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CHECK report for FGNet on tokay2

This page was generated on 2018-07-24 11:05:06 -0400 (Tue, 24 Jul 2018).

Package 486/1560HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FGNet 3.14.0
Sara Aibar
Snapshot Date: 2018-07-23 16:45:09 -0400 (Mon, 23 Jul 2018)
URL: https://git.bioconductor.org/packages/FGNet
Branch: RELEASE_3_7
Last Commit: 2ce55ef
Last Changed Date: 2018-04-30 10:35:31 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: FGNet
Version: 3.14.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FGNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings FGNet_3.14.0.tar.gz
StartedAt: 2018-07-24 01:52:34 -0400 (Tue, 24 Jul 2018)
EndedAt: 2018-07-24 01:56:55 -0400 (Tue, 24 Jul 2018)
EllapsedTime: 260.2 seconds
RetCode: 1
Status:  ERROR  
CheckDir: FGNet.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FGNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings FGNet_3.14.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/FGNet.Rcheck'
* using R version 3.5.1 RC (2018-06-24 r74929)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FGNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FGNet' version '3.14.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 '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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'FGNet-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotKegg
> ### Title: Plot KEGG pathway
> ### Aliases: plotKegg
> 
> ### ** Examples
> 
> 
> ###################################
> # Gene info
> genesYeast <- c("ADA2", "APC1", "APC11", "APC2", "APC4", "APC5", "APC9", "CDC16", 
+     "CDC23", "CDC26", "CDC27", "CFT1", "CFT2", "DCP1", "DOC1", "FIP1", 
+     "GCN5", "GLC7", "HFI1", "KEM1", "LSM1", "LSM2", "LSM3", "LSM4", 
+     "LSM5", "LSM6", "LSM7", "LSM8", "MPE1", "NGG1", "PAP1", "PAT1", 
+     "PFS2", "PTA1", "PTI1", "REF2", "RNA14", "RPN1", "RPN10", "RPN11", 
+     "RPN13", "RPN2", "RPN3", "RPN5", "RPN6", "RPN8", "RPT1", "RPT3", 
+     "RPT6", "SGF11", "SGF29", "SGF73", "SPT20", "SPT3", "SPT7", "SPT8", 
+     "TRA1", "YSH1", "YTH1")
> 
> # Gene expression (1=UP, -1=DW)
> genesYeastExpr <- setNames(c(rep(1,29), rep(-1,30)), genesYeast)
> 
> 
> ###################################
> # Plot pathway
> 
> # Specific pathway
> plotKegg("sce04111", genesYeastExpr, geneIDtype="GENENAME")

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

'select()' returned 1:1 mapping between keys and columns
[1] "Downloading files: 1/1"
trying URL 'http://www.genome.jp/kegg/pathway/sce/sce04111.png'
Content type 'image/png' length unknown
.......... .......... .......... .......... ..
downloaded 42 KB

trying URL 'http://www.genome.jp/kegg/pathway/map/map04111.png'
Content type 'image/png' length unknown
.......... .......... .......... .........
downloaded 39 KB

Start tag expected, '<' not found
Error: 1: Start tag expected, '<' not found
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'FGNet-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotKegg
> ### Title: Plot KEGG pathway
> ### Aliases: plotKegg
> 
> ### ** Examples
> 
> 
> ###################################
> # Gene info
> genesYeast <- c("ADA2", "APC1", "APC11", "APC2", "APC4", "APC5", "APC9", "CDC16", 
+     "CDC23", "CDC26", "CDC27", "CFT1", "CFT2", "DCP1", "DOC1", "FIP1", 
+     "GCN5", "GLC7", "HFI1", "KEM1", "LSM1", "LSM2", "LSM3", "LSM4", 
+     "LSM5", "LSM6", "LSM7", "LSM8", "MPE1", "NGG1", "PAP1", "PAT1", 
+     "PFS2", "PTA1", "PTI1", "REF2", "RNA14", "RPN1", "RPN10", "RPN11", 
+     "RPN13", "RPN2", "RPN3", "RPN5", "RPN6", "RPN8", "RPT1", "RPT3", 
+     "RPT6", "SGF11", "SGF29", "SGF73", "SPT20", "SPT3", "SPT7", "SPT8", 
+     "TRA1", "YSH1", "YTH1")
> 
> # Gene expression (1=UP, -1=DW)
> genesYeastExpr <- setNames(c(rep(1,29), rep(-1,30)), genesYeast)
> 
> 
> ###################################
> # Plot pathway
> 
> # Specific pathway
> plotKegg("sce04111", genesYeastExpr, geneIDtype="GENENAME")

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

'select()' returned 1:1 mapping between keys and columns
[1] "Downloading files: 1/1"
trying URL 'http://www.genome.jp/kegg/pathway/sce/sce04111.png'
Content type 'image/png' length unknown
.......... .......... .......... .......... ..
downloaded 42 KB

trying URL 'http://www.genome.jp/kegg/pathway/map/map04111.png'
Content type 'image/png' length unknown
.......... .......... .......... .........
downloaded 39 KB

Start tag expected, '<' not found
Error: 1: Start tag expected, '<' not found
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
   
  1 Test Suite : 
  FGNet RUnit Tests - 2 test functions, 1 error, 0 failures
  ERROR in test_fea_gtLinker_getResults: Error in fea_gtLinker_getResults(jobID = 1639610) : 
    Either the web server URL is wrong or the server is down.
  
  Test files with failing tests
  
     test_getResults_gtLinker.R 
       test_fea_gtLinker_getResults 
  
  
  Error in BiocGenerics:::testPackage("FGNet") : 
    unit tests failed for package FGNet
  Execution halted
** running tests for arch 'x64' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
   
  1 Test Suite : 
  FGNet RUnit Tests - 2 test functions, 1 error, 0 failures
  ERROR in test_fea_gtLinker_getResults: Error in fea_gtLinker_getResults(jobID = 1639610) : 
    Either the web server URL is wrong or the server is down.
  
  Test files with failing tests
  
     test_getResults_gtLinker.R 
       test_fea_gtLinker_getResults 
  
  
  Error in BiocGenerics:::testPackage("FGNet") : 
    unit tests failed for package FGNet
  Execution halted
* 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: 4 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/FGNet.Rcheck/00check.log'
for details.

Installation output

FGNet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/FGNet_3.14.0.tar.gz && rm -rf FGNet.buildbin-libdir && mkdir FGNet.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FGNet.buildbin-libdir FGNet_3.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL FGNet_3.14.0.zip && rm FGNet_3.14.0.tar.gz FGNet_3.14.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1464k  100 1464k    0     0  20.6M      0 --:--:-- --:--:-- --:--:-- 22.7M

install for i386

* installing *source* package 'FGNet' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FGNet'
    finding HTML links ... done
    FGNet-package                           html  
    FGNet_GUI                               html  
    FGNet_report                            html  
    analyzeNetwork                          html  
    clustersDistance                        html  
    data                                    html  
    fea2incidMat                            html  
    fea_david                               html  
    fea_gage                                html  
    fea_gtLinker                            html  
    fea_topGO                               html  
    format_david                            html  
    format_results                          html  
    functionalNetwork                       html  
    getTerms                                html  
    keywordsTerm                            html  
    plotGoAncestors                         html  
    plotKegg                                html  
    readGeneTermSets                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'FGNet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FGNet' as FGNet_3.14.0.zip
* DONE (FGNet)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'FGNet' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

FGNet.Rcheck/tests_i386/runTests.Rout.fail


R version 3.5.1 RC (2018-06-24 r74929) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
Timing stopped at: 1.36 0.59 2.17
Error in fea_gtLinker_getResults(jobID = 1639610) : 
  Either the web server URL is wrong or the server is down.


RUNIT TEST PROTOCOL -- Tue Jul 24 01:56:44 2018 
*********************************************** 
Number of test functions: 2 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
FGNet RUnit Tests - 2 test functions, 1 error, 0 failures
ERROR in test_fea_gtLinker_getResults: Error in fea_gtLinker_getResults(jobID = 1639610) : 
  Either the web server URL is wrong or the server is down.

Test files with failing tests

   test_getResults_gtLinker.R 
     test_fea_gtLinker_getResults 


Error in BiocGenerics:::testPackage("FGNet") : 
  unit tests failed for package FGNet
Execution halted

FGNet.Rcheck/tests_x64/runTests.Rout.fail


R version 3.5.1 RC (2018-06-24 r74929) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
Timing stopped at: 1.3 0.55 2.07
Error in fea_gtLinker_getResults(jobID = 1639610) : 
  Either the web server URL is wrong or the server is down.


RUNIT TEST PROTOCOL -- Tue Jul 24 01:56:48 2018 
*********************************************** 
Number of test functions: 2 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
FGNet RUnit Tests - 2 test functions, 1 error, 0 failures
ERROR in test_fea_gtLinker_getResults: Error in fea_gtLinker_getResults(jobID = 1639610) : 
  Either the web server URL is wrong or the server is down.

Test files with failing tests

   test_getResults_gtLinker.R 
     test_fea_gtLinker_getResults 


Error in BiocGenerics:::testPackage("FGNet") : 
  unit tests failed for package FGNet
Execution halted

Example timings

FGNet.Rcheck/examples_i386/FGNet-Ex.timings

nameusersystemelapsed
FGNet-package000
FGNet_GUI0.020.000.02
FGNet_report0.010.000.01
analyzeNetwork1.580.606.10
clustersDistance0.220.012.47
fea2incidMat1.140.133.48
fea_david3.090.233.34
fea_gage000
fea_gtLinker 0.31 0.0563.53
fea_topGO0.020.000.02
format_david0.590.121.04
format_results000
functionalNetwork1.090.032.81
getTerms0.270.003.45
keywordsTerm0.210.031.95
plotGoAncestors2.880.113.01

FGNet.Rcheck/examples_x64/FGNet-Ex.timings

nameusersystemelapsed
FGNet-package000
FGNet_GUI000
FGNet_report000
analyzeNetwork1.280.703.90
clustersDistance0.200.032.41
fea2incidMat1.100.102.94
fea_david2.860.122.99
fea_gage000
fea_gtLinker 0.41 0.0863.67
fea_topGO000
format_david0.810.030.89
format_results000
functionalNetwork1.080.072.92
getTerms0.200.012.35
keywordsTerm0.220.001.97
plotGoAncestors3.120.198.21