1s autopkgtest [20:03:24]: starting date and time: 2024-03-23 20:03:24+0000 1s autopkgtest [20:03:24]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 1s autopkgtest [20:03:24]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.23t2om08/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@bos02-ppc64el-4.secgroup --name adt-noble-ppc64el-r-cran-spatstat.model-20240323-200322-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 387s autopkgtest [20:09:50]: testbed dpkg architecture: ppc64el 387s autopkgtest [20:09:50]: testbed apt version: 2.7.12 387s autopkgtest [20:09:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 388s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 394s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 394s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 394s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 394s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3981 kB] 394s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 394s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 394s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 394s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 394s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4276 kB] 394s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 394s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 394s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 394s Fetched 9666 kB in 4s (2616 kB/s) 394s Reading package lists... 396s Reading package lists... 396s Building dependency tree... 396s Reading state information... 396s Calculating upgrade... 396s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 396s Reading package lists... 397s Building dependency tree... 397s Reading state information... 397s 0 upgraded, 0 newly installed, 0 to remove and 244 not upgraded. 398s sh: Attempting to set up Debian/Ubuntu apt sources automatically 398s sh: Distribution appears to be Ubuntu 398s Reading package lists... 399s Building dependency tree... 399s Reading state information... 399s eatmydata is already the newest version (131-1). 399s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 399s Reading package lists... 403s Building dependency tree... 403s Reading state information... 403s dbus is already the newest version (1.14.10-4ubuntu1). 403s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 403s Reading package lists... 403s Building dependency tree... 403s Reading state information... 403s rng-tools-debian is already the newest version (2.4). 403s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 403s Reading package lists... 403s Building dependency tree... 403s Reading state information... 403s The following packages will be REMOVED: 403s cloud-init* python3-configobj* python3-debconf* 403s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 403s After this operation, 3256 kB disk space will be freed. 403s (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 ... 70156 files and directories currently installed.) 403s Removing cloud-init (24.1.2-0ubuntu1) ... 403s Removing python3-configobj (5.0.8-3) ... 403s Removing python3-debconf (1.5.86) ... 403s Processing triggers for man-db (2.12.0-3) ... 403s (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 ... 69767 files and directories currently installed.) 403s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 403s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 403s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 403s invoke-rc.d: policy-rc.d denied execution of try-restart. 403s Reading package lists... 403s Building dependency tree... 403s Reading state information... 403s linux-generic is already the newest version (6.8.0-11.11+1). 403s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 403s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 403s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 403s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 406s Reading package lists... 406s Reading package lists... 406s Building dependency tree... 406s Reading state information... 406s Calculating upgrade... 407s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 407s Reading package lists... 407s Building dependency tree... 407s Reading state information... 407s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 407s autopkgtest [20:10:10]: rebooting testbed after setup commands that affected boot 451s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 467s autopkgtest [20:11:00]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 469s autopkgtest [20:11:12]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-spatstat.model 472s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-spatstat.model 3.2-8-1 (dsc) [2597 B] 472s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-spatstat.model 3.2-8-1 (tar) [804 kB] 472s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-spatstat.model 3.2-8-1 (diff) [3384 B] 472s gpgv: Signature made Tue Oct 24 08:22:10 2023 UTC 472s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 472s gpgv: issuer "tille@debian.org" 472s gpgv: Can't check signature: No public key 472s dpkg-source: warning: cannot verify inline signature for ./r-cran-spatstat.model_3.2-8-1.dsc: no acceptable signature found 472s autopkgtest [20:11:15]: testing package r-cran-spatstat.model version 3.2-8-1 473s autopkgtest [20:11:16]: build not needed 477s autopkgtest [20:11:20]: test run-unit-test: preparing testbed 489s Reading package lists... 489s Building dependency tree... 489s Reading state information... 489s Starting pkgProblemResolver with broken count: 0 489s Starting 2 pkgProblemResolver with broken count: 0 489s Done 489s The following additional packages will be installed: 489s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 489s fonts-mathjax libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 489s libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b 489s libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-mathjax liblapack3 liblerc4 489s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 489s libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 489s libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 489s libxss1 libxt6 littler r-base-core r-cran-abind r-cran-codetools 489s r-cran-deldir r-cran-foreach r-cran-glmnet r-cran-goftest r-cran-gsl 489s r-cran-iterators r-cran-lattice r-cran-littler r-cran-locfit r-cran-matrix 489s r-cran-mgcv r-cran-nleqslv r-cran-nlme r-cran-pkgkitten r-cran-polyclip 489s r-cran-rcpp r-cran-rcppeigen r-cran-rpart r-cran-shape r-cran-sm 489s r-cran-spatial r-cran-spatstat r-cran-spatstat.data r-cran-spatstat.explore 489s r-cran-spatstat.geom r-cran-spatstat.linnet r-cran-spatstat.model 489s r-cran-spatstat.random r-cran-spatstat.sparse r-cran-spatstat.utils 489s r-cran-survival r-cran-tensor unzip x11-common xdg-utils zip 489s Suggested packages: 489s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 489s fonts-mathjax-extras fonts-stix libjs-mathjax-doc tcl8.6 tk8.6 elpa-ess 489s r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-knitr r-cran-testthat 489s r-cran-xfun r-cran-rmarkdown r-cran-getopt r-cran-interp r-cran-gam 489s r-cran-inline 489s Recommended packages: 489s r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl 489s libx11-protocol-perl x11-utils x11-xserver-utils 489s The following NEW packages will be installed: 489s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 489s fonts-dejavu-mono fonts-mathjax libblas3 libcairo2 libdatrie1 libdeflate0 489s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 libgslcblas0 489s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-mathjax 489s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 489s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 489s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 489s libxft2 libxrender1 libxss1 libxt6 littler r-base-core r-cran-abind 489s r-cran-codetools r-cran-deldir r-cran-foreach r-cran-glmnet r-cran-goftest 489s r-cran-gsl r-cran-iterators r-cran-lattice r-cran-littler r-cran-locfit 489s r-cran-matrix r-cran-mgcv r-cran-nleqslv r-cran-nlme r-cran-pkgkitten 489s r-cran-polyclip r-cran-rcpp r-cran-rcppeigen r-cran-rpart r-cran-shape 489s r-cran-sm r-cran-spatial r-cran-spatstat r-cran-spatstat.data 489s r-cran-spatstat.explore r-cran-spatstat.geom r-cran-spatstat.linnet 489s r-cran-spatstat.model r-cran-spatstat.random r-cran-spatstat.sparse 489s r-cran-spatstat.utils r-cran-survival r-cran-tensor unzip x11-common 489s xdg-utils zip 489s 0 upgraded, 84 newly installed, 0 to remove and 0 not upgraded. 489s Need to get 97.1 MB/97.1 MB of archives. 489s After this operation, 215 MB of additional disk space will be used. 489s Get:1 /tmp/autopkgtest.nzJ8xp/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [768 B] 489s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 489s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 489s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 489s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 489s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig ppc64el 2.15.0-1ubuntu1 [192 kB] 489s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 489s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 489s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 489s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 489s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 489s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 489s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB] 489s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libdatrie1 ppc64el 0.2.13-3 [25.1 kB] 489s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 489s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 489s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 489s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 489s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgslcblas0 ppc64el 2.7.1+dfsg-6ubuntu1 [85.3 kB] 489s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgsl27 ppc64el 2.7.1+dfsg-6ubuntu1 [1064 kB] 489s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 489s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 489s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libice6 ppc64el 2:1.0.10-1build2 [49.3 kB] 489s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 489s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 489s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 489s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 489s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai-data all 0.1.29-2 [158 kB] 489s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai0 ppc64el 0.1.29-2 [21.4 kB] 489s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el libpango-1.0-0 ppc64el 1.51.0+ds-4 [266 kB] 489s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangoft2-1.0-0 ppc64el 1.51.0+ds-4 [49.5 kB] 489s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangocairo-1.0-0 ppc64el 1.51.0+ds-4 [31.2 kB] 489s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper1 ppc64el 1.1.29 [13.5 kB] 489s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper-utils ppc64el 1.1.29 [8710 B] 489s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB] 489s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el libsm6 ppc64el 2:1.2.3-1build2 [18.5 kB] 489s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el libtcl8.6 ppc64el 8.6.13+dfsg-2 [1179 kB] 489s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 489s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB] 489s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 489s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] 489s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el libxss1 ppc64el 1:1.2.3-1build2 [8982 B] 489s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libtk8.6 ppc64el 8.6.14-1 [944 kB] 490s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libxt6 ppc64el 1:1.2.1-1.1 [198 kB] 490s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el zip ppc64el 3.0-13 [192 kB] 490s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el unzip ppc64el 6.0-28ubuntu3 [192 kB] 490s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 490s Get:48 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base-core ppc64el 4.3.2-1build1 [27.4 MB] 492s Get:49 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-littler ppc64el 0.3.19-1 [95.1 kB] 492s Get:50 http://ftpmaster.internal/ubuntu noble/universe ppc64el littler all 0.3.19-1 [2472 B] 492s Get:51 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-abind all 1.4-5-2 [63.6 kB] 492s Get:52 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-codetools all 0.2-19-1 [90.5 kB] 492s Get:53 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-deldir ppc64el 2.0-4-1 [273 kB] 492s Get:54 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-iterators all 1.0.14-1 [336 kB] 492s Get:55 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-foreach all 1.5.2-1 [124 kB] 492s Get:56 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-lattice ppc64el 0.22-5-1 [1343 kB] 492s Get:57 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-matrix ppc64el 1.6-5-1 [4057 kB] 492s Get:58 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-shape all 1.4.6-1 [770 kB] 492s Get:59 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-survival ppc64el 3.5-8-1 [6160 kB] 493s Get:60 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 493s Get:61 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-rcpp ppc64el 1.0.12-1 [1989 kB] 493s Get:62 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-rcppeigen ppc64el 0.3.3.9.4-1 [1216 kB] 493s Get:63 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 493s Get:64 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-glmnet ppc64el 4.1-8-1 [1978 kB] 493s Get:65 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-goftest ppc64el 1.2-3-1 [60.2 kB] 493s Get:66 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-gsl ppc64el 2.1-8-1 [492 kB] 493s Get:67 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-locfit ppc64el 1.5-9.8-1 [570 kB] 493s Get:68 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-nlme ppc64el 3.1.164-1 [2281 kB] 493s Get:69 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-mgcv ppc64el 1.9-1-1 [3393 kB] 494s Get:70 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-nleqslv ppc64el 3.3.5-1 [106 kB] 494s Get:71 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-polyclip ppc64el 1.10-6-1 [121 kB] 494s Get:72 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-rpart ppc64el 4.1.23-1 [672 kB] 494s Get:73 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-sm ppc64el 2.2-6.0-1 [795 kB] 494s Get:74 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatial ppc64el 7.3-17-1 [137 kB] 494s Get:75 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.utils ppc64el 3.0-4-1 [362 kB] 494s Get:76 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.data all 3.0-4-1 [4090 kB] 494s Get:77 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.geom ppc64el 3.2-8-1 [3855 kB] 494s Get:78 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.random ppc64el 3.2-2-1 [1146 kB] 494s Get:79 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-tensor all 1.5-4 [15.7 kB] 494s Get:80 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.sparse ppc64el 3.0-3-1 [219 kB] 494s Get:81 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.explore ppc64el 3.2-5-1 [3294 kB] 494s Get:82 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.model ppc64el 3.2-8-1 [3290 kB] 494s Get:83 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.linnet ppc64el 3.1-3-1 [1415 kB] 494s Get:84 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat ppc64el 3.0-7-1 [3817 kB] 495s Preconfiguring packages ... 495s Fetched 97.1 MB in 9s (11.0 MB/s) 495s Selecting previously unselected package fonts-dejavu-mono. 495s (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 ... 69712 files and directories currently installed.) 495s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 495s Unpacking fonts-dejavu-mono (2.37-8) ... 495s Selecting previously unselected package fonts-dejavu-core. 495s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 495s Unpacking fonts-dejavu-core (2.37-8) ... 495s Selecting previously unselected package fontconfig-config. 495s Preparing to unpack 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unselected package libdeflate0:ppc64el. 496s Preparing to unpack .../13-libdeflate0_1.19-1_ppc64el.deb ... 496s Unpacking libdeflate0:ppc64el (1.19-1) ... 496s Selecting previously unselected package libgfortran5:ppc64el. 496s Preparing to unpack .../14-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 496s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 496s Selecting previously unselected package libgomp1:ppc64el. 496s Preparing to unpack .../15-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 496s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 496s Selecting previously unselected package libgraphite2-3:ppc64el. 496s Preparing to unpack .../16-libgraphite2-3_1.3.14-2_ppc64el.deb ... 496s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 496s Selecting previously unselected package libgslcblas0:ppc64el. 496s Preparing to unpack .../17-libgslcblas0_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 496s Unpacking libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 496s Selecting previously unselected package libgsl27:ppc64el. 496s Preparing to unpack .../18-libgsl27_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 496s Unpacking libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 496s Selecting previously unselected package libharfbuzz0b:ppc64el. 496s Preparing to unpack .../19-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 496s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 496s Selecting previously unselected package x11-common. 496s Preparing to unpack .../20-x11-common_1%3a7.7+23ubuntu2_all.deb ... 496s Unpacking x11-common (1:7.7+23ubuntu2) ... 496s Selecting previously unselected package libice6:ppc64el. 496s Preparing to unpack .../21-libice6_2%3a1.0.10-1build2_ppc64el.deb ... 496s Unpacking libice6:ppc64el (2:1.0.10-1build2) ... 496s Selecting previously unselected package libjpeg-turbo8:ppc64el. 496s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 496s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 496s Selecting previously unselected package libjpeg8:ppc64el. 496s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 496s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 496s Selecting previously unselected package liblapack3:ppc64el. 496s Preparing to unpack .../24-liblapack3_3.12.0-3_ppc64el.deb ... 496s Unpacking liblapack3:ppc64el (3.12.0-3) ... 496s Selecting previously unselected package liblerc4:ppc64el. 496s Preparing to unpack .../25-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 496s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 496s Selecting previously unselected package libthai-data. 496s Preparing to unpack .../26-libthai-data_0.1.29-2_all.deb ... 496s Unpacking libthai-data (0.1.29-2) ... 496s Selecting previously unselected package libthai0:ppc64el. 496s Preparing to unpack .../27-libthai0_0.1.29-2_ppc64el.deb ... 496s Unpacking libthai0:ppc64el (0.1.29-2) ... 496s Selecting previously unselected package libpango-1.0-0:ppc64el. 496s Preparing to unpack .../28-libpango-1.0-0_1.51.0+ds-4_ppc64el.deb ... 496s Unpacking libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 496s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 496s Preparing to unpack .../29-libpangoft2-1.0-0_1.51.0+ds-4_ppc64el.deb ... 496s Unpacking libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 496s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 496s Preparing to unpack .../30-libpangocairo-1.0-0_1.51.0+ds-4_ppc64el.deb ... 496s Unpacking libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 496s Selecting previously unselected package libpaper1:ppc64el. 496s Preparing to unpack .../31-libpaper1_1.1.29_ppc64el.deb ... 496s Unpacking libpaper1:ppc64el (1.1.29) ... 496s Selecting previously unselected package libpaper-utils. 496s Preparing to unpack .../32-libpaper-utils_1.1.29_ppc64el.deb ... 496s Unpacking libpaper-utils (1.1.29) ... 496s Selecting previously unselected package libsharpyuv0:ppc64el. 496s Preparing to unpack .../33-libsharpyuv0_1.3.2-0.4_ppc64el.deb ... 506s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ... 506s Selecting previously unselected package libsm6:ppc64el. 506s Preparing to unpack .../34-libsm6_2%3a1.2.3-1build2_ppc64el.deb ... 506s Unpacking libsm6:ppc64el (2:1.2.3-1build2) ... 506s Selecting previously unselected package libtcl8.6:ppc64el. 506s Preparing to unpack .../35-libtcl8.6_8.6.13+dfsg-2_ppc64el.deb ... 506s Unpacking libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 506s Selecting previously unselected package libjbig0:ppc64el. 506s Preparing to unpack .../36-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 506s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 506s Selecting previously unselected package libwebp7:ppc64el. 506s Preparing to unpack .../37-libwebp7_1.3.2-0.4_ppc64el.deb ... 506s Unpacking libwebp7:ppc64el (1.3.2-0.4) ... 506s Selecting previously unselected package libtiff6:ppc64el. 506s Preparing to unpack .../38-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ... 506s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 506s Selecting previously unselected package libxft2:ppc64el. 506s Preparing to unpack .../39-libxft2_2.3.6-1_ppc64el.deb ... 506s Unpacking libxft2:ppc64el (2.3.6-1) ... 506s Selecting previously unselected package libxss1:ppc64el. 506s Preparing to unpack .../40-libxss1_1%3a1.2.3-1build2_ppc64el.deb ... 506s Unpacking libxss1:ppc64el (1:1.2.3-1build2) ... 506s Selecting previously unselected package libtk8.6:ppc64el. 506s Preparing to unpack .../41-libtk8.6_8.6.14-1_ppc64el.deb ... 506s Unpacking libtk8.6:ppc64el (8.6.14-1) ... 506s Selecting previously unselected package libxt6:ppc64el. 506s Preparing to unpack .../42-libxt6_1%3a1.2.1-1.1_ppc64el.deb ... 506s Unpacking libxt6:ppc64el (1:1.2.1-1.1) ... 506s Selecting previously unselected package zip. 506s Preparing to unpack .../43-zip_3.0-13_ppc64el.deb ... 506s Unpacking zip (3.0-13) ... 506s Selecting previously unselected package unzip. 506s Preparing to unpack .../44-unzip_6.0-28ubuntu3_ppc64el.deb ... 506s Unpacking unzip (6.0-28ubuntu3) ... 506s Selecting previously unselected package xdg-utils. 506s Preparing to unpack .../45-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 506s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 506s Selecting previously unselected package r-base-core. 506s Preparing to unpack .../46-r-base-core_4.3.2-1build1_ppc64el.deb ... 506s Unpacking r-base-core (4.3.2-1build1) ... 506s Selecting previously unselected package r-cran-littler. 506s Preparing to unpack .../47-r-cran-littler_0.3.19-1_ppc64el.deb ... 506s Unpacking r-cran-littler (0.3.19-1) ... 506s Selecting previously unselected package littler. 506s Preparing to unpack .../48-littler_0.3.19-1_all.deb ... 506s Unpacking littler (0.3.19-1) ... 506s Selecting previously unselected package r-cran-abind. 506s Preparing to unpack .../49-r-cran-abind_1.4-5-2_all.deb ... 506s Unpacking r-cran-abind (1.4-5-2) ... 506s Selecting previously unselected package r-cran-codetools. 506s Preparing to unpack .../50-r-cran-codetools_0.2-19-1_all.deb ... 506s Unpacking r-cran-codetools (0.2-19-1) ... 506s Selecting previously unselected package r-cran-deldir. 506s Preparing to unpack .../51-r-cran-deldir_2.0-4-1_ppc64el.deb ... 506s Unpacking r-cran-deldir (2.0-4-1) ... 506s Selecting previously unselected package r-cran-iterators. 506s Preparing to unpack .../52-r-cran-iterators_1.0.14-1_all.deb ... 506s Unpacking r-cran-iterators (1.0.14-1) ... 506s Selecting previously unselected package r-cran-foreach. 506s Preparing to unpack .../53-r-cran-foreach_1.5.2-1_all.deb ... 506s Unpacking r-cran-foreach (1.5.2-1) ... 506s Selecting previously unselected package r-cran-lattice. 506s Preparing to unpack .../54-r-cran-lattice_0.22-5-1_ppc64el.deb ... 506s Unpacking r-cran-lattice (0.22-5-1) ... 506s Selecting previously unselected package r-cran-matrix. 506s Preparing to unpack .../55-r-cran-matrix_1.6-5-1_ppc64el.deb ... 506s Unpacking r-cran-matrix (1.6-5-1) ... 506s Selecting previously unselected package r-cran-shape. 506s Preparing to unpack .../56-r-cran-shape_1.4.6-1_all.deb ... 506s Unpacking r-cran-shape (1.4.6-1) ... 506s Selecting previously unselected package r-cran-survival. 506s Preparing to unpack .../57-r-cran-survival_3.5-8-1_ppc64el.deb ... 506s Unpacking r-cran-survival (3.5-8-1) ... 506s Selecting previously unselected package r-cran-pkgkitten. 506s Preparing to unpack .../58-r-cran-pkgkitten_0.2.3-1_all.deb ... 506s Unpacking r-cran-pkgkitten (0.2.3-1) ... 506s Selecting previously unselected package r-cran-rcpp. 506s Preparing to unpack .../59-r-cran-rcpp_1.0.12-1_ppc64el.deb ... 506s Unpacking r-cran-rcpp (1.0.12-1) ... 506s Selecting previously unselected package r-cran-rcppeigen. 506s Preparing to unpack .../60-r-cran-rcppeigen_0.3.3.9.4-1_ppc64el.deb ... 506s Unpacking r-cran-rcppeigen (0.3.3.9.4-1) ... 506s Selecting previously unselected package libjs-mathjax. 506s Preparing to unpack .../61-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 506s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 506s Selecting previously unselected package r-cran-glmnet. 506s Preparing to unpack .../62-r-cran-glmnet_4.1-8-1_ppc64el.deb ... 506s Unpacking r-cran-glmnet (4.1-8-1) ... 506s Selecting previously unselected package r-cran-goftest. 506s Preparing to unpack .../63-r-cran-goftest_1.2-3-1_ppc64el.deb ... 506s Unpacking r-cran-goftest (1.2-3-1) ... 506s Selecting previously unselected package r-cran-gsl. 506s Preparing to unpack .../64-r-cran-gsl_2.1-8-1_ppc64el.deb ... 506s Unpacking r-cran-gsl (2.1-8-1) ... 506s Selecting previously unselected package r-cran-locfit. 506s Preparing to unpack .../65-r-cran-locfit_1.5-9.8-1_ppc64el.deb ... 506s Unpacking r-cran-locfit (1.5-9.8-1) ... 506s Selecting previously unselected package r-cran-nlme. 506s Preparing to unpack .../66-r-cran-nlme_3.1.164-1_ppc64el.deb ... 506s Unpacking r-cran-nlme (3.1.164-1) ... 506s Selecting previously unselected package r-cran-mgcv. 506s Preparing to unpack .../67-r-cran-mgcv_1.9-1-1_ppc64el.deb ... 506s Unpacking r-cran-mgcv (1.9-1-1) ... 506s Selecting previously unselected package r-cran-nleqslv. 506s Preparing to unpack .../68-r-cran-nleqslv_3.3.5-1_ppc64el.deb ... 506s Unpacking r-cran-nleqslv (3.3.5-1) ... 506s Selecting previously unselected package r-cran-polyclip. 506s Preparing to unpack .../69-r-cran-polyclip_1.10-6-1_ppc64el.deb ... 506s Unpacking r-cran-polyclip (1.10-6-1) ... 506s Selecting previously unselected package r-cran-rpart. 506s Preparing to unpack .../70-r-cran-rpart_4.1.23-1_ppc64el.deb ... 506s Unpacking r-cran-rpart (4.1.23-1) ... 506s Selecting previously unselected package r-cran-sm. 506s Preparing to unpack .../71-r-cran-sm_2.2-6.0-1_ppc64el.deb ... 506s Unpacking r-cran-sm (2.2-6.0-1) ... 506s Selecting previously unselected package r-cran-spatial. 506s Preparing to unpack .../72-r-cran-spatial_7.3-17-1_ppc64el.deb ... 506s Unpacking r-cran-spatial (7.3-17-1) ... 506s Selecting previously unselected package r-cran-spatstat.utils. 506s Preparing to unpack .../73-r-cran-spatstat.utils_3.0-4-1_ppc64el.deb ... 506s Unpacking r-cran-spatstat.utils (3.0-4-1) ... 506s Selecting previously unselected package r-cran-spatstat.data. 506s Preparing to unpack .../74-r-cran-spatstat.data_3.0-4-1_all.deb ... 506s Unpacking r-cran-spatstat.data (3.0-4-1) ... 506s Selecting previously unselected package r-cran-spatstat.geom. 506s Preparing to unpack .../75-r-cran-spatstat.geom_3.2-8-1_ppc64el.deb ... 506s Unpacking r-cran-spatstat.geom (3.2-8-1) ... 506s Selecting previously unselected package r-cran-spatstat.random. 506s Preparing to unpack .../76-r-cran-spatstat.random_3.2-2-1_ppc64el.deb ... 506s Unpacking r-cran-spatstat.random (3.2-2-1) ... 506s Selecting previously unselected package r-cran-tensor. 506s Preparing to unpack .../77-r-cran-tensor_1.5-4_all.deb ... 506s Unpacking r-cran-tensor (1.5-4) ... 506s Selecting previously unselected package r-cran-spatstat.sparse. 506s Preparing to unpack .../78-r-cran-spatstat.sparse_3.0-3-1_ppc64el.deb ... 506s Unpacking r-cran-spatstat.sparse (3.0-3-1) ... 506s Selecting previously unselected package r-cran-spatstat.explore. 506s Preparing to unpack .../79-r-cran-spatstat.explore_3.2-5-1_ppc64el.deb ... 506s Unpacking r-cran-spatstat.explore (3.2-5-1) ... 506s Selecting previously unselected package r-cran-spatstat.model. 506s Preparing to unpack .../80-r-cran-spatstat.model_3.2-8-1_ppc64el.deb ... 506s Unpacking r-cran-spatstat.model (3.2-8-1) ... 506s Selecting previously unselected package r-cran-spatstat.linnet. 506s Preparing to unpack .../81-r-cran-spatstat.linnet_3.1-3-1_ppc64el.deb ... 506s Unpacking r-cran-spatstat.linnet (3.1-3-1) ... 506s Selecting previously unselected package r-cran-spatstat. 506s Preparing to unpack .../82-r-cran-spatstat_3.0-7-1_ppc64el.deb ... 506s Unpacking r-cran-spatstat (3.0-7-1) ... 506s Selecting previously unselected package autopkgtest-satdep. 506s Preparing to unpack .../83-1-autopkgtest-satdep.deb ... 506s Unpacking autopkgtest-satdep (0) ... 506s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 506s Setting up libpixman-1-0:ppc64el (0.42.2-1) ... 506s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ... 506s Setting up libpaper1:ppc64el (1.1.29) ... 506s 506s Creating config file /etc/papersize with new version 506s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 506s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 506s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 506s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 506s Setting up libdatrie1:ppc64el (0.2.13-3) ... 506s Setting up libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 506s Setting up libxcb-render0:ppc64el (1.15-1) ... 506s Setting up unzip (6.0-28ubuntu3) ... 506s Setting up x11-common (1:7.7+23ubuntu2) ... 506s Setting up libdeflate0:ppc64el (1.19-1) ... 506s Setting up libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 506s Setting up libxcb-shm0:ppc64el (1.15-1) ... 506s Setting up libpaper-utils (1.1.29) ... 506s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 506s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 506s Setting up zip (3.0-13) ... 506s Setting up libblas3:ppc64el (3.12.0-3) ... 506s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 506s Setting up fonts-dejavu-mono (2.37-8) ... 506s Setting up libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 506s Setting up fonts-dejavu-core (2.37-8) ... 506s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 506s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 506s Setting up libwebp7:ppc64el (1.3.2-0.4) ... 506s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 506s Setting up libthai-data (0.1.29-2) ... 506s Setting up libxss1:ppc64el (1:1.2.3-1build2) ... 506s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 506s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 506s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 506s Setting up libice6:ppc64el (2:1.0.10-1build2) ... 506s Setting up 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Removing autopkgtest-satdep (0) ... 509s autopkgtest [20:11:52]: test run-unit-test: [----------------------- 509s BEGIN TEST testsAtoC.R 509s 509s R version 4.3.2 (2023-10-31) -- "Eye Holes" 509s Copyright (C) 2023 The R Foundation for Statistical Computing 509s Platform: powerpc64le-unknown-linux-gnu (64-bit) 509s 509s R is free software and comes with ABSOLUTELY NO WARRANTY. 509s You are welcome to redistribute it under certain conditions. 509s Type 'license()' or 'licence()' for distribution details. 509s 509s R is a collaborative project with many contributors. 509s Type 'contributors()' for more information and 509s 'citation()' on how to cite R or R packages in publications. 509s 509s Type 'demo()' for some demos, 'help()' for on-line help, or 509s 'help.start()' for an HTML browser interface to help. 509s Type 'q()' to quit R. 509s 509s > #' 509s > #' Header for all (concatenated) test files 509s > #' 509s > #' Require spatstat.model 509s > #' Obtain environment variable controlling tests. 509s > #' 509s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 509s > 509s > require(spatstat.model) 509s Loading required package: spatstat.model 509s Loading required package: spatstat.data 510s Loading required package: spatstat.geom 510s spatstat.geom 3.2-8 510s Loading required package: spatstat.random 510s spatstat.random 3.2-2 510s Loading required package: spatstat.explore 510s Loading required package: nlme 510s spatstat.explore 3.2-5 510s Loading required package: rpart 511s spatstat.model 3.2-8 511s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 511s > ALWAYS <- TRUE 511s > cat(paste("--------- Executing", 511s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 511s + "test code -----------\n")) 511s --------- Executing **RESTRICTED** subset of test code ----------- 511s > #' tests/aucroc.R 511s > #' 511s > #' AUC and ROC code 511s > #' 511s > #' $Revision: 1.6 $ $Date: 2020/11/02 06:26:45 $ 511s > 511s > local({ 511s + if(FULLTEST) { 511s + fit <- kppm(redwood ~ I(y-x)) 511s + a <- roc(fit) 511s + b <- auc(fit) 511s + fet <- ppm(amacrine~x+y+marks) 511s + d <- roc(fet) 511s + e <- auc(fet) 511s + } 511s + }) 511s > ## tests/cdf.test.R 511s > 511s > 511s > local({ 511s + NSIM <- 9 511s + op <- spatstat.options(ndummy.min=16, npixel=32) 511s + if(FULLTEST) { 511s + ## Monte Carlo test for Gibbs model 511s + fit <- ppm(cells ~ 1, Strauss(0.07)) 511s + cdf.test(fit, "x", nsim=NSIM) 511s + 511s + ## cdf.test.slrm 511s + fut <- slrm(japanesepines ~ x + y) 511s + Z <- distmap(japanesepines) 511s + cdf.test(fut, Z) 511s + } 511s + reset.spatstat.options() 511s + }) 511s > 511s > 511s > #' 511s > #' tests/contrib.R 511s > #' 511s > #' Tests for user-contributed code in spatstat 511s > #' 511s > #' $Revision: 1.4 $ $Date: 2021/04/17 02:32:24 $ 511s > 511s > local({ 511s + #' Jinhom 511s + #' Marie-Colette van Lieshout and Ottmar Cronie 511s + X <- redwood3 511s + if(FULLTEST) { 511s + fit <- ppm(X ~ polynom(x,y,2)) 511s + } else { 511s + X <- X[c(TRUE,FALSE)] 511s + spatstat.options(npixel=32, ndummy.min=16) 511s + fit <- ppm(X ~ x) 511s + } 511s + lam <- predict(fit) 511s + lamX <- fitted(fit, dataonly=TRUE) 511s + lmin <- 0.9 * min(lam) 511s + g1 <- Ginhom(X, lambda=fit, update=TRUE) 511s + if(FULLTEST) { 511s + g2 <- Ginhom(X, lambda=fit, update=FALSE, lmin = lmin) 511s + g3 <- Ginhom(X, lambda=lam, lmin=lmin) 511s + g4 <- Ginhom(X, lambda=lamX, lmin=lmin) 511s + } 511s + if(ALWAYS) { 511s + f2 <- Finhom(X, lambda=fit, update=FALSE) 511s + } 511s + if(FULLTEST) { 511s + f1 <- Finhom(X, lambda=fit, update=TRUE) 511s + f3 <- Finhom(X, lambda=lam, lmin=lmin) 511s + } 511s + if(!FULLTEST) reset.spatstat.options() 511s + }) 511s > 511s BEGIN TEST testsD.R 511s 511s R version 4.3.2 (2023-10-31) -- "Eye Holes" 511s Copyright (C) 2023 The R Foundation for Statistical Computing 511s Platform: powerpc64le-unknown-linux-gnu (64-bit) 511s 511s R is free software and comes with ABSOLUTELY NO WARRANTY. 511s You are welcome to redistribute it under certain conditions. 511s Type 'license()' or 'licence()' for distribution details. 511s 511s R is a collaborative project with many contributors. 511s Type 'contributors()' for more information and 511s 'citation()' on how to cite R or R packages in publications. 511s 511s Type 'demo()' for some demos, 'help()' for on-line help, or 511s 'help.start()' for an HTML browser interface to help. 511s Type 'q()' to quit R. 511s 511s > #' 511s > #' Header for all (concatenated) test files 511s > #' 511s > #' Require spatstat.model 511s > #' Obtain environment variable controlling tests. 511s > #' 511s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 511s > 511s > require(spatstat.model) 511s Loading required package: spatstat.model 511s Loading required package: spatstat.data 512s Loading required package: spatstat.geom 512s spatstat.geom 3.2-8 512s Loading required package: spatstat.random 512s spatstat.random 3.2-2 512s Loading required package: spatstat.explore 512s Loading required package: nlme 512s spatstat.explore 3.2-5 512s Loading required package: rpart 512s spatstat.model 3.2-8 512s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 512s > ALWAYS <- TRUE 512s > cat(paste("--------- Executing", 512s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 512s + "test code -----------\n")) 512s --------- Executing **RESTRICTED** subset of test code ----------- 512s > #' 512s > #' tests/deltasuffstat.R 512s > #' 512s > #' Explicit tests of 'deltasuffstat' 512s > #' 512s > #' $Revision: 1.4 $ $Date: 2021/01/22 08:08:48 $ 512s > 512s > if(!FULLTEST) 512s + spatstat.options(npixel=32, ndummy.min=16) 512s > 512s > if(ALWAYS) { # depends on C code 512s + local({ 512s + 512s + disagree <- function(x, y, tol=1e-7) { !is.null(x) && !is.null(y) && max(abs(x-y)) > tol } 512s + 512s + flydelta <- function(model, modelname="") { 512s + ## Check execution of different algorithms for 'deltasuffstat' 512s + dSS <- deltasuffstat(model, sparseOK=TRUE) 512s + dBS <- deltasuffstat(model, sparseOK=TRUE, use.special=FALSE, force=TRUE) 512s + dBF <- deltasuffstat(model, sparseOK=FALSE, use.special=FALSE, force=TRUE) 512s + ## Compare results 512s + if(disagree(dBS, dSS)) 512s + stop(paste(modelname, "model: Brute force algorithm disagrees with special algorithm")) 512s + if(disagree(dBF, dBS)) 512s + stop(paste(modelname, "model: Sparse and full versions of brute force algorithm disagree")) 512s + return(invisible(NULL)) 512s + } 512s + 512s + modelS <- ppm(cells ~ x, Strauss(0.13), nd=10) 512s + flydelta(modelS, "Strauss") 512s + 512s + antsub <- ants[c(FALSE,TRUE,FALSE)] 512s + rmat <- matrix(c(130, 90, 90, 60), 2, 2) 512s + 512s + modelM <- ppm(antsub ~ 1, MultiStrauss(rmat), nd=16) 512s + flydelta(modelM, "MultiStrauss") 512s + 512s + modelA <- ppm(antsub ~ 1, HierStrauss(rmat, archy=c(2,1)), nd=16) 512s + flydelta(modelA, "HierStrauss") 512s + }) 512s + 512s + } 532s > 532s > reset.spatstat.options() 532s Loading required package: spatstat.model 532s Loading required package: spatstat.data 532s > #' 532s > #' tests/density.R 532s > #' 532s > #' Test behaviour of density() methods, 532s > #' relrisk(), Smooth() 532s > #' and inhomogeneous summary functions 532s > #' and idw, adaptive.density, intensity 532s > #' 532s > #' $Revision: 1.62 $ $Date: 2022/05/22 11:14:51 $ 532s > #' 532s > 532s > if(!FULLTEST) 532s + spatstat.options(npixel=32, ndummy.min=16) 532s > 532s > 532s > local({ 532s + ## likewise 'relrisk.ppm' 532s + fit <- ppm(ants ~ x) 532s + rants <- function(..., model=fit) { 532s + a <- relrisk(model, sigma=100, se=TRUE, ...) 532s + return(TRUE) 532s + } 532s + if(ALWAYS) { 532s + rants() 532s + rants(diggle=TRUE) 532s + rants(edge=FALSE) 532s + rants(at="points") 532s + rants(casecontrol=FALSE) 532s + rants(relative=TRUE) 532s + } 532s + if(FULLTEST) { 532s + rants(diggle=TRUE, at="points") 532s + rants(edge=FALSE, at="points") 532s + rants(casecontrol=FALSE, relative=TRUE) 532s + rants(casecontrol=FALSE,at="points") 532s + rants(relative=TRUE,at="points") 532s + rants(casecontrol=FALSE, relative=TRUE,at="points") 532s + rants(relative=TRUE, control="Cataglyphis", case="Messor") 532s + rants(relative=TRUE, control="Cataglyphis", case="Messor", at="points") 532s + } 532s + ## more than 2 types 532s + fut <- ppm(sporophores ~ x) 532s + if(ALWAYS) { 532s + rants(model=fut) 532s + } 532s + if(FULLTEST) { 532s + rants(model=fut, at="points") 532s + rants(model=fut, relative=TRUE, at="points") 532s + } 532s + if(FULLTEST) { 532s + ## cases of 'intensity' etc 532s + a <- intensity(ppm(amacrine ~ 1)) 532s + } 532s + }) 532s > 532s > reset.spatstat.options() 532s > 532s > #' 532s > #' tests/diagnostique.R 532s > #' 532s > #' Diagnostic tools such as diagnose.ppm, qqplot.ppm 532s > #' 532s > #' $Revision: 1.6 $ $Date: 2020/04/28 12:58:26 $ 532s > #' 532s > 532s > if(FULLTEST) { 532s + local({ 532s + fit <- ppm(cells ~ x) 532s + diagE <- diagnose.ppm(fit, type="eem") 532s + diagI <- diagnose.ppm(fit, type="inverse") 532s + diagP <- diagnose.ppm(fit, type="Pearson") 532s + plot(diagE, which="all") 532s + plot(diagI, which="smooth") 532s + plot(diagP, which="x") 532s + plot(diagP, which="marks", plot.neg="discrete") 532s + plot(diagP, which="marks", plot.neg="contour") 532s + plot(diagP, which="smooth", srange=c(-5,5)) 532s + plot(diagP, which="smooth", plot.smooth="contour") 532s + plot(diagP, which="smooth", plot.smooth="image") 532s + 532s + fitS <- ppm(cells ~ x, Strauss(0.08)) 532s + diagES <- diagnose.ppm(fitS, type="eem", clip=FALSE) 532s + diagIS <- diagnose.ppm(fitS, type="inverse", clip=FALSE) 532s + diagPS <- diagnose.ppm(fitS, type="Pearson", clip=FALSE) 532s + plot(diagES, which="marks", plot.neg="imagecontour") 532s + plot(diagPS, which="marks", plot.neg="discrete") 532s + plot(diagPS, which="marks", plot.neg="contour") 532s + plot(diagPS, which="smooth", plot.smooth="image") 532s + plot(diagPS, which="smooth", plot.smooth="contour") 532s + plot(diagPS, which="smooth", plot.smooth="persp") 532s + 532s + #' infinite reach, not border-corrected 532s + fut <- ppm(cells ~ x, Softcore(0.5), correction="isotropic") 532s + diagnose.ppm(fut) 532s + 532s + #' 532s + diagPX <- diagnose.ppm(fit, type="Pearson", cumulative=FALSE) 532s + plot(diagPX, which="y") 532s + 532s + #' simulation based 532s + e <- envelope(cells, nsim=4, savepatterns=TRUE, savefuns=TRUE) 532s + Plist <- rpoispp(40, nsim=5) 532s + 532s + qf <- qqplot.ppm(fit, nsim=4, expr=e, plot.it=FALSE) 532s + print(qf) 532s + qp <- qqplot.ppm(fit, nsim=5, expr=Plist, fast=FALSE) 532s + print(qp) 532s + qp <- qqplot.ppm(fit, nsim=5, expr=expression(rpoispp(40)), plot.it=FALSE) 532s + print(qp) 532s + qg <- qqplot.ppm(fit, nsim=5, style="classical", plot.it=FALSE) 532s + print(qg) 532s + 532s + #' lurking.ppm 532s + #' covariate is numeric vector 532s + fitx <- ppm(cells ~ x) 532s + yvals <- coords(as.ppp(quad.ppm(fitx)))[,"y"] 532s + lurking(fitx, yvals) 532s + #' covariate is stored but is not used in model 532s + Z <- as.im(function(x,y){ x+y }, Window(cells)) 532s + fitxx <- ppm(cells ~ x, data=solist(Zed=Z), allcovar=TRUE) 532s + lurking(fitxx, expression(Zed)) 532s + #' envelope is a ppplist; length < nsim; glmdata=NULL 532s + fit <- ppm(cells ~ 1) 532s + stuff <- lurking(fit, expression(x), envelope=Plist, plot.sd=FALSE) 532s + #' plot.lurk 532s + plot(stuff, shade=NULL) 532s + }) 532s + } 532s > 532s > #' 532s > #' tests/deepeepee.R 532s > #' 532s > #' Tests for determinantal point process models 532s > #' 532s > #' $Revision: 1.9 $ $Date: 2022/04/24 09:14:46 $ 532s > 532s > local({ 532s + if(ALWAYS) { 532s + #' simulate.dppm 532s + jpines <- residualspaper$Fig1 532s + fit <- dppm(jpines ~ 1, dppGauss) 532s + set.seed(10981) 532s + simulate(fit, W=square(5)) 532s + } 532s + if(FULLTEST) { 532s + #' simulate.detpointprocfamily - code blocks 532s + model <- dppGauss(lambda=100, alpha=.05, d=2) 532s + simulate(model, seed=1999, correction="border") 532s + u <- is.stationary(model) 532s + #' other methods for dppm 532s + kay <- Kmodel(fit) 532s + gee <- pcfmodel(fit) 532s + lam <- intensity(fit) 532s + arr <- reach(fit) 532s + pah <- parameters(fit) 532s + #' a user bug report - matrix dimension error 532s + set.seed(256) 532s + dat <- simulate( dppGauss(lambda = 8.5, alpha = 0.1, d = 2), nsim = 1) 532s + } 532s + if(FULLTEST) { 532s + ## cover print.summary.dppm 532s + jpines <- japanesepines[c(TRUE,FALSE,FALSE,FALSE)] 532s + print(summary(dppm(jpines ~ 1, dppGauss))) 532s + print(summary(dppm(jpines ~ 1, dppGauss, method="c"))) 532s + print(summary(dppm(jpines ~ 1, dppGauss, method="p"))) 532s + print(summary(dppm(jpines ~ 1, dppGauss, method="a"))) 532s + } 532s + #' dppeigen code blocks 532s + if(ALWAYS) { 532s + mod <- dppMatern(lambda=2, alpha=0.01, nu=1, d=2) 532s + uT <- dppeigen(mod, trunc=1.1, Wscale=c(1,1), stationary=TRUE) 532s + } 532s + if(FULLTEST) { 532s + uF <- dppeigen(mod, trunc=1.1, Wscale=c(1,1), stationary=FALSE) 532s + vT <- dppeigen(mod, trunc=0.98, Wscale=c(1,1), stationary=TRUE) 532s + vF <- dppeigen(mod, trunc=0.98, Wscale=c(1,1), stationary=FALSE) 532s + } 532s + }) 532s > 532s BEGIN TEST testsEtoF.R 532s 532s R version 4.3.2 (2023-10-31) -- "Eye Holes" 532s Copyright (C) 2023 The R Foundation for Statistical Computing 532s Platform: powerpc64le-unknown-linux-gnu (64-bit) 532s 532s R is free software and comes with ABSOLUTELY NO WARRANTY. 532s You are welcome to redistribute it under certain conditions. 532s Type 'license()' or 'licence()' for distribution details. 532s 532s R is a collaborative project with many contributors. 532s Type 'contributors()' for more information and 532s 'citation()' on how to cite R or R packages in publications. 532s 532s Type 'demo()' for some demos, 'help()' for on-line help, or 532s 'help.start()' for an HTML browser interface to help. 532s Type 'q()' to quit R. 532s 532s > #' 532s > #' Header for all (concatenated) test files 532s > #' 532s > #' Require spatstat.model 532s > #' Obtain environment variable controlling tests. 532s > #' 532s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 532s > 532s > require(spatstat.model) 532s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 532s > ALWAYS <- TRUE 532s > cat(paste("--------- Executing", 532s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 532s + "test code -----------\n")) 532s --------- Executing **RESTRICTED** subset of test code ----------- 532s > # 532s > # tests/envelopes.R 532s > # 532s > # Test validity of envelope data 532s > # 532s > # $Revision: 1.28 $ $Date: 2022/11/24 01:35:26 $ 532s > # 532s > 532s > local({ 532s + 532s + 532s + checktheo <- function(fit) { 532s + fitname <- deparse(substitute(fit)) 532s + en <- envelope(fit, nsim=4, verbose=FALSE, nrep=1e3) 532s + nama <- names(en) 532s + expecttheo <- is.poisson(fit) && is.stationary(fit) 532s + context <- paste("Envelope of", fitname) 532s + if(expecttheo) { 532s + if(!("theo" %in% nama)) 532s + stop(paste(context, "did not contain", sQuote("theo"))) 532s + if("mmean" %in% nama) 532s + stop(paste(context, "unexpectedly contained", sQuote("mmean"))) 532s + } else { 532s + if("theo" %in% nama) 532s + stop(paste(context, "unexpectedly contained", sQuote("theo"))) 532s + if(!("mmean" %in% nama)) 532s + stop(paste(context, "did not contain", sQuote("mmean"))) 532s + } 532s + cat(paste(context, "has correct format\n")) 532s + } 532s + 532s + if(ALWAYS) { 532s + checktheo(ppm(cells ~x)) 532s + } 532s + if(FULLTEST) { 532s + checktheo(ppm(cells)) 532s + checktheo(ppm(cells ~1, Strauss(0.1))) 532s + } 532s + 532s + 532s + #' check savefuns/savepatterns with global 532s + fit <- ppm(cells~x) 532s + if(ALWAYS) Ef <- envelope(fit, Kest, nsim=4, savefuns=TRUE, global=TRUE) 532s + if(FULLTEST) Ep <- envelope(fit, Kest, nsim=4, savepatterns=TRUE, global=TRUE) 532s + #' check handling of 'dangerous' cases 532s + if(FULLTEST) { 532s + fut <- ppm(redwood ~ x) 532s + Ek <- envelope(fut, Kinhom, update=FALSE, nsim=4) 532s + kfut <- kppm(redwood3 ~ x) 532s + Ekk <- envelope(kfut, Kinhom, lambda=density(redwood3), nsim=7) 532s + } 532s + 532s + 532s + if(ALWAYS) { # invokes C code 532s + fit <- ppm(japanesepines ~ 1, Strauss(0.04)) 532s + e6 <- envelope(fit, Kest, nsim=4, fix.n=TRUE) 532s + fit2 <- ppm(amacrine ~ 1, Strauss(0.03)) 532s + e7 <- envelope(fit2, Gcross, nsim=4, fix.marks=TRUE) 532s + } 532s + 532s + 532s + if(FULLTEST) { 532s + fit <- ppm(cells ~ 1, Strauss(0.07)) 532s + U <- envelope(fit, nsim=3, simulate=expression(runifpoint(20))) 532s + kfit <- kppm(redwood3 ~ x) 532s + UU <- envelope(kfit, nsim=7, simulate=expression(simulate(kfit, drop=TRUE))) 532s + VV <- envelope(kfit, nsim=7, weights=1:7) 532s + MM <- envelope(kfit, nsim=7, Kinhom, lambda=density(redwood3)) 532s + } 532s + 532s + if(FULLTEST) { 532s + #' envelope computations in other functions 532s + P <- lurking(cells, expression(x), envelope=TRUE, nsim=9) 532s + print(P) 532s + #' re-using envelope objects in other functions 532s + A <- envelope(cells, nsim=9, savepatterns=TRUE, savefuns=TRUE) 532s + S <- lurking(cells, expression(x), envelope=A, nsim=9) 532s + #' envelope.envelope 532s + B <- envelope(cells, nsim=5, savepatterns=TRUE, savefuns=FALSE) 532s + envelope(B) 532s + } 532s + 532s + 532s + 532s + ## close 'local' 532s + }) 532s Envelope of ppm(cells ~ x) has correct format 532s Generating 8 simulated realisations of fitted Poisson model (4 to estimate the 532s mean and 4 to calculate envelopes) ... 532s 1, 2, 3, 4, 5, 6, 7, 532s 8. 532s 532s Done. 532s Generating 4 simulated realisations of fitted Gibbs model with fixed number of 532s points ... 532s 1, 2, 3, 532s 4. 532s 532s Done. 532s Generating 4 simulated realisations of fitted Gibbs model with fixed number of 532s points of each type ... 532s 1, 2, 3, 532s 4. 532s 532s Done. 532s > #' tests/enveltest.R 532s > #' Envelope tests (dclf.test, mad.test) 532s > #' and two-stage tests (bits.test, dg.test, bits.envelope, dg.envelope) 532s > #' 532s > #' $Revision: 1.3 $ $Date: 2020/04/28 12:58:26 $ 532s > #' 532s > if(FULLTEST) { 532s + local({ 532s + #' handling of NA function values (due to empty point patterns) 532s + set.seed(1234) 532s + X <- rThomas(5, 0.05, 10) 532s + fit <- kppm(X ~ 1, "Thomas") 532s + set.seed(100000) 532s + dclf.test(fit) 532s + set.seed(909) 532s + dg.test(fit, nsim=9) 532s + #' other code blocks 532s + dclf.test(fit, rinterval=c(0, 3), nsim=9) 532s + envelopeTest(X, exponent=3, clamp=TRUE, nsim=9) 532s + }) 532s + } 532s > # 532s > # tests/fastgeyer.R 532s > # 532s > # checks validity of fast C implementation of Geyer interaction 532s > # 532s > # $Revision: 1.4 $ $Date: 2020/04/28 12:58:26 $ 532s > # 532s > if(FULLTEST) { # depends on hardware 532s + local({ 532s + X <- redwood 532s + Q <- quadscheme(X) 532s + U <- union.quad(Q) 532s + EP <- equalpairs.quad(Q) 532s + G <- Geyer(0.11, 2) 532s + # The value r=0.11 is chosen to avoid hardware numerical effects (gcc bug 323). 532s + # It avoids being close any value of pairdist(redwood). 532s + # The nearest such values are 0.1077.. and 0.1131.. 532s + # By contrast if r = 0.1 there are values differing from 0.1 by 3e-17 532s + a <- pairsat.family$eval(X,U,EP,G$pot,G$par,"border") 532s + b <- G$fasteval(X,U,EP,G$pot,G$par,"border") 532s + if(!all(a==b)) 532s + stop("Results of Geyer()$fasteval and pairsat.family$eval do not match") 532s + # ... 532s + # and again for a non-integer value of 'sat' 532s + # (spotted by Thordis Linda Thorarinsdottir) 532s + G <- Geyer(0.11, 2.5) 532s + a <- pairsat.family$eval(X,U,EP,G$pot,G$par,"border") 532s + b <- G$fasteval(X,U,EP,G$pot,G$par,"border") 532s + if(!all(a==b)) 532s + stop("Results of Geyer()$fasteval and pairsat.family$eval do not match when sat is not an integer") 532s + # and again for sat < 1 532s + # (spotted by Rolf) 532s + G <- Geyer(0.11, 0.5) 532s + a <- pairsat.family$eval(X,U,EP,G$pot,G$par,"border") 532s + b <- G$fasteval(X,U,EP,G$pot,G$par,"border") 532s + if(!all(a==b)) 532s + stop("Results of Geyer()$fasteval and pairsat.family$eval do not match when sat < 1") 532s + }) 532s + } 532s > 532s > #' tests/formuli.R 532s > #' 532s > #' Test machinery for manipulating formulae 532s > #' 532s > #' $Revision: 1.7 $ $Date: 2020/04/28 12:58:26 $ 532s > 532s > local({ 532s + 532s + ff <- function(A, deletevar, B) { 532s + D <- reduceformula(A, deletevar) 532s + if(!spatstat.utils::identical.formulae(D, B)) { 532s + AD <- as.expression(substitute(reduceformula(A,d), 532s + list(A=A, d=deletevar))) 532s + stop(paste(AD, "\n\tyields ", spatstat.utils::pasteFormula(D), 532s + " instead of ", spatstat.utils::pasteFormula(B)), 532s + call.=FALSE) 532s + } 532s + invisible(NULL) 532s + } 532s + 532s + ff(~ x + z, "x", ~z) 532s + 532s + ff(y ~ x + z, "x", y~z) 532s + 532s + ff(~ I(x^2) + z, "x", ~z) 532s + 532s + ff(y ~ poly(x,2) + poly(z,3), "x", y ~poly(z,3)) 532s + 532s + ff(y ~ x + z, "g", y ~ x + z) 532s + 532s + reduceformula(y ~ x+z, "g", verbose=TRUE) 532s + reduceformula(y ~ sin(x-z), "z", verbose=TRUE) 532s + 532s + illegal.iformula(~str*g, itags="str", dfvarnames=c("marks", "g", "x", "y")) 532s + }) 532s NULL 532s > 532s > 532s > 532s > ## 532s > ## tests/funnymarks.R 532s > ## 532s > ## tests involving strange mark values 532s > ## $Revision: 1.7 $ $Date: 2020/04/28 12:58:26 $ 532s > 532s > if(ALWAYS) { # depends on locale 532s + local({ 532s + ## ppm() where mark levels contain illegal characters 532s + hyphenated <- c("a", "not-a") 532s + spaced <- c("U", "non U") 532s + suffixed <- c("a+", "a*") 532s + charred <- c("+", "*") 532s + 532s + irad <- matrix(0.1, 2,2) 532s + hrad <- matrix(0.005, 2, 2) 532s + 532s + tryit <- function(types, X, irad, hrad) { 532s + levels(marks(X)) <- types 532s + fit <- ppm(X ~marks + polynom(x,y,2), 532s + MultiStraussHard(types=types,iradii=irad,hradii=hrad)) 532s + print(fit) 532s + print(coef(fit)) 532s + val <- fitted(fit) 532s + pred <- predict(fit) 532s + return(invisible(NULL)) 532s + } 532s + 532s + tryit(hyphenated, amacrine, irad, hrad) 532s + tryit(spaced, amacrine, irad, hrad) 532s + tryit(suffixed, amacrine, irad, hrad) 532s + tryit(charred, amacrine, irad, hrad) 532s + 532s + ## marks which are dates 532s + X <- cells 532s + n <- npoints(X) 532s + endoftime <- rep(ISOdate(2001,1,1), n) 532s + eotDate <- rep(as.Date("2001-01-01"), n) 532s + markformat(endoftime) 532s + markformat(eotDate) 532s + marks(X) <- endoftime 532s + print(X) 532s + Y <- X %mark% data.frame(id=1:42, date=endoftime, dd=eotDate) 532s + print(Y) 532s + md <- markformat(endoftime) 532s + 532s + ## mark formats 532s + Z <- Y 532s + marks(Z) <- marks(Z)[1,,drop=FALSE] 532s + ms <- markformat(solist(cells, redwood)) 532s + marks(Z) <- factor(1:npoints(Z)) 532s + marks(Z)[12] <- NA 532s + mz <- is.multitype(Z) 532s + cZ <- coerce.marks.numeric(Z) 532s + marks(Z) <- data.frame(n=1:npoints(Z), 532s + a=factor(sample(letters, npoints(Z), replace=TRUE))) 532s + cZ <- coerce.marks.numeric(Z) 532s + stopifnot(is.multitype(cells %mark% data.frame(a=factor(1:npoints(cells))))) 532s + 532s + a <- numeric.columns(finpines) 532s + b1 <- numeric.columns(amacrine) 532s + b2 <- coerce.marks.numeric(amacrine) 532s + d <- numeric.columns(cells) 532s + f <- numeric.columns(longleaf) 532s + ff <- data.frame(a=factor(letters[1:10]), y=factor(sample(letters, 10))) 532s + numeric.columns(ff) 532s + 532s + ## mark operations 532s + df <- data.frame(x=1:2, y=sample(letters, 2)) 532s + h <- hyperframe(z=1:2, p=solist(cells, cells)) 532s + a <- NULL %mrep% 3 532s + a <- 1:4 %mrep% 3 532s + a <- df %mrep% 3 532s + a <- h %mrep% 3 532s + b <- markcbind(df, h) 532s + b <- markcbind(h, df) 532s + }) 532s + } 532s Nonstationary Multitype Strauss Hardcore process 532s Fitted to point pattern dataset ‘X’ 532s 532s Possible marks: ‘a’ and ‘not-a’ 532s 532s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 532s 532s Fitted trend coefficients: 532s (Intercept) marksnot-a x y I(x^2) I(x * y) 532s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 532s I(y^2) 532s -0.5425654 532s 532s 2 types of points 532s Possible types: 532s [1] a not-a 532s Interaction radii: 532s a not-a 532s a 0.1 0.1 532s not-a 0.1 0.1 532s Hardcore radii: 532s a not-a 532s a 0.005 0.005 532s not-a 0.005 0.005 532s Fitted interaction parameters gamma_ij 532s a not-a 532s a 0.2699920 0.8920719 532s not-a 0.8920719 0.2694374 532s 532s Relevant coefficients: 532s markaxa markaxnot.a marknot.axnot.a 532s -1.3093629 -0.1142086 -1.3114192 532s 532s For standard errors, type coef(summary(x)) 532s (Intercept) marksnot-a x y I(x^2) 532s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 532s I(x * y) I(y^2) markaxa markaxnot.a marknot.axnot.a 532s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 532s Nonstationary Multitype Strauss Hardcore process 532s Fitted to point pattern dataset ‘X’ 532s 532s Possible marks: ‘U’ and ‘non U’ 532s 532s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 532s 532s Fitted trend coefficients: 532s (Intercept) marksnon U x y I(x^2) I(x * y) 532s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 532s I(y^2) 532s -0.5425654 532s 532s 2 types of points 532s Possible types: 532s [1] U non U 532s Interaction radii: 532s U non U 532s U 0.1 0.1 532s non U 0.1 0.1 532s Hardcore radii: 532s U non U 532s U 0.005 0.005 532s non U 0.005 0.005 532s Fitted interaction parameters gamma_ij 532s U non U 532s U 0.2699920 0.8920719 532s non U 0.8920719 0.2694374 532s 532s Relevant coefficients: 532s markUxU markUxnon.U marknon.Uxnon.U 532s -1.3093629 -0.1142086 -1.3114192 532s 532s For standard errors, type coef(summary(x)) 532s (Intercept) marksnon U x y I(x^2) 532s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 532s I(x * y) I(y^2) markUxU markUxnon.U marknon.Uxnon.U 532s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 532s Nonstationary Multitype Strauss Hardcore process 532s Fitted to point pattern dataset ‘X’ 532s 532s Possible marks: ‘a+’ and ‘a*’ 532s 532s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 532s 532s Fitted trend coefficients: 532s (Intercept) marksa* x y I(x^2) I(x * y) 532s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 532s I(y^2) 532s -0.5425654 532s 532s 2 types of points 532s Possible types: 532s [1] a+ a* 532s Interaction radii: 532s a+ a* 532s a+ 0.1 0.1 532s a* 0.1 0.1 532s Hardcore radii: 532s a+ a* 532s a+ 0.005 0.005 532s a* 0.005 0.005 532s Fitted interaction parameters gamma_ij 532s a+ a* 532s a+ 0.2699920 0.8920719 532s a* 0.8920719 0.2694374 532s 532s Relevant coefficients: 532s marka.xa. marka.xa..1 marka..1xa..1 532s -1.3093629 -0.1142086 -1.3114192 532s 532s For standard errors, type coef(summary(x)) 532s (Intercept) marksa* x y I(x^2) 532s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 532s I(x * y) I(y^2) marka.xa. marka.xa..1 marka..1xa..1 532s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 532s Nonstationary Multitype Strauss Hardcore process 532s Fitted to point pattern dataset ‘X’ 532s 532s Possible marks: ‘+’ and ‘*’ 532s 532s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 532s 532s Fitted trend coefficients: 532s (Intercept) marks* x y I(x^2) I(x * y) 532s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 532s I(y^2) 532s -0.5425654 532s 532s 2 types of points 532s Possible types: 532s [1] + * 532s Interaction radii: 532s + * 532s + 0.1 0.1 532s * 0.1 0.1 532s Hardcore radii: 532s + * 532s + 0.005 0.005 532s * 0.005 0.005 532s Fitted interaction parameters gamma_ij 532s + * 532s + 0.2699920 0.8920719 532s * 0.8920719 0.2694374 532s 532s Relevant coefficients: 532s markX.xX. markX.xX..1 markX..1xX..1 532s -1.3093629 -0.1142086 -1.3114192 532s 532s For standard errors, type coef(summary(x)) 532s (Intercept) marks* x y I(x^2) 532s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 532s I(x * y) I(y^2) markX.xX. markX.xX..1 markX..1xX..1 532s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 532s Marked planar point pattern: 42 points 532s marks are dates, of class ‘POSIXt’ 532s window: rectangle = [0, 1] x [0, 1] units 532s Marked planar point pattern: 42 points 532s Mark variables: id, date, dd 532s window: rectangle = [0, 1] x [0, 1] units 532s > 532s BEGIN TEST testsGtoJ.R 532s 532s R version 4.3.2 (2023-10-31) -- "Eye Holes" 532s Copyright (C) 2023 The R Foundation for Statistical Computing 532s Platform: powerpc64le-unknown-linux-gnu (64-bit) 532s 532s R is free software and comes with ABSOLUTELY NO WARRANTY. 532s You are welcome to redistribute it under certain conditions. 532s Type 'license()' or 'licence()' for distribution details. 532s 532s R is a collaborative project with many contributors. 532s Type 'contributors()' for more information and 532s 'citation()' on how to cite R or R packages in publications. 532s 532s Type 'demo()' for some demos, 'help()' for on-line help, or 532s 'help.start()' for an HTML browser interface to help. 532s Type 'q()' to quit R. 532s 532s > #' 532s > #' Header for all (concatenated) test files 532s > #' 532s > #' Require spatstat.model 532s > #' Obtain environment variable controlling tests. 532s > #' 532s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 532s > 532s > require(spatstat.model) 532s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 532s > ALWAYS <- TRUE 532s > cat(paste("--------- Executing", 532s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 532s + "test code -----------\n")) 532s --------- Executing **RESTRICTED** subset of test code ----------- 532s > #' 532s > #' tests/hobjects.R 532s > #' 532s > #' Validity of methods for ppm(... method="ho") 532s > #' 532s > #' $Revision: 1.4 $ $Date: 2022/06/18 10:14:44 $ 532s > 532s > 532s > if(FULLTEST) { 532s + local({ 532s + set.seed(42) 532s + fit <- ppm(cells ~1, Strauss(0.1), improve.type="ho", nsim=10) 532s + fitx <- ppm(cells ~offset(x), Strauss(0.1), improve.type="ho", nsim=10) 532s + 532s + a <- AIC(fit) 532s + ax <- AIC(fitx) 532s + 532s + f <- fitted(fit) 532s + fx <- fitted(fitx) 532s + 532s + p <- predict(fit) 532s + px <- predict(fitx) 532s + }) 532s + } 532s > 532s > 532s > #' tests/hypotests.R 532s > #' Hypothesis tests 532s > #' 532s > #' $Revision: 1.10 $ $Date: 2023/07/17 07:30:48 $ 532s > 532s > if(FULLTEST) { 532s + local({ 532s + 532s + #' scan test with baseline 532s + fit <- ppm(cells ~ x) 532s + lam <- predict(fit) 532s + rr <- c(0.05, 1) 532s + scan.test(cells, rr, nsim=5, 532s + method="poisson", baseline=fit, alternative="less") 532s + scan.test(cells, rr, nsim=5, 532s + method="poisson", baseline=lam, alternative="less") 532s + }) 532s + } 532s > #' 532s > #' tests/interact.R 532s > #' 532s > #' Support for interaction objects 532s > #' 532s > #' $Revision: 1.2 $ $Date: 2020/04/28 12:58:26 $ 532s > 532s > if(FULLTEST) { 532s + local({ 532s + #' print.intermaker 532s + Strauss 532s + Geyer 532s + Ord 532s + #' intermaker 532s + BS <- get("BlankStrauss", envir=environment(Strauss)) 532s + BD <- function(r) { instantiate.interact(BS, list(r=r)) } 532s + BlueDanube <- intermaker(BD, BS) 532s + }) 532s + } 532s > 532s > #' tests/ippm.R 532s > #' Tests of 'ippm' class 532s > #' $Revision: 1.6 $ $Date: 2020/04/28 12:58:26 $ 532s > 532s > if(FULLTEST) { 532s + local({ 532s + # .......... set up example from help file ................. 532s + nd <- 10 532s + gamma0 <- 3 532s + delta0 <- 5 532s + POW <- 3 532s + # Terms in intensity 532s + Z <- function(x,y) { -2*y } 532s + f <- function(x,y,gamma,delta) { 1 + exp(gamma - delta * x^POW) } 532s + # True intensity 532s + lamb <- function(x,y,gamma,delta) { 200 * exp(Z(x,y)) * f(x,y,gamma,delta) } 532s + # Simulate realisation 532s + lmax <- max(lamb(0,0,gamma0,delta0), lamb(1,1,gamma0,delta0)) 532s + set.seed(42) 532s + X <- rpoispp(lamb, lmax=lmax, win=owin(), gamma=gamma0, delta=delta0) 532s + # Partial derivatives of log f 532s + DlogfDgamma <- function(x,y, gamma, delta) { 532s + topbit <- exp(gamma - delta * x^POW) 532s + topbit/(1 + topbit) 532s + } 532s + DlogfDdelta <- function(x,y, gamma, delta) { 532s + topbit <- exp(gamma - delta * x^POW) 532s + - (x^POW) * topbit/(1 + topbit) 532s + } 532s + # irregular score 532s + Dlogf <- list(gamma=DlogfDgamma, delta=DlogfDdelta) 532s + # fit model 532s + fit <- ippm(X ~Z + offset(log(f)), 532s + covariates=list(Z=Z, f=f), 532s + iScore=Dlogf, 532s + start=list(gamma=1, delta=1), 532s + nd=nd) 532s + # fit model with logistic likelihood but without iScore 532s + fitlo <- ippm(X ~Z + offset(log(f)), 532s + method="logi", 532s + covariates=list(Z=Z, f=f), 532s + start=list(gamma=1, delta=1), 532s + nd=nd) 532s + 532s + ## ............. test ippm class support ...................... 532s + Ar <- model.matrix(fit) 532s + Ai <- model.matrix(fit, irregular=TRUE) 532s + An <- model.matrix(fit, irregular=TRUE, keepNA=FALSE) 532s + AS <- model.matrix(fit, irregular=TRUE, subset=(abs(Z) < 0.5)) 532s + 532s + Zr <- model.images(fit) 532s + Zi <- model.images(fit, irregular=TRUE) 532s + ## update.ippm 532s + fit2 <- update(fit, . ~ . + I(Z^2)) 532s + fit0 <- update(fit, 532s + . ~ . - Z, 532s + start=list(gamma=2, delta=4)) 532s + oldfit <- ippm(X, 532s + ~Z + offset(log(f)), 532s + covariates=list(Z=Z, f=f), 532s + iScore=Dlogf, 532s + start=list(gamma=1, delta=1), 532s + nd=nd) 532s + oldfit2 <- update(oldfit, . ~ . + I(Z^2)) 532s + oldfit0 <- update(oldfit, 532s + . ~ . - Z, 532s + start=list(gamma=2, delta=4)) 532s + ## again with logistic 532s + fitlo2 <- update(fitlo, . ~ . + I(Z^2)) 532s + fitlo0 <- update(fitlo, 532s + . ~ . - Z, 532s + start=list(gamma=2, delta=4)) 532s + oldfitlo <- ippm(X, 532s + ~Z + offset(log(f)), 532s + method="logi", 532s + covariates=list(Z=Z, f=f), 532s + start=list(gamma=1, delta=1), 532s + nd=nd) 532s + oldfitlo2 <- update(oldfitlo, . ~ . + I(Z^2)) 532s + oldfitlo0 <- update(oldfitlo, 532s + . ~ . - Z, 532s + start=list(gamma=2, delta=4)) 532s + ## anova.ppm including ippm objects 532s + fit0 <- update(fit, . ~ Z) 532s + fit0lo <- update(fitlo, . ~ Z) 532s + A <- anova(fit0, fit) 532s + Alo <- anova(fit0lo, fitlo) 532s + }) 532s + } 532s > 532s BEGIN TEST testsK.R 532s 532s R version 4.3.2 (2023-10-31) -- "Eye Holes" 532s Copyright (C) 2023 The R Foundation for Statistical Computing 532s Platform: powerpc64le-unknown-linux-gnu (64-bit) 532s 532s R is free software and comes with ABSOLUTELY NO WARRANTY. 532s You are welcome to redistribute it under certain conditions. 532s Type 'license()' or 'licence()' for distribution details. 532s 532s R is a collaborative project with many contributors. 532s Type 'contributors()' for more information and 532s 'citation()' on how to cite R or R packages in publications. 532s 532s Type 'demo()' for some demos, 'help()' for on-line help, or 532s 'help.start()' for an HTML browser interface to help. 532s Type 'q()' to quit R. 532s 532s > #' 532s > #' Header for all (concatenated) test files 532s > #' 532s > #' Require spatstat.model 532s > #' Obtain environment variable controlling tests. 532s > #' 532s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 532s > 532s > require(spatstat.model) 532s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 532s > ALWAYS <- TRUE 532s > cat(paste("--------- Executing", 532s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 532s + "test code -----------\n")) 532s --------- Executing **RESTRICTED** subset of test code ----------- 532s > # 532s > # tests/kppm.R 532s > # 532s > # $Revision: 1.39 $ $Date: 2023/10/21 04:25:51 $ 532s > # 532s > # Test functionality of kppm that once depended on RandomFields 532s > # Test update.kppm for old style kppm objects 532s > 532s > if(!FULLTEST) 532s + spatstat.options(npixel=32, ndummy.min=16) 532s > 532s > local({ 532s + 532s + fit <- kppm(redwood ~1, "Thomas") # sic 532s + fitx <- kppm(redwood ~x, "Thomas", verbose=TRUE) 532s + if(FULLTEST) { 532s + fitx <- update(fit, ~ . + x) 532s + fitM <- update(fit, clusters="MatClust") 532s + fitC <- update(fit, cells) 532s + fitCx <- update(fit, cells ~ x) 532s + #' 532s + Wsub <- owin(c(0, 0.5), c(-0.5, 0)) 532s + Zsub <- (bdist.pixels(Window(redwood)) > 0.1) 532s + fitWsub <- kppm(redwood ~1, "Thomas", subset=Wsub) 532s + fitZsub <- kppm(redwood ~1, "Thomas", subset=Zsub) 532s + fitWsub 532s + 532s + #' various methods 532s + ff <- as.fv(fitx) 532s + uu <- unitname(fitx) 532s + unitname(fitCx) <- "furlong" 532s + mo <- model.images(fitCx) 532s + p <- psib(fit) 532s + px <- psib(fitx) 532s + } 532s + if(ALWAYS) { 532s + Y <- simulate(fitx, seed=42, saveLambda=TRUE)[[1]] 532s + } 532s + 532s + if(FULLTEST) { 532s + #' vcov.kppm different algorithms 532s + vc <- vcov(fitx) 532s + vc2 <- vcov(fitx, fast=TRUE) 532s + vc3 <- vcov(fitx, fast=TRUE, splitup=TRUE) 532s + vc4 <- vcov(fitx, splitup=TRUE) 532s + 532s + ## other code blocks 532s + a <- varcount(fitx, function(x,y){x+1}) # always positive 532s + a <- varcount(fitx, function(x,y){y-1}) # always negative 532s + a <- varcount(fitx, function(x,y){x+y}) # positive or negative 532s + 532s + #' improve.kppm 532s + fitI <- update(fit, improve.type="quasi") 532s + fitxI <- update(fitx, improve.type="quasi") 532s + fitxIs <- update(fitx, improve.type="quasi", fast=FALSE) 532s + #' vcov.kppm 532s + vcI <- vcov(fitxI) 532s + } 532s + 532s + ## plot.kppm including predict.kppm 532s + if(ALWAYS) { 532s + fitMC <- kppm(redwood ~ x, "Thomas") 532s + plot(fitMC) 532s + } 532s + if(FULLTEST) { 532s + fitCL <- kppm(redwood ~ x, "Thomas", method="c") 532s + fitPA <- kppm(redwood ~ x, "Thomas", method="p") 532s + plot(fitCL) 532s + plot(fitPA) 532s + 532s + ## fit with composite likelihood method [thanks to Abdollah Jalilian] 532s + fut <- kppm(redwood ~ x, "VarGamma", method="clik2", nu.ker=-3/8) 532s + kfut <- as.fv(fut) 532s + } 532s + 532s + if(ALWAYS) { 532s + fit0 <- kppm(redwood ~1, "LGCP") 532s + is.poisson(fit0) 532s + Y0 <- simulate(fit0, saveLambda=TRUE)[[1]] 532s + stopifnot(is.ppp(Y0)) 532s + p0 <- psib(fit0) # issues a warning 532s + 532s + if(FULLTEST) { 532s + ## fit LGCP using K function: slow 532s + fit1 <- kppm(redwood ~x, "LGCP", 532s + covmodel=list(model="matern", nu=0.3), 532s + control=list(maxit=3)) 532s + Y1 <- simulate(fit1, saveLambda=TRUE)[[1]] 532s + stopifnot(is.ppp(Y1)) 532s + } 532s + 532s + ## fit LGCP using pcf 532s + fit1p <- kppm(redwood ~x, "LGCP", 532s + covmodel=list(model="matern", nu=0.3), 532s + statistic="pcf") 532s + Y1p <- simulate(fit1p, saveLambda=TRUE)[[1]] 532s + stopifnot(is.ppp(Y1p)) 532s + 532s + ## .. and using different fitting methods 532s + if(FULLTEST) { 532s + fit1pClik <- update(fit1p, method="clik") 532s + fit1pPalm <- update(fit1p, method="palm") 532s + } 532s + 532s + ## shortcut evaluation of pcf 532s + ## (the code being tested is in spatstat.random::clusterinfo.R) 532s + if(FULLTEST) { 532s + putSpatstatVariable("RFshortcut", TRUE) 532s + fitGshort <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="gauss")) 532s + fitSshort <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="stable", alpha=1)) 532s + putSpatstatVariable("RFshortcut", FALSE) 532s + fitGlong <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="gauss")) 532s + fitSlong <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="stable", alpha=1)) 532s + discrepG <- unlist(parameters(fitGshort)) - unlist(parameters(fitGlong)) 532s + discrepS <- unlist(parameters(fitSshort)) - unlist(parameters(fitSlong)) 532s + print(discrepG) 532s + print(discrepS) 532s + if(max(abs(discrepG) > 0.01)) 532s + stop("Discrepancy in short-cut fitting of Gaussian LGCP") 532s + if(max(abs(discrepS) > 0.01)) 532s + stop("Discrepancy in short-cut fitting of stable LGCP") 532s + } 532s + 532s + ## image covariate (a different code block) 532s + xx <- as.im(function(x,y) x, Window(redwood)) 532s + fit1xx <- update(fit1p, . ~ xx, data=solist(xx=xx)) 532s + Y1xx <- simulate(fit1xx, saveLambda=TRUE)[[1]] 532s + stopifnot(is.ppp(Y1xx)) 532s + if(FULLTEST) { 532s + fit1xxVG <- update(fit1xx, clusters="VarGamma", nu=-1/4) 532s + Y1xxVG <- simulate(fit1xxVG, saveLambda=TRUE)[[1]] 532s + stopifnot(is.ppp(Y1xxVG)) 532s + } 532s + fit1xxLG <- update(fit1xx, clusters="LGCP", 532s + covmodel=list(model="matern", nu=0.3), 532s + statistic="pcf") 532s + Y1xxLG <- simulate(fit1xxLG, saveLambda=TRUE, drop=TRUE) 532s + stopifnot(is.ppp(Y1xxLG)) 532s + 532s + # ... and Abdollah's code 532s + if(FULLTEST) { 532s + fit2 <- kppm(redwood ~x, cluster="Cauchy", statistic="K") 532s + Y2 <- simulate(fit2, saveLambda=TRUE)[[1]] 532s + stopifnot(is.ppp(Y2)) 532s + } 532s + } 532s + 532s + }) 532s Fitting cluster model 532s Retrieved cluster model information 532s Algorithm parameters: 532s $rmax 532s NULL 532s 532s $q 532s [1] 0.25 532s 532s $p 532s [1] 2 532s 532s $rmin 532s NULL 532s 532s Using point pattern data 532s Starting parameters: 532s kappa sigma2 532s 62.000000000 0.006173033 532s Calculating summary function...Done. 532s Starting minimum contrast fit 532s Returned from minimum contrast fit 532s Returning from clusterfit 532s > 532s > if(FULLTEST) { 532s + local({ 532s + #' various code blocks 532s + fut <- kppm(redwood, ~x) 532s + fet <- update(fut, redwood3) 532s + fot <- update(fut, trend=~y) 532s + fit <- kppm(redwoodfull ~ x) 532s + Y <- simulate(fit, window=redwoodfull.extra$regionII, saveLambda=TRUE) 532s + gut <- improve.kppm(fit, type="wclik1") 532s + gut <- improve.kppm(fit, vcov=TRUE, fast.vcov=TRUE, save.internals=TRUE) 532s + hut <- kppm(redwood ~ x, method="clik", weightfun=NULL) 532s + hut <- kppm(redwood ~ x, method="palm", weightfun=NULL) 532s + mut <- kppm(redwood) 532s + nut <- update(mut, Y) 532s + if(TRUE) { 532s + #' Bug in rLGCP spotted by Tilman Davies 532s + X <- rLGCP("matern", function(x,y) { 1 - 0.4* y }, 532s + var=2, scale=0.7, nu=0.5, win = square(10), 532s + dimyx=c(32,64)) 532s + } 532s + }) 532s + } 532s > 532s > if(FULLTEST) { 532s + local({ 532s + #' minimum contrast code 532s + K <- Kest(redwood) 532s + a <- matclust.estK(K) 532s + a <- thomas.estK(K) 532s + a <- cauchy.estK(K) 532s + a <- vargamma.estK(K) 532s + a <- lgcp.estK(K) 532s + 532s + print(a) 532s + u <- unitname(a) 532s + 532s + g <- pcf(redwood) 532s + a <- matclust.estpcf(g) 532s + a <- thomas.estpcf(g) 532s + a <- cauchy.estpcf(g) 532s + a <- vargamma.estpcf(g) 532s + a <- lgcp.estpcf(g) 532s + 532s + #' auxiliary functions 532s + b <- resolve.vargamma.shape(nu.pcf=1.5) 532s + Z <- clusterfield("Thomas", kappa=1, scale=0.2) 532s + 532s + aa <- NULL 532s + aa <- accumulateStatus(simpleMessage("Woof"), aa) 532s + aa <- accumulateStatus(simpleMessage("Sit"), aa) 532s + aa <- accumulateStatus(simpleMessage("Woof"), aa) 532s + printStatusList(aa) 532s + 532s + RMIN <- 0.01 532s + fit <- kppm(redwood ~ 1, ctrl=list(rmin=RMIN,q=1/2)) 532s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 532s + stop("kppm did not handle parameter 'rmin' in argument 'ctrl' ") 532s + fit <- kppm(redwood ~ 1, ctrl=list(rmin=0,q=1/2), rmin=RMIN) 532s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 532s + stop("kppm did not handle parameter 'rmin' in argument 'ctrl'") 532s + 532s + RMIN <- 2 532s + fit <- dppm(swedishpines~1, dppGauss(), ctrl=list(rmin=RMIN,q=1)) 532s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 532s + stop("dppm did not handle parameter 'rmin' in argument 'ctrl'") 532s + fit <- dppm(swedishpines~1, dppGauss(), ctrl=list(rmin=0,q=1), rmin=RMIN) 532s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 532s + stop("dppm did not handle argument 'rmin'") 532s + }) 532s + } 532s > 532s > 532s > 532s > if(FULLTEST) { 532s + local({ 532s + #' cover a few code blocks 532s + fut <- kppm(redwood ~ x, method="clik") 532s + print(summary(fut)) 532s + a <- residuals(fut) 532s + fut2 <- kppm(redwood ~ x, "LGCP", method="palm") 532s + print(summary(fut2)) 532s + b <- residuals(fut2) 532s + #' 532s + po <- ppm(redwood ~ 1) 532s + A <- kppmComLik(redwood, Xname="redwood", po=po, clusters="Thomas", 532s + statistic="pcf", statargs=list(), control=list(), 532s + weightfun=NULL, rmax=0.1) 532s + A <- kppmPalmLik(redwood, Xname="redwood", po=po, clusters="Thomas", 532s + statistic="pcf", statargs=list(), control=list(), 532s + weightfun=NULL, rmax=0.1) 532s + }) 532s + } 532s > 532s > reset.spatstat.options() 532s > 532s > #' 532s > #' tests/Kfuns.R 532s > #' 532s > #' Various K and L functions and pcf 532s > #' 532s > #' $Revision: 1.43 $ $Date: 2022/06/17 01:47:08 $ 532s > #' 532s > #' Assumes 'EveryStart.R' was run 532s > 532s > if(FULLTEST) { 532s + Cells <- cells 532s + Amacrine <- amacrine 532s + Redwood <- redwood 532s + } else { 532s + ## reduce numbers of data + dummy points 532s + spatstat.options(npixel=32, ndummy.min=16) 532s + Cells <- cells[c(FALSE, TRUE)] 532s + Amacrine <- amacrine[c(FALSE, TRUE)] 532s + Redwood <- redwood[c(FALSE, TRUE)] 532s + } 532s > 532s > 532s > if(FULLTEST) { 532s + local({ 532s + #' code blocks using fitted model to determine intensity 532s + #' Kinhom 532s + X <- rpoispp(function(x,y) { 100 * x }, 100, square(1)) 532s + fut <- ppm(X ~ x) 532s + Kio <- Kinhom(X, fut, update=FALSE) 532s + Kiu <- Kinhom(X, fut, update=TRUE, diagonal=FALSE) 532s + fit <- ppm(Amacrine ~ marks) 532s + #' lohboot Linhom 532s + Zred <- predict(ppm(Redwood ~ x+y)) 532s + Lred <- lohboot(Redwood, Linhom, lambda=Zred) 532s + #' Kmulti.inhom 532s + K1 <- Kcross.inhom(Amacrine, lambdaX=fit) 532s + On <- split(Amacrine)$on 532s + Off <- split(Amacrine)$off 532s + K4 <- Kcross.inhom(Amacrine, lambdaI=ppm(On), lambdaJ=ppm(Off)) 532s + #' local K functions 532s + fut <- ppm(swedishpines ~ polynom(x,y,2)) 532s + Z <- predict(fut) 532s + Lam <- fitted(fut, dataonly=TRUE) 532s + a <- localLinhom(swedishpines, lambda=fut) 532s + a <- localLinhom(swedishpines, lambda=Z) 532s + a <- localLinhom(swedishpines, lambda=Lam) 532s + a <- localLinhom(swedishpines, lambda=Z, correction="none") 532s + a <- localLinhom(swedishpines, lambda=Z, correction="translate") 532s + #' local cross K functions 532s + fat <- ppm(Amacrine ~ x * marks) 532s + Zed <- predict(fat) 532s + Lum <- fitted(fat, dataonly=TRUE) 532s + moff <- (marks(Amacrine) == "off") 532s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed) 532s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Lum) 532s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=fat) 532s + a <- localLcross.inhom(Amacrine, from="off", to="on", 532s + lambdaFrom=Lum[moff], lambdaTo=Lum[!moff]) 532s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 532s + correction="none") 532s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 532s + correction="translate") 532s + #' cases of resolve.lambdacross 532s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=fat) 532s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=fat, update=FALSE) 532s + h <- resolve.lambdacross(Amacrine, moff, !moff, 532s + lambdaI=fat, lambdaJ=fat) 532s + h <- resolve.lambdacross(Amacrine, moff, !moff, 532s + lambdaI=fat, lambdaJ=fat, 532s + update=FALSE) 532s + #' lohboot 532s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", lambdaX=Zed) 532s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", lambdaX=Lum) 532s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", lambdaX=fat) 532s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", 532s + lambdaFrom=Lum[moff], lambdaTo=Lum[!moff]) 532s + #' 532s + #' residual K functions etc 532s + #' 532s + rco <- compareFit(Cells, Kcom, 532s + interaction=anylist(P=Poisson(), S=Strauss(0.08)), 532s + same="trans", different="tcom") 532s + fit <- ppm(Cells ~ x, Strauss(0.07)) 532s + K <- Kcom(Cells, model=fit, restrict=TRUE) 532s + }) 532s + } 532s > 532s > reset.spatstat.options() 532s > 532s BEGIN TEST testsL.R 532s 532s R version 4.3.2 (2023-10-31) -- "Eye Holes" 532s Copyright (C) 2023 The R Foundation for Statistical Computing 532s Platform: powerpc64le-unknown-linux-gnu (64-bit) 532s 532s R is free software and comes with ABSOLUTELY NO WARRANTY. 532s You are welcome to redistribute it under certain conditions. 532s Type 'license()' or 'licence()' for distribution details. 532s 532s R is a collaborative project with many contributors. 532s Type 'contributors()' for more information and 532s 'citation()' on how to cite R or R packages in publications. 532s 532s Type 'demo()' for some demos, 'help()' for on-line help, or 532s 'help.start()' for an HTML browser interface to help. 532s Type 'q()' to quit R. 532s 532s > #' 532s > #' Header for all (concatenated) test files 532s > #' 532s > #' Require spatstat.model 532s > #' Obtain environment variable controlling tests. 532s > #' 532s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 532s > 532s > require(spatstat.model) 532s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 532s > ALWAYS <- TRUE 532s > cat(paste("--------- Executing", 532s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 532s + "test code -----------\n")) 532s --------- Executing **RESTRICTED** subset of test code ----------- 532s > ## 532s > ## tests/legacy.R 532s > ## 532s > ## Test that current version of spatstat is compatible with outmoded usage 532s > ## $Revision: 1.3 $ $Date: 2020/04/29 08:55:17 $ 532s > 532s > if(FULLTEST) { 532s + local({ 532s + 532s + ## (1) Old syntax of ppm 532s + ppm(cells, ~x) 532s + 532s + ## (2) Old syntax of MultiStrauss etc. 532s + r <- matrix(3, 2, 2) 532s + a <- MultiStrauss( , r) 532s + a <- MultiStrauss(NULL, r) 532s + a <- MultiHard(, r) 532s + 532s + h <- r/2 532s + a <- MultiStraussHard( , r, h) 532s + 532s + NULL 532s + }) 532s + } 532s > #' 532s > #' tests/leverinf.R 532s > #' 532s > #' leverage and influence for Gibbs models 532s > #' 532s > #' $Revision: 1.35 $ $Date: 2022/06/18 10:15:17 $ 532s > #' 532s > 532s > if(FULLTEST) { 532s + Cells <- cells 532s + Amacrine <- amacrine 532s + Redwood <- redwood 532s + } else { 532s + ## reduce number of data + dummy points 532s + spatstat.options(npixel=32, ndummy.min=16) 532s + Cells <- cells[c(FALSE,TRUE)] 532s + Redwood <- redwood[c(FALSE, TRUE)] 532s + Amacrine <- amacrine[c(FALSE, TRUE)] 532s + } 532s > 532s > local({ 532s + cat("Running non-sparse algorithm...", fill=TRUE) 532s + # original non-sparse algorithm 532s + Leverage <- function(...) leverage(..., sparseOK=FALSE) 532s + Influence <- function(...) influence(..., sparseOK=FALSE) 532s + Dfbetas <- function(...) dfbetas(..., sparseOK=FALSE) 532s + if(ALWAYS) { 532s + ## Strauss()$delta2 532s + fitS <- ppm(Cells ~ x, Strauss(0.12), rbord=0) 532s + levS <- Leverage(fitS) 532s + infS <- Influence(fitS) 532s + dfbS <- Dfbetas(fitS) 532s + ## Geyer()$delta2 532s + fitG <- ppm(Redwood ~ 1, Geyer(0.1, 2), rbord=0) 532s + levG <- Leverage(fitG) 532s + infG <- Influence(fitG) 532s + ## AreaInter()$delta2 532s + fitA <- ppm(Cells ~ 1, AreaInter(0.06), rbord=0, nd=11) 532s + levA <- Leverage(fitA) 532s + infA <- Influence(fitA) 532s + ## pairwise.family$delta2 532s + fitD <- ppm(Cells ~ 1, DiggleGatesStibbard(0.12), rbord=0) 532s + levD <- Leverage(fitD) 532s + infD <- Influence(fitD) 532s + ## DiggleGratton() special code 532s + fitDG <- ppm(Cells ~ 1, DiggleGratton(0.05, 0.12), rbord=0) 532s + levDG <- Leverage(fitDG) 532s + infDG <- Influence(fitDG) 532s + ## ppmInfluence; offset is present; coefficient vector has length 0 532s + fitH <- ppm(Cells ~ 1, Hardcore(0.07)) 532s + levH <- Leverage(fitH) 532s + infH <- Influence(fitH) 532s + ## ppmInfluence; hard core 532s + fitSH <- ppm(Cells ~ 1, StraussHard(0.07, 0.01)) 532s + levSH <- Leverage(fitSH) 532s + infSH <- Influence(fitSH) 532s + ## ppmInfluence; offset is present; coefficient vector has length 1 532s + fitHx <- ppm(Cells ~ x, Hardcore(0.07), rbord=0) 532s + levHx <- Leverage(fitHx) 532s + infHx <- Influence(fitHx) 532s + ## multitype 532s + futAm <- ppm(Amacrine ~ x + marks, Strauss(0.07)) 532s + levAm <- leverage(futAm) 532s + } 532s + 532s + if(FULLTEST) { 532s + ## ......... class support ............................. 532s + ## other methods for classes leverage.ppm and influence.ppm 532s + ## not elsewhere tested 532s + cat("Testing class support...", fill=TRUE) 532s + w <- domain(levS) 532s + w <- Window(infS) 532s + vv <- shift(levS, c(1.2, 1.3)) 532s + vv <- shift(infS, c(1.2, 1.3)) 532s + A <- quadrats(Window(Cells), 2) 532s + a <- integral(levS,domain=A) 532s + b <- integral(infS,domain=A) 532s + u <- Smooth(levS, sigma=0.07) 532s + v <- Smooth(infS, sigma=0.1) 532s + ## plot options 532s + plot(levS, what="exact") 532s + plot(levS, what="nearest") 532s + contour(levS, what="nearest") 532s + persp(levS, what="nearest") 532s + ## plotting for multitype models 532s + plot(levAm) 532s + contour(levAm) 532s + persp(levAm) 532s + plot(levAm, multiplot=FALSE) 532s + contour(levAm, multiplot=FALSE) 532s + } 532s + 532s + if(ALWAYS) { 532s + ## .......... compare algorithms ......................... 532s + ## divide and recombine algorithm 532s + cat("Reduce maximum block side to 50,000 ...", fill=TRUE) 532s + op <- spatstat.options(maxmatrix=50000) 532s + ## non-sparse 532s + levSB <- Leverage(fitS) 532s + infSB <- Influence(fitS) 532s + dfbSB <- Dfbetas(fitS) 532s + } 532s + 532s + chk <- function(x, y, what, 532s + from="single-block and multi-block", 532s + thresh=1e-12) { 532s + if(max(abs(x-y)) > thresh) 532s + stop(paste("Different results for", what, "obtained from", 532s + from, "algorithms"), 532s + call.=FALSE) 532s + invisible(NULL) 532s + } 532s + 532s + if(ALWAYS) { 532s + cat("Compare single-block to multi-block...", fill=TRUE) 532s + chk(marks(as.ppp(infS)), marks(as.ppp(infSB)), "influence") 532s + chk(as.im(levS), as.im(levSB), "leverage") 532s + chk(dfbS$val, dfbSB$val, "dfbetas$value") 532s + chk(dfbS$density, dfbSB$density, "dfbetas$density") 532s + } 532s + 532s + if(FULLTEST) { 532s + ## also check case of zero cif 532s + cat("Check zero cif cases...", fill=TRUE) 532s + levHB <- Leverage(fitH) 532s + infHB <- Influence(fitH) 532s + dfbHB <- Dfbetas(fitH) 532s + levHxB <- Leverage(fitHx) 532s + infHxB <- Influence(fitHx) 532s + dfbHxB <- Dfbetas(fitHx) 532s + } 532s + 532s + ## run all code segments 532s + Everything <- function(model, ...) { ppmInfluence(model, ..., what="all") } 532s + 532s + if(FULLTEST) { 532s + cat("Run full code on AreaInteraction model...", fill=TRUE) 532s + pmiA <- Everything(fitA) 532s + 532s + ## sparse algorithm, with blocks 532s + cat("Run sparse algorithm with blocks...", fill=TRUE) 532s + pmiSSB <- Everything(fitS, sparseOK=TRUE) 532s + ## also check case of zero cif 532s + pmiHSB <- Everything(fitH, sparseOK=TRUE) 532s + pmiSHSB <- Everything(fitSH, sparseOK=TRUE) 532s + pmiHxSB <- Everything(fitHx, sparseOK=TRUE) 532s + 532s + cat("Reinstate maxmatrix...", fill=TRUE) 532s + spatstat.options(op) 532s + } 532s + 532s + if(ALWAYS) { 532s + ## sparse algorithm, no blocks 532s + cat("Compare sparse and non-sparse results...", fill=TRUE) 532s + pmi <- Everything(fitS, sparseOK=TRUE) 532s + levSp <- pmi$leverage 532s + infSp <- pmi$influence 532s + dfbSp <- pmi$dfbetas 532s + chks <- function(...) chk(..., from="sparse and non-sparse") 532s + 532s + chks(marks(as.ppp(infS)), marks(as.ppp(infSp)), "influence") 532s + chks(as.im(levS), as.im(levSp), "leverage") 532s + chks(dfbS$val, dfbSp$val, "dfbetas$value") 532s + chks(dfbS$density, dfbSp$density, "dfbetas$density") 532s + } 532s + 532s + if(ALWAYS) { 532s + #' case of zero cif 532s + cat("zero cif...", fill=TRUE) 532s + pmiH <- Everything(fitH, sparseOK=TRUE) 532s + pmiSH <- Everything(fitSH, sparseOK=TRUE) 532s + pmiHx <- Everything(fitHx, sparseOK=TRUE) 532s + } 532s + if(FULLTEST) { 532s + #' other code blocks - check execution only 532s + cat("other code blocks...", fill=TRUE) 532s + a <- Everything(fitS) 532s + a <- Everything(fitS, method="interpreted") 532s + a <- Everything(fitS, method="interpreted", entrywise=FALSE) 532s + a <- Everything(fitS, entrywise=FALSE) 532s + #' zero cif 532s + b <- Everything(fitSH) 532s + b <- Everything(fitSH, method="interpreted") 532s + b <- Everything(fitSH, method="interpreted", entrywise=FALSE) 532s + b <- Everything(fitSH, entrywise=FALSE) 532s + } 532s + #' NOTE: code for irregular parameters is tested below, and in 'make bookcheck' 532s + 532s + ## ........... logistic fits ....................... 532s + cat("Logistic fits...", fill=TRUE) 532s + #' special algorithm for delta2 532s + fitSlogi <- ppm(Cells ~ x, Strauss(0.12), rbord=0, method="logi") 532s + 532s + if(FULLTEST) { 532s + pmiSlogi <- Everything(fitSlogi) 532s + #' special algorithm for delta2 532s + fitGlogi <- ppm(Redwood ~ 1, Geyer(0.1, 2), rbord=0, method="logi") 532s + pmiGlogi <- Everything(fitGlogi) 532s + #' generic algorithm for delta2 532s + fitDlogi <- ppm(Cells ~ 1, DiggleGatesStibbard(0.12), 532s + rbord=0, method="logi") 532s + pmiDlogi <- Everything(fitDlogi) 532s + #' generic algorithm for delta2 : offset; zero-dimensional 532s + fitHlogi <- ppm(Cells ~ 1, Hardcore(0.07), method="logi") 532s + pmiHlogi <- Everything(fitHlogi) 532s + #' generic algorithm for delta2 : offset; 1-dimensional 532s + fitHxlogi <- ppm(Cells ~ x, Hardcore(0.07), rbord=0, method="logi") 532s + pmiHxlogi <- Everything(fitHxlogi) 532s + #' plotting 532s + plot(leverage(fitSlogi)) 532s + plot(influence(fitSlogi)) 532s + plot(dfbetas(fitSlogi)) 532s + } 532s + 532s + if(ALWAYS) { 532s + #' other code blocks - check execution only 532s + cat("Other code blocks...", fill=TRUE) 532s + b <- Everything(fitSlogi) # i.e. full set of results 532s + b <- Everything(fitSlogi, method="interpreted") 532s + b <- Everything(fitSlogi, method="interpreted", entrywise=FALSE) 532s + b <- Everything(fitSlogi, entrywise=FALSE) 532s + } 532s + 532s + #' irregular parameters 532s + cat("Irregular parameters...", fill=TRUE) 532s + ytoa <- function(x,y, alpha=1) { y^alpha } 532s + lam <- function(x,y,alpha=1) { exp(4 + y^alpha) } 532s + set.seed(90210) 532s + X <- rpoispp(lam, alpha=2) 532s + iScor <- list(alpha=function(x,y,alpha) { alpha * y^(alpha-1) } ) 532s + iHess <- list(alpha=function(x,y,alpha) { alpha * (alpha-1) * y^(alpha-2) } ) 532s + gogo <- function(tag, ..., iS=iScor, iH=iHess) { 532s + cat(tag, fill=TRUE) 532s + #' compute all leverage+influence terms 532s + ppmInfluence(..., what="all", iScore=iS, iHessian=iH) 532s + } 532s + gogogo <- function(hdr, fit) { 532s + cat(hdr, fill=TRUE) 532s + force(fit) 532s + #' try all code options 532s + d <- gogo("a", fit) 532s + d <- gogo("b", fit, method="interpreted") 532s + d <- gogo("c", fit, method="interpreted", entrywise=FALSE) 532s + d <- gogo("d", fit, entrywise=FALSE) 532s + invisible(NULL) 532s + } 532s + gogogo("Offset model...", 532s + ippm(X ~ offset(ytoa), start=list(alpha=1), iterlim=40)) 532s + gogogo("Offset model (logistic) ...", 532s + ippm(X ~ offset(ytoa), start=list(alpha=1), 532s + method="logi", iterlim=40)) 532s + gogogo("Offset+x model...", 532s + ippm(X ~ x + offset(ytoa), start=list(alpha=1), iterlim=40)) 532s + gogogo("Offset+x model (logistic) ...", 532s + ippm(X ~ x + offset(ytoa), start=list(alpha=1), 532s + method="logi", iterlim=40)) 532s + gogogo("Offset model Strauss ...", 532s + ippm(X ~ offset(ytoa), Strauss(0.07), start=list(alpha=1), iterlim=40)) 532s + gogogo("Offset model Strauss (logistic) ...", 532s + ippm(X ~ offset(ytoa), Strauss(0.07), start=list(alpha=1), 532s + method="logi", iterlim=40)) 532s + if(FULLTEST) { 532s + gogogo("Offset+x model Strauss ...", 532s + ippm(X ~ x + offset(ytoa), Strauss(0.07), start=list(alpha=1), 532s + iterlim=40)) 532s + gogogo("Offset+x model Strauss (logistic)...", 532s + ippm(X ~ x + offset(ytoa), Strauss(0.07), start=list(alpha=1), 532s + method="logi", iterlim=40)) 532s + } 532s + #' 532s + if(FULLTEST) { 532s + set.seed(452) 532s + foo <- ppm(Cells ~ 1, Strauss(0.15), improve.type="ho", nsim=5) 532s + aa <- Everything(foo) 532s + 532s + #' Gradient and Hessian obtained by symbolic differentiation 532s + f <- deriv(expression((1+x)^a), 532s + "a", function.arg=c("x", "y", "a"), 532s + hessian=TRUE) 532s + #' check they can be extracted 532s + fit <- ippm(Cells ~offset(f), start=list(a=0.7)) 532s + Everything(fit) 532s + } 532s + }) 532s Running non-sparse algorithm... 532s Loading required package: spatstat.geom 532s spatstat.geom 3.2-8 532s Loading required package: spatstat.random 532s spatstat.random 3.2-2 532s Loading required package: spatstat.explore 532s Loading required package: nlme 532s spatstat.explore 3.2-5 532s Loading required package: rpart 532s spatstat.model 3.2-8 532s The formula does not involve “g” and is therefore unchanged 532s Don't know how to reduce the term “sin(x - z)” 532s Warning messages: 532s 1: In is.multitype.ppp(Z) : some mark values are NA in the point pattern Z 532s 2: Factor-valued marks were converted to integer codes 532s 3: Factor-valued mark variable ‘a’ was converted to integer codes 532s 4: Factor-valued marks were converted to integer codes 532s Loading required package: spatstat.model 532s Loading required package: spatstat.data 532s Loading required package: spatstat.geom 532s spatstat.geom 3.2-8 532s Loading required package: spatstat.random 532s spatstat.random 3.2-2 532s Loading required package: spatstat.explore 532s Loading required package: nlme 532s spatstat.explore 3.2-5 532s Loading required package: rpart 532s spatstat.model 3.2-8 532s Loading required package: spatstat.model 532s Loading required package: spatstat.data 532s Loading required package: spatstat.geom 532s spatstat.geom 3.2-8 532s Loading required package: spatstat.random 532s spatstat.random 3.2-2 532s Loading required package: spatstat.explore 532s Loading required package: nlme 532s spatstat.explore 3.2-5 532s Loading required package: rpart 532s spatstat.model 3.2-8 532s Warning messages: 532s 1: Internal error: fvlabels truncated the function name 532s 2: Internal error: fvlabels truncated the function name 532s 3: Internal error: fvlabels truncated the function name 532s 4: In psib.kppm(fit0) : The model is not a cluster process 532s 5: The value of the empirical function ‘pcf’ for r= 0 was Inf. Range of r values was reset to [0.00048828125, 0.25] 532s 6: The value of the empirical function ‘pcf’ for r= 0 was Inf. Range of r values was reset to [0.00048828125, 0.25] 532s 7: The value of the empirical function ‘pcf’ for r= 0 was Inf. Range of r values was reset to [0.00048828125, 0.25] 532s Loading required package: spatstat.model 532s Loading required package: spatstat.data 532s Loading required package: spatstat.geom 532s spatstat.geom 3.2-8 532s Loading required package: spatstat.random 532s spatstat.random 3.2-2 532s Loading required package: spatstat.explore 532s Loading required package: nlme 532s spatstat.explore 3.2-5 532s Loading required package: rpart 532s spatstat.model 3.2-8 536s Reduce maximum block side to 50,000 ... 537s Compare single-block to multi-block... 537s Compare sparse and non-sparse results... 537s zero cif... 539s Logistic fits... 539s Other code blocks... 542s Irregular parameters... 542s Offset model... 542s a 542s b 542s c 543s d 543s Offset model (logistic) ... 544s a 544s b 544s c 545s d 545s Offset+x model... 546s a 546s b 546s c 552s d 552s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points 552s Offset+x model (logistic) ... 552s a 552s b 552s c 552s d 552s Offset model Strauss ... 552s a 552s b 552s c 552s d 552s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points 552s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points 552s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points 552s Offset model Strauss (logistic) ... 553s a 553s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points 553s b 553s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points 554s c 554s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points 555s d 555s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points 555s There were 11 warnings (use warnings() to see them) 555s > 555s > reset.spatstat.options() 555s > 555s BEGIN TEST testsM.R 555s 555s R version 4.3.2 (2023-10-31) -- "Eye Holes" 555s Copyright (C) 2023 The R Foundation for Statistical Computing 555s Platform: powerpc64le-unknown-linux-gnu (64-bit) 555s 555s R is free software and comes with ABSOLUTELY NO WARRANTY. 555s You are welcome to redistribute it under certain conditions. 555s Type 'license()' or 'licence()' for distribution details. 555s 555s R is a collaborative project with many contributors. 555s Type 'contributors()' for more information and 555s 'citation()' on how to cite R or R packages in publications. 555s 555s Type 'demo()' for some demos, 'help()' for on-line help, or 555s 'help.start()' for an HTML browser interface to help. 555s Type 'q()' to quit R. 555s 555s > #' 555s > Loading required package: spatstat.model 555s Loading required package: spatstat.data 555s #' Header for all (concatenated) test files 555s > #' 555s > #' Require spatstat.model 555s > #' Obtain environment variable controlling tests. 555s > #' 555s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 555s > 555s > require(spatstat.model) 556s Loading required package: spatstat.geom 556s spatstat.geom 3.2-8 556s Loading required package: spatstat.random 556s spatstat.random 3.2-2 556s Loading required package: spatstat.explore 556s Loading required package: nlme 557s spatstat.explore 3.2-5 557s Loading required package: rpart 557s spatstat.model 3.2-8 557s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 557s > ALWAYS <- TRUE 557s > cat(paste("--------- Executing", 557s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 557s + "test code -----------\n")) 557s --------- Executing **RESTRICTED** subset of test code ----------- 557s > ## 557s > ## tests/marcelino.R 557s > ## 557s > ## $Revision: 1.4 $ $Date: 2020/04/30 02:18:23 $ 557s > ## 557s > 557s > local({ 557s + if(FULLTEST) { 557s + Y <- split(urkiola) 557s + B <- Y$birch 557s + O <- Y$oak 557s + B.lam <- predict (ppm(B ~polynom(x,y,2)), type="trend") 557s + O.lam <- predict (ppm(O ~polynom(x,y,2)), type="trend") 557s + 557s + Kinhom(B, lambda=B.lam, correction="iso") 557s + Kinhom(B, lambda=B.lam, correction="border") 557s + 557s + Kcross.inhom(urkiola, i="birch", j="oak", B.lam, O.lam) 557s + Kcross.inhom(urkiola, i="birch", j="oak", B.lam, O.lam, correction = "iso") 557s + Kcross.inhom(urkiola, i="birch", j="oak", B.lam, O.lam, correction = "border") 557s + } 557s + }) 557s > 557s > 557s > #' tests/mctests.R 557s > #' Monte Carlo tests 557s > #' (mad.test, dclf.test, envelopeTest, hasenvelope) 557s > #' $Revision: 1.5 $ $Date: 2022/05/23 04:09:49 $ 557s > 557s > 557s > local({ 557s + if(FULLTEST) { 557s + fitx <- ppm(redwood~x) 557s + ax <- envelopeTest(fitx, exponent=2, nsim=9, savefuns=TRUE) 557s + print(ax) 557s + } 557s + }) 557s > 557s > 557s > # 557s > # tests/mppm.R 557s > # 557s > # Basic tests of mppm 557s > # 557s > # $Revision: 1.23 $ $Date: 2022/07/08 04:55:13 $ 557s > # 557s > 557s > if(!FULLTEST) 557s + spatstat.options(npixel=32, ndummy.min=16) 557s > 557s > local({ 557s + ## test interaction formulae and subfits 557s + fit1 <- mppm(Points ~ group, simba, 557s + hyperframe(po=Poisson(), str=Strauss(0.1)), 557s + iformula=~ifelse(group=="control", po, str)) 557s + fit2 <- mppm(Points ~ group, simba, 557s + hyperframe(po=Poisson(), str=Strauss(0.1)), 557s + iformula=~str/id) 557s + fit2w <- mppm(Points ~ group, simba, 557s + hyperframe(po=Poisson(), str=Strauss(0.1)), 557s + iformula=~str/id, weights=runif(nrow(simba))) 557s + # currently invalid 557s + # fit3 <- mppm(Points ~ group, simba, 557s + # hyperframe(po=Poisson(), pie=PairPiece(c(0.05,0.1))), 557s + # iformula=~I((group=="control") * po) + I((group=="treatment") * pie)) 557s + 557s + fit1 557s + fit2 557s + fit2w 557s + # fit3 557s + 557s + if(FULLTEST) { 557s + ## run summary.mppm which currently sits in spatstat-internal.Rd 557s + summary(fit1) 557s + summary(fit2) 557s + summary(fit2w) 557s + # summary(fit3) 557s + } 557s + 557s + ## test vcov algorithm 557s + vcov(fit1) 557s + vcov(fit2) 557s + # vcov(fit3) 557s + 557s + if(FULLTEST) { 557s + fit4 <- mppm(Points ~ group, simba, hyperframe(str=Strauss(0.1)), iformula=~str/group) 557s + fit4 557s + summary(fit4) 557s + vcov(fit4) 557s + fit0 <- mppm(Points ~ group, simba) 557s + anova(fit0, fit4, test="Chi") 557s + ## [bug from Fernando Milesi] 557s + fit5 <- mppm(Wat ~ id, 557s + data=hyperframe(Wat=waterstriders), 557s + interaction=StraussHard(4.5, 1.5), 557s + iformula=~Interaction:id) 557s + fit5 557s + summary(fit5) 557s + vcov(fit5) 557s + } 557s + 557s + ## test subfits algorithm 557s + if(FULLTEST) { 557s + s1 <- subfits(fit1) 557s + s2 <- subfits(fit2) 557s + # s3 <- subfits(fit3) 557s + s4 <- subfits(fit4) 557s + s5 <- subfits(fit5) 557s + 557s + ## validity of results of subfits() 557s + p1 <- solapply(s1, predict) 557s + p2 <- solapply(s2, predict) 557s + # p3 <- solapply(s3, predict) 557s + p4 <- solapply(s4, predict) 557s + p5 <- solapply(s5, predict) 557s + } 557s + }) 559s > 559s > local({ 559s + if(FULLTEST) { 559s + ## cases of predict.mppm 559s + W <- solapply(waterstriders, Window) 559s + Fakes <- solapply(W, runifpoint, n=30) 559s + FakeDist <- solapply(Fakes, distfun) 559s + H <- hyperframe(Bugs=waterstriders, 559s + D=FakeDist) 559s + fit <- mppm(Bugs ~ D, data=H) 559s + p1 <- predict(fit) 559s + p2 <- predict(fit, locations=Fakes) 559s + p3 <- predict(fit, locations=solapply(W, erosion, r=4)) 559s + locn <- as.data.frame(do.call(cbind, lapply(Fakes, coords))) 559s + df <- data.frame(id=sample(1:3, nrow(locn), replace=TRUE), 559s + D=runif(nrow(locn))) 559s + p4 <- predict(fit, locations=locn, newdata=df) 559s + 559s + fitG <- mppm(Bugs ~ D, data=H, use.gam=TRUE) 559s + p1G <- predict(fitG) 559s + p2G <- predict(fitG, locations=Fakes) 559s + p3G <- predict(fitG, locations=solapply(W, erosion, r=4)) 559s + p4G <- predict(fitG, locations=locn, newdata=df) 559s + } 559s + }) 559s > 559s > local({ 559s + ## [thanks to Sven Wagner] 559s + ## factor covariate, with some levels unused in some rows 559s + if(FULLTEST) { 559s + set.seed(14921788) 559s + H <- hyperframe(X=replicate(3, runifpoint(20), simplify=FALSE), 559s + Z=solist(as.im(function(x,y){x}, owin()), 559s + as.im(function(x,y){y}, owin()), 559s + as.im(function(x,y){x+y}, owin()))) 559s + H$Z <- solapply(H$Z, cut, breaks=(0:4)/2) 559s + 559s + fit6 <- mppm(X ~ Z, H) 559s + v6 <- vcov(fit6) 559s + s6 <- subfits(fit6) 559s + p6 <- solapply(s6, predict) 559s + 559s + ## random effects 559s + fit7 <- mppm(X ~ Z, H, random=~1|id) 559s + v7 <- vcov(fit7) 559s + s7 <- subfits(fit7) 559s + p7 <- solapply(s7, predict) 559s + 559s + fit7a <- mppm(X ~ Z, H, random=~x|id) 559s + v7a <- vcov(fit7a) 559s + s7a <- subfits(fit7a) 559s + p7a <- solapply(s7a, predict) 559s + 559s + ## multitype: collisions in vcov.ppm, predict.ppm 559s + H$X <- lapply(H$X, rlabel, labels=factor(c("a","b")), permute=FALSE) 559s + M <- MultiStrauss(matrix(0.1, 2, 2), c("a","b")) 559s + fit8 <- mppm(X ~ Z, H, M) 559s + v8 <- vcov(fit8, fine=TRUE) 559s + s8 <- subfits(fit8) 559s + p8 <- lapply(s8, predict) 559s + c8 <- lapply(s8, predict, type="cif") 559s + 559s + fit9 <- mppm(X ~ Z, H, M, iformula=~Interaction * id) 559s + v9 <- vcov(fit9, fine=TRUE) 559s + s9 <- subfits(fit9) 559s + p9 <- lapply(s9, predict) 559s + c9 <- lapply(s9, predict, type="cif") 559s + 559s + ## and a simple error in recognising 'marks' 559s + fit10 <- mppm(X ~ marks, H) 559s + } 559s + }) 559s > 559s > local({ 559s + if(FULLTEST) { 559s + ## test handling of offsets and zero cif values in mppm 559s + H <- hyperframe(Y = waterstriders) 559s + (fit1 <- mppm(Y ~ 1, data=H, Hardcore(1.5))) 559s + (fit2 <- mppm(Y ~ 1, data=H, StraussHard(7, 1.5))) 559s + (fit3 <- mppm(Y ~ 1, data=H, Hybrid(S=Strauss(7), H=Hardcore(1.5)))) 559s + s1 <- subfits(fit1) 559s + s2 <- subfits(fit2) 559s + s3 <- subfits(fit3) 559s + 559s + ## prediction, in training/testing context 559s + ## (example from Markus Herrmann and Ege Rubak) 559s + X <- waterstriders 559s + dist <- solapply(waterstriders, 559s + function(z) distfun(runifpoint(1, Window(z)))) 559s + i <- 3 559s + train <- hyperframe(pattern = X[-i], dist = dist[-i]) 559s + test <- hyperframe(pattern = X[i], dist = dist[i]) 559s + fit <- mppm(pattern ~ dist, data = train) 559s + pred <- predict(fit, type="cif", newdata=test, verbose=TRUE) 559s + 559s + ## examples from Robert Aue 559s + GH <- Hybrid(G=Geyer(r=0.1, sat=3), H=Hardcore(0.01)) 559s + res <- mppm(Points ~ 1, interaction = GH, data=demohyper) 559s + print(summary(res)) 559s + sub <- subfits(res, verbose=TRUE) 559s + print(sub) 559s + } 559s + }) 559s > 559s > local({ 559s + if(FULLTEST) { 559s + ## test handling of interaction coefficients in multitype case 559s + set.seed(42) 559s + XX <- as.solist(replicate(3, rthin(amacrine, 0.8), simplify=FALSE)) 559s + H <- hyperframe(X=XX) 559s + M <- MultiStrauss(matrix(0.1, 2, 2), levels(marks(amacrine))) 559s + fit <- mppm(X ~ 1, H, M) 559s + co <- coef(fit) 559s + subco <- sapply(subfits(fit), coef) 559s + if(max(abs(subco - co)) > 0.001) 559s + stop("Wrong coefficient values in subfits, for multitype interaction") 559s + } 559s + }) 559s > 559s > local({ 559s + if(FULLTEST) { 559s + ## test lurking.mppm 559s + ## example from 'mppm' 559s + n <- 7 559s + H <- hyperframe(V=1:n, 559s + U=runif(n, min=-1, max=1)) 559s + H$Z <- setcov(square(1)) 559s + H$U <- with(H, as.im(U, as.rectangle(Z))) 559s + H$Y <- with(H, rpoispp(eval.im(exp(2+3*Z)))) 559s + fit <- mppm(Y ~ Z + U + V, data=H) 559s + 559s + lurking(fit, expression(Z), type="P") 559s + lurking(fit, expression(V), type="raw") # design covariate 559s + lurking(fit, expression(U), type="raw") # image, constant in each row 559s + lurking(fit, H$Z, type="P") # list of images 559s + } 559s + }) 559s > 559s > local({ 559s + if(FULLTEST) { 559s + ## test anova.mppm code blocks and scoping problem 559s + H <- hyperframe(X=waterstriders) 559s + mod0 <- mppm(X~1, data=H, Poisson()) 559s + modxy <- mppm(X~x+y, data=H, Poisson()) 559s + mod0S <- mppm(X~1, data=H, Strauss(2)) 559s + modxyS <- mppm(X~x+y, data=H, Strauss(2)) 559s + anova(mod0, modxy, test="Chi") 559s + anova(mod0S, modxyS, test="Chi") 559s + anova(modxy, test="Chi") 559s + anova(modxyS, test="Chi") 559s + #' models with random effects (example from Marcelino de la Cruz) 559s + mod0r <- mppm(X~1, data=H, Poisson(), random = ~1|id) 559s + modxr <- mppm(X~x, data=H, Poisson(), random = ~1|id) 559s + anova(mod0r, modxr, test="Chi") 559s + } 559s + }) 559s > 559s > local({ 559s + if(FULLTEST) { 559s + ## test multitype stuff 559s + foo <- flu[1:3,] 559s + msh <- MultiStraussHard(iradii=matrix(100, 2, 2), 559s + hradii=matrix(10,2,2), 559s + types=levels(marks(foo$pattern[[1]]))) 559s + msh0 <- MultiStraussHard(iradii=matrix(100, 2, 2), 559s + hradii=matrix(10,2,2)) 559s + fit <- mppm(pattern ~ 1, data=foo, interaction=msh0) 559s + print(fit) 559s + print(summary(fit)) 559s + v <- vcov(fit) 559s + } 559s + }) 559s > 559s > reset.spatstat.options() 559s > #' 559s > #' tests/msr.R 559s > #' 559s > #' $Revision: 1.5 $ $Date: 2020/11/30 07:27:44 $ 559s > #' 559s > #' Tests of code for measures 559s > #' 559s > 559s > if(FULLTEST) { 559s + local({ 559s + 559s + ## cases of 'msr' 559s + Q <- quadscheme(cells) 559s + nQ <- n.quad(Q) 559s + nX <- npoints(cells) 559s + A <- matrix(nX * 3, nX, 3) 559s + B <- matrix(nQ * 3, nQ, 3) 559s + 559s + m <- msr(Q, A, B) 559s + 559s + M <- msr(Q, A, 1) 559s + M <- msr(Q, 1, B) 559s + M <- msr(Q, A, B[,1]) 559s + M <- msr(Q, A[,1], B) 559s + M <- msr(Q, A, B[,1,drop=FALSE]) 559s + M <- msr(Q, A[,1,drop=FALSE], B) 559s + 559s + ## methods 559s + a <- summary(m) 559s + b <- is.marked(m) 559s + w <- as.owin(m) 559s + z <- domain(m) 559s + ss <- scalardilate(m, 2) 559s + tt <- rescale(m, 2) 559s + ee <- rotate(m, pi/4) 559s + aa <- affine(m, mat=diag(c(1,2)), vec=c(0,1)) 559s + ff <- flipxy(m) 559s + 559s + am <- augment.msr(m, sigma=0.08) 559s + ua <- update(am) 559s + 559s + rr <- residuals(ppm(cells ~ x)) 559s + mm <- residuals(ppm(amacrine ~ x)) 559s + ss <- residuals(ppm(amacrine ~ x), type="score") 559s + gg <- rescale(ss, 1/662, c("micron", "microns")) 559s + 559s + plot(mm) 559s + plot(mm, multiplot=FALSE) 559s + plot(mm, equal.markscale=TRUE, equal.ribbon=TRUE) 559s + plot(ss) 559s + plot(ss, multiplot=FALSE) 559s + }) 559s + } 559s > 559s BEGIN TEST testsNtoO.R 559s 559s R version 4.3.2 (2023-10-31) -- "Eye Holes" 559s Copyright (C) 2023 The R Foundation for Statistical Computing 559s Platform: powerpc64le-unknown-linux-gnu (64-bit) 559s 559s R is free software and comes with ABSOLUTELY NO WARRANTY. 559s You are welcome to redistribute it under certain conditions. 559s Type 'license()' or 'licence()' for distribution details. 559s 559s R is a collaborative project with many contributors. 559s Type 'contributors()' for more information and 559s 'citation()' on how to cite R or R packages in publications. 559s 559s Type 'demo()' for some demos, 'help()' for on-line help, or 559s 'help.start()' for an HTML browser interface to help. 559s Type 'q()' to quit R. 559s 559s > #' 559s > #' Header for all (concatenated) test files 559s > #' 559s > #' Require spatstat.model 559s > #' Obtain environment variable controlling tests. 559s Loading required package: spatstat.model 559s Loading required package: spatstat.data 559s > #' 559s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 559s > 559s > require(spatstat.model) 562s Loading required package: spatstat.geom 562s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 562s > ALWAYS <- TRUE 562s > cat(paste("--------- Executing", 562s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 562s + "test code -----------\n")) 562s --------- Executing **RESTRICTED** subset of test code ----------- 562s > # 562s > # tests/NAinCov.R 562s > # 562s > # Testing the response to the presence of NA's in covariates 562s > # 562s > # $Revision: 1.8 $ $Date: 2022/05/22 08:37:38 $ 562s > 562s > if(FULLTEST) { 562s + local({ 562s + X <- runifpoint(42) 562s + Y <- as.im(function(x,y) { x+y }, owin()) 562s + Y[owin(c(0.2,0.4),c(0.2,0.4))] <- NA 562s + # fit model: should produce a warning but no failure 562s + misfit <- ppm(X ~Y, covariates=list(Y=Y)) 562s + # prediction 562s + Z <- predict(misfit, type="trend", se=TRUE) 562s + # covariance matrix: all should be silent 562s + v <- vcov(misfit) 562s + ss <- vcov(misfit, what="internals") 562s + }) 562s + } 562s > 562s BEGIN TEST testsP1.R 562s 562s R version 4.3.2 (2023-10-31) -- "Eye Holes" 562s Copyright (C) 2023 The R Foundation for Statistical Computing 562s Platform: powerpc64le-unknown-linux-gnu (64-bit) 562s 562s R is free software and comes with ABSOLUTELY NO WARRANTY. 562s You are welcome to redistribute it under certain conditions. 562s Type 'license()' or 'licence()' for distribution details. 562s 562s R is a collaborative project with many contributors. 562s Type 'contributors()' for more information and 562s 'citation()' on how to cite R or R packages in publications. 562s 562s Type 'demo()' for some demos, 'help()' for on-line help, or 562s 'help.start()' for an HTML browser interface to help. 562s Type 'q()' to quit R. 562s 562s > #' 562s > #' Header for all (concatenated) test files 562s > #' 562s > #' Require spatstat.model 562s > #' Obtain environment variable controlling tests. 562s > #' 562s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 562s > 562s > require(spatstat.model) 562s spatstat.geom 3.2-8 562s Loading required package: spatstat.random 562s spatstat.random 3.2-2 562s Loading required package: spatstat.explore 562s Loading required package: nlme 562s spatstat.explore 3.2-5 562s Loading required package: rpart 562s spatstat.model 3.2-8 562s Loading required package: spatstat.model 562s Loading required package: spatstat.data 562s Loading required package: spatstat.geom 562s spatstat.geom 3.2-8 562s Loading required package: spatstat.random 562s spatstat.random 3.2-2 562s Loading required package: spatstat.explore 562s Loading required package: nlme 562s spatstat.explore 3.2-5 562s Loading required package: rpart 562s spatstat.model 3.2-8 562s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 562s > ALWAYS <- TRUE 562s > cat(paste("--------- Executing", 562s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 562s + "test code -----------\n")) 562s --------- Executing **RESTRICTED** subset of test code ----------- 562s > ## 562s > ## tests/percy.R 562s > ## 562s > ## Tests of Percus-Yevick approximations 562s > ## 562s > ## $Revision: 1.3 $ $Date: 2020/04/30 05:23:52 $ 562s > 562s > if(FULLTEST) { 562s + local({ 562s + fit <- ppm(swedishpines ~1, DiggleGatesStibbard(6)) 562s + K <- Kmodel(fit) 562s + }) 562s + } 562s > 562s > ## 562s > ## tests/pixelgripes.R 562s > ## Problems related to pixellation of windows 562s > ## 562s > ## $Revision: 1.8 $ $Date: 2022/10/23 06:21:10 $ 562s > 562s > if(FULLTEST) { 562s + local({ 562s + 562s + ## From Philipp Hunziker: bug in rNeymanScott (etc) 562s + ## Create an irregular window 562s + PM <- matrix(c(1,0,0.5,1,0,0), 3, 2, byrow=TRUE) 562s + P <- owin(poly=PM) 562s + ## Generate Matern points 562s + X <- rMatClust(50, 0.05, 5, win=P) 562s + ## Some distance function as a covariate 562s + distorigin <- function(x, y) { sqrt(x^2 + y^2) } 562s + ## No covariates: works fine 562s + fit0 <- kppm(X ~ 1, clusters="MatClust") 562s + Y0 <- simulate(fit0, retry=0) 562s + ## Covariates: Simulation fails 562s + fit1 <- kppm(X ~ distorigin, clusters="MatClust") 562s + Y1 <- simulate(fit1, retry=0) 562s + 562s + }) 562s + } 562s > 562s BEGIN TEST testsP2.R 562s 562s R version 4.3.2 (2023-10-31) -- "Eye Holes" 562s Copyright (C) 2023 The R Foundation for Statistical Computing 562s Platform: powerpc64le-unknown-linux-gnu (64-bit) 562s 562s R is free software and comes with ABSOLUTELY NO WARRANTY. 562s You are welcome to redistribute it under certain conditions. 562s Type 'license()' or 'licence()' for distribution details. 562s 562s R is a collaborative project with many contributors. 562s Type 'contributors()' for more information and 562s 'citation()' on how to cite R or R packages in publications. 562s 562s Type 'demo()' for some demos, 'help()' for on-line help, or 562s 'help.start()' for an HTML browser interface to help. 562s Type 'q()' to quit R. 562s 563s > #' 563s > #' Header for all (concatenated) test files 563s > #' 563s > #' Require spatstat.model 563s > #' Obtain environment variable controlling tests. 563s > #' 563s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 563s > 563s > require(spatstat.model) 563s Loading required package: spatstat.model 563s Loading required package: spatstat.data 564s Loading required package: spatstat.geom 564s spatstat.geom 3.2-8 564s Loading required package: spatstat.random 564s spatstat.random 3.2-2 564s Loading required package: spatstat.explore 564s Loading required package: nlme 564s spatstat.explore 3.2-5 564s Loading required package: rpart 564s spatstat.model 3.2-8 564s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 564s > ALWAYS <- TRUE 564s > cat(paste("--------- Executing", 564s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 564s + "test code -----------\n")) 564s --------- Executing **RESTRICTED** subset of test code ----------- 564s > # 564s > # tests/ppmBadData.R 564s > # 564s > # $Revision: 1.6 $ $Date: 2020/04/30 05:23:52 $ 564s > 564s > # Testing robustness of ppm and support functions 564s > # when data are rubbish 564s > 564s > local({ 564s + if(ALWAYS) { 564s + ## from Rolf: very large proportion of data is NA 564s + SEED <- 42 564s + K <- 101 564s + A <- 500 564s + X <- seq(0, A, length=K) 564s + G <- expand.grid(x=X, y=X) 564s + FOO <- function(x,y) { sin(x)^2 + cos(y)^2 } 564s + M1 <- im(matrix(FOO(G$x, G$y), K, K), xcol=X, yrow=X) 564s + M <- im(matrix(FOO(G$x, G$y), K, K)) 564s + BAR <- function(x) { exp(-6.618913 + 5.855337 * x - 8.432483 * x^2) } 564s + V <- im(BAR(M$v), xcol=X, yrow=X) 564s + # V <- eval.im(exp(-6.618913 + 5.855337 * M - 8.432483 * M^2)) 564s + set.seed(SEED) 564s + Y <- rpoispp(V) 564s + fY <- ppm(Y ~cv + I(cv^2), data=list(cv=M), correction="translate") 564s + diagnose.ppm(fY) 564s + lurking(fY, covariate=as.im(function(x,y){x}, square(A)), type="raw") 564s + } 564s + 564s + if(ALWAYS) { 564s + ## from Andrew Bevan: numerical overflow, ill-conditioned Fisher information 564s + SEED <- 42 564s + 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))) 564s + ## Trend on raster grid 564s + rain <- as.im(X=function(x,y) { x^2 + y^2 }, W=nongranite, dimyx=100) 564s + ## Generate a point pattern via a Lennard-Jones process 564s + set.seed(SEED) 564s + mod4<- rmhmodel(cif="lennard", 564s + par=list(beta=1, sigma=250, epsilon=2.2), 564s + trend=rain, w=nongranite) 564s + ljtr<- rmh(mod4, start=list(n.start=80), control=list(p=1, nrep=1e5)) 564s + 564s + ## Fit a point process model to the pattern with rain as a covariate 564s + ## NOTE INCORRECT TREND FORMULA 564s + ljtrmod <- ppm(ljtr, trend= ~ Z, interaction=NULL, data=list(Z=rain)) 564s + ss <- summary(ljtrmod) 564s + } 564s + 564s + if(FULLTEST) { 564s + ## From Ege 564s + ## Degenerate but non-null argument 'covariates' 564s + xx <- list() 564s + names(xx) <- character(0) 564s + fit <- ppm(cells ~x, covariates = xx) 564s + st <- summary(fit) 564s + } 564s + 564s + }) 564s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 564s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 565s Error in solve.default(M) : 565s system is computationally singular: reciprocal condition number = 5.72254e-18 565s In addition: Warning messages: 565s 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, 565s 2: Some infinite, NA or NaN increments were removed 565s 3: Numerical underflow detected: sigma is probably too small 565s 4: Some infinite, NA or NaN increments were removed 565s Error in solve.default(M) : 565s system is computationally singular: reciprocal condition number = 5.72254e-18 565s In addition: Warning message: 565s Cannot compute variance: Fisher information matrix is singular 565s Warning message: 565s Cannot compute variance: Fisher information matrix is singular 565s > 565s > 565s > 565s > #' tests/ppmclass.R 565s > #' 565s > #' Class support for ppm 565s > #' 565s > #' $Revision: 1.9 $ $Date: 2022/03/07 03:26:09 $ 565s > 565s > if(FULLTEST) { 565s + local({ 565s + #' (1) print.ppm, summary.ppm, print.summary.ppm 565s + Z <- as.im(function(x,y){x}, Window(cells)) 565s + fitZ <- ppm(cells ~ Z) 565s + print(fitZ) 565s + print(summary(fitZ)) 565s + #' logistic 565s + fitl <- ppm(swedishpines ~ x+y, method="logi") 565s + print(fitl) 565s + print(summary(fitl)) 565s + #' Model with covariate arguments 565s + f <- function(x,y,b) { x+b } 565s + fitf <- ppm(cells ~ f, covfunargs=list(b=1)) 565s + print(fitf) 565s + print(summary(fitf)) 565s + #' Invalid model 565s + fitN <- ppm(redwood ~ 1, Strauss(0.1)) 565s + print(fitN) 565s + print(summary(fitN)) 565s + #' standard errors in output 565s + fat <- ppm(cells ~ x, Strauss(0.12)) 565s + op <- spatstat.options(print.ppm.SE='always') 565s + print(fat) 565s + spatstat.options(print.ppm.SE='never') 565s + print(fat) 565s + print(fitZ) 565s + spatstat.options(op) 565s + 565s + ## (2) plot.ppm 565s + plot(fitZ) 565s + plot(fat, trend=FALSE, cif=FALSE, se=FALSE) 565s + 565s + ## (3) emend.ppm 565s + fitZe <- emend(fitZ, trace=TRUE) 565s + ZZ <- Z 565s + fitZZ <- ppm(cells ~ Z + ZZ) 565s + fitZZe <- emend(fitZZ, trace=TRUE) 565s + fitOK <- ppm(redwood ~1, Strauss(0.1), emend=TRUE) 565s + print(fitOK) 565s + fitNot <- ppm(redwood ~1, Strauss(0.1)) 565s + fitSlow <- emend(fitNot, trace=TRUE) 565s + print(fitSlow) 565s + op <- spatstat.options(project.fast=TRUE) 565s + fitFast <- emend(fitNot, trace=TRUE) 565s + print(fitFast) 565s + fitZZe <- emend(fitZZ, trace=TRUE) 565s + spatstat.options(op) 565s + 565s + #' (4) methods for other generics 565s + logLik(fitZ, absolute=TRUE) 565s + unitname(fitZ) 565s + unitname(fat) <- c("metre", "metres") 565s + is.expandable(fitf) 565s + fit0 <- update(fitZ, . ~ 1) 565s + anova(fit0, fitZ, override=TRUE) 565s + interactionfamilyname(fat) 565s + interactionorder(fat) 565s + hardcoredist(fat) 565s + 565s + #' (5) miscellaneous 565s + 565s + ## example from Robert Aue - handling offsets 565s + X <- demohyper$Points[[1]] 565s + GH <- Hybrid(G=Geyer(r=0.1, sat=3), H=Hardcore(0.01)) 565s + fit <- ppm(X ~ 1, GH) 565s + valid.ppm(fit) 565s + 565s + #' hard core distance of hybrid 565s + hardcoredist(fit) 565s + #' interaction order of hybrid 565s + interactionorder(fit) 565s + 565s + #' case of boundingbox 565s + boundingbox(cells, ppm(cells ~ 1)) 565s + }) 565s + 565s + reset.spatstat.options() 565s + } 565s > # 565s > # tests/ppmgam.R 565s > # 565s > # Test ppm with use.gam=TRUE 565s > # 565s > # $Revision: 1.4 $ $Date: 2020/04/30 05:23:52 $ 565s > # 565s > 565s > if(FULLTEST) { 565s + local({ 565s + fit <- ppm(nztrees ~s(x,y), use.gam=TRUE) 565s + mm <- model.matrix(fit) 565s + mf <- model.frame(fit) 565s + v <- vcov(fit) 565s + prd <- predict(fit) 565s + }) 565s + } 565s > #' 565s > #' tests/ppmlogi.R 565s > #' 565s > #' Tests of ppm(method='logi') 565s > #' and related code (predict, leverage etc) 565s > #' 565s > #' $Revision: 1.15 $ $Date: 2020/04/30 05:23:52 $ 565s > #' 565s > 565s > local({ 565s + if(FULLTEST) { 565s + fit <- ppm(cells ~x, method="logi") 565s + f <- fitted(fit) 565s + p <- predict(fit) 565s + u <- summary(fit) 565s + fitS <- ppm(cells ~x, Strauss(0.12), method="logi") 565s + fS <- fitted(fitS) 565s + pS <- predict(fitS) 565s + uS <- summary(fitS) 565s + print(uS) 565s + 565s + plot(leverage(fit)) 565s + plot(influence(fit)) 565s + plot(dfbetas(fit)) 565s + plot(leverage(fitS)) 565s + plot(influence(fitS)) 565s + plot(dfbetas(fitS)) 565s + } 565s + 565s + if(FULLTEST) { 565s + #' same with hard core - A1 is singular 565s + fitH <- ppm(cells ~x, Strauss(0.08), method="logi") 565s + print(fitH) 565s + fH <- fitted(fitH) 565s + pH <- predict(fitH) 565s + uH <- summary(fitH) 565s + print(uH) 565s + plot(leverage(fitH)) 565s + plot(influence(fitH)) 565s + plot(dfbetas(fitH)) 565s + } 565s + 565s + if(FULLTEST) { 565s + #' logistic fit to data frame of covariates 565s + z <- c(rep(TRUE, 5), rep(FALSE, 5)) 565s + df <- data.frame(A=z + 2* runif(10), 565s + B=runif(10)) 565s + Y <- quadscheme.logi(runifpoint(5), runifpoint(5)) 565s + fut <- ppm(Y ~ A+B, data=df, method="logi") 565s + sf <- summary(fut) 565s + print(sf) 565s + } 565s + 565s + if(FULLTEST) { 565s + #' vblogit code, just to check that it runs. 565s + fee <- ppm(cells ~ x, method="VBlogi", nd=21) 565s + print(fee) 565s + summary(fee) 565s + logLik(fee) 565s + AIC(fee) 565s + extractAIC(fee) 565s + Z <- predict(fee) 565s + summary(Z) 565s + print(fee$internal$glmfit) # print.vblogit 565s + } 565s + }) 565s > 565s > # 565s > # tests/ppmmarkorder.R 565s > # 565s > # $Revision: 1.4 $ $Date: 2020/04/30 05:23:52 $ 565s > # 565s > # Test that predict.ppm, plot.ppm and plot.fitin 565s > # tolerate marks with levels that are not in alpha order 565s > # 565s > if(ALWAYS) { # locale-dependent? 565s + local({ 565s + X <- amacrine 565s + levels(marks(X)) <- c("ZZZ", "AAA") 565s + fit <- ppm(X ~marks, MultiStrauss(c("ZZZ","AAA"), matrix(0.06, 2, 2))) 565s + aa <- predict(fit, type="trend") 565s + bb <- predict(fit, type="cif") 565s + plot(fit) 565s + plot(fitin(fit)) 565s + }) 565s + } 566s > 566s > 566s > # 566s > # tests/ppmscope.R 566s > # 567s > # Test things that might corrupt the internal format of ppm objects 567s > # 567s > # $Revision: 1.7 $ $Date: 2022/01/19 09:18:20 $ 567s > # 567s > 567s > if(ALWAYS) { # dependent on R version? 567s + local({ 567s + 567s + ## (1) Scoping problem that can arise when ppm splits the data 567s + fit <- ppm(bei ~elev, data=bei.extra) 567s + mm <- model.matrix(fit) 567s + 567s + ## (2) Fast update mechanism 567s + fit1 <- ppm(cells ~x+y, Strauss(0.07)) 567s + fit2 <- update(fit1, ~y) 567s + fit3 <- update(fit2, ~x) 567s + 567s + ## (3) New formula-based syntax 567s + attach(bei.extra) 567s + slfit <- ppm(bei ~ grad) 567s + sl2fit <- update(slfit, ~grad + I(grad^2)) 567s + slfitup <- update(slfit, use.internal=TRUE) 567s + sl2fitup <- update(sl2fit, use.internal=TRUE) 567s + 567s + ## (4) anova.ppm 567s + fut1 <- ppm(cells ~ 1, Strauss(0.1)) 567s + futx <- ppm(cells ~ x, Strauss(0.1)) 567s + anova(fut1, test="Chi") 567s + anova(futx, test="Chi") 567s + fut1a <- ppm(cells ~ 1, Strauss(0.1), rbord=0) 567s + anova(fut1a, futx, test="Chi") 567s + fut1d <- ppm(cells ~ 1, Strauss(0.1), nd=23) 567s + anova(fut1d, futx, test="Chi") 567s + ## This now works! 567s + futxyg <- ppm(cells ~ x + s(y), Strauss(0.1), use.gam=TRUE) 567s + anova(futx, futxyg) 567s + ## marked 567s + fatP <- ppm(amacrine ~ marks) 567s + fatM <- ppm(amacrine ~ marks, MultiStrauss(matrix(0.07, 2, 2))) 567s + anova(fatP, fatM, test="Chi") 567s + 567s + ## (5) expansion of "." in update.ppm 567s + fitb <- ppm(bei ~ . , data=bei.extra) 567s + step(fitb) 567s + }) 567s + } 569s Start: AIC=42295.11 569s ~elev + grad 569s 569s Df AIC 569s 42295 569s - elev 1 42383 569s - grad 1 42760 569s Nonstationary Poisson process 569s Fitted to point pattern dataset ‘bei’ 569s 569s Log intensity: ~elev + grad 569s 569s Fitted trend coefficients: 569s (Intercept) elev grad 569s -8.56355220 0.02143995 5.84646680 569s 569s Estimate S.E. CI95.lo CI95.hi Ztest Zval 569s (Intercept) -8.56355220 0.341113849 -9.23212306 -7.89498134 *** -25.104675 569s elev 0.02143995 0.002287866 0.01695581 0.02592408 *** 9.371155 569s grad 5.84646680 0.255781018 5.34514522 6.34778838 *** 22.857313 569s > grep# 569s function (pattern, x, ignore.case = FALSE, perl = FALSE, value = FALSE, 569s fixed = FALSE, useBytes = FALSE, invert = FALSE) 569s { 569s pattern <- as.character(pattern) 569s if (is.factor(x) && length(levx <- levels(x)) < length(x) && 569s !is.na(pattern[1L])) { 569s value <- is.character(idxna <- suppressWarnings(grep(pattern, 569s NA_character_, ignore.case, perl, value, fixed, useBytes, 569s invert))) 569s idx <- logical(length(levx)) 569s idx[grep(pattern, levx, ignore.case, perl, FALSE, fixed, 569s useBytes, invert)] <- TRUE 569s idx <- idx[x] 569s if (length(idxna)) 569s idx[is.na(x)] <- TRUE 569s idx <- which(idx) 569s if (value) { 569s idx <- x[idx] 569s structure(as.character(idx), names = names(idx)) 569s } 569s else idx 569s } 569s else { 569s if (!is.character(x)) 569s x <- structure(as.character(x), names = names(x)) 569s .Internal(grep(pattern, x, ignore.case, value, perl, 569s fixed, useBytes, invert)) 569s } 569s } 569s 569s 569s > # tests/ppmtricks.R 569s > # 569s > Warning messages: 569s 1: anova.ppm now computes the *adjusted* deviances when the models are not Poisson processes. 569s 2: Models were re-fitted using a common value of 'rbord' 569s 3: Models were re-fitted using a common quadrature scheme 569s 4: Models were re-fitted with use.gam=TRUE 569s 5: Deviance adjustment is not available for gam fits; unadjusted composite deviance calculated. 569s 6: Models were re-fitted using a common value of 'rbord' 569s # Test backdoor exits, hidden options, internals and tricks in ppm 569s > # 569s > # $Revision: 1.19 $ $Date: 2020/04/30 05:23:52 $ 569s > # 569s > local({ 569s + 569s + ## (1) skip.border 569s + if(ALWAYS) { # needed below 569s + fit <- ppm(cells, ~1, Strauss(0.1), skip.border=TRUE) 569s + } 569s + 569s + ## (2) subset arguments of different kinds 569s + if(FULLTEST) { 569s + fut <- ppm(cells ~ x, subset=(x > 0.5)) 569s + fot <- ppm(cells ~ x, subset=(x > 0.5), method="logi") 569s + W <- owin(c(0.4, 0.8), c(0.2, 0.7)) 569s + fut <- ppm(cells ~ x, subset=W) 569s + fot <- ppm(cells ~ x, subset=W, method="logi") 569s + V <- as.im(inside.owin, Window(cells), w=W) 569s + fet <- ppm(cells ~ x, subset=V) 569s + fet <- ppm(cells ~ x, subset=V, method="logi") 569s + } 569s + 569s + ## (3) profilepl -> ppm 569s + ## uses 'skip.border' and 'precomputed' 569s + ## also tests scoping for covariates 569s + if(FULLTEST) { 569s + splants <- split(ants) 569s + mess <- splants[["Messor"]] 569s + cats <- splants[["Cataglyphis"]] 569s + ss <- data.frame(r=seq(60,120,by=20),hc=29/6) 569s + dM <- distmap(mess,dimyx=256) 569s + mungf <- profilepl(ss, StraussHard, cats ~ dM) 569s + mungp <- profilepl(ss, StraussHard, trend=~dM, Q=cats) 569s + } 569s + 569s + ## (4) splitting large quadschemes into blocks 569s + if(FULLTEST) { 569s + mop <- spatstat.options(maxmatrix=5000) 569s + qr <- quadBlockSizes(quadscheme(cells)) 569s + pr <- predict(ppm(cells ~ x, AreaInter(0.05))) 569s + spatstat.options(mop) 569s + qr <- quadBlockSizes(quadscheme(cells)) 569s + } 569s + 569s + ## (5) shortcuts in summary.ppm 569s + ## and corresponding behaviour of print.summary.ppm 569s + if(FULLTEST) { 569s + print(summary(fit, quick=TRUE)) 569s + print(summary(fit, quick="entries")) 569s + print(summary(fit, quick="no prediction")) 569s + print(summary(fit, quick="no variances")) 569s + } 569s + 569s + ## (6) suffstat.R 569s + if(ALWAYS) { 569s + fitP <- update(fit, Poisson()) 569s + suffstat.poisson(fitP, cells) 569s + fit0 <- killinteraction(fit) 569s + suffstat.poisson(fit0, cells) 569s + } 569s + 569s + ## (7) various support for class ppm 569s + if(FULLTEST) { 569s + fut <- kppm(redwood ~ x) 569s + A <- quad.ppm(fut) 569s + Z <- as.im(function(x,y){x}, Window(cells)) 569s + fitZ <- ppm(cells ~ Z) 569s + U <- getppmOriginalCovariates(fitZ) 569s + } 569s + 569s + ## (8) support for class profilepl 569s + if(FULLTEST) { 569s + rr <- data.frame(r=seq(0.05, 0.15, by=0.02)) 569s + ps <- profilepl(rr, Strauss, cells) 569s + ## plot(ps) ## covered in plot.profilepl.Rd 569s + simulate(ps, nrep=1e4) 569s + parameters(ps) 569s + fitin(ps) 569s + predict(ps, type="cif") 569s + } 569s + 569s + ## (9) class 'plotppm' 569s + if(FULLTEST) { 569s + fut <- ppm(amacrine ~ marks + polynom(x,y,2), Strauss(0.07)) 569s + p <- plot(fut, plot.it=FALSE) 569s + print(p) 569s + plot(p, how="contour") 569s + plot(p, how="persp") 569s + } 569s + 569s + ## (10) ppm -> mpl.engine -> mpl.prepare 569s + if(ALWAYS) { # includes C code 569s + fit <- ppm(cells, NULL) 569s + fit <- ppm(cells ~ x, clipwin=square(0.7)) 569s + fit <- ppm(cells ~ x, subset=square(0.7)) 569s + DG <- as.im(function(x,y){x+y < 1}, square(1)) 569s + fit <- ppm(cells ~ x, subset=DG) 569s + fit <- ppm(cells ~ x, GLM=glm) 569s + fit <- ppm(cells ~ x, famille=quasi(link='log', variance='mu')) 569s + fit <- ppm(cells ~ x, Hardcore(0.07), skip.border=TRUE, splitInf=TRUE) 569s + } 569s + 569s + ## (11) unidentifiable model (triggers an error in ppm) 569s + if(FULLTEST) { 569s + Q <- quadscheme(cells) 569s + M <- mpl.prepare(Q, cells, as.ppp(Q), trend=~1, covariates=NULL, 569s + interaction=Hardcore(0.3), correction="none") 569s + } 569s + }) 569s > 569s > reset.spatstat.options() 569s > # 569s > # tests/prediction.R 569s > # 569s > # Things that might go wrong with predict() 569s > # 569s > # $Revision: 1.20 $ $Date: 2020/04/30 05:41:59 $ 569s > # 569s > 569s > local({ 569s + if(ALWAYS) { 569s + ## test of 'covfunargs' - platform dependent? 569s + f <- function(x,y,a){ y - a } 569s + fit <- ppm(cells ~x + f, covariates=list(f=f), covfunargs=list(a=1/2)) 569s + p <- predict(fit) 569s + 569s + ## prediction involving 0 * NA 569s + qc <- quadscheme(cells, nd=10) 569s + r <- minnndist(as.ppp(qc))/10 569s + fit <- ppm(qc ~ 1, Strauss(r)) # model has NA for interaction coefficient 569s + p1 <- predict(fit) 569s + p2 <- predict(fit, type="cif", ngrid=10) 569s + stopifnot(all(is.finite(as.matrix(p1)))) 569s + stopifnot(all(is.finite(as.matrix(p2)))) 569s + } 569s + 569s + if(FULLTEST) { 569s + ## test of 'new.coef' mechanism 569s + fut <- ppm(cells ~ x, Strauss(0.15), rbord=0) 569s + p0 <- predict(fut, type="cif") 569s + pe <- predict(fut, type="cif", new.coef=coef(fut)) 569s + pn <- predict(fut, type="cif", new.coef=unname(coef(fut))) 569s + if(max(abs(pe-p0)) > 0.01) 569s + stop("new.coef mechanism is broken!") 569s + if(max(abs(pn-p0)) > 0.01) 569s + stop("new.coef mechanism gives wrong answer, for unnamed vectors") 569s + #' adaptcoef 569s + a <- c(A=1,B=2,Z=42) 569s + b <- c(B=41,A=0) 569s + ab <- adaptcoef(a, b, drop=TRUE) 569s + } 569s + 569s + if(FULLTEST) { 569s + ## tests of relrisk.ppm 569s + fut <- ppm(amacrine ~ x * marks) 569s + a <- relrisk(fut, control=2, relative=TRUE) 569s + a <- relrisk(fut, se=TRUE) 569s + a <- relrisk(fut, relative=TRUE, se=TRUE) 569s + fut <- ppm(sporophores ~ marks + x) 569s + a <- relrisk(fut, control=2, relative=TRUE) 569s + a <- relrisk(fut, se=TRUE) 569s + a <- relrisk(fut, relative=TRUE, se=TRUE) 569s + 569s + ## untested cases of predict.ppm 569s + fit0 <- ppm(cells) 569s + a <- predict(fit0, interval="confidence") 569s + a <- predict(fit0, interval="confidence", type="count") 569s + fit <- ppm(cells ~ x) 569s + b <- predict(fit, se=TRUE, locations=cells) 569s + b <- predict(fit, se=TRUE, interval="confidence") 569s + b <- predict(fit, type="count", se=TRUE) 569s + b <- predict(fit, type="count", window=square(0.5), se=TRUE) 569s + b <- predict(fit, type="count", window=quadrats(cells, 3), se=TRUE) 569s + d <- predict(fit, type="count", interval="prediction", se=TRUE) 569s + d <- predict(fit, type="count", interval="confidence", se=TRUE) 569s + d <- predict(fit, interval="confidence", se=TRUE) 569s + foot <- ppm(cells ~ x, StraussHard(0.12)) 569s + d <- predict(foot, ignore.hardcore=TRUE) 569s + dX <- predict(foot, ignore.hardcore=TRUE, locations=cells) 569s + 569s + ## superseded usages 569s + b <- predict(fit, type="se", getoutofjail=TRUE) 569s + b <- predict(fit, type="se", locations=cells) # warning 569s + b <- predict(fit, total=TRUE) 569s + b <- predict(fit, total=square(0.5)) 569s + b <- predict(fit, total=quadrats(cells, 3)) 569s + 569s + ## supporting code 569s + u <- model.se.image(fit, square(0.5)) 569s + u <- model.se.image(fit, square(0.5), what="cv") 569s + u <- model.se.image(fit, square(0.5), what="ce") 569s + co <- c(Intercept=5, slope=3, kink=2) 569s + re <- c("Intercept", "slope") 569s + a <- fill.coefs(co, re) # warning 569s + b <- fill.coefs(co, rev(names(co))) 569s + d <- fill.coefs(co, letters[1:3]) 569s + ## model matrix etc 569s + v <- model.frame(ppm(cells)) 569s + fut <- ppm(cells ~ x, Strauss(0.1)) 569s + v <- model.matrix(fut, subset=(x<0.5), keepNA=FALSE) 569s + df <- data.frame(x=runif(10), y=runif(10), 569s + Interaction=sample(0:1, 10, TRUE)) 569s + m10 <- PPMmodelmatrix(fut, data=df) 569s + mmm <- PPMmodelmatrix(fut, Q=quad.ppm(fut)) 569s + #' effectfun for Gibbs 569s + effectfun(fut, "x") 569s + effectfun(fut, "x", se.fit=TRUE) 569s + #' implicit covariate when there is only one 569s + effectfun(fut) 569s + effectfun(fut, se.fit=TRUE) 569s + #' given covariate 569s + dlin <- distfun(copper$SouthLines) 569s + copfit <- ppm(copper$SouthPoints ~ dlin, Geyer(1,1)) 569s + effectfun(copfit, "dlin") 569s + effectfun(copfit) 569s + #' covariate that is not used in model 569s + effectfun(fut, "y", x=0) 569s + futS <- ppm(cells ~ 1, Strauss(0.1)) 569s + effectfun(futS, "x") 569s + effectfun(futS, "y") 569s + #' factor covariate 569s + fot <- ppm(amacrine~x+marks) 569s + effectfun(fot, "marks", x=0.5, se.fit=TRUE) 569s + #' covariate retained but not used 569s + W <- Window(swedishpines) 569s + a <- solist(A=funxy(function(x,y){x < 20}, W), 569s + B=funxy(function(x,y){factor(x < 20)}, W)) 569s + fvt <- ppm(swedishpines ~ A, data=a, allcovar=TRUE) 569s + effectfun(fvt, "A", se.fit=TRUE) 569s + effectfun(fvt, "B", A=TRUE, se.fit=TRUE) 569s + 569s + ## ppm with covariate values in data frame 569s + X <- rpoispp(42) 569s + Q <- quadscheme(X) 569s + weirdfunction <- function(x,y){ 10 * x^2 + 5 * sin(10 * y) } 569s + Zvalues <- weirdfunction(x.quad(Q), y.quad(Q)) 569s + fot <- ppm(Q ~ y + Z, data=data.frame(Z=Zvalues)) 569s + effectfun(fot, "y", Z=0) 569s + effectfun(fot, "Z", y=0) 569s + 569s + #' multitype 569s + modX <- ppm(amacrine ~ polynom(x,2)) 569s + effectfun(modX) 569s + effectfun(modX, "x") 569s + modXM <- ppm(amacrine ~ marks*polynom(x,2)) 569s + effectfun(modXM, "x", marks="on") 569s + modXYM <- ppm(amacrine ~ marks*polynom(x,y,2)) 569s + effectfun(modXYM, "x", y=0, marks="on") 569s + 569s + df <- as.data.frame(simulate(modXM, drop=TRUE)) 569s + df$marks <- as.character(df$marks) 569s + dfpr <- predict(modXM, locations=df) 569s + } 569s + }) 569s > 569s > # 569s > # tests/project.ppm.R 569s > # 569s > # $Revision: 1.7 $ $Date: 2020/04/30 05:41:59 $ 569s > # 569s > # Tests of projection mechanism 569s > # 569s > 569s > local({ 569s + chk <- function(m) { 569s + if(!valid.ppm(m)) stop("Projected model was still not valid") 569s + return(invisible(NULL)) 569s + } 569s + 569s + if(FULLTEST) { 569s + ## a very unidentifiable model 569s + fit <- ppm(cells ~Z, Strauss(1e-06), covariates=list(Z=0)) 569s + chk(emend(fit)) 569s + ## multitype 569s + r <- matrix(1e-06, 2, 2) 569s + fit2 <- ppm(amacrine ~1, MultiStrauss(types=c("off", "on"), radii=r)) 569s + chk(emend(fit2)) 569s + ## complicated multitype 569s + fit3 <- ppm(amacrine ~1, MultiStraussHard(types=c("off", "on"), 569s + iradii=r, hradii=r/5)) 569s + chk(emend(fit3)) 569s + 569s + #' code coverage 569s + op <- spatstat.options(project.fast=TRUE) 569s + fut <- emend(fit, trace=TRUE) 569s + chk(fut) 569s + spatstat.options(op) 569s + 569s + #' hierarchical 569s + ra <- r 569s + r[2,1] <- NA 569s + fit4 <- ppm(amacrine ~1, HierStrauss(types=c("off", "on"), radii=r)) 569s + chk(emend(fit4)) 569s + #' complicated hierarchical 569s + fit5 <- ppm(amacrine ~1, HierStraussHard(types=c("off", "on"), 569s + iradii=r, hradii=r/5)) 569s + chk(emend(fit5)) 569s + 569s + ## hybrids 569s + r0 <- min(nndist(redwood)) 569s + ra <- 1.25 * r0 569s + rb <- 0.8 * r0 569s + f1 <- ppm(redwood ~1, Hybrid(A=Strauss(ra), B=Geyer(0.1, 2)), project=TRUE) 569s + chk(f1) 569s + f2 <- ppm(redwood ~1, Hybrid(A=Strauss(rb), B=Geyer(0.1, 2)), project=TRUE) 569s + chk(f2) 569s + f3 <- ppm(redwood ~1, Hybrid(A=Strauss(ra), B=Strauss(0.1)), project=TRUE) 569s + chk(f3) 569s + f4 <- ppm(redwood ~1, Hybrid(A=Strauss(rb), B=Strauss(0.1)), project=TRUE) 569s + chk(f4) 569s + f5 <- ppm(redwood ~1, Hybrid(A=Hardcore(rb), B=Strauss(0.1)), project=TRUE) 569s + chk(f5) 569s + f6 <- ppm(redwood ~1, Hybrid(A=Hardcore(rb), B=Geyer(0.1, 2)), project=TRUE) 569s + chk(f6) 569s + f7 <- ppm(redwood ~1, Hybrid(A=Geyer(rb, 1), B=Strauss(0.1)), project=TRUE) 569s + chk(f7) 569s + } 569s + }) 569s > 569s > reset.spatstat.options() 569s > 569s BEGIN TEST testsQ.R 569s 569s R version 4.3.2 (2023-10-31) -- "Eye Holes" 569s Copyright (C) 2023 The R Foundation for Statistical Computing 569s Platform: powerpc64le-unknown-linux-gnu (64-bit) 569s 569s R is free software and comes with ABSOLUTELY NO WARRANTY. 569s You are welcome to redistribute it under certain conditions. 569s Type 'license()' or 'licence()' for distribution details. 569s 569s R is a collaborative project with many contributors. 569s Type 'contributors()' for more information and 569s 'citation()' on how to cite R or R packages in publications. 569s 569s Type 'demo()' for some demos, 'help()' for on-line help, or 569s 'help.start()' for an HTML browser interface to help. 569s Type 'q()' to quit R. 569s 579s > #' 579s > #' Header for all (concatenated) test files 579s Loading required package: spatstat.model 579s Loading required package: spatstat.data 579s Loading required package: spatstat.geom 579s > #' 579s > #' Require spatstat.model 579s > #' Obtain environment variable controlling tests. 579s > #' 579s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 579s > 579s > require(spatstat.model) 579s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 579s > ALWAYS <- TRUE 579s > cat(paste("--------- Executing", 579s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 579s + "test code -----------\n")) 579s --------- Executing **RESTRICTED** subset of test code ----------- 579s > 579s BEGIN TEST testsR1.R 579s 579s R version 4.3.2 (2023-10-31) -- "Eye Holes" 579s Copyright (C) 2023 The R Foundation for Statistical Computing 579s Platform: powerpc64le-unknown-linux-gnu (64-bit) 579s 579s R is free software and comes with ABSOLUTELY NO WARRANTY. 579s You are welcome to redistribute it under certain conditions. 579s Type 'license()' or 'licence()' for distribution details. 579s 579s R is a collaborative project with many contributors. 579s Type 'contributors()' for more information and 579s 'citation()' on how to cite R or R packages in publications. 579s 579s Type 'demo()' for some demos, 'help()' for on-line help, or 579s 'help.start()' for an HTML browser interface to help. 579s Type 'q()' to quit R. 579s 579s > #' 579s > #' Header for all (concatenated) test files 579s > #' 579s > #' Require spatstat.model 579s > #' Obtain environment variable controlling tests. 579s > #' 579s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 579s > 579s > require(spatstat.model) 579s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 579s > ALWAYS <- TRUE 579s > cat(paste("--------- Executing", 579s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 579s + "test code -----------\n")) 579s --------- Executing **RESTRICTED** subset of test code ----------- 579s > #' tests/resid.R 579s > #' 579s > #' Stuff related to residuals and residual diagnostics 579s > #' including residual summary functions 579s > #' 579s > #' $Revision: 1.7 $ $Date: 2022/05/22 08:43:31 $ 579s > #' 579s > 579s > local({ 579s + fit <- ppm(cells ~x, Strauss(r=0.15)) 579s + rr <- residuals(fit, quad=quadscheme(cells, nd=128)) 579s + diagnose.ppm(fit, cumulative=FALSE, type="pearson") 579s + 579s + if(FULLTEST) { 579s + diagnose.ppm(fit, cumulative=FALSE) 579s + 579s + fitoff <- ppm(cells ~ sin(x) + offset(y)) 579s + plot(a <- parres(fitoff, "x")) 579s + plot(b <- parres(fitoff, "y")) 579s + print(a) 579s + print(b) 579s + 579s + d <- diagnose.ppm(fit, which="marks") 579s + plot(d, plot.neg="discrete") 579s + plot(d, plot.neg="imagecontour") 579s + 579s + d <- diagnose.ppm(fit, type="pearson", which="smooth") 579s + plot(d, plot.smooth="image") 579s + plot(d, plot.smooth="contour") 579s + plot(d, plot.smooth="imagecontour") 579s + 579s + d <- diagnose.ppm(fit, type="pearson", which="x") 579s + plot(d) 579s + d <- diagnose.ppm(fit, type="pearson", which="y") 579s + plot(d) 579s + 579s + diagnose.ppm(fit, type="pearson", which="x", cumulative=FALSE) 579s + diagnose.ppm(fit, type="pearson", which="x", cumulative=FALSE) 579s + diagnose.ppm(fit, type="raw", plot.neg="discrete", plot.smooth="image") 579s + diagnose.ppm(fit, type="pearson", plot.neg="contour", plot.smooth="contour") 579s + 579s + diagnose.ppm(fitoff, type="raw", which="smooth", plot.smooth="persp") 579s + diagnose.ppm(fitoff, type="pearson", plot.neg="imagecontour") 579s + 579s + plot(Frame(letterR), main="") 579s + ploterodewin(letterR, erosion(letterR, 0.05), main="jeans") 579s + W <- as.mask(letterR) 579s + plot(Frame(W), main="") 579s + ploterodewin(W, erosion(W, 0.05), main="JeAnS") 579s + 579s + #' entangled terms in model 579s + U <- as.im(1, owin()) 579s + Z <- as.im(function(x,y) x, owin()) 579s + X <- runifpoint(40) 579s + fut <- ppm(X ~ Z:U) 579s + a <- parres(fut, "Z") 579s + futoff <- ppm(X ~ offset(Z*U)) 579s + a <- parres(futoff, "Z") 579s + 579s + #' residual summary functions 579s + pt <- psst(cells, interaction=Strauss(0.1), fun=nndcumfun) 579s + } 579s + }) 579s > 579s > 579s > 579s > ## 579s > ## tests/rhohat.R 579s > ## 579s > ## Test all combinations of options for rhohatCalc 579s > ## 579s > ## $Revision: 1.6 $ $Date: 2022/05/22 08:03:48 $ 579s > 579s > local({ 579s + if(FULLTEST) { 579s + X <- rpoispp(function(x,y){exp(3+3*x)}) 579s + Z <- as.im(function(x,y) { x }, Window(X)) 579s + f <- funxy(function(x,y) { y + 1 }, Window(X)) 579s + 579s + 579s + ## rhohat.ppm 579s + fit <- ppm(X ~x) 579s + rhofitA <- rhohat(fit, "x") 579s + rhofitB <- rhohat(fit, "x", method="reweight") 579s + rhofitC <- rhohat(fit, "x", method="transform") 579s + rhofitD <- rhohat(fit, Z) 579s + rhofitD <- rhohat(fit, Z, positiveCI=TRUE) 579s + lam <- predict(fit) 579s + 579s + 579s + ## Horvitz-Thompson 579s + rhofitAH <- rhohat(fit, "x", horvitz=TRUE) 579s + rhofitBH <- rhohat(fit, "x", method="reweight", horvitz=TRUE) 579s + rhofitCH <- rhohat(fit, "x", method="transform", horvitz=TRUE) 579s + 579s + r2myx <- rho2hat(fit, "y", "x") 579s + r2myxw <- rho2hat(fit, "y", "x", method="reweight") 579s + plot(r2myx) 579s + plot(r2myxw) 579s + print(r2myxw) 579s + predict(r2myxw) 579s + predict(r2myxw, relative=TRUE) 579s + } 579s + }) 579s > 579s BEGIN TEST testsR2.R 579s 579s R version 4.3.2 (2023-10-31) -- "Eye Holes" 579s Copyright (C) 2023 The R Foundation for Statistical Computing 579s Platform: powerpc64le-unknown-linux-gnu (64-bit) 579s 579s R is free software and comes with ABSOLUTELY NO WARRANTY. 579s You are welcome to redistribute it under certain conditions. 579s Type 'license()' or 'licence()' for distribution details. 579s 579s R is a collaborative project with many contributors. 579s Type 'contributors()' for more information and 579s 'citation()' on how to cite R or R packages in publications. 579s 579s Type 'demo()' for some demos, 'help()' for on-line help, or 579s 'help.start()' for an HTML browser interface to help. 579s Type 'q()' to quit R. 579s 579s > #' 579s > #' Header for all (concatenated) test files 579s > #' 579s > #' Require spatstat.model 579s > #' Obtain environment variable controlling tests. 579s > #' 579s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 579s > 579s > require(spatstat.model) 579s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 579s > ALWAYS <- TRUE 579s > cat(paste("--------- Executing", 579s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 579s + "test code -----------\n")) 579s --------- Executing **RESTRICTED** subset of test code ----------- 579s > # 579s > # tests/rmhExpand.R 579s > # 579s > # test decisions about expansion of simulation window 579s > # 579s > # $Revision: 1.9 $ $Date: 2022/10/23 01:17:33 $ 579s > # 579s > 579s > local({ 579s + if(FULLTEST) { 579s + ## check expansion in rmhmodel.ppm 579s + fit <- ppm(cells ~x) 579s + mod <- rmhmodel(fit) 579s + is.expandable(mod) 579s + wsim <- as.rectangle(mod$trend) 579s + ## work around changes in 'unitname' 579s + wcel <- as.owin(cells) 579s + unitname(wcel) <- unitname(cells) 579s + ## test 579s + if(!identical(wsim, wcel)) 579s + stop("Expansion occurred improperly in rmhmodel.ppm") 579s + } 579s + }) 579s > 579s > 579s > 579s > # 579s > # tests/rmhTrend.R 579s > # 579s > # Problems with trend images (rmhmodel.ppm or rmhEngine) 579s > # 579s > 579s > if(ALWAYS) { 579s + local({ 579s + set.seed(42) 579s + 579s + # Bug folder 37 of 8 feb 2011 579s + # rmhmodel.ppm -> predict.ppm 579s + # + rmhResolveTypes -> is.subset.owin 579s + 579s + Z <- rescale(demopat, 7000) 579s + X <- unmark(Z) 579s + X1 <- split(Z)[[1]] 579s + Int <- density(X,dimyx=200) 579s + Lint <- eval.im(log(npoints(X1)*Int/npoints(X))) 579s + M <- as.owin(Int) 579s + MR <- intersect.owin(M,scalardilate(M,0.5,origin="midpoint")) 579s + X1 <- X1[MR] 579s + Fut <- ppm(X1~offset(Lint),covariates=list(Lint=Lint), 579s + inter=BadGey(r=c(0.03,0.05),sat=3)) 579s + Y <- rmh(Fut,control=list(expand=M,nrep=1e3), verbose=FALSE) 579s + 579s + }) 579s + } 579s > # 579s > # tests/rmhmodel.ppm.R 579s > # 579s > # $Revision: 1.10 $ $Date: 2020/05/01 05:29:42 $ 579s > # 579s > # Case-by-case tests of rmhmodel.ppm 579s > # 579s > 579s > if(FULLTEST) { 579s + local({ 579s + f <- ppm(cells) 579s + m <- rmhmodel(f) 579s + 579s + f <- ppm(cells ~x) 579s + m <- rmhmodel(f) 579s + 579s + f <- ppm(cells ~1, Strauss(0.1)) 579s + m <- rmhmodel(f) 579s + 579s + f <- ppm(cells ~1, StraussHard(r=0.1,hc=0.05)) 579s + m <- rmhmodel(f) 579s + print(m) 579s + 579s + f <- ppm(cells ~1, Hardcore(0.07)) 579s + m <- rmhmodel(f) 579s + 579s + f <- ppm(cells ~1, DiggleGratton(0.05,0.1)) 579s + m <- rmhmodel(f) 579s + 579s + f <- ppm(cells ~1, Softcore(0.5), correction="isotropic") 579s + m <- rmhmodel(f) 579s + 579s + f <- ppm(cells ~1, Geyer(0.07,2)) 579s + m <- rmhmodel(f) 579s + 579s + f <- ppm(cells ~1, BadGey(c(0.07,0.1,0.13),2)) 579s + m <- rmhmodel(f) 579s + 579s + f <- ppm(cells ~1, PairPiece(r = c(0.05, 0.1, 0.2))) 579s + m <- rmhmodel(f) 579s + 579s + f <- ppm(cells ~1, AreaInter(r=0.06)) 579s + m <- rmhmodel(f) 579s + print(m) 579s + 579s + # multitype 579s + 579s + r <- matrix(0.07, 2, 2) 579s + f <- ppm(amacrine ~1, MultiStrauss(c("off","on"),r)) 579s + m <- rmhmodel(f) 579s + print(m) 579s + 579s + h <- matrix(min(nndist(amacrine))/2, 2, 2) 579s + f <- ppm(amacrine ~1, MultiStraussHard(c("off","on"),r, h)) 579s + m <- rmhmodel(f) 579s + 579s + diag(r) <- NA 579s + diag(h) <- NA 579s + f <- ppm(amacrine ~1, MultiStrauss(c("off","on"),r)) 579s + m <- rmhmodel(f) 579s + 579s + f <- ppm(amacrine ~1, MultiStraussHard(c("off","on"),r, h)) 579s + m <- rmhmodel(f) 579s + 579s + # multitype data, interaction not dependent on type 579s + 579s + f <- ppm(amacrine ~marks, Strauss(0.05)) 579s + m <- rmhmodel(f) 579s + print(m) 579s + 579s + # trends 579s + 579s + f <- ppm(cells ~x, Strauss(0.1)) 579s + m <- rmhmodel(f) 579s + 579s + f <- ppm(cells ~y, StraussHard(r=0.1,hc=0.05)) 579s + m <- rmhmodel(f) 579s + 579s + f <- ppm(cells ~x+y, Hardcore(0.07)) 579s + m <- rmhmodel(f) 579s + print(m) 579s + 579s + f <- ppm(cells ~polynom(x,y,2), Softcore(0.5), correction="isotropic") 579s + m <- rmhmodel(f) 579s + 579s + # covariates 579s + 579s + Z <- as.im(function(x,y){ x^2+y^2 }, as.owin(cells)) 579s + f <- ppm(cells ~z, covariates=list(z=Z)) 579s + m <- rmhmodel(f) 579s + m <- rmhmodel(f, control=list(p=1)) 579s + print(m) 579s + 579s + Zim <- as.im(Z, as.owin(cells)) 579s + f <- ppm(cells ~z, covariates=list(z=Zim)) 579s + m <- rmhmodel(f) 579s + 579s + Z <- as.im(function(x,y){ x^2+y }, as.owin(amacrine)) 579s + f <- ppm(amacrine ~z + marks, covariates=list(z=Z)) 579s + m <- rmhmodel(f) 579s + print(m) 579s + m <- rmhmodel(f, control=list(p=1)) 579s + m <- rmhmodel(f, control=list(p=1,fixall=TRUE)) 579s + print(m) 579s + 579s + Zim <- as.im(Z, as.owin(amacrine)) 579s + f <- ppm(amacrine ~z + marks, covariates=list(z=Zim)) 579s + m <- rmhmodel(f) 579s + print(m) 579s + 579s + }) 579s + } 579s > # 579s > # tests/rmhmodelHybrids.R 579s > # 579s > # Test that rmhmodel.ppm and rmhmodel.default 579s > # work on Hybrid interaction models 579s > # 579s > # $Revision: 1.6 $ $Date: 2022/10/23 01:17:56 $ 579s > # 579s > 579s > if(ALWAYS) { # involves C code 579s + local({ 579s + 579s + ## ......... rmhmodel.ppm ....................... 579s + fit1 <- ppm(redwood ~1, 579s + Hybrid(A=Strauss(0.02), B=Geyer(0.1, 2), C=Geyer(0.15, 1))) 579s + m1 <- rmhmodel(fit1) 579s + m1 579s + reach(m1) 579s + 579s + ## Test of handling 'IsOffset' 579s + fit2 <- ppm(cells ~1, Hybrid(H=Hardcore(0.05), G=Geyer(0.15, 2))) 579s + m2 <- rmhmodel(fit2) 579s + ## also test C code for hybrid interaction with hard core 579s + fakecells <- rmh(fit2, nrep=1e4) 579s + 579s + ## Test of handling Poisson components 579s + fit3 <- ppm(cells ~1, Hybrid(P=Poisson(), S=Strauss(0.05))) 579s + X3 <- rmh(fit3, control=list(nrep=1e3,expand=1), verbose=FALSE) 579s + 579s + 579s + }) 579s + } 579s Extracting model information...Evaluating trend...done. 579s Extracting model information...Evaluating trend...done. 579s Extracting model information...Evaluating trend...done. 579s Checking arguments..determining simulation windows...Starting simulation. 579s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 579s > 579s > # 579s > # tests/rmh.ppm.R 579s > # 579s > # $Revision: 1.5 $ $Date: 2020/05/01 05:29:42 $ 579s > # 579s > # Examples removed from rmh.ppm.Rd 579s > # stripped down to minimal tests of validity 579s > # 579s > 579s > local({ 579s + op <- spatstat.options() 579s + spatstat.options(rmh.nrep=10, npixel=10, ndummy.min=10) 579s + spatstat.options(project.fast=TRUE) 579s + Nrep <- 10 579s + 579s + X <- swedishpines 579s + if(FULLTEST) { 579s + ## Poisson process 579s + fit <- ppm(X ~1, Poisson()) 579s + Xsim <- rmh(fit) 579s + } 579s + if(ALWAYS) { # Gibbs model => C code 579s + ## Strauss process 579s + fit <- ppm(X ~1, Strauss(r=7)) 579s + Xsim <- rmh(fit) 579s + 579s + ## Strauss process simulated on a larger window 579s + ## then clipped to original window 579s + Xsim <- rmh(fit, control=list(nrep=Nrep, expand=1.1, periodic=TRUE)) 579s + 579s + ## Extension of model to another window (thanks to Tuomas Rajala) 579s + Xsim <- rmh(fit, w=square(2)) 579s + Xsim <- simulate(fit, w=square(2)) 579s + 579s + ## Strauss - hard core process 579s + ## fit <- ppm(X ~1, StraussHard(r=7,hc=2)) 579s + ## Xsim <- rmh(fit, start=list(n.start=X$n)) 579s + 579s + ## Geyer saturation process 579s + ## fit <- ppm(X ~1, Geyer(r=7,sat=2)) 579s + ## Xsim <- rmh(fit, start=list(n.start=X$n)) 579s + 579s + ## Area-interaction process 579s + fit <- ppm(X ~1, AreaInter(r=7)) 579s + Xsim <- rmh(fit, start=list(n.start=X$n)) 579s + 579s + ## Penttinen process 579s + fit <- ppm(X ~1, Penttinen(r=7)) 579s + Xsim <- rmh(fit, start=list(n.start=X$n)) 579s + 579s + ## soft core interaction process 579s + ## X <- quadscheme(X, nd=50) 579s + ## fit <- ppm(X ~1, Softcore(kappa=0.1), correction="isotropic") 579s + ## Xsim <- rmh(fit, start=list(n.start=X$n)) 579s + 579s + ## Diggle-Gratton pairwise interaction model 579s + ## fit <- ppm(cells ~1, DiggleGratton(0.05, 0.1)) 579s + ## Xsim <- rmh(fit, start=list(n.start=cells$n)) 579s + ## plot(Xsim, main="simulation from fitted Diggle-Gratton model") 579s + 579s + 579s + ## piecewise-constant pairwise interaction function 579s + X <- rSSI(0.05, 100) 579s + fit <- ppm(X ~1, PairPiece(seq(0.02, 0.1, by=0.01))) 579s + Xsim <- rmh(fit) 579s + } 579s + 579s + ## marked point pattern 579s + Y <- amacrine 579s + 579s + if(FULLTEST) { 579s + #' marked Poisson models 579s + fit <- ppm(Y) 579s + Ysim <- rmh(fit) 579s + 579s + fit <- ppm(Y~marks) 579s + Ysim <- rmh(fit) 579s + 579s + fit <- ppm(Y~x) 579s + Ysim <- rmh(fit) 579s + 579s + fit <- ppm(Y~marks+x) 579s + Ysim <- rmh(fit) 579s + } 579s + 579s + if(ALWAYS) { 579s + #' multitype Strauss 579s + typ <- levels(Y$marks) 579s + MS <- MultiStrauss(types = typ, 579s + radii=matrix(0.07, ncol=2, nrow=2)) 579s + 579s + fit <- ppm(Y~marks*x, MS) 579s + Ysim <- rmh(fit) 579s + 579s + #' multitype Hardcore 579s + h0 <- minnndist(unmark(Y)) * 0.95 579s + MH <- MultiHard(types = typ, 579s + hradii=matrix(h0, ncol=2, nrow=2)) 579s + fit <- ppm(Y ~ marks+x, MH) 579s + Ysim <- rmh(fit) 579s + #' other code blocks 579s + Ysim <- rmh(fit, control=list(periodic=TRUE, expand=1)) 579s + Ysim <- rmh(fit, control=list(periodic=FALSE, expand=1)) 579s + #' multihard core with invalid initial state 579s + Ydouble <- superimpose(Y, rjitter(Y, h0/10)) 579s + Ysim <- rmh(fit, start=list(x.start=Ydouble)) 579s + 579s + #' Lennard-Jones 579s + fut <- ppm(unmark(longleaf) ~ 1, LennardJones(), rbord=1) 579s + Ysim <- rmh(fut) 579s + Ysim <- rmh(fut, control=list(periodic=TRUE, expand=1)) 579s + } 579s + 579s + spatstat.options(op) 579s + }) 579s Extracting model information...Evaluating trend...done. 579s Checking arguments..determining simulation windows...Starting simulation. 579s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 579s Extracting model information...Evaluating trend...done. 579s Checking arguments..determining simulation windows...Starting simulation. 579s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 579s Extracting model information...Evaluating trend...done. 579s Checking arguments..determining simulation windows...Starting simulation. 579s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 579s Extracting model information...Evaluating trend...done. 579s Checking arguments..determining simulation windows...Starting simulation. 579s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 579s Extracting model information...Evaluating trend...done. 579s Checking arguments..determining simulation windows...Starting simulation. 579s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 579s Model is invalid - projecting it 579s spatstat.geom 3.2-8 579s Loading required package: spatstat.random 579s spatstat.random 3.2-2 579s Loading required package: spatstat.explore 579s Loading required package: nlme 579s spatstat.explore 3.2-5 579s Loading required package: rpart 579s spatstat.model 3.2-8 579s Loading required package: spatstat.model 579s Loading required package: spatstat.data 579s Loading required package: spatstat.geom 579s spatstat.geom 3.2-8 579s Loading required package: spatstat.random 579s spatstat.random 3.2-2 579s Loading required package: spatstat.explore 579s Loading required package: nlme 579s spatstat.explore 3.2-5 579s Loading required package: rpart 579s spatstat.model 3.2-8 579s Loading required package: spatstat.model 579s Loading required package: spatstat.data 579s Loading required package: spatstat.geom 579s spatstat.geom 3.2-8 579s Loading required package: spatstat.random 579s spatstat.random 3.2-2 579s Loading required package: spatstat.explore 579s Loading required package: nlme 579s spatstat.explore 3.2-5 579s Loading required package: rpart 579s spatstat.model 3.2-8 579s Extracting model information...Evaluating trend...done. 579s Checking arguments..determining simulation windows...Starting simulation. 579s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 580s Extracting model information...Evaluating trend...done. 580s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 580s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 580s Extracting model information...Evaluating trend...done. 580s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 580s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 580s Extracting model information...Evaluating trend...done. 580s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 580s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 580s Extracting model information...Evaluating trend...done. 580s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 580s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 580s Extracting model information...Evaluating trend...done. 580s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 580s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 581s Extracting model information...Evaluating trend...done. 581s Checking arguments..determining simulation windows...Starting simulation. 581s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 581s Extracting model information...Evaluating trend...done. 581s Checking arguments..determining simulation windows...Starting simulation. 581s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 581s > 581s > 581s > reset.spatstat.options() 581s > #' 581s > #' tests/rmhsnoopy.R 581s > #' 581s > #' Test the rmh interactive debugger 581s > #' 581s > #' $Revision: 1.11 $ $Date: 2022/10/23 01:19:00 $ 581s > 581s > if(ALWAYS) { # may depend on platform 581s + local({ 581s + R <- 0.1 581s + ## fit a model and prepare to simulate 581s + model <- ppm(amacrine ~ marks + x, Strauss(R)) 581s + siminfo <- rmh(model, preponly=TRUE) 581s + Wsim <- siminfo$control$internal$w.sim 581s + Wclip <- siminfo$control$internal$w.clip 581s + if(is.null(Wclip)) Wclip <- Window(cells) 581s + 581s + ## determine debugger interface panel geometry 581s + Xinit <- runifpoint(ex=amacrine)[1:40] 581s + P <- rmhsnoop(Wsim=Wsim, Wclip=Wclip, R=R, 581s + xcoords=Xinit$x, 581s + ycoords=Xinit$y, 581s + mlevels=levels(marks(Xinit)), 581s + mcodes=as.integer(marks(Xinit)) - 1L, 581s + irep=3L, itype=1L, 581s + proptype=1, proplocn=c(0.5, 0.5), propmark=0, propindx=0, 581s + numerator=42, denominator=24, 581s + panel.only=TRUE) 581s + boxes <- P$boxes 581s + clicknames <- names(P$clicks) 581s + boxcentres <- do.call(concatxy, lapply(boxes, centroid.owin)) 581s + 581s + ## design a sequence of clicks 581s + actionsequence <- c("Up", "Down", "Left", "Right", 581s + "At Proposal", "Zoom Out", "Zoom In", "Reset", 581s + "Accept", "Reject", "Print Info", 581s + "Next Iteration", "Next Shift", "Next Death", 581s + "Skip 10", "Skip 100", "Skip 1000", "Skip 10,000", 581s + "Skip 100,000", "Exit Debugger") 581s + actionsequence <- match(actionsequence, clicknames) 581s + actionsequence <- actionsequence[!is.na(actionsequence)] 581s + xy <- lapply(boxcentres, "[", actionsequence) 581s + 581s + ## queue the click sequence 581s + spatstat.utils::queueSpatstatLocator(xy$x,xy$y) 581s + 581s + ## go 581s + rmh(model, snoop=TRUE) 581s + }) 581s + } 581s Extracting model information...Evaluating trend...done. 581s Checking arguments..determining simulation windows...Evaluating trend integral...Extracting model information...Evaluating trend...done. 581s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 581s Initial state... 581s Creating debugger environment..Done. 581s Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 583s 583s 583s ------------------- 583s Iteration 0 583s Simulation window: 583s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 583s Clipping window: 583s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 583s Current state: 583s Marked planar point pattern: 72 points 583s Multitype, with levels = off, on 583s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 583s Proposal type: Shift 583s Shift data point 18 from current location (0.290108, 0.0160037, “off”) to 583s new location (0.620599, 0.378428, “off”) 583s Hastings ratio = 6831.92992943048 / 14545.6615344207 = 0.469688498750192 583s Fate of proposal: Rejected 585s Marked planar point pattern: 350 points 585s Multitype, with levels = off, on 585s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 585s Pattern was generated by Metropolis-Hastings simulation. 585s > 585s BEGIN TEST testsS.R 585s 585s R version 4.3.2 (2023-10-31) -- "Eye Holes" 585s Copyright (C) 2023 The R Foundation for Statistical Computing 585s Platform: powerpc64le-unknown-linux-gnu (64-bit) 585s 585s R is free software and comes with ABSOLUTELY NO WARRANTY. 585s You are welcome to redistribute it under certain conditions. 585s Type 'license()' or 'licence()' for distribution details. 585s 585s R is a collaborative project with many contributors. 585s Type 'contributors()' for more information and 585s 'citation()' on how to cite R or R packages in publications. 585s 585s Type 'demo()' for some demos, 'help()' for on-line help, or 585s 'help.start()' for an HTML browser interface to help. 585s Type 'q()' to quit R. 585s 585s > #' 585s > #' Header for all (concatenated) test files 585s > #' 585s > #' Require spatstat.model 585s > #' Obtain environment variable controlling tests. 585s > #' 585s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 585s > 585s > require(spatstat.model) 585s Loading required package: spatstat.model 585s Loading required package: spatstat.data 586s Loading required package: spatstat.geom 586s spatstat.geom 3.2-8 586s Loading required package: spatstat.random 586s spatstat.random 3.2-2 586s Loading required package: spatstat.explore 586s Loading required package: nlme 586s spatstat.explore 3.2-5 586s Loading required package: rpart 586s spatstat.model 3.2-8 586s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 586s > ALWAYS <- TRUE 586s > cat(paste("--------- Executing", 586s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 586s + "test code -----------\n")) 586s --------- Executing **RESTRICTED** subset of test code ----------- 586s > # 586s > # tests/slrm.R 586s > # 586s > # $Revision: 1.3 $ $Date: 2020/05/01 09:59:59 $ 586s > # 586s > # Test slrm fitting and prediction when there are NA's 586s > # 586s > 586s > if(ALWAYS) { 586s + local({ 586s + X <- copper$SouthPoints 586s + W <- owin(poly=list(x=c(0,35,35,1),y=c(1,1,150,150))) 586s + Y <- X[W] 586s + fit <- slrm(Y ~ x+y) 586s + pred <- predict(fit) 586s + extractAIC(fit) 586s + fitx <- update(fit, . ~ x) 586s + simulate(fitx, seed=42) 586s + if(FULLTEST) { 586s + unitname(fitx) 586s + unitname(fitx) <- "km" 586s + 586s + mur <- solapply(murchison,rescale, 1000, "km") 586s + mur$dfault <- distfun(mur$faults) 586s + fut <- slrm(gold ~ dfault, data=mur, splitby="greenstone") 586s + A <- model.images(fut) 586s + } 586s + }) 586s + } 587s > 587s > 587s > # 587s > # tests/step.R 587s > # 587s > # $Revision: 1.5 $ $Date: 2020/05/01 09:59:59 $ 587s > # 587s > # test for step() operation 587s > # 587s > if(FULLTEST) { 587s + local({ 587s + Z <- as.im(function(x,y){ x^3 - y^2 }, nztrees$window) 587s + fitP <- ppm(nztrees ~x+y+Z, covariates=list(Z=Z)) 587s + step(fitP) 587s + fitS <- update(fitP, Strauss(7)) 587s + step(fitS) 587s + fitM <- ppm(amacrine ~ marks*(x+y), 587s + MultiStrauss(types=levels(marks(amacrine)), radii=matrix(0.04, 2, 2))) 587s + step(fitM) 587s + }) 587s + } 587s > 587s > 587s > 587s > 587s BEGIN TEST testsT.R 587s 587s R version 4.3.2 (2023-10-31) -- "Eye Holes" 587s Copyright (C) 2023 The R Foundation for Statistical Computing 587s Platform: powerpc64le-unknown-linux-gnu (64-bit) 587s 587s R is free software and comes with ABSOLUTELY NO WARRANTY. 587s You are welcome to redistribute it under certain conditions. 587s Type 'license()' or 'licence()' for distribution details. 587s 587s R is a collaborative project with many contributors. 587s Type 'contributors()' for more information and 587s 'citation()' on how to cite R or R packages in publications. 587s 587s Type 'demo()' for some demos, 'help()' for on-line help, or 587s 'help.start()' for an HTML browser interface to help. 587s Type 'q()' to quit R. 587s 587s > #' 587s > #' Header for all (concatenated) test files 587s > #' 587s > #' Require spatstat.model 587s > #' Obtain environment variable controlling tests. 587s > #' 587s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 587s > 587s > require(spatstat.model) 587s Loading required package: spatstat.model 587s Loading required package: spatstat.data 588s Loading required package: spatstat.geom 588s spatstat.geom 3.2-8 588s Loading required package: spatstat.random 588s spatstat.random 3.2-2 588s Loading required package: spatstat.explore 588s Loading required package: nlme 588s spatstat.explore 3.2-5 588s Loading required package: rpart 588s spatstat.model 3.2-8 588s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 588s > ALWAYS <- TRUE 588s > cat(paste("--------- Executing", 588s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 588s + "test code -----------\n")) 588s --------- Executing **RESTRICTED** subset of test code ----------- 588s > # 588s > # tests/testaddvar.R 588s > # 588s > # test addvar options 588s > # 588s > # $Revision: 1.3 $ $Date: 2020/05/02 01:32:58 $ 588s > 588s > if(FULLTEST) { 588s + local({ 588s + X <- rpoispp(function(x,y){exp(3+3*x)}) 588s + model <- ppm(X ~y) 588s + addvar(model, "x", crosscheck=TRUE) 588s + addvar(model, "x", bw.input="quad") 588s + w <- square(0.5) 588s + addvar(model, "x", subregion=w) 588s + addvar(model, "x", subregion=w, bw.input="points") 588s + Z <- as.im(function(x,y) { x }, Window(X)) 588s + addvar(model, Z) 588s + }) 588s + } 588s > # 588s > # tests/testparres.R 588s > # 588s > # additional test of parres 588s > # 588s > # $Revision: 1.8 $ $Date: 2022/05/20 06:59:59 $ 588s > # 588s > 588s > if(FULLTEST) { 588s + local({ 588s + X <- rpoispp(function(x,y){exp(3+x+2*x^2)}) 588s + model <- ppm(X ~x+y) 588s + 588s + # options in parres (and code blocks in print.parres) 588s + parres(model, "x") 588s + parres(model, "x", smooth.effect=TRUE) 588s + parres(model, "x", bw.input="quad") 588s + w <- square(0.5) 588s + parres(model, "x", subregion=w) 588s + parres(model, "x", subregion=w, bw.input="quad") 588s + f <- function(x,y) { x + y } 588s + parres(model, f) 588s + 588s + # check whether 'update.ppm' has messed up internals 588s + mod2 <- update(model, ~x) 588s + parres(mod2, "x") 588s + 588s + #' other kinds of covariates 588s + mod3 <- ppm(X ~ x + offset(y)) 588s + parres(mod3, "offset(y)") 588s + Z <- distmap(runifpoint(3)) 588s + parres(mod3, Z) 588s + mod4 <- ppm(X ~ sin(x), data=solist(B=Z)) 588s + parres(mod4, "sin(x)") 588s + parres(mod4, "B") 588s + 588s + #' models with interaction 588s + mod5 <- ppm(cells ~ x, AreaInter(0.06)) 588s + parres(mod5, "x") 588s + dlin <- distfun(copper$SouthLines) 588s + copfit <- ppm(copper$SouthPoints ~ dlin, Geyer(1,1)) 588s + parres(copfit, "dlin") 588s + 588s + #' covariate need not be specified if there is only one. 588s + parres(mod5) 588s + parres(copfit) 588s + 588s + #' infrastructure 588s + ltuae <- evaluateCovariate(42, cells) 588s + LTUAE <- evaluateCovariate(ltuae, cells) 588s + 588s + fit <- ppm(amacrine ~ x * marks, nd=16) 588s + dmat <- model.depends(fit) 588s + check.separable(dmat, "x", c(x=FALSE, marks=FALSE), FALSE) 588s + check.separable(dmat, "x", c(FALSE, FALSE), FALSE) 588s + check.separable(dmat, "x", c(x=FALSE, marks=TRUE), FALSE) 588s + }) 588s + } 588s > #' 588s > #' tests/threedee.R 588s > #' 588s > #' Tests of 3D code 588s > #' 588s > #' $Revision: 1.8 $ $Date: 2020/05/02 01:32:58 $ 588s > #' 588s > 588s > local({ 588s + X <- runifpoint3(30) 588s + Y <- runifpoint3(20) 588s + if(FULLTEST) { 588s + A <- runifpoint3(10, nsim=2) 588s + Z <- ppsubset(X, 2:4) 588s + } 588s + ## 588s + if(ALWAYS) { # includes C code 588s + d <- pairdist(X, periodic=TRUE, squared=TRUE) 588s + d <- crossdist(X, Y, squared=TRUE) 588s + d <- crossdist(X, Y, squared=TRUE, periodic=TRUE) 588s + #' 588s + h <- has.close(X, 0.2) 588s + h <- has.close(X, 0.2, periodic=TRUE) 588s + h <- has.close(X, 0.2, Y=Y) 588s + h <- has.close(X, 0.2, Y=Y, periodic=TRUE) 588s + #' code blocks not otherwise reached 588s + rmax <- 0.6 * max(nndist(X)) 588s + g <- G3est(X, rmax=rmax, correction="rs") 588s + g <- G3est(X, rmax=rmax, correction="km") 588s + g <- G3est(X, rmax=rmax, correction="Hanisch") 588s + g <- G3est(X, rmax=rmax, sphere="ideal") 588s + g <- G3est(X, rmax=rmax, sphere="digital") 588s + v <- sphere.volume() 588s + v <- digital.volume() 588s + #' older code 588s + co <- coords(X) 588s + xx <- co$x 588s + yy <- co$y 588s + zz <- co$z 588s + gg1 <- g3engine(xx, yy, zz, correction="Hanisch G3") 588s + gg2 <- g3engine(xx, yy, zz, correction="minus sampling") 588s + ff1 <- f3engine(xx, yy, zz, correction="no") 588s + ff2 <- f3engine(xx, yy, zz, correction="minus sampling") 588s + } 588s + ## 588s + if(ALWAYS) { 588s + #'class support 588s + X <- runifpoint3(10) 588s + print(X) 588s + print(X %mark% runif(10)) 588s + print(X %mark% factor(letters[c(1:5,5:1)])) 588s + print(X %mark% data.frame(a=1:10, b=runif(10))) 588s + da <- as.Date(paste0("2020-01-0", c(1:5,5:1))) 588s + print(X %mark% da) 588s + print(X %mark% data.frame(a=1:10, b=da)) 588s + } 588s + }) 588s Three-dimensional point pattern: 10 points 588s Box: [0, 1] x [0, 1] x [0, 1] units 588s Marked three-dimensional point pattern: 10 points 588s marks are numeric, of storage type ‘double’ 588s Box: [0, 1] x [0, 1] x [0, 1] units 588s Marked three-dimensional point pattern: 10 points 588s Multitype, with levels = a, b, c, d, e 588s Box: [0, 1] x [0, 1] x [0, 1] units 588s Marked three-dimensional point pattern: 10 points 588s Mark variables: a, b 588s Box: [0, 1] x [0, 1] x [0, 1] units 588s Marked three-dimensional point pattern: 10 points 588s marks are dates, of class ‘Date’ 588s Box: [0, 1] x [0, 1] x [0, 1] units 588s Marked three-dimensional point pattern: 10 points 588s Mark variables: a, b 588s Box: [0, 1] x [0, 1] x [0, 1] units 588s > # 588s > # tests/triplets.R 588s > # 588s > # test code for triplet interaction 588s > # 588s > # $Revision: 1.9 $ $Date: 2022/05/22 08:45:38 $ 588s > # 588s > if(ALWAYS) { # C code, platform dependence 588s + local({ 588s + #' valid model 588s + fit <- ppm(cells ~1, Triplets(0.1)) 588s + fit 588s + suffstat(fit) 588s + #' invalid model 588s + fitR <- ppm(redwood ~1, Triplets(0.1)) 588s + fitR 588s + suffstat(fitR) 588s + #' hard core (zero triangles, coefficient is NA) 588s + fit0 <- ppm(cells ~1, Triplets(0.05)) 588s + fit0 588s + suffstat(fit0) 588s + #' bug case (1 triangle in data) 588s + fit1 <- ppm(cells ~1, Triplets(0.15)) 588s + fit1 588s + suffstat(fit1) 588s + #' simulation 588s + X <- simulate(fit) 588s + mod <- list(cif="triplets",par=list(beta=50,gamma=0.2,r=0.07), w=square(1)) 588s + Xm <- rmh(model=mod,start=list(n.start=5), control=list(nrep=1e5)) 588s + #' hard core 588s + mod$par$gamma <- 0 588s + XmHard <- rmh(model=mod,start=list(n.start=5), control=list(nrep=1e5)) 588s + }) 588s + } 588s Warning messages: 588s 1: In G3est: unrecognised argument ‘sphere’ was ignored 588s 2: In G3est: unrecognised argument ‘sphere’ was ignored 590s Checking arguments..determining simulation windows...Starting simulation. 590s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 591s Checking arguments..determining simulation windows...Starting simulation. 591s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 591s > 591s BEGIN TEST testsUtoZ.R 591s 591s R version 4.3.2 (2023-10-31) -- "Eye Holes" 591s Copyright (C) 2023 The R Foundation for Statistical Computing 591s Platform: powerpc64le-unknown-linux-gnu (64-bit) 591s 591s R is free software and comes with ABSOLUTELY NO WARRANTY. 591s You are welcome to redistribute it under certain conditions. 591s Type 'license()' or 'licence()' for distribution details. 591s 591s R is a collaborative project with many contributors. 591s Type 'contributors()' for more information and 591s 'citation()' on how to cite R or R packages in publications. 591s 591s Type 'demo()' for some demos, 'help()' for on-line help, or 591s 'help.start()' for an HTML browser interface to help. 591s Type 'q()' to quit R. 591s 591s > #' 591s > #' Header for all (concatenated) test files 591s > #' 591s > #' Require spatstat.model 591s > #' Obtain environment variable controlling tests. 591s > #' 591s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 591s > 591s > require(spatstat.model) 591s Loading required package: spatstat.model 591s Loading required package: spatstat.data 592s Loading required package: spatstat.geom 592s spatstat.geom 3.2-8 592s Loading required package: spatstat.random 592s spatstat.random 3.2-2 592s Loading required package: spatstat.explore 592s Loading required package: nlme 593s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 593s > ALWAYS <- TRUE 593s > cat(paste("--------- Executing", 593s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 593s + "test code -----------\n")) 593s --------- Executing **RESTRICTED** subset of test code ----------- 593s > # 593s > # tests/undoc.R 593s > # 593s > # $Revision: 1.16 $ $Date: 2020/11/02 07:06:49 $ 593s > # 593s > # Test undocumented hacks, experimental code, etc 593s > 593s > 593s > local({ 593s + if(FULLTEST) { 593s + ## cases of 'pickoption' 593s + aliases <- c(Lenin="Ulyanov", Stalin="Djugashvili", Trotsky="Bronstein") 593s + surname <- "Trot" 593s + pickoption("leader", surname, aliases) 593s + pickoption("leader", surname, aliases, exact=TRUE, die=FALSE) 593s + } 593s + if(ALWAYS) { 593s + ## pixellate.ppp accepts a data frame of weights 593s + pixellate(cells, weights=data.frame(a=1:42, b=42:1)) 593s + ## test parts of 'rmhsnoop' that don't require interaction with user 593s + rmhSnoopEnv(cells, Window(cells), 0.1) 593s + } 593s + if(FULLTEST) { 593s + ## Berman-Turner frame 593s + A <- bt.frame(quadscheme(cells), ~x, Strauss(0.07), rbord=0.07) 593s + print(A) 593s + ## digestCovariates 593s + D <- distfun(cells) 593s + Z <- distmap(cells) 593s + U <- dirichlet(cells) 593s + stopifnot(is.scov(D)) 593s + stopifnot(is.scov(Z)) 593s + stopifnot(is.scov(U)) 593s + stopifnot(is.scov("x")) 593s + dg <- digestCovariates(D=D,Z=Z,U=U,"x",list(A="x", B=D)) 593s + ## 593s + a <- getfields(dg, c("A", "D", "niets"), fatal=FALSE) 593s + ## util.R 593s + gg <- pointgrid(owin(), 7) 593s + checkbigmatrix(1000000L, 1000000L, FALSE, TRUE) 593s + spatstatDiagnostic("whatever") 593s + M <- list(list(a=2, b=FALSE), 593s + list(a=2, b=TRUE)) 593s + stopifnot(!allElementsIdentical(M)) 593s + stopifnot(allElementsIdentical(M, "a")) 593s + ## 593s + A <- Strauss(0.1) 593s + A <- reincarnate.interact(A) 593s + ## 593s + ## special lists 593s + B <- solist(a=cells, b=redwood, c=japanesepines) 593s + BB <- as.ppplist(B) 593s + BL <- as.layered(B) 593s + DB <- as.imlist(lapply(B, density)) 593s + is.solist(B) 593s + is.ppplist(B) 593s + is.imlist(DB) 593s + ## case of density.ppplist 593s + DEB <- density(BB, se=TRUE) 593s + } 593s + 593s + if(ALWAYS) { 593s + ## fft 593s + z <- matrix(1:16, 4, 4) 593s + a <- fft2D(z, west=FALSE) 593s + if(fftwAvailable()) 593s + b <- fft2D(z, west=TRUE) 593s + } 593s + 593s + if(ALWAYS) { 593s + ## experimental interactions 593s + pot <- function(d, par) { d <= 0.1 } 593s + A <- Saturated(pot) 593s + print(A) 593s + A <- update(A, name="something") 593s + ppm(amacrine ~ x, A, rbord=0.1) 593s + } 593s + 593s + if(ALWAYS) { # platform dependent 593s + #' version-checking 593s + now <- Sys.Date() 593s + versioncurrency.spatstat(now + 80, FALSE) 593s + versioncurrency.spatstat(now + 140, FALSE) 593s + versioncurrency.spatstat(now + 400, FALSE) 593s + versioncurrency.spatstat(now + 1000) 593s + } 593s + 593s + if(FULLTEST) { 593s + #' general Ord interaction 593s + gradual <- function(d, pars) { 593s + y <- pmax(0, 0.005 - d)/0.005 593s + if(is.matrix(d)) y <- matrix(y, nrow(d), ncol(d)) 593s + return(y) 593s + } 593s + B <- Ord(gradual, "gradual Ord process") 593s + } 593s + }) 593s Saturated pairwise interaction family 593s Interaction:Saturated spatstat.explore 3.2-5 593s Loading required package: rpart 593s spatstat.model 3.2-8 593s process with user-defined potential 593s Potential function: 593s function (d, par) 593s { 593s d <= 0.1 593s } 593s 593s > 593s > 593s > ## 593s > ## tests/updateppm.R 593s > ## 593s > ## Check validity of update.ppm 593s > ## 593s > ## $Revision: 1.8 $ $Date: 2022/10/23 01:19:19 $ 593s > 593s > local({ 593s + if(ALWAYS) { 593s + require(spatstat.utils) 593s + h <- function(m1, m2) { 593s + mc <- short.deparse(sys.call()) 593s + cat(paste(mc, "\t... ")) 593s + m1name <- short.deparse(substitute(m1)) 593s + m2name <- short.deparse(substitute(m2)) 593s + if(!identical(names(coef(m1)), names(coef(m2)))) 593s + stop(paste("Differing results for", m1name, "and", m2name, 593s + "in updateppm.R"), 593s + call.=FALSE) 593s + cat("OK\n") 593s + } 593s + 593s + X <- redwood[c(TRUE,FALSE)] 593s + Y <- redwood[c(FALSE,TRUE)] 593s + fit0f <- ppm(X ~ 1, nd=8) 593s + fit0p <- ppm(X, ~1, nd=8) 593s + fitxf <- ppm(X ~ x, nd=8) 593s + fitxp <- ppm(X, ~x, nd=8) 593s + 593s + cat("Basic consistency ...\n") 593s + h(fit0f, fit0p) 593s + h(fitxf, fitxp) 593s + 593s + cat("\nTest correct handling of model formulas ...\n") 593s + h(update(fitxf, Y), fitxf) 593s + h(update(fitxf, Q=Y), fitxf) 593s + h(update(fitxf, Y~x), fitxf) 593s + h(update(fitxf, Q=Y~x), fitxf) 593s + h(update(fitxf, ~x), fitxf) 593s + } 593s + 593s + if(FULLTEST) { 593s + h(update(fitxf, Y~1), fit0f) 593s + h(update(fitxf, ~1), fit0f) 593s + h(update(fit0f, Y~x), fitxf) 593s + h(update(fit0f, ~x), fitxf) 593s + 593s + h(update(fitxp, Y), fitxp) 593s + h(update(fitxp, Q=Y), fitxp) 593s + h(update(fitxp, Y~x), fitxp) 593s + h(update(fitxp, Q=Y~x), fitxp) 593s + h(update(fitxp, ~x), fitxp) 593s + 593s + h(update(fitxp, Y~1), fit0p) 593s + h(update(fitxp, ~1), fit0p) 593s + h(update(fit0p, Y~x), fitxp) 593s + h(update(fit0p, ~x), fitxp) 593s + } 593s + 593s + if(ALWAYS) { 593s + cat("\nTest scope handling for left hand side ...\n") 593s + X <- Y 593s + h(update(fitxf), fitxf) 593s + } 593s + 593s + if(ALWAYS) { 593s + cat("\nTest scope handling for right hand side ...\n") 593s + Z <- distmap(X) 593s + fitZf <- ppm(X ~ Z) 593s + fitZp <- ppm(X, ~ Z) 593s + h(update(fitxf, X ~ Z), fitZf) 593s + } 593s + if(FULLTEST) { 593s + h(update(fitxp, X ~ Z), fitZp) 593s + h(update(fitxf, . ~ Z), fitZf) 593s + h(update(fitZf, . ~ x), fitxf) 593s + h(update(fitZf, . ~ . - Z), fit0f) 593s + h(update(fitxp, . ~ Z), fitZp) 593s + h(update(fitZp, . ~ . - Z), fit0p) 593s + h(update(fit0p, . ~ . + Z), fitZp) 593s + h(update(fitZf, . ~ . ), fitZf) 593s + h(update(fitZp, . ~ . ), fitZp) 593s + } 593s + if(ALWAYS) { 593s + cat("\nTest use of internal data ...\n") 593s + h(update(fitZf, ~ x, use.internal=TRUE), fitxf) 593s + fitsin <- update(fitZf, X~sin(Z)) 593s + h(update(fitZf, ~ sin(Z), use.internal=TRUE), fitsin) 593s + } 593s + if(FULLTEST) { 593s + cat("\nTest step() ... ") 593s + fut <- ppm(X ~ Z + x + y, nd=8) 593s + fut0 <- step(fut, trace=0) 593s + cat("OK\n") 593s + } 593s + 593s + }) 593s Loading required package: spatstat.utils 593s Basic consistency ... 593s h(fit0f, fit0p) ... OK 593s h(fitxf, fitxp) ... OK 593s 593s Test correct handling of model formulas ... 593s h(update(fitxf, Y), fitxf) ... OK 593s h(update(fitxf, Q = Y), fitxf) ... OK 593s h(update(fitxf, Y ~ x), fitxf) ... OK 593s h(update(fitxf, Q = Y ~ x), fitxf) ... OK 593s h(update(fitxf, ~x), fitxf) ... OK 593s 593s Test scope handling for left hand side ... 593s h(update(fitxf), fitxf) ... OK 593s 593s Test scope handling for right hand side ... 593s h(update(fitxf, X ~ Z), fitZf) ... OK 593s 593s Test use of internal data ... 593s h(update(fitZf, ~x, use.internal = TRUE), fitxf) ... OK 593s h(update(fitZf, ~sin(Z), use.internal = TRUE), fitsin) ... OK 593s > # 593s > # tests/vcovppm.R 593s > # 593s > # Check validity of vcov.ppm algorithms 593s > # 593s > # Thanks to Ege Rubak 593s > # 593s > # $Revision: 1.12 $ $Date: 2020/05/02 01:32:58 $ 593s > # 593s > 593s > local({ 593s + 593s + set.seed(42) 593s + X <- rStrauss(200, .5, .05) 593s + model <- ppm(X, inter = Strauss(.05)) 593s + 593s + if(ALWAYS) { 593s + b <- vcov(model, generic = TRUE, algorithm = "basic") 593s + v <- vcov(model, generic = TRUE, algorithm = "vector") 593s + vc <- vcov(model, generic = TRUE, algorithm = "vectorclip") 593s + vn <- vcov(model, generic = FALSE) 593s + 593s + disagree <- function(x, y, tol=1e-7) { max(abs(x-y)) > tol } 593s + asymmetric <- function(x) { disagree(x, t(x)) } 593s + 593s + if(asymmetric(b)) 593s + stop("Non-symmetric matrix produced by vcov.ppm 'basic' algorithm") 593s + if(asymmetric(v)) 593s + stop("Non-symmetric matrix produced by vcov.ppm 'vector' algorithm") 593s + if(asymmetric(vc)) 593s + stop("Non-symmetric matrix produced by vcov.ppm 'vectorclip' algorithm") 593s + if(asymmetric(vn)) 593s + stop("Non-symmetric matrix produced by vcov.ppm Strauss algorithm") 593s + 593s + if(disagree(v, b)) 593s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'basic' ") 593s + if(disagree(v, vc)) 593s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'vectorclip' ") 593s + if(disagree(vn, vc)) 593s + stop("Disagreement between vcov.ppm generic and Strauss algorithms") 593s + } 593s + 593s + if(ALWAYS) { # C code 593s + ## Geyer code 593s + xx <- c(0.7375956, 0.6851697, 0.6399788, 0.6188382) 593s + yy <- c(0.5816040, 0.6456319, 0.5150633, 0.6191592) 593s + Y <- ppp(xx, yy, window=square(1)) 593s + modelY <- ppm(Y ~1, Geyer(0.1, 1)) 593s + 593s + b <- vcov(modelY, generic = TRUE, algorithm = "basic") 593s + v <- vcov(modelY, generic = TRUE, algorithm = "vector") 593s + vc <- vcov(modelY, generic = TRUE, algorithm = "vectorclip") 593s + 593s + if(asymmetric(b)) 593s + stop("Non-symmetric matrix produced by vcov.ppm 'basic' algorithm for Geyer model") 593s + if(asymmetric(v)) 593s + stop("Non-symmetric matrix produced by vcov.ppm 'vector' algorithm for Geyer model") 593s + if(asymmetric(vc)) 593s + stop("Non-symmetric matrix produced by vcov.ppm 'vectorclip' algorithm for Geyer model") 593s + 593s + if(disagree(v, b)) 593s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'basic' for Geyer model") 593s + if(disagree(v, vc)) 593s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'vectorclip' for Geyer model") 593s + } 593s + 593s + if(ALWAYS) { # C code 593s + ## tests of 'deltasuffstat' code 593s + ## Handling of offset terms 593s + modelH <- ppm(cells ~x, Hardcore(0.05)) 593s + a <- vcov(modelH, generic=TRUE) ## may fall over 593s + b <- vcov(modelH, generic=FALSE) 593s + if(disagree(a, b)) 593s + stop("Disagreement between vcov.ppm algorithms for Hardcore model") 593s + 593s + ## Correctness of pairwise.family$delta2 593s + modelZ <- ppm(amacrine ~1, MultiStrauss(radii=matrix(0.1, 2, 2))) 593s + b <- vcov(modelZ, generic=FALSE) 593s + g <- vcov(modelZ, generic=TRUE) 593s + if(disagree(b, g)) 593s + stop("Disagreement between vcov.ppm algorithms for MultiStrauss model") 593s + 593s + ## Test that 'deltasuffstat' works for Hybrids 593s + modelHyb <- ppm(japanesepines ~ 1, Hybrid(Strauss(0.05), Strauss(0.1))) 593s + vHyb <- vcov(modelHyb) 593s + } 593s + 593s + if(FULLTEST) { 593s + ## Code blocks for other choices of 'what' 593s + model <- ppm(X ~ 1, Strauss(.05)) 593s + cG <- vcov(model, what="corr") 593s + cP <- vcov(update(model, Poisson()), what="corr") 593s + ## outdated usage 593s + cX <- vcov(model, A1dummy=TRUE) 593s + 593s + ## Model with zero-length coefficient vector 593s + lam <- intensity(X) 593s + f <- function(x,y) { rep(lam, length(x)) } 593s + model0 <- ppm(X ~ offset(log(f)) - 1) 593s + dd <- vcov(model0) 593s + cc <- vcov(model0, what="corr") 593s + 593s + ## Model with NA coefficients 593s + fit <- ppm(X ~ log(f)) 593s + vcov(fit) 593s + fitE <- emend(fit, trace=TRUE) 593s + 593s + ## Other weird stuff 593s + su <- suffloc(ppm(X ~ x)) 593s + } 593s + }) 595s > 595s autopkgtest [20:13:18]: test run-unit-test: -----------------------] 599s autopkgtest [20:13:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 599s run-unit-test PASS 599s autopkgtest [20:13:22]: test pkg-r-autopkgtest: preparing testbed 850s autopkgtest [20:17:33]: testbed dpkg architecture: ppc64el 850s autopkgtest [20:17:33]: testbed apt version: 2.7.12 850s autopkgtest [20:17:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 851s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 851s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 851s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 851s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3981 kB] 852s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 852s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 852s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 852s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 852s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 852s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4276 kB] 852s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 852s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 852s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 856s Fetched 9666 kB in 3s (3731 kB/s) 856s Reading package lists... 858s Reading package lists... 858s Building dependency tree... 858s Reading state information... 858s Calculating upgrade... 859s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 859s Reading package lists... 859s Building dependency tree... 859s Reading state information... 859s 0 upgraded, 0 newly installed, 0 to remove and 244 not upgraded. 860s sh: Attempting to set up Debian/Ubuntu apt sources automatically 860s sh: Distribution appears to be Ubuntu 861s Reading package lists... 861s Building dependency tree... 861s Reading state information... 861s eatmydata is already the newest version (131-1). 861s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 861s Reading package lists... 861s Building dependency tree... 862s Reading state information... 862s dbus is already the newest version (1.14.10-4ubuntu1). 862s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 862s Reading package lists... 862s Building dependency tree... 862s Reading state information... 862s rng-tools-debian is already the newest version (2.4). 862s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 862s Reading package lists... 862s Building dependency tree... 862s Reading state information... 863s The following packages will be REMOVED: 863s cloud-init* python3-configobj* python3-debconf* 863s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 863s After this operation, 3256 kB disk space will be freed. 863s (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 ... 70156 files and directories currently installed.) 863s Removing cloud-init (24.1.2-0ubuntu1) ... 864s Removing python3-configobj (5.0.8-3) ... 864s Removing python3-debconf (1.5.86) ... 864s Processing triggers for man-db (2.12.0-3) ... 864s (Reading database ... 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linux-generic is already the newest version (6.8.0-11.11+1). 866s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 866s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 866s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 866s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 869s Reading package lists... 869s Reading package lists... 869s Building dependency tree... 869s Reading state information... 870s Calculating upgrade... 870s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 870s Reading package lists... 870s Building dependency tree... 870s Reading state information... 870s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 870s autopkgtest [20:17:53]: rebooting testbed after setup commands that affected boot 1057s Reading package lists... 1057s Building dependency tree... 1057s Reading state information... 1057s Starting pkgProblemResolver with broken count: 0 1057s Starting 2 pkgProblemResolver with broken count: 0 1057s Done 1058s The following additional packages will be installed: 1058s build-essential cpp cpp-13 cpp-13-powerpc64le-linux-gnu 1058s cpp-powerpc64le-linux-gnu dctrl-tools fontconfig fontconfig-config 1058s fonts-dejavu-core fonts-dejavu-mono fonts-mathjax g++ g++-13 1058s g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-13 1058s gcc-13-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gfortran gfortran-13 1058s gfortran-13-powerpc64le-linux-gnu gfortran-powerpc64le-linux-gnu 1058s icu-devtools libasan8 libatomic1 libblas-dev libblas3 libbz2-dev 1058s libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdatrie1 1058s libdeflate0 libfontconfig1 libgcc-13-dev libgfortran-13-dev libgfortran5 1058s libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libice6 1058s libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 1058s libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-mathjax liblapack-dev 1058s liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 libncurses-dev 1058s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 1058s libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 1058s libpixman-1-0 libpkgconf3 libpng-dev libquadmath0 libreadline-dev 1058s libsharpyuv0 libsm6 libstdc++-13-dev libtcl8.6 libthai-data libthai0 1058s libtiff6 libtk8.6 libtsan2 libubsan1 libwebp7 libxcb-render0 libxcb-shm0 1058s libxft2 libxrender1 libxss1 libxt6 linux-libc-dev littler pkg-config 1058s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev r-cran-abind 1058s r-cran-codetools r-cran-deldir r-cran-foreach r-cran-glmnet r-cran-goftest 1058s r-cran-gsl r-cran-iterators r-cran-lattice r-cran-littler r-cran-matrix 1058s r-cran-mgcv r-cran-nleqslv r-cran-nlme r-cran-pkgkitten r-cran-polyclip 1058s r-cran-rcpp r-cran-rcppeigen r-cran-rpart r-cran-shape r-cran-sm 1058s r-cran-spatial r-cran-spatstat r-cran-spatstat.data r-cran-spatstat.explore 1058s r-cran-spatstat.geom r-cran-spatstat.linnet r-cran-spatstat.model 1058s r-cran-spatstat.random r-cran-spatstat.sparse r-cran-spatstat.utils 1058s r-cran-survival r-cran-tensor rpcsvc-proto unzip x11-common xdg-utils zip 1058s zlib1g-dev 1058s Suggested packages: 1058s cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib 1058s manpages-dev autoconf automake libtool flex bison gdb gcc-doc 1058s gdb-powerpc64le-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev 1058s liblapack-doc glibc-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info 1058s | gsl-ref-html icu-doc fonts-mathjax-extras fonts-stix libjs-mathjax-doc 1058s liblzma-doc ncurses-doc readline-doc libstdc++-13-doc tcl8.6 tk8.6 elpa-ess 1058s r-doc-info | r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base 1058s texlive-plain-generic texlive-fonts-recommended texlive-fonts-extra 1058s texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo 1058s r-cran-knitr r-cran-testthat r-cran-xfun r-cran-rmarkdown r-cran-getopt 1058s r-cran-inline 1058s Recommended packages: 1058s bzip2-doc manpages manpages-dev libc-devtools libpng-tools r-recommended 1058s r-doc-html r-cran-locfit libfile-mimeinfo-perl libnet-dbus-perl 1058s libx11-protocol-perl x11-utils x11-xserver-utils 1058s The following NEW packages will be installed: 1058s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-powerpc64le-linux-gnu 1058s cpp-powerpc64le-linux-gnu dctrl-tools fontconfig fontconfig-config 1058s fonts-dejavu-core fonts-dejavu-mono fonts-mathjax g++ g++-13 1058s g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-13 1058s gcc-13-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gfortran gfortran-13 1058s gfortran-13-powerpc64le-linux-gnu gfortran-powerpc64le-linux-gnu 1058s icu-devtools libasan8 libatomic1 libblas-dev libblas3 libbz2-dev 1058s libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdatrie1 1058s libdeflate0 libfontconfig1 libgcc-13-dev libgfortran-13-dev libgfortran5 1058s libgomp1 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libice6 1058s libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 1058s libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-mathjax liblapack-dev 1058s liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 libncurses-dev 1058s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 1058s libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 1058s libpixman-1-0 libpkgconf3 libpng-dev libquadmath0 libreadline-dev 1058s libsharpyuv0 libsm6 libstdc++-13-dev libtcl8.6 libthai-data libthai0 1058s libtiff6 libtk8.6 libtsan2 libubsan1 libwebp7 libxcb-render0 libxcb-shm0 1058s libxft2 libxrender1 libxss1 libxt6 linux-libc-dev littler pkg-config 1058s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev r-cran-abind 1058s r-cran-codetools r-cran-deldir r-cran-foreach r-cran-glmnet r-cran-goftest 1058s r-cran-gsl r-cran-iterators r-cran-lattice r-cran-littler r-cran-matrix 1058s r-cran-mgcv r-cran-nleqslv r-cran-nlme r-cran-pkgkitten r-cran-polyclip 1058s r-cran-rcpp r-cran-rcppeigen r-cran-rpart r-cran-shape r-cran-sm 1058s r-cran-spatial r-cran-spatstat r-cran-spatstat.data r-cran-spatstat.explore 1058s r-cran-spatstat.geom r-cran-spatstat.linnet r-cran-spatstat.model 1058s r-cran-spatstat.random r-cran-spatstat.sparse r-cran-spatstat.utils 1058s r-cran-survival r-cran-tensor rpcsvc-proto unzip x11-common xdg-utils zip 1058s zlib1g-dev 1058s 0 upgraded, 142 newly installed, 0 to remove and 0 not upgraded. 1058s Need to get 193 MB/193 MB of archives. 1058s After this operation, 590 MB of additional disk space will be used. 1058s Get:1 /tmp/autopkgtest.nzJ8xp/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [764 B] 1058s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu6 [21.3 kB] 1058s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el linux-libc-dev ppc64el 6.8.0-11.11 [1585 kB] 1058s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4 [167 kB] 1058s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el rpcsvc-proto ppc64el 1.4.2-0ubuntu6 [82.3 kB] 1058s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6-dev ppc64el 2.39-0ubuntu6 [2102 kB] 1059s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libisl23 ppc64el 0.26-3 [864 kB] 1059s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libmpc3 ppc64el 1.3.1-1 [61.2 kB] 1059s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [10.7 MB] 1059s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-13 ppc64el 13.2.0-17ubuntu2 [1038 B] 1059s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [5330 B] 1059s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp ppc64el 4:13.2.0-7ubuntu1 [22.5 kB] 1059s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libcc1-0 ppc64el 14-20240303-1ubuntu1 [48.1 kB] 1059s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 1059s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libitm1 ppc64el 14-20240303-1ubuntu1 [32.4 kB] 1059s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libatomic1 ppc64el 14-20240303-1ubuntu1 [10.7 kB] 1059s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libasan8 ppc64el 14-20240303-1ubuntu1 [2973 kB] 1059s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el liblsan0 ppc64el 14-20240303-1ubuntu1 [1325 kB] 1059s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libtsan2 ppc64el 14-20240303-1ubuntu1 [2734 kB] 1059s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libubsan1 ppc64el 14-20240303-1ubuntu1 [1194 kB] 1059s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libquadmath0 ppc64el 14-20240303-1ubuntu1 [158 kB] 1059s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libgcc-13-dev ppc64el 13.2.0-17ubuntu2 [1581 kB] 1060s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [20.6 MB] 1060s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-13 ppc64el 13.2.0-17ubuntu2 [477 kB] 1060s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [1224 B] 1060s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc ppc64el 4:13.2.0-7ubuntu1 [5022 B] 1060s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libstdc++-13-dev ppc64el 13.2.0-17ubuntu2 [2445 kB] 1060s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [12.2 MB] 1060s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-13 ppc64el 13.2.0-17ubuntu2 [14.5 kB] 1060s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [968 B] 1060s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el g++ ppc64el 4:13.2.0-7ubuntu1 [1086 B] 1060s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B] 1060s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el dctrl-tools ppc64el 2.24-3build2 [70.6 kB] 1060s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 1061s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 1061s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 1061s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 1061s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig ppc64el 2.15.0-1ubuntu1 [192 kB] 1061s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 1061s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 1061s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran-13-dev ppc64el 13.2.0-17ubuntu2 [604 kB] 1061s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el gfortran-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [11.2 MB] 1061s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el gfortran-13 ppc64el 13.2.0-17ubuntu2 [10.3 kB] 1061s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el gfortran-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [1030 B] 1061s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el gfortran ppc64el 4:13.2.0-7ubuntu1 [1170 B] 1061s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el icu-devtools ppc64el 74.2-1ubuntu1 [246 kB] 1061s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 1061s Get:48 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas-dev ppc64el 3.12.0-3 [301 kB] 1061s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el libbz2-dev ppc64el 1.0.8-5ubuntu1 [51.2 kB] 1061s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 1061s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 1061s Get:52 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 1061s Get:53 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 1061s Get:54 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB] 1061s Get:55 http://ftpmaster.internal/ubuntu noble/main ppc64el libdatrie1 ppc64el 0.2.13-3 [25.1 kB] 1061s Get:56 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 1061s Get:57 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 1061s Get:58 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgslcblas0 ppc64el 2.7.1+dfsg-6ubuntu1 [85.3 kB] 1061s Get:59 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgsl27 ppc64el 2.7.1+dfsg-6ubuntu1 [1064 kB] 1061s Get:60 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 1061s Get:61 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 1061s Get:62 http://ftpmaster.internal/ubuntu noble/main ppc64el libice6 ppc64el 2:1.0.10-1build2 [49.3 kB] 1061s Get:63 http://ftpmaster.internal/ubuntu noble/main ppc64el libicu-dev ppc64el 74.2-1ubuntu1 [12.5 MB] 1061s Get:64 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 1061s Get:65 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8-dev ppc64el 2.1.5-2ubuntu1 [357 kB] 1061s Get:66 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 1061s Get:67 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8-dev ppc64el 8c-2ubuntu11 [1484 B] 1061s Get:68 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-dev ppc64el 8c-2ubuntu11 [1486 B] 1061s Get:69 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 1062s Get:70 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack-dev ppc64el 3.12.0-3 [6100 kB] 1062s Get:71 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 1062s Get:72 http://ftpmaster.internal/ubuntu noble/main ppc64el libncurses-dev ppc64el 6.4+20240113-1ubuntu1 [485 kB] 1062s Get:73 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai-data all 0.1.29-2 [158 kB] 1062s Get:74 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai0 ppc64el 0.1.29-2 [21.4 kB] 1062s Get:75 http://ftpmaster.internal/ubuntu noble/main ppc64el libpango-1.0-0 ppc64el 1.51.0+ds-4 [266 kB] 1062s Get:76 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangoft2-1.0-0 ppc64el 1.51.0+ds-4 [49.5 kB] 1062s Get:77 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangocairo-1.0-0 ppc64el 1.51.0+ds-4 [31.2 kB] 1062s Get:78 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper1 ppc64el 1.1.29 [13.5 kB] 1062s Get:79 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper-utils ppc64el 1.1.29 [8710 B] 1062s Get:80 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-16-0 ppc64el 10.42-4ubuntu1 [245 kB] 1062s Get:81 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-32-0 ppc64el 10.42-4ubuntu1 [228 kB] 1062s Get:82 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-posix3 ppc64el 10.42-4ubuntu1 [7016 B] 1062s Get:83 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-dev ppc64el 10.42-4ubuntu1 [794 kB] 1062s Get:84 http://ftpmaster.internal/ubuntu noble/main ppc64el libpkgconf3 ppc64el 1.8.1-2 [36.9 kB] 1062s Get:85 http://ftpmaster.internal/ubuntu noble/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg-3ubuntu1 [902 kB] 1062s Get:86 http://ftpmaster.internal/ubuntu noble/main ppc64el libpng-dev ppc64el 1.6.43-1 [327 kB] 1062s Get:87 http://ftpmaster.internal/ubuntu noble/main ppc64el libreadline-dev ppc64el 8.2-3 [226 kB] 1062s Get:88 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB] 1062s Get:89 http://ftpmaster.internal/ubuntu noble/main ppc64el libsm6 ppc64el 2:1.2.3-1build2 [18.5 kB] 1062s Get:90 http://ftpmaster.internal/ubuntu noble/main ppc64el libtcl8.6 ppc64el 8.6.13+dfsg-2 [1179 kB] 1062s Get:91 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 1062s Get:92 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB] 1062s Get:93 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 1062s Get:94 http://ftpmaster.internal/ubuntu noble/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] 1062s Get:95 http://ftpmaster.internal/ubuntu noble/main ppc64el libxss1 ppc64el 1:1.2.3-1build2 [8982 B] 1062s Get:96 http://ftpmaster.internal/ubuntu noble/main ppc64el libtk8.6 ppc64el 8.6.14-1 [944 kB] 1062s Get:97 http://ftpmaster.internal/ubuntu noble/main ppc64el libxt6 ppc64el 1:1.2.1-1.1 [198 kB] 1062s Get:98 http://ftpmaster.internal/ubuntu noble/main ppc64el zip ppc64el 3.0-13 [192 kB] 1062s Get:99 http://ftpmaster.internal/ubuntu noble/main ppc64el unzip ppc64el 6.0-28ubuntu3 [192 kB] 1062s Get:100 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 1062s Get:101 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base-core ppc64el 4.3.2-1build1 [27.4 MB] 1063s Get:102 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-littler ppc64el 0.3.19-1 [95.1 kB] 1063s Get:103 http://ftpmaster.internal/ubuntu noble/universe ppc64el littler all 0.3.19-1 [2472 B] 1063s Get:104 http://ftpmaster.internal/ubuntu noble/main ppc64el pkgconf-bin ppc64el 1.8.1-2 [22.0 kB] 1063s Get:105 http://ftpmaster.internal/ubuntu noble/main ppc64el pkgconf ppc64el 1.8.1-2 [16.7 kB] 1063s Get:106 http://ftpmaster.internal/ubuntu noble/main ppc64el pkg-config ppc64el 1.8.1-2 [7170 B] 1063s Get:107 http://ftpmaster.internal/ubuntu noble/main ppc64el liblzma-dev ppc64el 5.4.5-0.3 [243 kB] 1063s Get:108 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base-dev all 4.3.2-1build1 [4336 B] 1063s Get:109 http://ftpmaster.internal/ubuntu noble/universe ppc64el pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 1063s Get:110 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-abind all 1.4-5-2 [63.6 kB] 1063s Get:111 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-codetools all 0.2-19-1 [90.5 kB] 1063s Get:112 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-deldir ppc64el 2.0-4-1 [273 kB] 1063s Get:113 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-iterators all 1.0.14-1 [336 kB] 1063s Get:114 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-foreach all 1.5.2-1 [124 kB] 1063s Get:115 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-lattice ppc64el 0.22-5-1 [1343 kB] 1063s Get:116 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-matrix ppc64el 1.6-5-1 [4057 kB] 1064s Get:117 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-shape all 1.4.6-1 [770 kB] 1064s Get:118 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-survival ppc64el 3.5-8-1 [6160 kB] 1064s Get:119 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 1064s Get:120 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-rcpp ppc64el 1.0.12-1 [1989 kB] 1064s Get:121 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-rcppeigen ppc64el 0.3.3.9.4-1 [1216 kB] 1064s Get:122 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 1064s Get:123 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-glmnet ppc64el 4.1-8-1 [1978 kB] 1065s Get:124 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-goftest ppc64el 1.2-3-1 [60.2 kB] 1065s Get:125 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-gsl ppc64el 2.1-8-1 [492 kB] 1065s Get:126 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-nlme ppc64el 3.1.164-1 [2281 kB] 1065s Get:127 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-mgcv ppc64el 1.9-1-1 [3393 kB] 1065s Get:128 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-nleqslv ppc64el 3.3.5-1 [106 kB] 1065s Get:129 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-polyclip ppc64el 1.10-6-1 [121 kB] 1065s Get:130 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-rpart ppc64el 4.1.23-1 [672 kB] 1065s Get:131 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-sm ppc64el 2.2-6.0-1 [795 kB] 1065s Get:132 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatial ppc64el 7.3-17-1 [137 kB] 1065s Get:133 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.utils ppc64el 3.0-4-1 [362 kB] 1065s Get:134 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.data all 3.0-4-1 [4090 kB] 1065s Get:135 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.geom ppc64el 3.2-8-1 [3855 kB] 1066s Get:136 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.random ppc64el 3.2-2-1 [1146 kB] 1066s Get:137 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-tensor all 1.5-4 [15.7 kB] 1066s Get:138 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.sparse ppc64el 3.0-3-1 [219 kB] 1066s Get:139 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.explore ppc64el 3.2-5-1 [3294 kB] 1066s Get:140 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.model ppc64el 3.2-8-1 [3290 kB] 1066s Get:141 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat.linnet ppc64el 3.1-3-1 [1415 kB] 1066s Get:142 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-spatstat ppc64el 3.0-7-1 [3817 kB] 1067s Preconfiguring packages ... 1067s Fetched 193 MB in 9s (22.1 MB/s) 1067s Selecting previously unselected package libc-dev-bin. 1067s (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 ... 69712 files and directories currently installed.) 1067s Preparing to unpack .../000-libc-dev-bin_2.39-0ubuntu6_ppc64el.deb ... 1067s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 1067s Selecting previously unselected package linux-libc-dev:ppc64el. 1067s Preparing to unpack .../001-linux-libc-dev_6.8.0-11.11_ppc64el.deb ... 1067s Unpacking linux-libc-dev:ppc64el (6.8.0-11.11) ... 1067s Selecting previously unselected package libcrypt-dev:ppc64el. 1067s Preparing to unpack .../002-libcrypt-dev_1%3a4.4.36-4_ppc64el.deb ... 1067s Unpacking libcrypt-dev:ppc64el (1:4.4.36-4) ... 1067s Selecting previously unselected package rpcsvc-proto. 1067s Preparing to unpack .../003-rpcsvc-proto_1.4.2-0ubuntu6_ppc64el.deb ... 1067s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 1067s Selecting previously unselected package libc6-dev:ppc64el. 1067s Preparing to unpack .../004-libc6-dev_2.39-0ubuntu6_ppc64el.deb ... 1067s Unpacking libc6-dev:ppc64el (2.39-0ubuntu6) ... 1068s Selecting previously unselected package libisl23:ppc64el. 1068s Preparing to unpack .../005-libisl23_0.26-3_ppc64el.deb ... 1068s Unpacking libisl23:ppc64el (0.26-3) ... 1068s Selecting previously unselected package libmpc3:ppc64el. 1068s Preparing to unpack .../006-libmpc3_1.3.1-1_ppc64el.deb ... 1068s Unpacking libmpc3:ppc64el (1.3.1-1) ... 1068s Selecting previously unselected package cpp-13-powerpc64le-linux-gnu. 1068s Preparing to unpack .../007-cpp-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 1068s Unpacking cpp-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 1068s Selecting previously unselected package cpp-13. 1068s Preparing to unpack .../008-cpp-13_13.2.0-17ubuntu2_ppc64el.deb ... 1068s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 1068s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 1068s Preparing to unpack .../009-cpp-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 1068s Unpacking cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 1068s Selecting previously unselected package cpp. 1068s Preparing to unpack .../010-cpp_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 1068s Unpacking cpp (4:13.2.0-7ubuntu1) ... 1068s Selecting previously unselected package libcc1-0:ppc64el. 1068s Preparing to unpack .../011-libcc1-0_14-20240303-1ubuntu1_ppc64el.deb ... 1068s Unpacking libcc1-0:ppc64el (14-20240303-1ubuntu1) ... 1068s Selecting previously unselected package libgomp1:ppc64el. 1068s Preparing to unpack .../012-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 1068s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 1068s Selecting previously unselected package libitm1:ppc64el. 1068s Preparing to unpack .../013-libitm1_14-20240303-1ubuntu1_ppc64el.deb ... 1068s Unpacking libitm1:ppc64el (14-20240303-1ubuntu1) ... 1068s Selecting previously unselected package libatomic1:ppc64el. 1068s Preparing to unpack .../014-libatomic1_14-20240303-1ubuntu1_ppc64el.deb ... 1068s Unpacking libatomic1:ppc64el (14-20240303-1ubuntu1) ... 1068s Selecting previously unselected package libasan8:ppc64el. 1068s Preparing to unpack .../015-libasan8_14-20240303-1ubuntu1_ppc64el.deb ... 1068s Unpacking libasan8:ppc64el (14-20240303-1ubuntu1) ... 1068s Selecting previously unselected package liblsan0:ppc64el. 1068s Preparing to unpack .../016-liblsan0_14-20240303-1ubuntu1_ppc64el.deb ... 1068s Unpacking liblsan0:ppc64el (14-20240303-1ubuntu1) ... 1068s Selecting previously unselected package libtsan2:ppc64el. 1068s Preparing to unpack .../017-libtsan2_14-20240303-1ubuntu1_ppc64el.deb ... 1068s Unpacking libtsan2:ppc64el (14-20240303-1ubuntu1) ... 1068s Selecting previously unselected package libubsan1:ppc64el. 1068s Preparing to unpack .../018-libubsan1_14-20240303-1ubuntu1_ppc64el.deb ... 1068s Unpacking libubsan1:ppc64el (14-20240303-1ubuntu1) ... 1068s Selecting previously unselected package libquadmath0:ppc64el. 1068s Preparing to unpack .../019-libquadmath0_14-20240303-1ubuntu1_ppc64el.deb ... 1068s Unpacking libquadmath0:ppc64el (14-20240303-1ubuntu1) ... 1068s Selecting previously unselected package libgcc-13-dev:ppc64el. 1068s Preparing to unpack .../020-libgcc-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 1068s Unpacking libgcc-13-dev:ppc64el (13.2.0-17ubuntu2) ... 1068s Selecting previously unselected package gcc-13-powerpc64le-linux-gnu. 1068s Preparing to unpack .../021-gcc-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 1068s Unpacking gcc-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 1069s Selecting previously unselected package gcc-13. 1069s Preparing to unpack .../022-gcc-13_13.2.0-17ubuntu2_ppc64el.deb ... 1069s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 1069s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 1069s Preparing to unpack .../023-gcc-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 1069s Unpacking gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 1069s Selecting previously unselected package gcc. 1069s Preparing to unpack .../024-gcc_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 1069s Unpacking gcc (4:13.2.0-7ubuntu1) ... 1069s Selecting previously unselected package libstdc++-13-dev:ppc64el. 1069s Preparing to unpack .../025-libstdc++-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 1069s Unpacking libstdc++-13-dev:ppc64el (13.2.0-17ubuntu2) ... 1069s Selecting previously unselected package g++-13-powerpc64le-linux-gnu. 1069s Preparing to unpack .../026-g++-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 1069s Unpacking g++-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 1070s Selecting previously unselected package g++-13. 1070s Preparing to unpack .../027-g++-13_13.2.0-17ubuntu2_ppc64el.deb ... 1070s Unpacking g++-13 (13.2.0-17ubuntu2) ... 1070s Selecting previously unselected package g++-powerpc64le-linux-gnu. 1070s Preparing to unpack .../028-g++-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 1070s Unpacking g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 1070s Selecting previously unselected package g++. 1070s Preparing to unpack .../029-g++_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 1070s Unpacking g++ (4:13.2.0-7ubuntu1) ... 1070s Selecting previously unselected package build-essential. 1070s Preparing to unpack .../030-build-essential_12.10ubuntu1_ppc64el.deb ... 1070s Unpacking build-essential (12.10ubuntu1) ... 1070s Selecting previously unselected package dctrl-tools. 1070s Preparing to unpack .../031-dctrl-tools_2.24-3build2_ppc64el.deb ... 1070s Unpacking dctrl-tools (2.24-3build2) ... 1070s Selecting previously unselected package fonts-dejavu-mono. 1070s Preparing to unpack .../032-fonts-dejavu-mono_2.37-8_all.deb ... 1070s Unpacking fonts-dejavu-mono (2.37-8) ... 1070s Selecting previously unselected package fonts-dejavu-core. 1070s Preparing to unpack .../033-fonts-dejavu-core_2.37-8_all.deb ... 1070s Unpacking fonts-dejavu-core (2.37-8) ... 1070s Selecting previously unselected package fontconfig-config. 1070s Preparing to unpack .../034-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 1070s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 1070s Selecting previously unselected package libfontconfig1:ppc64el. 1070s Preparing to unpack .../035-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 1070s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 1070s Selecting previously unselected package fontconfig. 1070s Preparing to unpack .../036-fontconfig_2.15.0-1ubuntu1_ppc64el.deb ... 1070s Unpacking fontconfig (2.15.0-1ubuntu1) ... 1070s Selecting previously unselected package fonts-mathjax. 1070s Preparing to unpack .../037-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 1070s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 1070s Selecting previously unselected package libgfortran5:ppc64el. 1070s Preparing to unpack .../038-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 1070s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 1070s Selecting previously unselected package libgfortran-13-dev:ppc64el. 1070s Preparing to unpack .../039-libgfortran-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 1070s Unpacking libgfortran-13-dev:ppc64el (13.2.0-17ubuntu2) ... 1070s Selecting previously unselected package gfortran-13-powerpc64le-linux-gnu. 1070s Preparing to unpack .../040-gfortran-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 1070s Unpacking gfortran-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 1071s Selecting previously unselected package gfortran-13. 1071s Preparing to unpack .../041-gfortran-13_13.2.0-17ubuntu2_ppc64el.deb ... 1071s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 1071s Selecting previously unselected package gfortran-powerpc64le-linux-gnu. 1071s Preparing to unpack .../042-gfortran-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 1071s Unpacking gfortran-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 1071s Selecting previously unselected package gfortran. 1071s Preparing to unpack .../043-gfortran_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 1071s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 1071s Selecting previously unselected package icu-devtools. 1071s Preparing to unpack .../044-icu-devtools_74.2-1ubuntu1_ppc64el.deb ... 1071s Unpacking icu-devtools (74.2-1ubuntu1) ... 1071s Selecting previously unselected package libblas3:ppc64el. 1071s Preparing to unpack .../045-libblas3_3.12.0-3_ppc64el.deb ... 1071s Unpacking libblas3:ppc64el (3.12.0-3) ... 1071s Selecting previously unselected package libblas-dev:ppc64el. 1071s Preparing to unpack .../046-libblas-dev_3.12.0-3_ppc64el.deb ... 1071s Unpacking libblas-dev:ppc64el (3.12.0-3) ... 1071s Selecting previously unselected package libbz2-dev:ppc64el. 1071s Preparing to unpack .../047-libbz2-dev_1.0.8-5ubuntu1_ppc64el.deb ... 1071s Unpacking libbz2-dev:ppc64el (1.0.8-5ubuntu1) ... 1071s Selecting previously unselected package libpixman-1-0:ppc64el. 1071s Preparing to unpack .../048-libpixman-1-0_0.42.2-1_ppc64el.deb ... 1071s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ... 1071s Selecting previously unselected package libxcb-render0:ppc64el. 1071s Preparing to unpack .../049-libxcb-render0_1.15-1_ppc64el.deb ... 1071s Unpacking libxcb-render0:ppc64el (1.15-1) ... 1071s Selecting previously unselected package libxcb-shm0:ppc64el. 1071s Preparing to unpack .../050-libxcb-shm0_1.15-1_ppc64el.deb ... 1071s Unpacking libxcb-shm0:ppc64el (1.15-1) ... 1071s Selecting previously unselected package libxrender1:ppc64el. 1071s Preparing to unpack .../051-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... 1071s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... 1071s Selecting previously unselected package libcairo2:ppc64el. 1071s Preparing to unpack .../052-libcairo2_1.18.0-1_ppc64el.deb ... 1071s Unpacking libcairo2:ppc64el (1.18.0-1) ... 1071s Selecting previously unselected package libdatrie1:ppc64el. 1071s Preparing to unpack .../053-libdatrie1_0.2.13-3_ppc64el.deb ... 1071s Unpacking libdatrie1:ppc64el (0.2.13-3) ... 1071s Selecting previously unselected package libdeflate0:ppc64el. 1071s Preparing to unpack .../054-libdeflate0_1.19-1_ppc64el.deb ... 1071s Unpacking libdeflate0:ppc64el (1.19-1) ... 1071s Selecting previously unselected package libgraphite2-3:ppc64el. 1071s Preparing to unpack .../055-libgraphite2-3_1.3.14-2_ppc64el.deb ... 1071s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 1071s Selecting previously unselected package libgslcblas0:ppc64el. 1071s Preparing to unpack .../056-libgslcblas0_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 1071s Unpacking libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 1071s Selecting previously unselected package libgsl27:ppc64el. 1071s Preparing to unpack .../057-libgsl27_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 1071s Unpacking libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 1071s Selecting previously unselected package libharfbuzz0b:ppc64el. 1071s Preparing to unpack .../058-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 1071s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 1071s Selecting previously unselected package x11-common. 1071s Preparing to unpack .../059-x11-common_1%3a7.7+23ubuntu2_all.deb ... 1071s Unpacking x11-common (1:7.7+23ubuntu2) ... 1071s Selecting previously unselected package libice6:ppc64el. 1071s Preparing to unpack .../060-libice6_2%3a1.0.10-1build2_ppc64el.deb ... 1071s Unpacking libice6:ppc64el (2:1.0.10-1build2) ... 1071s Selecting previously unselected package libicu-dev:ppc64el. 1071s Preparing to unpack .../061-libicu-dev_74.2-1ubuntu1_ppc64el.deb ... 1071s Unpacking libicu-dev:ppc64el (74.2-1ubuntu1) ... 1071s Selecting previously unselected package libjpeg-turbo8:ppc64el. 1071s Preparing to unpack .../062-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 1071s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 1071s Selecting previously unselected package libjpeg-turbo8-dev:ppc64el. 1071s Preparing to unpack .../063-libjpeg-turbo8-dev_2.1.5-2ubuntu1_ppc64el.deb ... 1071s Unpacking libjpeg-turbo8-dev:ppc64el (2.1.5-2ubuntu1) ... 1071s Selecting previously unselected package libjpeg8:ppc64el. 1071s Preparing to unpack .../064-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 1071s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 1071s Selecting previously unselected package libjpeg8-dev:ppc64el. 1071s Preparing to unpack .../065-libjpeg8-dev_8c-2ubuntu11_ppc64el.deb ... 1071s Unpacking libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 1071s Selecting previously unselected package libjpeg-dev:ppc64el. 1071s Preparing to unpack .../066-libjpeg-dev_8c-2ubuntu11_ppc64el.deb ... 1071s Unpacking libjpeg-dev:ppc64el (8c-2ubuntu11) ... 1071s Selecting previously unselected package liblapack3:ppc64el. 1071s Preparing to unpack .../067-liblapack3_3.12.0-3_ppc64el.deb ... 1071s Unpacking liblapack3:ppc64el (3.12.0-3) ... 1072s Selecting previously unselected package liblapack-dev:ppc64el. 1072s Preparing to unpack .../068-liblapack-dev_3.12.0-3_ppc64el.deb ... 1072s Unpacking liblapack-dev:ppc64el (3.12.0-3) ... 1072s Selecting previously unselected package liblerc4:ppc64el. 1072s Preparing to unpack .../069-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 1072s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 1072s Selecting previously unselected package libncurses-dev:ppc64el. 1072s Preparing to unpack .../070-libncurses-dev_6.4+20240113-1ubuntu1_ppc64el.deb ... 1072s Unpacking libncurses-dev:ppc64el (6.4+20240113-1ubuntu1) ... 1072s Selecting previously unselected package libthai-data. 1072s Preparing to unpack .../071-libthai-data_0.1.29-2_all.deb ... 1072s Unpacking libthai-data (0.1.29-2) ... 1072s Selecting previously unselected package libthai0:ppc64el. 1072s Preparing to unpack .../072-libthai0_0.1.29-2_ppc64el.deb ... 1072s Unpacking libthai0:ppc64el (0.1.29-2) ... 1072s Selecting previously unselected package libpango-1.0-0:ppc64el. 1072s Preparing to unpack .../073-libpango-1.0-0_1.51.0+ds-4_ppc64el.deb ... 1072s Unpacking libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 1072s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 1072s Preparing to unpack .../074-libpangoft2-1.0-0_1.51.0+ds-4_ppc64el.deb ... 1072s Unpacking libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 1072s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 1072s Preparing to unpack .../075-libpangocairo-1.0-0_1.51.0+ds-4_ppc64el.deb ... 1072s Unpacking libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 1072s Selecting previously unselected package libpaper1:ppc64el. 1072s Preparing to unpack .../076-libpaper1_1.1.29_ppc64el.deb ... 1072s Unpacking libpaper1:ppc64el (1.1.29) ... 1072s Selecting previously unselected package libpaper-utils. 1072s Preparing to unpack .../077-libpaper-utils_1.1.29_ppc64el.deb ... 1072s Unpacking libpaper-utils (1.1.29) ... 1072s Selecting previously unselected package libpcre2-16-0:ppc64el. 1072s Preparing to unpack .../078-libpcre2-16-0_10.42-4ubuntu1_ppc64el.deb ... 1072s Unpacking libpcre2-16-0:ppc64el (10.42-4ubuntu1) ... 1072s Selecting previously unselected package libpcre2-32-0:ppc64el. 1072s Preparing to unpack .../079-libpcre2-32-0_10.42-4ubuntu1_ppc64el.deb ... 1072s Unpacking libpcre2-32-0:ppc64el (10.42-4ubuntu1) ... 1072s Selecting previously unselected package libpcre2-posix3:ppc64el. 1072s Preparing to unpack .../080-libpcre2-posix3_10.42-4ubuntu1_ppc64el.deb ... 1072s Unpacking libpcre2-posix3:ppc64el (10.42-4ubuntu1) ... 1072s Selecting previously unselected package libpcre2-dev:ppc64el. 1072s Preparing to unpack .../081-libpcre2-dev_10.42-4ubuntu1_ppc64el.deb ... 1072s Unpacking libpcre2-dev:ppc64el (10.42-4ubuntu1) ... 1072s Selecting previously unselected package libpkgconf3:ppc64el. 1072s Preparing to unpack .../082-libpkgconf3_1.8.1-2_ppc64el.deb ... 1072s Unpacking libpkgconf3:ppc64el (1.8.1-2) ... 1072s Selecting previously unselected package zlib1g-dev:ppc64el. 1072s Preparing to unpack .../083-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_ppc64el.deb ... 1072s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg-3ubuntu1) ... 1072s Selecting previously unselected package libpng-dev:ppc64el. 1072s Preparing to unpack .../084-libpng-dev_1.6.43-1_ppc64el.deb ... 1072s Unpacking libpng-dev:ppc64el (1.6.43-1) ... 1072s Selecting previously unselected package libreadline-dev:ppc64el. 1072s Preparing to unpack .../085-libreadline-dev_8.2-3_ppc64el.deb ... 1072s Unpacking libreadline-dev:ppc64el (8.2-3) ... 1072s Selecting previously unselected package libsharpyuv0:ppc64el. 1072s Preparing to unpack .../086-libsharpyuv0_1.3.2-0.4_ppc64el.deb ... 1072s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ... 1072s Selecting previously unselected package libsm6:ppc64el. 1072s Preparing to unpack .../087-libsm6_2%3a1.2.3-1build2_ppc64el.deb ... 1072s Unpacking libsm6:ppc64el (2:1.2.3-1build2) ... 1072s Selecting previously unselected package libtcl8.6:ppc64el. 1072s Preparing to unpack .../088-libtcl8.6_8.6.13+dfsg-2_ppc64el.deb ... 1072s Unpacking libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 1072s Selecting previously unselected package libjbig0:ppc64el. 1072s Preparing to unpack .../089-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 1072s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 1072s Selecting previously unselected package libwebp7:ppc64el. 1072s Preparing to unpack .../090-libwebp7_1.3.2-0.4_ppc64el.deb ... 1072s Unpacking libwebp7:ppc64el (1.3.2-0.4) ... 1072s Selecting previously unselected package libtiff6:ppc64el. 1072s Preparing to unpack .../091-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ... 1072s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 1072s Selecting previously unselected package libxft2:ppc64el. 1072s Preparing to unpack .../092-libxft2_2.3.6-1_ppc64el.deb ... 1072s Unpacking libxft2:ppc64el (2.3.6-1) ... 1072s Selecting previously unselected package libxss1:ppc64el. 1072s Preparing to unpack .../093-libxss1_1%3a1.2.3-1build2_ppc64el.deb ... 1072s Unpacking libxss1:ppc64el (1:1.2.3-1build2) ... 1072s Selecting previously unselected package libtk8.6:ppc64el. 1072s Preparing to unpack .../094-libtk8.6_8.6.14-1_ppc64el.deb ... 1072s Unpacking libtk8.6:ppc64el (8.6.14-1) ... 1072s Selecting previously unselected package libxt6:ppc64el. 1072s Preparing to unpack .../095-libxt6_1%3a1.2.1-1.1_ppc64el.deb ... 1072s Unpacking libxt6:ppc64el (1:1.2.1-1.1) ... 1072s Selecting previously unselected package zip. 1072s Preparing to unpack .../096-zip_3.0-13_ppc64el.deb ... 1072s Unpacking zip (3.0-13) ... 1072s Selecting previously unselected package unzip. 1072s Preparing to unpack .../097-unzip_6.0-28ubuntu3_ppc64el.deb ... 1072s Unpacking unzip (6.0-28ubuntu3) ... 1073s Selecting previously unselected package xdg-utils. 1073s Preparing to unpack .../098-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 1073s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 1073s Selecting previously unselected package r-base-core. 1073s Preparing to unpack .../099-r-base-core_4.3.2-1build1_ppc64el.deb ... 1073s Unpacking r-base-core (4.3.2-1build1) ... 1073s Selecting previously unselected package r-cran-littler. 1073s Preparing to unpack .../100-r-cran-littler_0.3.19-1_ppc64el.deb ... 1073s Unpacking r-cran-littler (0.3.19-1) ... 1073s Selecting previously unselected package littler. 1073s Preparing to unpack .../101-littler_0.3.19-1_all.deb ... 1073s Unpacking littler (0.3.19-1) ... 1073s Selecting previously unselected package pkgconf-bin. 1073s Preparing to unpack .../102-pkgconf-bin_1.8.1-2_ppc64el.deb ... 1073s Unpacking pkgconf-bin (1.8.1-2) ... 1073s Selecting previously unselected package pkgconf:ppc64el. 1073s Preparing to unpack .../103-pkgconf_1.8.1-2_ppc64el.deb ... 1073s Unpacking pkgconf:ppc64el (1.8.1-2) ... 1073s Selecting previously unselected package pkg-config:ppc64el. 1073s Preparing to unpack .../104-pkg-config_1.8.1-2_ppc64el.deb ... 1073s Unpacking pkg-config:ppc64el (1.8.1-2) ... 1073s Selecting previously unselected package liblzma-dev:ppc64el. 1073s Preparing to unpack .../105-liblzma-dev_5.4.5-0.3_ppc64el.deb ... 1073s Unpacking liblzma-dev:ppc64el (5.4.5-0.3) ... 1073s Selecting previously unselected package r-base-dev. 1073s Preparing to unpack .../106-r-base-dev_4.3.2-1build1_all.deb ... 1073s Unpacking r-base-dev (4.3.2-1build1) ... 1073s Selecting previously unselected package pkg-r-autopkgtest. 1073s Preparing to unpack .../107-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 1073s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 1073s Selecting previously unselected package r-cran-abind. 1073s Preparing to unpack .../108-r-cran-abind_1.4-5-2_all.deb ... 1073s Unpacking r-cran-abind (1.4-5-2) ... 1073s Selecting previously unselected package r-cran-codetools. 1073s Preparing to unpack .../109-r-cran-codetools_0.2-19-1_all.deb ... 1073s Unpacking r-cran-codetools (0.2-19-1) ... 1073s Selecting previously unselected package r-cran-deldir. 1073s Preparing to unpack .../110-r-cran-deldir_2.0-4-1_ppc64el.deb ... 1073s Unpacking r-cran-deldir (2.0-4-1) ... 1073s Selecting previously unselected package r-cran-iterators. 1073s Preparing to unpack .../111-r-cran-iterators_1.0.14-1_all.deb ... 1073s Unpacking r-cran-iterators (1.0.14-1) ... 1073s Selecting previously unselected package r-cran-foreach. 1073s Preparing to unpack .../112-r-cran-foreach_1.5.2-1_all.deb ... 1073s Unpacking r-cran-foreach (1.5.2-1) ... 1073s Selecting previously unselected package r-cran-lattice. 1073s Preparing to unpack .../113-r-cran-lattice_0.22-5-1_ppc64el.deb ... 1073s Unpacking r-cran-lattice (0.22-5-1) ... 1073s Selecting previously unselected package r-cran-matrix. 1073s Preparing to unpack .../114-r-cran-matrix_1.6-5-1_ppc64el.deb ... 1073s Unpacking r-cran-matrix (1.6-5-1) ... 1073s Selecting previously unselected package r-cran-shape. 1073s Preparing to unpack .../115-r-cran-shape_1.4.6-1_all.deb ... 1073s Unpacking r-cran-shape (1.4.6-1) ... 1073s Selecting previously unselected package r-cran-survival. 1073s Preparing to unpack .../116-r-cran-survival_3.5-8-1_ppc64el.deb ... 1073s Unpacking r-cran-survival (3.5-8-1) ... 1074s Selecting previously unselected package r-cran-pkgkitten. 1074s Preparing to unpack .../117-r-cran-pkgkitten_0.2.3-1_all.deb ... 1074s Unpacking r-cran-pkgkitten (0.2.3-1) ... 1074s Selecting previously unselected package r-cran-rcpp. 1074s Preparing to unpack .../118-r-cran-rcpp_1.0.12-1_ppc64el.deb ... 1074s Unpacking r-cran-rcpp (1.0.12-1) ... 1074s Selecting previously unselected package r-cran-rcppeigen. 1074s Preparing to unpack .../119-r-cran-rcppeigen_0.3.3.9.4-1_ppc64el.deb ... 1074s Unpacking r-cran-rcppeigen (0.3.3.9.4-1) ... 1074s Selecting previously unselected package libjs-mathjax. 1074s Preparing to unpack .../120-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 1074s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 1075s Selecting previously unselected package r-cran-glmnet. 1075s Preparing to unpack .../121-r-cran-glmnet_4.1-8-1_ppc64el.deb ... 1075s Unpacking r-cran-glmnet (4.1-8-1) ... 1075s Selecting previously unselected package r-cran-goftest. 1075s Preparing to unpack .../122-r-cran-goftest_1.2-3-1_ppc64el.deb ... 1075s Unpacking r-cran-goftest (1.2-3-1) ... 1075s Selecting previously unselected package r-cran-gsl. 1075s Preparing to unpack .../123-r-cran-gsl_2.1-8-1_ppc64el.deb ... 1075s Unpacking r-cran-gsl (2.1-8-1) ... 1075s Selecting previously unselected package r-cran-nlme. 1075s Preparing to unpack .../124-r-cran-nlme_3.1.164-1_ppc64el.deb ... 1075s Unpacking r-cran-nlme (3.1.164-1) ... 1075s Selecting previously unselected package r-cran-mgcv. 1075s Preparing to unpack .../125-r-cran-mgcv_1.9-1-1_ppc64el.deb ... 1075s Unpacking r-cran-mgcv (1.9-1-1) ... 1075s Selecting previously unselected package r-cran-nleqslv. 1075s Preparing to unpack .../126-r-cran-nleqslv_3.3.5-1_ppc64el.deb ... 1075s Unpacking r-cran-nleqslv (3.3.5-1) ... 1075s Selecting previously unselected package r-cran-polyclip. 1075s Preparing to unpack .../127-r-cran-polyclip_1.10-6-1_ppc64el.deb ... 1075s Unpacking r-cran-polyclip (1.10-6-1) ... 1075s Selecting previously unselected package r-cran-rpart. 1075s Preparing to unpack .../128-r-cran-rpart_4.1.23-1_ppc64el.deb ... 1075s Unpacking r-cran-rpart (4.1.23-1) ... 1076s Selecting previously unselected package r-cran-sm. 1076s Preparing to unpack .../129-r-cran-sm_2.2-6.0-1_ppc64el.deb ... 1076s Unpacking r-cran-sm (2.2-6.0-1) ... 1076s Selecting previously unselected package r-cran-spatial. 1076s Preparing to unpack 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.../140-r-cran-spatstat_3.0-7-1_ppc64el.deb ... 1076s Unpacking r-cran-spatstat (3.0-7-1) ... 1076s Selecting previously unselected package autopkgtest-satdep. 1076s Preparing to unpack .../141-2-autopkgtest-satdep.deb ... 1076s Unpacking autopkgtest-satdep (0) ... 1076s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 1076s Setting up libpixman-1-0:ppc64el (0.42.2-1) ... 1076s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ... 1076s Setting up libpaper1:ppc64el (1.1.29) ... 1076s 1076s Creating config file /etc/papersize with new version 1076s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 1076s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 1076s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 1076s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 1076s Setting up libdatrie1:ppc64el (0.2.13-3) ... 1076s Setting up libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 1076s Setting up libxcb-render0:ppc64el (1.15-1) ... 1076s Setting up unzip (6.0-28ubuntu3) ... 1076s Setting up x11-common (1:7.7+23ubuntu2) ... 1077s Setting up libdeflate0:ppc64el (1.19-1) ... 1077s Setting up linux-libc-dev:ppc64el (6.8.0-11.11) ... 1077s Setting up libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 1077s Setting up libxcb-shm0:ppc64el (1.15-1) ... 1077s Setting up libpaper-utils (1.1.29) ... 1077s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 1077s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 1077s Setting up libpcre2-16-0:ppc64el (10.42-4ubuntu1) ... 1077s Setting up zip (3.0-13) ... 1077s Setting up libpcre2-32-0:ppc64el (10.42-4ubuntu1) ... 1077s Setting up libblas3:ppc64el (3.12.0-3) ... 1077s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 1077s Setting up libpkgconf3:ppc64el (1.8.1-2) ... 1077s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 1077s Setting up libquadmath0:ppc64el (14-20240303-1ubuntu1) ... 1077s Setting up fonts-dejavu-mono (2.37-8) ... 1077s Setting up libmpc3:ppc64el (1.3.1-1) ... 1077s Setting up libatomic1:ppc64el (14-20240303-1ubuntu1) ... 1077s Setting up libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 1077s Setting up icu-devtools (74.2-1ubuntu1) ... 1077s Setting up fonts-dejavu-core (2.37-8) ... 1077s Setting up pkgconf-bin (1.8.1-2) ... 1077s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 1077s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 1077s Setting up libwebp7:ppc64el (1.3.2-0.4) ... 1077s Setting up liblzma-dev:ppc64el (5.4.5-0.3) ... 1077s Setting up libubsan1:ppc64el (14-20240303-1ubuntu1) ... 1077s Setting up libpcre2-posix3:ppc64el (10.42-4ubuntu1) ... 1077s Setting up libcrypt-dev:ppc64el (1:4.4.36-4) ... 1077s Setting up libasan8:ppc64el (14-20240303-1ubuntu1) ... 1077s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 1077s Setting up libthai-data (0.1.29-2) ... 1077s Setting up libxss1:ppc64el (1:1.2.3-1build2) ... 1077s Setting up libtsan2:ppc64el (14-20240303-1ubuntu1) ... 1077s Setting up libisl23:ppc64el (0.26-3) ... 1077s Setting up libc-dev-bin (2.39-0ubuntu6) ... 1077s Setting up cpp-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 1077s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 1077s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 1077s Setting up libcc1-0:ppc64el (14-20240303-1ubuntu1) ... 1077s Setting up liblsan0:ppc64el (14-20240303-1ubuntu1) ... 1077s Setting up libblas-dev:ppc64el (3.12.0-3) ... 1077s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so to provide /usr/lib/powerpc64le-linux-gnu/libblas.so (libblas.so-powerpc64le-linux-gnu) in auto mode 1077s Setting up dctrl-tools (2.24-3build2) ... 1077s Setting up libitm1:ppc64el (14-20240303-1ubuntu1) ... 1077s Setting up cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 1077s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 1077s Setting up libice6:ppc64el (2:1.0.10-1build2) ... 1077s Setting up liblapack3:ppc64el (3.12.0-3) ... 1077s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 1077s Setting up cpp-13 (13.2.0-17ubuntu2) ... 1077s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 1077s Setting up pkgconf:ppc64el (1.8.1-2) ... 1077s Setting up libthai0:ppc64el (0.1.29-2) ... 1077s Setting up liblapack-dev:ppc64el (3.12.0-3) ... 1077s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so (liblapack.so-powerpc64le-linux-gnu) in auto mode 1077s Setting up pkg-config:ppc64el (1.8.1-2) ... 1077s Setting up libgcc-13-dev:ppc64el (13.2.0-17ubuntu2) ... 1077s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 1077s Setting up cpp (4:13.2.0-7ubuntu1) ... 1077s Setting up libc6-dev:ppc64el (2.39-0ubuntu6) ... 1077s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 1077s Setting up libgfortran-13-dev:ppc64el (13.2.0-17ubuntu2) ... 1077s Setting up libsm6:ppc64el (2:1.2.3-1build2) ... 1077s Setting up libicu-dev:ppc64el (74.2-1ubuntu1) ... 1077s Setting up libstdc++-13-dev:ppc64el (13.2.0-17ubuntu2) ... 1077s Setting up libbz2-dev:ppc64el (1.0.8-5ubuntu1) ... 1077s Setting up fontconfig (2.15.0-1ubuntu1) ... 1079s Regenerating fonts cache... done. 1079s Setting up libjpeg-turbo8-dev:ppc64el (2.1.5-2ubuntu1) ... 1079s Setting up libxft2:ppc64el (2.3.6-1) ... 1079s Setting up libncurses-dev:ppc64el (6.4+20240113-1ubuntu1) ... 1079s Setting up libpcre2-dev:ppc64el (10.42-4ubuntu1) ... 1079s Setting up libtk8.6:ppc64el (8.6.14-1) ... 1079s Setting up libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 1079s Setting up libreadline-dev:ppc64el (8.2-3) ... 1079s Setting up libcairo2:ppc64el (1.18.0-1) ... 1079s Setting up gcc-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 1079s Setting up gcc-13 (13.2.0-17ubuntu2) ... 1079s Setting up libxt6:ppc64el (1:1.2.1-1.1) ... 1079s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg-3ubuntu1) ... 1079s Setting up libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 1079s Setting up libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 1079s Setting up libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 1079s Setting up gfortran-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 1079s Setting up libpng-dev:ppc64el (1.6.43-1) ... 1079s Setting up libjpeg-dev:ppc64el (8c-2ubuntu11) ... 1079s Setting up g++-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 1079s Setting up gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 1079s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 1079s Setting up r-base-core (4.3.2-1build1) ... 1079s 1079s Creating config file /etc/R/Renviron with new version 1079s Setting up r-cran-lattice (0.22-5-1) ... 1079s Setting up r-cran-nlme (3.1.164-1) ... 1079s Setting up r-cran-spatstat.utils (3.0-4-1) ... 1079s Setting up r-cran-tensor (1.5-4) ... 1079s Setting up r-cran-pkgkitten (0.2.3-1) ... 1079s Setting up g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 1079s Setting up r-cran-littler (0.3.19-1) ... 1079s Setting up r-cran-nleqslv (3.3.5-1) ... 1079s Setting up r-cran-rcpp (1.0.12-1) ... 1079s Setting up r-cran-codetools (0.2-19-1) ... 1079s Setting up g++-13 (13.2.0-17ubuntu2) ... 1079s Setting up littler (0.3.19-1) ... 1079s Setting up r-cran-gsl (2.1-8-1) ... 1079s Setting up r-cran-spatial (7.3-17-1) ... 1079s Setting up r-cran-iterators (1.0.14-1) ... 1079s Setting up r-cran-abind (1.4-5-2) ... 1079s Setting up r-cran-foreach (1.5.2-1) ... 1079s Setting up r-cran-sm (2.2-6.0-1) ... 1079s Setting up r-cran-polyclip (1.10-6-1) ... 1079s Setting up gcc (4:13.2.0-7ubuntu1) ... 1079s Setting up r-cran-deldir (2.0-4-1) ... 1079s Setting up r-cran-goftest (1.2-3-1) ... 1079s Setting up r-cran-shape (1.4.6-1) ... 1079s Setting up gfortran-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 1079s Setting up r-cran-matrix (1.6-5-1) ... 1079s Setting up r-cran-spatstat.sparse (3.0-3-1) ... 1079s Setting up r-cran-mgcv (1.9-1-1) ... 1079s Setting up g++ (4:13.2.0-7ubuntu1) ... 1079s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 1079s Setting up build-essential (12.10ubuntu1) ... 1079s Setting up r-cran-rcppeigen (0.3.3.9.4-1) ... 1079s Setting up r-cran-survival (3.5-8-1) ... 1079s Setting up gfortran (4:13.2.0-7ubuntu1) ... 1079s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 1079s 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 1079s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 1079s 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 1079s Setting up r-cran-spatstat.data (3.0-4-1) ... 1079s Setting up r-cran-spatstat.geom (3.2-8-1) ... 1079s Setting up r-cran-glmnet (4.1-8-1) ... 1079s Setting up r-base-dev (4.3.2-1build1) ... 1079s Setting up r-cran-rpart (4.1.23-1) ... 1079s Setting up r-cran-spatstat.random (3.2-2-1) ... 1079s Setting up r-cran-spatstat.explore (3.2-5-1) ... 1079s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 1079s Setting up r-cran-spatstat.model (3.2-8-1) ... 1079s Setting up r-cran-spatstat.linnet (3.1-3-1) ... 1079s Setting up r-cran-spatstat (3.0-7-1) ... 1079s Setting up autopkgtest-satdep (0) ... 1079s Processing triggers for man-db (2.12.0-3) ... 1081s Processing triggers for install-info (7.1-3) ... 1081s Processing triggers for libc-bin (2.39-0ubuntu6) ... 1086s (Reading database ... 82755 files and directories currently installed.) 1086s Removing autopkgtest-satdep (0) ... 1088s autopkgtest [20:21:31]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 1088s autopkgtest [20:21:31]: test pkg-r-autopkgtest: [----------------------- 1089s Test: Try to load the R library spatstat.model 1089s 1089s R version 4.3.2 (2023-10-31) -- "Eye Holes" 1089s Copyright (C) 2023 The R Foundation for Statistical Computing 1089s Platform: powerpc64le-unknown-linux-gnu (64-bit) 1089s 1089s R is free software and comes with ABSOLUTELY NO WARRANTY. 1089s You are welcome to redistribute it under certain conditions. 1089s Type 'license()' or 'licence()' for distribution details. 1089s 1089s R is a collaborative project with many contributors. 1089s Type 'contributors()' for more information and 1089s 'citation()' on how to cite R or R packages in publications. 1089s 1089s Type 'demo()' for some demos, 'help()' for on-line help, or 1089s 'help.start()' for an HTML browser interface to help. 1089s Type 'q()' to quit R. 1089s 1089s > library('spatstat.model') 1089s Loading required package: spatstat.data 1090s Loading required package: spatstat.geom 1090s spatstat.geom 3.2-8 1090s Loading required package: spatstat.random 1090s spatstat.random 3.2-2 1090s Loading required package: spatstat.explore 1090s Loading required package: nlme 1090s spatstat.explore 3.2-5 1090s Loading required package: rpart 1090s spatstat.model 3.2-8 1090s > 1090s > 1090s Other tests are currently unsupported! 1090s They will be progressively added. 1090s autopkgtest [20:21:33]: test pkg-r-autopkgtest: -----------------------] 1091s pkg-r-autopkgtest PASS 1091s autopkgtest [20:21:34]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 1091s autopkgtest [20:21:34]: @@@@@@@@@@@@@@@@@@@@ summary 1091s run-unit-test PASS 1091s pkg-r-autopkgtest PASS 1126s Creating nova instance adt-noble-ppc64el-r-cran-spatstat.model-20240323-200322-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)... 1126s Creating nova instance adt-noble-ppc64el-r-cran-spatstat.model-20240323-200322-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240323.img (UUID ff8abf95-5243-4ea5-b7f5-3bf690534a1d)...