut, relative=TRUE, se=TRUE) 413s + fut <- ppm(sporophores ~ marks + x) 413s + a <- relrisk(fut, control=2, relative=TRUE) 413s + a <- relrisk(fut, se=TRUE) 413s + a <- relrisk(fut, relative=TRUE, se=TRUE) 413s + 413s + ## untested cases of predict.ppm 413s + fit0 <- ppm(cells) 413s + a <- predict(fit0, interval="confidence") 413s + a <- predict(fit0, interval="confidence", type="count") 413s + fit <- ppm(cells ~ x) 413s + b <- predict(fit, se=TRUE, locations=cells) 413s + b <- predict(fit, se=TRUE, interval="confidence") 413s + b <- predict(fit, type="count", se=TRUE) 413s + b <- predict(fit, type="count", window=square(0.5), se=TRUE) 413s + b <- predict(fit, type="count", window=quadrats(cells, 3), se=TRUE) 413s + d <- predict(fit, type="count", interval="prediction", se=TRUE) 413s + d <- predict(fit, type="count", interval="confidence", se=TRUE) 413s + d <- predict(fit, interval="confidence", se=TRUE) 413s + foot <- ppm(cells ~ x, StraussHard(0.12)) 413s + d <- predict(foot, ignore.hardcore=TRUE) 413s + dX <- predict(foot, ignore.hardcore=TRUE, locations=cells) 413s + 413s + ## superseded usages 413s + b <- predict(fit, type="se", getoutofjail=TRUE) 413s + b <- predict(fit, type="se", locations=cells) # warning 413s + b <- predict(fit, total=TRUE) 413s + b <- predict(fit, total=square(0.5)) 413s + b <- predict(fit, total=quadrats(cells, 3)) 413s + 413s + ## supporting code 413s + u <- model.se.image(fit, square(0.5)) 413s + u <- model.se.image(fit, square(0.5), what="cv") 413s + u <- model.se.image(fit, square(0.5), what="ce") 413s + co <- c(Intercept=5, slope=3, kink=2) 413s + re <- c("Intercept", "slope") 413s + a <- fill.coefs(co, re) # warning 413s + b <- fill.coefs(co, rev(names(co))) 413s + d <- fill.coefs(co, letters[1:3]) 413s + ## model matrix etc 413s + v <- model.frame(ppm(cells)) 413s + fut <- ppm(cells ~ x, Strauss(0.1)) 413s + v <- model.matrix(fut, subset=(x<0.5), keepNA=FALSE) 413s + df <- data.frame(x=runif(10), y=runif(10), 413s + Interaction=sample(0:1, 10, TRUE)) 413s + m10 <- PPMmodelmatrix(fut, data=df) 413s + mmm <- PPMmodelmatrix(fut, Q=quad.ppm(fut)) 413s + #' effectfun for Gibbs 413s + effectfun(fut, "x") 413s + effectfun(fut, "x", se.fit=TRUE) 413s + #' implicit covariate when there is only one 413s + effectfun(fut) 413s + effectfun(fut, se.fit=TRUE) 413s + #' given covariate 413s + dlin <- distfun(copper$SouthLines) 413s + copfit <- ppm(copper$SouthPoints ~ dlin, Geyer(1,1)) 413s + effectfun(copfit, "dlin") 413s + effectfun(copfit) 413s + #' covariate that is not used in model 413s + effectfun(fut, "y", x=0) 413s + futS <- ppm(cells ~ 1, Strauss(0.1)) 413s + effectfun(futS, "x") 413s + effectfun(futS, "y") 413s + #' factor covariate 413s + fot <- ppm(amacrine~x+marks) 413s + effectfun(fot, "marks", x=0.5, se.fit=TRUE) 413s + #' covariate retained but not used 413s + W <- Window(swedishpines) 413s + a <- solist(A=funxy(function(x,y){x < 20}, W), 413s + B=funxy(function(x,y){factor(x < 20)}, W)) 413s + fvt <- ppm(swedishpines ~ A, data=a, allcovar=TRUE) 413s + effectfun(fvt, "A", se.fit=TRUE) 413s + effectfun(fvt, "B", A=TRUE, se.fit=TRUE) 413s + 413s + ## ppm with covariate values in data frame 413s + X <- rpoispp(42) 413s + Q <- quadscheme(X) 413s + weirdfunction <- function(x,y){ 10 * x^2 + 5 * sin(10 * y) } 413s + Zvalues <- weirdfunction(x.quad(Q), y.quad(Q)) 413s + fot <- ppm(Q ~ y + Z, data=data.frame(Z=Zvalues)) 413s + effectfun(fot, "y", Z=0) 413s + effectfun(fot, "Z", y=0) 413s + 413s + #' multitype 413s + modX <- ppm(amacrine ~ polynom(x,2)) 413s + effectfun(modX) 413s + effectfun(modX, "x") 413s + modXM <- ppm(amacrine ~ marks*polynom(x,2)) 413s + effectfun(modXM, "x", marks="on") 413s + modXYM <- ppm(amacrine ~ marks*polynom(x,y,2)) 413s + effectfun(modXYM, "x", y=0, marks="on") 413s + 413s + df <- as.data.frame(simulate(modXM, drop=TRUE)) 413s + df$marks <- as.character(df$marks) 413s + dfpr <- predict(modXM, locations=df) 413s + } 413s + }) 413s > 413s > # 413s > # tests/project.ppm.R 413s > # 413s > # $Revision: 1.7 $ $Date: 2020/04/30 05:41:59 $ 413s > # 413s > # Tests of projection mechanism 413s > # 413s > 413s > local({ 413s + chk <- function(m) { 413s + if(!valid.ppm(m)) stop("Projected model was still not valid") 413s + return(invisible(NULL)) 413s + } 413s + 413s + if(FULLTEST) { 413s + ## a very unidentifiable model 413s + fit <- ppm(cells ~Z, Strauss(1e-06), covariates=list(Z=0)) 413s + chk(emend(fit)) 413s + ## multitype 413s + r <- matrix(1e-06, 2, 2) 413s + fit2 <- ppm(amacrine ~1, MultiStrauss(types=c("off", "on"), radii=r)) 413s + chk(emend(fit2)) 413s + ## complicated multitype 413s + fit3 <- ppm(amacrine ~1, MultiStraussHard(types=c("off", "on"), 413s + iradii=r, hradii=r/5)) 413s + chk(emend(fit3)) 413s + 413s + #' code coverage 413s + op <- spatstat.options(project.fast=TRUE) 413s + fut <- emend(fit, trace=TRUE) 413s + chk(fut) 413s + spatstat.options(op) 413s + 413s + #' hierarchical 413s + ra <- r 413s + r[2,1] <- NA 413s + fit4 <- ppm(amacrine ~1, HierStrauss(types=c("off", "on"), radii=r)) 413s + chk(emend(fit4)) 413s + #' complicated hierarchical 413s + fit5 <- ppm(amacrine ~1, HierStraussHard(types=c("off", "on"), 413s + iradii=r, hradii=r/5)) 413s + chk(emend(fit5)) 413s + 413s + ## hybrids 413s + r0 <- min(nndist(redwood)) 413s + ra <- 1.25 * r0 413s + rb <- 0.8 * r0 413s + f1 <- ppm(redwood ~1, Hybrid(A=Strauss(ra), B=Geyer(0.1, 2)), project=TRUE) 413s + chk(f1) 413s + f2 <- ppm(redwood ~1, Hybrid(A=Strauss(rb), B=Geyer(0.1, 2)), project=TRUE) 413s + chk(f2) 413s + f3 <- ppm(redwood ~1, Hybrid(A=Strauss(ra), B=Strauss(0.1)), project=TRUE) 413s + chk(f3) 413s + f4 <- ppm(redwood ~1, Hybrid(A=Strauss(rb), B=Strauss(0.1)), project=TRUE) 413s + chk(f4) 413s + f5 <- ppm(redwood ~1, Hybrid(A=Hardcore(rb), B=Strauss(0.1)), project=TRUE) 413s + chk(f5) 413s + f6 <- ppm(redwood ~1, Hybrid(A=Hardcore(rb), B=Geyer(0.1, 2)), project=TRUE) 413s + chk(f6) 413s + f7 <- ppm(redwood ~1, Hybrid(A=Geyer(rb, 1), B=Strauss(0.1)), project=TRUE) 413s + chk(f7) 413s + } 413s + }) 413s > 413s > reset.spatstat.options() 413s > 413s BEGIN TEST testsQ.R 413s 413s R version 4.3.2 (2023-10-31) -- "Eye Holes" 413s Copyright (C) 2023 The R Foundation for Statistical Computing 413s Platform: s390x-ibm-linux-gnu (64-bit) 413s 413s R is free software and comes with ABSOLUTELY NO WARRANTY. 413s You are welcome to redistribute it under certain conditions. 413s Type 'license()' or 'licence()' for distribution details. 413s 413s R is a collaborative project with many contributors. 413s Type 'contributors()' for more information and 413s 'citation()' on how to cite R or R packages in publications. 413s 413s Type 'demo()' for some demos, 'help()' for on-line help, or 413s 'help.start()' for an HTML browser interface to help. 413s Type 'q()' to quit R. 413s 413s > #' 413s > #' Header for all (concatenated) test files 413s > #' 413s > #' Require spatstat.model 413s > #' Obtain environment variable controlling tests. 413s > #' 413s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 413s > 413s > require(spatstat.model) 413s Loading required package: spatstat.model 413s Loading required package: spatstat.data 426s Loading required package: spatstat.geom 426s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 426s > ALWAYS <- TRUE 426s > cat(paste("--------- Executing", 426s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 426s + "test code -----------\n")) 426s --------- Executing **RESTRICTED** subset of test code ----------- 426s > 426s spatstat.geom 3.2-8 426s Loading required package: spatstat.random 426s spatstat.random 3.2-2 426s Loading required package: spatstat.explore 426s Loading required package: nlme 426s spatstat.explore 3.2-5 426s Loading required package: rpart 426s spatstat.model 3.2-8 426s Loading required package: spatstat.model 426s Loading required package: spatstat.data 426s Loading required package: spatstat.geom 426s spatstat.geom 3.2-8 426s Loading required package: spatstat.random 426s spatstat.random 3.2-2 426s Loading required package: spatstat.explore 426s Loading required package: nlme 426s spatstat.explore 3.2-5 426s Loading required package: rpart 426s spatstat.model 3.2-8 426s Loading required package: spatstat.model 426s Loading required package: spatstat.data 426s Loading required package: spatstat.geom 426s spatstat.geom 3.2-8 426s Loading required package: spatstat.random 426s spatstat.random 3.2-2 426s Loading required package: spatstat.explore 426s Loading required package: nlme 426s spatstat.explore 3.2-5 426s Loading required package: rpart 426s spatstat.model 3.2-8 426s BEGIN TEST testsR1.R 426s 426s R version 4.3.2 (2023-10-31) -- "Eye Holes" 426s Copyright (C) 2023 The R Foundation for Statistical Computing 426s Platform: s390x-ibm-linux-gnu (64-bit) 426s 426s R is free software and comes with ABSOLUTELY NO WARRANTY. 426s You are welcome to redistribute it under certain conditions. 426s Type 'license()' or 'licence()' for distribution details. 426s 426s R is a collaborative project with many contributors. 426s Type 'contributors()' for more information and 426s 'citation()' on how to cite R or R packages in publications. 426s 426s Type 'demo()' for some demos, 'help()' for on-line help, or 426s 'help.start()' for an HTML browser interface to help. 426s Type 'q()' to quit R. 426s 426s > #' 426s > #' Header for all (concatenated) test files 426s > #' 426s > #' Require spatstat.model 426s > #' Obtain environment variable controlling tests. 426s > #' 426s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 426s > 426s > require(spatstat.model) 426s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 426s > ALWAYS <- TRUE 426s > cat(paste("--------- Executing", 426s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 426s + "test code -----------\n")) 426s --------- Executing **RESTRICTED** subset of test code ----------- 426s > #' tests/resid.R 426s > #' 426s > #' Stuff related to residuals and residual diagnostics 426s > #' including residual summary functions 426s > #' 426s > #' $Revision: 1.7 $ $Date: 2022/05/22 08:43:31 $ 426s > #' 426s > 426s > local({ 426s + fit <- ppm(cells ~x, Strauss(r=0.15)) 426s + rr <- residuals(fit, quad=quadscheme(cells, nd=128)) 426s + diagnose.ppm(fit, cumulative=FALSE, type="pearson") 426s + 426s + if(FULLTEST) { 426s + diagnose.ppm(fit, cumulative=FALSE) 426s + 426s + fitoff <- ppm(cells ~ sin(x) + offset(y)) 426s + plot(a <- parres(fitoff, "x")) 426s + plot(b <- parres(fitoff, "y")) 426s + print(a) 426s + print(b) 426s + 426s + d <- diagnose.ppm(fit, which="marks") 426s + plot(d, plot.neg="discrete") 426s + plot(d, plot.neg="imagecontour") 426s + 426s + d <- diagnose.ppm(fit, type="pearson", which="smooth") 426s + plot(d, plot.smooth="image") 426s + plot(d, plot.smooth="contour") 426s + plot(d, plot.smooth="imagecontour") 426s + 426s + d <- diagnose.ppm(fit, type="pearson", which="x") 426s + plot(d) 426s + d <- diagnose.ppm(fit, type="pearson", which="y") 426s + plot(d) 426s + 426s + diagnose.ppm(fit, type="pearson", which="x", cumulative=FALSE) 426s + diagnose.ppm(fit, type="pearson", which="x", cumulative=FALSE) 426s + diagnose.ppm(fit, type="raw", plot.neg="discrete", plot.smooth="image") 426s + diagnose.ppm(fit, type="pearson", plot.neg="contour", plot.smooth="contour") 426s + 426s + diagnose.ppm(fitoff, type="raw", which="smooth", plot.smooth="persp") 426s + diagnose.ppm(fitoff, type="pearson", plot.neg="imagecontour") 426s + 426s + plot(Frame(letterR), main="") 426s + ploterodewin(letterR, erosion(letterR, 0.05), main="jeans") 426s + W <- as.mask(letterR) 426s + plot(Frame(W), main="") 426s + ploterodewin(W, erosion(W, 0.05), main="JeAnS") 426s + 426s + #' entangled terms in model 426s + U <- as.im(1, owin()) 426s + Z <- as.im(function(x,y) x, owin()) 426s + X <- runifpoint(40) 426s + fut <- ppm(X ~ Z:U) 426s + a <- parres(fut, "Z") 426s + futoff <- ppm(X ~ offset(Z*U)) 426s + a <- parres(futoff, "Z") 426s + 426s + #' residual summary functions 426s + pt <- psst(cells, interaction=Strauss(0.1), fun=nndcumfun) 426s + } 426s + }) 426s > 426s > 426s > 426s > ## 426s > ## tests/rhohat.R 426s > ## 426s > ## Test all combinations of options for rhohatCalc 426s > ## 426s > ## $Revision: 1.6 $ $Date: 2022/05/22 08:03:48 $ 426s > 426s > local({ 426s + if(FULLTEST) { 426s + X <- rpoispp(function(x,y){exp(3+3*x)}) 426s + Z <- as.im(function(x,y) { x }, Window(X)) 426s + f <- funxy(function(x,y) { y + 1 }, Window(X)) 426s + 426s + 426s + ## rhohat.ppm 426s + fit <- ppm(X ~x) 426s + rhofitA <- rhohat(fit, "x") 426s + rhofitB <- rhohat(fit, "x", method="reweight") 426s + rhofitC <- rhohat(fit, "x", method="transform") 426s + rhofitD <- rhohat(fit, Z) 426s + rhofitD <- rhohat(fit, Z, positiveCI=TRUE) 426s + lam <- predict(fit) 426s + 426s + 426s + ## Horvitz-Thompson 426s + rhofitAH <- rhohat(fit, "x", horvitz=TRUE) 426s + rhofitBH <- rhohat(fit, "x", method="reweight", horvitz=TRUE) 426s + rhofitCH <- rhohat(fit, "x", method="transform", horvitz=TRUE) 426s + 426s + r2myx <- rho2hat(fit, "y", "x") 426s + r2myxw <- rho2hat(fit, "y", "x", method="reweight") 426s + plot(r2myx) 426s + plot(r2myxw) 426s + print(r2myxw) 426s + predict(r2myxw) 426s + predict(r2myxw, relative=TRUE) 426s + } 426s + }) 426s > 426s BEGIN TEST testsR2.R 426s 426s R version 4.3.2 (2023-10-31) -- "Eye Holes" 426s Copyright (C) 2023 The R Foundation for Statistical Computing 426s Platform: s390x-ibm-linux-gnu (64-bit) 426s 426s R is free software and comes with ABSOLUTELY NO WARRANTY. 426s You are welcome to redistribute it under certain conditions. 426s Type 'license()' or 'licence()' for distribution details. 426s 426s R is a collaborative project with many contributors. 426s Type 'contributors()' for more information and 426s 'citation()' on how to cite R or R packages in publications. 426s 426s Type 'demo()' for some demos, 'help()' for on-line help, or 426s 'help.start()' for an HTML browser interface to help. 426s Type 'q()' to quit R. 426s 426s > #' 426s > #' Header for all (concatenated) test files 426s > #' 426s > #' Require spatstat.model 426s > #' Obtain environment variable controlling tests. 426s > #' 426s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 426s > 426s > require(spatstat.model) 426s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 426s > ALWAYS <- TRUE 426s > cat(paste("--------- Executing", 426s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 426s + "test code -----------\n")) 426s --------- Executing **RESTRICTED** subset of test code ----------- 426s > # 426s > # tests/rmhExpand.R 426s > # 426s > # test decisions about expansion of simulation window 426s > # 426s > # $Revision: 1.9 $ $Date: 2022/10/23 01:17:33 $ 426s > # 426s > 426s > local({ 426s + if(FULLTEST) { 426s + ## check expansion in rmhmodel.ppm 426s + fit <- ppm(cells ~x) 426s + mod <- rmhmodel(fit) 426s + is.expandable(mod) 426s + wsim <- as.rectangle(mod$trend) 426s + ## work around changes in 'unitname' 426s + wcel <- as.owin(cells) 426s + unitname(wcel) <- unitname(cells) 426s + ## test 426s + if(!identical(wsim, wcel)) 426s + stop("Expansion occurred improperly in rmhmodel.ppm") 426s + } 426s + }) 426s > 426s > 426s > 426s > # 426s > # tests/rmhTrend.R 426s > # 426s > # Problems with trend images (rmhmodel.ppm or rmhEngine) 426s > # 426s > 426s > if(ALWAYS) { 426s + local({ 426s + set.seed(42) 426s + 426s + # Bug folder 37 of 8 feb 2011 426s + # rmhmodel.ppm -> predict.ppm 426s + # + rmhResolveTypes -> is.subset.owin 426s + 426s + Z <- rescale(demopat, 7000) 426s + X <- unmark(Z) 426s + X1 <- split(Z)[[1]] 426s + Int <- density(X,dimyx=200) 426s + Lint <- eval.im(log(npoints(X1)*Int/npoints(X))) 426s + M <- as.owin(Int) 426s + MR <- intersect.owin(M,scalardilate(M,0.5,origin="midpoint")) 426s + X1 <- X1[MR] 426s + Fut <- ppm(X1~offset(Lint),covariates=list(Lint=Lint), 426s + inter=BadGey(r=c(0.03,0.05),sat=3)) 426s + Y <- rmh(Fut,control=list(expand=M,nrep=1e3), verbose=FALSE) 426s + 426s + }) 426s + } 426s > # 426s > # tests/rmhmodel.ppm.R 426s > # 426s > # $Revision: 1.10 $ $Date: 2020/05/01 05:29:42 $ 426s > # 426s > # Case-by-case tests of rmhmodel.ppm 426s > # 426s > 426s > if(FULLTEST) { 426s + local({ 426s + f <- ppm(cells) 426s + m <- rmhmodel(f) 426s + 426s + f <- ppm(cells ~x) 426s + m <- rmhmodel(f) 426s + 426s + f <- ppm(cells ~1, Strauss(0.1)) 426s + m <- rmhmodel(f) 426s + 426s + f <- ppm(cells ~1, StraussHard(r=0.1,hc=0.05)) 426s + m <- rmhmodel(f) 426s + print(m) 426s + 426s + f <- ppm(cells ~1, Hardcore(0.07)) 426s + m <- rmhmodel(f) 426s + 426s + f <- ppm(cells ~1, DiggleGratton(0.05,0.1)) 426s + m <- rmhmodel(f) 426s + 426s + f <- ppm(cells ~1, Softcore(0.5), correction="isotropic") 426s + m <- rmhmodel(f) 426s + 426s + f <- ppm(cells ~1, Geyer(0.07,2)) 426s + m <- rmhmodel(f) 426s + 426s + f <- ppm(cells ~1, BadGey(c(0.07,0.1,0.13),2)) 426s + m <- rmhmodel(f) 426s + 426s + f <- ppm(cells ~1, PairPiece(r = c(0.05, 0.1, 0.2))) 426s + m <- rmhmodel(f) 426s + 426s + f <- ppm(cells ~1, AreaInter(r=0.06)) 426s + m <- rmhmodel(f) 426s + print(m) 426s + 426s + # multitype 426s + 426s + r <- matrix(0.07, 2, 2) 426s + f <- ppm(amacrine ~1, MultiStrauss(c("off","on"),r)) 426s + m <- rmhmodel(f) 426s + print(m) 426s + 426s + h <- matrix(min(nndist(amacrine))/2, 2, 2) 426s + f <- ppm(amacrine ~1, MultiStraussHard(c("off","on"),r, h)) 426s + m <- rmhmodel(f) 426s + 426s + diag(r) <- NA 426s + diag(h) <- NA 426s + f <- ppm(amacrine ~1, MultiStrauss(c("off","on"),r)) 426s + m <- rmhmodel(f) 426s + 426s + f <- ppm(amacrine ~1, MultiStraussHard(c("off","on"),r, h)) 426s + m <- rmhmodel(f) 426s + 426s + # multitype data, interaction not dependent on type 426s + 426s + f <- ppm(amacrine ~marks, Strauss(0.05)) 426s + m <- rmhmodel(f) 426s + print(m) 426s + 426s + # trends 426s + 426s + f <- ppm(cells ~x, Strauss(0.1)) 426s + m <- rmhmodel(f) 426s + 426s + f <- ppm(cells ~y, StraussHard(r=0.1,hc=0.05)) 426s + m <- rmhmodel(f) 426s + 426s + f <- ppm(cells ~x+y, Hardcore(0.07)) 426s + m <- rmhmodel(f) 426s + print(m) 426s + 426s + f <- ppm(cells ~polynom(x,y,2), Softcore(0.5), correction="isotropic") 426s + m <- rmhmodel(f) 426s + 426s + # covariates 426s + 426s + Z <- as.im(function(x,y){ x^2+y^2 }, as.owin(cells)) 426s + f <- ppm(cells ~z, covariates=list(z=Z)) 426s + m <- rmhmodel(f) 426s + m <- rmhmodel(f, control=list(p=1)) 426s + print(m) 426s + 426s + Zim <- as.im(Z, as.owin(cells)) 426s + f <- ppm(cells ~z, covariates=list(z=Zim)) 426s + m <- rmhmodel(f) 426s + 426s + Z <- as.im(function(x,y){ x^2+y }, as.owin(amacrine)) 426s + f <- ppm(amacrine ~z + marks, covariates=list(z=Z)) 426s + m <- rmhmodel(f) 426s + print(m) 426s + m <- rmhmodel(f, control=list(p=1)) 426s + m <- rmhmodel(f, control=list(p=1,fixall=TRUE)) 426s + print(m) 426s + 426s + Zim <- as.im(Z, as.owin(amacrine)) 426s + f <- ppm(amacrine ~z + marks, covariates=list(z=Zim)) 426s + m <- rmhmodel(f) 426s + print(m) 426s + 426s + }) 426s + } 426s > # 426s > # tests/rmhmodelHybrids.R 426s > # 426s > # Test that rmhmodel.ppm and rmhmodel.default 426s > # work on Hybrid interaction models 426s > # 426s > # $Revision: 1.6 $ $Date: 2022/10/23 01:17:56 $ 426s > # 426s > 426s > if(ALWAYS) { # involves C code 426s + local({ 426s + 426s + ## ......... rmhmodel.ppm ....................... 426s + fit1 <- ppm(redwood ~1, 426s + Hybrid(A=Strauss(0.02), B=Geyer(0.1, 2), C=Geyer(0.15, 1))) 426s + m1 <- rmhmodel(fit1) 426s + m1 426s + reach(m1) 426s + 426s + ## Test of handling 'IsOffset' 426s + fit2 <- ppm(cells ~1, Hybrid(H=Hardcore(0.05), G=Geyer(0.15, 2))) 426s + m2 <- rmhmodel(fit2) 426s + ## also test C code for hybrid interaction with hard core 426s + fakecells <- rmh(fit2, nrep=1e4) 426s + 426s + ## Test of handling Poisson components 426s + fit3 <- ppm(cells ~1, Hybrid(P=Poisson(), S=Strauss(0.05))) 426s + X3 <- rmh(fit3, control=list(nrep=1e3,expand=1), verbose=FALSE) 426s + 426s + 426s + }) 426s + } 426s Extracting model information...Evaluating trend...done. 426s Extracting model information...Evaluating trend...done. 426s Extracting model information...Evaluating trend...done. 426s Checking arguments..determining simulation windows...Starting simulation. 426s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 426s > 426s > # 426s > # tests/rmh.ppm.R 426s > # 426s > # $Revision: 1.5 $ $Date: 2020/05/01 05:29:42 $ 426s > # 426s > # Examples removed from rmh.ppm.Rd 426s > # stripped down to minimal tests of validity 426s > # 426s > 426s > local({ 426s + op <- spatstat.options() 426s + spatstat.options(rmh.nrep=10, npixel=10, ndummy.min=10) 426s + spatstat.options(project.fast=TRUE) 426s + Nrep <- 10 426s + 426s + X <- swedishpines 426s + if(FULLTEST) { 426s + ## Poisson process 426s + fit <- ppm(X ~1, Poisson()) 426s + Xsim <- rmh(fit) 426s + } 426s + if(ALWAYS) { # Gibbs model => C code 426s + ## Strauss process 426s + fit <- ppm(X ~1, Strauss(r=7)) 426s + Xsim <- rmh(fit) 426s + 426s + ## Strauss process simulated on a larger window 426s + ## then clipped to original window 426s + Xsim <- rmh(fit, control=list(nrep=Nrep, expand=1.1, periodic=TRUE)) 426s + 426s + ## Extension of model to another window (thanks to Tuomas Rajala) 426s + Xsim <- rmh(fit, w=square(2)) 426s + Xsim <- simulate(fit, w=square(2)) 426s + 426s + ## Strauss - hard core process 426s + ## fit <- ppm(X ~1, StraussHard(r=7,hc=2)) 426s + ## Xsim <- rmh(fit, start=list(n.start=X$n)) 426s + 426s + ## Geyer saturation process 426s + ## fit <- ppm(X ~1, Geyer(r=7,sat=2)) 426s + ## Xsim <- rmh(fit, start=list(n.start=X$n)) 426s + 426s + ## Area-interaction process 426s + fit <- ppm(X ~1, AreaInter(r=7)) 426s + Xsim <- rmh(fit, start=list(n.start=X$n)) 426s + 426s + ## Penttinen process 426s + fit <- ppm(X ~1, Penttinen(r=7)) 426s + Xsim <- rmh(fit, start=list(n.start=X$n)) 426s + 426s + ## soft core interaction process 426s + ## X <- quadscheme(X, nd=50) 426s + ## fit <- ppm(X ~1, Softcore(kappa=0.1), correction="isotropic") 426s + ## Xsim <- rmh(fit, start=list(n.start=X$n)) 426s + 426s + ## Diggle-Gratton pairwise interaction model 426s + ## fit <- ppm(cells ~1, DiggleGratton(0.05, 0.1)) 426s + ## Xsim <- rmh(fit, start=list(n.start=cells$n)) 426s + ## plot(Xsim, main="simulation from fitted Diggle-Gratton model") 426s + 426s + 426s + ## piecewise-constant pairwise interaction function 426s + X <- rSSI(0.05, 100) 426s + fit <- ppm(X ~1, PairPiece(seq(0.02, 0.1, by=0.01))) 426s + Xsim <- rmh(fit) 426s + } 426s + 426s + ## marked point pattern 426s + Y <- amacrine 426s + 426s + if(FULLTEST) { 426s + #' marked Poisson models 426s + fit <- ppm(Y) 426s + Ysim <- rmh(fit) 426s + 426s + fit <- ppm(Y~marks) 426s + Ysim <- rmh(fit) 426s + 426s + fit <- ppm(Y~x) 426s + Ysim <- rmh(fit) 426s + 426s + fit <- ppm(Y~marks+x) 426s + Ysim <- rmh(fit) 426s + } 426s + 426s + if(ALWAYS) { 426s + #' multitype Strauss 426s + typ <- levels(Y$marks) 426s + MS <- MultiStrauss(types = typ, 426s + radii=matrix(0.07, ncol=2, nrow=2)) 426s + 426s + fit <- ppm(Y~marks*x, MS) 426s + Ysim <- rmh(fit) 426s + 426s + #' multitype Hardcore 426s + h0 <- minnndist(unmark(Y)) * 0.95 426s + MH <- MultiHard(types = typ, 426s + hradii=matrix(h0, ncol=2, nrow=2)) 426s + fit <- ppm(Y ~ marks+x, MH) 426s + Ysim <- rmh(fit) 426s + #' other code blocks 426s + Ysim <- rmh(fit, control=list(periodic=TRUE, expand=1)) 426s + Ysim <- rmh(fit, control=list(periodic=FALSE, expand=1)) 426s + #' multihard core with invalid initial state 426s + Ydouble <- superimpose(Y, rjitter(Y, h0/10)) 426s + Ysim <- rmh(fit, start=list(x.start=Ydouble)) 426s + 426s + #' Lennard-Jones 426s + fut <- ppm(unmark(longleaf) ~ 1, LennardJones(), rbord=1) 426s + Ysim <- rmh(fut) 426s + Ysim <- rmh(fut, control=list(periodic=TRUE, expand=1)) 426s + } 426s + 426s + spatstat.options(op) 426s + }) 426s Extracting model information...Evaluating trend...done. 426s Checking arguments..determining simulation windows...Starting simulation. 426s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 426s Extracting model information...Evaluating trend...done. 426s Checking arguments..determining simulation windows...Starting simulation. 426s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 426s Extracting model information...Evaluating trend...done. 426s Checking arguments..determining simulation windows...Starting simulation. 426s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 427s Extracting model information...Evaluating trend...done. 427s Checking arguments..determining simulation windows...Starting simulation. 427s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 427s Extracting model information...Evaluating trend...done. 427s Checking arguments..determining simulation windows...Starting simulation. 427s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 427s Model is invalid - projecting it 427s Extracting model information...Evaluating trend...done. 427s Checking arguments..determining simulation windows...Starting simulation. 427s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 428s Extracting model information...Evaluating trend...done. 428s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 428s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 429s Extracting model information...Evaluating trend...done. 429s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 429s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 429s Extracting model information...Evaluating trend...done. 429s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 429s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 429s Extracting model information...Evaluating trend...done. 429s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 429s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 429s Extracting model information...Evaluating trend...done. 429s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 429s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 430s Extracting model information...Evaluating trend...done. 430s Checking arguments..determining simulation windows...Starting simulation. 430s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 430s Extracting model information...Evaluating trend...done. 430s Checking arguments..determining simulation windows...Starting simulation. 430s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 430s > 430s > 430s > reset.spatstat.options() 430s > #' 430s > #' tests/rmhsnoopy.R 430s > #' 430s > #' Test the rmh interactive debugger 430s > #' 430s > #' $Revision: 1.11 $ $Date: 2022/10/23 01:19:00 $ 430s > 430s > if(ALWAYS) { # may depend on platform 430s + local({ 430s + R <- 0.1 430s + ## fit a model and prepare to simulate 430s + model <- ppm(amacrine ~ marks + x, Strauss(R)) 430s + siminfo <- rmh(model, preponly=TRUE) 430s + Wsim <- siminfo$control$internal$w.sim 430s + Wclip <- siminfo$control$internal$w.clip 430s + if(is.null(Wclip)) Wclip <- Window(cells) 430s + 430s + ## determine debugger interface panel geometry 430s + Xinit <- runifpoint(ex=amacrine)[1:40] 430s + P <- rmhsnoop(Wsim=Wsim, Wclip=Wclip, R=R, 430s + xcoords=Xinit$x, 430s + ycoords=Xinit$y, 430s + mlevels=levels(marks(Xinit)), 430s + mcodes=as.integer(marks(Xinit)) - 1L, 430s + irep=3L, itype=1L, 430s + proptype=1, proplocn=c(0.5, 0.5), propmark=0, propindx=0, 430s + numerator=42, denominator=24, 430s + panel.only=TRUE) 430s + boxes <- P$boxes 430s + clicknames <- names(P$clicks) 430s + boxcentres <- do.call(concatxy, lapply(boxes, centroid.owin)) 430s + 430s + ## design a sequence of clicks 430s + actionsequence <- c("Up", "Down", "Left", "Right", 430s + "At Proposal", "Zoom Out", "Zoom In", "Reset", 430s + "Accept", "Reject", "Print Info", 430s + "Next Iteration", "Next Shift", "Next Death", 430s + "Skip 10", "Skip 100", "Skip 1000", "Skip 10,000", 430s + "Skip 100,000", "Exit Debugger") 430s + actionsequence <- match(actionsequence, clicknames) 430s + actionsequence <- actionsequence[!is.na(actionsequence)] 430s + xy <- lapply(boxcentres, "[", actionsequence) 430s + 430s + ## queue the click sequence 430s + spatstat.utils::queueSpatstatLocator(xy$x,xy$y) 430s + 430s + ## go 430s + rmh(model, snoop=TRUE) 430s + }) 430s + } 430s Extracting model information...Evaluating trend...done. 430s Checking arguments..determining simulation windows...Evaluating trend integral...Extracting model information...Evaluating trend...done. 430s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 430s Initial state... 430s Creating debugger environment..Done. 431s Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 432s 432s 432s ------------------- 432s Iteration 0 432s Simulation window: 432s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 432s Clipping window: 432s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 432s Current state: 432s Marked planar point pattern: 72 points 432s Multitype, with levels = off, on 432s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 432s Proposal type: Shift 432s Shift data point 18 from current location (0.290108, 0.0160037, “off”) to 432s new location (0.620599, 0.378428, “off”) 432s Hastings ratio = 6831.92992943093 / 14545.6615344216 = 0.469688498750194 432s Fate of proposal: Rejected 435s Marked planar point pattern: 350 points 435s Multitype, with levels = off, on 435s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 435s Pattern was generated by Metropolis-Hastings simulation. 435s > 435s BEGIN TEST testsS.R 435s 435s R version 4.3.2 (2023-10-31) -- "Eye Holes" 435s Copyright (C) 2023 The R Foundation for Statistical Computing 435s Platform: s390x-ibm-linux-gnu (64-bit) 435s 435s R is free software and comes with ABSOLUTELY NO WARRANTY. 435s You are welcome to redistribute it under certain conditions. 435s Type 'license()' or 'licence()' for distribution details. 435s 435s R is a collaborative project with many contributors. 435s Type 'contributors()' for more information and 435s 'citation()' on how to cite R or R packages in publications. 435s 435s Type 'demo()' for some demos, 'help()' for on-line help, or 435s 'help.start()' for an HTML browser interface to help. 435s Type 'q()' to quit R. 435s 435s > #' 435s > #' Header for all (concatenated) test files 435s > #' 435s > #' Require spatstat.model 435s > #' Obtain environment variable controlling tests. 435s > #' 435s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 435s > 435s > require(spatstat.model) 435s Loading required package: spatstat.model 435s Loading required package: spatstat.data 437s Loading required package: spatstat.geom 437s spatstat.geom 3.2-8 437s Loading required package: spatstat.random 437s spatstat.random 3.2-2 437s Loading required package: spatstat.explore 437s Loading required package: nlme 437s spatstat.explore 3.2-5 437s Loading required package: rpart 437s spatstat.model 3.2-8 437s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 437s > ALWAYS <- TRUE 437s > cat(paste("--------- Executing", 437s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 437s + "test code -----------\n")) 437s --------- Executing **RESTRICTED** subset of test code ----------- 437s > # 437s > # tests/slrm.R 437s > # 437s > # $Revision: 1.3 $ $Date: 2020/05/01 09:59:59 $ 437s > # 437s > # Test slrm fitting and prediction when there are NA's 437s > # 437s > 437s > if(ALWAYS) { 437s + local({ 437s + X <- copper$SouthPoints 437s + W <- owin(poly=list(x=c(0,35,35,1),y=c(1,1,150,150))) 437s + Y <- X[W] 437s + fit <- slrm(Y ~ x+y) 437s + pred <- predict(fit) 437s + extractAIC(fit) 437s + fitx <- update(fit, . ~ x) 437s + simulate(fitx, seed=42) 437s + if(FULLTEST) { 437s + unitname(fitx) 437s + unitname(fitx) <- "km" 437s + 437s + mur <- solapply(murchison,rescale, 1000, "km") 437s + mur$dfault <- distfun(mur$faults) 437s + fut <- slrm(gold ~ dfault, data=mur, splitby="greenstone") 437s + A <- model.images(fut) 437s + } 437s + }) 437s + } 437s > 437s > 437s > # 437s > # tests/step.R 437s > # 437s > # $Revision: 1.5 $ $Date: 2020/05/01 09:59:59 $ 437s > # 437s > # test for step() operation 437s > # 437s > if(FULLTEST) { 437s + local({ 437s + Z <- as.im(function(x,y){ x^3 - y^2 }, nztrees$window) 437s + fitP <- ppm(nztrees ~x+y+Z, covariates=list(Z=Z)) 437s + step(fitP) 437s + fitS <- update(fitP, Strauss(7)) 437s + step(fitS) 437s + fitM <- ppm(amacrine ~ marks*(x+y), 437s + MultiStrauss(types=levels(marks(amacrine)), radii=matrix(0.04, 2, 2))) 437s + step(fitM) 437s + }) 437s + } 437s > 437s > 437s > 437s > 438s BEGIN TEST testsT.R 438s 438s R version 4.3.2 (2023-10-31) -- "Eye Holes" 438s Copyright (C) 2023 The R Foundation for Statistical Computing 438s Platform: s390x-ibm-linux-gnu (64-bit) 438s 438s R is free software and comes with ABSOLUTELY NO WARRANTY. 438s You are welcome to redistribute it under certain conditions. 438s Type 'license()' or 'licence()' for distribution details. 438s 438s R is a collaborative project with many contributors. 438s Type 'contributors()' for more information and 438s 'citation()' on how to cite R or R packages in publications. 438s 438s Type 'demo()' for some demos, 'help()' for on-line help, or 438s 'help.start()' for an HTML browser interface to help. 438s Type 'q()' to quit R. 438s 438s > #' 438s > #' Header for all (concatenated) test files 438s > #' 438s > #' Require spatstat.model 438s > #' Obtain environment variable controlling tests. 438s > #' 438s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 438s > 438s > require(spatstat.model) 438s Loading required package: spatstat.model 438s Loading required package: spatstat.data 439s Loading required package: spatstat.geom 439s spatstat.geom 3.2-8 439s Loading required package: spatstat.random 439s spatstat.random 3.2-2 439s Loading required package: spatstat.explore 439s Loading required package: nlme 439s spatstat.explore 3.2-5 439s Loading required package: rpart 439s spatstat.model 3.2-8 439s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 439s > ALWAYS <- TRUE 439s > cat(paste("--------- Executing", 439s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 439s + "test code -----------\n")) 439s --------- Executing **RESTRICTED** subset of test code ----------- 439s > # 439s > # tests/testaddvar.R 439s > # 439s > # test addvar options 439s > # 439s > # $Revision: 1.3 $ $Date: 2020/05/02 01:32:58 $ 439s > 439s > if(FULLTEST) { 439s + local({ 439s + X <- rpoispp(function(x,y){exp(3+3*x)}) 439s + model <- ppm(X ~y) 439s + addvar(model, "x", crosscheck=TRUE) 439s + addvar(model, "x", bw.input="quad") 439s + w <- square(0.5) 439s + addvar(model, "x", subregion=w) 439s + addvar(model, "x", subregion=w, bw.input="points") 439s + Z <- as.im(function(x,y) { x }, Window(X)) 439s + addvar(model, Z) 439s + }) 439s + } 439s > # 439s > # tests/testparres.R 439s > # 439s > # additional test of parres 439s > # 439s > # $Revision: 1.8 $ $Date: 2022/05/20 06:59:59 $ 439s > # 439s > 439s > if(FULLTEST) { 439s + local({ 439s + X <- rpoispp(function(x,y){exp(3+x+2*x^2)}) 439s + model <- ppm(X ~x+y) 439s + 439s + # options in parres (and code blocks in print.parres) 439s + parres(model, "x") 439s + parres(model, "x", smooth.effect=TRUE) 439s + parres(model, "x", bw.input="quad") 439s + w <- square(0.5) 439s + parres(model, "x", subregion=w) 439s + parres(model, "x", subregion=w, bw.input="quad") 439s + f <- function(x,y) { x + y } 439s + parres(model, f) 439s + 439s + # check whether 'update.ppm' has messed up internals 439s + mod2 <- update(model, ~x) 439s + parres(mod2, "x") 439s + 439s + #' other kinds of covariates 439s + mod3 <- ppm(X ~ x + offset(y)) 439s + parres(mod3, "offset(y)") 439s + Z <- distmap(runifpoint(3)) 439s + parres(mod3, Z) 439s + mod4 <- ppm(X ~ sin(x), data=solist(B=Z)) 439s + parres(mod4, "sin(x)") 439s + parres(mod4, "B") 439s + 439s + #' models with interaction 439s + mod5 <- ppm(cells ~ x, AreaInter(0.06)) 439s + parres(mod5, "x") 439s + dlin <- distfun(copper$SouthLines) 439s + copfit <- ppm(copper$SouthPoints ~ dlin, Geyer(1,1)) 439s + parres(copfit, "dlin") 439s + 439s + #' covariate need not be specified if there is only one. 439s + parres(mod5) 439s + parres(copfit) 439s + 439s + #' infrastructure 439s + ltuae <- evaluateCovariate(42, cells) 439s + LTUAE <- evaluateCovariate(ltuae, cells) 439s + 439s + fit <- ppm(amacrine ~ x * marks, nd=16) 439s + dmat <- model.depends(fit) 439s + check.separable(dmat, "x", c(x=FALSE, marks=FALSE), FALSE) 439s + check.separable(dmat, "x", c(FALSE, FALSE), FALSE) 439s + check.separable(dmat, "x", c(x=FALSE, marks=TRUE), FALSE) 439s + }) 439s + } 439s > #' 439s > #' tests/threedee.R 439s > #' 439s > #' Tests of 3D code 439s > #' 439s > #' $Revision: 1.8 $ $Date: 2020/05/02 01:32:58 $ 439s > #' 439s > 439s > local({ 439s + X <- runifpoint3(30) 439s + Y <- runifpoint3(20) 439s + if(FULLTEST) { 439s + A <- runifpoint3(10, nsim=2) 439s + Z <- ppsubset(X, 2:4) 439s + } 439s + ## 439s + if(ALWAYS) { # includes C code 439s + d <- pairdist(X, periodic=TRUE, squared=TRUE) 439s + d <- crossdist(X, Y, squared=TRUE) 439s + d <- crossdist(X, Y, squared=TRUE, periodic=TRUE) 439s + #' 439s + h <- has.close(X, 0.2) 439s + h <- has.close(X, 0.2, periodic=TRUE) 439s + h <- has.close(X, 0.2, Y=Y) 439s + h <- has.close(X, 0.2, Y=Y, periodic=TRUE) 439s + #' code blocks not otherwise reached 439s + rmax <- 0.6 * max(nndist(X)) 439s + g <- G3est(X, rmax=rmax, correction="rs") 439s + g <- G3est(X, rmax=rmax, correction="km") 439s + g <- G3est(X, rmax=rmax, correction="Hanisch") 439s + g <- G3est(X, rmax=rmax, sphere="ideal") 439s + g <- G3est(X, rmax=rmax, sphere="digital") 439s + v <- sphere.volume() 439s + v <- digital.volume() 439s + #' older code 439s + co <- coords(X) 439s + xx <- co$x 439s + yy <- co$y 439s + zz <- co$z 439s + gg1 <- g3engine(xx, yy, zz, correction="Hanisch G3") 439s + gg2 <- g3engine(xx, yy, zz, correction="minus sampling") 439s + ff1 <- f3engine(xx, yy, zz, correction="no") 439s + ff2 <- f3engine(xx, yy, zz, correction="minus sampling") 439s + } 439s + ## 439s + if(ALWAYS) { 439s + #'class support 439s + X <- runifpoint3(10) 439s + print(X) 439s + print(X %mark% runif(10)) 439s + print(X %mark% factor(letters[c(1:5,5:1)])) 439s + print(X %mark% data.frame(a=1:10, b=runif(10))) 439s + da <- as.Date(paste0("2020-01-0", c(1:5,5:1))) 439s + print(X %mark% da) 439s + print(X %mark% data.frame(a=1:10, b=da)) 439s + } 439s + }) 439s Three-dimensional point pattern: 10 points 439s Box: [0, 1] x [0, 1] x [0, 1] units 439s Marked three-dimensional point pattern: 10 points 439s marks are numeric, of storage type ‘double’ 439s Box: [0, 1] x [0, 1] x [0, 1] units 439s Marked three-dimensional point pattern: 10 points 439s Multitype, with levels = a, b, c, d, e 439s Box: [0, 1] x [0, 1] x [0, 1] units 439s Marked three-dimensional point pattern: 10 points 439s Mark variables: a, b 439s Box: [0, 1] x [0, 1] x [0, 1] units 439s Marked three-dimensional point pattern: 10 points 439s marks are dates, of class ‘Date’ 439s Box: [0, 1] x [0, 1] x [0, 1] units 439s Marked three-dimensional Warning messages: 439s 1: In G3est: unrecognised argument ‘sphere’ was ignored 439s 2: In G3est: unrecognised argument ‘sphere’ was ignored 439s point pattern: 10 points 439s Mark variables: a, b 439s Box: [0, 1] x [0, 1] x [0, 1] units 439s > # 439s > # tests/triplets.R 439s > # 439s > # test code for triplet interaction 439s > # 439s > # $Revision: 1.9 $ $Date: 2022/05/22 08:45:38 $ 439s > # 439s > if(ALWAYS) { # C code, platform dependence 439s + local({ 439s + #' valid model 439s + fit <- ppm(cells ~1, Triplets(0.1)) 439s + fit 439s + suffstat(fit) 439s + #' invalid model 439s + fitR <- ppm(redwood ~1, Triplets(0.1)) 439s + fitR 439s + suffstat(fitR) 439s + #' hard core (zero triangles, coefficient is NA) 439s + fit0 <- ppm(cells ~1, Triplets(0.05)) 439s + fit0 439s + suffstat(fit0) 439s + #' bug case (1 triangle in data) 439s + fit1 <- ppm(cells ~1, Triplets(0.15)) 439s + fit1 439s + suffstat(fit1) 439s + #' simulation 439s + X <- simulate(fit) 439s + mod <- list(cif="triplets",par=list(beta=50,gamma=0.2,r=0.07), w=square(1)) 439s + Xm <- rmh(model=mod,start=list(n.start=5), control=list(nrep=1e5)) 439s + #' hard core 439s + mod$par$gamma <- 0 439s + XmHard <- rmh(model=mod,start=list(n.start=5), control=list(nrep=1e5)) 439s + }) 439s + } 442s Checking arguments..determining simulation windows...Starting simulation. 442s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 442s Checking arguments..determining simulation windows...Starting simulation. 442s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 443s > 443s BEGIN TEST testsUtoZ.R 443s 443s R version 4.3.2 (2023-10-31) -- "Eye Holes" 443s Copyright (C) 2023 The R Foundation for Statistical Computing 443s Platform: s390x-ibm-linux-gnu (64-bit) 443s 443s R is free software and comes with ABSOLUTELY NO WARRANTY. 443s You are welcome to redistribute it under certain conditions. 443s Type 'license()' or 'licence()' for distribution details. 443s 443s R is a collaborative project with many contributors. 443s Type 'contributors()' for more information and 443s 'citation()' on how to cite R or R packages in publications. 443s 443s Type 'demo()' for some demos, 'help()' for on-line help, or 443s 'help.start()' for an HTML browser interface to help. 443s Type 'q()' to quit R. 443s 443s > #' 443s > #' Header for all (concatenated) test files 443s > #' 443s > #' Require spatstat.model 443s > #' Obtain environment variable controlling tests. 443s > #' 443s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 443s > 443s > require(spatstat.model) 443s Loading required package: spatstat.model 443s Loading required package: spatstat.data 444s Loading required package: spatstat.geom 444s spatstat.geom 3.2-8 444s Loading required package: spatstat.random 444s spatstat.random 3.2-2 444s Loading required package: spatstat.explore 444s Loading required package: nlme 445s spatstat.explore 3.2-5 445s Loading required package: rpart 445s spatstat.model 3.2-8 445s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 445s > ALWAYS <- TRUE 445s > cat(paste("--------- Executing", 445s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 445s + "test code -----------\n")) 445s --------- Executing **RESTRICTED** subset of test code ----------- 445s > # 445s > # tests/undoc.R 445s > # 445s > # $Revision: 1.16 $ $Date: 2020/11/02 07:06:49 $ 445s > # 445s > # Test undocumented hacks, experimental code, etc 445s > 445s > 445s > local({ 445s + if(FULLTEST) { 445s + ## cases of 'pickoption' 445s + aliases <- c(Lenin="Ulyanov", Stalin="Djugashvili", Trotsky="Bronstein") 445s + surname <- "Trot" 445s + pickoption("leader", surname, aliases) 445s + pickoption("leader", surname, aliases, exact=TRUE, die=FALSE) 445s + } 445s + if(ALWAYS) { 445s + ## pixellate.ppp accepts a data frame of weights 445s + pixellate(cells, weights=data.frame(a=1:42, b=42:1)) 445s + ## test parts of 'rmhsnoop' that don't require interaction with user 445s + rmhSnoopEnv(cells, Window(cells), 0.1) 445s + } 445s + if(FULLTEST) { 445s + ## Berman-Turner frame 445s + A <- bt.frame(quadscheme(cells), ~x, Strauss(0.07), rbord=0.07) 445s + print(A) 445s + ## digestCovariates 445s + D <- distfun(cells) 445s + Z <- distmap(cells) 445s + U <- dirichlet(cells) 445s + stopifnot(is.scov(D)) 445s + stopifnot(is.scov(Z)) 445s + stopifnot(is.scov(U)) 445s + stopifnot(is.scov("x")) 445s + dg <- digestCovariates(D=D,Z=Z,U=U,"x",list(A="x", B=D)) 445s + ## 445s + a <- getfields(dg, c("A", "D", "niets"), fatal=FALSE) 445s + ## util.R 445s + gg <- pointgrid(owin(), 7) 445s + checkbigmatrix(1000000L, 1000000L, FALSE, TRUE) 445s + spatstatDiagnostic("whatever") 445s + M <- list(list(a=2, b=FALSE), 445s + list(a=2, b=TRUE)) 445s + stopifnot(!allElementsIdentical(M)) 445s + stopifnot(allElementsIdentical(M, "a")) 445s + ## 445s + A <- Strauss(0.1) 445s + A <- reincarnate.interact(A) 445s + ## 445s + ## special lists 445s + B <- solist(a=cells, b=redwood, c=japanesepines) 445s + BB <- as.ppplist(B) 445s + BL <- as.layered(B) 445s + DB <- as.imlist(lapply(B, density)) 445s + is.solist(B) 445s + is.ppplist(B) 445s + is.imlist(DB) 445s + ## case of density.ppplist 445s + DEB <- density(BB, se=TRUE) 445s + } 445s + 445s + if(ALWAYS) { 445s + ## fft 445s + z <- matrix(1:16, 4, 4) 445s + a <- fft2D(z, west=FALSE) 445s + if(fftwAvailable()) 445s + b <- fft2D(z, west=TRUE) 445s + } 445s + 445s + if(ALWAYS) { 445s + ## experimental interactions 445s + pot <- function(d, par) { d <= 0.1 } 445s + A <- Saturated(pot) 445s + print(A) 445s + A <- update(A, name="something") 445s + ppm(amacrine ~ x, A, rbord=0.1) 445s + } 445s + 445s + if(ALWAYS) { # platform dependent 445s + #' version-checking 445s + now <- Sys.Date() 445s + versioncurrency.spatstat(now + 80, FALSE) 445s + versioncurrency.spatstat(now + 140, FALSE) 445s + versioncurrency.spatstat(now + 400, FALSE) 445s + versioncurrency.spatstat(now + 1000) 445s + } 445s + 445s + if(FULLTEST) { 445s + #' general Ord interaction 445s + gradual <- function(d, pars) { 445s + y <- pmax(0, 0.005 - d)/0.005 445s + if(is.matrix(d)) y <- matrix(y, nrow(d), ncol(d)) 445s + return(y) 445s + } 445s + B <- Ord(gradual, "gradual Ord process") 445s + } 445s + }) 445s Saturated pairwise interaction family 445s Interaction:Saturated process with user-defined potential 445s Potential function: 445s function (d, par) 445s { 445s d <= 0.1 445s } 445s 445s > 445s > 445s > ## 445s > ## tests/updateppm.R 445s > ## 445s > ## Check validity of update.ppm 445s > ## 445s > ## $Revision: 1.8 $ $Date: 2022/10/23 01:19:19 $ 445s > 445s > local({ 445s + if(ALWAYS) { 445s + require(spatstat.utils) 445s + h <- function(m1, m2) { 445s + mc <- short.deparse(sys.call()) 445s + cat(paste(mc, "\t... ")) 445s + m1name <- short.deparse(substitute(m1)) 445s + m2name <- short.deparse(substitute(m2)) 445s + if(!identical(names(coef(m1)), names(coef(m2)))) 445s + stop(paste("Differing results for", m1name, "and", m2name, 445s + "in updateppm.R"), 445s + call.=FALSE) 445s + cat("OK\n") 445s + } 445s + 445s + X <- redwood[c(TRUE,FALSE)] 445s + Y <- redwood[c(FALSE,TRUE)] 445s + fit0f <- ppm(X ~ 1, nd=8) 445s + fit0p <- ppm(X, ~1, nd=8) 445s + fitxf <- ppm(X ~ x, nd=8) 445s + fitxp <- ppm(X, ~x, nd=8) 445s + 445s + cat("Basic consistency ...\n") 445s + h(fit0f, fit0p) 445s + h(fitxf, fitxp) 445s + 445s + cat("\nTest correct handling of model formulas ...\n") 445s + h(update(fitxf, Y), fitxf) 445s + h(update(fitxf, Q=Y), fitxf) 445s + h(update(fitxf, Y~x), fitxf) 445s + h(update(fitxf, Q=Y~x), fitxf) 445s + h(update(fitxf, ~x), fitxf) 445s + Loading required package: spatstat.utils 445s } 445s + 445s + if(FULLTEST) { 445s + h(update(fitxf, Y~1), fit0f) 445s + h(update(fitxf, ~1), fit0f) 445s + h(update(fit0f, Y~x), fitxf) 445s + h(update(fit0f, ~x), fitxf) 445s + 445s + h(update(fitxp, Y), fitxp) 445s + h(update(fitxp, Q=Y), fitxp) 445s + h(update(fitxp, Y~x), fitxp) 445s + h(update(fitxp, Q=Y~x), fitxp) 445s + h(update(fitxp, ~x), fitxp) 445s + 445s + h(update(fitxp, Y~1), fit0p) 445s + h(update(fitxp, ~1), fit0p) 445s + h(update(fit0p, Y~x), fitxp) 445s + h(update(fit0p, ~x), fitxp) 445s + } 445s + 445s + if(ALWAYS) { 445s + cat("\nTest scope handling for left hand side ...\n") 445s + X <- Y 445s + h(update(fitxf), fitxf) 445s + } 445s + 445s + if(ALWAYS) { 445s + cat("\nTest scope handling for right hand side ...\n") 445s + Z <- distmap(X) 445s + fitZf <- ppm(X ~ Z) 445s + fitZp <- ppm(X, ~ Z) 445s + h(update(fitxf, X ~ Z), fitZf) 445s + } 445s + if(FULLTEST) { 445s + h(update(fitxp, X ~ Z), fitZp) 445s + h(update(fitxf, . ~ Z), fitZf) 445s + h(update(fitZf, . ~ x), fitxf) 445s + h(update(fitZf, . ~ . - Z), fit0f) 445s + h(update(fitxp, . ~ Z), fitZp) 445s + h(update(fitZp, . ~ . - Z), fit0p) 445s + h(update(fit0p, . ~ . + Z), fitZp) 445s + h(update(fitZf, . ~ . ), fitZf) 445s + h(update(fitZp, . ~ . ), fitZp) 445s + } 445s + if(ALWAYS) { 445s + cat("\nTest use of internal data ...\n") 445s + h(update(fitZf, ~ x, use.internal=TRUE), fitxf) 445s + fitsin <- update(fitZf, X~sin(Z)) 445s + h(update(fitZf, ~ sin(Z), use.internal=TRUE), fitsin) 445s + } 445s + if(FULLTEST) { 445s + cat("\nTest step() ... ") 445s + fut <- ppm(X ~ Z + x + y, nd=8) 445s + fut0 <- step(fut, trace=0) 445s + cat("OK\n") 445s + } 445s + 445s + }) 445s Basic consistency ... 445s h(fit0f, fit0p) ... OK 445s h(fitxf, fitxp) ... OK 445s 445s Test correct handling of model formulas ... 445s h(update(fitxf, Y), fitxf) ... OK 445s h(update(fitxf, Q = Y), fitxf) ... OK 445s h(update(fitxf, Y ~ x), fitxf) ... OK 445s h(update(fitxf, Q = Y ~ x), fitxf) ... OK 445s h(update(fitxf, ~x), fitxf) ... OK 445s 445s Test scope handling for left hand side ... 445s h(update(fitxf), fitxf) ... OK 445s 445s Test scope handling for right hand side ... 445s h(update(fitxf, X ~ Z), fitZf) ... OK 445s 445s Test use of internal data ... 445s h(update(fitZf, ~x, use.internal = TRUE), fitxf) ... OK 445s h(update(fitZf, ~sin(Z), use.internal = TRUE), fitsin) ... OK 445s > # 445s > # tests/vcovppm.R 445s > # 445s > # Check validity of vcov.ppm algorithms 445s > # 445s > # Thanks to Ege Rubak 445s > # 445s > # $Revision: 1.12 $ $Date: 2020/05/02 01:32:58 $ 445s > # 445s > 445s > local({ 445s + 445s + set.seed(42) 445s + X <- rStrauss(200, .5, .05) 445s + model <- ppm(X, inter = Strauss(.05)) 445s + 445s + if(ALWAYS) { 445s + b <- vcov(model, generic = TRUE, algorithm = "basic") 445s + v <- vcov(model, generic = TRUE, algorithm = "vector") 445s + vc <- vcov(model, generic = TRUE, algorithm = "vectorclip") 445s + vn <- vcov(model, generic = FALSE) 445s + 445s + disagree <- function(x, y, tol=1e-7) { max(abs(x-y)) > tol } 445s + asymmetric <- function(x) { disagree(x, t(x)) } 445s + 445s + if(asymmetric(b)) 445s + stop("Non-symmetric matrix produced by vcov.ppm 'basic' algorithm") 445s + if(asymmetric(v)) 445s + stop("Non-symmetric matrix produced by vcov.ppm 'vector' algorithm") 445s + if(asymmetric(vc)) 445s + stop("Non-symmetric matrix produced by vcov.ppm 'vectorclip' algorithm") 445s + if(asymmetric(vn)) 445s + stop("Non-symmetric matrix produced by vcov.ppm Strauss algorithm") 445s + 445s + if(disagree(v, b)) 445s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'basic' ") 445s + if(disagree(v, vc)) 445s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'vectorclip' ") 445s + if(disagree(vn, vc)) 445s + stop("Disagreement between vcov.ppm generic and Strauss algorithms") 445s + } 445s + 445s + if(ALWAYS) { # C code 445s + ## Geyer code 445s + xx <- c(0.7375956, 0.6851697, 0.6399788, 0.6188382) 445s + yy <- c(0.5816040, 0.6456319, 0.5150633, 0.6191592) 445s + Y <- ppp(xx, yy, window=square(1)) 445s + modelY <- ppm(Y ~1, Geyer(0.1, 1)) 445s + 445s + b <- vcov(modelY, generic = TRUE, algorithm = "basic") 445s + v <- vcov(modelY, generic = TRUE, algorithm = "vector") 445s + vc <- vcov(modelY, generic = TRUE, algorithm = "vectorclip") 445s + 445s + if(asymmetric(b)) 445s + stop("Non-symmetric matrix produced by vcov.ppm 'basic' algorithm for Geyer model") 445s + if(asymmetric(v)) 445s + stop("Non-symmetric matrix produced by vcov.ppm 'vector' algorithm for Geyer model") 445s + if(asymmetric(vc)) 445s + stop("Non-symmetric matrix produced by vcov.ppm 'vectorclip' algorithm for Geyer model") 445s + 445s + if(disagree(v, b)) 445s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'basic' for Geyer model") 445s + if(disagree(v, vc)) 445s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'vectorclip' for Geyer model") 445s + } 445s + 445s + if(ALWAYS) { # C code 445s + ## tests of 'deltasuffstat' code 445s + ## Handling of offset terms 445s + modelH <- ppm(cells ~x, Hardcore(0.05)) 445s + a <- vcov(modelH, generic=TRUE) ## may fall over 445s + b <- vcov(modelH, generic=FALSE) 445s + if(disagree(a, b)) 445s + stop("Disagreement between vcov.ppm algorithms for Hardcore model") 445s + 445s + ## Correctness of pairwise.family$delta2 445s + modelZ <- ppm(amacrine ~1, MultiStrauss(radii=matrix(0.1, 2, 2))) 445s + b <- vcov(modelZ, generic=FALSE) 445s + g <- vcov(modelZ, generic=TRUE) 445s + if(disagree(b, g)) 445s + stop("Disagreement between vcov.ppm algorithms for MultiStrauss model") 445s + 445s + ## Test that 'deltasuffstat' works for Hybrids 445s + modelHyb <- ppm(japanesepines ~ 1, Hybrid(Strauss(0.05), Strauss(0.1))) 445s + vHyb <- vcov(modelHyb) 445s + } 445s + 445s + if(FULLTEST) { 445s + ## Code blocks for other choices of 'what' 445s + model <- ppm(X ~ 1, Strauss(.05)) 445s + cG <- vcov(model, what="corr") 445s + cP <- vcov(update(model, Poisson()), what="corr") 445s + ## outdated usage 445s + cX <- vcov(model, A1dummy=TRUE) 445s + 445s + ## Model with zero-length coefficient vector 445s + lam <- intensity(X) 445s + f <- function(x,y) { rep(lam, length(x)) } 445s + model0 <- ppm(X ~ offset(log(f)) - 1) 445s + dd <- vcov(model0) 445s + cc <- vcov(model0, what="corr") 445s + 445s + ## Model with NA coefficients 445s + fit <- ppm(X ~ log(f)) 445s + vcov(fit) 445s + fitE <- emend(fit, trace=TRUE) 445s + 445s + ## Other weird stuff 445s + su <- suffloc(ppm(X ~ x)) 445s + } 445s + }) 448s > 449s autopkgtest [16:17:44]: test run-unit-test: -----------------------] 450s autopkgtest [16:17:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 450s run-unit-test PASS 450s autopkgtest [16:17:45]: test pkg-r-autopkgtest: preparing testbed 558s autopkgtest [16:19:33]: testbed dpkg architecture: s390x 559s autopkgtest [16:19:34]: testbed apt version: 2.7.12 559s autopkgtest [16:19:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 559s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 559s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 559s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 560s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 560s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 560s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [652 kB] 560s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 560s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 560s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 560s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4143 kB] 560s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 560s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [46.8 kB] 560s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 563s Fetched 9495 kB in 3s (3547 kB/s) 563s Reading package lists... 565s Reading package lists... 566s Building dependency tree... 566s Reading state information... 566s Calculating upgrade... 566s The following packages will be upgraded: 566s cloud-init debianutils fonts-ubuntu-console libbsd0 libc-bin libc6 locales 566s python3-markupsafe 566s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 566s Need to get 8499 kB of archives. 566s After this operation, 9216 B disk space will be freed. 566s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.17 [90.1 kB] 566s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libc6 s390x 2.39-0ubuntu6 [2847 kB] 567s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libc-bin s390x 2.39-0ubuntu6 [654 kB] 567s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libbsd0 s390x 0.12.1-1 [46.7 kB] 567s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x locales all 2.39-0ubuntu6 [4232 kB] 567s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 567s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x python3-markupsafe s390x 2.1.5-1build1 [12.8 kB] 567s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x cloud-init all 24.1.2-0ubuntu1 [597 kB] 568s Preconfiguring packages ... 568s Fetched 8499 kB in 1s (8901 kB/s) 568s (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 ... 51778 files and directories currently installed.) 568s Preparing to unpack .../debianutils_5.17_s390x.deb ... 568s Unpacking debianutils (5.17) over (5.16) ... 568s Setting up debianutils (5.17) ... 568s (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 ... 51778 files and directories currently installed.) 568s Preparing to unpack .../libc6_2.39-0ubuntu6_s390x.deb ... 568s Unpacking libc6:s390x (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 568s Setting up libc6:s390x (2.39-0ubuntu6) ... 569s (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 ... 51778 files and directories currently installed.) 569s Preparing to unpack .../libc-bin_2.39-0ubuntu6_s390x.deb ... 569s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 569s Setting up libc-bin (2.39-0ubuntu6) ... 569s (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 ... 51778 files and directories currently installed.) 569s Preparing to unpack .../libbsd0_0.12.1-1_s390x.deb ... 569s Unpacking libbsd0:s390x (0.12.1-1) over (0.11.8-1) ... 569s Preparing to unpack .../locales_2.39-0ubuntu6_all.deb ... 569s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 569s Preparing to unpack .../fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 569s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 569s Preparing to unpack .../python3-markupsafe_2.1.5-1build1_s390x.deb ... 569s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 569s Preparing to unpack .../cloud-init_24.1.2-0ubuntu1_all.deb ... 570s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 570s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 570s Setting up cloud-init (24.1.2-0ubuntu1) ... 572s Setting up locales (2.39-0ubuntu6) ... 572s Generating locales (this might take a while)... 574s en_US.UTF-8... done 574s Generation complete. 574s Setting up python3-markupsafe (2.1.5-1build1) ... 574s Setting up libbsd0:s390x (0.12.1-1) ... 574s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 575s Processing triggers for man-db (2.12.0-3) ... 575s Processing triggers for libc-bin (2.39-0ubuntu6) ... 576s Reading package lists... 577s Building dependency tree... 577s Reading state information... 577s 0 upgraded, 0 newly installed, 0 to remove and 234 not upgraded. 577s Unknown architecture, assuming PC-style ttyS0 577s sh: Attempting to set up Debian/Ubuntu apt sources automatically 577s sh: Distribution appears to be Ubuntu 578s Reading package lists... 579s Building dependency tree... 579s Reading state information... 579s eatmydata is already the newest version (131-1). 579s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 579s Reading package lists... 579s Building dependency tree... 579s Reading state information... 579s dbus is already the newest version (1.14.10-4ubuntu1). 579s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 579s Reading package lists... 580s Building dependency tree... 580s Reading state information... 580s rng-tools-debian is already the newest version (2.4). 580s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 580s Reading package lists... 580s Building dependency tree... 580s Reading state information... 581s The following packages will be REMOVED: 581s cloud-init* python3-configobj* python3-debconf* 581s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 581s After this operation, 3256 kB disk space will be freed. 581s (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 ... 51777 files and directories currently installed.) 581s Removing cloud-init (24.1.2-0ubuntu1) ... 581s Removing python3-configobj (5.0.8-3) ... 581s Removing python3-debconf (1.5.86) ... 582s Processing triggers for man-db (2.12.0-3) ... 582s (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 ... 51388 files and directories currently installed.) 582s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 582s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 582s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 582s invoke-rc.d: policy-rc.d denied execution of try-restart. 583s Reading package lists... 583s Building dependency tree... 583s Reading state information... 583s linux-generic is already the newest version (6.8.0-11.11+1). 583s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 584s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 584s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 584s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 587s Reading package lists... 587s Reading package lists... 587s Building dependency tree... 587s Reading state information... 587s Calculating upgrade... 587s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 587s Reading package lists... 588s Building dependency tree... 588s Reading state information... 588s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 588s autopkgtest [16:20:03]: rebooting testbed after setup commands that affected boot 618s Reading package lists... 618s Building dependency tree... 618s Reading state information... 619s Starting pkgProblemResolver with broken count: 0 619s Starting 2 pkgProblemResolver with broken count: 0 619s Done 619s The following additional packages will be installed: 619s build-essential cpp cpp-13 cpp-13-s390x-linux-gnu cpp-s390x-linux-gnu 619s dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 619s fonts-mathjax g++ g++-13 g++-13-s390x-linux-gnu g++-s390x-linux-gnu gcc 619s gcc-13 gcc-13-base gcc-13-s390x-linux-gnu gcc-s390x-linux-gnu gfortran 619s gfortran-13 gfortran-13-s390x-linux-gnu gfortran-s390x-linux-gnu 619s icu-devtools libasan8 libatomic1 libblas-dev libblas3 libbz2-dev 619s libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdatrie1 619s libdeflate0 libfontconfig1 libfreetype6 libgcc-13-dev libgfortran-13-dev 619s libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b 619s libice6 libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 619s libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-mathjax liblapack-dev 619s liblapack3 liblzma-dev libmpc3 libncurses-dev libpango-1.0-0 619s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-16-0 619s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 619s libpng-dev libreadline-dev libsharpyuv0 libsm6 libstdc++-13-dev libtcl8.6 619s libthai-data libthai0 libtiff6 libtk8.6 libubsan1 libwebp7 libxcb-render0 619s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 linux-libc-dev littler 619s pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev 619s r-cran-abind r-cran-codetools r-cran-deldir r-cran-foreach r-cran-glmnet 619s r-cran-goftest r-cran-gsl r-cran-iterators r-cran-lattice r-cran-littler 619s r-cran-matrix r-cran-mgcv r-cran-nleqslv r-cran-nlme r-cran-pkgkitten 619s r-cran-polyclip r-cran-rcpp r-cran-rcppeigen r-cran-rpart r-cran-shape 619s r-cran-sm r-cran-spatial r-cran-spatstat r-cran-spatstat.data 619s r-cran-spatstat.explore r-cran-spatstat.geom r-cran-spatstat.linnet 619s r-cran-spatstat.model r-cran-spatstat.random r-cran-spatstat.sparse 619s r-cran-spatstat.utils r-cran-survival r-cran-tensor rpcsvc-proto unzip 619s x11-common xdg-utils zip zlib1g-dev 619s Suggested packages: 619s cpp-doc gcc-13-locales cpp-13-doc debtags g++-multilib g++-13-multilib 619s gcc-13-doc gcc-multilib manpages-dev autoconf automake libtool flex bison 619s gdb gcc-doc gcc-13-multilib gdb-s390x-linux-gnu gfortran-multilib 619s gfortran-doc gfortran-13-multilib gfortran-13-doc libcoarrays-dev 619s liblapack-doc glibc-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info 619s | gsl-ref-html icu-doc fonts-mathjax-extras fonts-stix libjs-mathjax-doc 619s liblzma-doc ncurses-doc readline-doc libstdc++-13-doc tcl8.6 tk8.6 elpa-ess 619s r-doc-info | r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base 619s texlive-plain-generic texlive-fonts-recommended texlive-fonts-extra 619s texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo 619s r-cran-knitr r-cran-testthat r-cran-xfun r-cran-rmarkdown r-cran-getopt 619s r-cran-inline 619s Recommended packages: 619s bzip2-doc manpages manpages-dev libc-devtools libpng-tools r-recommended 619s r-doc-html r-cran-locfit libfile-mimeinfo-perl libnet-dbus-perl 619s libx11-protocol-perl x11-utils x11-xserver-utils 619s The following NEW packages will be installed: 619s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-s390x-linux-gnu 619s cpp-s390x-linux-gnu dctrl-tools fontconfig fontconfig-config 619s fonts-dejavu-core fonts-dejavu-mono fonts-mathjax g++ g++-13 619s g++-13-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-13 gcc-13-base 619s gcc-13-s390x-linux-gnu gcc-s390x-linux-gnu gfortran gfortran-13 619s gfortran-13-s390x-linux-gnu gfortran-s390x-linux-gnu icu-devtools libasan8 619s libatomic1 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev libcairo2 619s libcc1-0 libcrypt-dev libdatrie1 libdeflate0 libfontconfig1 libfreetype6 619s libgcc-13-dev libgfortran-13-dev libgfortran5 libgomp1 libgraphite2-3 619s libgsl27 libgslcblas0 libharfbuzz0b libice6 libicu-dev libisl23 libitm1 619s libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev 619s libjs-mathjax liblapack-dev liblapack3 liblzma-dev libmpc3 libncurses-dev 619s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 619s libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 619s libpixman-1-0 libpkgconf3 libpng-dev libreadline-dev libsharpyuv0 libsm6 619s libstdc++-13-dev libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libubsan1 619s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 619s linux-libc-dev littler pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin 619s r-base-core r-base-dev r-cran-abind r-cran-codetools r-cran-deldir 619s r-cran-foreach r-cran-glmnet r-cran-goftest r-cran-gsl r-cran-iterators 619s r-cran-lattice r-cran-littler r-cran-matrix r-cran-mgcv r-cran-nleqslv 619s r-cran-nlme r-cran-pkgkitten r-cran-polyclip r-cran-rcpp r-cran-rcppeigen 619s r-cran-rpart r-cran-shape r-cran-sm r-cran-spatial r-cran-spatstat 619s r-cran-spatstat.data r-cran-spatstat.explore r-cran-spatstat.geom 619s r-cran-spatstat.linnet r-cran-spatstat.model r-cran-spatstat.random 619s r-cran-spatstat.sparse r-cran-spatstat.utils r-cran-survival r-cran-tensor 619s rpcsvc-proto unzip x11-common xdg-utils zip zlib1g-dev 619s 0 upgraded, 140 newly installed, 0 to remove and 0 not upgraded. 619s Need to get 181 MB/181 MB of archives. 619s After this operation, 502 MB of additional disk space will be used. 619s Get:1 /tmp/autopkgtest.qd1hMn/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [764 B] 619s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-base s390x 13.2.0-17ubuntu2 [47.4 kB] 619s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libc-dev-bin s390x 2.39-0ubuntu6 [20.2 kB] 619s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x linux-libc-dev s390x 6.8.0-11.11 [1590 kB] 620s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt-dev s390x 1:4.4.36-4 [135 kB] 620s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x rpcsvc-proto s390x 1.4.2-0ubuntu6 [64.7 kB] 620s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libc6-dev s390x 2.39-0ubuntu6 [1629 kB] 620s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libisl23 s390x 0.26-3 [722 kB] 620s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libmpc3 s390x 1.3.1-1 [54.9 kB] 620s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13-s390x-linux-gnu s390x 13.2.0-17ubuntu2 [9929 kB] 621s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13 s390x 13.2.0-17ubuntu2 [1026 B] 621s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x cpp-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [5308 B] 621s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x cpp s390x 4:13.2.0-7ubuntu1 [22.4 kB] 621s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libcc1-0 s390x 14-20240303-1ubuntu1 [49.9 kB] 621s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 621s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libitm1 s390x 14-20240303-1ubuntu1 [31.1 kB] 621s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libatomic1 s390x 14-20240303-1ubuntu1 [9392 B] 621s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libasan8 s390x 14-20240303-1ubuntu1 [2998 kB] 621s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libubsan1 s390x 14-20240303-1ubuntu1 [1186 kB] 621s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-13-dev s390x 13.2.0-17ubuntu2 [1003 kB] 621s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-s390x-linux-gnu s390x 13.2.0-17ubuntu2 [19.1 MB] 622s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13 s390x 13.2.0-17ubuntu2 [467 kB] 622s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x gcc-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [1208 B] 622s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x gcc s390x 4:13.2.0-7ubuntu1 [5014 B] 622s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++-13-dev s390x 13.2.0-17ubuntu2 [2430 kB] 622s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x g++-13-s390x-linux-gnu s390x 13.2.0-17ubuntu2 [11.3 MB] 622s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x g++-13 s390x 13.2.0-17ubuntu2 [14.4 kB] 622s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x g++-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [956 B] 622s Get:29 http://ftpmaster.internal/ubuntu noble/main s390x g++ s390x 4:13.2.0-7ubuntu1 [1096 B] 622s Get:30 http://ftpmaster.internal/ubuntu noble/main s390x build-essential s390x 12.10ubuntu1 [4930 B] 622s Get:31 http://ftpmaster.internal/ubuntu noble/main s390x dctrl-tools s390x 2.24-3build2 [65.4 kB] 622s Get:32 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 622s Get:33 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 622s Get:34 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 622s Get:35 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 622s Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 622s Get:37 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig s390x 2.15.0-1ubuntu1 [191 kB] 622s Get:38 http://ftpmaster.internal/ubuntu noble/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 622s Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 622s Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran-13-dev s390x 13.2.0-17ubuntu2 [623 kB] 622s Get:41 http://ftpmaster.internal/ubuntu noble/main s390x gfortran-13-s390x-linux-gnu s390x 13.2.0-17ubuntu2 [10.4 MB] 623s Get:42 http://ftpmaster.internal/ubuntu noble/main s390x gfortran-13 s390x 13.2.0-17ubuntu2 [10.3 kB] 623s Get:43 http://ftpmaster.internal/ubuntu noble/main s390x gfortran-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [1016 B] 623s Get:44 http://ftpmaster.internal/ubuntu noble/main s390x gfortran s390x 4:13.2.0-7ubuntu1 [1174 B] 623s Get:45 http://ftpmaster.internal/ubuntu noble/main s390x icu-devtools s390x 74.2-1ubuntu1 [224 kB] 623s Get:46 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 623s Get:47 http://ftpmaster.internal/ubuntu noble/main s390x libblas-dev s390x 3.12.0-3 [239 kB] 623s Get:48 http://ftpmaster.internal/ubuntu noble/main s390x libbz2-dev s390x 1.0.8-5ubuntu1 [39.4 kB] 623s Get:49 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB] 623s Get:50 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB] 623s Get:51 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B] 623s Get:52 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB] 623s Get:53 http://ftpmaster.internal/ubuntu noble/main s390x libcairo2 s390x 1.18.0-1 [578 kB] 623s Get:54 http://ftpmaster.internal/ubuntu noble/main s390x libdatrie1 s390x 0.2.13-3 [22.6 kB] 623s Get:55 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 623s Get:56 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] 623s Get:57 http://ftpmaster.internal/ubuntu noble/universe s390x libgslcblas0 s390x 2.7.1+dfsg-6ubuntu1 [147 kB] 623s Get:58 http://ftpmaster.internal/ubuntu noble/universe s390x libgsl27 s390x 2.7.1+dfsg-6ubuntu1 [1069 kB] 623s Get:59 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2 [515 kB] 623s Get:60 http://ftpmaster.internal/ubuntu noble/main s390x x11-common all 1:7.7+23ubuntu2 [23.4 kB] 623s Get:61 http://ftpmaster.internal/ubuntu noble/main s390x libice6 s390x 2:1.0.10-1build2 [40.8 kB] 623s Get:62 http://ftpmaster.internal/ubuntu noble/main s390x libicu-dev s390x 74.2-1ubuntu1 [11.9 MB] 623s Get:63 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 623s Get:64 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8-dev s390x 2.1.5-2ubuntu1 [264 kB] 623s Get:65 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 623s Get:66 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8-dev s390x 8c-2ubuntu11 [1484 B] 624s Get:67 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-dev s390x 8c-2ubuntu11 [1484 B] 624s Get:68 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 624s Get:69 http://ftpmaster.internal/ubuntu noble/main s390x liblapack-dev s390x 3.12.0-3 [5983 kB] 624s Get:70 http://ftpmaster.internal/ubuntu noble/main s390x libncurses-dev s390x 6.4+20240113-1ubuntu1 [412 kB] 624s Get:71 http://ftpmaster.internal/ubuntu noble/main s390x libthai-data all 0.1.29-2 [158 kB] 624s Get:72 http://ftpmaster.internal/ubuntu noble/main s390x libthai0 s390x 0.1.29-2 [20.6 kB] 624s Get:73 http://ftpmaster.internal/ubuntu noble/main s390x libpango-1.0-0 s390x 1.51.0+ds-4 [240 kB] 624s Get:74 http://ftpmaster.internal/ubuntu noble/main s390x libpangoft2-1.0-0 s390x 1.51.0+ds-4 [43.6 kB] 624s Get:75 http://ftpmaster.internal/ubuntu noble/main s390x libpangocairo-1.0-0 s390x 1.51.0+ds-4 [28.9 kB] 624s Get:76 http://ftpmaster.internal/ubuntu noble/main s390x libpaper1 s390x 1.1.29 [13.3 kB] 624s Get:77 http://ftpmaster.internal/ubuntu noble/main s390x libpaper-utils s390x 1.1.29 [8452 B] 624s Get:78 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-16-0 s390x 10.42-4ubuntu1 [229 kB] 624s Get:79 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-32-0 s390x 10.42-4ubuntu1 [217 kB] 624s Get:80 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-posix3 s390x 10.42-4ubuntu1 [6704 B] 624s Get:81 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-dev s390x 10.42-4ubuntu1 [805 kB] 624s Get:82 http://ftpmaster.internal/ubuntu noble/main s390x libpkgconf3 s390x 1.8.1-2 [30.4 kB] 624s Get:83 http://ftpmaster.internal/ubuntu noble/main s390x zlib1g-dev s390x 1:1.3.dfsg-3ubuntu1 [905 kB] 624s Get:84 http://ftpmaster.internal/ubuntu noble/main s390x libpng-dev s390x 1.6.43-1 [277 kB] 624s Get:85 http://ftpmaster.internal/ubuntu noble/main s390x libreadline-dev s390x 8.2-3 [187 kB] 624s Get:86 http://ftpmaster.internal/ubuntu noble/main s390x libsharpyuv0 s390x 1.3.2-0.4 [14.8 kB] 624s Get:87 http://ftpmaster.internal/ubuntu noble/main s390x libsm6 s390x 2:1.2.3-1build2 [16.9 kB] 624s Get:88 http://ftpmaster.internal/ubuntu noble/main s390x libtcl8.6 s390x 8.6.13+dfsg-2 [948 kB] 624s Get:89 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu1 [29.8 kB] 624s Get:90 http://ftpmaster.internal/ubuntu noble/main s390x libwebp7 s390x 1.3.2-0.4 [207 kB] 624s Get:91 http://ftpmaster.internal/ubuntu noble/main s390x libtiff6 s390x 4.5.1+git230720-3ubuntu1 [253 kB] 624s Get:92 http://ftpmaster.internal/ubuntu noble/main s390x libxft2 s390x 2.3.6-1 [44.3 kB] 624s Get:93 http://ftpmaster.internal/ubuntu noble/main s390x libxss1 s390x 1:1.2.3-1build2 [8192 B] 624s Get:94 http://ftpmaster.internal/ubuntu noble/main s390x libtk8.6 s390x 8.6.14-1 [833 kB] 624s Get:95 http://ftpmaster.internal/ubuntu noble/main s390x libxt6 s390x 1:1.2.1-1.1 [166 kB] 624s Get:96 http://ftpmaster.internal/ubuntu noble/main s390x zip s390x 3.0-13 [175 kB] 624s Get:97 http://ftpmaster.internal/ubuntu noble/main s390x unzip s390x 6.0-28ubuntu3 [180 kB] 624s Get:98 http://ftpmaster.internal/ubuntu noble/main s390x xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 624s Get:99 http://ftpmaster.internal/ubuntu noble/universe s390x r-base-core s390x 4.3.2-1build1 [27.1 MB] 625s Get:100 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-littler s390x 0.3.19-1 [93.0 kB] 625s Get:101 http://ftpmaster.internal/ubuntu noble/universe s390x littler all 0.3.19-1 [2472 B] 625s Get:102 http://ftpmaster.internal/ubuntu noble/main s390x pkgconf-bin s390x 1.8.1-2 [20.8 kB] 625s Get:103 http://ftpmaster.internal/ubuntu noble/main s390x pkgconf s390x 1.8.1-2 [16.7 kB] 625s Get:104 http://ftpmaster.internal/ubuntu noble/main s390x pkg-config s390x 1.8.1-2 [7170 B] 625s Get:105 http://ftpmaster.internal/ubuntu noble/main s390x liblzma-dev s390x 5.4.5-0.3 [215 kB] 626s Get:106 http://ftpmaster.internal/ubuntu noble/universe s390x r-base-dev all 4.3.2-1build1 [4336 B] 626s Get:107 http://ftpmaster.internal/ubuntu noble/universe s390x pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 626s Get:108 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-abind all 1.4-5-2 [63.6 kB] 626s Get:109 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-codetools all 0.2-19-1 [90.5 kB] 626s Get:110 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-deldir s390x 2.0-4-1 [271 kB] 626s Get:111 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-iterators all 1.0.14-1 [336 kB] 626s Get:112 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-foreach all 1.5.2-1 [124 kB] 626s Get:113 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-lattice s390x 0.22-5-1 [1341 kB] 626s Get:114 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-matrix s390x 1.6-5-1 [3983 kB] 626s Get:115 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-shape all 1.4.6-1 [770 kB] 626s Get:116 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-survival s390x 3.5-8-1 [6161 kB] 626s Get:117 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 626s Get:118 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rcpp s390x 1.0.12-1 [1985 kB] 626s Get:119 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rcppeigen s390x 0.3.3.9.4-1 [1187 kB] 626s Get:120 http://ftpmaster.internal/ubuntu noble/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 627s Get:121 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-glmnet s390x 4.1-8-1 [1942 kB] 627s Get:122 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-goftest s390x 1.2-3-1 [59.2 kB] 627s Get:123 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-gsl s390x 2.1-8-1 [490 kB] 627s Get:124 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-nlme s390x 3.1.164-1 [2268 kB] 627s Get:125 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-mgcv s390x 1.9-1-1 [3348 kB] 627s Get:126 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-nleqslv s390x 3.3.5-1 [104 kB] 627s Get:127 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-polyclip s390x 1.10-6-1 [119 kB] 627s Get:128 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rpart s390x 4.1.23-1 [667 kB] 627s Get:129 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-sm s390x 2.2-6.0-1 [792 kB] 627s Get:130 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatial s390x 7.3-17-1 [134 kB] 627s Get:131 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.utils s390x 3.0-4-1 [361 kB] 627s Get:132 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.data all 3.0-4-1 [4090 kB] 627s Get:133 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.geom s390x 3.2-8-1 [3829 kB] 627s Get:134 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.random s390x 3.2-2-1 [1146 kB] 627s Get:135 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-tensor all 1.5-4 [15.7 kB] 627s Get:136 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.sparse s390x 3.0-3-1 [217 kB] 627s Get:137 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.explore s390x 3.2-5-1 [3289 kB] 628s Get:138 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.model s390x 3.2-8-1 [3290 kB] 628s Get:139 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat.linnet s390x 3.1-3-1 [1411 kB] 628s Get:140 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-spatstat s390x 3.0-7-1 [3817 kB] 629s Preconfiguring packages ... 629s Fetched 181 MB in 9s (20.1 MB/s) 629s Selecting previously unselected package gcc-13-base:s390x. 629s (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 ... 51331 files and directories currently installed.) 629s Preparing to unpack .../000-gcc-13-base_13.2.0-17ubuntu2_s390x.deb ... 629s Unpacking gcc-13-base:s390x (13.2.0-17ubuntu2) ... 629s Selecting previously unselected package libc-dev-bin. 629s Preparing to unpack .../001-libc-dev-bin_2.39-0ubuntu6_s390x.deb ... 629s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 629s Selecting previously unselected package linux-libc-dev:s390x. 629s Preparing to unpack .../002-linux-libc-dev_6.8.0-11.11_s390x.deb ... 629s Unpacking linux-libc-dev:s390x (6.8.0-11.11) ... 629s Selecting previously unselected package libcrypt-dev:s390x. 629s Preparing to unpack .../003-libcrypt-dev_1%3a4.4.36-4_s390x.deb ... 629s Unpacking libcrypt-dev:s390x (1:4.4.36-4) ... 630s Selecting previously unselected package rpcsvc-proto. 630s Preparing to unpack .../004-rpcsvc-proto_1.4.2-0ubuntu6_s390x.deb ... 630s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 630s Selecting previously unselected package libc6-dev:s390x. 630s Preparing to unpack .../005-libc6-dev_2.39-0ubuntu6_s390x.deb ... 630s Unpacking libc6-dev:s390x (2.39-0ubuntu6) ... 630s Selecting previously unselected package libisl23:s390x. 630s Preparing to unpack .../006-libisl23_0.26-3_s390x.deb ... 630s Unpacking libisl23:s390x (0.26-3) ... 630s Selecting previously unselected package libmpc3:s390x. 630s Preparing to unpack .../007-libmpc3_1.3.1-1_s390x.deb ... 630s Unpacking libmpc3:s390x (1.3.1-1) ... 630s Selecting previously unselected package cpp-13-s390x-linux-gnu. 630s Preparing to unpack .../008-cpp-13-s390x-linux-gnu_13.2.0-17ubuntu2_s390x.deb ... 630s Unpacking cpp-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 630s Selecting previously unselected package cpp-13. 630s Preparing to unpack .../009-cpp-13_13.2.0-17ubuntu2_s390x.deb ... 630s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 630s Selecting previously unselected package cpp-s390x-linux-gnu. 630s Preparing to unpack .../010-cpp-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... 630s Unpacking cpp-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 630s Selecting previously unselected package cpp. 630s Preparing to unpack .../011-cpp_4%3a13.2.0-7ubuntu1_s390x.deb ... 630s Unpacking cpp (4:13.2.0-7ubuntu1) ... 630s Selecting previously unselected package libcc1-0:s390x. 630s Preparing to unpack .../012-libcc1-0_14-20240303-1ubuntu1_s390x.deb ... 630s Unpacking libcc1-0:s390x (14-20240303-1ubuntu1) ... 630s Selecting previously unselected package libgomp1:s390x. 630s Preparing to unpack .../013-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 630s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 630s Selecting previously unselected package libitm1:s390x. 630s Preparing to unpack .../014-libitm1_14-20240303-1ubuntu1_s390x.deb ... 630s Unpacking libitm1:s390x (14-20240303-1ubuntu1) ... 630s Selecting previously unselected package libatomic1:s390x. 630s Preparing to unpack .../015-libatomic1_14-20240303-1ubuntu1_s390x.deb ... 630s Unpacking libatomic1:s390x (14-20240303-1ubuntu1) ... 630s Selecting previously unselected package libasan8:s390x. 630s Preparing to unpack .../016-libasan8_14-20240303-1ubuntu1_s390x.deb ... 630s Unpacking libasan8:s390x (14-20240303-1ubuntu1) ... 630s Selecting previously unselected package libubsan1:s390x. 630s Preparing to unpack .../017-libubsan1_14-20240303-1ubuntu1_s390x.deb ... 630s Unpacking libubsan1:s390x (14-20240303-1ubuntu1) ... 631s Selecting previously unselected package libgcc-13-dev:s390x. 631s Preparing to unpack .../018-libgcc-13-dev_13.2.0-17ubuntu2_s390x.deb ... 631s Unpacking libgcc-13-dev:s390x (13.2.0-17ubuntu2) ... 631s Selecting previously unselected package gcc-13-s390x-linux-gnu. 631s Preparing to unpack .../019-gcc-13-s390x-linux-gnu_13.2.0-17ubuntu2_s390x.deb ... 631s Unpacking gcc-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 631s Selecting previously unselected package gcc-13. 631s Preparing to unpack .../020-gcc-13_13.2.0-17ubuntu2_s390x.deb ... 631s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 631s Selecting previously unselected package gcc-s390x-linux-gnu. 631s Preparing to unpack .../021-gcc-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... 631s Unpacking gcc-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 631s Selecting previously unselected package gcc. 631s Preparing to unpack .../022-gcc_4%3a13.2.0-7ubuntu1_s390x.deb ... 631s Unpacking gcc (4:13.2.0-7ubuntu1) ... 631s Selecting previously unselected package libstdc++-13-dev:s390x. 631s Preparing to unpack .../023-libstdc++-13-dev_13.2.0-17ubuntu2_s390x.deb ... 631s Unpacking libstdc++-13-dev:s390x (13.2.0-17ubuntu2) ... 631s Selecting previously unselected package g++-13-s390x-linux-gnu. 631s Preparing to unpack .../024-g++-13-s390x-linux-gnu_13.2.0-17ubuntu2_s390x.deb ... 631s Unpacking g++-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 632s Selecting previously unselected package g++-13. 632s Preparing to unpack .../025-g++-13_13.2.0-17ubuntu2_s390x.deb ... 632s Unpacking g++-13 (13.2.0-17ubuntu2) ... 632s Selecting previously unselected package g++-s390x-linux-gnu. 632s Preparing to unpack .../026-g++-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... 632s Unpacking g++-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 632s Selecting previously unselected package g++. 632s Preparing to unpack .../027-g++_4%3a13.2.0-7ubuntu1_s390x.deb ... 632s Unpacking g++ (4:13.2.0-7ubuntu1) ... 632s Selecting previously unselected package build-essential. 632s Preparing to unpack .../028-build-essential_12.10ubuntu1_s390x.deb ... 632s Unpacking build-essential (12.10ubuntu1) ... 632s Selecting previously unselected package dctrl-tools. 632s Preparing to unpack .../029-dctrl-tools_2.24-3build2_s390x.deb ... 632s Unpacking dctrl-tools (2.24-3build2) ... 632s Selecting previously unselected package libfreetype6:s390x. 632s Preparing to unpack .../030-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 632s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 632s Selecting previously unselected package fonts-dejavu-mono. 632s Preparing to unpack .../031-fonts-dejavu-mono_2.37-8_all.deb ... 632s Unpacking fonts-dejavu-mono (2.37-8) ... 632s Selecting previously unselected package fonts-dejavu-core. 632s Preparing to unpack .../032-fonts-dejavu-core_2.37-8_all.deb ... 632s Unpacking fonts-dejavu-core (2.37-8) ... 632s Selecting previously unselected package fontconfig-config. 632s Preparing to unpack .../033-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 632s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 632s Selecting previously unselected package libfontconfig1:s390x. 632s Preparing to unpack .../034-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 632s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 632s Selecting previously unselected package fontconfig. 632s Preparing to unpack .../035-fontconfig_2.15.0-1ubuntu1_s390x.deb ... 632s Unpacking fontconfig (2.15.0-1ubuntu1) ... 632s Selecting previously unselected package fonts-mathjax. 632s Preparing to unpack .../036-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 632s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 632s Selecting previously unselected package libgfortran5:s390x. 632s Preparing to unpack .../037-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 632s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 632s Selecting previously unselected package libgfortran-13-dev:s390x. 632s Preparing to unpack .../038-libgfortran-13-dev_13.2.0-17ubuntu2_s390x.deb ... 632s Unpacking libgfortran-13-dev:s390x (13.2.0-17ubuntu2) ... 633s Selecting previously unselected package gfortran-13-s390x-linux-gnu. 633s Preparing to unpack .../039-gfortran-13-s390x-linux-gnu_13.2.0-17ubuntu2_s390x.deb ... 633s Unpacking gfortran-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 633s Selecting previously unselected package gfortran-13. 633s Preparing to unpack .../040-gfortran-13_13.2.0-17ubuntu2_s390x.deb ... 633s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 633s Selecting previously unselected package gfortran-s390x-linux-gnu. 633s Preparing to unpack .../041-gfortran-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... 633s Unpacking gfortran-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 633s Selecting previously unselected package gfortran. 633s Preparing to unpack .../042-gfortran_4%3a13.2.0-7ubuntu1_s390x.deb ... 633s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 633s Selecting previously unselected package icu-devtools. 633s Preparing to unpack .../043-icu-devtools_74.2-1ubuntu1_s390x.deb ... 633s Unpacking icu-devtools (74.2-1ubuntu1) ... 633s Selecting previously unselected package libblas3:s390x. 633s Preparing to unpack .../044-libblas3_3.12.0-3_s390x.deb ... 633s Unpacking libblas3:s390x (3.12.0-3) ... 633s Selecting previously unselected package libblas-dev:s390x. 633s Preparing to unpack .../045-libblas-dev_3.12.0-3_s390x.deb ... 633s Unpacking libblas-dev:s390x (3.12.0-3) ... 633s Selecting previously unselected package libbz2-dev:s390x. 633s Preparing to unpack .../046-libbz2-dev_1.0.8-5ubuntu1_s390x.deb ... 633s Unpacking libbz2-dev:s390x (1.0.8-5ubuntu1) ... 633s Selecting previously unselected package libpixman-1-0:s390x. 633s Preparing to unpack .../047-libpixman-1-0_0.42.2-1_s390x.deb ... 633s Unpacking libpixman-1-0:s390x (0.42.2-1) ... 633s Selecting previously unselected package libxcb-render0:s390x. 633s Preparing to unpack .../048-libxcb-render0_1.15-1_s390x.deb ... 633s Unpacking libxcb-render0:s390x (1.15-1) ... 633s Selecting previously unselected package libxcb-shm0:s390x. 633s Preparing to unpack .../049-libxcb-shm0_1.15-1_s390x.deb ... 633s Unpacking libxcb-shm0:s390x (1.15-1) ... 633s Selecting previously unselected package libxrender1:s390x. 633s Preparing to unpack .../050-libxrender1_1%3a0.9.10-1.1_s390x.deb ... 633s Unpacking libxrender1:s390x (1:0.9.10-1.1) ... 633s Selecting previously unselected package libcairo2:s390x. 633s Preparing to unpack .../051-libcairo2_1.18.0-1_s390x.deb ... 633s Unpacking libcairo2:s390x (1.18.0-1) ... 633s Selecting previously unselected package libdatrie1:s390x. 633s Preparing to unpack .../052-libdatrie1_0.2.13-3_s390x.deb ... 633s Unpacking libdatrie1:s390x (0.2.13-3) ... 633s Selecting previously unselected package libdeflate0:s390x. 633s Preparing to unpack .../053-libdeflate0_1.19-1_s390x.deb ... 633s Unpacking libdeflate0:s390x (1.19-1) ... 633s Selecting previously unselected package libgraphite2-3:s390x. 633s Preparing to unpack .../054-libgraphite2-3_1.3.14-2_s390x.deb ... 633s Unpacking libgraphite2-3:s390x (1.3.14-2) ... 633s Selecting previously unselected package libgslcblas0:s390x. 633s Preparing to unpack .../055-libgslcblas0_2.7.1+dfsg-6ubuntu1_s390x.deb ... 633s Unpacking libgslcblas0:s390x (2.7.1+dfsg-6ubuntu1) ... 633s Selecting previously unselected package libgsl27:s390x. 633s Preparing to unpack .../056-libgsl27_2.7.1+dfsg-6ubuntu1_s390x.deb ... 633s Unpacking libgsl27:s390x (2.7.1+dfsg-6ubuntu1) ... 633s Selecting previously unselected package libharfbuzz0b:s390x. 633s Preparing to unpack .../057-libharfbuzz0b_8.3.0-2_s390x.deb ... 633s Unpacking libharfbuzz0b:s390x (8.3.0-2) ... 633s Selecting previously unselected package x11-common. 633s Preparing to unpack .../058-x11-common_1%3a7.7+23ubuntu2_all.deb ... 633s Unpacking x11-common (1:7.7+23ubuntu2) ... 633s Selecting previously unselected package libice6:s390x. 633s Preparing to unpack .../059-libice6_2%3a1.0.10-1build2_s390x.deb ... 633s Unpacking libice6:s390x (2:1.0.10-1build2) ... 633s Selecting previously unselected package libicu-dev:s390x. 633s Preparing to unpack .../060-libicu-dev_74.2-1ubuntu1_s390x.deb ... 633s Unpacking libicu-dev:s390x (74.2-1ubuntu1) ... 634s Selecting previously unselected package libjpeg-turbo8:s390x. 634s Preparing to unpack .../061-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 634s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 634s Selecting previously unselected package libjpeg-turbo8-dev:s390x. 634s Preparing to unpack .../062-libjpeg-turbo8-dev_2.1.5-2ubuntu1_s390x.deb ... 634s Unpacking libjpeg-turbo8-dev:s390x (2.1.5-2ubuntu1) ... 634s Selecting previously unselected package libjpeg8:s390x. 634s Preparing to unpack .../063-libjpeg8_8c-2ubuntu11_s390x.deb ... 634s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 634s Selecting previously unselected package libjpeg8-dev:s390x. 634s Preparing to unpack .../064-libjpeg8-dev_8c-2ubuntu11_s390x.deb ... 634s Unpacking libjpeg8-dev:s390x (8c-2ubuntu11) ... 634s Selecting previously unselected package libjpeg-dev:s390x. 634s Preparing to unpack .../065-libjpeg-dev_8c-2ubuntu11_s390x.deb ... 634s Unpacking libjpeg-dev:s390x (8c-2ubuntu11) ... 634s Selecting previously unselected package liblapack3:s390x. 634s Preparing to unpack .../066-liblapack3_3.12.0-3_s390x.deb ... 634s Unpacking liblapack3:s390x (3.12.0-3) ... 634s Selecting previously unselected package liblapack-dev:s390x. 634s Preparing to unpack .../067-liblapack-dev_3.12.0-3_s390x.deb ... 634s Unpacking liblapack-dev:s390x (3.12.0-3) ... 634s Selecting previously unselected package libncurses-dev:s390x. 634s Preparing to unpack .../068-libncurses-dev_6.4+20240113-1ubuntu1_s390x.deb ... 634s Unpacking libncurses-dev:s390x (6.4+20240113-1ubuntu1) ... 634s Selecting previously unselected package libthai-data. 634s Preparing to unpack .../069-libthai-data_0.1.29-2_all.deb ... 634s Unpacking libthai-data (0.1.29-2) ... 634s Selecting previously unselected package libthai0:s390x. 634s Preparing to unpack .../070-libthai0_0.1.29-2_s390x.deb ... 634s Unpacking libthai0:s390x (0.1.29-2) ... 634s Selecting previously unselected package libpango-1.0-0:s390x. 634s Preparing to unpack .../071-libpango-1.0-0_1.51.0+ds-4_s390x.deb ... 634s Unpacking libpango-1.0-0:s390x (1.51.0+ds-4) ... 634s Selecting previously unselected package libpangoft2-1.0-0:s390x. 634s Preparing to unpack .../072-libpangoft2-1.0-0_1.51.0+ds-4_s390x.deb ... 634s Unpacking libpangoft2-1.0-0:s390x (1.51.0+ds-4) ... 634s Selecting previously unselected package libpangocairo-1.0-0:s390x. 634s Preparing to unpack .../073-libpangocairo-1.0-0_1.51.0+ds-4_s390x.deb ... 634s Unpacking libpangocairo-1.0-0:s390x (1.51.0+ds-4) ... 634s Selecting previously unselected package libpaper1:s390x. 634s Preparing to unpack .../074-libpaper1_1.1.29_s390x.deb ... 634s Unpacking libpaper1:s390x (1.1.29) ... 635s Selecting previously unselected package libpaper-utils. 635s Preparing to unpack .../075-libpaper-utils_1.1.29_s390x.deb ... 635s Unpacking libpaper-utils (1.1.29) ... 635s Selecting previously unselected package libpcre2-16-0:s390x. 635s Preparing to unpack .../076-libpcre2-16-0_10.42-4ubuntu1_s390x.deb ... 635s Unpacking libpcre2-16-0:s390x (10.42-4ubuntu1) ... 635s Selecting previously unselected package libpcre2-32-0:s390x. 635s Preparing to unpack .../077-libpcre2-32-0_10.42-4ubuntu1_s390x.deb ... 635s Unpacking libpcre2-32-0:s390x (10.42-4ubuntu1) ... 635s Selecting previously unselected package libpcre2-posix3:s390x. 635s Preparing to unpack .../078-libpcre2-posix3_10.42-4ubuntu1_s390x.deb ... 635s Unpacking libpcre2-posix3:s390x (10.42-4ubuntu1) ... 635s Selecting previously unselected package libpcre2-dev:s390x. 635s Preparing to unpack .../079-libpcre2-dev_10.42-4ubuntu1_s390x.deb ... 635s Unpacking libpcre2-dev:s390x (10.42-4ubuntu1) ... 635s Selecting previously unselected package libpkgconf3:s390x. 635s Preparing to unpack .../080-libpkgconf3_1.8.1-2_s390x.deb ... 635s Unpacking libpkgconf3:s390x (1.8.1-2) ... 635s Selecting previously unselected package zlib1g-dev:s390x. 635s Preparing to unpack .../081-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_s390x.deb ... 635s Unpacking zlib1g-dev:s390x (1:1.3.dfsg-3ubuntu1) ... 635s Selecting previously unselected package libpng-dev:s390x. 635s Preparing to unpack .../082-libpng-dev_1.6.43-1_s390x.deb ... 635s Unpacking libpng-dev:s390x (1.6.43-1) ... 635s Selecting previously unselected package libreadline-dev:s390x. 635s Preparing to unpack .../083-libreadline-dev_8.2-3_s390x.deb ... 635s Unpacking libreadline-dev:s390x (8.2-3) ... 635s Selecting previously unselected package libsharpyuv0:s390x. 635s Preparing to unpack .../084-libsharpyuv0_1.3.2-0.4_s390x.deb ... 635s Unpacking libsharpyuv0:s390x (1.3.2-0.4) ... 635s Selecting previously unselected package libsm6:s390x. 635s Preparing to unpack .../085-libsm6_2%3a1.2.3-1build2_s390x.deb ... 635s Unpacking libsm6:s390x (2:1.2.3-1build2) ... 635s Selecting previously unselected package libtcl8.6:s390x. 635s Preparing to unpack .../086-libtcl8.6_8.6.13+dfsg-2_s390x.deb ... 635s Unpacking libtcl8.6:s390x (8.6.13+dfsg-2) ... 635s Selecting previously unselected package libjbig0:s390x. 635s Preparing to unpack .../087-libjbig0_2.1-6.1ubuntu1_s390x.deb ... 635s Unpacking libjbig0:s390x (2.1-6.1ubuntu1) ... 635s Selecting previously unselected package libwebp7:s390x. 635s Preparing to unpack .../088-libwebp7_1.3.2-0.4_s390x.deb ... 635s Unpacking libwebp7:s390x (1.3.2-0.4) ... 635s Selecting previously unselected package libtiff6:s390x. 635s Preparing to unpack .../089-libtiff6_4.5.1+git230720-3ubuntu1_s390x.deb ... 635s Unpacking libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 635s Selecting previously unselected package libxft2:s390x. 635s Preparing to unpack .../090-libxft2_2.3.6-1_s390x.deb ... 635s Unpacking libxft2:s390x (2.3.6-1) ... 635s Selecting previously unselected package libxss1:s390x. 635s Preparing to unpack .../091-libxss1_1%3a1.2.3-1build2_s390x.deb ... 635s Unpacking libxss1:s390x (1:1.2.3-1build2) ... 635s Selecting previously unselected package libtk8.6:s390x. 635s Preparing to unpack .../092-libtk8.6_8.6.14-1_s390x.deb ... 635s Unpacking libtk8.6:s390x (8.6.14-1) ... 635s Selecting previously unselected package libxt6:s390x. 635s Preparing to unpack .../093-libxt6_1%3a1.2.1-1.1_s390x.deb ... 635s Unpacking libxt6:s390x (1:1.2.1-1.1) ... 635s Selecting previously unselected package zip. 635s Preparing to unpack .../094-zip_3.0-13_s390x.deb ... 635s Unpacking zip (3.0-13) ... 635s Selecting previously unselected package unzip. 635s Preparing to unpack .../095-unzip_6.0-28ubuntu3_s390x.deb ... 635s Unpacking unzip (6.0-28ubuntu3) ... 635s Selecting previously unselected package xdg-utils. 635s Preparing to unpack .../096-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 635s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 635s Selecting previously unselected package r-base-core. 635s Preparing to unpack .../097-r-base-core_4.3.2-1build1_s390x.deb ... 635s Unpacking r-base-core (4.3.2-1build1) ... 636s Selecting previously unselected package r-cran-littler. 636s Preparing to unpack .../098-r-cran-littler_0.3.19-1_s390x.deb ... 636s Unpacking r-cran-littler (0.3.19-1) ... 636s Selecting previously unselected package littler. 636s Preparing to unpack .../099-littler_0.3.19-1_all.deb ... 636s Unpacking littler (0.3.19-1) ... 636s Selecting previously unselected package pkgconf-bin. 636s Preparing to unpack .../100-pkgconf-bin_1.8.1-2_s390x.deb ... 636s Unpacking pkgconf-bin (1.8.1-2) ... 636s Selecting previously unselected package pkgconf:s390x. 636s Preparing to unpack .../101-pkgconf_1.8.1-2_s390x.deb ... 636s Unpacking pkgconf:s390x (1.8.1-2) ... 636s Selecting previously unselected package pkg-config:s390x. 636s Preparing to unpack .../102-pkg-config_1.8.1-2_s390x.deb ... 636s Unpacking pkg-config:s390x (1.8.1-2) ... 636s Selecting previously unselected package liblzma-dev:s390x. 636s Preparing to unpack .../103-liblzma-dev_5.4.5-0.3_s390x.deb ... 636s Unpacking liblzma-dev:s390x (5.4.5-0.3) ... 636s Selecting previously unselected package r-base-dev. 636s Preparing to unpack .../104-r-base-dev_4.3.2-1build1_all.deb ... 636s Unpacking r-base-dev (4.3.2-1build1) ... 636s Selecting previously unselected package pkg-r-autopkgtest. 636s Preparing to unpack .../105-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 636s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 636s Selecting previously unselected package r-cran-abind. 636s Preparing to unpack .../106-r-cran-abind_1.4-5-2_all.deb ... 636s Unpacking r-cran-abind (1.4-5-2) ... 636s Selecting previously unselected package r-cran-codetools. 636s Preparing to unpack .../107-r-cran-codetools_0.2-19-1_all.deb ... 636s Unpacking r-cran-codetools (0.2-19-1) ... 636s Selecting previously unselected package r-cran-deldir. 636s Preparing to unpack .../108-r-cran-deldir_2.0-4-1_s390x.deb ... 636s Unpacking r-cran-deldir (2.0-4-1) ... 636s Selecting previously unselected package r-cran-iterators. 636s Preparing to unpack .../109-r-cran-iterators_1.0.14-1_all.deb ... 636s Unpacking r-cran-iterators (1.0.14-1) ... 636s Selecting previously unselected package r-cran-foreach. 636s Preparing to unpack .../110-r-cran-foreach_1.5.2-1_all.deb ... 636s Unpacking r-cran-foreach (1.5.2-1) ... 636s Selecting previously unselected package r-cran-lattice. 636s Preparing to unpack .../111-r-cran-lattice_0.22-5-1_s390x.deb ... 636s Unpacking r-cran-lattice (0.22-5-1) ... 636s Selecting previously unselected package r-cran-matrix. 636s Preparing to unpack .../112-r-cran-matrix_1.6-5-1_s390x.deb ... 636s Unpacking r-cran-matrix (1.6-5-1) ... 636s Selecting previously unselected package r-cran-shape. 636s Preparing to unpack .../113-r-cran-shape_1.4.6-1_all.deb ... 636s Unpacking r-cran-shape (1.4.6-1) ... 636s Selecting previously unselected package r-cran-survival. 636s Preparing to unpack .../114-r-cran-survival_3.5-8-1_s390x.deb ... 636s Unpacking r-cran-survival (3.5-8-1) ... 636s Selecting previously unselected package r-cran-pkgkitten. 636s Preparing to unpack .../115-r-cran-pkgkitten_0.2.3-1_all.deb ... 636s Unpacking r-cran-pkgkitten (0.2.3-1) ... 636s Selecting previously unselected package r-cran-rcpp. 636s Preparing to unpack .../116-r-cran-rcpp_1.0.12-1_s390x.deb ... 636s Unpacking r-cran-rcpp (1.0.12-1) ... 636s Selecting previously unselected package r-cran-rcppeigen. 636s Preparing to unpack .../117-r-cran-rcppeigen_0.3.3.9.4-1_s390x.deb ... 636s Unpacking r-cran-rcppeigen (0.3.3.9.4-1) ... 637s Selecting previously unselected package libjs-mathjax. 637s Preparing to unpack .../118-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 637s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 638s Selecting previously unselected package r-cran-glmnet. 638s Preparing to unpack .../119-r-cran-glmnet_4.1-8-1_s390x.deb ... 638s Unpacking r-cran-glmnet (4.1-8-1) ... 638s Selecting previously unselected package r-cran-goftest. 638s Preparing to unpack .../120-r-cran-goftest_1.2-3-1_s390x.deb ... 638s Unpacking r-cran-goftest (1.2-3-1) ... 638s Selecting previously unselected package r-cran-gsl. 638s Preparing to unpack .../121-r-cran-gsl_2.1-8-1_s390x.deb ... 638s Unpacking r-cran-gsl (2.1-8-1) ... 638s Selecting previously unselected package r-cran-nlme. 638s Preparing to unpack .../122-r-cran-nlme_3.1.164-1_s390x.deb ... 638s Unpacking r-cran-nlme (3.1.164-1) ... 638s Selecting previously unselected package r-cran-mgcv. 638s Preparing to unpack .../123-r-cran-mgcv_1.9-1-1_s390x.deb ... 638s Unpacking r-cran-mgcv (1.9-1-1) ... 638s Selecting previously unselected package r-cran-nleqslv. 638s Preparing to unpack .../124-r-cran-nleqslv_3.3.5-1_s390x.deb ... 638s Unpacking r-cran-nleqslv (3.3.5-1) ... 638s Selecting previously unselected package r-cran-polyclip. 638s Preparing to unpack .../125-r-cran-polyclip_1.10-6-1_s390x.deb ... 638s Unpacking r-cran-polyclip (1.10-6-1) ... 638s Selecting previously unselected package r-cran-rpart. 638s Preparing to unpack .../126-r-cran-rpart_4.1.23-1_s390x.deb ... 638s Unpacking r-cran-rpart (4.1.23-1) ... 638s Selecting previously unselected package r-cran-sm. 638s Preparing to unpack .../127-r-cran-sm_2.2-6.0-1_s390x.deb ... 638s Unpacking r-cran-sm (2.2-6.0-1) ... 638s Selecting previously unselected package r-cran-spatial. 638s Preparing to unpack .../128-r-cran-spatial_7.3-17-1_s390x.deb ... 638s Unpacking r-cran-spatial (7.3-17-1) ... 638s Selecting previously unselected package r-cran-spatstat.utils. 638s Preparing to unpack .../129-r-cran-spatstat.utils_3.0-4-1_s390x.deb ... 638s Unpacking r-cran-spatstat.utils (3.0-4-1) ... 638s Selecting previously unselected package r-cran-spatstat.data. 638s Preparing to unpack .../130-r-cran-spatstat.data_3.0-4-1_all.deb ... 638s Unpacking r-cran-spatstat.data (3.0-4-1) ... 638s Selecting previously unselected package r-cran-spatstat.geom. 638s Preparing to unpack .../131-r-cran-spatstat.geom_3.2-8-1_s390x.deb ... 638s Unpacking r-cran-spatstat.geom (3.2-8-1) ... 638s Selecting previously unselected package r-cran-spatstat.random. 638s Preparing to unpack .../132-r-cran-spatstat.random_3.2-2-1_s390x.deb ... 638s Unpacking r-cran-spatstat.random (3.2-2-1) ... 638s Selecting previously unselected package r-cran-tensor. 638s Preparing to unpack .../133-r-cran-tensor_1.5-4_all.deb ... 638s Unpacking r-cran-tensor (1.5-4) ... 638s Selecting previously unselected package r-cran-spatstat.sparse. 638s Preparing to unpack .../134-r-cran-spatstat.sparse_3.0-3-1_s390x.deb ... 638s Unpacking r-cran-spatstat.sparse (3.0-3-1) ... 638s Selecting previously unselected package r-cran-spatstat.explore. 638s Preparing to unpack .../135-r-cran-spatstat.explore_3.2-5-1_s390x.deb ... 638s Unpacking r-cran-spatstat.explore (3.2-5-1) ... 639s Selecting previously unselected package r-cran-spatstat.model. 639s Preparing to unpack .../136-r-cran-spatstat.model_3.2-8-1_s390x.deb ... 639s Unpacking r-cran-spatstat.model (3.2-8-1) ... 639s Selecting previously unselected package r-cran-spatstat.linnet. 639s Preparing to unpack .../137-r-cran-spatstat.linnet_3.1-3-1_s390x.deb ... 639s Unpacking r-cran-spatstat.linnet (3.1-3-1) ... 639s Selecting previously unselected package r-cran-spatstat. 639s Preparing to unpack .../138-r-cran-spatstat_3.0-7-1_s390x.deb ... 639s Unpacking r-cran-spatstat (3.0-7-1) ... 639s Selecting previously unselected package autopkgtest-satdep. 639s Preparing to unpack .../139-2-autopkgtest-satdep.deb ... 639s Unpacking autopkgtest-satdep (0) ... 639s Setting up libgraphite2-3:s390x (1.3.14-2) ... 639s Setting up libpixman-1-0:s390x (0.42.2-1) ... 639s Setting up libsharpyuv0:s390x (1.3.2-0.4) ... 639s Setting up libpaper1:s390x (1.1.29) ... 639s 639s Creating config file /etc/papersize with new version 639s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 639s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 639s Setting up libxrender1:s390x (1:0.9.10-1.1) ... 639s Setting up libdatrie1:s390x (0.2.13-3) ... 639s Setting up libgslcblas0:s390x (2.7.1+dfsg-6ubuntu1) ... 639s Setting up libxcb-render0:s390x (1.15-1) ... 639s Setting up unzip (6.0-28ubuntu3) ... 639s Setting up x11-common (1:7.7+23ubuntu2) ... 639s Setting up libdeflate0:s390x (1.19-1) ... 639s Setting up linux-libc-dev:s390x (6.8.0-11.11) ... 639s Setting up libgsl27:s390x (2.7.1+dfsg-6ubuntu1) ... 639s Setting up libxcb-shm0:s390x (1.15-1) ... 639s Setting up libpaper-utils (1.1.29) ... 639s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 639s Setting up libjbig0:s390x (2.1-6.1ubuntu1) ... 639s Setting up libpcre2-16-0:s390x (10.42-4ubuntu1) ... 639s Setting up zip (3.0-13) ... 639s Setting up libpcre2-32-0:s390x (10.42-4ubuntu1) ... 639s Setting up libblas3:s390x (3.12.0-3) ... 639s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 639s Setting up libpkgconf3:s390x (1.8.1-2) ... 639s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 639s Setting up gcc-13-base:s390x (13.2.0-17ubuntu2) ... 639s Setting up libfreetype6:s390x (2.13.2+dfsg-1) ... 639s Setting up fonts-dejavu-mono (2.37-8) ... 639s Setting up libmpc3:s390x (1.3.1-1) ... 639s Setting up libatomic1:s390x (14-20240303-1ubuntu1) ... 639s Setting up libtcl8.6:s390x (8.6.13+dfsg-2) ... 639s Setting up icu-devtools (74.2-1ubuntu1) ... 639s Setting up fonts-dejavu-core (2.37-8) ... 639s Setting up pkgconf-bin (1.8.1-2) ... 639s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 639s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 639s Setting up libwebp7:s390x (1.3.2-0.4) ... 639s Setting up liblzma-dev:s390x (5.4.5-0.3) ... 639s Setting up libubsan1:s390x (14-20240303-1ubuntu1) ... 639s Setting up libpcre2-posix3:s390x (10.42-4ubuntu1) ... 639s Setting up libcrypt-dev:s390x (1:4.4.36-4) ... 639s Setting up libasan8:s390x (14-20240303-1ubuntu1) ... 639s Setting up libharfbuzz0b:s390x (8.3.0-2) ... 639s Setting up libthai-data (0.1.29-2) ... 639s Setting up libxss1:s390x (1:1.2.3-1build2) ... 639s Setting up libisl23:s390x (0.26-3) ... 639s Setting up libc-dev-bin (2.39-0ubuntu6) ... 639s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 639s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 639s Setting up libcc1-0:s390x (14-20240303-1ubuntu1) ... 639s Setting up libblas-dev:s390x (3.12.0-3) ... 639s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so to provide /usr/lib/s390x-linux-gnu/libblas.so (libblas.so-s390x-linux-gnu) in auto mode 639s Setting up dctrl-tools (2.24-3build2) ... 639s Setting up libitm1:s390x (14-20240303-1ubuntu1) ... 639s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 639s Setting up libice6:s390x (2:1.0.10-1build2) ... 639s Setting up liblapack3:s390x (3.12.0-3) ... 639s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 639s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 640s Setting up pkgconf:s390x (1.8.1-2) ... 640s Setting up libthai0:s390x (0.1.29-2) ... 640s Setting up cpp-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 640s Setting up liblapack-dev:s390x (3.12.0-3) ... 640s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so to provide /usr/lib/s390x-linux-gnu/liblapack.so (liblapack.so-s390x-linux-gnu) in auto mode 640s Setting up pkg-config:s390x (1.8.1-2) ... 640s Setting up libgcc-13-dev:s390x (13.2.0-17ubuntu2) ... 640s Setting up libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 640s Setting up libc6-dev:s390x (2.39-0ubuntu6) ... 640s Setting up libfontconfig1:s390x (2.15.0-1ubuntu1) ... 640s Setting up libgfortran-13-dev:s390x (13.2.0-17ubuntu2) ... 640s Setting up libsm6:s390x (2:1.2.3-1build2) ... 640s Setting up libicu-dev:s390x (74.2-1ubuntu1) ... 640s Setting up libstdc++-13-dev:s390x (13.2.0-17ubuntu2) ... 640s Setting up libbz2-dev:s390x (1.0.8-5ubuntu1) ... 640s Setting up fontconfig (2.15.0-1ubuntu1) ... 642s Regenerating fonts cache... done. 642s Setting up libjpeg-turbo8-dev:s390x (2.1.5-2ubuntu1) ... 642s Setting up libxft2:s390x (2.3.6-1) ... 642s Setting up libncurses-dev:s390x (6.4+20240113-1ubuntu1) ... 642s Setting up libpcre2-dev:s390x (10.42-4ubuntu1) ... 642s Setting up cpp-13 (13.2.0-17ubuntu2) ... 642s Setting up cpp-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 642s Setting up libtk8.6:s390x (8.6.14-1) ... 642s Setting up libpango-1.0-0:s390x (1.51.0+ds-4) ... 642s Setting up libreadline-dev:s390x (8.2-3) ... 642s Setting up libcairo2:s390x (1.18.0-1) ... 642s Setting up gcc-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 642s Setting up gcc-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 642s Setting up g++-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 642s Setting up gcc-13 (13.2.0-17ubuntu2) ... 642s Setting up libxt6:s390x (1:1.2.1-1.1) ... 642s Setting up zlib1g-dev:s390x (1:1.3.dfsg-3ubuntu1) ... 642s Setting up cpp (4:13.2.0-7ubuntu1) ... 642s Setting up gfortran-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 642s Setting up libpangoft2-1.0-0:s390x (1.51.0+ds-4) ... 642s Setting up libjpeg8-dev:s390x (8c-2ubuntu11) ... 642s Setting up libpangocairo-1.0-0:s390x (1.51.0+ds-4) ... 642s Setting up g++-13 (13.2.0-17ubuntu2) ... 642s Setting up gfortran-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 642s Setting up libpng-dev:s390x (1.6.43-1) ... 642s Setting up libjpeg-dev:s390x (8c-2ubuntu11) ... 642s Setting up g++-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 642s Setting up gcc (4:13.2.0-7ubuntu1) ... 642s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 642s Setting up r-base-core (4.3.2-1build1) ... 642s 642s Creating config file /etc/R/Renviron with new version 642s Setting up r-cran-lattice (0.22-5-1) ... 642s Setting up r-cran-nlme (3.1.164-1) ... 642s Setting up r-cran-spatstat.utils (3.0-4-1) ... 642s Setting up g++ (4:13.2.0-7ubuntu1) ... 642s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 642s Setting up build-essential (12.10ubuntu1) ... 642s Setting up r-cran-tensor (1.5-4) ... 642s Setting up r-cran-pkgkitten (0.2.3-1) ... 642s Setting up r-cran-littler (0.3.19-1) ... 642s Setting up r-cran-nleqslv (3.3.5-1) ... 642s Setting up r-cran-rcpp (1.0.12-1) ... 642s Setting up r-cran-codetools (0.2-19-1) ... 642s Setting up littler (0.3.19-1) ... 642s Setting up r-cran-gsl (2.1-8-1) ... 642s Setting up r-cran-spatial (7.3-17-1) ... 642s Setting up r-cran-iterators (1.0.14-1) ... 642s Setting up r-cran-abind (1.4-5-2) ... 642s Setting up r-cran-foreach (1.5.2-1) ... 642s Setting up r-cran-sm (2.2-6.0-1) ... 642s Setting up r-cran-polyclip (1.10-6-1) ... 642s Setting up gfortran (4:13.2.0-7ubuntu1) ... 642s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 642s 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 642s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 642s 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 642s Setting up r-cran-deldir (2.0-4-1) ... 642s Setting up r-cran-goftest (1.2-3-1) ... 642s Setting up r-cran-shape (1.4.6-1) ... 642s Setting up r-cran-matrix (1.6-5-1) ... 642s Setting up r-cran-spatstat.sparse (3.0-3-1) ... 642s Setting up r-cran-mgcv (1.9-1-1) ... 642s Setting up r-cran-rcppeigen (0.3.3.9.4-1) ... 642s Setting up r-base-dev (4.3.2-1build1) ... 642s Setting up r-cran-survival (3.5-8-1) ... 642s Setting up r-cran-spatstat.data (3.0-4-1) ... 642s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 642s Setting up r-cran-spatstat.geom (3.2-8-1) ... 642s Setting up r-cran-glmnet (4.1-8-1) ... 642s Setting up r-cran-rpart (4.1.23-1) ... 642s Setting up r-cran-spatstat.random (3.2-2-1) ... 642s Setting up r-cran-spatstat.explore (3.2-5-1) ... 642s Setting up r-cran-spatstat.model (3.2-8-1) ... 642s Setting up r-cran-spatstat.linnet (3.1-3-1) ... 642s Setting up r-cran-spatstat (3.0-7-1) ... 642s Setting up autopkgtest-satdep (0) ... 642s Processing triggers for man-db (2.12.0-3) ... 643s Processing triggers for install-info (7.1-3) ... 643s Processing triggers for libc-bin (2.39-0ubuntu6) ... 649s (Reading database ... 64341 files and directories currently installed.) 649s Removing autopkgtest-satdep (0) ... 657s autopkgtest [16:21:12]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 657s autopkgtest [16:21:12]: test pkg-r-autopkgtest: [----------------------- 657s Test: Try to load the R library spatstat.model 657s 657s R version 4.3.2 (2023-10-31) -- "Eye Holes" 657s Copyright (C) 2023 The R Foundation for Statistical Computing 657s Platform: s390x-ibm-linux-gnu (64-bit) 657s 657s R is free software and comes with ABSOLUTELY NO WARRANTY. 657s You are welcome to redistribute it under certain conditions. 657s Type 'license()' or 'licence()' for distribution details. 657s 657s R is a collaborative project with many contributors. 657s Type 'contributors()' for more information and 657s 'citation()' on how to cite R or R packages in publications. 657s 657s Type 'demo()' for some demos, 'help()' for on-line help, or 657s 'help.start()' for an HTML browser interface to help. 657s Type 'q()' to quit R. 657s 657s > library('spatstat.model') 657s Loading required package: spatstat.data 659s Loading required package: spatstat.geom 659s spatstat.geom 3.2-8 659s Loading required package: spatstat.random 659s spatstat.random 3.2-2 659s Loading required package: spatstat.explore 659s Loading required package: nlme 659s spatstat.explore 3.2-5 659s Loading required package: rpart 659s spatstat.model 3.2-8 659s > 659s > 659s Other tests are currently unsupported! 659s They will be progressively added. 660s autopkgtest [16:21:15]: test pkg-r-autopkgtest: -----------------------] 660s autopkgtest [16:21:15]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 660s pkg-r-autopkgtest PASS 660s autopkgtest [16:21:15]: @@@@@@@@@@@@@@@@@@@@ summary 660s run-unit-test PASS 660s pkg-r-autopkgtest PASS 674s Creating nova instance adt-noble-s390x-r-cran-spatstat.model-20240323-161015-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240321.img (UUID a4b1c77c-a35e-4d28-a8d9-902a1febb465)... 674s Creating nova instance adt-noble-s390x-r-cran-spatstat.model-20240323-161015-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240321.img (UUID a4b1c77c-a35e-4d28-a8d9-902a1febb465)...