BioC 3.5: CHECK report for limmaGUI on toluca2

Package: limmaGUI

Version: 1.51.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings limmaGUI_1.51.0.tar.gz

StartedAt: 2017-04-23 05:52:50 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 05:55:27 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 156.6 seconds

RetCode: 0

Status:  OK

CheckDir: limmaGUI.Rcheck

Warnings: 0

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings limmaGUI_1.51.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/limmaGUI.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limmaGUI/DESCRIPTION’ ... OK
* this is package ‘limmaGUI’ version ‘1.51.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘limmaGUI’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AboutNormalization: no visible binding for global variable
  ‘.limmaGUIglobals’
BChelp: no visible global function definition for ‘help’
ChooseContrastsParameterization: no visible binding for global variable
  ‘limmaGUIenvironment’
ChooseContrastsParameterization: no visible binding for global variable
  ‘ParameterizationNamesVec’
ChooseContrastsParameterization: no visible binding for global variable
  ‘parameterizationIndex’
ChooseContrastsParameterization: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseContrastsParameterization : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
ChooseContrastsParameterization : onCancel: no visible binding for
  global variable ‘.limmaGUIglobals’
ChooseContrastsParameterization : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
ChooseEbayesStatistic: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseEbayesStatistic : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseEbayesStatistic : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
ChooseEbayesStatistic : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
ChooseParameterization: no visible binding for global variable
  ‘limmaGUIenvironment’
ChooseParameterization: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseParameterization : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseParameterization : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
ChooseParameterization : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
ChoosePlotSymbolByClicking: no visible binding for global variable
  ‘.limmaGUIglobals’
ChoosePlotSymbolByClicking : ChoosePlotSymbol: no visible global
  function definition for ‘par’
ChoosePlotSymbolByClicking : ChoosePlotSymbol: no visible global
  function definition for ‘plot’
ChoosePlotSymbolByClicking : ChoosePlotSymbol: no visible global
  function definition for ‘abline’
ChoosePlotSymbolByClicking : ChoosePlotSymbol: no visible global
  function definition for ‘points’
ChoosePlotSymbolByClicking : ChoosePlotSymbol: no visible global
  function definition for ‘text’
ChoosePlotSymbolByClicking : LeftClick: no visible binding for global
  variable ‘.limmaGUIglobals’
ChoosePlotSymbolByClicking : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
ChoosePlotSymbolByClicking : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
ChooseSpotType: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseSpotType : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseSpotType : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseSpotType : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
ComputeContrasts: no visible binding for global variable
  ‘limmaGUIenvironment’
ComputeContrasts: no visible binding for global variable
  ‘.limmaGUIglobals’
ComputeLinearModelFit: no visible binding for global variable
  ‘limmaGUIenvironment’
ComputeLinearModelFit: no visible binding for global variable
  ‘.limmaGUIglobals’
ComputeLinearModelFit : GetDupCor: no visible binding for global
  variable ‘.limmaGUIglobals’
ComputeLinearModelFit : GetDupCor : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
ComputeLinearModelFit : GetDupCor : onCancel: no visible binding for
  global variable ‘.limmaGUIglobals’
ComputeLinearModelFit : GetDupCor : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
CreateNewParameterization: no visible binding for global variable
  ‘limmaGUIenvironment’
CreateNewParameterization: no visible binding for global variable
  ‘.limmaGUIglobals’
CreateTreeAndList: no visible binding for global variable
  ‘limmaGUIenvironment’
CreateTreeAndList: no visible binding for global variable
  ‘.limmaGUIglobals’
DeleteContrastsParameterization: no visible binding for global variable
  ‘limmaGUIenvironment’
DeleteContrastsParameterization: no visible binding for global variable
  ‘.limmaGUIglobals’
DeleteParameterization: no visible binding for global variable
  ‘limmaGUIenvironment’
DeleteParameterization: no visible binding for global variable
  ‘.limmaGUIglobals’
DupCorBoxPlot: no visible binding for global variable
  ‘limmaGUIenvironment’
DupCorBoxPlot: no visible binding for global variable
  ‘.limmaGUIglobals’
DupCorBoxPlot : plotDupCor: no visible global function definition for
  ‘par’
DupCorBoxPlot : plotDupCor: no visible global function definition for
  ‘boxplot’
DupCorBoxPlot : plotDupCor: no visible global function definition for
  ‘title’
DupCorBoxPlot: no visible global function definition for ‘plot.new’
ExportAvalues: no visible binding for global variable
  ‘limmaGUIenvironment’
ExportAvalues: no visible global function definition for ‘write.table’
ExportHTMLreport: no visible binding for global variable
  ‘limmaGUIenvironment’
ExportHTMLreport: no visible binding for global variable
  ‘.limmaGUIglobals’
ExportHTMLreport : plotFunction: no visible global function definition
  for ‘plot.scale.box’
ExportHTMLreport: no visible global function definition for
  ‘write.table’
ExportHTMLreport : AvgMAPlotFunction: no visible global function
  definition for ‘plot’
ExportHTMLreport : AvgMAPlotFunction: no visible global function
  definition for ‘text’
ExportHTMLreport : AvgMAPlotFunction2: no visible global function
  definition for ‘plot’
ExportHTMLreport : AvgMAPlotFunction2: no visible global function
  definition for ‘text’
ExportHTMLreport : plotEbayesBoxPlot: no visible global function
  definition for ‘par’
ExportHTMLreport : plotEbayesBoxPlot: no visible global function
  definition for ‘grid’
ExportMvalues: no visible binding for global variable
  ‘limmaGUIenvironment’
ExportMvalues: no visible global function definition for ‘write.table’
GetBackgroundCorrectionMethod: no visible binding for global variable
  ‘.limmaGUIglobals’
GetBackgroundCorrectionMethod: no visible binding for global variable
  ‘limmaGUIenvironment’
GetBackgroundCorrectionMethod : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetBackgroundCorrectionMethod : onOK: no visible binding for global
  variable ‘limmaGUIenvironment’
GetBackgroundCorrectionMethod : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
GetBetweenArrayNormalizationMethod: no visible binding for global
  variable ‘.limmaGUIglobals’
GetBetweenArrayNormalizationMethod: no visible binding for global
  variable ‘limmaGUIenvironment’
GetBetweenArrayNormalizationMethod : onOK: no visible binding for
  global variable ‘limmaGUIenvironment’
GetBetweenArrayNormalizationMethod : onOK: no visible binding for
  global variable ‘.limmaGUIglobals’
GetBetweenArrayNormalizationMethod : <anonymous>: no visible binding
  for global variable ‘.limmaGUIglobals’
GetBetweenArrayNormalizationMethod : <anonymous>: no visible global
  function definition for ‘help’
GetCoef: no visible binding for global variable ‘limmaGUIenvironment’
GetCoef: no visible binding for global variable ‘.limmaGUIglobals’
GetCoef : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetCoef : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetCoef : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetComponentsToExportInHTMLreport: no visible binding for global
  variable ‘limmaGUIenvironment’
GetComponentsToExportInHTMLreport: no visible binding for global
  variable ‘.limmaGUIglobals’
GetComponentsToExportInHTMLreport : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetComponentsToExportInHTMLreport : onCancel: no visible binding for
  global variable ‘.limmaGUIglobals’
GetComponentsToExportInHTMLreport : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
GetContrastsParameterizationName: no visible binding for global
  variable ‘.limmaGUIglobals’
GetContrastsParameterizationName : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetContrastsParameterizationName : onCancel: no visible binding for
  global variable ‘.limmaGUIglobals’
GetContrastsParameterizationName : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
GetContrastsParameterizationNames: no visible binding for global
  variable ‘limmaGUIenvironment’
GetDEcutoff: no visible binding for global variable ‘.limmaGUIglobals’
GetDEcutoff : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetDEcutoff : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetDEcutoff : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetDesignOrContrasts: no visible binding for global variable
  ‘limmaGUIenvironment’
GetDesignOrContrasts: no visible binding for global variable
  ‘.limmaGUIglobals’
GetDesignOrContrasts : GetDesignOrContrastsTable: no visible binding
  for global variable ‘.limmaGUIglobals’
GetDesignOrContrasts : GetDesignOrContrastsTable : onOK: no visible
  binding for global variable ‘limmaGUIenvironment’
GetDesignOrContrasts : GetDesignOrContrastsTable : onOK: no visible
  binding for global variable ‘.limmaGUIglobals’
GetDesignOrContrasts : GetDesignOrContrastsTable : onCancel: no visible
  binding for global variable ‘.limmaGUIglobals’
GetDesignOrContrasts : GetDesignOrContrastsTable :
  openDesignOrContrastsMatrixFile: no visible global function
  definition for ‘read.table’
GetDesignOrContrasts : GetDesignOrContrastsTable :
  saveDesignOrContrastsMatrixFile: no visible global function
  definition for ‘write.table’
GetDesignOrContrasts : GetDesignOrContrastsTable : <anonymous>: no
  visible binding for global variable ‘.limmaGUIglobals’
GetDesignOrContrasts : OnAdvanced: no visible binding for global
  variable ‘limmaGUIenvironment’
GetDesignOrContrasts : OnAdvanced: no visible binding for global
  variable ‘.limmaGUIglobals’
GetDesignOrContrasts : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetDesignOrContrasts : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetDesignOrContrasts : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetGeneLabelsOptions: no visible binding for global variable
  ‘.limmaGUIglobals’
GetGeneLabelsOptions : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetGeneLabelsOptions : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetGeneLabelsOptions : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetGenePixFlagWeightings: no visible binding for global variable
  ‘.limmaGUIglobals’
GetGenePixFlagWeightings : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetGenePixFlagWeightings : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetGenePixFlagWeightings : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetImageAnalysisColumnHeadings: no visible binding for global variable
  ‘.limmaGUIglobals’
GetImageAnalysisColumnHeadings : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetImageAnalysisColumnHeadings : onCancel: no visible binding for
  global variable ‘.limmaGUIglobals’
GetImageAnalysisColumnHeadings : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
GetImageProcessingFileType: no visible binding for global variable
  ‘.limmaGUIglobals’
GetImageProcessingFileType: no visible binding for global variable
  ‘limmaGUIenvironment’
GetImageProcessingFileType : onOther: no visible binding for global
  variable ‘.limmaGUIglobals’
GetImageProcessingFileType : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetImageProcessingFileType : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetImageProcessingFileType : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetJpegOrPngParams: no visible binding for global variable
  ‘.limmaGUIglobals’
GetJpegOrPngParams : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetJpegOrPngParams : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetJpegOrPngParams : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetJpegOrPngX11Params: no visible binding for global variable
  ‘.limmaGUIglobals’
GetJpegOrPngX11Params : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetJpegOrPngX11Params : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetJpegOrPngX11Params : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetLowessType: no visible binding for global variable
  ‘.limmaGUIglobals’
GetLowessType : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetLowessType : onHelp: no visible global function definition for
  ‘help’
GetLowessType : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetNEWxlim: no visible binding for global variable ‘.limmaGUIglobals’
GetNEWxlim : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetNEWxlim : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetNEWxlim : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetNormexpOffsetValue: no visible binding for global variable
  ‘.limmaGUIglobals’
GetNormexpOffsetValue : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetNormexpOffsetValue : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetNormexpOffsetValue : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetNumParametersNoTargets: no visible binding for global variable
  ‘limmaGUIenvironment’
GetNumParametersNoTargets: no visible binding for global variable
  ‘.limmaGUIglobals’
GetNumParametersNoTargets : onOK: no visible binding for global
  variable ‘limmaGUIenvironment’
GetNumParametersNoTargets : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetNumParametersNoTargets : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetNumParametersNoTargets : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetPValueCutoff: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPValueCutoff : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPValueCutoff : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPValueCutoff : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetParameterNames: no visible binding for global variable
  ‘limmaGUIenvironment’
GetParameterizationName: no visible binding for global variable
  ‘.limmaGUIglobals’
GetParameterizationName : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetParameterizationName : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetParameterizationName : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetParametersAndOrContrasts: no visible binding for global variable
  ‘limmaGUIenvironment’
GetParametersAndOrContrasts: no visible binding for global variable
  ‘.limmaGUIglobals’
GetParametersAndOrContrasts : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetParametersAndOrContrasts : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetParametersAndOrContrasts : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
GetPlotLabels: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotLabels : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotLabels : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotLabels : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotSize: no visible binding for global variable ‘.limmaGUIglobals’
GetPlotSize : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotSize : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotSize : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotTitle: no visible binding for global variable ‘.limmaGUIglobals’
GetPlotTitle : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotTitle : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotTitle : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetReducedDuplicateSpacing: no visible binding for global variable
  ‘limmaGUIenvironment’
GetSlideNum: no visible binding for global variable
  ‘limmaGUIenvironment’
GetSlideNum: no visible binding for global variable ‘.limmaGUIglobals’
GetSlideNum : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetSlideNum : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetSlideNum : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetSpotTypesForLinearModel: no visible binding for global variable
  ‘limmaGUIenvironment’
GetSpotTypesForLinearModel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetSpotTypesForLinearModel : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetSpotTypesForLinearModel : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetSpotTypesForLinearModel : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetSpotTypesIncludedNames: no visible binding for global variable
  ‘limmaGUIenvironment’
GetWithinArrayNormalizationMethod: no visible binding for global
  variable ‘.limmaGUIglobals’
GetWithinArrayNormalizationMethod: no visible binding for global
  variable ‘limmaGUIenvironment’
GetWithinArrayNormalizationMethod : onOK: no visible binding for global
  variable ‘limmaGUIenvironment’
GetWithinArrayNormalizationMethod : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetWithinArrayNormalizationMethod : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
GetWithinArrayNormalizationMethod : <anonymous>: no visible global
  function definition for ‘help’
GetWtAreaParams: no visible binding for global variable
  ‘.limmaGUIglobals’
GetWtAreaParams : onOK: no visible binding for global variable
  ‘limmaGUIenvironment’
GetWtAreaParams : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetWtAreaParams : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetWtAreaParams : <anonymous>: no visible global function definition
  for ‘help’
GetWtAreaParams : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetlimmaDataSetName: no visible binding for global variable
  ‘limmaGUIenvironment’
GetlimmaDataSetName: no visible binding for global variable
  ‘.limmaGUIglobals’
GetlimmaDataSetName : onOK: no visible binding for global variable
  ‘limmaGUIenvironment’
GetlimmaDataSetName : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetlmFitMethod: no visible binding for global variable
  ‘.limmaGUIglobals’
GetlmFitMethod: no visible binding for global variable
  ‘limmaGUIenvironment’
GetlmFitMethod : onOK: no visible binding for global variable
  ‘limmaGUIenvironment’
GetlmFitMethod : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetlmFitMethod : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
HTMLplotUsingFunction: no visible binding for global variable
  ‘.HTML.file’
HTMLplotUsingFunction: no visible global function definition for
  ‘dev.print’
HTMLplotUsingFunction: no visible binding for global variable ‘png’
HTMLplotUsingFunction: no visible global function definition for
  ‘bitmap’
HTMLplotUsingFunction: no visible global function definition for ‘png’
HTMLplotUsingFunction: no visible global function definition for
  ‘dev.off’
HTMLplotUsingFunction: no visible binding for global variable ‘jpeg’
HTMLplotUsingFunction: no visible global function definition for ‘jpeg’
HTMLplotUsingFunction: no visible binding for global variable ‘gif’
HeatDiagramDialog: no visible binding for global variable
  ‘.limmaGUIglobals’
HeatDiagramDialog : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
HeatDiagramDialog : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
HeatDiagramDialog : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
HeatDiagramPlot: no visible binding for global variable
  ‘limmaGUIenvironment’
HeatDiagramPlot: no visible binding for global variable
  ‘.limmaGUIglobals’
HeatDiagramPlot : plotHD: no visible global function definition for
  ‘par’
HeatDiagramPlot : plotHD: no visible global function definition for
  ‘title’
HeatDiagramPlot: no visible global function definition for ‘plot.new’
HowManyDups: no visible binding for global variable
  ‘limmaGUIenvironment’
HowManyDups: no visible binding for global variable ‘.limmaGUIglobals’
HowManyDups : onOK: no visible binding for global variable
  ‘limmaGUIenvironment’
HowManyDups : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
HowManyDups : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
HowManyDups : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
ImageArrayPlot: no visible binding for global variable
  ‘limmaGUIenvironment’
ImageArrayPlot: no visible binding for global variable
  ‘.limmaGUIglobals’
ImageArrayPlot : plotImageArray: no visible global function definition
  for ‘par’
ImageArrayPlot : <anonymous>: no visible global function definition for
  ‘par’
ImageArrayPlot: no visible global function definition for ‘plot.new’
ImageArrayPlotDialog: no visible binding for global variable
  ‘limmaGUIenvironment’
ImageArrayPlotDialog: no visible binding for global variable
  ‘.limmaGUIglobals’
ImageArrayPlotDialog : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
ImageArrayPlotDialog : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
ImageArrayPlotDialog : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
ImportMA: no visible binding for global variable ‘limmaGUIenvironment’
ImportMA: no visible binding for global variable ‘.limmaGUIglobals’
ImportMA: no visible global function definition for ‘new’
ImportMADialog: no visible binding for global variable
  ‘.limmaGUIglobals’
ImportMADialog : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
ImportMADialog : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
ImportMADialog : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
InitNewParameterization: no visible binding for global variable
  ‘limmaGUIenvironment’
InitNewParameterization: no visible binding for global variable
  ‘.limmaGUIglobals’
LogOddsPlot: no visible binding for global variable
  ‘limmaGUIenvironment’
LogOddsPlot: no visible binding for global variable ‘.limmaGUIglobals’
LogOddsPlot : plotLogOdds: no visible global function definition for
  ‘par’
LogOddsPlot : plotLogOdds: no visible global function definition for
  ‘plot’
LogOddsPlot : plotLogOdds: no visible global function definition for
  ‘title’
LogOddsPlot : plotLogOdds: no visible global function definition for
  ‘text’
LogOddsPlot: no visible global function definition for ‘plot.new’
MAPlot: no visible binding for global variable ‘limmaGUIenvironment’
MAPlot: no visible binding for global variable ‘.limmaGUIglobals’
MAPlot: no visible global function definition for ‘new’
MAPlot : plotFun: no visible global function definition for ‘par’
MAPlot : plotFun: ... may be used in an incorrect context:
  plotPrintTipLoess(RG, maLayout, array = slidenum, span = 0.4, ...)
MAPlot : plotFun: no visible global function definition for ‘plot’
MAPlot : plotFun: no visible global function definition for ‘plot.mva’
MAPlot : plotFun: no visible global function definition for ‘title’
MAPlot: no visible global function definition for ‘plot.new’
MAPlotAvg: no visible binding for global variable ‘limmaGUIenvironment’
MAPlotAvg: no visible binding for global variable ‘.limmaGUIglobals’
MAPlotAvg : plotAvgMA: no visible global function definition for ‘par’
MAPlotAvg : plotAvgMA: no visible global function definition for ‘plot’
MAPlotAvg : plotAvgMA: no visible global function definition for
  ‘title’
MAPlotAvg : plotAvgMA: no visible global function definition for ‘text’
MAPlotAvg : plotAvgMA: no visible binding for global variable
  ‘limmaGUIenvironment’
MAPlotAvg : plotAvgMA: no visible global function definition for
  ‘points’
MAPlotAvg : plotAvgMA: no visible global function definition for
  ‘legend’
MAPlotAvg: no visible global function definition for ‘plot.new’
MBoxPlot: no visible binding for global variable ‘limmaGUIenvironment’
MBoxPlot: no visible binding for global variable ‘.limmaGUIglobals’
MBoxPlot : plot.scale.box0: no visible global function definition for
  ‘par’
MBoxPlot : plot.scale.box0: no visible global function definition for
  ‘plot.scale.box’
MBoxPlot : plot.scale.box0: no visible global function definition for
  ‘rainbow’
MBoxPlot : plot.scale.box0: no visible global function definition for
  ‘title’
MBoxPlot : plot.scale.box0: no visible global function definition for
  ‘boxplot’
MBoxPlot : plot.scale.box0: no visible global function definition for
  ‘abline’
MBoxPlot: no visible global function definition for ‘plot.new’
MMPlot: no visible binding for global variable ‘limmaGUIenvironment’
MMPlot: no visible binding for global variable ‘.limmaGUIglobals’
MMPlot : plotMM: no visible global function definition for ‘par’
MMPlot : plotMM: no visible global function definition for ‘plot’
MMPlot : plotMM: no visible global function definition for ‘title’
MMPlot : plotMM: no visible global function definition for ‘points’
MMPlot: no visible global function definition for ‘plot.new’
NewLimmaFile: no visible binding for global variable
  ‘limmaGUIenvironment’
NormalizeNow: no visible binding for global variable
  ‘limmaGUIenvironment’
NormalizeNow: no visible binding for global variable ‘.limmaGUIglobals’
OpenALimmaFile: no visible binding for global variable
  ‘limmaGUIenvironment’
OpenALimmaFile: no visible global function definition for ‘new’
OpenGALFile: no visible binding for global variable
  ‘limmaGUIenvironment’
OpenGALandTargetsandSpotTypesfiles : onOK: no visible binding for
  global variable ‘limmaGUIenvironment’
OpenGALandTargetsandSpotTypesfiles : onHelp: no visible global function
  definition for ‘browseURL’
OpenSpotTypesFile: no visible binding for global variable
  ‘limmaGUIenvironment’
OpenSpotTypesFile: no visible global function definition for
  ‘read.table’
OpenTargetsFile: no visible binding for global variable
  ‘limmaGUIenvironment’
OpenTargetsFile: no visible global function definition for ‘read.table’
PlotOptions: no visible binding for global variable ‘.limmaGUIglobals’
PlotOptions : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
PlotOptions : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
PrintTipGroupMAPlot: no visible binding for global variable
  ‘limmaGUIenvironment’
PrintTipGroupMAPlot: no visible binding for global variable
  ‘.limmaGUIglobals’
PrintTipGroupMAPlot : PrintTipGroupPlot: no visible global function
  definition for ‘par’
PrintTipGroupMAPlot: no visible global function definition for
  ‘plot.new’
QQTplot: no visible binding for global variable ‘limmaGUIenvironment’
QQTplot: no visible binding for global variable ‘.limmaGUIglobals’
QQTplot : plotQQT: no visible global function definition for ‘par’
QQTplot : plotQQT: no visible global function definition for ‘abline’
QQTplot: no visible global function definition for ‘plot.new’
ReadImageProcessingFiles: no visible binding for global variable
  ‘limmaGUIenvironment’
ReadImageProcessingFiles: no visible binding for global variable
  ‘.limmaGUIglobals’
ReadImageProcessingFiles: no visible global function definition for
  ‘read.table’
SaveAsLimmaFile: no visible binding for global variable
  ‘limmaGUIenvironment’
SaveAsLimmaFile: no visible binding for global variable
  ‘.limmaGUIglobals’
SaveGraphAsJpeg: no visible global function definition for ‘bitmap’
SaveGraphAsJpeg: no visible global function definition for ‘jpeg’
SaveGraphAsJpeg: no visible global function definition for ‘dev.off’
SaveGraphAsPDF: no visible global function definition for ‘pdf’
SaveGraphAsPDF: no visible global function definition for ‘dev.off’
SaveGraphAsPNG: no visible global function definition for ‘bitmap’
SaveGraphAsPNG: no visible global function definition for ‘png’
SaveGraphAsPNG: no visible global function definition for ‘dev.off’
SaveGraphAsPostscript: no visible global function definition for
  ‘postscript’
SaveGraphAsPostscript: no visible global function definition for
  ‘dev.off’
SaveLimmaFile: no visible binding for global variable
  ‘limmaGUIenvironment’
SaveLimmaFile: no visible binding for global variable
  ‘.limmaGUIglobals’
SelectPlotSymbols: no visible binding for global variable
  ‘.limmaGUIglobals’
SelectPlotSymbols: no visible global function definition for ‘rgb’
SelectPlotSymbols: no visible global function definition for ‘col2rgb’
SelectPlotSymbols : onBrowse: no visible binding for global variable
  ‘.limmaGUIglobals’
SelectPlotSymbols : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
SelectPlotSymbols : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
SelectPlotSymbols : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
SetLayoutParameters: no visible binding for global variable
  ‘limmaGUIenvironment’
SetLayoutParameters: no visible binding for global variable
  ‘.limmaGUIglobals’
SetLayoutParameters : GetFromGAL: no visible binding for global
  variable ‘limmaGUIenvironment’
SetLayoutParameters : onOK: no visible binding for global variable
  ‘limmaGUIenvironment’
SetLayoutParameters : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
SetLayoutParameters : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
SetLayoutParameters : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
SetWD: no visible binding for global variable ‘.limmaGUIglobals’
TclRequire: no visible binding for global variable ‘.limmaGUIglobals’
TclRequire : onDestroy: no visible binding for global variable
  ‘.limmaGUIglobals’
TclRequire : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
TclRequire : onOK: no visible binding for global variable
  ‘limmaGUIenvironment’
UpDownOrBoth: no visible binding for global variable ‘.limmaGUIglobals’
UpDownOrBoth : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
UpDownOrBoth : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
UpdateSpotTypesStatus: no visible binding for global variable
  ‘limmaGUIenvironment’
VennDiagramPlot: no visible binding for global variable
  ‘limmaGUIenvironment’
VennDiagramPlot: no visible binding for global variable
  ‘.limmaGUIglobals’
VennDiagramPlot : plotVennDiagram: no visible global function
  definition for ‘par’
VennDiagramPlot: no visible global function definition for ‘plot.new’
ViewDesignOrContrastsMatrixAsPairs: no visible binding for global
  variable ‘limmaGUIenvironment’
ViewDesignOrContrastsMatrixAsPairs: no visible binding for global
  variable ‘.limmaGUIglobals’
ViewDesignOrContrastsMatrixAsPairs : onOK: no visible binding for
  global variable ‘.limmaGUIglobals’
ViewDesignOrContrastsMatrixAsPairs : <anonymous>: no visible binding
  for global variable ‘.limmaGUIglobals’
ViewDesignOrContrastsMatrixInTable: no visible binding for global
  variable ‘limmaGUIenvironment’
ViewDesignOrContrastsMatrixInTable: no visible binding for global
  variable ‘.limmaGUIglobals’
ViewDesignOrContrastsMatrixInTable : onClose: no visible binding for
  global variable ‘.limmaGUIglobals’
ViewDesignOrContrastsMatrixInTable : onSaveDesignOrContrastsMatrixAs:
  no visible global function definition for ‘write.table’
ViewDesignOrContrastsMatrixInTable : <anonymous>: no visible binding
  for global variable ‘.limmaGUIglobals’
ViewExistingContrastsParameterization: no visible binding for global
  variable ‘limmaGUIenvironment’
ViewExistingContrastsParameterization: no visible binding for global
  variable ‘.limmaGUIglobals’
ViewExistingParameterization: no visible binding for global variable
  ‘limmaGUIenvironment’
ViewExistingParameterization: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewRNATargets: no visible binding for global variable
  ‘limmaGUIenvironment’
ViewRNATargets: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewRNATargets : onClose: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewRNATargets : saveTargetsFile: no visible global function definition
  for ‘write.table’
ViewRNATargets : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewSpotTypes: no visible binding for global variable
  ‘limmaGUIenvironment’
ViewSpotTypes: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewSpotTypes : onUpdate: no visible binding for global variable
  ‘limmaGUIenvironment’
ViewSpotTypes : onUpdate: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewSpotTypes : onClose: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewSpotTypes : openSpotTypesFile: no visible global function
  definition for ‘read.table’
ViewSpotTypes : saveSpotTypesFile: no visible global function
  definition for ‘write.table’
ViewSpotTypes : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
WithinBetweenOrBoth: no visible binding for global variable
  ‘.limmaGUIglobals’
WithinBetweenOrBoth : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
WithinBetweenOrBoth : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
chooseDir: no visible binding for global variable ‘.limmaGUIglobals’
ebayesBoxPlots: no visible binding for global variable
  ‘limmaGUIenvironment’
ebayesBoxPlots: no visible binding for global variable
  ‘.limmaGUIglobals’
ebayesBoxPlots : plotEbayesBoxPlot: no visible global function
  definition for ‘par’
ebayesBoxPlots : plotEbayesBoxPlot: no visible global function
  definition for ‘grid’
ebayesBoxPlots: no visible binding for global variable
  ‘limmaDataSetNameText’
ebayesBoxPlots: no visible global function definition for ‘plot.new’
evalRcode: no visible binding for global variable ‘.limmaGUIglobals’
evalRcode : SaveRSourceFile: no visible global function definition for
  ‘tkputs’
evalRcode : runOverall: no visible binding for global variable
  ‘.limmaGUIglobals’
evalRcode : runOverall: no visible binding for global variable
  ‘limmaGUIenvironment’
evalRcode : runOverall: no visible global function definition for
  ‘plot.new’
evalRcode : runOverall : SaveTextResults: no visible global function
  definition for ‘tkputs’
evalRcode : MakeLimmaGUIMenu: no visible global function definition for
  ‘GetMenuName’
evalRcode : MakeLimmaGUIMenu: no visible global function definition for
  ‘addMenuItem’
evalRcode : HTMLhelp: no visible global function definition for
  ‘help.start’
imageplotlimmaGUI: no visible global function definition for ‘col2rgb’
imageplotlimmaGUI: no visible global function definition for ‘rgb’
imageplotlimmaGUI: no visible global function definition for ‘par’
imageplotlimmaGUI: no visible global function definition for ‘image’
imageplotlimmaGUI: no visible global function definition for ‘lines’
initGlobals: no visible binding for global variable
  ‘limmaGUIenvironment’
initGlobals: no visible global function definition for ‘new’
initGlobals: no visible binding for '<<-' assignment to
  ‘NEOffsetDefault’
initGlobals: no visible binding for global variable ‘NEOffsetDefault’
limmaGUI: no visible binding for global variable ‘limmaGUIenvironment’
limmaGUI: no visible binding for global variable ‘.limmaGUIglobals’
limmaGUI : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
limmaGUI: no visible global function definition for ‘read.table’
limmaGUIhelp: no visible global function definition for ‘browseURL’
limmaHelp: no visible global function definition for ‘browseURL’
lmFitMethodHelp: no visible global function definition for ‘help’
onDestroy: no visible binding for global variable ‘limmaGUIenvironment’
onExit: no visible binding for global variable ‘limmaGUIenvironment’
onExit: no visible binding for global variable ‘.limmaGUIglobals’
plotMAColorCoded: no visible binding for global variable
  ‘limmaGUIenvironment’
plotMAColorCoded: no visible binding for global variable
  ‘.limmaGUIglobals’
plotMAColorCoded : plotMA0: no visible global function definition for
  ‘par’
plotMAColorCoded : plotMA0: no visible global function definition for
  ‘title’
plotMAColorCoded: no visible global function definition for ‘plot.new’
read.marrayTools: no visible global function definition for
  ‘read.table’
read.marrayTools: no visible global function definition for ‘new’
showCitations: no visible global function definition for ‘citation’
showGAL: no visible binding for global variable ‘limmaGUIenvironment’
showGAL: no visible binding for global variable ‘.limmaGUIglobals’
showGAL: no visible global function definition for ‘write.table’
showGAL : SaveGAL: no visible global function definition for
  ‘write.table’
showTopTable: no visible binding for global variable
  ‘limmaGUIenvironment’
showTopTable: no visible binding for global variable ‘.limmaGUIglobals’
showTopTable : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
showTopTable : onHelp: no visible global function definition for ‘help’
showTopTable : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
showTopTable : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
showTopTable : SaveTopTable: no visible global function definition for
  ‘write.table’
showTopTable: no visible global function definition for ‘write.table’
vennDiagramlimmaGUI: no visible global function definition for ‘par’
vennDiagramlimmaGUI: no visible global function definition for ‘plot’
vennDiagramlimmaGUI: no visible global function definition for ‘lines’
vennDiagramlimmaGUI: no visible global function definition for ‘text’
vennDiagramlimmaGUI: no visible global function definition for ‘rect’
Undefined global functions or variables:
  .HTML.file .limmaGUIglobals GetMenuName NEOffsetDefault
  ParameterizationNamesVec abline addMenuItem bitmap boxplot browseURL
  citation col2rgb dev.off dev.print gif grid help help.start image
  jpeg legend limmaDataSetNameText limmaGUIenvironment lines new par
  parameterizationIndex pdf plot plot.mva plot.new plot.scale.box png
  points postscript rainbow read.table rect rgb text title tkputs
  write.table
Consider adding
  importFrom("grDevices", "bitmap", "col2rgb", "dev.off", "dev.print",
             "jpeg", "pdf", "png", "postscript", "rainbow", "rgb")
  importFrom("graphics", "abline", "boxplot", "grid", "image", "legend",
             "lines", "par", "plot", "plot.new", "points", "rect",
             "text", "title")
  importFrom("methods", "new")
  importFrom("utils", "browseURL", "citation", "help", "help.start",
             "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘LinModIntro.tex’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/limmaGUI.Rcheck/00check.log’
for details.

* installing *source* package ‘limmaGUI’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (limmaGUI)