##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:limmaGUI.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings limmaGUI_1.83.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/limmaGUI.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'limmaGUI/DESCRIPTION' ... OK
* this is package 'limmaGUI' version '1.83.0'
* 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 whether package 'limmaGUI' can be installed ... OK
* checking installed package size ... INFO
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
* 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 code 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 whether startup messages can be suppressed ... 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'
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 : 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'
ComputeContrasts: no visible global function definition for 'ebayes'
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'
ComputeLinearModelFit: no visible global function definition for
  'ebayes'
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'
ExportAvalues: no visible binding for global variable
  'limmaGUIenvironment'
ExportHTMLreport: no visible binding for global variable
  'limmaGUIenvironment'
ExportHTMLreport: no visible binding for global variable
  '.limmaGUIglobals'
ExportHTMLreport: no visible global function definition for 'toptable'
ExportMvalues: no visible binding for global variable
  'limmaGUIenvironment'
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'
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 : <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 : <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'
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 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 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'
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'
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'
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'
MAPlot: no visible binding for global variable 'limmaGUIenvironment'
MAPlot: no visible binding for global variable '.limmaGUIglobals'
MAPlotAvg: no visible binding for global variable 'limmaGUIenvironment'
MAPlotAvg: no visible binding for global variable '.limmaGUIglobals'
MAPlotAvg : plotAvgMA: no visible binding for global variable
  'limmaGUIenvironment'
MBoxPlot: no visible binding for global variable 'limmaGUIenvironment'
MBoxPlot: no visible binding for global variable '.limmaGUIglobals'
MMPlot: no visible binding for global variable 'limmaGUIenvironment'
MMPlot: no visible binding for global variable '.limmaGUIglobals'
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'
OpenGALFile: no visible binding for global variable
  'limmaGUIenvironment'
OpenGALandTargetsandSpotTypesfiles : onOK: no visible binding for
  global variable 'limmaGUIenvironment'
OpenSpotTypesFile: no visible binding for global variable
  'limmaGUIenvironment'
OpenTargetsFile: no visible binding for global variable
  'limmaGUIenvironment'
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'
QQTplot: no visible binding for global variable 'limmaGUIenvironment'
QQTplot: no visible binding for global variable '.limmaGUIglobals'
ReadImageProcessingFiles: no visible binding for global variable
  'limmaGUIenvironment'
ReadImageProcessingFiles: no visible binding for global variable
  '.limmaGUIglobals'
SaveAsLimmaFile: no visible binding for global variable
  'limmaGUIenvironment'
SaveAsLimmaFile: no visible binding for global variable
  '.limmaGUIglobals'
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 : 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'
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 : <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 : <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 : <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: no visible binding for global variable
  'limmaDataSetNameText'
evalRcode: no visible binding for global variable '.limmaGUIglobals'
evalRcode : runOverall: no visible binding for global variable
  '.limmaGUIglobals'
evalRcode : runOverall: no visible binding for global variable
  'limmaGUIenvironment'
initGlobals: no visible binding for global variable
  'limmaGUIenvironment'
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'
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'
showGAL: no visible binding for global variable 'limmaGUIenvironment'
showGAL: no visible binding for global variable '.limmaGUIglobals'
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 : onCancel: no visible binding for global variable
  '.limmaGUIglobals'
showTopTable : <anonymous>: no visible binding for global variable
  '.limmaGUIglobals'
showTopTable: no visible global function definition for 'toptable'
Undefined global functions or variables:
  .HTML.file .limmaGUIglobals NEOffsetDefault ParameterizationNamesVec
  ebayes gif limmaDataSetNameText limmaGUIenvironment
  parameterizationIndex toptable
* 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' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc/meat/limmaGUI.Rcheck/00check.log'
for details.