CRAN Package Check Results for Package biomod2

Last updated on 2015-07-04 03:48:01.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.1-64 5.38 87.30 92.68 NOTE
r-devel-linux-x86_64-debian-gcc 3.1-64 4.79 83.47 88.26 NOTE
r-devel-linux-x86_64-fedora-clang 3.1-64 182.23 NOTE
r-devel-linux-x86_64-fedora-gcc 3.1-64 172.86 NOTE
r-devel-osx-x86_64-clang 3.1-64 148.38 NOTE
r-devel-windows-ix86+x86_64 3.1-64 15.00 119.00 134.00 NOTE
r-patched-linux-x86_64 3.1-64 4.86 83.66 88.52 NOTE
r-patched-solaris-sparc 3.1-64 1053.00 NOTE
r-patched-solaris-x86 3.1-64 228.50 NOTE
r-release-linux-x86_64 3.1-64 4.87 84.56 89.42 NOTE
r-release-osx-x86_64-mavericks 3.1-64 NOTE
r-release-windows-ix86+x86_64 3.1-64 22.00 123.00 145.00 NOTE
r-oldrel-windows-ix86+x86_64 3.1-64 22.00 167.00 189.00 NOTE

Check Details

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-clang, 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: Error while checking: invalid ‘envir’ argument
    .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: Error while checking: invalid ‘envir’ argument
    .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: Error while checking: invalid ‘envir’ argument
    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’
    Undefined global functions or variables:
     abline as.formula axis colorRampPalette colors combn cor dev.new
     dev.off glm gray jpeg layout legend median na.omit par pdf plot.new
     png points polygon postscript qt rainbow read.csv rug sd terms tiff
     write.table
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

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: Error while checking: invalid 'envir' argument
    .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: Error while checking: invalid 'envir' argument
    .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: Error while checking: invalid 'envir' argument
    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 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 qt rainbow read.csv rug
     scaled.models sd terms tiff write.table
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

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
Flavor: r-devel-windows-ix86+x86_64