CRAN Package Check Results for Package geostatsp

Last updated on 2021-03-01 04:46:59 CET.

Check Details

Version: 1.8.2
Check: package dependencies
Result: NOTE
    Package which this enhances but not available for checking: 'INLA'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.8.2
Check: installed package size
Result: NOTE
     installed size is 6.0Mb
     sub-directories of 1Mb or more:
     data 3.8Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.8.2
Check: data for non-ASCII characters
Result: NOTE
     Note: found 4 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.8.2
Check: examples
Result: ERROR
    Running examples in ‘geostatsp-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: glgm-methods
    > ### Title: Generalized Linear Geostatistical Models
    > ### Aliases: glgm glgm-methods glgm,ANY,ANY,ANY,ANY-method
    > ### glgm,formula,Raster,ANY,ANY-method
    > ### glgm,formula,Spatial,ANY,ANY-method
    > ### glgm,formula,data.frame,Raster,data.frame-method lgcp
    >
    > ### ** Examples
    >
    > # use the 'safe' version of INLA on linux systems
    > if(Sys.info()['sysname'] =='Linux' &
    + requireNamespace("INLA", quietly = TRUE)) {
    + INLA::inla.setOption(inla.call = system.file(paste("bin/linux/",
    + ifelse(.Machine$sizeof.pointer == 4, "32", "64"),
    + 'bit/inla.static', sep=''), package="INLA")) }
    >
    > # geostatistical model for the swiss rainfall data
    > require("geostatsp")
    > data("swissRain")
    > swissRain$lograin = log(swissRain$rain)
    > swissFit = glgm(formula="lograin", data=swissRain,
    + grid=30,
    + covariates=swissAltitude, family="gaussian",
    + buffer=2000,
    + prior = list(sd=1, range=100*1000, sdObs = 2),
    + control.inla = list(strategy='gaussian')
    + )
    >
    > if(!is.null(swissFit$parameters) ) {
    +
    + swissExc = excProb(swissFit, threshold=log(25))
    +
    + swissExcRE = excProb(swissFit$inla$marginals.random$space,
    + log(1.5),template=swissFit$raster)
    +
    + swissFit$parameters$summary
    +
    + matplot(
    + swissFit$parameters$range$postK[,'x'],
    + swissFit$parameters$range$postK[,c('y','prior')],
    + type="l", lty=1, xlim = c(0, 1000),
    + xlab = 'km', ylab='dens')
    + legend('topright', lty=1, col=1:2, legend=c('post','prior'))
    +
    + plot(swissFit$raster[["predict.exp"]])
    +
    + mycol = c("green","yellow","orange","red")
    + mybreaks = c(0, 0.2, 0.8, 0.95, 1)
    + plot(swissBorder)
    + plot(swissExc, breaks=mybreaks, col=mycol,add=TRUE,legend=FALSE)
    + plot(swissBorder, add=TRUE)
    + legend("topleft",legend=mybreaks, fill=c(NA,mycol))
    +
    +
    + plot(swissBorder)
    + plot(swissExcRE, breaks=mybreaks, col=mycol,add=TRUE,legend=FALSE)
    + plot(swissBorder, add=TRUE)
    + legend("topleft",legend=mybreaks, fill=c(NA,mycol))
    + }
    >
    >
    >
    >
    > # a log-Gaussian Cox process example
    >
    > myPoints = SpatialPoints(cbind(rbeta(100,2,2), rbeta(100,3,4)))
    > myPoints@bbox = cbind(c(0,0), c(1,1))
    >
    > mycov = raster(matrix(rbinom(100, 1, 0.5), 10, 10), 0, 1, 0, 1)
    > names(mycov)="x1"
    >
    >
    > res = lgcp(
    + formula=~factor(x1),
    + data=myPoints,
    + grid=20, covariates=mycov,
    + prior=list(sd=c(0.9, 1.1), range=c(0.4, 0.41),
    + control.inla = list(strategy='gaussian'))
    + )
    > if(requireNamespace("INLA", quietly = TRUE)) {
    + plot(res$raster[["predict.exp"]])
    + plot(myPoints,add=TRUE,col="#0000FF30",cex=0.5)
    + }
    Warning in min(x) : no non-missing arguments to min; returning Inf
    Warning in max(x) : no non-missing arguments to max; returning -Inf
    Warning in min(x) : no non-missing arguments to min; returning Inf
    Warning in max(x) : no non-missing arguments to max; returning -Inf
    Error in plot.window(...) : need finite 'xlim' values
    Calls: plot -> plot -> plot.default -> localWindow -> plot.window
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.8.2
Check: tests
Result: ERROR
     Running ‘RFsimulate.R’ [12s/14s]
     Running ‘krige.R’
     Running ‘lgcp.R’ [9s/13s]
     Running ‘lgm.R’ [17s/21s]
     Running ‘lgmRaster.R’ [320s/233s]
     Running ‘likfitLgm.R’ [11s/15s]
     Running ‘matern.R’
     Running ‘maternGmrfPrec.R’ [11s/15s]
     Running ‘profLlgm.R’ [14s/16s]
     Running ‘simLgcp.R’ [16s/23s]
     Running ‘stackRasterList.R’
    Running the tests in ‘tests/lgcp.R’ failed.
    Complete output:
     > options("rgdal_show_exportToProj4_warnings"="none")
     > if(Sys.info()['sysname'] =='Linux' &
     + requireNamespace("INLA", quietly=TRUE)) {
     + INLA::inla.setOption(inla.call =
     + system.file(paste(
     + "bin/linux/",
     + ifelse(
     + .Machine$sizeof.pointer == 4,
     + "32", "64"),
     + 'bit/inla.static', sep=''),
     + package="INLA"))
     + }
     >
     >
     > havePackages = c(
     + 'INLA' = requireNamespace('INLA', quietly=TRUE)
     + )
     >
     > print(havePackages)
     INLA
     TRUE
     >
     > # as in example
     > require('geostatsp')
     Loading required package: geostatsp
     Loading required package: Matrix
     Loading required package: raster
     Loading required package: sp
     > myPoints = SpatialPoints(cbind(rbeta(100,2,2), rbeta(100,3,4)))
     > myPoints@bbox = cbind(c(0,0), c(1,1))
     >
     > mycov = raster(matrix(rbinom(100, 1, 0.5), 10, 10), 0, 1, 0, 1)
     > names(mycov)="x1"
     >
     > if(all(havePackages)) {
     +
     + res = lgcp(
     + formula=~factor(x1),
     + data=myPoints,
     + grid=20,
     + covariates=mycov,
     + priorCI=list(sd=c(u=0.1, alpha = 0.01), range=c(0.4, 0.41))
     + )
     +
     + knitr::kable(res$parameters$summary, digits=3)
     +
     + plot(res$raster[["predict.exp"]])
     + plot(myPoints,add=TRUE,col="#0000FF30",cex=0.5)
     +
     +
     + # intercept only
     +
     + res = lgcp(
     + data=myPoints,
     + grid=20,
     + covariates=mycov,
     + formula=~1,
     + priorCI=list(sd=c(0.9, 1.1), range=c(0.4, 0.41))
     + )
     +
     + knitr::kable(res$parameters$summary, digits=3)
     +
     + plot(res$raster[["predict.exp"]])
     + plot(myPoints,add=TRUE,col="#0000FF30",cex=0.5)
     +
     + if(interactive() | Sys.info()['user'] =='patrick') {
     +
     + # some missing values
     +
     + temp = values(mycov)
     + temp[1:4] = NA
     + values(mycov) = temp
     +
     + res = lgcp(data=myPoints, grid=20, covariates=mycov,
     + formula=~factor(x1),
     + priorCI=list(sd=c(0.9, 1.1), range=c(0.4, 0.41))
     + )
     +
     + plot(res$raster[["predict.exp"]])
     + plot(myPoints,add=TRUE,col="#0000FF30",cex=0.5)
     +
     + data('murder')
     + data('torontoPop')
     + myCov = list(
     + pop=torontoPdens,
     + inc = log(torontoIncome)
     + )
     +
     + formula = ~ inc + offset(pop, log=TRUE)
     +
     + resL=lgcp(formula, data=murder,
     + grid=squareRaster(murder, 30),
     + covariates=myCov,
     + border=torontoBorder)
     +
     + resO = lgcp( ~ inc + pop,
     + data=murder,
     + grid=squareRaster(murder, 30),
     + covariates=list(inc=myCov$inc, pop=log(myCov$pop)),
     + border=torontoBorder)
     +
     + rbind(resL$param$summary, resO$param$summary)
     +
     +
     +
     + }
     + }
     Error in plot.window(...) : need finite 'xlim' values
     Calls: plot -> plot -> plot.default -> localWindow -> plot.window
     In addition: Warning messages:
     1: In kable_pipe(x = character(0), caption = NULL, escape = TRUE) :
     The table should have a header (column names)
     2: In min(x) : no non-missing arguments to min; returning Inf
     3: In max(x) : no non-missing arguments to max; returning -Inf
     4: In min(x) : no non-missing arguments to min; returning Inf
     5: In max(x) : no non-missing arguments to max; returning -Inf
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.8.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘glgm.Rnw’ using knitr
    Quitting from lines 72-119 (glgm.Rnw)
    Error: processing vignette 'glgm.Rnw' failed with diagnostics:
    incorrect number of dimensions
    --- failed re-building ‘glgm.Rnw’
    
    --- re-building ‘lgcp.Rnw’ using knitr
    --- finished re-building ‘lgcp.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘glgm.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.8.2
Check: dependencies in R code
Result: NOTE
    No protocol specified
    No protocol specified
Flavor: r-oldrel-macos-x86_64