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Package 345/631HostnameOS / ArchBUILDCHECKBUILD BIN
limmaGUI 1.35.0
Keith Satterley
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/limmaGUI
Last Changed Rev: 72083 / Revision: 72575
Last Changed Date: 2012-12-20 09:36:07 -0800 (Thu, 20 Dec 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: limmaGUI
Version: 1.35.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings limmaGUI_1.35.0.tar.gz
StartedAt: 2013-01-16 03:55:28 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 03:56:31 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 63.0 seconds
RetCode: 0
Status:  OK 
CheckDir: limmaGUI.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/limmaGUI.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limmaGUI/DESCRIPTION’ ... OK
* this is package ‘limmaGUI’ version ‘1.35.0’
* 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 ... NOTE
Found the following hidden files and directories:
  inst/doc/Bob/.xvpics
  inst/doc/Swirl/.xvpics
  inst/doc/Weaver/.xvpics
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘limmaGUI’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 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
File ‘limmaGUI/R/zzz.R’:
  .First.lib has wrong argument list ‘libname, pkgname, where’
  .First.lib calls:
    require("tcltk", character.only = TRUE)
    require(limma)
    require(limma)
    cat(paste("\nWarning: ActiveTcl could not be found in the Windows Registry.\n"))
    cat(paste("\nEither it has not been installed or it has not been installed with sufficient privileges.\n\n"))
    cat(paste("\nlimmaGUI requires the Tcl/Tk extensions Tktable and BWidget which are not distributed with R,\n"))
    cat(paste("\nbut they are distributed with ActiveTcl.\n"))
    cat(paste("\nActiveTcl was found in the Windows Registry (for CURRENT_USER), installed in",     TclPath, sep = "\n"))
    cat(paste("\nThis directory will be added to the Tcl search path to enable limmaGUI\n"))
    cat(paste("to find the Tktable and BWidget extensions.\n"))
    cat(paste("\nActiveTcl was found in the Windows Registry (for LOCAL_MACHINE), installed in",     TclPath2, sep = "\n"))
    cat(paste("\nThis directory will be added to the Tcl search path to enable limmaGUI\n"))
    cat(paste("to find the Tktable and BWidget extensions.\n"))
    cat(paste("\nlimmaGUI can be launched by typing limmaGUI() or by using the pull-down menu.\n"))
    cat(paste("\nlimmaGUI can be launched by typing limmaGUI()\n"))

Package startup functions should have two arguments with names starting
  with ‘lib’ and ‘pkg’, respectively.
Package startup functions should not change the search path.
Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

ExportHTMLreport: warning in exists("X11", env = .GlobalEnv): partial
  argument match of 'env' to 'envir'
HTMLplotUsingFunction: warning in exists("X11", env = .GlobalEnv):
  partial argument match of 'env' to 'envir'
HTMLplotUsingFunction: warning in assign(".HTML.graph", TRUE, env =
  get("HTMLenv", envir = .GlobalEnv)): partial argument match of 'env'
  to 'envir'
LogOddsPlot: warning in exists("X11", env = .GlobalEnv): partial
  argument match of 'env' to 'envir'
MAPlot: warning in exists("X11", env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
MAPlotAvg: warning in exists("X11", env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
MMPlot: warning in exists("X11", env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
QQTplot: warning in exists("X11", env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
SaveGraphAsJpeg: warning in exists("X11", env = .GlobalEnv): partial
  argument match of 'env' to 'envir'
SaveGraphAsJpeg: warning in jpeg(file = jpegFileName, width =
  jpegParams$width, height = jpegParams$height, pointsize =
  jpegParams$pointsize, bg = jpegParams$bg): partial argument match of
  'file' to 'filename'
SaveGraphAsPNG: warning in exists("X11", env = .GlobalEnv): partial
  argument match of 'env' to 'envir'
SaveGraphAsPNG: warning in png(file = pngFileName, width =
  pngParams$width, height = pngParams$height, pointsize =
  pngParams$pointsize, bg = pngParams$bg): partial argument match of
  'file' to 'filename'
SelectPlotSymbols: warning in exists("X11", env = .GlobalEnv): partial
  argument match of 'env' to 'envir'
limmaGUI: warning in exists("X11", env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
AboutNormalization: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseContrastsParameterization: no visible binding for global variable
  ‘limmaGUIenvironment’
ChooseContrastsParameterization: no visible binding for global variable
  ‘ParameterizationNamesVec’
ChooseContrastsParameterization: no visible binding for global variable
  ‘parameterizationIndex’
ChooseContrastsParameterization: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseContrastsParameterization : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
ChooseContrastsParameterization : onCancel: no visible binding for
  global variable ‘.limmaGUIglobals’
ChooseContrastsParameterization : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
ChooseEbayesStatistic: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseEbayesStatistic : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseEbayesStatistic : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
ChooseEbayesStatistic : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
ChooseParameterization: no visible binding for global variable
  ‘limmaGUIenvironment’
ChooseParameterization: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseParameterization : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseParameterization : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
ChooseParameterization : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
ChoosePlotSymbolByClicking: no visible binding for global variable
  ‘.limmaGUIglobals’
ChoosePlotSymbolByClicking : LeftClick: no visible binding for global
  variable ‘.limmaGUIglobals’
ChoosePlotSymbolByClicking : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
ChoosePlotSymbolByClicking : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
ChooseSpotType: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseSpotType : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseSpotType : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
ChooseSpotType : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
ComputeContrasts: no visible binding for global variable
  ‘limmaGUIenvironment’
ComputeContrasts: no visible binding for global variable
  ‘.limmaGUIglobals’
ComputeLinearModelFit: no visible binding for global variable
  ‘limmaGUIenvironment’
ComputeLinearModelFit: no visible binding for global variable
  ‘.limmaGUIglobals’
ComputeLinearModelFit : GetDupCor: no visible binding for global
  variable ‘.limmaGUIglobals’
ComputeLinearModelFit : GetDupCor : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
ComputeLinearModelFit : GetDupCor : onCancel: no visible binding for
  global variable ‘.limmaGUIglobals’
ComputeLinearModelFit : GetDupCor : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
CreateNewParameterization: no visible binding for global variable
  ‘limmaGUIenvironment’
CreateNewParameterization: no visible binding for global variable
  ‘.limmaGUIglobals’
CreateTreeAndList: no visible binding for global variable
  ‘limmaGUIenvironment’
CreateTreeAndList: no visible binding for global variable
  ‘.limmaGUIglobals’
DeleteContrastsParameterization: no visible binding for global variable
  ‘limmaGUIenvironment’
DeleteContrastsParameterization: no visible binding for global variable
  ‘.limmaGUIglobals’
DeleteParameterization: no visible binding for global variable
  ‘limmaGUIenvironment’
DeleteParameterization: no visible binding for global variable
  ‘.limmaGUIglobals’
DupCorBoxPlot: no visible binding for global variable
  ‘limmaGUIenvironment’
DupCorBoxPlot: no visible binding for global variable
  ‘.limmaGUIglobals’
ExportAvalues: no visible binding for global variable
  ‘limmaGUIenvironment’
ExportHTMLreport: no visible binding for global variable
  ‘limmaGUIenvironment’
ExportHTMLreport: no visible binding for global variable
  ‘.limmaGUIglobals’
ExportHTMLreport : plotFunction: no visible global function definition
  for ‘plot.scale.box’
ExportMvalues: no visible binding for global variable
  ‘limmaGUIenvironment’
GetBackgroundCorrectionMethod: no visible binding for global variable
  ‘.limmaGUIglobals’
GetBackgroundCorrectionMethod: no visible binding for global variable
  ‘limmaGUIenvironment’
GetBackgroundCorrectionMethod : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetBackgroundCorrectionMethod : onOK: no visible binding for global
  variable ‘limmaGUIenvironment’
GetBackgroundCorrectionMethod : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
GetBetweenArrayNormalizationMethod: no visible binding for global
  variable ‘.limmaGUIglobals’
GetBetweenArrayNormalizationMethod: no visible binding for global
  variable ‘limmaGUIenvironment’
GetBetweenArrayNormalizationMethod : onOK: no visible binding for
  global variable ‘limmaGUIenvironment’
GetBetweenArrayNormalizationMethod : onOK: no visible binding for
  global variable ‘.limmaGUIglobals’
GetBetweenArrayNormalizationMethod : <anonymous>: no visible binding
  for global variable ‘.limmaGUIglobals’
GetCoef: no visible binding for global variable ‘limmaGUIenvironment’
GetCoef: no visible binding for global variable ‘.limmaGUIglobals’
GetCoef : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetCoef : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetCoef : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetComponentsToExportInHTMLreport: no visible binding for global
  variable ‘limmaGUIenvironment’
GetComponentsToExportInHTMLreport: no visible binding for global
  variable ‘.limmaGUIglobals’
GetComponentsToExportInHTMLreport : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetComponentsToExportInHTMLreport : onCancel: no visible binding for
  global variable ‘.limmaGUIglobals’
GetComponentsToExportInHTMLreport : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
GetContrastsParameterizationName: no visible binding for global
  variable ‘.limmaGUIglobals’
GetContrastsParameterizationName : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetContrastsParameterizationName : onCancel: no visible binding for
  global variable ‘.limmaGUIglobals’
GetContrastsParameterizationName : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
GetContrastsParameterizationNames: no visible binding for global
  variable ‘limmaGUIenvironment’
GetDEcutoff: no visible binding for global variable ‘.limmaGUIglobals’
GetDEcutoff : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetDEcutoff : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetDEcutoff : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetDesignOrContrasts: no visible binding for global variable
  ‘limmaGUIenvironment’
GetDesignOrContrasts: no visible binding for global variable
  ‘.limmaGUIglobals’
GetDesignOrContrasts : GetDesignOrContrastsTable: no visible binding
  for global variable ‘.limmaGUIglobals’
GetDesignOrContrasts : GetDesignOrContrastsTable : onOK: no visible
  binding for global variable ‘limmaGUIenvironment’
GetDesignOrContrasts : GetDesignOrContrastsTable : onOK: no visible
  binding for global variable ‘.limmaGUIglobals’
GetDesignOrContrasts : GetDesignOrContrastsTable : onCancel: no visible
  binding for global variable ‘.limmaGUIglobals’
GetDesignOrContrasts : GetDesignOrContrastsTable : <anonymous>: no
  visible binding for global variable ‘.limmaGUIglobals’
GetDesignOrContrasts : OnAdvanced: no visible binding for global
  variable ‘limmaGUIenvironment’
GetDesignOrContrasts : OnAdvanced: no visible binding for global
  variable ‘.limmaGUIglobals’
GetDesignOrContrasts : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetDesignOrContrasts : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetDesignOrContrasts : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetGeneLabelsOptions: no visible binding for global variable
  ‘.limmaGUIglobals’
GetGeneLabelsOptions : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetGeneLabelsOptions : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetGeneLabelsOptions : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetGenePixFlagWeightings: no visible binding for global variable
  ‘.limmaGUIglobals’
GetGenePixFlagWeightings : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetGenePixFlagWeightings : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetGenePixFlagWeightings : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetImageAnalysisColumnHeadings: no visible binding for global variable
  ‘.limmaGUIglobals’
GetImageAnalysisColumnHeadings : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetImageAnalysisColumnHeadings : onCancel: no visible binding for
  global variable ‘.limmaGUIglobals’
GetImageAnalysisColumnHeadings : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
GetImageProcessingFileType: no visible binding for global variable
  ‘.limmaGUIglobals’
GetImageProcessingFileType: no visible binding for global variable
  ‘limmaGUIenvironment’
GetImageProcessingFileType : onOther: no visible binding for global
  variable ‘.limmaGUIglobals’
GetImageProcessingFileType : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetImageProcessingFileType : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetImageProcessingFileType : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetJpegOrPngParams: no visible binding for global variable
  ‘.limmaGUIglobals’
GetJpegOrPngParams : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetJpegOrPngParams : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetJpegOrPngParams : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetJpegOrPngX11Params: no visible binding for global variable
  ‘.limmaGUIglobals’
GetJpegOrPngX11Params : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetJpegOrPngX11Params : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetJpegOrPngX11Params : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetLowessType: no visible binding for global variable
  ‘.limmaGUIglobals’
GetLowessType : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetLowessType : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetNEWxlim: no visible binding for global variable ‘.limmaGUIglobals’
GetNEWxlim : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetNEWxlim : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetNEWxlim : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetNormexpOffsetValue: no visible binding for global variable
  ‘.limmaGUIglobals’
GetNormexpOffsetValue : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetNormexpOffsetValue : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetNormexpOffsetValue : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetNumParametersNoTargets: no visible binding for global variable
  ‘limmaGUIenvironment’
GetNumParametersNoTargets: no visible binding for global variable
  ‘.limmaGUIglobals’
GetNumParametersNoTargets : onOK: no visible binding for global
  variable ‘limmaGUIenvironment’
GetNumParametersNoTargets : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetNumParametersNoTargets : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetNumParametersNoTargets : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetPValueCutoff: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPValueCutoff : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPValueCutoff : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPValueCutoff : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetParameterNames: no visible binding for global variable
  ‘limmaGUIenvironment’
GetParameterizationName: no visible binding for global variable
  ‘.limmaGUIglobals’
GetParameterizationName : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetParameterizationName : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetParameterizationName : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetParametersAndOrContrasts: no visible binding for global variable
  ‘limmaGUIenvironment’
GetParametersAndOrContrasts: no visible binding for global variable
  ‘.limmaGUIglobals’
GetParametersAndOrContrasts : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetParametersAndOrContrasts : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetParametersAndOrContrasts : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
GetPlotLabels: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotLabels : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotLabels : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotLabels : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotSize: no visible binding for global variable ‘.limmaGUIglobals’
GetPlotSize : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotSize : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotSize : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotTitle: no visible binding for global variable ‘.limmaGUIglobals’
GetPlotTitle : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotTitle : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetPlotTitle : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetReducedDuplicateSpacing: no visible binding for global variable
  ‘limmaGUIenvironment’
GetSlideNum: no visible binding for global variable
  ‘limmaGUIenvironment’
GetSlideNum: no visible binding for global variable ‘.limmaGUIglobals’
GetSlideNum : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetSlideNum : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetSlideNum : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetSpotTypesForLinearModel: no visible binding for global variable
  ‘limmaGUIenvironment’
GetSpotTypesForLinearModel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetSpotTypesForLinearModel : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetSpotTypesForLinearModel : onCancel: no visible binding for global
  variable ‘.limmaGUIglobals’
GetSpotTypesForLinearModel : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetSpotTypesIncludedNames: no visible binding for global variable
  ‘limmaGUIenvironment’
GetWithinArrayNormalizationMethod: no visible binding for global
  variable ‘.limmaGUIglobals’
GetWithinArrayNormalizationMethod: no visible binding for global
  variable ‘limmaGUIenvironment’
GetWithinArrayNormalizationMethod : onOK: no visible binding for global
  variable ‘limmaGUIenvironment’
GetWithinArrayNormalizationMethod : onOK: no visible binding for global
  variable ‘.limmaGUIglobals’
GetWithinArrayNormalizationMethod : <anonymous>: no visible binding for
  global variable ‘.limmaGUIglobals’
GetWtAreaParams: no visible binding for global variable
  ‘.limmaGUIglobals’
GetWtAreaParams : onOK: no visible binding for global variable
  ‘limmaGUIenvironment’
GetWtAreaParams : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetWtAreaParams : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
GetWtAreaParams : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
GetlimmaDataSetName: no visible binding for global variable
  ‘limmaGUIenvironment’
GetlimmaDataSetName: no visible binding for global variable
  ‘.limmaGUIglobals’
GetlimmaDataSetName : onOK: no visible binding for global variable
  ‘limmaGUIenvironment’
GetlimmaDataSetName : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
GetlmFitMethod: no visible binding for global variable
  ‘.limmaGUIglobals’
GetlmFitMethod: no visible binding for global variable
  ‘limmaGUIenvironment’
GetlmFitMethod : onOK: no visible binding for global variable
  ‘limmaGUIenvironment’
GetlmFitMethod : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
GetlmFitMethod : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
HTMLplotUsingFunction: no visible binding for global variable
  ‘.HTML.file’
HTMLplotUsingFunction: no visible binding for global variable ‘gif’
HeatDiagramDialog: no visible binding for global variable
  ‘.limmaGUIglobals’
HeatDiagramDialog : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
HeatDiagramDialog : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
HeatDiagramDialog : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
HeatDiagramPlot: no visible binding for global variable
  ‘limmaGUIenvironment’
HeatDiagramPlot: no visible binding for global variable
  ‘.limmaGUIglobals’
HowManyDups: no visible binding for global variable
  ‘limmaGUIenvironment’
HowManyDups: no visible binding for global variable ‘.limmaGUIglobals’
HowManyDups : onOK: no visible binding for global variable
  ‘limmaGUIenvironment’
HowManyDups : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
HowManyDups : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
HowManyDups : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
ImageArrayPlot: no visible binding for global variable
  ‘limmaGUIenvironment’
ImageArrayPlot: no visible binding for global variable
  ‘.limmaGUIglobals’
ImageArrayPlotDialog: no visible binding for global variable
  ‘limmaGUIenvironment’
ImageArrayPlotDialog: no visible binding for global variable
  ‘.limmaGUIglobals’
ImageArrayPlotDialog : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
ImageArrayPlotDialog : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
ImageArrayPlotDialog : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
ImportMA: no visible binding for global variable ‘limmaGUIenvironment’
ImportMA: no visible binding for global variable ‘.limmaGUIglobals’
ImportMADialog: no visible binding for global variable
  ‘.limmaGUIglobals’
ImportMADialog : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
ImportMADialog : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
ImportMADialog : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
InitNewParameterization: no visible binding for global variable
  ‘limmaGUIenvironment’
InitNewParameterization: no visible binding for global variable
  ‘.limmaGUIglobals’
LogOddsPlot: no visible binding for global variable
  ‘limmaGUIenvironment’
LogOddsPlot: no visible binding for global variable ‘.limmaGUIglobals’
MAPlot: no visible binding for global variable ‘limmaGUIenvironment’
MAPlot: no visible binding for global variable ‘.limmaGUIglobals’
MAPlot : plotFun: ... may be used in an incorrect context:
  plotPrintTipLoess(RG, maLayout, array = slidenum, span = 0.4, ...)
MAPlot : plotFun: no visible global function definition for ‘plot.mva’
MAPlotAvg: no visible binding for global variable ‘limmaGUIenvironment’
MAPlotAvg: no visible binding for global variable ‘.limmaGUIglobals’
MAPlotAvg : plotAvgMA: no visible binding for global variable
  ‘limmaGUIenvironment’
MBoxPlot: no visible binding for global variable ‘limmaGUIenvironment’
MBoxPlot: no visible binding for global variable ‘.limmaGUIglobals’
MBoxPlot : plot.scale.box0: no visible global function definition for
  ‘plot.scale.box’
MMPlot: no visible binding for global variable ‘limmaGUIenvironment’
MMPlot: no visible binding for global variable ‘.limmaGUIglobals’
NewLimmaFile: no visible binding for global variable
  ‘limmaGUIenvironment’
NormalizeNow: no visible binding for global variable
  ‘limmaGUIenvironment’
NormalizeNow: no visible binding for global variable ‘.limmaGUIglobals’
OpenALimmaFile: no visible binding for global variable
  ‘limmaGUIenvironment’
OpenGALFile: no visible binding for global variable
  ‘limmaGUIenvironment’
OpenGALandTargetsandSpotTypesfiles : onOK: no visible binding for
  global variable ‘limmaGUIenvironment’
OpenSpotTypesFile: no visible binding for global variable
  ‘limmaGUIenvironment’
OpenTargetsFile: no visible binding for global variable
  ‘limmaGUIenvironment’
PlotOptions: no visible binding for global variable ‘.limmaGUIglobals’
PlotOptions : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
PlotOptions : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
PrintTipGroupMAPlot: no visible binding for global variable
  ‘limmaGUIenvironment’
PrintTipGroupMAPlot: no visible binding for global variable
  ‘.limmaGUIglobals’
QQTplot: no visible binding for global variable ‘limmaGUIenvironment’
QQTplot: no visible binding for global variable ‘.limmaGUIglobals’
ReadImageProcessingFiles: no visible binding for global variable
  ‘limmaGUIenvironment’
ReadImageProcessingFiles: no visible binding for global variable
  ‘.limmaGUIglobals’
SaveAsLimmaFile: no visible binding for global variable
  ‘limmaGUIenvironment’
SaveAsLimmaFile: no visible binding for global variable
  ‘.limmaGUIglobals’
SaveLimmaFile: no visible binding for global variable
  ‘limmaGUIenvironment’
SaveLimmaFile: no visible binding for global variable
  ‘.limmaGUIglobals’
SelectPlotSymbols: no visible binding for global variable
  ‘.limmaGUIglobals’
SelectPlotSymbols : onBrowse: no visible binding for global variable
  ‘.limmaGUIglobals’
SelectPlotSymbols : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
SelectPlotSymbols : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
SelectPlotSymbols : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
SetLayoutParameters: no visible binding for global variable
  ‘limmaGUIenvironment’
SetLayoutParameters: no visible binding for global variable
  ‘.limmaGUIglobals’
SetLayoutParameters : GetFromGAL: no visible binding for global
  variable ‘limmaGUIenvironment’
SetLayoutParameters : onOK: no visible binding for global variable
  ‘limmaGUIenvironment’
SetLayoutParameters : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
SetLayoutParameters : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
SetLayoutParameters : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
SetWD: no visible binding for global variable ‘.limmaGUIglobals’
TclRequire: no visible binding for global variable ‘.limmaGUIglobals’
TclRequire : onDestroy: no visible binding for global variable
  ‘.limmaGUIglobals’
TclRequire : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
TclRequire : onOK: no visible binding for global variable
  ‘limmaGUIenvironment’
UpDownOrBoth: no visible binding for global variable ‘.limmaGUIglobals’
UpDownOrBoth : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
UpDownOrBoth : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
UpdateSpotTypesStatus: no visible binding for global variable
  ‘limmaGUIenvironment’
VennDiagramPlot: no visible binding for global variable
  ‘limmaGUIenvironment’
VennDiagramPlot: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewDesignOrContrastsMatrixAsPairs: no visible binding for global
  variable ‘limmaGUIenvironment’
ViewDesignOrContrastsMatrixAsPairs: no visible binding for global
  variable ‘.limmaGUIglobals’
ViewDesignOrContrastsMatrixAsPairs : onOK: no visible binding for
  global variable ‘.limmaGUIglobals’
ViewDesignOrContrastsMatrixAsPairs : <anonymous>: no visible binding
  for global variable ‘.limmaGUIglobals’
ViewDesignOrContrastsMatrixInTable: no visible binding for global
  variable ‘limmaGUIenvironment’
ViewDesignOrContrastsMatrixInTable: no visible binding for global
  variable ‘.limmaGUIglobals’
ViewDesignOrContrastsMatrixInTable : onClose: no visible binding for
  global variable ‘.limmaGUIglobals’
ViewDesignOrContrastsMatrixInTable : <anonymous>: no visible binding
  for global variable ‘.limmaGUIglobals’
ViewExistingContrastsParameterization: no visible binding for global
  variable ‘limmaGUIenvironment’
ViewExistingContrastsParameterization: no visible binding for global
  variable ‘.limmaGUIglobals’
ViewExistingParameterization: no visible binding for global variable
  ‘limmaGUIenvironment’
ViewExistingParameterization: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewRNATargets: no visible binding for global variable
  ‘limmaGUIenvironment’
ViewRNATargets: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewRNATargets : onClose: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewRNATargets : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewSpotTypes: no visible binding for global variable
  ‘limmaGUIenvironment’
ViewSpotTypes: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewSpotTypes : onUpdate: no visible binding for global variable
  ‘limmaGUIenvironment’
ViewSpotTypes : onUpdate: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewSpotTypes : onClose: no visible binding for global variable
  ‘.limmaGUIglobals’
ViewSpotTypes : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
WithinBetweenOrBoth: no visible binding for global variable
  ‘.limmaGUIglobals’
WithinBetweenOrBoth : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
WithinBetweenOrBoth : <anonymous>: no visible binding for global
  variable ‘.limmaGUIglobals’
chooseDir: no visible binding for global variable ‘.limmaGUIglobals’
ebayesBoxPlots: no visible binding for global variable
  ‘limmaGUIenvironment’
ebayesBoxPlots: no visible binding for global variable
  ‘.limmaGUIglobals’
ebayesBoxPlots: no visible binding for global variable
  ‘limmaDataSetNameText’
evalRcode: no visible binding for global variable ‘.limmaGUIglobals’
evalRcode : SaveRSourceFile: no visible global function definition for
  ‘tkputs’
evalRcode : runOverall: no visible binding for global variable
  ‘.limmaGUIglobals’
evalRcode : runOverall: no visible binding for global variable
  ‘limmaGUIenvironment’
evalRcode : runOverall : SaveTextResults: no visible global function
  definition for ‘tkputs’
evalRcode : MakeLimmaGUIMenu: no visible global function definition for
  ‘GetMenuName’
evalRcode : MakeLimmaGUIMenu: no visible global function definition for
  ‘addMenuItem’
initGlobals: no visible binding for global variable
  ‘limmaGUIenvironment’
initGlobals: no visible binding for '<<-' assignment to
  ‘NEOffsetDefault’
initGlobals: no visible binding for global variable ‘NEOffsetDefault’
limmaGUI: no visible binding for global variable ‘limmaGUIenvironment’
limmaGUI: no visible binding for global variable ‘.limmaGUIglobals’
limmaGUI: possible error in Try(limmaGUIglobals$mainTreeHeight, 20):
  unused argument (20)
limmaGUI : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
onDestroy: no visible binding for global variable ‘limmaGUIenvironment’
onExit: no visible binding for global variable ‘limmaGUIenvironment’
onExit: no visible binding for global variable ‘.limmaGUIglobals’
plotMAColorCoded: no visible binding for global variable
  ‘limmaGUIenvironment’
plotMAColorCoded: no visible binding for global variable
  ‘.limmaGUIglobals’
showGAL: no visible binding for global variable ‘limmaGUIenvironment’
showGAL: no visible binding for global variable ‘.limmaGUIglobals’
showTopTable: no visible binding for global variable
  ‘limmaGUIenvironment’
showTopTable: no visible binding for global variable ‘.limmaGUIglobals’
showTopTable : onOK: no visible binding for global variable
  ‘.limmaGUIglobals’
showTopTable : onCancel: no visible binding for global variable
  ‘.limmaGUIglobals’
showTopTable : <anonymous>: no visible binding for global variable
  ‘.limmaGUIglobals’
* 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’ ... NOTE
The following files should probably not be installed:
  ‘LinModIntro.tex’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* 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

NOTE: There were 3 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/limmaGUI.Rcheck/00check.log’
for details.

limmaGUI.Rcheck/00install.out:

* installing *source* package ‘limmaGUI’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘extract.Rnw’ 
   ‘limmaGUI.Rnw’ 
** testing if installed package can be loaded

* DONE (limmaGUI)