oneChannelGUI 1.19.4
Raffaele A Calogero
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oneChannelGUI | | Last Changed Rev: 56323 / Revision: 56603 | | Last Changed Date: 2011-06-20 02:30:33 -0700 (Mon, 20 Jun 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/oneChannelGUI.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'oneChannelGUI/DESCRIPTION' ... OK
* this is package 'oneChannelGUI' version '1.19.4'
* 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 installed package size ... NOTE
installed size is 9.3Mb
sub-directories of 1Mb or more:
doc 8.0Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking 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
.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 '.affylmGUIglobals'
ExportNormalizedExpressionValues1: no visible binding for global
variable 'affylmGUIenvironment'
ExportfeatureNames: no visible binding for global variable
'.affylmGUIglobals'
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'
NewLimmaFileNGS: 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'
SaveLimmaFile: no visible binding for global variable
'affylmGUIenvironment'
SaveLimmaFile: no visible binding for global variable
'.affylmGUIglobals'
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'
bowtieDownload: no visible binding for global variable
'.affylmGUIglobals'
bowtieDownload: no visible binding for global variable
'affylmGUIenvironment'
bowtieDownload: no visible global function definition for
'.bowtieGenomes'
bowtieDownload : onCancel: no visible binding for global variable
'.affylmGUIglobals'
bowtieDownload : onOK: no visible binding for global variable
'.affylmGUIglobals'
bowtieDownload : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
bowtieGenomes: no visible binding for global variable
'.affylmGUIglobals'
bowtieGenomes : onCancel: no visible binding for global variable
'.affylmGUIglobals'
bowtieGenomes : onOK: no visible binding for global variable
'.affylmGUIglobals'
bowtieGenomes : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
bowtieRun : onOK: no visible binding for global variable
'affylmGUIenvironment'
bowtieRun: no visible binding for global variable
'affylmGUIenvironment'
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 '.affylmGUIglobals'
changeMenu: no visible binding for global variable
'affylmGUIenvironment'
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'
edgeRNorm: no visible global function definition for 'plotMDS.dge'
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'
extPckInfo: 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: 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
'.affylmGUIglobals'
geneExonLibs: no visible binding for global variable
'affylmGUIenvironment'
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
'.affylmGUIglobals'
ngsperlDownload: no visible binding for global variable
'affylmGUIenvironment'
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'
qcMDS: no visible global function definition for 'plotMDS.dge'
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 '.affylmGUIglobals'
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'
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: 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
'.affylmGUIglobals'
whichKindOfArray: no visible binding for global variable
'affylmGUIenvironment'
whichKindOfArray: no visible binding for '<<-' assignment to
'ReturnVal'
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
Note: significantly better compression could be obtained
by using tools::resaveRdaFiles() or R CMD build --resave-data
old_size new_size compress
bofa.rda 101Kb 17Kb bzip2
hsfa.rda 166Kb 28Kb bzip2
mmfa.rda 107Kb 18Kb bzip2
ncHs.data.rda 94Kb 74Kb xz
ncMm.data.rda 64Kb 48Kb xz
ncRn.data.rda 65Kb 49Kb xz
rnfa.rda 66Kb 12Kb bzip2
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
'/Users/biocbuild/bbs-2.9-bioc/meat/oneChannelGUI.Rcheck/00check.log'
for details
* 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
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'Exon-level.analysis.Rnw'
'RNAseq.Rnw'
'gene-level.analysis.Rnw'
'install.Rnw'
'standAloneFunctions.Rnw'
'whatIsNew.Rnw'
** testing if installed package can be loaded
To begin, type oneChannelGUI()
* DONE (oneChannelGUI)