Sara Aibar
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/FGNet |
| Branch: RELEASE_3_9 |
| Last Commit: 85a050d |
| Last Changed Date: 2019-05-02 11:53:46 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:28:50 -0400 (Wed, 16 Oct 2019).
| Package 547/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| FGNet 3.18.0 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 | |
| Package: FGNet |
| Version: 3.18.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FGNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings FGNet_3.18.0.tar.gz |
| StartedAt: 2019-10-16 03:41:01 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:42:27 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 85.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FGNet.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FGNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings FGNet_3.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/FGNet.Rcheck' * using R version 3.6.1 (2019-07-05) * 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 '3.18.0' * 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 :: 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 : : no visible global function definition for 'write.table' fea_david : : no visible global function definition for 'getIdTypes' fea_david: no visible global function definition for 'setAnnotationCategories' fea_david : : 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 : : no visible global function definition for 'genesInTerm' fea_topGO : : no visible global function definition for 'sigGenes' fillCombosColumns : : 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 : : no visible global function definition for 'setNames' goTreeLinks: no visible global function definition for 'data' goTreeLinks: no visible binding for global variable 'GOBPPARENTS' goTreeLinks: no visible binding for global variable 'GOMFPARENTS' goTreeLinks: no visible binding for global variable 'GOCCPARENTS' keywordsTerm: no visible global function definition for 'quantile' loadEset: no visible global function definition for 'gtkCheckButton' loadFileDialog: no visible global function definition for 'data' loadFileDialog: no visible global function definition for 'gtkFileChooserDialog' loadFileDialog: no visible binding for global variable 'GtkResponseType' loadFileDialog: no visible global function definition for 'read.table' loadFileDialog: no visible global function definition for 'gtkTextBufferNew' loadFileDialog: no visible global function definition for 'gtkTextBufferSetText' loadFileDialog: no visible global function definition for 'gtkTextViewSetBuffer' loadInstPkg: no visible global function definition for 'installed.packages' loadInstPkg: no visible global function definition for 'gtkDialogNewWithButtons' loadInstPkg: no visible binding for global variable 'GtkResponseType' loadInstPkg: no visible global function definition for 'gtkLabel' loadInstPkg: no visible global function definition for 'install.packages' plotFGNet: no visible global function definition for 'setNames' plotFGNet: no visible global function definition for 'plot' plotFGNet: no visible global function definition for 'legend' plotFGNet: no visible global function definition for 'title' plotFGNet_bipartite: no visible global function definition for 'setNames' plotGoAncestors: no visible binding for global variable 'GOBPPARENTS' plotGoAncestors: no visible binding for global variable 'GOMFPARENTS' plotGoAncestors: no visible binding for global variable 'GOCCPARENTS' plotGoAncestors : : 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 : : 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 : : no visible global function definition for 'gtkComboBoxNewText' 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 '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 ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed plotGoAncestors 4.51 0.92 5.51 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed plotGoAncestors 4.33 1.03 5.56 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.9-bioc/meat/FGNet.Rcheck/00check.log' for details.
FGNet.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/FGNet_3.18.0.tar.gz && rm -rf FGNet.buildbin-libdir && mkdir FGNet.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FGNet.buildbin-libdir FGNet_3.18.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL FGNet_3.18.0.zip && rm FGNet_3.18.0.tar.gz FGNet_3.18.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 1464k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1464k 100 1464k 0 0 6440k 0 --:--:-- --:--:-- --:--:-- 6627k
install for i386
* installing *source* package 'FGNet' ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'FGNet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FGNet' as FGNet_3.18.0.zip
* DONE (FGNet)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'FGNet' successfully unpacked and MD5 sums checked
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FGNet.Rcheck/tests_i386/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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")
RUNIT TEST PROTOCOL -- Wed Oct 16 03:42:20 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
1.12 0.10 1.26
|
FGNet.Rcheck/tests_x64/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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")
RUNIT TEST PROTOCOL -- Wed Oct 16 03:42:21 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
1.17 0.10 1.26
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FGNet.Rcheck/examples_i386/FGNet-Ex.timings
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FGNet.Rcheck/examples_x64/FGNet-Ex.timings
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