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Package 317/467HostnameOS / ArchBUILDCHECKBUILD BIN
oneChannelGUI 1.18.7
Raffaele A Calogero
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/oneChannelGUI
Last Changed Rev: 56797 / Revision: 59457
Last Changed Date: 2011-07-18 08:59:07 -0700 (Mon, 18 Jul 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: oneChannelGUI
Version: 1.18.7
Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch oneChannelGUI_1.18.7.tar.gz
StartedAt: 2011-10-20 15:42:29 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 15:50:42 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 493.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: oneChannelGUI.Rcheck
Warnings: 2

Command output

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/oneChannelGUI.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.18.7'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'oneChannelGUI' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
* 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 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 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'
.gettingEG: no visible binding for global variable 'huex.annotation'
.gettingEG: no visible binding for global variable 'moex.annotation'
.gettingEG: no visible binding for global variable 'raex.annotation'
.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'
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'
GOenrichment: no visible binding for global variable 'huex.annotation'
GOenrichment: no visible binding for global variable 'moex.annotation'
GOenrichment: no visible binding for global variable 'raex.annotation'
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'
IPAlistFilter: no visible binding for global variable 'huex.annotation'
IPAlistFilter: no visible binding for global variable 'moex.annotation'
IPAlistFilter: no visible binding for global variable 'raex.annotation'
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'
extractAffyids: no visible binding for global variable
  'huex.annotation'
extractAffyids: no visible binding for global variable
  'moex.annotation'
extractAffyids: no visible binding for global variable
  'raex.annotation'
extractmirTargets: no visible binding for global variable
  '.affylmGUIglobals'
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 'huex.annotation'
limma2paired: no visible binding for global variable 'moex.annotation'
limma2paired: no visible binding for global variable 'raex.annotation'
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'
rankProd: no visible global function definition for 'getDataEnv'
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'
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 'huex.annotation'
showTopTable: no visible binding for global variable 'moex.annotation'
showTopTable: no visible binding for global variable 'raex.annotation'
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'
templA: no visible binding for global variable 'huex.annotation'
templA: no visible binding for global variable 'moex.annotation'
templA: no visible binding for global variable 'raex.annotation'
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'
variantSI: no visible binding for global variable 'huex.variantexons'
variantSI: no visible binding for global variable 'moex.variantexons'
variantSI: no visible binding for global variable 'raex.variantexons'
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  Warning: large data file(s) saved inefficiently:
            size ASCII compress
  bofa.rda 101Kb  TRUE     none
  hsfa.rda 166Kb  TRUE     none
  mmfa.rda 107Kb  TRUE     none
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   NGS.Rnw
   install.Rnw
   oneChannelGUI.Rnw
   standAloneFunctions.Rnw
   whatIsNew.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, 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
** 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