CRAN Package Check Results for Package geostatsp

Last updated on 2020-04-30 07:48:33 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	1.8.0	27.71	434.12	461.83	NOTE
r-devel-linux-x86_64-debian-gcc	1.8.0	21.85	320.75	342.60	NOTE
r-devel-linux-x86_64-fedora-clang	1.8.0			429.23	ERROR
r-devel-linux-x86_64-fedora-gcc	1.8.0			506.23	ERROR
r-devel-windows-ix86+x86_64	1.8.0	64.00	528.00	592.00	NOTE
r-patched-linux-x86_64	1.8.0	23.46	418.56	442.02	NOTE
r-patched-solaris-x86	1.8.0			841.40	NOTE
r-release-linux-x86_64	1.8.0	22.35	419.09	441.44	NOTE
r-release-osx-x86_64	1.8.0				NOTE
r-release-windows-ix86+x86_64	1.8.0	48.00	544.00	592.00	NOTE
r-oldrel-osx-x86_64	1.8.0				NOTE
r-oldrel-windows-ix86+x86_64	1.8.0	42.00	574.00	616.00	NOTE

Check Details

Version: 1.8.0
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-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.8.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘mapmisc’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.8.0
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-osx-x86_64, r-release-windows-ix86+x86_64, r-oldrel-osx-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.8.0
Check: examples
Result: ERROR
    Running examples in ‘geostatsp-Ex.R’ failed
    The error most likely occurred in:

    > ### Name: loaloa
    > ### Title: Loaloa prevalence data from 197 village surveys
    > ### Aliases: loaloa elevationLoa eviLoa ltLoa tempLoa
    > ### Keywords: datasets
    >
    > ### ** Examples
    >
    >
    >
    > data("loaloa")
    > plot(loaloa, main="loaloa villages")
    >
    > # elevation
    > plot(elevationLoa, col=terrain.colors(100), main="elevation")
    > points(loaloa)
    >
    > # vegetation index
    > plot(eviLoa, main="evi")
    > points(loaloa)
    >
    > plot(tempLoa, main="temperature")
    > points(loaloa)
    >
    >
    >
    > # land type, a categorical variable
    > plot(ltLoa)
    > mapmisc::legendBreaks("bottomleft",ltLoa, bty='n')
    Error in loadNamespace(name) : there is no package called ‘mapmisc’
    Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.8.0
Check: tests
Result: ERROR
     Running ‘RFsimulate.R’ [12s/14s]
     Running ‘krige.R’
     Running ‘lgcp.R’
     Running ‘lgm.R’ [19s/19s]
     Running ‘lgmRaster.R’ [92s/56s]
     Running ‘likfitLgm.R’ [12s/12s]
     Running ‘matern.R’
     Running ‘maternGmrfPrec.R’ [11s/11s]
     Running ‘profLlgm.R’ [14s/12s]
     Running ‘simLgcp.R’
     Running ‘stackRasterList.R’
    Running the tests in ‘tests/lgmRaster.R’ failed.
    Complete output:
     > #+ setup
     > library('geostatsp')
     Loading required package: Matrix
     Loading required package: raster
     Loading required package: sp
     > #'
     >
     > #' # simulated data
     >
     >
     > #+ simData
     > if(.Platform$OS.type == 'windows') {
     + Ncell = 30
     + } else {
     + Ncell = 40
     + }
     > myRaster = squareRaster(extent(0,6000,0,6000), Ncell)
     >
     > myParam=c(oneminusar=0.1, conditionalVariance=2.5^2,shape=2)
     > myQ = maternGmrfPrec(myRaster, param=myParam)
     > attributes(myQ)$info$optimalShape
     shape variance range cellSize
     4.092496 110.524266 900.000000 150.000000
     > set.seed(0)
     > mySim = RFsimulate(attributes(myQ)$info$optimalShape, myRaster)
     New output format of RFsimulate: S4 object of class 'RFsp';
     for a bare, but faster array format use 'RFoptions(spConform=FALSE)'.
     >
     > otherPar = c(intercept=1, beta = 2, tau=10)
     > myCov = myRaster
     > values(myCov) = rep(seq(-1,1,len=ncol(myCov)), nrow(myCov))
     >
     > myLambda = otherPar['intercept'] + otherPar['beta'] * myCov + mySim
     > myY = myLambda
     > values(myY)=rnorm(prod(dim(myLambda)),values(myLambda), sd=otherPar['tau'])
     >
     > names(myCov) = 'x'
     > names(myY) = gsub("^layer\\.","sim", names(mySim))
     > #'
     >
     >
     >
     > #+ plotSim, fig.cap='simulated data', fig.subcap =c('random effect','observed')
     > plot(mySim)
     >
     > plot(myY)
     > #'
     >
     > #' grid search
     >
     > #+ simGrid
     > myResR = lgm(formula = sim ~ x,
     + data=raster::stack(myY, myCov),
     + oneminusar = exp(seq(log(0.05), log(0.2),len=25)),
     + nugget = exp(seq(log(5), log(100),len=21)), shape=2,
     + adjustEdges=TRUE,
     + mc.cores=1+(.Platform$OS.type=='unix') )
     > #'
     >
     > #+ simPlot
     > Sbreaks = c(-100000,-50,-20,-10, -5, -2, -1,0)
     >
     > myCol = mapmisc::colourScale(
     + breaks = Sbreaks + max(myResR$array[,-1,'logLreml',], na.rm=TRUE),
     + style='fixed',
     + col=terrain.colors
     + )
     Error in loadNamespace(name) : there is no package called 'mapmisc'
     Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.8.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘glgm.Rnw’ using knitr
    Failed with error: 'there is no package called 'INLA''
    Quitting from lines 47-59 (glgm.Rnw)
    Error: processing vignette 'glgm.Rnw' failed with diagnostics:
    there is no package called 'mapmisc'
    --- failed re-building ‘glgm.Rnw’

    --- re-building ‘lgcp.Rnw’ using knitr
    Failed with error: 'there is no package called 'INLA''
    Quitting from lines 30-34 (lgcp.Rnw)
    Error: processing vignette 'lgcp.Rnw' failed with diagnostics:
    there is no package called 'mapmisc'
    --- failed re-building ‘lgcp.Rnw’

    SUMMARY: processing the following files failed:
     ‘glgm.Rnw’ ‘lgcp.Rnw’

    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.8.0
Check: tests
Result: ERROR
     Running ‘RFsimulate.R’ [12s/12s]
     Running ‘krige.R’
     Running ‘lgcp.R’ [46s/36s]
     Running ‘lgm.R’ [18s/18s]
     Running ‘lgmRaster.R’ [95s/55s]
     Running ‘likfitLgm.R’ [11s/12s]
     Running ‘matern.R’
     Running ‘maternGmrfPrec.R’ [11s/11s]
     Running ‘profLlgm.R’ [16s/13s]
     Running ‘simLgcp.R’ [17s/17s]
     Running ‘stackRasterList.R’
    Running the tests in ‘tests/lgmRaster.R’ failed.
    Complete output:
     > #+ setup
     > library('geostatsp')
     Loading required package: Matrix
     Loading required package: raster
     Loading required package: sp
     > #'
     >
     > #' # simulated data
     >
     >
     > #+ simData
     > if(.Platform$OS.type == 'windows') {
     + Ncell = 30
     + } else {
     + Ncell = 40
     + }
     > myRaster = squareRaster(extent(0,6000,0,6000), Ncell)
     >
     > myParam=c(oneminusar=0.1, conditionalVariance=2.5^2,shape=2)
     > myQ = maternGmrfPrec(myRaster, param=myParam)
     > attributes(myQ)$info$optimalShape
     shape variance range cellSize
     4.092496 110.524266 900.000000 150.000000
     > set.seed(0)
     > mySim = RFsimulate(attributes(myQ)$info$optimalShape, myRaster)
     New output format of RFsimulate: S4 object of class 'RFsp';
     for a bare, but faster array format use 'RFoptions(spConform=FALSE)'.
     >
     > otherPar = c(intercept=1, beta = 2, tau=10)
     > myCov = myRaster
     > values(myCov) = rep(seq(-1,1,len=ncol(myCov)), nrow(myCov))
     >
     > myLambda = otherPar['intercept'] + otherPar['beta'] * myCov + mySim
     > myY = myLambda
     > values(myY)=rnorm(prod(dim(myLambda)),values(myLambda), sd=otherPar['tau'])
     >
     > names(myCov) = 'x'
     > names(myY) = gsub("^layer\\.","sim", names(mySim))
     > #'
     >
     >
     >
     > #+ plotSim, fig.cap='simulated data', fig.subcap =c('random effect','observed')
     > plot(mySim)
     >
     > plot(myY)
     > #'
     >
     > #' grid search
     >
     > #+ simGrid
     > myResR = lgm(formula = sim ~ x,
     + data=raster::stack(myY, myCov),
     + oneminusar = exp(seq(log(0.05), log(0.2),len=25)),
     + nugget = exp(seq(log(5), log(100),len=21)), shape=2,
     + adjustEdges=TRUE,
     + mc.cores=1+(.Platform$OS.type=='unix') )
     > #'
     >
     > #+ simPlot
     > Sbreaks = c(-100000,-50,-20,-10, -5, -2, -1,0)
     >
     > myCol = mapmisc::colourScale(
     + breaks = Sbreaks + max(myResR$array[,-1,'logLreml',], na.rm=TRUE),
     + style='fixed',
     + col=terrain.colors
     + )
     Error in loadNamespace(name) : there is no package called 'mapmisc'
     Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.8.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘glgm.Rnw’ using knitr
    Quitting from lines 47-59 (glgm.Rnw)
    Error: processing vignette 'glgm.Rnw' failed with diagnostics:
    there is no package called 'mapmisc'
    --- failed re-building ‘glgm.Rnw’

    --- re-building ‘lgcp.Rnw’ using knitr
    Quitting from lines 30-34 (lgcp.Rnw)
    Error: processing vignette 'lgcp.Rnw' failed with diagnostics:
    there is no package called 'mapmisc'
    --- failed re-building ‘lgcp.Rnw’

    SUMMARY: processing the following files failed:
     ‘glgm.Rnw’ ‘lgcp.Rnw’

    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.8.0
Check: dependencies in R code
Result: NOTE
No protocol specified
No protocol specified
Flavor: r-oldrel-osx-x86_64