Package: RCy3

Version: 2.3.12

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_2.3.12.tar.gz

StartedAt: 2019-04-09 04:49:07 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:50:37 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 90.1 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_2.3.12.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RCy3.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.3.12’
* 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-3.9-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/3.6/Resources/library’
* installing *source* package ‘RCy3’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RCy3)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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 
  0.373   0.148   0.469 

name	user	system	elapsed
AddToGroup	0.000	0.000	0.001
RemoveFromGroup	0	0	0
addCyEdges	0.000	0.001	0.000
addCyNodes	0.001	0.000	0.001
applyFilter	0.000	0.000	0.001
bundleEdges	0.000	0.001	0.001
clearEdgePropertyBypass	0	0	0
clearNetworkCenterBypass	0	0	0
clearNetworkPropertyBypass	0.000	0.000	0.001
clearNetworkZoomBypass	0	0	0
clearNodeOpacityBypass	0	0	0
clearNodePropertyBypass	0.000	0.000	0.001
clearSelection	0.000	0.001	0.000
cloneNetwork	0.000	0.000	0.001
closeSession	0.001	0.000	0.000
collapseGroup	0.001	0.000	0.001
commandEcho	0.000	0.000	0.001
commandOpenDialog	0.000	0.000	0.001
commandPause	0	0	0
commandQuit	0	0	0
commandRunFile	0	0	0
commandSleep	0.000	0.000	0.001
commandsAPI	0	0	0
commandsGET	0.000	0.000	0.001
commandsHelp	0	0	0
commandsPOST	0.000	0.000	0.001
commandsRun	0	0	0
copyVisualStyle	0.000	0.000	0.001
createColumnFilter	0.001	0.000	0.000
createCompositeFilter	0.001	0.000	0.001
createDegreeFilter	0	0	0
createGraphFromNetwork	0	0	0
createGroup	0.000	0.000	0.001
createIgraphFromNetwork	0	0	0
createNetworkFromDataFrames	0.000	0.001	0.001
createNetworkFromGraph	0	0	0
createNetworkFromIgraph	0.000	0.001	0.001
createSubnetwork	0.000	0.000	0.001
createVisualStyle	0	0	0
cybrowserClose	0.000	0.001	0.000
cybrowserDialog	0.000	0.000	0.001
cybrowserHide	0.000	0.000	0.001
cybrowserList	0	0	0
cybrowserSend	0	0	0
cybrowserShow	0.000	0.001	0.001
cybrowserVersion	0	0	0
cyrestAPI	0.001	0.000	0.000
cyrestDELETE	0.000	0.001	0.000
cyrestGET	0	0	0
cyrestPOST	0.000	0.001	0.001
cyrestPUT	0.000	0.000	0.001
cytoscapeApiVersions	0.000	0.000	0.001
cytoscapeFreeMemory	0.001	0.000	0.001
cytoscapeMemoryStatus	0.000	0.000	0.001
cytoscapeNumberOfCores	0.000	0.001	0.000
cytoscapePing	0	0	0
cytoscapeVersionInfo	0.001	0.001	0.000
deleteAllNetworks	0.000	0.000	0.001
deleteDuplicateEdges	0.000	0.000	0.001
deleteGroup	0	0	0
deleteNetwork	0.000	0.000	0.001
deleteSelectedEdges	0	0	0
deleteSelectedNodes	0.001	0.000	0.000
deleteSelfLoops	0	0	0
deleteStyleMapping	0.000	0.000	0.001
deleteTableColumn	0.000	0.001	0.001
deleteVisualStyle	0.001	0.000	0.001
diffusionAdvanced	0.000	0.001	0.000
diffusionBasic	0	0	0
disableApp	0.001	0.000	0.001
dockPanel	0.001	0.000	0.000
enableApp	0	0	0
expandGroup	0.000	0.000	0.001
exportFilters	0	0	0
exportImage	0.000	0.000	0.001
exportNetwork	0	0	0
exportNetworkToNDEx	0.000	0.000	0.001
exportVisualStyles	0.000	0.000	0.001
fitContent	0	0	0
floatPanel	0.001	0.001	0.000
getAllEdges	0	0	0
getAllNodes	0	0	0
getAppInformation	0	0	0
getAppStatus	0.001	0.000	0.000
getAppUpdates	0	0	0
getArrowShapes	0.000	0.000	0.001
getAvailableApps	0.001	0.000	0.001
getBackgroundColorDefault	0	0	0
getCollectionList	0.001	0.000	0.001
getCollectionName	0	0	0
getCollectionNetworks	0.001	0.001	0.000
getCollectionSuid	0	0	0
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getEdgeLineStyle	0	0	0
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getFilterList	0	0	0
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getInstalledApps	0	0	0
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getNetworkCount	0	0	0
getNetworkList	0.001	0.000	0.001
getNetworkNDExId	0.000	0.000	0.001
getNetworkName	0	0	0
getNetworkProperty	0	0	0
getNetworkSuid	0.001	0.000	0.001
getNetworkViewSuid	0.000	0.000	0.001
getNetworkViews	0.000	0.000	0.001
getNetworkZoom	0.000	0.000	0.001
getNodeColor	0.001	0.000	0.000
getNodeCount	0.001	0.000	0.001
getNodeHeight	0.000	0.000	0.001
getNodeProperty	0.000	0.000	0.001
getNodeSelectionColorDefault	0.000	0.000	0.001
getNodeShapes	0.000	0.001	0.001
getNodeSize	0	0	0
getNodeWidth	0.000	0.000	0.001
getSelectedEdgeCount	0.001	0.000	0.000
getSelectedEdges	0.000	0.001	0.000
getSelectedNodeCount	0.000	0.000	0.001
getSelectedNodes	0	0	0
getStyleDependencies	0.000	0.000	0.001
getTableColumnNames	0	0	0
getTableColumnTypes	0.001	0.000	0.000
getTableColumns	0	0	0
getTableValue	0	0	0
getUninstalledApps	0.000	0.001	0.000
getVisualPropertyDefault	0	0	0
getVisualPropertyNames	0.001	0.000	0.001
getVisualStyleNames	0.000	0.000	0.001
hideAllPanels	0.001	0.000	0.001
hideEdges	0.000	0.000	0.001
hideNodes	0.000	0.000	0.001
hidePanel	0	0	0
hideSelectedEdges	0	0	0
hideSelectedNodes	0	0	0
importFilters	0	0	0
importNetworkFromFile	0.000	0.001	0.000
importNetworkFromNDEx	0	0	0
importVisualStyles	0.001	0.000	0.000
installApp	0	0	0
invertEdgeSelection	0	0	0
invertNodeSelection	0	0	0
layoutCopycat	0.000	0.000	0.001
layoutNetwork	0	0	0
listGroups	0.001	0.000	0.000
lockNodeDimensions	0.000	0.000	0.001
makeSimpleGraph	0.117	0.002	0.119
makeSimpleIgraph	0.019	0.001	0.019
mapTableColumn	0	0	0
mapVisualProperty	0.000	0.000	0.001
matchArrowColorToEdge	0.000	0.000	0.001
openAppStore	0.000	0.000	0.001
openSession	0.001	0.000	0.000
removeNodeCustomGraphics	0.001	0.000	0.001
renameNetwork	0.001	0.000	0.000
renameTableColumn	0.001	0.000	0.000
saveSession	0.001	0.001	0.000
selectAllEdges	0.001	0.001	0.001
selectAllNodes	0.001	0.001	0.000
selectEdges	0.001	0.001	0.001
selectEdgesAdjacentToSelectedNodes	0	0	0
selectEdgesConnectingSelectedNodes	0.000	0.000	0.001
selectFirstNeighbors	0	0	0
selectNodes	0.000	0.000	0.001
selectNodesConnectedBySelectedEdges	0.001	0.000	0.000
setBackgroundColorDefault	0.000	0.001	0.000
setCurrentNetwork	0.000	0.000	0.001
setCurrentView	0.000	0.001	0.000
setEdgeColorBypass	0.001	0.000	0.000
setEdgeColorDefault	0.000	0.000	0.001
setEdgeColorMapping	0.000	0.001	0.000
setEdgeFontFaceBypass	0	0	0
setEdgeFontSizeBypass	0	0	0
setEdgeFontSizeDefault	0	0	0
setEdgeLabelBypass	0	0	0
setEdgeLabelColorBypass	0.001	0.000	0.000
setEdgeLabelMapping	0	0	0
setEdgeLabelOpacityBypass	0.000	0.000	0.001
setEdgeLineStyleBypass	0	0	0
setEdgeLineStyleDefault	0.001	0.000	0.000
setEdgeLineStyleMapping	0	0	0
setEdgeLineWidthBypass	0.000	0.000	0.001
setEdgeLineWidthDefault	0	0	0
setEdgeLineWidthMapping	0.001	0.000	0.000
setEdgeOpacityBypass	0.000	0.001	0.000
setEdgeOpacityMapping	0	0	0
setEdgePropertyBypass	0.001	0.000	0.000
setEdgeSelectionColorDefault	0.000	0.001	0.000
setEdgeSourceArrowColorBypass	0	0	0
setEdgeSourceArrowColorDefault	0	0	0
setEdgeSourceArrowColorMapping	0	0	0
setEdgeSourceArrowMapping	0.001	0.000	0.000
setEdgeSourceArrowShapeBypass	0.000	0.001	0.000
setEdgeSourceArrowShapeDefault	0.001	0.000	0.001
setEdgeTargetArrowColorBypass	0.000	0.000	0.001
setEdgeTargetArrowColorDefault	0.000	0.001	0.001
setEdgeTargetArrowColorMapping	0.000	0.000	0.001
setEdgeTargetArrowMapping	0.000	0.000	0.001
setEdgeTargetArrowShapeBypass	0.001	0.000	0.001
setEdgeTargetArrowShapeDefault	0.000	0.000	0.001
setEdgeTooltipBypass	0.000	0.001	0.001
setEdgeTooltipMapping	0.000	0.000	0.001
setLayoutProperties	0	0	0
setNetworkCenterBypass	0	0	0
setNetworkPropertyBypass	0.001	0.000	0.000
setNetworkZoomBypass	0	0	0
setNodeBorderColorBypass	0.000	0.000	0.001
setNodeBorderColorDefault	0.001	0.000	0.001
setNodeBorderColorMapping	0.000	0.000	0.001
setNodeBorderOpacityBypass	0.001	0.000	0.000
setNodeBorderWidthBypass	0	0	0
setNodeBorderWidthDefault	0	0	0
setNodeBorderWidthMapping	0	0	0
setNodeColorBypass	0	0	0
setNodeColorDefault	0	0	0
setNodeColorMapping	0.001	0.000	0.001
setNodeComboOpacityMapping	0.001	0.000	0.000
setNodeCustomBarChart	0	0	0
setNodeCustomBoxChart	0.001	0.000	0.000
setNodeCustomHeatMapChart	0	0	0
setNodeCustomLineChart	0.000	0.000	0.001
setNodeCustomLinearGradient	0.001	0.000	0.001
setNodeCustomPieChart	0	0	0
setNodeCustomPosition	0.001	0.000	0.000
setNodeCustomRadialGradient	0.000	0.000	0.001
setNodeCustomRingChart	0.000	0.001	0.000
setNodeFillOpacityBypass	0.000	0.000	0.001
setNodeFontSizeBypass	0	0	0
setNodeFontSizeDefault	0.000	0.000	0.001
setNodeHeightBypass	0	0	0
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setNodeLabelColorBypass	0.001	0.000	0.000
setNodeLabelColorDefault	0	0	0
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setNodeLabelOpacityBypass	0	0	0
setNodeOpacityBypass	0.000	0.000	0.001
setNodePropertyBypass	0	0	0
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setNodeShapeMapping	0	0	0
setNodeSizeBypass	0.001	0.000	0.000
setNodeSizeDefault	0.000	0.001	0.001
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setNodeTooltipMapping	0.000	0.000	0.001
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syncNodeCustomGraphicsSize	0.001	0.000	0.000
toggleGraphicsDetails	0	0	0
unhideAll	0	0	0
unhideEdges	0	0	0
unhideNodes	0.000	0.000	0.001
uninstallApp	0.001	0.001	0.000
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updateNetworkInNDEx	0.000	0.001	0.000
updateStyleDefaults	0.001	0.000	0.001
updateStyleMapping	0.000	0.000	0.001