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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:28:53 -0400 (Tue, 09 Apr 2019).
| Package 538/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| FGNet 3.17.0 Sara Aibar
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| 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 |
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### Running command:
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### /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
###
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* 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
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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
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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
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fea_david : <anonymous>: no visible global function definition for
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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
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fea_gtLinker_getResults: no visible global function definition for
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fea_gtLinker_getResults: no visible global function definition for
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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
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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
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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
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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
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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
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loadInstPkg: no visible binding for global variable ‘GtkResponseType’
loadInstPkg: no visible global function definition for ‘gtkLabel’
loadInstPkg: no visible global function definition for
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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
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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
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processGenesField: no visible global function definition for
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processGenesField: no visible global function definition for
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processGenesField: no visible global function definition for
‘gtkTextBufferGetStartIter’
processGenesField: no visible global function definition for
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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
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readFEAresults: no visible global function definition for ‘gtkLabel’
readGeneTermSets: no visible global function definition for ‘data’
readGeneTermSets: no visible global function definition for
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refList: no visible global function definition for ‘columns’
refList: no visible global function definition for ‘keys’
selectAPI: no visible global function definition for
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selectAPI: no visible global function definition for
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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
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selectWs_fillFields: no visible global function definition for
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selectWs_fillFields: no visible global function definition for
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selectWs_fillFields: no visible global function definition for
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selectWs_fillFields: no visible global function definition for
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selectWs_fillFields: no visible binding for global variable
‘GtkResponseType’
selectWs_fillFields: no visible global function definition for
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setColors: no visible global function definition for ‘rainbow’
submitQuery: no visible global function definition for ‘data’
submitQuery: no visible global function definition for
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submitQuery: no visible global function definition for
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submitQuery: no visible global function definition for ‘gtkLabel’
submitQuery: no visible global function definition for
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submitQuery: no visible global function definition for ‘readList’
submitQuery: no visible global function definition for
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submitQuery: no visible global function definition for
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tabDavid_fill: no visible global function definition for ‘gtkHBox’
tabDavid_fill: no visible global function definition for
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tabDavid_fill: no visible global function definition for
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tabDavid_fill: no visible global function definition for
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tabDavid_fill: no visible global function definition for
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tabDavid_fill: no visible binding for global variable ‘GtkShadowType’
tabDavid_fill: no visible global function definition for
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tabDavid_fill: no visible global function definition for
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tabDavid_fill: no visible global function definition for
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tabDavid_fill: no visible global function definition for
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tabFEA_fill: no visible global function definition for
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tabFEA_fill: no visible binding for global variable ‘GtkShadowType’
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tabFEA_fill: no visible global function definition for
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tabFEA_fill: no visible global function definition for ‘setNames’
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tabFEA_fill: no visible global function definition for
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tabFEA_fill: no visible global function definition for
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tabFEA_fill: no visible global function definition for
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tabFEA_fill: no visible global function definition for
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tabFEA_fill: no visible global function definition for
‘gtkTextBufferSetText’
tabFEA_fill: no visible global function definition for
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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
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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
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tabGTL_fill: no visible global function definition for
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tabGTL_fill: no visible global function definition for
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tabGTL_fill: no visible global function definition for ‘gtkFrame’
tabGTL_fill: no visible global function definition for
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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’
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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
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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
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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
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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
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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.
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)
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
FGNet.Rcheck/FGNet-Ex.timings
| name | user | system | elapsed | |
| FGNet-package | 0.000 | 0.001 | 0.001 | |
| FGNet_GUI | 0.000 | 0.001 | 0.001 | |
| FGNet_report | 0.000 | 0.000 | 0.001 | |
| analyzeNetwork | 0.000 | 0.000 | 0.001 | |
| clustersDistance | 0 | 0 | 0 | |
| fea2incidMat | 0.000 | 0.000 | 0.001 | |
| fea_david | 3.393 | 0.166 | 3.595 | |
| fea_gage | 0.001 | 0.001 | 0.001 | |
| fea_gtLinker | 0.001 | 0.000 | 0.001 | |
| fea_topGO | 0.000 | 0.001 | 0.001 | |
| format_david | 0.854 | 0.076 | 0.942 | |
| format_results | 0 | 0 | 0 | |
| functionalNetwork | 0.001 | 0.001 | 0.001 | |
| getTerms | 0.001 | 0.000 | 0.000 | |
| keywordsTerm | 0.000 | 0.000 | 0.001 | |
| plotGoAncestors | 5.320 | 0.443 | 5.812 | |
| plotKegg | 0.244 | 0.028 | 0.279 | |