Package: RCy3

Version: 2.0.88

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCy3.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCy3_2.0.88.tar.gz

StartedAt: 2018-10-16 23:33:34 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:34:40 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 65.9 seconds

RetCode: 0

Status:  OK

CheckDir: RCy3.Rcheck

Warnings: 0

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCy3.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCy3_2.0.88.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/RCy3.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCy3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCy3’ version ‘2.0.88’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RCy3’ 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
createNetworkFromDataFrames: no visible binding for global variable
  ‘SUID’
Undefined global functions or variables:
  SUID
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/RCy3.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RCy3
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RCy3’ ...
** R
** 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 (RCy3)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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.

> # tests disabled as the Bioconductor build system no longer supports interactive sessions
> #require(RCy3) || stop("unable to load RCy3")
> #BiocGenerics:::testPackage('RCy3')
> 
> proc.time()
   user  system elapsed 
  0.259   0.059   0.284 

name	user	system	elapsed
AddToGroup	0.001	0.000	0.001
RemoveFromGroup	0.001	0.000	0.001
addCyEdges	0.001	0.000	0.000
addCyNodes	0.001	0.000	0.001
clearEdgePropertyBypass	0.001	0.000	0.001
clearNetworkCenterBypass	0.001	0.001	0.002
clearNetworkPropertyBypass	0.001	0.000	0.001
clearNetworkZoomBypass	0.001	0.001	0.001
clearNodeOpacityBypass	0.002	0.000	0.001
clearNodePropertyBypass	0.001	0.000	0.001
clearSelection	0.001	0.000	0.001
cloneNetwork	0.001	0.000	0.001
closeSession	0.001	0.001	0.001
collapseGroup	0.001	0.000	0.001
commandEcho	0.001	0.000	0.001
commandOpenDialog	0.001	0.000	0.001
commandPause	0.001	0.000	0.001
commandQuit	0.001	0.000	0.001
commandRunFile	0.001	0.000	0.001
commandSleep	0.001	0.000	0.001
commandsAPI	0.001	0.000	0.002
commandsGET	0.001	0.000	0.001
commandsHelp	0.001	0.000	0.001
commandsPOST	0.001	0.000	0.001
commandsRun	0.001	0.000	0.001
copyVisualStyle	0.001	0.000	0.001
createGraphFromNetwork	0.001	0.000	0.001
createGroup	0.001	0.000	0.001
createIgraphFromNetwork	0.001	0.000	0.001
createNetworkFromDataFrames	0.001	0.001	0.001
createNetworkFromGraph	0.001	0.000	0.001
createNetworkFromIgraph	0.001	0.000	0.001
createSubnetwork	0.000	0.001	0.001
createVisualStyle	0.001	0.000	0.001
cybrowserClose	0.001	0.000	0.001
cybrowserDialog	0.000	0.001	0.001
cybrowserHide	0.001	0.000	0.001
cybrowserList	0.001	0.000	0.001
cybrowserSend	0.001	0.000	0.001
cybrowserShow	0.001	0.000	0.001
cybrowserVersion	0.001	0.001	0.001
cyrestAPI	0.001	0.000	0.001
cyrestDELETE	0.001	0.000	0.001
cyrestGET	0.000	0.000	0.001
cyrestPOST	0.001	0.000	0.001
cyrestPUT	0.000	0.000	0.001
cytoscapeApiVersions	0.001	0.000	0.001
cytoscapeFreeMemory	0.001	0.000	0.001
cytoscapeMemoryStatus	0.001	0.000	0.001
cytoscapeNumberOfCores	0.001	0.000	0.001
cytoscapePing	0.002	0.000	0.001
cytoscapeVersionInfo	0.001	0.000	0.001
deleteAllNetworks	0.001	0.000	0.002
deleteGroup	0.001	0.000	0.001
deleteNetwork	0.001	0.000	0.001
deleteSelectedEdges	0.001	0.000	0.001
deleteSelectedNodes	0.001	0.000	0.001
deleteTableColumn	0.001	0.000	0.001
diffusionAdvanced	0.001	0.001	0.001
diffusionBasic	0.001	0.000	0.001
disableApp	0.001	0.000	0.001
dockPanel	0.001	0.001	0.001
enableApp	0.001	0.000	0.002
expandGroup	0.001	0.000	0.000
exportImage	0.001	0.001	0.001
exportNetwork	0.001	0.000	0.001
exportNetworkToNDEx	0.001	0.000	0.001
exportVisualStyles	0.001	0.000	0.001
fitContent	0.001	0.000	0.001
floatPanel	0.001	0.000	0.000
getAllEdges	0.001	0.000	0.000
getAllNodes	0.001	0.000	0.001
getAppInformation	0.001	0.000	0.001
getAppStatus	0.001	0.000	0.001
getAppUpdates	0.002	0.001	0.001
getArrowShapes	0.001	0.000	0.002
getAvailableApps	0.001	0.000	0.001
getBackgroundColorDefault	0.001	0.001	0.002
getCollectionList	0.001	0.000	0.001
getCollectionName	0.001	0.000	0.000
getCollectionNetworks	0.001	0.000	0.001
getCollectionSuid	0.001	0.001	0.001
getDisabledApps	0.001	0.000	0.001
getEdgeColor	0.001	0.000	0.000
getEdgeCount	0.002	0.000	0.001
getEdgeLineStyle	0.001	0.001	0.001
getEdgeLineWidth	0.001	0.000	0.002
getEdgeProperty	0.001	0.000	0.001
getEdgeSelectionColorDefault	0.001	0.000	0.001
getEdgeTargetArrowShape	0.001	0.000	0.002
getFirstNeighbors	0.001	0.000	0.002
getGroupInfo	0.001	0.000	0.000
getInstalledApps	0.001	0.000	0.001
getLayoutNameMapping	0.001	0.000	0.001
getLayoutNames	0.001	0.000	0.001
getLayoutPropertyNames	0.001	0.000	0.001
getLayoutPropertyType	0.001	0.000	0.001
getLayoutPropertyValue	0.002	0.000	0.001
getLineStyles	0.001	0.000	0.001
getNetworkCenter	0.001	0.000	0.001
getNetworkCount	0.001	0.001	0.001
getNetworkList	0.002	0.000	0.001
getNetworkNDExId	0.001	0.000	0.000
getNetworkName	0.000	0.000	0.001
getNetworkProperty	0.001	0.000	0.000
getNetworkSuid	0.001	0.000	0.001
getNetworkViewSuid	0.000	0.000	0.001
getNetworkViews	0.001	0.000	0.001
getNetworkZoom	0.001	0.000	0.001
getNodeColor	0.001	0.000	0.001
getNodeCount	0.001	0.000	0.001
getNodeHeight	0.001	0.000	0.001
getNodeProperty	0.000	0.000	0.001
getNodeSelectionColorDefault	0.000	0.000	0.001
getNodeShapes	0.000	0.000	0.001
getNodeSize	0	0	0
getNodeWidth	0.000	0.000	0.001
getSelectedEdgeCount	0.000	0.000	0.001
getSelectedEdges	0.000	0.000	0.001
getSelectedNodeCount	0	0	0
getSelectedNodes	0.000	0.001	0.000
getStyleDependencies	0.001	0.000	0.002
getTableColumnNames	0.001	0.000	0.001
getTableColumnTypes	0.001	0.000	0.001
getTableColumns	0.001	0.000	0.001
getTableValue	0.001	0.000	0.002
getUninstalledApps	0.001	0.000	0.001
getVisualPropertyDefault	0.001	0.000	0.001
getVisualPropertyNames	0.001	0.000	0.001
getVisualStyleNames	0.001	0.001	0.002
hideAllPanels	0.001	0.000	0.001
hideEdges	0.000	0.000	0.001
hideNodes	0.001	0.000	0.001
hidePanel	0.001	0.000	0.001
hideSelectedEdges	0.001	0.000	0.001
hideSelectedNodes	0.001	0.000	0.001
importNetworkFromFile	0.001	0.000	0.000
importNetworkFromNDEx	0.001	0.000	0.001
installApp	0.001	0.000	0.001
invertEdgeSelection	0.001	0.000	0.001
invertNodeSelection	0.000	0.000	0.001
layoutCopycat	0.001	0.000	0.001
layoutNetwork	0.001	0.000	0.001
listGroups	0.001	0.000	0.001
lockNodeDimensions	0.001	0.000	0.001
makeSimpleGraph	0.081	0.002	0.083
makeSimpleIgraph	0.017	0.001	0.018
mapTableColumn	0.001	0.000	0.001
mapVisualProperty	0	0	0
matchArrowColorToEdge	0.001	0.000	0.001
openAppStore	0.001	0.000	0.001
openSession	0.001	0.000	0.001
renameNetwork	0.002	0.000	0.002
renameTableColumn	0.001	0.001	0.001
saveSession	0.001	0.000	0.001
selectAllEdges	0.001	0.000	0.002
selectAllNodes	0.002	0.000	0.002
selectEdges	0.001	0.000	0.001
selectEdgesAdjacentToSelectedNodes	0.001	0.000	0.001
selectEdgesConnectingSelectedNodes	0.001	0.000	0.002
selectFirstNeighbors	0.002	0.000	0.001
selectNodes	0.001	0.000	0.002
setBackgroundColorDefault	0.001	0.000	0.001
setCurrentNetwork	0.001	0.001	0.002
setCurrentView	0.001	0.000	0.001
setEdgeColorBypass	0.001	0.000	0.001
setEdgeColorDefault	0.001	0.000	0.001
setEdgeColorMapping	0.001	0.000	0.001
setEdgeFontFaceBypass	0.001	0.001	0.001
setEdgeFontSizeBypass	0.001	0.000	0.001
setEdgeFontSizeDefault	0.001	0.000	0.002
setEdgeLabelBypass	0.001	0.000	0.001
setEdgeLabelColorBypass	0.001	0.000	0.001
setEdgeLabelMapping	0.001	0.000	0.001
setEdgeLabelOpacityBypass	0.001	0.000	0.001
setEdgeLineStyleBypass	0.001	0.000	0.001
setEdgeLineStyleDefault	0.001	0.000	0.003
setEdgeLineStyleMapping	0.001	0.001	0.001
setEdgeLineWidthBypass	0.001	0.000	0.001
setEdgeLineWidthDefault	0.001	0.000	0.001
setEdgeLineWidthMapping	0.001	0.000	0.001
setEdgeOpacityBypass	0.001	0.001	0.001
setEdgeOpacityMapping	0.001	0.000	0.000
setEdgePropertyBypass	0.002	0.000	0.002
setEdgeSelectionColorDefault	0.001	0.000	0.002
setEdgeSourceArrowColorBypass	0.001	0.000	0.002
setEdgeSourceArrowColorDefault	0.001	0.000	0.002
setEdgeSourceArrowColorMapping	0.001	0.000	0.000
setEdgeSourceArrowMapping	0.001	0.000	0.001
setEdgeSourceArrowShapeBypass	0.001	0.000	0.001
setEdgeSourceArrowShapeDefault	0.001	0.000	0.001
setEdgeTargetArrowColorBypass	0.001	0.000	0.000
setEdgeTargetArrowColorDefault	0.001	0.000	0.002
setEdgeTargetArrowColorMapping	0.001	0.000	0.001
setEdgeTargetArrowMapping	0.001	0.000	0.001
setEdgeTargetArrowShapeBypass	0.001	0.000	0.001
setEdgeTargetArrowShapeDefault	0.001	0.000	0.001
setEdgeTooltipBypass	0.001	0.000	0.000
setEdgeTooltipMapping	0.001	0.000	0.001
setLayoutProperties	0.001	0.000	0.002
setNetworkCenterBypass	0.001	0.000	0.001
setNetworkPropertyBypass	0.001	0.000	0.001
setNetworkZoomBypass	0.001	0.000	0.001
setNodeBorderColorBypass	0.001	0.001	0.002
setNodeBorderColorDefault	0	0	0
setNodeBorderColorMapping	0.002	0.000	0.001
setNodeBorderOpacityBypass	0.001	0.000	0.002
setNodeBorderWidthBypass	0.001	0.000	0.001
setNodeBorderWidthDefault	0.001	0.001	0.001
setNodeBorderWidthMapping	0.001	0.000	0.001
setNodeColorBypass	0.001	0.000	0.002
setNodeColorDefault	0.001	0.000	0.002
setNodeColorMapping	0.001	0.000	0.001
setNodeComboOpacityMapping	0.001	0.001	0.001
setNodeFillOpacityBypass	0.001	0.000	0.001
setNodeFontSizeBypass	0	0	0
setNodeFontSizeDefault	0.000	0.001	0.001
setNodeHeightBypass	0.000	0.000	0.001
setNodeLabelBypass	0	0	0
setNodeLabelColorBypass	0.000	0.000	0.001
setNodeLabelColorDefault	0.001	0.000	0.001
setNodeLabelMapping	0.001	0.000	0.000
setNodeLabelOpacityBypass	0.001	0.000	0.001
setNodeOpacityBypass	0.001	0.000	0.001
setNodePropertyBypass	0.001	0.000	0.000
setNodeSelectionColorDefault	0.001	0.000	0.001
setNodeShapeBypass	0.001	0.000	0.001
setNodeShapeDefault	0.001	0.000	0.001
setNodeShapeMapping	0.001	0.000	0.001
setNodeSizeBypass	0.001	0.000	0.001
setNodeSizeDefault	0.001	0.000	0.002
setNodeSizeMapping	0.001	0.000	0.001
setNodeTooltipMapping	0.002	0.000	0.001
setNodeWidthBypass	0.001	0.001	0.002
setStyleDependencies	0.001	0.000	0.000
setVisualPropertyDefault	0.001	0.000	0.001
setVisualStyle	0.001	0.001	0.002
syncNodeCustomGraphicsSize	0.001	0.000	0.001
toggleGraphicsDetails	0.001	0.000	0.002
unhideAll	0.002	0.000	0.001
unhideEdges	0.001	0.000	0.001
unhideNodes	0.000	0.000	0.001
uninstallApp	0.000	0.000	0.001
updateApp	0.001	0.000	0.001
updateNetworkInNDEx	0.001	0.000	0.001
updateStyleDefaults	0.001	0.000	0.001
updateStyleMapping	0.001	0.000	0.001