oneChannelGUI 1.17.10
Raffaele A Calogero
| Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oneChannelGUI | | Last Changed Rev: 53129 / Revision: 53255 | | Last Changed Date: 2011-02-23 14:35:36 -0800 (Wed, 23 Feb 2011) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | [ WARNINGS ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.4) / i386 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/oneChannelGUI.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oneChannelGUI/DESCRIPTION' ... OK
* this is package 'oneChannelGUI' version '1.17.10'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'oneChannelGUI' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
.GetContrasts: no visible binding for global variable
'affylmGUIenvironment'
.GetContrasts: no visible global function definition for 'limmaExon'
.aptDir: no visible binding for global variable '.affylmGUIglobals'
.consistentFilter: no visible binding for global variable
'.affylmGUIglobals'
.consistentFilter: no visible binding for global variable
'affylmGUIenvironment'
.consistentFilter : onOK: no visible binding for global variable
'affylmGUIenvironment'
.consistentFilter : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
.downloadLibs: no visible binding for global variable
'.affylmGUIglobals'
.downloadLibs: no visible binding for global variable
'affylmGUIenvironment'
.exonTopTable: no visible binding for global variable
'affylmGUIenvironment'
.fromNGStoDf: no visible binding for global variable 'tmpIR'
.gettingEG: no visible binding for global variable
'affylmGUIenvironment'
.gettingOneEG: no visible binding for global variable
'.affylmGUIglobals'
.gettingOneEG: no visible binding for global variable
'affylmGUIenvironment'
.mappingWgenominator: no visible binding for global variable
'affylmGUIenvironment'
.pamr.confusion.mod: no visible binding for global variable
'which.is.max'
.rawpCheckExons: no visible binding for global variable
'affylmGUIenvironment'
.rawpCheckExons: no visible binding for global variable
'.affylmGUIglobals'
.resize: no visible binding for global variable '.affylmGUIglobals'
.resize: no visible binding for global variable 'affylmGUIenvironment'
.resize : onOK: no visible binding for global variable
'affylmGUIenvironment'
.resize : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
AptMidas: no visible binding for global variable 'affylmGUIenvironment'
AptMidas: no visible binding for global variable '.affylmGUIglobals'
AptMidas: no visible binding for global variable 'tmp'
AptMidas: no visible binding for global variable 'tt'
ComputeContrasts: no visible binding for global variable
'affylmGUIenvironment'
ComputeLinearModelFit: no visible binding for global variable
'affylmGUIenvironment'
ComputeLinearModelFit: no visible binding for global variable
'.affylmGUIglobals'
EG2probeset: no visible binding for global variable '.affylmGUIglobals'
EG2probeset: no visible binding for global variable
'affylmGUIenvironment'
EG2probeset : OpenAFile: no visible binding for global variable
'.affylmGUIglobals'
ExportNormalizedExpressionValues: no visible binding for global
variable 'affylmGUIenvironment'
ExportNormalizedExpressionValues1: no visible binding for global
variable 'affylmGUIenvironment'
ExportfeatureNames: no visible binding for global variable
'affylmGUIenvironment'
GOenrichment: no visible binding for global variable
'.affylmGUIglobals'
GOenrichment: no visible binding for global variable
'affylmGUIenvironment'
GOenrichment : onOK: no visible binding for '<<-' assignment to
'ReturnVal'
GOenrichment : onOK: no visible binding for global variable
'.affylmGUIglobals'
GOenrichment : onCancel: no visible binding for global variable
'.affylmGUIglobals'
GOenrichment : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
GOenrichment: no visible binding for global variable 'ReturnVal'
GOenrichment : OpenAFile: no visible binding for global variable
'.affylmGUIglobals'
GetNormalizationMethod: no visible binding for global variable
'.affylmGUIglobals'
GetNormalizationMethod : onCancel: no visible binding for global
variable '.affylmGUIglobals'
GetNormalizationMethod : onOK: no visible binding for global variable
'.affylmGUIglobals'
GetNormalizationMethod : <anonymous>: no visible binding for global
variable '.affylmGUIglobals'
IPAlistFilter: no visible binding for global variable
'affylmGUIenvironment'
IPAlistFilter: no visible binding for global variable
'.affylmGUIglobals'
ML.edesign: no visible binding for global variable
'affylmGUIenvironment'
ML.edesign: no visible binding for global variable '.affylmGUIglobals'
ML.edesign : onClose: no visible binding for global variable
'.affylmGUIglobals'
ML.edesign : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
NGSreformat: no visible binding for global variable
'affylmGUIenvironment'
NGSreformat : onOK: no visible binding for global variable
'affylmGUIenvironment'
NewLimmaFile: no visible binding for global variable
'affylmGUIenvironment'
NormalizeNow: no visible binding for global variable
'affylmGUIenvironment'
NormalizeNow: no visible binding for global variable
'.affylmGUIglobals'
OpenAFile: no visible binding for global variable '.affylmGUIglobals'
OpenAGeoFile: no visible binding for global variable
'.affylmGUIglobals'
OpenAGeoFile: no visible binding for global variable
'affylmGUIenvironment'
OpenALimmaFile: no visible binding for global variable
'affylmGUIenvironment'
OpenBeadStudioFiles : onOK: no visible binding for global variable
'affylmGUIenvironment'
OpenBeadStudioFiles: no visible binding for global variable
'affylmGUIenvironment'
OpenCDFandTargetsfiles : onOK: no visible binding for global variable
'affylmGUIenvironment'
OpenCDFandTargetsfiles: no visible binding for global variable
'affylmGUIenvironment'
OpenExonandTargetsfiles : onOK: no visible binding for global variable
'affylmGUIenvironment'
OpenExonandTargetsfiles: no visible binding for global variable
'affylmGUIenvironment'
OpenExonandTargetsfiles: no visible binding for '<<-' assignment to
'ReturnValX'
OpenExonandTargetsfiles : onOK: no visible binding for '<<-' assignment
to 'ReturnValX'
OpenExonandTargetsfiles: no visible binding for global variable
'ReturnValX'
OpenGeoFiles : onOK: no visible binding for global variable
'affylmGUIenvironment'
OpenGeoFiles: no visible binding for global variable
'affylmGUIenvironment'
OpenGeoFiles: no visible binding for global variable 'geoVSbioc'
OpenLargefiles : onOK: no visible binding for global variable
'affylmGUIenvironment'
OpenLargefiles: no visible binding for global variable
'affylmGUIenvironment'
OpenNgsfiles : onOK: no visible binding for global variable
'affylmGUIenvironment'
OpenNgsfiles: no visible binding for global variable
'affylmGUIenvironment'
OpenmiRExpress : onOK: no visible binding for global variable
'affylmGUIenvironment'
OpenmiRExpress: no visible binding for global variable
'affylmGUIenvironment'
OpenmiRProfiles : onOK: no visible binding for global variable
'affylmGUIenvironment'
OpenmiRProfiles: no visible binding for global variable
'affylmGUIenvironment'
OpenmiRShrimp : onOK: no visible binding for global variable
'affylmGUIenvironment'
OpenmiRShrimp: no visible binding for global variable
'affylmGUIenvironment'
OpenmiRanalyserfiles : onOK: no visible binding for global variable
'affylmGUIenvironment'
OpenmiRanalyserfiles: no visible binding for global variable
'affylmGUIenvironment'
PlotOptionsv1: no visible binding for global variable
'.affylmGUIglobals'
PlotOptionsv1 : onOK: no visible binding for global variable
'.affylmGUIglobals'
PlotOptionsv1 : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
Reads2logos: no visible binding for global variable '.affylmGUIglobals'
Reads2logos: no visible binding for global variable
'affylmGUIenvironment'
Reads2logos : onOK: no visible binding for global variable
'affylmGUIenvironment'
Reads2logos : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
Reads2logos : onCancel: no visible binding for global variable
'.affylmGUIglobals'
Reads2logos : onOK: no visible binding for global variable
'.affylmGUIglobals'
RmiRInterface: no visible binding for global variable
'.affylmGUIglobals'
RmiRInterface : onOK: no visible binding for global variable
'.affylmGUIglobals'
RmiRInterface : onCancel: no visible binding for global variable
'.affylmGUIglobals'
RmiRInterface : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
SaveAsLimmaFile: no visible binding for global variable
'.affylmGUIglobals'
SaveAsLimmaFile: no visible binding for global variable
'affylmGUIenvironment'
SetED: no visible binding for global variable '.affylmGUIglobals'
VennDiagram: no visible binding for global variable '.affylmGUIglobals'
VennDiagram : onCancel: no visible binding for global variable
'.affylmGUIglobals'
VennDiagram : onOK: no visible binding for global variable
'.affylmGUIglobals'
VennDiagram : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
VennDiagram: no visible binding for global variable
'affylmGUIenvironment'
VennDiagram : plotFunction: no visible binding for global variable
'include'
VennDiagram: no visible global function definition for 'tkrplot'
addAnnLib: no visible binding for global variable
'affylmGUIenvironment'
addAnnLib: no visible binding for global variable '.affylmGUIglobals'
addAnnLib : onOK: no visible binding for global variable
'affylmGUIenvironment'
addAnnLib : onOK: no visible binding for global variable
'.affylmGUIglobals'
addAnnLib : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
affyPlotMA: no visible binding for global variable
'affylmGUIenvironment'
affyPlotMA: no visible binding for global variable '.affylmGUIglobals'
affyPlotMA : plotFunction: no visible binding for global variable
'.affylmGUIglobals'
affyPlotMA : CopyToClip: no visible global function definition for
'tkrreplot'
affyPlotMA: no visible global function definition for 'tkrplot'
annotateNGSeset: no visible binding for global variable
'.affylmGUIglobals'
annotateNGSeset: no visible binding for global variable
'affylmGUIenvironment'
aptFolder: no visible binding for global variable '.affylmGUIglobals'
aptFolder: no visible binding for global variable
'affylmGUIenvironment'
bayseqInterface: no visible binding for global variable
'.affylmGUIglobals'
bayseqInterface : onOK: no visible binding for global variable
'affylmGUIenvironment'
bayseqInterface : onOK: no visible binding for global variable
'.affylmGUIglobals'
bayseqInterface : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
bayseqInterface: no visible binding for global variable
'affylmGUIenvironment'
bayseqInterface : onOK: no visible binding for '<<-' assignment to
'ReturnVal'
bayseqInterface : onCancel: no visible binding for '<<-' assignment to
'ReturnVal'
bayseqInterface : onCancel: no visible binding for global variable
'.affylmGUIglobals'
bayseqInterface: no visible binding for global variable 'ReturnVal'
biomartFilter: no visible binding for global variable
'.affylmGUIglobals'
buildingLocalAnnotation: no visible binding for global variable
'.affylmGUIglobals'
buildingLocalAnnotation : onOK: no visible binding for global variable
'affylmGUIenvironment'
buildingLocalAnnotation : <anonymous>: no visible binding for global
variable '.affylmGUIglobals'
buildingLocalAnnotation: no visible binding for global variable
'affylmGUIenvironment'
buildingLocalAnnotation : onOK: no visible binding for '<<-' assignment
to 'ReturnNetaffx'
buildingLocalAnnotation : onOK: no visible binding for global variable
'.affylmGUIglobals'
buildingLocalAnnotation : onCancel: no visible binding for global
variable '.affylmGUIglobals'
buildingLocalAnnotation: no visible binding for global variable
'ReturnNetaffx'
changeMenu: no visible binding for global variable
'affylmGUIenvironment'
changeMenu: no visible binding for global variable '.affylmGUIglobals'
chooseEDir: no visible binding for global variable '.affylmGUIglobals'
colExtract: no visible binding for global variable '.affylmGUIglobals'
colExtract : onOK: no visible binding for global variable
'affylmGUIenvironment'
colExtract : onOK: no visible binding for global variable
'.affylmGUIglobals'
colExtract : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
colExtract: no visible binding for global variable
'affylmGUIenvironment'
combineGeoMSF: no visible binding for global variable
'.affylmGUIglobals'
combineGeoMSF : onOK: no visible binding for global variable
'.affylmGUIglobals'
combineGeoMSF : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
combineGeoMSF: no visible binding for global variable
'affylmGUIenvironment'
combining2eSet: no visible binding for global variable
'.affylmGUIglobals'
consistentFilters: no visible binding for global variable
'.affylmGUIglobals'
consistentFilters: no visible binding for global variable
'affylmGUIenvironment'
consistentFilters : onOK: no visible binding for '<<-' assignment to
'ReturnFilter'
consistentFilters : onOK: no visible binding for global variable
'.affylmGUIglobals'
consistentFilters : onCancel: no visible binding for global variable
'.affylmGUIglobals'
consistentFilters : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
consistentFilters: no visible binding for global variable
'ReturnFilter'
consistentFilters : onOK: no visible binding for global variable
'affylmGUIenvironment'
cosieWrapper: no visible binding for global variable
'affylmGUIenvironment'
cosieWrapper: no visible binding for global variable
'.affylmGUIglobals'
createGeoTarget: no visible binding for global variable
'.affylmGUIglobals'
crosshybFilter: no visible binding for global variable
'affylmGUIenvironment'
crosshybFilter: no visible binding for global variable
'.affylmGUIglobals'
crosshybFilter : onCancel: no visible binding for global variable
'.affylmGUIglobals'
crosshybFilter : onOK: no visible binding for global variable
'.affylmGUIglobals'
crosshybFilter : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
ctrtrtHeatmap: no visible binding for global variable
'affylmGUIenvironment'
ctrtrtHeatmap: no visible binding for global variable
'.affylmGUIglobals'
dabgFilter: no visible binding for global variable
'affylmGUIenvironment'
dabgFilter: no visible binding for global variable '.affylmGUIglobals'
dabgFilter : onOK: no visible binding for '<<-' assignment to
'ReturnVal'
dabgFilter : onOK: no visible binding for global variable
'.affylmGUIglobals'
dabgFilter : onCancel: no visible binding for '<<-' assignment to
'ReturnVal'
dabgFilter : onCancel: no visible binding for global variable
'.affylmGUIglobals'
dabgFilter : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
dabgFilter: no visible binding for global variable 'ReturnVal'
delete.ML: no visible binding for global variable
'affylmGUIenvironment'
delete.ML: no visible binding for global variable '.affylmGUIglobals'
deleteLocalData: no visible binding for global variable
'.affylmGUIglobals'
dfMAplot: no visible binding for global variable '.affylmGUIglobals'
dfMAplot : onOK: no visible binding for '<<-' assignment to 'ReturnVal'
dfMAplot : onOK: no visible binding for global variable
'.affylmGUIglobals'
dfMAplot : onCancel: no visible binding for global variable
'.affylmGUIglobals'
dfMAplot : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
dfMAplot: no visible binding for global variable 'ReturnVal'
eSet4meV: no visible binding for global variable 'affylmGUIenvironment'
edgeRNorm: no visible binding for global variable '.affylmGUIglobals'
edgeRNorm: no visible binding for global variable
'affylmGUIenvironment'
edgerInterface: no visible binding for global variable
'affylmGUIenvironment'
edgerInterface: no visible binding for global variable
'.affylmGUIglobals'
edgerInterface : onOK: no visible binding for global variable
'affylmGUIenvironment'
edgerInterface : onOK: no visible binding for global variable
'.affylmGUIglobals'
edgerInterface : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
edgerInterface : onOK: no visible binding for '<<-' assignment to
'ReturnVal'
edgerInterface : onCancel: no visible binding for '<<-' assignment to
'ReturnVal'
edgerInterface : onCancel: no visible binding for global variable
'.affylmGUIglobals'
edgerInterface: no visible binding for global variable 'ReturnVal'
erankProdAltSpl: no visible binding for global variable
'affylmGUIenvironment'
erankProdAltSpl: no visible binding for global variable
'.affylmGUIglobals'
erankProdAltSpl : onCancel: no visible binding for global variable
'.affylmGUIglobals'
erankProdAltSpl : onOK: no visible binding for global variable
'.affylmGUIglobals'
erankProdAltSpl : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
erankProdAltSpl: no visible binding for '<<-' assignment to 'ReturnVal'
erankProdAltSpl : onOK: no visible binding for '<<-' assignment to
'ReturnVal'
erankProdAltSpl: no visible binding for global variable 'ReturnVal'
erankProdAltSplFilter: no visible binding for global variable
'affylmGUIenvironment'
erankProdAltSplFilter: no visible binding for global variable
'.affylmGUIglobals'
erankProdAltSplFilter : onOK: no visible binding for global variable
'affylmGUIenvironment'
erankProdAltSplFilter : <anonymous>: no visible binding for global
variable '.affylmGUIglobals'
exonContrasts: no visible binding for global variable
'affylmGUIenvironment'
exonTopTableExtract: no visible binding for global variable
'affylmGUIenvironment'
exonTopTableExtract: no visible binding for global variable
'.affylmGUIglobals'
exonTopTableExtract : onOK: no visible binding for global variable
'affylmGUIenvironment'
exonTopTableExtract : <anonymous>: no visible binding for global
variable '.affylmGUIglobals'
exonsSpecific2as: no visible binding for global variable
'.affylmGUIglobals'
exonsSpecific2as: no visible binding for global variable
'affylmGUIenvironment'
exportFASTA: no visible binding for global variable '.affylmGUIglobals'
exportFASTA : onCancel: no visible binding for global variable
'.affylmGUIglobals'
exportFASTA : onOK: no visible binding for global variable
'.affylmGUIglobals'
exportFASTA : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
extractAffyids: no visible binding for global variable
'.affylmGUIglobals'
extractAffyids: no visible binding for global variable
'affylmGUIenvironment'
extractAffyids : onOK: no visible binding for global variable
'affylmGUIenvironment'
extractAffyids : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
extractAffyids : OpenAFile: no visible binding for global variable
'.affylmGUIglobals'
extractmirTargets: no visible binding for global variable
'.affylmGUIglobals'
extractmirTargets: no visible binding for global variable 'mySel1'
extractmirTargets : onOK: no visible binding for global variable
'affylmGUIenvironment'
extractmirTargets : onOK: no visible binding for global variable
'.affylmGUIglobals'
extractmirTargets : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
extractmirTargets: no visible binding for global variable
'affylmGUIenvironment'
filteringTable: no visible binding for global variable
'.affylmGUIglobals'
filteringmiRtargets: no visible binding for global variable
'.affylmGUIglobals'
filteringmiRtargets : onCancel: no visible binding for global variable
'.affylmGUIglobals'
filteringmiRtargets : onOK: no visible binding for global variable
'.affylmGUIglobals'
filteringmiRtargets : <anonymous>: no visible binding for global
variable '.affylmGUIglobals'
geneExonLibs: no visible binding for global variable
'affylmGUIenvironment'
geneExonLibs: no visible binding for global variable
'.affylmGUIglobals'
genomePlot: no visible binding for global variable '.affylmGUIglobals'
genomePlot: no visible binding for global variable
'affylmGUIenvironment'
genomePlot : onOK: no visible binding for global variable
'affylmGUIenvironment'
genomePlot : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
genomePlot: no visible binding for global variable
'crosshybraex.annotation'
getNGSannotation: no visible binding for '<<-' assignment to
'ReturnAnn'
getNGSannotation: no visible binding for global variable
'.affylmGUIglobals'
getNGSannotation : onOK: no visible binding for '<<-' assignment to
'ReturnAnn'
getNGSannotation : onOK: no visible binding for global variable
'.affylmGUIglobals'
getNGSannotation : onCancel: no visible binding for global variable
'.affylmGUIglobals'
getNGSannotation : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
getNGSannotation: no visible binding for global variable 'ReturnAnn'
getNGSannotation: no visible binding for global variable
'affylmGUIenvironment'
initialize.extAffylmGUI: no visible binding for global variable
'affylmGUIenvironment'
initialize.extAffylmGUI: no visible binding for global variable
'.affylmGUIglobals'
inspecting.one.splice.index: no visible binding for global variable
'.affylmGUIglobals'
inspecting.one.splice.index: no visible binding for global variable
'affylmGUIenvironment'
inspecting.one.splice.index : onOK: no visible binding for global
variable 'affylmGUIenvironment'
inspecting.one.splice.index : <anonymous>: no visible binding for
global variable '.affylmGUIglobals'
inspecting.splice.index: no visible binding for global variable
'.affylmGUIglobals'
inspecting.splice.index: no visible binding for global variable
'affylmGUIenvironment'
intensityFilter: no visible binding for global variable
'.affylmGUIglobals'
intensityFilter : onOK: no visible binding for '<<-' assignment to
'ReturnVal'
intensityFilter : onOK: no visible binding for global variable
'.affylmGUIglobals'
intensityFilter : onCancel: no visible binding for '<<-' assignment to
'ReturnVal'
intensityFilter : onCancel: no visible binding for global variable
'.affylmGUIglobals'
intensityFilter : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
intensityFilter: no visible binding for global variable 'ReturnVal'
intronicBg: no visible binding for global variable
'affylmGUIenvironment'
intronicBg: no visible binding for global variable '.affylmGUIglobals'
intronicBg : onOK: no visible binding for global variable
'affylmGUIenvironment'
intronicBg : onOK: no visible binding for global variable
'.affylmGUIglobals'
intronicBg : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
iqrFilter: no visible binding for global variable '.affylmGUIglobals'
iqrFilter : onCancel: no visible binding for global variable
'.affylmGUIglobals'
iqrFilter : onOK: no visible binding for global variable
'.affylmGUIglobals'
iqrFilter : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
largedatasetNorm: no visible binding for global variable
'affylmGUIenvironment'
largedatasetNorm: no visible binding for global variable
'.affylmGUIglobals'
largedatasetNorm : onCancel: no visible binding for global variable
'.affylmGUIglobals'
largedatasetNorm : onOK: no visible binding for global variable
'.affylmGUIglobals'
largedatasetNorm : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
libraryFilesDir: no visible binding for global variable
'.affylmGUIglobals'
limma2paired: no visible binding for global variable
'affylmGUIenvironment'
limma2paired: no visible binding for global variable
'.affylmGUIglobals'
limma2paired : onOK: no visible binding for global variable
'.affylmGUIglobals'
limma2paired : onHelp: possible error in help("topTable", htmlhelp =
TRUE): unused argument(s) (htmlhelp = TRUE)
limma2paired : onCancel: no visible binding for global variable
'.affylmGUIglobals'
limma2paired : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
limma2paired: no visible binding for global variable 'annlib'
limmaExons: no visible binding for global variable
'affylmGUIenvironment'
limmaExons: no visible binding for global variable '.affylmGUIglobals'
listFilter: no visible binding for global variable
'affylmGUIenvironment'
listFilter: no visible binding for global variable '.affylmGUIglobals'
listFilter : OpenAFile: no visible binding for global variable
'.affylmGUIglobals'
log2Conversion: no visible binding for global variable
'affylmGUIenvironment'
log2Conversion: no visible binding for global variable
'.affylmGUIglobals'
mRNAmiRCor: no visible binding for global variable '.affylmGUIglobals'
mRNAmiRCor: no visible binding for global variable
'affylmGUIenvironment'
mRNAmiRCor : onOK: no visible binding for '<<-' assignment to
'ReturnVal'
mRNAmiRCor : onOK: no visible binding for global variable
'.affylmGUIglobals'
mRNAmiRCor : onCancel: no visible binding for '<<-' assignment to
'ReturnVal'
mRNAmiRCor : onCancel: no visible binding for global variable
'.affylmGUIglobals'
mRNAmiRCor : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
mRNAmiRCor: no visible binding for global variable 'ReturnVal'
mRNAmiRCor : .OpenAmiRFile: no visible binding for global variable
'.affylmGUIglobals'
mRNAmiRCor: possible error in Try(tkmessageBox(title = "Filtering by
correlation", message = "The data set in oneChannelGUI and the miR
data have the samples organized in different way!\nPlease modify the
miRdata file to have the same samples organization as in the Target
name of the dataset load in oneChannelGUI."), type = "error"): unused
argument(s) (type = "error")
mRNAmiRCor: possible error in Try(tkmessageBox(title = "Filtering by
correlation", message = "The data set in oneChannelGUI and the miR
data do not contain the same number of samples!"), type = "error"):
unused argument(s) (type = "error")
makeBED15: no visible binding for global variable '.affylmGUIglobals'
mapping2RefSeq: no visible binding for global variable
'.affylmGUIglobals'
mapping2RefSeq: no visible binding for global variable
'affylmGUIenvironment'
mapping2ensembl: no visible binding for global variable
'.affylmGUIglobals'
mapping2ensembl: no visible binding for global variable
'affylmGUIenvironment'
mapping2exon: no visible binding for global variable
'.affylmGUIglobals'
mapping2exon: no visible binding for global variable
'affylmGUIenvironment'
masigpro: no visible binding for global variable 'affylmGUIenvironment'
masigpro: no visible binding for global variable '.affylmGUIglobals'
masigpro : onOK: no visible binding for global variable
'.affylmGUIglobals'
masigpro : onCancel: no visible binding for global variable
'.affylmGUIglobals'
masigpro : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
masigpro.edesign: no visible binding for global variable
'affylmGUIenvironment'
masigpro.edesign: no visible binding for global variable
'.affylmGUIglobals'
masigpro.edesign : onClose: no visible binding for global variable
'.affylmGUIglobals'
masigpro.edesign : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
masigpro.view: no visible binding for global variable
'affylmGUIenvironment'
masigpro.view: no visible binding for global variable
'.affylmGUIglobals'
masigpro.view : onCancel: no visible binding for global variable
'.affylmGUIglobals'
masigpro.view : onOK: no visible binding for global variable
'.affylmGUIglobals'
masigpro.view : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
masigpro.view : plotFunction: no visible binding for global variable
'include'
masigpro.view: no visible global function definition for 'tkrplot'
masigpro.view : onOK: no visible binding for global variable
'affylmGUIenvironment'
meVDownload: no visible binding for global variable '.affylmGUIglobals'
meVDownload: no visible binding for global variable
'affylmGUIenvironment'
metaArrayIC: no visible binding for global variable
'affylmGUIenvironment'
metaArrayIC: no visible binding for global variable '.affylmGUIglobals'
metaArrayMerge : OpenAFile: no visible binding for global variable
'.affylmGUIglobals'
metaArrayMerge: no visible binding for global variable
'affylmGUIenvironment'
metaArrayMerge: no visible binding for global variable
'.affylmGUIglobals'
metaArrayMerge : onCancel: no visible binding for global variable
'.affylmGUIglobals'
metaArrayMerge : onOK: no visible binding for global variable
'.affylmGUIglobals'
metaArrayMerge : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
midasFilter: no visible binding for global variable
'affylmGUIenvironment'
midasFilter: no visible binding for global variable '.affylmGUIglobals'
midasFilter : onOK: no visible binding for global variable
'affylmGUIenvironment'
midasFilter : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
myExpresso: no visible binding for global variable
'affylmGUIenvironment'
myExpresso: no visible binding for global variable '.affylmGUIglobals'
ngsperlDownload: no visible binding for global variable
'affylmGUIenvironment'
ngsperlDownload: no visible binding for global variable
'.affylmGUIglobals'
normBoxplot: no visible binding for global variable
'affylmGUIenvironment'
normBoxplot: no visible binding for global variable '.affylmGUIglobals'
ocPlotHist: no visible binding for global variable
'affylmGUIenvironment'
ocPlotHist: no visible binding for global variable '.affylmGUIglobals'
ocPlotHist : onCancel: no visible binding for global variable
'.affylmGUIglobals'
ocPlotHist : onOK: no visible binding for global variable
'.affylmGUIglobals'
ocPlotHist : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
ocPlotPCA: no visible binding for global variable
'affylmGUIenvironment'
ocPlotPCA: no visible binding for global variable '.affylmGUIglobals'
ocPlotPCA : onCancel: no visible binding for global variable
'.affylmGUIglobals'
ocPlotPCA : onOK: no visible binding for global variable
'.affylmGUIglobals'
ocPlotPCA : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
oneChannelGUI: no visible binding for global variable
'affylmGUIenvironment'
oneChannelGUI: no visible binding for global variable
'.affylmGUIglobals'
plierToZero: no visible binding for global variable
'affylmGUIenvironment'
plierToZero: no visible binding for global variable '.affylmGUIglobals'
plotGO: no visible binding for global variable 'affylmGUIenvironment'
plotGO: no visible binding for global variable '.affylmGUIglobals'
plotGO : onOK: no visible binding for global variable
'affylmGUIenvironment'
plotGO : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
plotGO : onCancel: no visible binding for global variable
'.affylmGUIglobals'
plotGO : onOK: no visible binding for global variable
'.affylmGUIglobals'
plotVariantSI: no visible binding for global variable
'.affylmGUIglobals'
plotVariantSI : onOK: no visible binding for global variable
'affylmGUIenvironment'
plotVariantSI : onOK: no visible binding for global variable
'.affylmGUIglobals'
plotVariantSI : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
plotVariantSI: no visible binding for global variable
'affylmGUIenvironment'
qcMDS: no visible binding for global variable 'affylmGUIenvironment'
qcMDS: no visible binding for global variable '.affylmGUIglobals'
rankProd: no visible binding for global variable 'affylmGUIenvironment'
rankProd: no visible binding for global variable '.affylmGUIglobals'
rankProd : onOK: no visible binding for '<<-' assignment to 'ReturnVal'
rankProd : onOK: no visible binding for global variable
'.affylmGUIglobals'
rankProd : onCancel: no visible binding for '<<-' assignment to
'ReturnVal'
rankProd : onCancel: no visible binding for global variable
'.affylmGUIglobals'
rankProd : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
rankProd: no visible binding for global variable 'ReturnVal'
rankingConversion: no visible binding for global variable
'affylmGUIenvironment'
rankingConversion: no visible binding for global variable
'.affylmGUIglobals'
rawBoxplotPN: no visible binding for global variable
'affylmGUIenvironment'
rawBoxplotPN: no visible binding for global variable
'.affylmGUIglobals'
rawpCheck: no visible binding for global variable
'affylmGUIenvironment'
rawpCheck: no visible binding for global variable '.affylmGUIglobals'
recoverUnfiltered: no visible binding for global variable
'.affylmGUIglobals'
recoverUnfiltered: no visible binding for global variable
'affylmGUIenvironment'
recoverUnfiltered: no visible binding for global variable 'x.exon'
refiningPeaks: no visible binding for global variable
'affylmGUIenvironment'
refiningPeaks: no visible binding for global variable
'.affylmGUIglobals'
refiningPeaks : onOK: no visible binding for global variable
'affylmGUIenvironment'
refiningPeaks : onOK: no visible binding for global variable
'.affylmGUIglobals'
refiningPeaks : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
reformatGdl: no visible binding for global variable '.affylmGUIglobals'
reformatGdl: no visible binding for global variable
'affylmGUIenvironment'
reformatGdl : onOK: no visible binding for global variable
'affylmGUIenvironment'
reformatGdl : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
refseqDownload: no visible binding for global variable
'.affylmGUIglobals'
refseqDownload: no visible binding for global variable
'affylmGUIenvironment'
retrieveMirTargets: no visible binding for global variable
'.affylmGUIglobals'
retrieveMirTargets : onCancel: no visible binding for global variable
'.affylmGUIglobals'
retrieveMirTargets : onOK: no visible binding for global variable
'.affylmGUIglobals'
retrieveMirTargets : <anonymous>: no visible binding for global
variable '.affylmGUIglobals'
retrieveMirTargets : onOK: no visible binding for global variable
'affylmGUIenvironment'
retrieveMirTargets: no visible binding for global variable
'affylmGUIenvironment'
retrieveMirTargets: no visible binding for global variable 'mycol'
retrieveMirTargets: no visible binding for global variable 'miRnum'
retrievePSRseq: no visible binding for global variable
'.affylmGUIglobals'
retrievePSRseq: no visible binding for global variable
'affylmGUIenvironment'
retrievePSRseq1gid: no visible binding for global variable
'.affylmGUIglobals'
retrievePSRseq1gid: no visible binding for global variable
'affylmGUIenvironment'
retrievePSRseq1gid : onOK: no visible binding for global variable
'affylmGUIenvironment'
retrievePSRseq1gid : <anonymous>: no visible binding for global
variable '.affylmGUIglobals'
reviqrFilter: no visible binding for global variable
'.affylmGUIglobals'
reviqrFilter : onCancel: no visible binding for global variable
'.affylmGUIglobals'
reviqrFilter : onOK: no visible binding for global variable
'.affylmGUIglobals'
reviqrFilter : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
runningJetta: no visible binding for global variable
'.affylmGUIglobals'
runningJetta: no visible binding for global variable
'affylmGUIenvironment'
runningJetta: no visible binding for global variable 'tmp'
runningJetta : onOK: no visible binding for global variable
'.affylmGUIglobals'
runningJetta : onOK: no visible binding for global variable
'affylmGUIenvironment'
runningJetta : onCancel: no visible binding for global variable
'.affylmGUIglobals'
runningJetta : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
runningJetta: no visible global function definition for 'jetta.do.mads'
runningJetta: no visible global function definition for
'jetta.read.expression'
runningJetta: no visible global function definition for
'jetta.read.mads.output'
sample.size.evaluation: no visible binding for global variable
'affylmGUIenvironment'
sample.size.evaluation: no visible binding for global variable
'.affylmGUIglobals'
sample.size.evaluation : onOK: no visible binding for global variable
'affylmGUIenvironment'
sample.size.evaluation : <anonymous>: no visible binding for global
variable '.affylmGUIglobals'
sample.size.evaluation : common.sd: no visible binding for global
variable 'affylmGUIenvironment'
sample.size.evaluation : onCancel: no visible binding for global
variable '.affylmGUIglobals'
sample.size.evaluation : onOK: no visible binding for global variable
'.affylmGUIglobals'
sample.size.evaluation1: no visible binding for global variable
'affylmGUIenvironment'
sample.size.evaluation1: no visible binding for global variable
'.affylmGUIglobals'
sample.size.evaluation1 : onCancel: no visible binding for global
variable '.affylmGUIglobals'
sample.size.evaluation1 : onOK: no visible binding for global variable
'.affylmGUIglobals'
sample.size.evaluation1 : <anonymous>: no visible binding for global
variable '.affylmGUIglobals'
sample.size.evaluation1 : common.sd: no visible binding for global
variable 'affylmGUIenvironment'
showDataset: no visible binding for global variable
'affylmGUIenvironment'
showTopTable: no visible binding for global variable
'affylmGUIenvironment'
showTopTable : onHelp: possible error in help("topTable", htmlhelp =
TRUE): unused argument(s) (htmlhelp = TRUE)
showTopTable: no visible binding for global variable 'annlib'
siggenes: no visible binding for global variable 'affylmGUIenvironment'
siggenes: no visible binding for global variable '.affylmGUIglobals'
siggenes : onOK: no visible binding for global variable
'affylmGUIenvironment'
siggenes : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
simFilter: no visible binding for global variable '.affylmGUIglobals'
simFilter : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
spliceIndex: no visible binding for global variable
'affylmGUIenvironment'
spliceIndex: no visible binding for global variable '.affylmGUIglobals'
startmeV: no visible binding for global variable 'affylmGUIenvironment'
startmeV: no visible binding for global variable '.affylmGUIglobals'
targetWidget: possible error in sub("^/?([^/]*/)*", "", widgetfiles,
extended = TRUE): unused argument(s) (extended = TRUE)
templA: no visible binding for global variable 'affylmGUIenvironment'
templA: no visible binding for global variable '.affylmGUIglobals'
templA : onCancel: no visible binding for global variable
'.affylmGUIglobals'
templA : onOK: no visible binding for global variable
'.affylmGUIglobals'
templA : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
trainTest: no visible binding for global variable
'affylmGUIenvironment'
trainTest: no visible binding for global variable '.affylmGUIglobals'
trainTest : onOK: no visible binding for global variable
'.affylmGUIglobals'
trainTest : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
trainTest : onCancel: no visible binding for global variable
'.affylmGUIglobals'
trainTest: possible error in Try(x = exprs(testAffyData)): unused
argument(s) (x = exprs(testAffyData))
trainTest : onOK: no visible binding for global variable
'affylmGUIenvironment'
updateLibs: no visible binding for global variable '.affylmGUIglobals'
updateLibs: no visible global function definition for
'biocinstallRepos'
variantExons: no visible binding for global variable
'.affylmGUIglobals'
variantSI: no visible binding for global variable '.affylmGUIglobals'
variantSI: no visible binding for global variable
'affylmGUIenvironment'
whichKindOfArray: no visible binding for global variable
'affylmGUIenvironment'
whichKindOfArray: no visible binding for '<<-' assignment to
'ReturnVal'
whichKindOfArray: no visible binding for global variable
'.affylmGUIglobals'
whichKindOfArray : onOK: no visible binding for '<<-' assignment to
'ReturnVal'
whichKindOfArray : onOK: no visible binding for global variable
'.affylmGUIglobals'
whichKindOfArray : onCancel: no visible binding for global variable
'.affylmGUIglobals'
whichKindOfArray : <anonymous>: no visible binding for global variable
'.affylmGUIglobals'
whichKindOfArray: no visible binding for global variable 'ReturnVal'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignettes without corresponding PDF:
D:/biocbld/bbs-2.8-bioc/meat/oneChannelGUI.Rcheck/00_pkg_src/oneChannelGUI/inst/doc/NGS.Rnw
D:/biocbld/bbs-2.8-bioc/meat/oneChannelGUI.Rcheck/00_pkg_src/oneChannelGUI/inst/doc/install.Rnw
D:/biocbld/bbs-2.8-bioc/meat/oneChannelGUI.Rcheck/00_pkg_src/oneChannelGUI/inst/doc/oneChannelGUI.Rnw
D:/biocbld/bbs-2.8-bioc/meat/oneChannelGUI.Rcheck/00_pkg_src/oneChannelGUI/inst/doc/standAloneFunctions.Rnw
SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
'D:/biocbld/bbs-2.8-bioc/meat/oneChannelGUI.Rcheck/00check.log'
for details
* installing *source* package 'oneChannelGUI' ...
** R
** data
** inst
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: affy
Loading required package: affyio
Loading required package: widgetTools
Loading required package: DynDoc
Loading required package: tools
Loading required package: Category
Loading required package: AnnotationDbi
Loading required package: graph
Loading required package: DBI
Attaching package: 'IRanges'
The following object(s) are masked from 'package:graph':
union
The following object(s) are masked from 'package:Biobase':
updateObject
The following object(s) are masked from 'package:base':
Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
Attaching package: 'baySeq'
The following object(s) are masked from 'package:IRanges':
rbind
The following object(s) are masked from 'package:base':
rbind
Loading required package: Rsamtools
Loading required package: GenomicRanges
Loading required package: Biostrings
Attaching package: 'Biostrings'
The following object(s) are masked from 'package:graph':
complement
Attaching package: 'Rsamtools'
The following object(s) are masked from 'package:DynDoc':
path
Loading required package: ShortRead
Loading required package: lattice
Attaching package: 'ShortRead'
The following object(s) are masked from 'package:affy':
intensity
Loading required package: intervals
Attaching package: 'intervals'
The following object(s) are masked from 'package:Biostrings':
type
The following object(s) are masked from 'package:IRanges':
reduce
Loading required package: genomeIntervals
Attaching package: 'genomeIntervals'
The following object(s) are masked from 'package:GenomicRanges':
strand, strand<-
Loading required package: grid
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
To begin, type oneChannelGUI()
* DONE (oneChannelGUI)