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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FGNet_3.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/FGNet.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘3.10.0’
* 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 9.2Mb
sub-directories of 1Mb or more:
doc 8.7Mb
* 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 ... 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, cbind, colMeans, colSums, colnames, 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
'select()' returned 1:1 mapping between keys and columns
[1] "Downloading files: 1/1"
trying URL 'http://www.genome.jp/kegg-bin/download?entry=sce04111&format=kgml'
downloaded 1 bytes
trying URL 'http://www.genome.jp/kegg/pathway/sce/sce04111.png'
Content type 'image/png' length 43060 bytes (42 KB)
==================================================
downloaded 42 KB
trying URL 'http://www.genome.jp/kegg/pathway/map/map04111.png'
Content type 'image/png' length 40513 bytes (39 KB)
==================================================
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 ‘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 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/FGNet.Rcheck/00check.log’
for details.