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CHECK report for FGNet on merida2

This page was generated on 2019-04-09 13:28:53 -0400 (Tue, 09 Apr 2019).

Package 538/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FGNet 3.17.0
Sara Aibar
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/FGNet
Branch: master
Last Commit: 72c43b1
Last Changed Date: 2018-10-30 11:54:32 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: FGNet
Version: 3.17.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FGNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FGNet_3.17.0.tar.gz
StartedAt: 2019-04-09 00:51:47 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:52:52 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 65.0 seconds
RetCode: 0
Status:  OK 
CheckDir: FGNet.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FGNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FGNet_3.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/FGNet.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘3.17.0’
* 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 ... OK
* 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 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
  ‘install.packages’
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 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
  install.packages 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",
             "install.packages", "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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotGoAncestors 5.32  0.443   5.812
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/FGNet.Rcheck/00check.log’
for details.



Installation output

FGNet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FGNet
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘FGNet’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FGNet)

Tests output

FGNet.Rcheck/tests/runTests.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("FGNet")


RUNIT TEST PROTOCOL -- Tue Apr  9 00:52:46 2019 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
FGNet RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.198   0.142   1.314 

Example timings

FGNet.Rcheck/FGNet-Ex.timings

nameusersystemelapsed
FGNet-package0.0000.0010.001
FGNet_GUI0.0000.0010.001
FGNet_report0.0000.0000.001
analyzeNetwork0.0000.0000.001
clustersDistance000
fea2incidMat0.0000.0000.001
fea_david3.3930.1663.595
fea_gage0.0010.0010.001
fea_gtLinker0.0010.0000.001
fea_topGO0.0000.0010.001
format_david0.8540.0760.942
format_results000
functionalNetwork0.0010.0010.001
getTerms0.0010.0000.000
keywordsTerm0.0000.0000.001
plotGoAncestors5.3200.4435.812
plotKegg0.2440.0280.279