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BioC 3.4: CHECK report for FGNet on morelia

This page was generated on 2017-04-15 16:25:04 -0400 (Sat, 15 Apr 2017).

Package 414/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FGNet 3.8.0
Sara Aibar
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/FGNet
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: FGNet
Version: 3.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FGNet_3.8.0.tar.gz
StartedAt: 2017-04-15 02:02:06 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 02:05:02 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 176.7 seconds
RetCode: 0
Status:  OK 
CheckDir: FGNet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FGNet_3.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/FGNet.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FGNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FGNet’ version ‘3.8.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FGNet’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc   8.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking 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
FGNet_GUI: no visible global function definition for ‘data’
FGNet_GUI: no visible global function definition for ‘gtkWindowNew’
FGNet_GUI: no visible global function definition for ‘gtkStatusbar’
FGNet_GUI: no visible global function definition for ‘gtkNotebookNew’
FGNet_GUI: no visible global function definition for ‘setNames’
FGNet_GUI: no visible global function definition for
  ‘gtkNotebookInsertPage’
FGNet_GUI: no visible global function definition for ‘gtkLabelNew’
FGNet_GUI: no visible global function definition for ‘gtkVBoxNew’
FGNet_GUI: no visible global function definition for ‘gSignalConnect’
FGNet_report: no visible global function definition for ‘data’
SOAPQuery: no visible global function definition for
  ‘basicTextGatherer’
SOAPQuery: no visible global function definition for ‘curlPerform’
SOAPQuery: no visible global function definition for ‘parseHTTPHeader’
actDeactGenes: no visible global function definition for ‘data’
actDeactGenes: no visible global function definition for
  ‘gtkWidgetSetSensitive’
analyzeNetwork: no visible global function definition for ‘data’
analyzeNetwork: no visible global function definition for ‘par’
analyzeNetwork: no visible global function definition for ‘boxplot’
analyzeNetwork: no visible global function definition for ‘box’
analyzeNetwork: no visible global function definition for ‘axis’
analyzeNetwork: no visible global function definition for ‘abline’
analyzeNetwork : <anonymous>: no visible global function definition for
  ‘quantile’
buildGeneSets: no visible global function definition for ‘columns’
buildGeneSets: no visible global function definition for ‘keys’
buildGeneSets: no visible global function definition for ‘select’
buildGeneSets: no visible binding for global variable ‘GO.db’
buildGeneSets: no visible binding for global variable ‘KEGGPATHID2NAME’
buildGeneSets: no visible binding for global variable
  ‘reactomePATHID2EXTID’
buildGeneSets: no visible binding for global variable
  ‘reactomeEXTID2PATHID’
buildGeneSets: no visible binding for global variable
  ‘reactomePATHID2NAME’
clustersDistance: no visible global function definition for ‘dist’
clustersDistance: no visible global function definition for ‘hclust’
clustersDistance: no visible global function definition for ‘layout’
clustersDistance: no visible global function definition for ‘par’
clustersDistance: no visible global function definition for ‘plot’
clustersDistance: no visible global function definition for ‘image’
clustersDistance: no visible global function definition for ‘box’
clustersDistance: no visible global function definition for ‘barplot’
clustersDistance: no visible global function definition for ‘axis’
createHTML_FEA_header: no visible global function definition for ‘data’
createHtml: no visible global function definition for ‘data’
createHtml: no visible global function definition for ‘setNames’
createHtml: no visible global function definition for ‘png’
createHtml: no visible global function definition for ‘dev.off’
createHtml: no visible global function definition for ‘write.table’
createHtml: no visible global function definition for ‘browseURL’
fea2incidMat: no visible global function definition for ‘setNames’
fea_david: no visible binding for global variable ‘DAVIDWebService’
fea_david: no visible global function definition for ‘addList’
fea_david : <anonymous>: no visible global function definition for
  ‘write.table’
fea_david : <anonymous>: no visible global function definition for
  ‘getIdTypes’
fea_david: no visible global function definition for
  ‘setAnnotationCategories’
fea_david : <anonymous>: no visible global function definition for
  ‘getAllAnnotationCategoryNames’
fea_david: no visible global function definition for
  ‘getClusterReportFile’
fea_david: no visible global function definition for ‘getCurlHandle’
fea_david: no visible global function definition for ‘postForm’
fea_gage: no visible global function definition for ‘exprs’
fea_gage: no visible global function definition for ‘data’
fea_gage: no visible global function definition for ‘gage’
fea_gage: no visible global function definition for ‘esset.grp’
fea_gage: no visible global function definition for ‘setNames’
fea_gage: no visible global function definition for ‘write.table’
fea_gtLinker_getResults: no visible global function definition for
  ‘url.exists’
fea_gtLinker_getResults: no visible global function definition for
  ‘download.file’
fea_gtLinker_getResults: no visible global function definition for
  ‘read.table’
fea_topGO: no visible global function definition for ‘groupGOTerms’
fea_topGO: no visible global function definition for ‘data’
fea_topGO: no visible global function definition for ‘new’
fea_topGO: no visible binding for global variable ‘GOFisherTest’
fea_topGO: no visible binding for global variable ‘annFUN.gene2GO’
fea_topGO: no visible global function definition for ‘getSigGroups’
fea_topGO: no visible global function definition for ‘GenTable’
fea_topGO : <anonymous>: no visible global function definition for
  ‘genesInTerm’
fea_topGO : <anonymous>: no visible global function definition for
  ‘sigGenes’
fillCombosColumns : <anonymous>: no visible global function definition
  for ‘gtkComboBoxAppendText’
formatResultsFile: no visible global function definition for ‘setNames’
formatResultsFile: no visible binding for global variable ‘rawResults’
format_david: no visible global function definition for ‘getURL’
format_david: no visible global function definition for ‘write.table’
format_gtLinker: no visible global function definition for ‘read.table’
format_gtLinker: no visible global function definition for ‘data’
format_gtLinker: no visible global function definition for
  ‘write.table’
format_results: no visible global function definition for ‘read.csv’
format_results: no visible global function definition for ‘write.table’
functionalNetwork: no visible global function definition for ‘setNames’
functionalNetwork: no visible global function definition for ‘data’
functionalNetwork: no visible global function definition for ‘col2rgb’
generateNetwork: no visible global function definition for ‘data’
generateNetwork: no visible global function definition for
  ‘gtkDialogNewWithButtons’
generateNetwork: no visible binding for global variable
  ‘GtkResponseType’
generateNetwork: no visible global function definition for ‘gtkLabel’
generateReport: no visible global function definition for ‘data’
generateReport: no visible global function definition for
  ‘gtkDialogNewWithButtons’
generateReport: no visible binding for global variable
  ‘GtkResponseType’
generateReport: no visible global function definition for ‘gtkLabel’
getTerms : <anonymous>: no visible global function definition for
  ‘setNames’
goTreeLinks: no visible global function definition for ‘data’
goTreeLinks: no visible binding for global variable ‘GOBPPARENTS’
goTreeLinks: no visible binding for global variable ‘GOMFPARENTS’
goTreeLinks: no visible binding for global variable ‘GOCCPARENTS’
keywordsTerm: no visible global function definition for ‘quantile’
loadEset: no visible global function definition for ‘gtkCheckButton’
loadFileDialog: no visible global function definition for ‘data’
loadFileDialog: no visible global function definition for
  ‘gtkFileChooserDialog’
loadFileDialog: no visible binding for global variable
  ‘GtkResponseType’
loadFileDialog: no visible global function definition for ‘read.table’
loadFileDialog: no visible global function definition for
  ‘gtkTextBufferNew’
loadFileDialog: no visible global function definition for
  ‘gtkTextBufferSetText’
loadFileDialog: no visible global function definition for
  ‘gtkTextViewSetBuffer’
loadInstPkg: no visible global function definition for
  ‘installed.packages’
loadInstPkg: no visible global function definition for
  ‘gtkDialogNewWithButtons’
loadInstPkg: no visible binding for global variable ‘GtkResponseType’
loadInstPkg: no visible global function definition for ‘gtkLabel’
loadInstPkg: no visible global function definition for ‘biocLite’
plotFGNet: no visible global function definition for ‘setNames’
plotFGNet: no visible global function definition for ‘plot’
plotFGNet: no visible global function definition for ‘legend’
plotFGNet: no visible global function definition for ‘title’
plotFGNet_bipartite: no visible global function definition for
  ‘setNames’
plotGoAncestors: no visible binding for global variable ‘GOBPPARENTS’
plotGoAncestors: no visible binding for global variable ‘GOMFPARENTS’
plotGoAncestors: no visible binding for global variable ‘GOCCPARENTS’
plotGoAncestors : <anonymous>: no visible binding for global variable
  ‘GOTERM’
plotGoAncestors: no visible global function definition for ‘png’
plotGoAncestors: no visible global function definition for ‘plot’
plotGoAncestors: no visible global function definition for ‘legend’
plotGoAncestors: no visible global function definition for ‘dev.off’
plotKegg: no visible global function definition for ‘data’
plotKegg: no visible global function definition for ‘columns’
plotKegg: no visible global function definition for ‘keys’
plotKegg: no visible global function definition for ‘select’
plotKegg: no visible global function definition for ‘setNames’
plotKegg: no visible binding for global variable ‘KEGGPATHID2NAME’
plotKegg: no visible global function definition for ‘download_KEGGfile’
plotKegg : <anonymous>: no visible global function definition for
  ‘download.file’
plotKegg: no visible global function definition for ‘parse_XMLfile’
plotKegg: no visible global function definition for ‘plot_profile’
processExpressionField: no visible global function definition for
  ‘gtkTextViewGetBuffer’
processExpressionField: no visible global function definition for
  ‘gtkTextBufferGetText’
processExpressionField: no visible global function definition for
  ‘gtkTextBufferGetStartIter’
processExpressionField: no visible global function definition for
  ‘gtkTextBufferGetEndIter’
processExpressionField: no visible global function definition for
  ‘setNames’
processFile: no visible binding for '<<-' assignment to ‘rawResults’
processFile: no visible global function definition for ‘read.table’
processFile: no visible binding for global variable ‘rawResults’
processFile: no visible global function definition for
  ‘gtkWidgetSetSensitive’
processGenesField: no visible global function definition for
  ‘gtkTextViewGetBuffer’
processGenesField: no visible global function definition for
  ‘gtkTextBufferGetText’
processGenesField: no visible global function definition for
  ‘gtkTextBufferGetStartIter’
processGenesField: no visible global function definition for
  ‘gtkTextBufferGetEndIter’
readFEAresults: no visible global function definition for ‘data’
readFEAresults: no visible global function definition for
  ‘gtkTextBufferNew’
readFEAresults: no visible global function definition for
  ‘gtkTextBufferSetText’
readFEAresults: no visible global function definition for
  ‘gtkTextViewSetBuffer’
readFEAresults: no visible global function definition for
  ‘gtkDialogNewWithButtons’
readFEAresults: no visible binding for global variable
  ‘GtkResponseType’
readFEAresults: no visible global function definition for ‘gtkLabel’
readGeneTermSets: no visible global function definition for ‘data’
readGeneTermSets: no visible global function definition for
  ‘read.table’
refList: no visible global function definition for ‘columns’
refList: no visible global function definition for ‘keys’
selectAPI: no visible global function definition for
  ‘gtkWidgetSetSensitive’
selectAPI: no visible global function definition for
  ‘gtkComboBoxAppendText’
selectAPI: no visible global function definition for ‘gtkCheckButton’
selectNetworkTool: no visible global function definition for ‘data’
selectNetworkTool: no visible global function definition for
  ‘gtkWidgetSetSensitive’
selectNetworkType: no visible global function definition for
  ‘gtkWidgetSetSensitive’
selectWs: no visible global function definition for
  ‘gtkWidgetSetSensitive’
selectWs_fillFields: no visible binding for global variable
  ‘DAVIDWebService’
selectWs_fillFields: no visible global function definition for
  ‘getIdTypes’
selectWs_fillFields: no visible global function definition for
  ‘getAllAnnotationCategoryNames’
selectWs_fillFields: no visible global function definition for
  ‘gtkComboBoxAppendText’
selectWs_fillFields: no visible global function definition for
  ‘gtkCheckButton’
selectWs_fillFields: no visible global function definition for
  ‘gtkWidgetSetSensitive’
selectWs_fillFields: no visible global function definition for
  ‘gtkDialogNewWithButtons’
selectWs_fillFields: no visible binding for global variable
  ‘GtkResponseType’
selectWs_fillFields: no visible global function definition for
  ‘gtkLabel’
setColors: no visible global function definition for ‘rainbow’
submitQuery: no visible global function definition for ‘data’
submitQuery: no visible global function definition for
  ‘gtkNotebookGetCurrentPage’
submitQuery: no visible global function definition for
  ‘gtkDialogNewWithButtons’
submitQuery: no visible binding for global variable ‘GtkResponseType’
submitQuery: no visible global function definition for ‘gtkLabel’
submitQuery: no visible global function definition for
  ‘gtkWidgetGetSensitive’
submitQuery: no visible global function definition for ‘readList’
submitQuery: no visible global function definition for
  ‘gtkNotebookSetCurrentPage’
submitQuery: no visible global function definition for
  ‘gtkTextBufferNew’
submitQuery: no visible global function definition for
  ‘gtkTextBufferSetText’
submitQuery: no visible global function definition for
  ‘gtkTextViewSetBuffer’
tabDavid_fill: no visible global function definition for ‘gtkVBox’
tabDavid_fill: no visible global function definition for ‘gtkFrame’
tabDavid_fill: no visible global function definition for ‘gtkHBox’
tabDavid_fill: no visible global function definition for
  ‘gtkRadioButtonNewWithLabelFromWidget’
tabDavid_fill: no visible global function definition for
  ‘gtkRadioButton’
tabDavid_fill: no visible global function definition for
  ‘gtkLinkButtonNewWithLabel’
tabDavid_fill: no visible global function definition for
  ‘gtkFrameSetShadowType’
tabDavid_fill: no visible binding for global variable ‘GtkShadowType’
tabDavid_fill: no visible global function definition for
  ‘gtkWidgetSetSensitive’
tabDavid_fill: no visible global function definition for ‘gtkEntryNew’
tabDavid_fill: no visible global function definition for ‘gtkButton’
tabDavid_fill: no visible global function definition for
  ‘gtkComboBoxNewText’
tabDavid_fill: no visible global function definition for
  ‘gtkScrolledWindow’
tabDavid_fill: no visible global function definition for ‘gtkVBoxNew’
tabDavid_fill: no visible global function definition for
  ‘gtkViewportNew’
tabDavid_fill: no visible global function definition for
  ‘gSignalConnect’
tabFEA_fill: no visible global function definition for ‘gtkHBox’
tabFEA_fill: no visible global function definition for ‘gtkFrame’
tabFEA_fill: no visible global function definition for
  ‘gtkFrameSetShadowType’
tabFEA_fill: no visible binding for global variable ‘GtkShadowType’
tabFEA_fill: no visible global function definition for ‘gtkEntryNew’
tabFEA_fill: no visible global function definition for ‘data’
tabFEA_fill: no visible global function definition for
  ‘installed.packages’
tabFEA_fill: no visible global function definition for ‘setNames’
tabFEA_fill: no visible global function definition for ‘gtkVBoxNew’
tabFEA_fill: no visible global function definition for ‘gtkFrameNew’
tabFEA_fill: no visible global function definition for ‘gtkVBox’
tabFEA_fill: no visible global function definition for
  ‘gtkScrolledWindow’
tabFEA_fill: no visible global function definition for
  ‘gtkTextViewNewWithBuffer’
tabFEA_fill: no visible global function definition for
  ‘pangoFontDescriptionFromString’
tabFEA_fill: no visible global function definition for
  ‘gtkTextBufferNew’
tabFEA_fill: no visible global function definition for
  ‘gtkTextBufferSetText’
tabFEA_fill: no visible global function definition for
  ‘gtkTextViewSetBuffer’
tabFEA_fill: no visible global function definition for ‘gtkButton’
tabFEA_fill: no visible global function definition for ‘gSignalConnect’
tabFEA_fill: no visible global function definition for ‘gtkViewportNew’
tabFEA_fill: no visible global function definition for ‘gtkNotebookNew’
tabFEA_fill: no visible binding for '<<-' assignment to ‘rawResults’
tabFEA_fill: no visible global function definition for
  ‘gtkNotebookInsertPage’
tabFEA_fill: no visible global function definition for ‘gtkLabelNew’
tabGTL_fill: no visible global function definition for ‘gtkVBox’
tabGTL_fill: no visible global function definition for
  ‘gtkComboBoxNewText’
tabGTL_fill: no visible global function definition for
  ‘gtkComboBoxAppendText’
tabGTL_fill: no visible global function definition for
  ‘gtkComboBoxSetTitle’
tabGTL_fill: no visible global function definition for ‘gtkFrame’
tabGTL_fill: no visible global function definition for
  ‘gtkFrameSetShadowType’
tabGTL_fill: no visible binding for global variable ‘GtkShadowType’
tabGTL_fill: no visible global function definition for ‘gtkVBoxNew’
tabGTL_fill: no visible global function definition for ‘gtkCheckButton’
tabGTL_fill: no visible global function definition for ‘gtkEntryNew’
tabGage_fill: no visible global function definition for ‘gtkVBox’
tabGage_fill: no visible global function definition for ‘gtkFrame’
tabGage_fill: no visible global function definition for ‘gtkVBoxNew’
tabGage_fill: no visible global function definition for
  ‘gtkFrameSetShadowType’
tabGage_fill: no visible binding for global variable ‘GtkShadowType’
tabGage_fill: no visible global function definition for ‘gtkHBox’
tabGage_fill: no visible global function definition for
  ‘gtkRadioButtonNewWithLabelFromWidget’
tabGage_fill: no visible global function definition for
  ‘gtkRadioButton’
tabGage_fill: no visible global function definition for ‘gtkEntryNew’
tabGage_fill: no visible global function definition for ‘gtkButton’
tabGage_fill: no visible global function definition for ‘gtkHBoxNew’
tabGage_fill: no visible global function definition for
  ‘gtkComboBoxNewText’
tabGage_fill: no visible global function definition for
  ‘gtkComboBoxAppendText’
tabGage_fill: no visible global function definition for
  ‘gtkCheckButton’
tabGage_fill: no visible global function definition for
  ‘gSignalConnect’
tabHelp_fill: no visible global function definition for ‘gtkHBox’
tabHelp_fill: no visible global function definition for ‘gtkVBox’
tabHelp_fill: no visible global function definition for ‘gtkLabel’
tabHelp_fill: no visible global function definition for ‘gtkFrame’
tabHelp_fill: no visible global function definition for
  ‘gtkFrameSetShadowType’
tabHelp_fill: no visible binding for global variable ‘GtkShadowType’
tabHelp_fill: no visible global function definition for ‘gtkEntryNew’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkHBox’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkTable’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkFrame’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkFrameSetShadowType’
tabNetwork_common_fill: no visible binding for global variable
  ‘GtkShadowType’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkScrolledWindow’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkTextViewNewWithBuffer’
tabNetwork_common_fill: no visible global function definition for
  ‘pangoFontDescriptionFromString’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkTextBufferNew’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkTextBufferSetText’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkTextViewSetBuffer’
tabNetwork_common_fill: no visible global function definition for
  ‘setNames’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkComboBoxNewText’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkComboBoxAppendText’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkComboBoxSetTitle’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkFrameNew’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkButton’
tabNetwork_common_fill: no visible global function definition for
  ‘gSignalConnect’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkVBoxNew’
tabNetwork_common_fill: no visible global function definition for
  ‘data’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkEntryNew’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkExpander’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkCheckButton’
tabNetwork_common_fill: no visible global function definition for
  ‘gtkWidgetSetSensitive’
tabNetwork_fill: no visible global function definition for ‘data’
tabNetwork_fill: no visible global function definition for
  ‘gtkNotebookNew’
tabNetwork_fill: no visible global function definition for
  ‘gtkNotebookInsertPage’
tabNetwork_fill: no visible global function definition for
  ‘gtkLabelNew’
tabNetwork_fill: no visible global function definition for
  ‘gSignalConnect’
tabOther_fill: no visible global function definition for ‘gtkVBox’
tabOther_fill: no visible global function definition for ‘gtkLabelNew’
tabOther_fill: no visible global function definition for ‘gtkExpander’
tabOther_fill: no visible global function definition for ‘gtkHBox’
tabOther_fill: no visible global function definition for
  ‘gtkCheckButton’
tabOther_fill: no visible global function definition for ‘setNames’
tabOther_fill: no visible global function definition for
  ‘gtkComboBoxNewText’
tabOther_fill: no visible global function definition for
  ‘gtkComboBoxAppendText’
tabOther_fill: no visible global function definition for ‘gtkFrame’
tabOther_fill: no visible global function definition for
  ‘gtkFrameSetShadowType’
tabOther_fill: no visible binding for global variable ‘GtkShadowType’
tabOther_fill: no visible global function definition for ‘gtkEntryNew’
tabOther_fill: no visible global function definition for ‘gtkButton’
tabOther_fill: no visible global function definition for
  ‘gSignalConnect’
tabOther_fill: no visible global function definition for
  ‘gtkWidgetSetSensitive’
tabOther_fill : <anonymous>: no visible global function definition for
  ‘gtkComboBoxNewText’
tabOther_fill : <anonymous>: no visible global function definition for
  ‘gtkFrame’
tabOther_fill : <anonymous>: no visible global function definition for
  ‘gtkFrameSetShadowType’
tabOther_fill : <anonymous>: no visible binding for global variable
  ‘GtkShadowType’
tabOther_fill : <anonymous>: no visible global function definition for
  ‘gtkHBox’
tabOther_fill: no visible global function definition for ‘gtkTable’
tabOther_fill: no visible global function definition for ‘gtkLabel’
tabPlotNetwork_fill: no visible global function definition for
  ‘gtkVBox’
tabPlotNetwork_fill: no visible global function definition for
  ‘gtkExpanderNew’
tabPlotNetwork_fill: no visible global function definition for
  ‘gtkHBox’
tabPlotNetwork_fill: no visible global function definition for
  ‘setNames’
tabPlotNetwork_fill: no visible global function definition for
  ‘gtkFrame’
tabPlotNetwork_fill: no visible global function definition for
  ‘gtkFrameSetShadowType’
tabPlotNetwork_fill: no visible binding for global variable
  ‘GtkShadowType’
tabPlotNetwork_fill: no visible global function definition for
  ‘gtkComboBoxNewText’
tabPlotNetwork_fill: no visible global function definition for
  ‘gtkComboBoxAppendText’
tabPlotNetwork_fill: no visible global function definition for
  ‘gtkCheckButton’
tabPlotNetwork_fill: no visible global function definition for
  ‘gtkWidgetSetSensitive’
tabPlotNetwork_fill: no visible global function definition for
  ‘gtkEntryNew’
tabPlotNetwork_fill: no visible global function definition for
  ‘gtkButton’
tabPlotNetwork_fill: no visible global function definition for
  ‘gSignalConnect’
tabReport_fill: no visible global function definition for ‘gtkVBox’
tabReport_fill: no visible global function definition for ‘gtkFrame’
tabReport_fill: no visible global function definition for ‘gtkVBoxNew’
tabReport_fill: no visible global function definition for
  ‘gtkCheckButton’
tabReport_fill: no visible global function definition for ‘gtkButton’
tabReport_fill: no visible global function definition for
  ‘gSignalConnect’
tabSubNetwork_fill: no visible global function definition for ‘gtkVBox’
tabSubNetwork_fill: no visible global function definition for ‘gtkHBox’
tabSubNetwork_fill: no visible global function definition for
  ‘gtkFrame’
tabSubNetwork_fill: no visible global function definition for
  ‘gtkFrameSetShadowType’
tabSubNetwork_fill: no visible binding for global variable
  ‘GtkShadowType’
tabSubNetwork_fill: no visible global function definition for
  ‘gtkEntryNew’
tabSubNetwork_fill: no visible global function definition for
  ‘gtkComboBoxNewText’
tabSubNetwork_fill: no visible global function definition for
  ‘gtkCheckButton’
tabSubNetwork_fill: no visible global function definition for
  ‘gtkFrameNew’
tabSubNetwork_fill: no visible global function definition for
  ‘gtkButton’
tabSubNetwork_fill: no visible global function definition for
  ‘gtkTable’
tabSubNetwork_fill: no visible global function definition for
  ‘gtkLabel’
tabTopGo_fill: no visible global function definition for ‘gtkVBox’
tabTopGo_fill: no visible global function definition for ‘gtkHBoxNew’
tabTopGo_fill: no visible global function definition for ‘gtkFrame’
tabTopGo_fill: no visible global function definition for
  ‘gtkFrameSetShadowType’
tabTopGo_fill: no visible binding for global variable ‘GtkShadowType’
tabTopGo_fill: no visible global function definition for
  ‘gtkComboBoxNewText’
tabTopGo_fill: no visible global function definition for
  ‘gtkComboBoxAppendText’
tabTopGo_fill: no visible global function definition for ‘gtkVBoxNew’
tabTopGo_fill: no visible global function definition for
  ‘gtkCheckButton’
tabTopGo_fill: no visible global function definition for ‘data’
tabTopGo_fill: no visible global function definition for
  ‘gtkScrolledWindow’
tabTopGo_fill: no visible global function definition for
  ‘gtkViewportNew’
tabTopGo_fill: no visible global function definition for ‘gtkEntryNew’
tabTopGo_fill: no visible global function definition for
  ‘gtkLinkButtonNewWithLabel’
viewFile: no visible global function definition for ‘View’
viewFile: no visible binding for global variable ‘rawResults’
Undefined global functions or variables:
  DAVIDWebService GO.db GOBPPARENTS GOCCPARENTS GOFisherTest
  GOMFPARENTS GOTERM GenTable GtkResponseType GtkShadowType
  KEGGPATHID2NAME View abline addList annFUN.gene2GO axis barplot
  basicTextGatherer biocLite box boxplot browseURL col2rgb columns
  curlPerform data dev.off dist download.file download_KEGGfile
  esset.grp exprs gSignalConnect gage genesInTerm
  getAllAnnotationCategoryNames getClusterReportFile getCurlHandle
  getIdTypes getSigGroups getURL groupGOTerms gtkButton gtkCheckButton
  gtkComboBoxAppendText gtkComboBoxNewText gtkComboBoxSetTitle
  gtkDialogNewWithButtons gtkEntryNew gtkExpander gtkExpanderNew
  gtkFileChooserDialog gtkFrame gtkFrameNew gtkFrameSetShadowType
  gtkHBox gtkHBoxNew gtkLabel gtkLabelNew gtkLinkButtonNewWithLabel
  gtkNotebookGetCurrentPage gtkNotebookInsertPage gtkNotebookNew
  gtkNotebookSetCurrentPage gtkRadioButton
  gtkRadioButtonNewWithLabelFromWidget gtkScrolledWindow gtkStatusbar
  gtkTable gtkTextBufferGetEndIter gtkTextBufferGetStartIter
  gtkTextBufferGetText gtkTextBufferNew gtkTextBufferSetText
  gtkTextViewGetBuffer gtkTextViewNewWithBuffer gtkTextViewSetBuffer
  gtkVBox gtkVBoxNew gtkViewportNew gtkWidgetGetSensitive
  gtkWidgetSetSensitive gtkWindowNew hclust image installed.packages
  keys layout legend new pangoFontDescriptionFromString par
  parseHTTPHeader parse_XMLfile plot plot_profile png postForm quantile
  rainbow rawResults reactomeEXTID2PATHID reactomePATHID2EXTID
  reactomePATHID2NAME read.csv read.table readList select
  setAnnotationCategories setNames sigGenes title url.exists
  write.table
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "png", "rainbow")
  importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
             "image", "layout", "legend", "par", "plot", "title")
  importFrom("methods", "new")
  importFrom("stats", "dist", "hclust", "quantile", "setNames")
  importFrom("utils", "View", "browseURL", "data", "download.file",
             "installed.packages", "read.csv", "read.table",
             "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plotGoAncestors   5.300  0.375   5.869
plotKegg          4.806  0.330   9.888
functionalNetwork 2.509  0.276  10.011
analyzeNetwork    1.879  0.108  24.661
fea2incidMat      1.598  0.134   9.130
fea_gtLinker      0.552  0.096   9.685
getTerms          0.190  0.079  10.232
keywordsTerm      0.167  0.064   7.295
clustersDistance  0.166  0.015  10.567
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/FGNet.Rcheck/00check.log’
for details.

FGNet.Rcheck/00install.out:

* installing *source* package ‘FGNet’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FGNet)

FGNet.Rcheck/FGNet-Ex.timings:

nameusersystemelapsed
FGNet-package0.0020.0010.002
FGNet_GUI0.0000.0000.001
FGNet_report0.0030.0010.003
analyzeNetwork 1.879 0.10824.661
clustersDistance 0.166 0.01510.567
fea2incidMat1.5980.1349.130
fea_david3.5960.2523.901
fea_gage0.0000.0000.001
fea_gtLinker0.5520.0969.685
fea_topGO0.0010.0000.002
format_david1.8390.1882.571
format_results0.0010.0000.001
functionalNetwork 2.509 0.27610.011
getTerms 0.190 0.07910.232
keywordsTerm0.1670.0647.295
plotGoAncestors5.3000.3755.869
plotKegg4.8060.3309.888