Sara Aibar
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/FGNet |
| Branch: RELEASE_3_6 |
| Last Commit: 62559b4 |
| Last Changed Date: 2017-10-30 12:40:09 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:23:32 -0400 (Thu, 12 Apr 2018).
| Package 462/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| FGNet 3.12.0 Sara Aibar
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: FGNet |
| Version: 3.12.0 |
| Command: rm -rf FGNet.buildbin-libdir FGNet.Rcheck && mkdir FGNet.buildbin-libdir FGNet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FGNet.buildbin-libdir FGNet_3.12.0.tar.gz >FGNet.Rcheck\00install.out 2>&1 && cp FGNet.Rcheck\00install.out FGNet-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=FGNet.buildbin-libdir --install="check:FGNet-install.out" --force-multiarch --no-vignettes --timings FGNet_3.12.0.tar.gz |
| StartedAt: 2018-04-11 23:57:25 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:59:57 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 151.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FGNet.Rcheck |
| Warnings: 0 |
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### Running command:
###
### rm -rf FGNet.buildbin-libdir FGNet.Rcheck && mkdir FGNet.buildbin-libdir FGNet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FGNet.buildbin-libdir FGNet_3.12.0.tar.gz >FGNet.Rcheck\00install.out 2>&1 && cp FGNet.Rcheck\00install.out FGNet-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=FGNet.buildbin-libdir --install="check:FGNet-install.out" --force-multiarch --no-vignettes --timings FGNet_3.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/FGNet.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '3.12.0'
* 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
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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
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analyzeNetwork: no visible global function definition for 'par'
analyzeNetwork: no visible global function definition for 'boxplot'
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analyzeNetwork: no visible global function definition for 'axis'
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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 'par'
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fea2incidMat: no visible global function definition for 'setNames'
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fea_david: no visible global function definition for
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fea_david: no visible global function definition for
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fea_david: no visible global function definition for 'getCurlHandle'
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fea_topGO : <anonymous>: no visible global function definition for
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fillCombosColumns : <anonymous>: no visible global function definition
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generateNetwork: no visible global function definition for
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generateNetwork: no visible binding for global variable
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generateReport: no visible binding for global variable
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generateReport: no visible global function definition for 'gtkLabel'
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goTreeLinks: no visible binding for global variable 'GOCCPARENTS'
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loadFileDialog: no visible global function definition for
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loadFileDialog: no visible global function definition for
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loadInstPkg: no visible global function definition for
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loadInstPkg: no visible binding for global variable 'GtkResponseType'
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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
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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'
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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
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plotKegg: no visible global function definition for 'parse_XMLfile'
plotKegg: no visible global function definition for 'plot_profile'
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processExpressionField: no visible global function definition for
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processExpressionField: no visible global function definition for
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processExpressionField: no visible global function definition for
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processExpressionField: no visible global function definition for
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processFile: no visible global function definition for 'read.table'
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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
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processGenesField: no visible global function definition for
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readFEAresults: no visible global function definition for
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readFEAresults: no visible global function definition for
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'gtkDialogNewWithButtons'
readFEAresults: no visible binding for global variable
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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
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selectWs: no visible global function definition for
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selectWs_fillFields: no visible binding for global variable
'DAVIDWebService'
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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
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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
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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
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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'
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tabHelp_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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'gtkEntryNew'
tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_fill: no visible global function definition for
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tabNetwork_fill: no visible global function definition for
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tabNetwork_fill: no visible global function definition for
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tabOther_fill: no visible global function definition for 'gtkHBox'
tabOther_fill: no visible global function definition for
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tabOther_fill: no visible global function definition for
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tabOther_fill: no visible global function definition for
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tabOther_fill: no visible global function definition for 'gtkFrame'
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tabOther_fill: no visible binding for global variable 'GtkShadowType'
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tabOther_fill: no visible global function definition for
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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
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tabPlotNetwork_fill: no visible global function definition for
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tabPlotNetwork_fill: no visible global function definition for
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tabPlotNetwork_fill: no visible global function definition for
'gtkFrameSetShadowType'
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tabPlotNetwork_fill: no visible global function definition for
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'gtkWidgetSetSensitive'
tabPlotNetwork_fill: no visible global function definition for
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'gtkButton'
tabPlotNetwork_fill: no visible global function definition for
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tabReport_fill: no visible global function definition for 'gtkVBox'
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tabReport_fill: no visible global function definition for
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tabReport_fill: no visible global function definition for
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tabSubNetwork_fill: no visible global function definition for
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tabSubNetwork_fill: no visible global function definition for
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tabSubNetwork_fill: no visible binding for global variable
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'gtkComboBoxNewText'
tabSubNetwork_fill: no visible global function definition for
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'gtkFrameNew'
tabSubNetwork_fill: no visible global function definition for
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tabSubNetwork_fill: no visible global function definition for
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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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotKegg 2.75 0.31 5.13
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotGoAncestors 4.89 0.16 5.16
plotKegg 4.34 0.28 6.45
* 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-3.6-bioc/meat/FGNet.Rcheck/00check.log'
for details.
FGNet.Rcheck/00install.out
install for i386
* installing *source* package 'FGNet' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'FGNet'
finding HTML links ... done
FGNet-package html
FGNet_GUI html
FGNet_report html
analyzeNetwork html
clustersDistance html
data html
fea2incidMat html
fea_david html
fea_gage html
fea_gtLinker html
fea_topGO html
format_david html
format_results html
functionalNetwork html
getTerms html
keywordsTerm html
plotGoAncestors html
plotKegg html
readGeneTermSets html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'FGNet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FGNet' as FGNet_3.12.0.zip
* DONE (FGNet)
In R CMD INSTALL
In R CMD INSTALL
|
FGNet.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("FGNet")
trying URL 'http://gtlinker.cnb.csic.es/jobs/1639610/global_hash'
Content type 'text/plain' length 3656 bytes
==================================================
downloaded 3656 bytes
Results downloaded to folder '1639610_gtLinker'
Metagroups and Gene-term sets tables saved as 1639610_gtLinker_formatted_metagroups.txt and 1639610_gtLinker_formatted_gtSets.txt.
RUNIT TEST PROTOCOL -- Wed Apr 11 23:59:44 2018
***********************************************
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
1.95 0.46 4.48
|
FGNet.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("FGNet")
trying URL 'http://gtlinker.cnb.csic.es/jobs/1639610/global_hash'
Content type 'text/plain' length 3656 bytes
==================================================
downloaded 3656 bytes
Results downloaded to folder '1639610_gtLinker'
Metagroups and Gene-term sets tables saved as 1639610_gtLinker_formatted_metagroups.txt and 1639610_gtLinker_formatted_gtSets.txt.
RUNIT TEST PROTOCOL -- Wed Apr 11 23:59:50 2018
***********************************************
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
2.31 0.35 5.09
|
|
FGNet.Rcheck/examples_i386/FGNet-Ex.timings
|
FGNet.Rcheck/examples_x64/FGNet-Ex.timings
|