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Package 292/436HostnameOS / ArchBUILDCHECKBUILD BIN
oneChannelGUI 1.17.10
Raffaele A Calogero
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oneChannelGUI
Last Changed Rev: 53129 / Revision: 53255
Last Changed Date: 2011-02-23 14:35:36 -0800 (Wed, 23 Feb 2011)
lamb2 Linux (openSUSE 11.2) / 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 [ WARNINGS ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  OK  OK 

Summary

Package: oneChannelGUI
Version: 1.17.10
Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings oneChannelGUI_1.17.10.tar.gz
StartedAt: 2011-02-24 21:04:35 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 21:16:19 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 704.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: oneChannelGUI.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/oneChannelGUI.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oneChannelGUI/DESCRIPTION' ... OK
* this is package 'oneChannelGUI' version '1.17.10'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'oneChannelGUI' can be installed ... 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
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
.GetContrasts: no visible binding for global variable
  'affylmGUIenvironment'
.GetContrasts: no visible global function definition for 'limmaExon'
.aptDir: no visible binding for global variable '.affylmGUIglobals'
.consistentFilter: no visible binding for global variable
  '.affylmGUIglobals'
.consistentFilter: no visible binding for global variable
  'affylmGUIenvironment'
.consistentFilter : onOK: no visible binding for global variable
  'affylmGUIenvironment'
.consistentFilter : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
.downloadLibs: no visible binding for global variable
  '.affylmGUIglobals'
.downloadLibs: no visible binding for global variable
  'affylmGUIenvironment'
.exonTopTable: no visible binding for global variable
  'affylmGUIenvironment'
.fromNGStoDf: no visible binding for global variable 'tmpIR'
.gettingEG: no visible binding for global variable
  'affylmGUIenvironment'
.gettingOneEG: no visible binding for global variable
  '.affylmGUIglobals'
.gettingOneEG: no visible binding for global variable
  'affylmGUIenvironment'
.mappingWgenominator: no visible binding for global variable
  'affylmGUIenvironment'
.pamr.confusion.mod: no visible binding for global variable
  'which.is.max'
.rawpCheckExons: no visible binding for global variable
  'affylmGUIenvironment'
.rawpCheckExons: no visible binding for global variable
  '.affylmGUIglobals'
.resize: no visible binding for global variable '.affylmGUIglobals'
.resize: no visible binding for global variable 'affylmGUIenvironment'
.resize : onOK: no visible binding for global variable
  'affylmGUIenvironment'
.resize : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
AptMidas: no visible binding for global variable 'affylmGUIenvironment'
AptMidas: no visible binding for global variable '.affylmGUIglobals'
AptMidas: no visible binding for global variable 'tmp'
AptMidas: no visible binding for global variable 'tt'
ComputeContrasts: no visible binding for global variable
  'affylmGUIenvironment'
ComputeLinearModelFit: no visible binding for global variable
  'affylmGUIenvironment'
ComputeLinearModelFit: no visible binding for global variable
  '.affylmGUIglobals'
EG2probeset: no visible binding for global variable '.affylmGUIglobals'
EG2probeset: no visible binding for global variable
  'affylmGUIenvironment'
EG2probeset : OpenAFile: no visible binding for global variable
  '.affylmGUIglobals'
ExportNormalizedExpressionValues: no visible binding for global
  variable 'affylmGUIenvironment'
ExportNormalizedExpressionValues1: no visible binding for global
  variable 'affylmGUIenvironment'
ExportfeatureNames: no visible binding for global variable
  'affylmGUIenvironment'
GOenrichment: no visible binding for global variable
  '.affylmGUIglobals'
GOenrichment: no visible binding for global variable
  'affylmGUIenvironment'
GOenrichment : onOK: no visible binding for '<<-' assignment to
  'ReturnVal'
GOenrichment : onOK: no visible binding for global variable
  '.affylmGUIglobals'
GOenrichment : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
GOenrichment : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
GOenrichment: no visible binding for global variable 'ReturnVal'
GOenrichment : OpenAFile: 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'
IPAlistFilter: no visible binding for global variable
  'affylmGUIenvironment'
IPAlistFilter: no visible binding for global variable
  '.affylmGUIglobals'
ML.edesign: no visible binding for global variable
  'affylmGUIenvironment'
ML.edesign: no visible binding for global variable '.affylmGUIglobals'
ML.edesign : onClose: no visible binding for global variable
  '.affylmGUIglobals'
ML.edesign : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
NGSreformat: no visible binding for global variable
  'affylmGUIenvironment'
NGSreformat : onOK: no visible binding for global variable
  'affylmGUIenvironment'
NewLimmaFile: no visible binding for global variable
  'affylmGUIenvironment'
NormalizeNow: no visible binding for global variable
  'affylmGUIenvironment'
NormalizeNow: no visible binding for global variable
  '.affylmGUIglobals'
OpenAFile: no visible binding for global variable '.affylmGUIglobals'
OpenAGeoFile: no visible binding for global variable
  '.affylmGUIglobals'
OpenAGeoFile: no visible binding for global variable
  'affylmGUIenvironment'
OpenALimmaFile: no visible binding for global variable
  'affylmGUIenvironment'
OpenBeadStudioFiles : onOK: no visible binding for global variable
  'affylmGUIenvironment'
OpenBeadStudioFiles: no visible binding for global variable
  'affylmGUIenvironment'
OpenCDFandTargetsfiles : onOK: no visible binding for global variable
  'affylmGUIenvironment'
OpenCDFandTargetsfiles: no visible binding for global variable
  'affylmGUIenvironment'
OpenExonandTargetsfiles : onOK: no visible binding for global variable
  'affylmGUIenvironment'
OpenExonandTargetsfiles: no visible binding for global variable
  'affylmGUIenvironment'
OpenExonandTargetsfiles: no visible binding for '<<-' assignment to
  'ReturnValX'
OpenExonandTargetsfiles : onOK: no visible binding for '<<-' assignment
  to 'ReturnValX'
OpenExonandTargetsfiles: no visible binding for global variable
  'ReturnValX'
OpenGeoFiles : onOK: no visible binding for global variable
  'affylmGUIenvironment'
OpenGeoFiles: no visible binding for global variable
  'affylmGUIenvironment'
OpenGeoFiles: no visible binding for global variable 'geoVSbioc'
OpenLargefiles : onOK: no visible binding for global variable
  'affylmGUIenvironment'
OpenLargefiles: no visible binding for global variable
  'affylmGUIenvironment'
OpenNgsfiles : onOK: no visible binding for global variable
  'affylmGUIenvironment'
OpenNgsfiles: no visible binding for global variable
  'affylmGUIenvironment'
OpenmiRExpress : onOK: no visible binding for global variable
  'affylmGUIenvironment'
OpenmiRExpress: no visible binding for global variable
  'affylmGUIenvironment'
OpenmiRProfiles : onOK: no visible binding for global variable
  'affylmGUIenvironment'
OpenmiRProfiles: no visible binding for global variable
  'affylmGUIenvironment'
OpenmiRShrimp : onOK: no visible binding for global variable
  'affylmGUIenvironment'
OpenmiRShrimp: no visible binding for global variable
  'affylmGUIenvironment'
OpenmiRanalyserfiles : onOK: no visible binding for global variable
  'affylmGUIenvironment'
OpenmiRanalyserfiles: no visible binding for global variable
  'affylmGUIenvironment'
PlotOptionsv1: no visible binding for global variable
  '.affylmGUIglobals'
PlotOptionsv1 : onOK: no visible binding for global variable
  '.affylmGUIglobals'
PlotOptionsv1 : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
Reads2logos: no visible binding for global variable '.affylmGUIglobals'
Reads2logos: no visible binding for global variable
  'affylmGUIenvironment'
Reads2logos : onOK: no visible binding for global variable
  'affylmGUIenvironment'
Reads2logos : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
Reads2logos : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
Reads2logos : onOK: no visible binding for global variable
  '.affylmGUIglobals'
RmiRInterface: no visible binding for global variable
  '.affylmGUIglobals'
RmiRInterface : onOK: no visible binding for global variable
  '.affylmGUIglobals'
RmiRInterface : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
RmiRInterface : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
SaveAsLimmaFile: no visible binding for global variable
  '.affylmGUIglobals'
SaveAsLimmaFile: no visible binding for global variable
  'affylmGUIenvironment'
SetED: no visible binding for global variable '.affylmGUIglobals'
VennDiagram: no visible binding for global variable '.affylmGUIglobals'
VennDiagram : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
VennDiagram : onOK: no visible binding for global variable
  '.affylmGUIglobals'
VennDiagram : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
VennDiagram: no visible binding for global variable
  'affylmGUIenvironment'
VennDiagram : plotFunction: no visible binding for global variable
  'include'
VennDiagram: no visible global function definition for 'tkrplot'
addAnnLib: no visible binding for global variable
  'affylmGUIenvironment'
addAnnLib: no visible binding for global variable '.affylmGUIglobals'
addAnnLib : onOK: no visible binding for global variable
  'affylmGUIenvironment'
addAnnLib : onOK: no visible binding for global variable
  '.affylmGUIglobals'
addAnnLib : <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'
affyPlotMA : CopyToClip: no visible global function definition for
  'tkrreplot'
affyPlotMA: no visible global function definition for 'tkrplot'
annotateNGSeset: no visible binding for global variable
  '.affylmGUIglobals'
annotateNGSeset: no visible binding for global variable
  'affylmGUIenvironment'
aptFolder: no visible binding for global variable '.affylmGUIglobals'
aptFolder: no visible binding for global variable
  'affylmGUIenvironment'
bayseqInterface: no visible binding for global variable
  '.affylmGUIglobals'
bayseqInterface : onOK: no visible binding for global variable
  'affylmGUIenvironment'
bayseqInterface : onOK: no visible binding for global variable
  '.affylmGUIglobals'
bayseqInterface : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
bayseqInterface: no visible binding for global variable
  'affylmGUIenvironment'
bayseqInterface : onOK: no visible binding for '<<-' assignment to
  'ReturnVal'
bayseqInterface : onCancel: no visible binding for '<<-' assignment to
  'ReturnVal'
bayseqInterface : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
bayseqInterface: no visible binding for global variable 'ReturnVal'
biomartFilter: no visible binding for global variable
  '.affylmGUIglobals'
buildingLocalAnnotation: no visible binding for global variable
  '.affylmGUIglobals'
buildingLocalAnnotation : onOK: no visible binding for global variable
  'affylmGUIenvironment'
buildingLocalAnnotation : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
buildingLocalAnnotation: no visible binding for global variable
  'affylmGUIenvironment'
buildingLocalAnnotation : onOK: no visible binding for '<<-' assignment
  to 'ReturnNetaffx'
buildingLocalAnnotation : onOK: no visible binding for global variable
  '.affylmGUIglobals'
buildingLocalAnnotation : onCancel: no visible binding for global
  variable '.affylmGUIglobals'
buildingLocalAnnotation: no visible binding for global variable
  'ReturnNetaffx'
changeMenu: no visible binding for global variable
  'affylmGUIenvironment'
changeMenu: no visible binding for global variable '.affylmGUIglobals'
chooseEDir: no visible binding for global variable '.affylmGUIglobals'
colExtract: no visible binding for global variable '.affylmGUIglobals'
colExtract : onOK: no visible binding for global variable
  'affylmGUIenvironment'
colExtract : onOK: no visible binding for global variable
  '.affylmGUIglobals'
colExtract : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
colExtract: no visible binding for global variable
  'affylmGUIenvironment'
combineGeoMSF: no visible binding for global variable
  '.affylmGUIglobals'
combineGeoMSF : onOK: no visible binding for global variable
  '.affylmGUIglobals'
combineGeoMSF : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
combineGeoMSF: no visible binding for global variable
  'affylmGUIenvironment'
combining2eSet: no visible binding for global variable
  '.affylmGUIglobals'
consistentFilters: no visible binding for global variable
  '.affylmGUIglobals'
consistentFilters: no visible binding for global variable
  'affylmGUIenvironment'
consistentFilters : onOK: no visible binding for '<<-' assignment to
  'ReturnFilter'
consistentFilters : onOK: no visible binding for global variable
  '.affylmGUIglobals'
consistentFilters : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
consistentFilters : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
consistentFilters: no visible binding for global variable
  'ReturnFilter'
consistentFilters : onOK: no visible binding for global variable
  'affylmGUIenvironment'
cosieWrapper: no visible binding for global variable
  'affylmGUIenvironment'
cosieWrapper: no visible binding for global variable
  '.affylmGUIglobals'
createGeoTarget: no visible binding for global variable
  '.affylmGUIglobals'
crosshybFilter: no visible binding for global variable
  'affylmGUIenvironment'
crosshybFilter: no visible binding for global variable
  '.affylmGUIglobals'
crosshybFilter : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
crosshybFilter : onOK: no visible binding for global variable
  '.affylmGUIglobals'
crosshybFilter : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
ctrtrtHeatmap: no visible binding for global variable
  'affylmGUIenvironment'
ctrtrtHeatmap: no visible binding for global variable
  '.affylmGUIglobals'
dabgFilter: no visible binding for global variable
  'affylmGUIenvironment'
dabgFilter: no visible binding for global variable '.affylmGUIglobals'
dabgFilter : onOK: no visible binding for '<<-' assignment to
  'ReturnVal'
dabgFilter : onOK: no visible binding for global variable
  '.affylmGUIglobals'
dabgFilter : onCancel: no visible binding for '<<-' assignment to
  'ReturnVal'
dabgFilter : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
dabgFilter : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
dabgFilter: no visible binding for global variable 'ReturnVal'
delete.ML: no visible binding for global variable
  'affylmGUIenvironment'
delete.ML: no visible binding for global variable '.affylmGUIglobals'
deleteLocalData: no visible binding for global variable
  '.affylmGUIglobals'
dfMAplot: no visible binding for global variable '.affylmGUIglobals'
dfMAplot : onOK: no visible binding for '<<-' assignment to 'ReturnVal'
dfMAplot : onOK: no visible binding for global variable
  '.affylmGUIglobals'
dfMAplot : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
dfMAplot : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
dfMAplot: no visible binding for global variable 'ReturnVal'
eSet4meV: no visible binding for global variable 'affylmGUIenvironment'
edgeRNorm: no visible binding for global variable '.affylmGUIglobals'
edgeRNorm: no visible binding for global variable
  'affylmGUIenvironment'
edgerInterface: no visible binding for global variable
  'affylmGUIenvironment'
edgerInterface: no visible binding for global variable
  '.affylmGUIglobals'
edgerInterface : onOK: no visible binding for global variable
  'affylmGUIenvironment'
edgerInterface : onOK: no visible binding for global variable
  '.affylmGUIglobals'
edgerInterface : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
edgerInterface : onOK: no visible binding for '<<-' assignment to
  'ReturnVal'
edgerInterface : onCancel: no visible binding for '<<-' assignment to
  'ReturnVal'
edgerInterface : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
edgerInterface: no visible binding for global variable 'ReturnVal'
erankProdAltSpl: no visible binding for global variable
  'affylmGUIenvironment'
erankProdAltSpl: no visible binding for global variable
  '.affylmGUIglobals'
erankProdAltSpl : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
erankProdAltSpl : onOK: no visible binding for global variable
  '.affylmGUIglobals'
erankProdAltSpl : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
erankProdAltSpl: no visible binding for '<<-' assignment to 'ReturnVal'
erankProdAltSpl : onOK: no visible binding for '<<-' assignment to
  'ReturnVal'
erankProdAltSpl: no visible binding for global variable 'ReturnVal'
erankProdAltSplFilter: no visible binding for global variable
  'affylmGUIenvironment'
erankProdAltSplFilter: no visible binding for global variable
  '.affylmGUIglobals'
erankProdAltSplFilter : onOK: no visible binding for global variable
  'affylmGUIenvironment'
erankProdAltSplFilter : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
exonContrasts: no visible binding for global variable
  'affylmGUIenvironment'
exonTopTableExtract: no visible binding for global variable
  'affylmGUIenvironment'
exonTopTableExtract: no visible binding for global variable
  '.affylmGUIglobals'
exonTopTableExtract : onOK: no visible binding for global variable
  'affylmGUIenvironment'
exonTopTableExtract : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
exonsSpecific2as: no visible binding for global variable
  '.affylmGUIglobals'
exonsSpecific2as: no visible binding for global variable
  'affylmGUIenvironment'
exportFASTA: no visible binding for global variable '.affylmGUIglobals'
exportFASTA : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
exportFASTA : onOK: no visible binding for global variable
  '.affylmGUIglobals'
exportFASTA : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
extractAffyids: no visible binding for global variable
  '.affylmGUIglobals'
extractAffyids: no visible binding for global variable
  'affylmGUIenvironment'
extractAffyids : onOK: no visible binding for global variable
  'affylmGUIenvironment'
extractAffyids : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
extractAffyids : OpenAFile: no visible binding for global variable
  '.affylmGUIglobals'
extractmirTargets: no visible binding for global variable
  '.affylmGUIglobals'
extractmirTargets: no visible binding for global variable 'mySel1'
extractmirTargets : onOK: no visible binding for global variable
  'affylmGUIenvironment'
extractmirTargets : onOK: no visible binding for global variable
  '.affylmGUIglobals'
extractmirTargets : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
extractmirTargets: no visible binding for global variable
  'affylmGUIenvironment'
filteringTable: no visible binding for global variable
  '.affylmGUIglobals'
filteringmiRtargets: no visible binding for global variable
  '.affylmGUIglobals'
filteringmiRtargets : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
filteringmiRtargets : onOK: no visible binding for global variable
  '.affylmGUIglobals'
filteringmiRtargets : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
geneExonLibs: no visible binding for global variable
  'affylmGUIenvironment'
geneExonLibs: no visible binding for global variable
  '.affylmGUIglobals'
genomePlot: no visible binding for global variable '.affylmGUIglobals'
genomePlot: no visible binding for global variable
  'affylmGUIenvironment'
genomePlot : onOK: no visible binding for global variable
  'affylmGUIenvironment'
genomePlot : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
genomePlot: no visible binding for global variable
  'crosshybraex.annotation'
getNGSannotation: no visible binding for '<<-' assignment to
  'ReturnAnn'
getNGSannotation: no visible binding for global variable
  '.affylmGUIglobals'
getNGSannotation : onOK: no visible binding for '<<-' assignment to
  'ReturnAnn'
getNGSannotation : onOK: no visible binding for global variable
  '.affylmGUIglobals'
getNGSannotation : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
getNGSannotation : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
getNGSannotation: no visible binding for global variable 'ReturnAnn'
getNGSannotation: no visible binding for global variable
  'affylmGUIenvironment'
initialize.extAffylmGUI: no visible binding for global variable
  'affylmGUIenvironment'
initialize.extAffylmGUI: no visible binding for global variable
  '.affylmGUIglobals'
inspecting.one.splice.index: no visible binding for global variable
  '.affylmGUIglobals'
inspecting.one.splice.index: no visible binding for global variable
  'affylmGUIenvironment'
inspecting.one.splice.index : onOK: no visible binding for global
  variable 'affylmGUIenvironment'
inspecting.one.splice.index : <anonymous>: no visible binding for
  global variable '.affylmGUIglobals'
inspecting.splice.index: no visible binding for global variable
  '.affylmGUIglobals'
inspecting.splice.index: no visible binding for global variable
  'affylmGUIenvironment'
intensityFilter: no visible binding for global variable
  '.affylmGUIglobals'
intensityFilter : onOK: no visible binding for '<<-' assignment to
  'ReturnVal'
intensityFilter : onOK: no visible binding for global variable
  '.affylmGUIglobals'
intensityFilter : onCancel: no visible binding for '<<-' assignment to
  'ReturnVal'
intensityFilter : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
intensityFilter : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
intensityFilter: no visible binding for global variable 'ReturnVal'
intronicBg: no visible binding for global variable
  'affylmGUIenvironment'
intronicBg: no visible binding for global variable '.affylmGUIglobals'
intronicBg : onOK: no visible binding for global variable
  'affylmGUIenvironment'
intronicBg : onOK: no visible binding for global variable
  '.affylmGUIglobals'
intronicBg : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
iqrFilter: no visible binding for global variable '.affylmGUIglobals'
iqrFilter : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
iqrFilter : onOK: no visible binding for global variable
  '.affylmGUIglobals'
iqrFilter : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
largedatasetNorm: no visible binding for global variable
  'affylmGUIenvironment'
largedatasetNorm: no visible binding for global variable
  '.affylmGUIglobals'
largedatasetNorm : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
largedatasetNorm : onOK: no visible binding for global variable
  '.affylmGUIglobals'
largedatasetNorm : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
libraryFilesDir: no visible binding for global variable
  '.affylmGUIglobals'
limma2paired: no visible binding for global variable
  'affylmGUIenvironment'
limma2paired: no visible binding for global variable
  '.affylmGUIglobals'
limma2paired : onOK: no visible binding for global variable
  '.affylmGUIglobals'
limma2paired : onHelp: possible error in help("topTable", htmlhelp =
  TRUE): unused argument(s) (htmlhelp = TRUE)
limma2paired : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
limma2paired : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
limma2paired: no visible binding for global variable 'annlib'
limmaExons: no visible binding for global variable
  'affylmGUIenvironment'
limmaExons: no visible binding for global variable '.affylmGUIglobals'
listFilter: no visible binding for global variable
  'affylmGUIenvironment'
listFilter: no visible binding for global variable '.affylmGUIglobals'
listFilter : OpenAFile: no visible binding for global variable
  '.affylmGUIglobals'
log2Conversion: no visible binding for global variable
  'affylmGUIenvironment'
log2Conversion: no visible binding for global variable
  '.affylmGUIglobals'
mRNAmiRCor: no visible binding for global variable '.affylmGUIglobals'
mRNAmiRCor: no visible binding for global variable
  'affylmGUIenvironment'
mRNAmiRCor : onOK: no visible binding for '<<-' assignment to
  'ReturnVal'
mRNAmiRCor : onOK: no visible binding for global variable
  '.affylmGUIglobals'
mRNAmiRCor : onCancel: no visible binding for '<<-' assignment to
  'ReturnVal'
mRNAmiRCor : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
mRNAmiRCor : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
mRNAmiRCor: no visible binding for global variable 'ReturnVal'
mRNAmiRCor : .OpenAmiRFile: no visible binding for global variable
  '.affylmGUIglobals'
mRNAmiRCor: possible error in Try(tkmessageBox(title = "Filtering by
  correlation", message = "The data set in oneChannelGUI and the miR
  data have the samples organized in different way!\nPlease modify the
  miRdata file to have the same samples organization as in the Target
  name of the dataset load in oneChannelGUI."), type = "error"): unused
  argument(s) (type = "error")
mRNAmiRCor: possible error in Try(tkmessageBox(title = "Filtering by
  correlation", message = "The data set in oneChannelGUI and the miR
  data do not contain the same number of samples!"), type = "error"):
  unused argument(s) (type = "error")
makeBED15: no visible binding for global variable '.affylmGUIglobals'
mapping2RefSeq: no visible binding for global variable
  '.affylmGUIglobals'
mapping2RefSeq: no visible binding for global variable
  'affylmGUIenvironment'
mapping2ensembl: no visible binding for global variable
  '.affylmGUIglobals'
mapping2ensembl: no visible binding for global variable
  'affylmGUIenvironment'
mapping2exon: no visible binding for global variable
  '.affylmGUIglobals'
mapping2exon: no visible binding for global variable
  'affylmGUIenvironment'
masigpro: no visible binding for global variable 'affylmGUIenvironment'
masigpro: no visible binding for global variable '.affylmGUIglobals'
masigpro : onOK: no visible binding for global variable
  '.affylmGUIglobals'
masigpro : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
masigpro : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
masigpro.edesign: no visible binding for global variable
  'affylmGUIenvironment'
masigpro.edesign: no visible binding for global variable
  '.affylmGUIglobals'
masigpro.edesign : onClose: no visible binding for global variable
  '.affylmGUIglobals'
masigpro.edesign : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
masigpro.view: no visible binding for global variable
  'affylmGUIenvironment'
masigpro.view: no visible binding for global variable
  '.affylmGUIglobals'
masigpro.view : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
masigpro.view : onOK: no visible binding for global variable
  '.affylmGUIglobals'
masigpro.view : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
masigpro.view : plotFunction: no visible binding for global variable
  'include'
masigpro.view: no visible global function definition for 'tkrplot'
masigpro.view : onOK: no visible binding for global variable
  'affylmGUIenvironment'
meVDownload: no visible binding for global variable '.affylmGUIglobals'
meVDownload: no visible binding for global variable
  'affylmGUIenvironment'
metaArrayIC: no visible binding for global variable
  'affylmGUIenvironment'
metaArrayIC: no visible binding for global variable '.affylmGUIglobals'
metaArrayMerge : OpenAFile: no visible binding for global variable
  '.affylmGUIglobals'
metaArrayMerge: no visible binding for global variable
  'affylmGUIenvironment'
metaArrayMerge: no visible binding for global variable
  '.affylmGUIglobals'
metaArrayMerge : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
metaArrayMerge : onOK: no visible binding for global variable
  '.affylmGUIglobals'
metaArrayMerge : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
midasFilter: no visible binding for global variable
  'affylmGUIenvironment'
midasFilter: no visible binding for global variable '.affylmGUIglobals'
midasFilter : onOK: no visible binding for global variable
  'affylmGUIenvironment'
midasFilter : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
myExpresso: no visible binding for global variable
  'affylmGUIenvironment'
myExpresso: no visible binding for global variable '.affylmGUIglobals'
ngsperlDownload: no visible binding for global variable
  'affylmGUIenvironment'
ngsperlDownload: no visible binding for global variable
  '.affylmGUIglobals'
normBoxplot: no visible binding for global variable
  'affylmGUIenvironment'
normBoxplot: no visible binding for global variable '.affylmGUIglobals'
ocPlotHist: no visible binding for global variable
  'affylmGUIenvironment'
ocPlotHist: no visible binding for global variable '.affylmGUIglobals'
ocPlotHist : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
ocPlotHist : onOK: no visible binding for global variable
  '.affylmGUIglobals'
ocPlotHist : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
ocPlotPCA: no visible binding for global variable
  'affylmGUIenvironment'
ocPlotPCA: no visible binding for global variable '.affylmGUIglobals'
ocPlotPCA : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
ocPlotPCA : onOK: no visible binding for global variable
  '.affylmGUIglobals'
ocPlotPCA : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
oneChannelGUI: no visible binding for global variable
  'affylmGUIenvironment'
oneChannelGUI: no visible binding for global variable
  '.affylmGUIglobals'
plierToZero: no visible binding for global variable
  'affylmGUIenvironment'
plierToZero: no visible binding for global variable '.affylmGUIglobals'
plotGO: no visible binding for global variable 'affylmGUIenvironment'
plotGO: no visible binding for global variable '.affylmGUIglobals'
plotGO : onOK: no visible binding for global variable
  'affylmGUIenvironment'
plotGO : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
plotGO : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
plotGO : onOK: no visible binding for global variable
  '.affylmGUIglobals'
plotVariantSI: no visible binding for global variable
  '.affylmGUIglobals'
plotVariantSI : onOK: no visible binding for global variable
  'affylmGUIenvironment'
plotVariantSI : onOK: no visible binding for global variable
  '.affylmGUIglobals'
plotVariantSI : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
plotVariantSI: no visible binding for global variable
  'affylmGUIenvironment'
qcMDS: no visible binding for global variable 'affylmGUIenvironment'
qcMDS: no visible binding for global variable '.affylmGUIglobals'
rankProd: no visible binding for global variable 'affylmGUIenvironment'
rankProd: no visible binding for global variable '.affylmGUIglobals'
rankProd : onOK: no visible binding for '<<-' assignment to 'ReturnVal'
rankProd : onOK: no visible binding for global variable
  '.affylmGUIglobals'
rankProd : onCancel: no visible binding for '<<-' assignment to
  'ReturnVal'
rankProd : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
rankProd : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
rankProd: no visible binding for global variable 'ReturnVal'
rankingConversion: no visible binding for global variable
  'affylmGUIenvironment'
rankingConversion: no visible binding for global variable
  '.affylmGUIglobals'
rawBoxplotPN: no visible binding for global variable
  'affylmGUIenvironment'
rawBoxplotPN: no visible binding for global variable
  '.affylmGUIglobals'
rawpCheck: no visible binding for global variable
  'affylmGUIenvironment'
rawpCheck: no visible binding for global variable '.affylmGUIglobals'
recoverUnfiltered: no visible binding for global variable
  '.affylmGUIglobals'
recoverUnfiltered: no visible binding for global variable
  'affylmGUIenvironment'
recoverUnfiltered: no visible binding for global variable 'x.exon'
refiningPeaks: no visible binding for global variable
  'affylmGUIenvironment'
refiningPeaks: no visible binding for global variable
  '.affylmGUIglobals'
refiningPeaks : onOK: no visible binding for global variable
  'affylmGUIenvironment'
refiningPeaks : onOK: no visible binding for global variable
  '.affylmGUIglobals'
refiningPeaks : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
reformatGdl: no visible binding for global variable '.affylmGUIglobals'
reformatGdl: no visible binding for global variable
  'affylmGUIenvironment'
reformatGdl : onOK: no visible binding for global variable
  'affylmGUIenvironment'
reformatGdl : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
refseqDownload: no visible binding for global variable
  '.affylmGUIglobals'
refseqDownload: no visible binding for global variable
  'affylmGUIenvironment'
retrieveMirTargets: no visible binding for global variable
  '.affylmGUIglobals'
retrieveMirTargets : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
retrieveMirTargets : onOK: no visible binding for global variable
  '.affylmGUIglobals'
retrieveMirTargets : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
retrieveMirTargets : onOK: no visible binding for global variable
  'affylmGUIenvironment'
retrieveMirTargets: no visible binding for global variable
  'affylmGUIenvironment'
retrieveMirTargets: no visible binding for global variable 'mycol'
retrieveMirTargets: no visible binding for global variable 'miRnum'
retrievePSRseq: no visible binding for global variable
  '.affylmGUIglobals'
retrievePSRseq: no visible binding for global variable
  'affylmGUIenvironment'
retrievePSRseq1gid: no visible binding for global variable
  '.affylmGUIglobals'
retrievePSRseq1gid: no visible binding for global variable
  'affylmGUIenvironment'
retrievePSRseq1gid : onOK: no visible binding for global variable
  'affylmGUIenvironment'
retrievePSRseq1gid : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
reviqrFilter: no visible binding for global variable
  '.affylmGUIglobals'
reviqrFilter : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
reviqrFilter : onOK: no visible binding for global variable
  '.affylmGUIglobals'
reviqrFilter : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
runningJetta: no visible binding for global variable
  '.affylmGUIglobals'
runningJetta: no visible binding for global variable
  'affylmGUIenvironment'
runningJetta: no visible binding for global variable 'tmp'
runningJetta : onOK: no visible binding for global variable
  '.affylmGUIglobals'
runningJetta : onOK: no visible binding for global variable
  'affylmGUIenvironment'
runningJetta : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
runningJetta : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
runningJetta: no visible global function definition for 'jetta.do.mads'
runningJetta: no visible global function definition for
  'jetta.read.expression'
runningJetta: no visible global function definition for
  'jetta.read.mads.output'
sample.size.evaluation: no visible binding for global variable
  'affylmGUIenvironment'
sample.size.evaluation: no visible binding for global variable
  '.affylmGUIglobals'
sample.size.evaluation : onOK: no visible binding for global variable
  'affylmGUIenvironment'
sample.size.evaluation : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
sample.size.evaluation : common.sd: no visible binding for global
  variable 'affylmGUIenvironment'
sample.size.evaluation : onCancel: no visible binding for global
  variable '.affylmGUIglobals'
sample.size.evaluation : onOK: no visible binding for global variable
  '.affylmGUIglobals'
sample.size.evaluation1: no visible binding for global variable
  'affylmGUIenvironment'
sample.size.evaluation1: no visible binding for global variable
  '.affylmGUIglobals'
sample.size.evaluation1 : onCancel: no visible binding for global
  variable '.affylmGUIglobals'
sample.size.evaluation1 : onOK: no visible binding for global variable
  '.affylmGUIglobals'
sample.size.evaluation1 : <anonymous>: no visible binding for global
  variable '.affylmGUIglobals'
sample.size.evaluation1 : common.sd: no visible binding for global
  variable 'affylmGUIenvironment'
showDataset: no visible binding for global variable
  'affylmGUIenvironment'
showTopTable: no visible binding for global variable
  'affylmGUIenvironment'
showTopTable : onHelp: possible error in help("topTable", htmlhelp =
  TRUE): unused argument(s) (htmlhelp = TRUE)
showTopTable: no visible binding for global variable 'annlib'
siggenes: no visible binding for global variable 'affylmGUIenvironment'
siggenes: no visible binding for global variable '.affylmGUIglobals'
siggenes : onOK: no visible binding for global variable
  'affylmGUIenvironment'
siggenes : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
simFilter: no visible binding for global variable '.affylmGUIglobals'
simFilter : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
spliceIndex: no visible binding for global variable
  'affylmGUIenvironment'
spliceIndex: no visible binding for global variable '.affylmGUIglobals'
startmeV: no visible binding for global variable 'affylmGUIenvironment'
startmeV: no visible binding for global variable '.affylmGUIglobals'
targetWidget: possible error in sub("^/?([^/]*/)*", "", widgetfiles,
  extended = TRUE): unused argument(s) (extended = TRUE)
templA: no visible binding for global variable 'affylmGUIenvironment'
templA: no visible binding for global variable '.affylmGUIglobals'
templA : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
templA : onOK: no visible binding for global variable
  '.affylmGUIglobals'
templA : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
trainTest: no visible binding for global variable
  'affylmGUIenvironment'
trainTest: no visible binding for global variable '.affylmGUIglobals'
trainTest : onOK: no visible binding for global variable
  '.affylmGUIglobals'
trainTest : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
trainTest : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
trainTest: possible error in Try(x = exprs(testAffyData)): unused
  argument(s) (x = exprs(testAffyData))
trainTest : onOK: no visible binding for global variable
  'affylmGUIenvironment'
updateLibs: no visible binding for global variable '.affylmGUIglobals'
updateLibs: no visible global function definition for
  'biocinstallRepos'
variantExons: no visible binding for global variable
  '.affylmGUIglobals'
variantSI: no visible binding for global variable '.affylmGUIglobals'
variantSI: no visible binding for global variable
  'affylmGUIenvironment'
whichKindOfArray: no visible binding for global variable
  'affylmGUIenvironment'
whichKindOfArray: no visible binding for '<<-' assignment to
  'ReturnVal'
whichKindOfArray: no visible binding for global variable
  '.affylmGUIglobals'
whichKindOfArray : onOK: no visible binding for '<<-' assignment to
  'ReturnVal'
whichKindOfArray : onOK: no visible binding for global variable
  '.affylmGUIglobals'
whichKindOfArray : onCancel: no visible binding for global variable
  '.affylmGUIglobals'
whichKindOfArray : <anonymous>: no visible binding for global variable
  '.affylmGUIglobals'
whichKindOfArray: no visible binding for global variable 'ReturnVal'
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignettes without corresponding PDF:


D:/biocbld/bbs-2.8-bioc/meat/oneChannelGUI.Rcheck/00_pkg_src/oneChannelGUI/inst/doc/NGS.Rnw
D:/biocbld/bbs-2.8-bioc/meat/oneChannelGUI.Rcheck/00_pkg_src/oneChannelGUI/inst/doc/install.Rnw
D:/biocbld/bbs-2.8-bioc/meat/oneChannelGUI.Rcheck/00_pkg_src/oneChannelGUI/inst/doc/oneChannelGUI.Rnw
D:/biocbld/bbs-2.8-bioc/meat/oneChannelGUI.Rcheck/00_pkg_src/oneChannelGUI/inst/doc/standAloneFunctions.Rnw
 SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/oneChannelGUI.Rcheck/00check.log'
for details

oneChannelGUI.Rcheck/00install.out:

* installing *source* package 'oneChannelGUI' ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

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

Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: affy
Loading required package: affyio
Loading required package: widgetTools
Loading required package: DynDoc
Loading required package: tools
Loading required package: Category
Loading required package: AnnotationDbi
Loading required package: graph
Loading required package: DBI

Attaching package: 'IRanges'

The following object(s) are masked from 'package:graph':

    union

The following object(s) are masked from 'package:Biobase':

    updateObject

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union


Attaching package: 'baySeq'

The following object(s) are masked from 'package:IRanges':

    rbind

The following object(s) are masked from 'package:base':

    rbind

Loading required package: Rsamtools
Loading required package: GenomicRanges
Loading required package: Biostrings

Attaching package: 'Biostrings'

The following object(s) are masked from 'package:graph':

    complement


Attaching package: 'Rsamtools'

The following object(s) are masked from 'package:DynDoc':

    path

Loading required package: ShortRead
Loading required package: lattice

Attaching package: 'ShortRead'

The following object(s) are masked from 'package:affy':

    intensity

Loading required package: intervals

Attaching package: 'intervals'

The following object(s) are masked from 'package:Biostrings':

    type

The following object(s) are masked from 'package:IRanges':

    reduce

Loading required package: genomeIntervals

Attaching package: 'genomeIntervals'

The following object(s) are masked from 'package:GenomicRanges':

    strand, strand<-

Loading required package: grid
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

To begin, type oneChannelGUI()

* DONE (oneChannelGUI)

oneChannelGUI.Rcheck/oneChannelGUI-Ex.timings:

nameusersystemelapsed
oneChannelGUI-package000
oneChannelGUI000