BioC 3.4: CHECK report for affylmGUI on moscato1

Package: affylmGUI

Version: 1.47.0

Command: rm -rf affylmGUI.buildbin-libdir affylmGUI.Rcheck && mkdir affylmGUI.buildbin-libdir affylmGUI.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affylmGUI.buildbin-libdir affylmGUI_1.47.0.tar.gz >affylmGUI.Rcheck\00install.out 2>&1 && cp affylmGUI.Rcheck\00install.out affylmGUI-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=affylmGUI.buildbin-libdir --install="check:affylmGUI-install.out" --force-multiarch --no-vignettes --timings affylmGUI_1.47.0.tar.gz

StartedAt: 2016-09-20 03:39:21 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:42:15 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 174.1 seconds

RetCode: 0

Status:  OK

CheckDir: affylmGUI.Rcheck

Warnings: 0

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###
### Running command:
###
###   rm -rf affylmGUI.buildbin-libdir affylmGUI.Rcheck && mkdir affylmGUI.buildbin-libdir affylmGUI.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affylmGUI.buildbin-libdir affylmGUI_1.47.0.tar.gz >affylmGUI.Rcheck\00install.out 2>&1 && cp affylmGUI.Rcheck\00install.out affylmGUI-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=affylmGUI.buildbin-libdir --install="check:affylmGUI-install.out" --force-multiarch --no-vignettes --timings affylmGUI_1.47.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/affylmGUI.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affylmGUI/DESCRIPTION' ... OK
* this is package 'affylmGUI' version '1.47.0'
* 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 'affylmGUI' can be installed ... OK
* checking installed package size ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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
.onAttach: no visible global function definition for 'winMenuAdd'
.onAttach: no visible global function definition for 'winMenuAddItem'
.onAttach: no visible global function definition for 'bringToTop'
ChooseCDF: no visible binding for global variable '.affylmGUIglobals'
ChooseCDF: no visible global function definition for
  'available.packages'
ChooseCDF: no visible global function definition for 'contrib.url'
ChooseCDF : onOK: no visible binding for global variable
  '.affylmGUIglobals'
ChooseCDF : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
ChooseCDF : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
ChooseContrastParameterization: no visible binding for global variable
  'affylmGUIenvironment'
ChooseContrastParameterization: no visible binding for global variable
  '.affylmGUIglobals'
ChooseContrastParameterization : onOK: no visible binding for global
  variable '.affylmGUIglobals'
ChooseContrastParameterization : onCancel: no visible binding for
  global variable '.affylmGUIglobals'
ChooseContrastParameterization : <anonymous>: no visible binding for
  global variable '.affylmGUIglobals'
ChooseEbayesStatistic: no visible binding for global variable
  '.affylmGUIglobals'
ChooseEbayesStatistic : onOK: no visible binding for global variable
  '.affylmGUIglobals'
ChooseEbayesStatistic : onCancel: no visible binding for global
  variable '.affylmGUIglobals'
ChooseEbayesStatistic : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
ComputeContrasts: no visible binding for global variable
  'affylmGUIenvironment'
ComputeLinearModelFit: no visible binding for global variable
  'affylmGUIenvironment'
ComputeLinearModelFit: no visible binding for global variable
  '.affylmGUIglobals'
ComputeLinearModelFit: no visible global function definition for
  'model.matrix'
DeleteContrastParameterization: no visible binding for global variable
  'affylmGUIenvironment'
DensityPlot: no visible binding for global variable
  'affylmGUIenvironment'
DensityPlot: no visible binding for global variable '.affylmGUIglobals'
DensityPlot : plotFunction: no visible global function definition for
  'par'
DensityPlot : plotFunction: no visible binding for global variable
  '.affylmGUIglobals'
DensityPlot : plotFunction: no visible global function definition for
  'title'
DensityPlot: no visible global function definition for 'plot.new'
DensityPlotAll: no visible binding for global variable
  'affylmGUIenvironment'
DensityPlotAll: no visible binding for global variable
  '.affylmGUIglobals'
DensityPlotAll : plotFunction: no visible global function definition
  for 'par'
DensityPlotAll : plotFunction: no visible binding for global variable
  '.affylmGUIglobals'
DensityPlotAll : plotFunction: no visible global function definition
  for 'legend'
DensityPlotAll : plotFunction: no visible binding for global variable
  'affylmGUIenvironment'
DensityPlotAll : plotFunction: no visible global function definition
  for 'title'
DensityPlotAll: no visible global function definition for 'plot.new'
ExportHTMLreport: no visible binding for global variable
  'affylmGUIenvironment'
ExportHTMLreport : plotFunction: no visible global function definition
  for 'par'
ExportHTMLreport : plotFunction: no visible global function definition
  for 'title'
ExportHTMLreport : plotFunction: no visible global function definition
  for 'plot'
ExportHTMLreport: no visible global function definition for
  'install.packages'
ExportHTMLreport: no visible global function definition for
  'write.table'
ExportNormalizedExpressionValues: no visible binding for global
  variable 'affylmGUIenvironment'
ExportNormalizedExpressionValues: no visible global function definition
  for 'write.table'
GetComponentsToExportInHTMLreport: no visible binding for global
  variable 'affylmGUIenvironment'
GetComponentsToExportInHTMLreport: no visible binding for global
  variable '.affylmGUIglobals'
GetComponentsToExportInHTMLreport : onOK: no visible binding for global
  variable '.affylmGUIglobals'
GetComponentsToExportInHTMLreport : onCancel: no visible binding for
  global variable '.affylmGUIglobals'
GetComponentsToExportInHTMLreport : <anonymous>: no visible binding for
  global variable '.affylmGUIglobals'
GetContrast: no visible binding for global variable '.affylmGUIglobals'
GetContrast: no visible binding for global variable
  'affylmGUIenvironment'
GetContrast : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetContrast : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetContrast : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
GetContrastNamesForHeatDiagram: no visible binding for global variable
  '.affylmGUIglobals'
GetContrastNamesForHeatDiagram : onOK: no visible binding for global
  variable '.affylmGUIglobals'
GetContrastNamesForHeatDiagram : onCancel: no visible binding for
  global variable '.affylmGUIglobals'
GetContrastNamesForHeatDiagram : <anonymous>: no visible binding for
  global variable '.affylmGUIglobals'
GetContrastParameterizationName: no visible binding for global variable
  '.affylmGUIglobals'
GetContrastParameterizationName : onOK: no visible binding for global
  variable '.affylmGUIglobals'
GetContrastParameterizationName : onCancel: no visible binding for
  global variable '.affylmGUIglobals'
GetContrastParameterizationName : <anonymous>: no visible binding for
  global variable '.affylmGUIglobals'
GetContrasts: no visible binding for global variable
  'affylmGUIenvironment'
GetContrasts : GetContrastsTable : openContrastsMatrixFile: no visible
  global function definition for 'read.table'
GetContrasts : GetContrastsTable : saveContrastsMatrixFile: no visible
  global function definition for 'write.table'
GetDEcutoff: no visible binding for global variable '.affylmGUIglobals'
GetDEcutoff : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetDEcutoff : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetDEcutoff : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
GetGeneLabelsOptions: no visible binding for global variable
  '.affylmGUIglobals'
GetGeneLabelsOptions : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetGeneLabelsOptions : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetGeneLabelsOptions : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
GetJpegOrPngParams: no visible binding for global variable
  '.affylmGUIglobals'
GetJpegOrPngParams : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetJpegOrPngParams : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetJpegOrPngParams : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
GetJpegOrPngX11Params: no visible binding for global variable
  '.affylmGUIglobals'
GetJpegOrPngX11Params : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetJpegOrPngX11Params : onCancel: no visible binding for global
  variable '.affylmGUIglobals'
GetJpegOrPngX11Params : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
GetLogPLMDataChoice: no visible binding for global variable
  '.affylmGUIglobals'
GetLogPLMDataChoice : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetLogPLMDataChoice : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetLogPLMDataChoice : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
GetMultipleContrasts: no visible binding for global variable
  '.affylmGUIglobals'
GetMultipleContrasts: no visible binding for global variable
  'affylmGUIenvironment'
GetMultipleContrasts : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetMultipleContrasts : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetMultipleContrasts : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
GetNormalizationMethod: no visible binding for global variable
  '.affylmGUIglobals'
GetNormalizationMethod : onCancel: no visible binding for global
  variable '.affylmGUIglobals'
GetNormalizationMethod : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetNormalizationMethod : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
GetPValueCutoff: no visible binding for global variable
  '.affylmGUIglobals'
GetPValueCutoff : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetPValueCutoff : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetPValueCutoff : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
GetParameterizationName: no visible binding for global variable
  '.affylmGUIglobals'
GetParameterizationName : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetParameterizationName : onCancel: no visible binding for global
  variable '.affylmGUIglobals'
GetParameterizationName : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
GetPlotLabels: no visible binding for global variable
  '.affylmGUIglobals'
GetPlotLabels : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetPlotLabels : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetPlotLabels : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
GetPlotSize: no visible binding for global variable '.affylmGUIglobals'
GetPlotSize : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetPlotSize : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetPlotSize : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
GetPlotTitle: no visible binding for global variable
  '.affylmGUIglobals'
GetPlotTitle : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetPlotTitle : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetPlotTitle : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
GetResidualTypeChoice: no visible binding for global variable
  '.affylmGUIglobals'
GetResidualTypeChoice : onCancel: no visible binding for global
  variable '.affylmGUIglobals'
GetResidualTypeChoice : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetResidualTypeChoice : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
GetSetNames: no visible binding for global variable '.affylmGUIglobals'
GetSetNames : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetSetNames : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetSetNames : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
GetSlideNum: no visible binding for global variable
  'affylmGUIenvironment'
GetSlideNum: no visible binding for global variable '.affylmGUIglobals'
GetSlideNum : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetSlideNum : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetSlideNum : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
GetSlideNums: no visible binding for global variable
  'affylmGUIenvironment'
GetSlideNums: no visible binding for global variable
  '.affylmGUIglobals'
GetSlideNums : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetSlideNums : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetSlideNums : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
GetWhichProbes: no visible binding for global variable
  '.affylmGUIglobals'
GetWhichProbes : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetWhichProbes : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetWhichProbes : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
GetWtAreaParams: no visible binding for global variable
  '.affylmGUIglobals'
GetWtAreaParams : onOK: no visible binding for global variable
  'affylmGUIenvironment'
GetWtAreaParams : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetWtAreaParams : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetWtAreaParams : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
GetWtFlagParams: no visible binding for global variable
  '.affylmGUIglobals'
GetWtFlagParams : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GetWtFlagParams : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GetWtFlagParams : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
GetWtFlagParams: no visible binding for global variable
  'affylmGUIenvironment'
GetlimmaDataSetName: no visible binding for global variable
  'affylmGUIenvironment'
GetlimmaDataSetName: no visible binding for global variable
  '.affylmGUIglobals'
GetlimmaDataSetName : onOK: no visible binding for global variable
  'affylmGUIenvironment'
GetlimmaDataSetName : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
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'
HeatDiagramDialog: no visible binding for global variable
  '.affylmGUIglobals'
HeatDiagramDialog : onOK: no visible binding for global variable
  '.affylmGUIglobals'
HeatDiagramDialog : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
HeatDiagramDialog : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
HeatDiagramPlot: no visible binding for global variable
  'affylmGUIenvironment'
HeatDiagramPlot: no visible global function definition for
  'available.packages'
HeatDiagramPlot: no visible global function definition for
  'contrib.url'
HeatDiagramPlot: no visible global function definition for
  'install.packages'
HeatDiagramPlot : plotFunction: no visible global function definition
  for 'par'
HeatDiagramPlot : plotFunction: no visible global function definition
  for 'title'
HeatDiagramPlot: no visible global function definition for 'plot.new'
ImageArrayPlot: no visible binding for global variable
  'affylmGUIenvironment'
ImageArrayPlot: no visible binding for global variable
  '.affylmGUIglobals'
ImageArrayPlot : plotFunction: no visible global function definition
  for 'par'
ImageArrayPlot : plotFunction: no visible binding for global variable
  '.affylmGUIglobals'
ImageArrayPlot : plotFunction: no visible global function definition
  for 'gray'
ImageArrayPlot : plotFunction: no visible global function definition
  for 'title'
ImageQualityResidualPlot: no visible binding for global variable
  'affylmGUIenvironment'
ImageQualityResidualPlot: no visible binding for global variable
  '.affylmGUIglobals'
ImageQualityResidualPlot : plotFunction: no visible global function
  definition for 'par'
ImageQualityResidualPlot : plotFunction: no visible binding for global
  variable '.affylmGUIglobals'
ImageQualityWeightPlot: no visible binding for global variable
  'affylmGUIenvironment'
ImageQualityWeightPlot: no visible binding for global variable
  '.affylmGUIglobals'
ImageQualityWeightPlot : plotFunction: no visible global function
  definition for 'par'
ImageQualityWeightPlot : plotFunction: no visible binding for global
  variable '.affylmGUIglobals'
IntensityHistogram: no visible binding for global variable
  'affylmGUIenvironment'
IntensityHistogram: no visible binding for global variable
  '.affylmGUIglobals'
IntensityHistogram : plotFunction: no visible global function
  definition for 'par'
IntensityHistogram : plotFunction: no visible binding for global
  variable '.affylmGUIglobals'
IntensityHistogram: no visible global function definition for
  'plot.new'
IntensityHistogramAll: no visible binding for global variable
  'affylmGUIenvironment'
IntensityHistogramAll: no visible binding for global variable
  '.affylmGUIglobals'
IntensityHistogramAll : plotFunction: no visible global function
  definition for 'par'
IntensityHistogramAll : plotFunction: no visible binding for global
  variable '.affylmGUIglobals'
IntensityHistogramAll: no visible global function definition for
  'plot.new'
LogOddsPlot: no visible binding for global variable
  'affylmGUIenvironment'
LogOddsPlot: no visible global function definition for
  'install.packages'
LogOddsPlot : plotFunction: no visible global function definition for
  'par'
LogOddsPlot : plotFunction: no visible global function definition for
  'plot'
LogOddsPlot : plotFunction: no visible global function definition for
  'title'
LogOddsPlot : plotFunction: no visible global function definition for
  'text'
LogOddsPlot: no visible global function definition for 'plot.new'
NUSEPlotAll: no visible binding for global variable
  'affylmGUIenvironment'
NUSEPlotAll: no visible binding for global variable '.affylmGUIglobals'
NUSEPlotAll : plotFunction: no visible global function definition for
  'par'
NUSEPlotAll : plotFunction: no visible binding for global variable
  '.affylmGUIglobals'
NUSEPlotAll: no visible global function definition for 'plot.new'
NewLimmaFile: no visible binding for global variable
  'affylmGUIenvironment'
NormalizeNow: no visible binding for global variable
  'affylmGUIenvironment'
NormalizeNow: no visible binding for global variable
  '.affylmGUIglobals'
NormalizedIntensityBoxPlot: no visible binding for global variable
  'affylmGUIenvironment'
NormalizedIntensityBoxPlot: no visible binding for global variable
  '.affylmGUIglobals'
NormalizedIntensityBoxPlot : plotFunction: no visible global function
  definition for 'par'
NormalizedIntensityBoxPlot : plotFunction: no visible binding for
  global variable '.affylmGUIglobals'
NormalizedIntensityBoxPlot : plotFunction: no visible global function
  definition for 'title'
NormalizedIntensityBoxPlot: no visible global function definition for
  'plot.new'
OpenALimmaFile: no visible binding for global variable
  'affylmGUIenvironment'
OpenCDFFile: no visible binding for global variable
  'affylmGUIenvironment'
OpenCDFFile: no visible global function definition for
  'install.packages'
OpenCDFandTargetsfiles : onOK: no visible binding for global variable
  'affylmGUIenvironment'
OpenCDFandTargetsfiles: no visible binding for global variable
  'affylmGUIenvironment'
OpenTargetsFile: no visible binding for global variable
  'affylmGUIenvironment'
OpenTargetsFile: no visible global function definition for 'read.table'
PlotOptions: no visible binding for global variable '.affylmGUIglobals'
PlotOptions : onOK: no visible binding for global variable
  '.affylmGUIglobals'
PlotOptions : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
QQTplot: no visible binding for global variable 'affylmGUIenvironment'
QQTplot : plotFunction: no visible global function definition for 'par'
QQTplot : plotFunction: no visible global function definition for
  'abline'
QQTplot: no visible global function definition for 'plot.new'
RLEPlotAll: no visible binding for global variable
  'affylmGUIenvironment'
RLEPlotAll: no visible binding for global variable '.affylmGUIglobals'
RLEPlotAll : plotFunction: no visible global function definition for
  'par'
RLEPlotAll : plotFunction: no visible binding for global variable
  '.affylmGUIglobals'
RLEPlotAll: no visible global function definition for 'plot.new'
RNADegradationPlotAll: no visible binding for global variable
  'affylmGUIenvironment'
RNADegradationPlotAll: no visible binding for global variable
  '.affylmGUIglobals'
RNADegradationPlotAll : plotFunction: no visible global function
  definition for 'par'
RNADegradationPlotAll : plotFunction: no visible binding for global
  variable '.affylmGUIglobals'
RNADegradationPlotAll : plotFunction: no visible global function
  definition for 'legend'
RNADegradationPlotAll: no visible global function definition for
  'plot.new'
RawIntensityBoxPlot: no visible binding for global variable
  'affylmGUIenvironment'
RawIntensityBoxPlot: no visible binding for global variable
  '.affylmGUIglobals'
RawIntensityBoxPlot : plotFunction: no visible global function
  definition for 'par'
RawIntensityBoxPlot : plotFunction: no visible binding for global
  variable '.affylmGUIglobals'
RawIntensityBoxPlot : plotFunction: no visible global function
  definition for 'title'
RawIntensityBoxPlot: no visible global function definition for
  'plot.new'
Resize: no visible binding for '<<-' assignment to 'LocalHScale'
Resize: no visible binding for '<<-' assignment to 'LocalVScale'
Resize: no visible binding for global variable 'LocalHScale'
Resize: no visible binding for global variable 'LocalVScale'
SaveAsLimmaFile: no visible binding for global variable
  'affylmGUIenvironment'
SaveAsLimmaFile: no visible binding for global variable
  '.affylmGUIglobals'
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
  'affylmGUIenvironment'
SaveLimmaFile: no visible binding for global variable
  '.affylmGUIglobals'
SetWD: no visible binding for global variable '.affylmGUIglobals'
TclRequire: no visible binding for global variable '.affylmGUIglobals'
TclRequire : onDestroy: no visible binding for global variable
  '.affylmGUIglobals'
TclRequire : onOK: no visible binding for global variable
  '.affylmGUIglobals'
TclRequire : onOK: no visible binding for global variable
  'affylmGUIenvironment'
UpDownOrBoth: no visible binding for global variable
  '.affylmGUIglobals'
UpDownOrBoth : onOK: no visible binding for global variable
  '.affylmGUIglobals'
UpDownOrBoth : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
VennDiagramPlot: no visible binding for global variable
  'affylmGUIenvironment'
VennDiagramPlot : plotFunction: no visible global function definition
  for 'par'
VennDiagramPlot: no visible global function definition for 'plot.new'
ViewContrastsMatrixAsPairs: no visible binding for global variable
  'affylmGUIenvironment'
ViewContrastsMatrixInTable: no visible binding for global variable
  'affylmGUIenvironment'
ViewContrastsMatrixInTable : onSaveContrastsMatrixAs: no visible global
  function definition for 'write.table'
ViewExistingContrastParameterization: no visible binding for global
  variable 'affylmGUIenvironment'
ViewRNATargets: no visible binding for global variable
  'affylmGUIenvironment'
ViewRNATargets: no visible binding for global variable
  '.affylmGUIglobals'
ViewRNATargets : onClose: no visible binding for global variable
  '.affylmGUIglobals'
ViewRNATargets : saveTargetsFile: no visible global function definition
  for 'write.table'
ViewRNATargets : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
affyHelp: no visible global function definition for 'browseURL'
affyPlotMA: no visible binding for global variable
  'affylmGUIenvironment'
affyPlotMA: no visible binding for global variable '.affylmGUIglobals'
affyPlotMA : plotFunction: no visible global function definition for
  'par'
affyPlotMA : plotFunction: no visible binding for global variable
  '.affylmGUIglobals'
affyPlotMA : plotFunction: no visible global function definition for
  'plot'
affyPlotMA : plotFunction: no visible global function definition for
  'title'
affyPlotMA: no visible global function definition for 'plot.new'
affyPlotMAcontrast: no visible binding for global variable
  'affylmGUIenvironment'
affyPlotMAcontrast: no visible global function definition for
  'available.packages'
affyPlotMAcontrast: no visible global function definition for
  'contrib.url'
affyPlotMAcontrast: no visible global function definition for
  'install.packages'
affyPlotMAcontrast : plotFunction: no visible global function
  definition for 'par'
affyPlotMAcontrast : plotFunction: no visible global function
  definition for 'plot'
affyPlotMAcontrast : plotFunction: no visible global function
  definition for 'title'
affyPlotMAcontrast : plotFunction: no visible global function
  definition for 'text'
affyPlotMAcontrast: no visible global function definition for
  'plot.new'
affylmGUI: no visible binding for global variable
  'affylmGUIenvironment'
affylmGUI: no visible binding for global variable '.affylmGUIglobals'
affylmGUI : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
affylmGUI: no visible global function definition for 'read.table'
affylmGUIhelp: no visible global function definition for 'browseURL'
chooseDir: no visible binding for global variable '.affylmGUIglobals'
evalRcode: no visible binding for global variable '.affylmGUIglobals'
evalRcode : SaveRSourceFile: no visible global function definition for
  'tkopen'
evalRcode : SaveRSourceFile: no visible global function definition for
  'tkputs'
evalRcode : SaveRSourceFile: no visible global function definition for
  'tkclose'
evalRcode : runOverall: no visible binding for global variable
  '.affylmGUIglobals'
evalRcode : runOverall: no visible binding for global variable
  'affylmGUIenvironment'
evalRcode : runOverall: no visible global function definition for
  'plot.new'
evalRcode : runOverall : SaveTextResults: no visible global function
  definition for 'tkopen'
evalRcode : runOverall : SaveTextResults: no visible global function
  definition for 'tkputs'
evalRcode : runOverall : SaveTextResults: no visible global function
  definition for 'tkclose'
evalRcode : HTMLhelp: no visible global function definition for
  'help.start'
generalPlotFunction: no visible binding for global variable
  '.affylmGUIglobals'
generalPlotFunction: no visible binding for global variable
  'affylmGUIenvironment'
generalPlotFunction: no visible global function definition for
  'plot.new'
initGlobals: no visible binding for global variable
  'affylmGUIenvironment'
limmaHelp: no visible global function definition for 'browseURL'
onDestroy: no visible binding for global variable
  'affylmGUIenvironment'
onExit: no visible binding for global variable 'affylmGUIenvironment'
onExit: no visible binding for global variable '.affylmGUIglobals'
showCitations: no visible global function definition for 'citation'
showTopTable: no visible binding for global variable
  'affylmGUIenvironment'
showTopTable : onOK: no visible binding for global variable
  'affylmGUIenvironment'
showTopTable : onHelp: no visible global function definition for 'help'
showTopTable: no visible global function definition for
  'install.packages'
showTopTable : SaveTopTable: no visible global function definition for
  'write.table'
showTopTable: no visible global function definition for 'write.table'
toptable2: no visible global function definition for 'p.adjust'
vennDiagramaffylmGUI: no visible global function definition for 'par'
vennDiagramaffylmGUI: no visible global function definition for 'plot'
vennDiagramaffylmGUI: no visible global function definition for 'lines'
vennDiagramaffylmGUI: no visible global function definition for 'text'
vennDiagramaffylmGUI: no visible global function definition for 'rect'
Undefined global functions or variables:
  .HTML.file .affylmGUIglobals LocalHScale LocalVScale abline
  affylmGUIenvironment available.packages bitmap bringToTop browseURL
  citation contrib.url dev.off dev.print gray help help.start
  install.packages jpeg legend lines model.matrix p.adjust par pdf plot
  plot.new png postscript read.table rect text title tkclose tkopen
  tkputs winMenuAdd winMenuAddItem write.table
Consider adding
  importFrom("grDevices", "bitmap", "bringToTop", "dev.off", "dev.print",
             "gray", "jpeg", "pdf", "png", "postscript")
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "plot.new", "rect", "text", "title")
  importFrom("stats", "model.matrix", "p.adjust")
  importFrom("utils", "available.packages", "browseURL", "citation",
             "contrib.url", "help", "help.start", "install.packages",
             "read.table", "winMenuAdd", "winMenuAddItem", "write.table")
to your NAMESPACE file.
* 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 installed files from 'inst/doc' ... OK
* 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: 1 NOTE
See
  'D:/biocbld/bbs-3.4-bioc/meat/affylmGUI.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'affylmGUI' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'boxplot' from package 'graphics' in package 'affyPLM'
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
Bioconductor version 3.4 (BiocInstaller 1.23.9), ?biocLite for help
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'boxplot' from package 'graphics' in package 'affyPLM'
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'

install for x64

* installing *source* package 'affylmGUI' ...
** testing if installed package can be loaded
Creating a generic function for 'boxplot' from package 'graphics' in package 'affyPLM'
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
* MD5 sums
packaged installation of 'affylmGUI' as affylmGUI_1.47.0.zip
* DONE (affylmGUI)