CRAN Package Check Results for Package dismo

Last updated on 2015-09-06 23:47:20.

Check Details

Version: 1.0-12
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
    .auctest: no visible global function definition for ‘wilcox.test’
    .avgDist: no visible global function definition for ‘median’
    .calibration: no visible global function definition for ‘glm’
    .calibration: no visible binding for global variable ‘binomial’
    .calibration: no visible global function definition for ‘pchisq’
    .calibration: no visible binding for global variable ‘poisson’
    .conversionError: no visible global function definition for ‘na.omit’
    .conversionError: no visible global function definition for
     ‘chisq.test’
    .doResponse: no visible global function definition for ‘par’
    .gbif_old: no visible global function definition for ‘flush.console’
    .gbif_old: no visible global function definition for ‘download.file’
    .generateHulls: no visible global function definition for ‘na.omit’
    .generateHulls: no visible global function definition for ‘chull’
    .generateHulls: no visible global function definition for ‘kmeans’
    .getECcrops: no visible global function definition for ‘data’
    .getECcrops: no visible binding for global variable ‘ECOcrops’
    .kAUC: no visible global function definition for ‘na.omit’
    .messi2b: no visible global function definition for ‘na.omit’
    .messi3: no visible global function definition for ‘na.omit’
    .messi4: no visible global function definition for ‘na.omit’
    .messix: no visible global function definition for ‘ecdf’
    .nobs: no visible global function definition for ‘na.omit’
    .nullRandom2: no visible global function definition for ‘flush.console’
    .precision: no visible global function definition for ‘na.omit’
    .richness: no visible global function definition for ‘na.omit’
    .voronoi: no visible global function definition for ‘na.omit’
    dcEvaluate: no visible global function definition for ‘na.omit’
    evaluate: no visible global function definition for ‘na.omit’
    evaluate: no visible global function definition for ‘cor.test’
    evaluateROCR: no visible global function definition for ‘na.omit’
    gbif: no visible global function definition for ‘download.file’
    gbif: no visible global function definition for ‘flush.console’
    gbm.holdout: no visible binding for global variable ‘weights’
    gbm.interactions: no visible global function definition for ‘lm’
    gbm.interactions: no visible global function definition for ‘resid’
    gbm.perspec: no visible global function definition for ‘glm’
    gbm.perspec: no visible binding for global variable ‘poisson’
    gbm.perspec: no visible global function definition for ‘fitted’
    gbm.perspec: no visible global function definition for ‘legend’
    gbm.plot: no visible global function definition for ‘par’
    gbm.plot: no visible global function definition for ‘loess’
    gbm.plot: no visible global function definition for ‘fitted’
    gbm.plot: no visible global function definition for ‘title’
    gbm.plot.fits: no visible global function definition for ‘par’
    gbm.plot.fits: no visible global function definition for ‘approx’
    gbm.plot.fits: no visible global function definition for ‘ppoints’
    gbm.plot.fits: no visible global function definition for ‘abline’
    gbm.plot.fits: no visible global function definition for ‘title’
    gbm.simplify: no visible global function definition for ‘runif’
    gbm.simplify: no visible binding for global variable ‘var’
    gbm.simplify: no visible global function definition for ‘abline’
    gbm.simplify: no visible global function definition for ‘title’
    gbm.step: no visible global function definition for ‘runif’
    gbm.step: no visible global function definition for ‘flush.console’
    gbm.step: no visible binding for global variable ‘var’
    gbm.step: no visible global function definition for ‘abline’
    gbm.step: no visible global function definition for ‘title’
    gbm.step: no visible global function definition for ‘cor’
    gbm.step: no visible global function definition for ‘approx’
    gbm.step: no visible global function definition for ‘ppoints’
    gbm.step: no visible global function definition for ‘var’
    geocode: no visible global function definition for ‘flush.console’
    gmap: no visible global function definition for ‘download.file’
    gmap: no visible global function definition for ‘col2rgb’
    gridSample: no visible global function definition for ‘na.omit’
    gridSample: no visible global function definition for ‘runif’
    kfold : singlefold: no visible global function definition for ‘runif’
    nicheEquivalency: no visible global function definition for
     ‘flush.console’
    nicheEquivalency : <anonymous>: no visible global function definition
     for ‘flush.console’
    nicheEquivalency: no visible binding for global variable ‘sd’
    nicheEquivalency: no visible global function definition for ‘pnorm’
    nullRandom: no visible global function definition for ‘flush.console’
    pointValues: no visible global function definition for ‘na.omit’
    randomPoints: no visible global function definition for ‘na.omit’
    voronoi: no visible global function definition for ‘na.omit’
    bioclim,data.frame-missing: no visible global function definition for
     ‘na.omit’
    biovars,matrix-matrix-matrix: no visible binding for global variable
     ‘sd’
    circles,SpatialPoints: no visible binding for global variable ‘r’
    density,DistModel: no visible global function definition for ‘par’
    domain,data.frame-missing: no visible global function definition for
     ‘na.omit’
    ecolim,matrix-matrix: no visible global function definition for
     ‘na.omit’
    ecolim,matrix-matrix: no visible global function definition for
     ‘approxfun’
    geoDist,data.frame: no visible global function definition for ‘na.omit’
    mahal,data.frame-missing: no visible global function definition for
     ‘na.omit’
    mahal,data.frame-missing: no visible global function definition for
     ‘var’
    maxent,Raster-ANY: no visible global function definition for ‘na.omit’
    maxent,data.frame-vector: no visible global function definition for
     ‘na.omit’
    maxent,data.frame-vector: no visible global function definition for
     ‘runif’
    maxent,data.frame-vector: no visible global function definition for
     ‘write.table’
    maxent,data.frame-vector: no visible global function definition for
     ‘read.csv’
    maxent,data.frame-vector: no visible global function definition for
     ‘packageDescription’
    pairs,DistModel : panelhist: no visible global function definition for
     ‘par’
    pairs,DistModel : panelhist: no visible global function definition for
     ‘rect’
    pairs,DistModel : panelcor: no visible global function definition for
     ‘par’
    persp,DistModel: no visible binding for global variable ‘median’
    plot,Bioclim-missing : myquantile: no visible global function
     definition for ‘na.omit’
    plot,Bioclim-missing: no visible global function definition for
     ‘polygon’
    plot,ECOCROPcrop-missing: no visible global function definition for
     ‘par’
    plot,EcoLim-ANY: no visible global function definition for ‘par’
    plot,MaxEnt-missing: no visible global function definition for
     ‘dotchart’
    predict,Bioclim: no visible global function definition for ‘na.omit’
    predict,Mahalanobis : <anonymous>: no visible global function
     definition for ‘mahalanobis’
    predict,MaxEnt: no visible global function definition for ‘na.omit’
    response,ANY: no visible binding for global variable ‘median’
    response,DistModel: no visible binding for global variable ‘median’
    response,MaxEntReplicates: no visible binding for global variable
     ‘median’
    show,MaxEnt: no visible global function definition for ‘browseURL’
    show,MaxEntReplicates: no visible global function definition for
     ‘browseURL’
    Undefined global functions or variables:
     ECOcrops abline approx approxfun binomial browseURL chisq.test chull
     col2rgb cor cor.test data dotchart download.file ecdf fitted
     flush.console glm kmeans legend lm loess mahalanobis median na.omit
     packageDescription par pchisq pnorm poisson polygon ppoints r
     read.csv rect resid runif sd title var weights wilcox.test
     write.table
    Consider adding
     importFrom("grDevices", "chull", "col2rgb")
     importFrom("graphics", "abline", "dotchart", "legend", "par",
     "polygon", "rect", "title")
     importFrom("stats", "approx", "approxfun", "binomial", "chisq.test",
     "cor", "cor.test", "ecdf", "fitted", "glm", "kmeans", "lm",
     "loess", "mahalanobis", "median", "na.omit", "pchisq",
     "pnorm", "poisson", "ppoints", "resid", "runif", "sd",
     "var", "weights", "wilcox.test")
     importFrom("utils", "browseURL", "data", "download.file",
     "flush.console", "packageDescription", "read.csv",
     "write.table")
    to your NAMESPACE.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64

Version: 1.0-12
Flags: --no-build-vignettes
Check: R code for possible problems
Result: NOTE
    .auctest: no visible global function definition for ‘wilcox.test’
    .avgDist: no visible global function definition for ‘median’
    .calibration: no visible global function definition for ‘glm’
    .calibration: no visible binding for global variable ‘binomial’
    .calibration: no visible global function definition for ‘pchisq’
    .calibration: no visible binding for global variable ‘poisson’
    .conversionError: no visible global function definition for ‘na.omit’
    .conversionError: no visible global function definition for
     ‘chisq.test’
    .doResponse: no visible global function definition for ‘par’
    .gbif_old: no visible global function definition for ‘flush.console’
    .gbif_old: no visible global function definition for ‘download.file’
    .generateHulls: no visible global function definition for ‘na.omit’
    .generateHulls: no visible global function definition for ‘chull’
    .generateHulls: no visible global function definition for ‘kmeans’
    .getECcrops: no visible global function definition for ‘data’
    .getECcrops: no visible binding for global variable ‘ECOcrops’
    .kAUC: no visible global function definition for ‘na.omit’
    .messi2b: no visible global function definition for ‘na.omit’
    .messi3: no visible global function definition for ‘na.omit’
    .messi4: no visible global function definition for ‘na.omit’
    .messix: no visible global function definition for ‘ecdf’
    .nobs: no visible global function definition for ‘na.omit’
    .nullRandom2: no visible global function definition for ‘flush.console’
    .precision: no visible global function definition for ‘na.omit’
    .richness: no visible global function definition for ‘na.omit’
    .voronoi: no visible global function definition for ‘na.omit’
    dcEvaluate: no visible global function definition for ‘na.omit’
    evaluate: no visible global function definition for ‘na.omit’
    evaluate: no visible global function definition for ‘cor.test’
    evaluateROCR: no visible global function definition for ‘na.omit’
    gbif: no visible global function definition for ‘download.file’
    gbif: no visible global function definition for ‘flush.console’
    gbm.holdout: no visible binding for global variable ‘weights’
    gbm.interactions: no visible global function definition for ‘lm’
    gbm.interactions: no visible global function definition for ‘resid’
    gbm.perspec: no visible global function definition for ‘glm’
    gbm.perspec: no visible binding for global variable ‘poisson’
    gbm.perspec: no visible global function definition for ‘fitted’
    gbm.perspec: no visible global function definition for ‘legend’
    gbm.plot: no visible global function definition for ‘par’
    gbm.plot: no visible global function definition for ‘loess’
    gbm.plot: no visible global function definition for ‘fitted’
    gbm.plot: no visible global function definition for ‘title’
    gbm.plot.fits: no visible global function definition for ‘par’
    gbm.plot.fits: no visible global function definition for ‘approx’
    gbm.plot.fits: no visible global function definition for ‘ppoints’
    gbm.plot.fits: no visible global function definition for ‘abline’
    gbm.plot.fits: no visible global function definition for ‘title’
    gbm.simplify: no visible global function definition for ‘runif’
    gbm.simplify: no visible binding for global variable ‘var’
    gbm.simplify: no visible global function definition for ‘abline’
    gbm.simplify: no visible global function definition for ‘title’
    gbm.step: no visible global function definition for ‘runif’
    gbm.step: no visible global function definition for ‘flush.console’
    gbm.step: no visible binding for global variable ‘var’
    gbm.step: no visible global function definition for ‘abline’
    gbm.step: no visible global function definition for ‘title’
    gbm.step: no visible global function definition for ‘cor’
    gbm.step: no visible global function definition for ‘approx’
    gbm.step: no visible global function definition for ‘ppoints’
    gbm.step: no visible global function definition for ‘var’
    geocode: no visible global function definition for ‘flush.console’
    gmap: no visible global function definition for ‘download.file’
    gmap: no visible global function definition for ‘col2rgb’
    gridSample: no visible global function definition for ‘na.omit’
    gridSample: no visible global function definition for ‘runif’
    kfold : singlefold: no visible global function definition for ‘runif’
    nicheEquivalency: no visible global function definition for
     ‘flush.console’
    nicheEquivalency : <anonymous>: no visible global function definition
     for ‘flush.console’
    nicheEquivalency: no visible binding for global variable ‘sd’
    nicheEquivalency: no visible global function definition for ‘pnorm’
    nullRandom: no visible global function definition for ‘flush.console’
    pointValues: no visible global function definition for ‘na.omit’
    randomPoints: no visible global function definition for ‘na.omit’
    voronoi: no visible global function definition for ‘na.omit’
    bioclim,data.frame-missing: no visible global function definition for
     ‘na.omit’
    biovars,matrix-matrix-matrix: no visible binding for global variable
     ‘sd’
    circles,SpatialPoints: no visible binding for global variable ‘r’
    density,DistModel: no visible global function definition for ‘par’
    domain,data.frame-missing: no visible global function definition for
     ‘na.omit’
    ecolim,matrix-matrix: no visible global function definition for
     ‘na.omit’
    ecolim,matrix-matrix: no visible global function definition for
     ‘approxfun’
    geoDist,data.frame: no visible global function definition for ‘na.omit’
    mahal,data.frame-missing: no visible global function definition for
     ‘na.omit’
    mahal,data.frame-missing: no visible global function definition for
     ‘var’
    maxent,Raster-ANY: no visible global function definition for ‘na.omit’
    maxent,data.frame-vector: no visible global function definition for
     ‘na.omit’
    maxent,data.frame-vector: no visible global function definition for
     ‘runif’
    maxent,data.frame-vector: no visible global function definition for
     ‘write.table’
    maxent,data.frame-vector: no visible global function definition for
     ‘read.csv’
    maxent,data.frame-vector: no visible global function definition for
     ‘packageDescription’
    pairs,DistModel : panelhist: no visible global function definition for
     ‘par’
    pairs,DistModel : panelhist: no visible global function definition for
     ‘rect’
    pairs,DistModel : panelcor: no visible global function definition for
     ‘par’
    persp,DistModel: no visible binding for global variable ‘median’
    plot,Bioclim-missing : myquantile: no visible global function
     definition for ‘na.omit’
    plot,Bioclim-missing: no visible global function definition for
     ‘polygon’
    plot,ECOCROPcrop-missing: no visible global function definition for
     ‘par’
    plot,EcoLim-ANY: no visible global function definition for ‘par’
    plot,MaxEnt-missing: no visible global function definition for
     ‘dotchart’
    predict,Bioclim: no visible global function definition for ‘na.omit’
    predict,Mahalanobis : <anonymous>: no visible global function
     definition for ‘mahalanobis’
    predict,MaxEnt: no visible global function definition for ‘na.omit’
    response,ANY: no visible binding for global variable ‘median’
    response,DistModel: no visible binding for global variable ‘median’
    response,MaxEntReplicates: no visible binding for global variable
     ‘median’
    show,MaxEnt: no visible global function definition for ‘browseURL’
    show,MaxEntReplicates: no visible global function definition for
     ‘browseURL’
    Undefined global functions or variables:
     ECOcrops abline approx approxfun binomial browseURL chisq.test chull
     col2rgb cor cor.test data dotchart download.file ecdf fitted
     flush.console glm kmeans legend lm loess mahalanobis median na.omit
     packageDescription par pchisq pnorm poisson polygon ppoints r
     read.csv rect resid runif sd title var weights wilcox.test
     write.table
    Consider adding
     importFrom("grDevices", "chull", "col2rgb")
     importFrom("graphics", "abline", "dotchart", "legend", "par",
     "polygon", "rect", "title")
     importFrom("stats", "approx", "approxfun", "binomial", "chisq.test",
     "cor", "cor.test", "ecdf", "fitted", "glm", "kmeans", "lm",
     "loess", "mahalanobis", "median", "na.omit", "pchisq",
     "pnorm", "poisson", "ppoints", "resid", "runif", "sd",
     "var", "weights", "wilcox.test")
     importFrom("utils", "browseURL", "data", "download.file",
     "flush.console", "packageDescription", "read.csv",
     "write.table")
    to your NAMESPACE.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0-12
Flags: --no-build-vignettes
Check: data for non-ASCII characters
Result: NOTE
     Note: found 106 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-patched-solaris-x86

Version: 1.0-12
Flags: --no-build-vignettes
Check: R code for possible problems
Result: NOTE
    circles,SpatialPoints: no visible binding for global variable ‘r’
    Undefined global functions or variables:
     r
Flavor: r-devel-osx-x86_64-clang

Version: 1.0-12
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
    circles,SpatialPoints : .local: no visible binding for global variable
     ‘r’
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0-12
Flags: --no-vignettes
Check: data for non-ASCII characters
Result: NOTE
     Note: found 106 marked UTF-8 strings
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0-12
Flags: --no-build-vignettes
Check: R code for possible problems
Result: NOTE
    circles,SpatialPoints : .local: no visible binding for global variable
     ‘r’
Flavor: r-patched-solaris-x86

Version: 1.0-12
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘rgdal’ ‘rgeos’
Flavor: r-release-osx-x86_64-mavericks

Version: 1.0-12
Check: data for non-ASCII characters
Result: NOTE
     Note: found 106 marked UTF-8 strings
Flavor: r-release-osx-x86_64-mavericks

Version: 1.0-12
Check: running R code from vignettes
Result: WARN
    Errors in running code in vignettes:
    when running code in ‘sdm.Rnw’
     ...
    
    > x <- circles(ac, d = 50000, lonlat = TRUE)
    Loading required namespace: rgeos
    Failed with error: ‘there is no package called ‘rgeos’’
    
    > library(rgeos)
    
     When sourcing ‘sdm.R’:
    Error: there is no package called ‘rgeos’
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 1.0-12
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: raster
    Loading required package: sp
    Loading required namespace: gbm
    Warning in persp.default(x = x.var, y = y.var, z = pred.matrix, zlim = z.range, :
     surface extends beyond the box
    Loading required package: survival
    Loading required package: lattice
    Loading required package: splines
    Loading required package: parallel
    Loaded gbm 2.1.1
    Checking rgeos availability: FALSE
     Note: when rgeos is not available, polygon geometry computations in maptools depend on gpclib,
     which has a restricted licence. It is disabled by default;
     to enable gpclib, type gpclibPermit()
    Loading required namespace: XML
    Loading required namespace: rgeos
    Failed with error: ‘there is no package called ‘rgeos’’
    
    Error: processing vignette 'sdm.Rnw' failed with diagnostics:
     chunk 24 (label = sdm18)
    Error in library(rgeos) : there is no package called ‘rgeos’
    Execution halted
Flavor: r-release-osx-x86_64-mavericks