Package: affylmGUI

Version: 1.13.1

Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check affylmGUI_1.13.1.tar.gz

StartedAt: 2008-04-09 03:34:17 -0700 (Wed, 09 Apr 2008)

EndedAt: 2008-04-09 03:35:07 -0700 (Wed, 09 Apr 2008)

EllapsedTime: 49.5 seconds

RetCode: 0

Status: OK

CheckDir: affylmGUI.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/home/biocbuild/bbs-2.2-bioc/meat/affylmGUI.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* using session charset: ISO8859-1
* checking for file 'affylmGUI/DESCRIPTION' ... OK
* this is package 'affylmGUI' version '1.13.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affylmGUI' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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
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'
affyPlotMA: no visible binding for global variable
  'affylmGUIenvironment'
affyPlotMA: no visible binding for global variable '.affylmGUIglobals'
affyPlotMA : plotFunction: no visible binding for global variable
  '.affylmGUIglobals'
affyPlotMAcontrast: no visible binding for global variable
  'affylmGUIenvironment'
ChooseCDF: no visible binding for global variable '.affylmGUIglobals'
ChooseCDF : onOK: no visible binding for global variable
  '.affylmGUIglobals'
ChooseCDF : onOK: no visible binding for global variable 'cdfDataFrame'
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'
chooseDir: 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'
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 binding for global variable
  '.affylmGUIglobals'
DensityPlotAll: no visible binding for global variable
  'affylmGUIenvironment'
DensityPlotAll: no visible binding for global variable
  '.affylmGUIglobals'
DensityPlotAll : plotFunction: no visible binding for global variable
  '.affylmGUIglobals'
DensityPlotAll : plotFunction: no visible binding for global variable
  'affylmGUIenvironment'
evalRcode: no visible binding for global variable '.affylmGUIglobals'
evalRcode : runOverall: no visible binding for global variable
  '.affylmGUIglobals'
evalRcode : runOverall: no visible binding for global variable
  'affylmGUIenvironment'
evalRcode : runOverall: no visible binding for global variable
  'tmpEvalRcodeResultsGraph'
ExportHTMLreport: no visible binding for global variable
  'affylmGUIenvironment'
ExportNormalizedExpressionValues: no visible binding for global
  variable 'affylmGUIenvironment'
generalPlotFunction: no visible binding for global variable
  '.affylmGUIglobals'
generalPlotFunction: no visible binding for global variable
  'affylmGUIenvironment'
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'
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'
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'
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'
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'
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'
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'
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'
HTMLplotUsingFunction: no visible binding for global variable
  '.HTML.file'
HTMLplotUsingFunction: no visible binding for global variable 'gif'
ImageArrayPlot: no visible binding for global variable
  'affylmGUIenvironment'
ImageArrayPlot: no visible binding for global variable
  '.affylmGUIglobals'
ImageArrayPlot : plotFunction: no visible binding for global variable
  '.affylmGUIglobals'
ImageQualityResidualPlot: no visible binding for global variable
  'affylmGUIenvironment'
ImageQualityResidualPlot: no visible binding for global variable
  '.affylmGUIglobals'
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 binding for global
  variable '.affylmGUIglobals'
initGlobals: no visible binding for global variable
  'affylmGUIenvironment'
IntensityHistogram: no visible binding for global variable
  'affylmGUIenvironment'
IntensityHistogram: no visible binding for global variable
  '.affylmGUIglobals'
IntensityHistogram : plotFunction: no visible binding for global
  variable '.affylmGUIglobals'
IntensityHistogramAll: no visible binding for global variable
  'affylmGUIenvironment'
IntensityHistogramAll: no visible binding for global variable
  '.affylmGUIglobals'
IntensityHistogramAll : plotFunction: no visible binding for global
  variable '.affylmGUIglobals'
LogOddsPlot: no visible binding for global variable
  'affylmGUIenvironment'
NewLimmaFile: no visible binding for global variable
  'affylmGUIenvironment'
NormalizedIntensityBoxPlot: no visible binding for global variable
  'affylmGUIenvironment'
NormalizedIntensityBoxPlot: no visible binding for global variable
  '.affylmGUIglobals'
NormalizedIntensityBoxPlot : plotFunction: no visible binding for
  global variable '.affylmGUIglobals'
NormalizeNow: no visible binding for global variable
  'affylmGUIenvironment'
NormalizeNow: no visible binding for global variable
  '.affylmGUIglobals'
NUSEPlotAll: no visible binding for global variable
  'affylmGUIenvironment'
NUSEPlotAll: no visible binding for global variable '.affylmGUIglobals'
NUSEPlotAll : plotFunction: no visible binding for global variable
  '.affylmGUIglobals'
onDestroy: no visible binding for global variable
  'affylmGUIenvironment'
onExit: no visible binding for global variable 'affylmGUIenvironment'
onExit: no visible binding for global variable '.affylmGUIglobals'
OpenALimmaFile: no visible binding for global variable
  'affylmGUIenvironment'
OpenCDFandTargetsfiles : onOK: no visible binding for global variable
  'affylmGUIenvironment'
OpenCDFandTargetsfiles: no visible binding for global variable
  'affylmGUIenvironment'
OpenCDFFile: no visible binding for global variable 'cdf'
OpenCDFFile: no visible binding for global variable
  'affylmGUIenvironment'
OpenTargetsFile: no visible binding for global variable
  'affylmGUIenvironment'
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'
RawIntensityBoxPlot: no visible binding for global variable
  'affylmGUIenvironment'
RawIntensityBoxPlot: no visible binding for global variable
  '.affylmGUIglobals'
RawIntensityBoxPlot : plotFunction: no visible binding for global
  variable '.affylmGUIglobals'
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'
RLEPlotAll: no visible binding for global variable
  'affylmGUIenvironment'
RLEPlotAll: no visible binding for global variable '.affylmGUIglobals'
RLEPlotAll : plotFunction: no visible binding for global variable
  '.affylmGUIglobals'
RNADegradationPlotAll: no visible binding for global variable
  'affylmGUIenvironment'
RNADegradationPlotAll: no visible binding for global variable
  '.affylmGUIglobals'
RNADegradationPlotAll : plotFunction: no visible binding for global
  variable '.affylmGUIglobals'
SaveAsLimmaFile: no visible binding for global variable
  'affylmGUIenvironment'
SaveAsLimmaFile: no visible binding for global variable
  '.affylmGUIglobals'
SaveLimmaFile: no visible binding for global variable
  'affylmGUIenvironment'
SaveLimmaFile: no visible binding for global variable
  '.affylmGUIglobals'
SetWD: no visible binding for global variable '.affylmGUIglobals'
showTopTable: no visible binding for global variable
  'affylmGUIenvironment'
showTopTable : onOK: no visible binding for global variable
  'affylmGUIenvironment'
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'
ViewContrastsMatrixAsPairs: no visible binding for global variable
  'affylmGUIenvironment'
ViewContrastsMatrixInTable: no visible binding for global variable
  'affylmGUIenvironment'
ViewExistingContrastParameterization: no visible binding for global
  variable 'affylmGUIenvironment'
ViewExistingContrastParameterization: possible error in
  ViewContrastsMatrixInTable(contrastsMatrix = "Contrasts",
  contrastsList, contrastParameterizationIndex): unused argument(s)
  (contrastParameterizationIndex)
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 : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating affylmGUI-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating affylmGUI-manual.tex ... OK
* checking affylmGUI-manual.tex using pdflatex ... OK

* Installing *source* package 'affylmGUI' ...
** R
** inst
** preparing package for lazy loading
Loading required package: limma
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: affy
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affyio
Loading required package: preprocessCore
** help
 >>> Building/Updating help pages for package 'affylmGUI'
     Formats: text html latex example 
  ALGchangeLog                      text    html    latex
  affylmGUI                         text    html    latex
** building package indices ...
* DONE (affylmGUI)