CRAN Package Check Results for Package biomod2

Last updated on 2016-02-08 03:46:42.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-gcc 3.1-64 4.51 85.39 89.90 WARN
r-devel-linux-x86_64-fedora-clang 3.1-64 173.95 WARN
r-devel-linux-x86_64-fedora-gcc 3.1-64 168.08 WARN
r-devel-osx-x86_64-clang 3.1-64 179.89 WARN
r-devel-windows-ix86+x86_64 3.1-64 23.00 140.00 163.00 WARN
r-patched-linux-x86_64 3.1-64 4.88 89.34 94.22 WARN
r-patched-solaris-sparc 3.1-64 1076.80 WARN
r-patched-solaris-x86 3.1-64 221.90 WARN
r-release-linux-x86_64 3.1-64 5.11 89.06 94.17 WARN
r-release-osx-x86_64-mavericks 3.1-64 NOTE
r-release-windows-ix86+x86_64 3.1-64 19.00 201.00 220.00 WARN
r-oldrel-windows-ix86+x86_64 3.1-64 32.00 236.00 268.00 WARN

Check Details

Version: 3.1-64
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘biomod2’
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-windows-ix86+x86_64

Version: 3.1-64
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘gam’ ‘mgcv’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 3.1-64
Check: R code for possible problems
Result: NOTE
    .BIOMOD_FormatingData.check.args: no visible global function definition
     for ‘na.omit’
    .Biomod.Models: no visible global function definition for ‘glm’
    .Biomod.Models: no visible global function definition for ‘read.csv’
    .Biomod.Models: no visible global function definition for ‘na.omit’
    .Biomod.Models.loop: no visible global function definition for
     ‘na.omit’
    .Prepare.Maxent.WorkDir: no visible global function definition for
     ‘write.table’
    .Rescaler5: no visible global function definition for ‘glm’
    .Rescaler5: no visible global function definition for ‘binomial’
    .Rescaler5: no visible binding for global variable ‘probit’
    .predict.EMci_biomod2_model.RasterStack: no visible binding for global
     variable ‘sd’
    .predict.EMci_biomod2_model.RasterStack: no visible global function
     definition for ‘qt’
    .predict.EMci_biomod2_model.data.frame: no visible binding for global
     variable ‘sd’
    .predict.EMci_biomod2_model.data.frame: no visible global function
     definition for ‘qt’
    .predict.EMmedian_biomod2_model.RasterStack: no visible binding for
     global variable ‘median’
    .predict.EMmedian_biomod2_model.data.frame: no visible binding for
     global variable ‘median’
    .scaling_model: no visible global function definition for ‘glm’
    .scaling_model: no visible global function definition for ‘binomial’
    .scaling_model: no visible binding for global variable ‘probit’
    .scope2: no visible global function definition for ‘as.formula’
    .scope2: no visible global function definition for ‘terms’
    BIOMOD_EnsembleModeling: no visible global function definition for
     ‘na.omit’
    BIOMOD_ModelingOptions: no visible global function definition for
     ‘binomial’
    CustomIndexMaker: no visible global function definition for ‘read.csv’
    Find.Optim.Stat: no visible global function definition for ‘median’
    ProbDensFunc: no visible global function definition for ‘pdf’
    ProbDensFunc: no visible global function definition for ‘jpeg’
    ProbDensFunc: no visible global function definition for ‘tiff’
    ProbDensFunc: no visible global function definition for ‘postscript’
    ProbDensFunc: no visible global function definition for ‘png’
    ProbDensFunc: no visible global function definition for ‘dev.new’
    ProbDensFunc: no visible global function definition for ‘par’
    ProbDensFunc: no visible global function definition for ‘colors’
    ProbDensFunc: no visible global function definition for ‘legend’
    ProbDensFunc: no visible global function definition for ‘abline’
    ProbDensFunc: no visible global function definition for
     ‘colorRampPalette’
    ProbDensFunc: no visible global function definition for ‘dev.off’
    level.plot: no visible global function definition for ‘gray’
    level.plot: no visible global function definition for ‘rainbow’
    level.plot: no visible global function definition for ‘colors’
    level.plot: no visible global function definition for ‘pdf’
    level.plot: no visible global function definition for ‘jpeg’
    level.plot: no visible global function definition for ‘tiff’
    level.plot: no visible global function definition for ‘postscript’
    level.plot: no visible global function definition for ‘layout’
    level.plot: no visible global function definition for ‘points’
    level.plot: no visible global function definition for ‘par’
    level.plot: no visible global function definition for ‘polygon’
    level.plot: no visible global function definition for ‘legend’
    level.plot: no visible global function definition for ‘dev.off’
    makeFormula: no visible global function definition for ‘combn’
    makeFormula: no visible global function definition for ‘as.formula’
    models_scores_graph : <anonymous> : <anonymous>: no visible global
     function definition for ‘sd’
    multiple.plot : pbox: no visible global function definition for
     ‘polygon’
    multiple.plot: no visible global function definition for ‘pdf’
    multiple.plot: no visible global function definition for ‘jpeg’
    multiple.plot: no visible global function definition for ‘tiff’
    multiple.plot: no visible global function definition for ‘postscript’
    multiple.plot: no visible global function definition for ‘dev.new’
    multiple.plot: no visible global function definition for ‘layout’
    multiple.plot: no visible global function definition for ‘par’
    multiple.plot: no visible global function definition for ‘dev.off’
    response.plot2: no visible global function definition for ‘median’
    response.plot2: no visible global function definition for ‘pdf’
    response.plot2: no visible global function definition for ‘jpeg’
    response.plot2: no visible global function definition for ‘tiff’
    response.plot2: no visible global function definition for ‘postscript’
    response.plot2: no visible global function definition for ‘layout’
    response.plot2: no visible global function definition for ‘par’
    response.plot2: no visible global function definition for ‘polygon’
    response.plot2: no visible global function definition for ‘rug’
    response.plot2: no visible global function definition for ‘axis’
    response.plot2: no visible global function definition for ‘points’
    response.plot2: no visible global function definition for ‘plot.new’
    response.plot2: no visible global function definition for
     ‘colorRampPalette’
    response.plot2: no visible global function definition for ‘dev.off’
    variables_importance: no visible global function definition for ‘cor’
    .Prepare.Maxent.Proj.WorkDir,data.frame: no visible global function
     definition for ‘write.table’
    .transform.outputs,list: missing arguments not allowed in calls to ‘c’
    .transform.outputs,list: no visible global function definition for
     ‘na.omit’
    Projection,ANY-ANY-data.frame: no visible binding for global variable
     ‘kept.models.name’
    Projection,ANY-ANY-data.frame: no visible binding for global variable
     ‘scaled.models’
    Projection,ANY-ANY-data.frame: no visible binding for global variable
     ‘models.options’
    Projection,ANY-ANY-data.frame : <anonymous> : <anonymous>: no visible
     binding for global variable ‘models.evaluation’
    getModelsPredictionEval,BIOMOD.models.out: no visible binding for
     global variable ‘models.prediction.eval’
    getProjection,BIOMOD.projection.out: no visible binding for global
     variable ‘bm_proj’
    plot,BIOMOD.formated.data-missing: no visible global function
     definition for ‘points’
    plot,BIOMOD.formated.data.PA-missing: no visible global function
     definition for ‘par’
    plot,BIOMOD.formated.data.PA-missing: no visible global function
     definition for ‘points’
    plot,BIOMOD.projection.out-missing: no visible global function
     definition for ‘colorRampPalette’
    sre.pseudo.abs.selection,ANY-RasterStack: no visible global function
     definition for ‘na.omit’
    Undefined global functions or variables:
     abline as.formula axis binomial bm_proj colorRampPalette colors combn
     cor dev.new dev.off glm gray jpeg kept.models.name layout legend
     median models.evaluation models.options models.prediction.eval
     na.omit par pdf plot.new png points polygon postscript probit qt
     rainbow read.csv rug scaled.models sd terms tiff write.table
    Consider adding
     importFrom("grDevices", "colorRampPalette", "colors", "dev.new",
     "dev.off", "gray", "jpeg", "pdf", "png", "postscript",
     "rainbow", "tiff")
     importFrom("graphics", "abline", "axis", "layout", "legend", "par",
     "plot.new", "points", "polygon", "rug")
     importFrom("stats", "as.formula", "binomial", "cor", "glm", "median",
     "na.omit", "qt", "sd", "terms")
     importFrom("utils", "combn", "read.csv", "write.table")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64

Version: 3.1-64
Check: R code for possible problems
Result: NOTE
    .transform.outputs,list : .local: missing arguments not allowed in
     calls to ‘c’
    Projection,ANY-ANY-data.frame : .local: no visible binding for global
     variable ‘kept.models.name’
    Projection,ANY-ANY-data.frame : .local: no visible binding for global
     variable ‘scaled.models’
    Projection,ANY-ANY-data.frame : .local: no visible binding for global
     variable ‘models.options’
    Projection,ANY-ANY-data.frame : .local : <anonymous> : <anonymous>: no
     visible binding for global variable ‘models.evaluation’
    getModelsPredictionEval,BIOMOD.models.out : .local: no visible binding
     for global variable ‘models.prediction.eval’
    getProjection,BIOMOD.projection.out : .local: no visible binding for
     global variable ‘bm_proj’
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 3.1-64
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: replacing previous import by ‘randomForest::margin’ when loading ‘biomod2’
Flavors: r-release-linux-x86_64, r-oldrel-windows-ix86+x86_64