affylmGUI 1.27.0
Keith Satterley
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affylmGUI | | Last Changed Rev: 54810 / Revision: 55359 | | Last Changed Date: 2011-04-13 18:14:51 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | [ OK ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/affylmGUI.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affylmGUI/DESCRIPTION' ... OK
* this is package 'affylmGUI' version '1.27.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affylmGUI' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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
ChooseCDF: no visible binding for global variable '.affylmGUIglobals'
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'
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'
ExportHTMLreport: no visible binding for global variable
'affylmGUIenvironment'
ExportNormalizedExpressionValues: 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'
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'
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'
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'
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'
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'
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 binding for
global variable '.affylmGUIglobals'
OpenALimmaFile: no visible binding for global variable
'affylmGUIenvironment'
OpenCDFFile: no visible binding for global variable
'affylmGUIenvironment'
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'
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'
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'
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'
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'
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'
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'
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'
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'
chooseDir: no visible binding for global variable '.affylmGUIglobals'
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'
generalPlotFunction: no visible binding for global variable
'.affylmGUIglobals'
generalPlotFunction: no visible binding for global variable
'affylmGUIenvironment'
initGlobals: no visible binding for global variable
'affylmGUIenvironment'
onDestroy: no visible binding for global variable
'affylmGUIenvironment'
onExit: no visible binding for global variable 'affylmGUIenvironment'
onExit: no visible binding for global variable '.affylmGUIglobals'
showTopTable: no visible binding for global variable
'affylmGUIenvironment'
showTopTable : onOK: no visible binding for global variable
'affylmGUIenvironment'
* 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 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package 'affylmGUI' ...
** R
** inst
** preparing package for lazy loading
Loading Tcl/Tk interface ... done
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'affylmGUI.Rnw'
'extract.Rnw'
** testing if installed package can be loaded
* DONE (affylmGUI)