BioC 3.3: CHECK report for affylmGUI on oaxaca

Package: affylmGUI

Version: 1.46.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings affylmGUI_1.46.0.tar.gz

StartedAt: 2016-10-12 23:08:11 -0700 (Wed, 12 Oct 2016)

EndedAt: 2016-10-12 23:10:26 -0700 (Wed, 12 Oct 2016)

EllapsedTime: 134.8 seconds

RetCode: 0

Status:  OK

CheckDir: affylmGUI.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings affylmGUI_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/affylmGUI.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affylmGUI/DESCRIPTION’ ... OK
* this is package ‘affylmGUI’ version ‘1.46.0’
* 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 ‘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
* 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
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 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
  write.table
Consider adding
  importFrom("grDevices", "bitmap", "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", "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 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 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
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/affylmGUI.Rcheck/00check.log’
for details.

* 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 3.3 (BiocInstaller 1.22.3), ?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’
* DONE (affylmGUI)