Package: RCy3

Version: 2.4.6

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_2.4.6.tar.gz

StartedAt: 2019-10-16 06:04:23 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:06:00 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 97.2 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_2.4.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RCy3.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.4.6’
* 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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 
  0.393   0.146   0.483 

name	user	system	elapsed
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RemoveFromGroup	0	0	0
addCyEdges	0	0	0
addCyNodes	0.000	0.000	0.001
applyFilter	0.000	0.000	0.001
bundleEdges	0.000	0.000	0.001
clearEdgePropertyBypass	0.000	0.000	0.001
clearNetworkCenterBypass	0.001	0.000	0.000
clearNetworkPropertyBypass	0	0	0
clearNetworkZoomBypass	0.001	0.000	0.001
clearNodeOpacityBypass	0	0	0
clearNodePropertyBypass	0.001	0.000	0.000
clearSelection	0.000	0.000	0.001
cloneNetwork	0.000	0.001	0.000
closeSession	0.001	0.000	0.000
collapseGroup	0	0	0
commandEcho	0.000	0.001	0.000
commandOpenDialog	0.001	0.000	0.000
commandPause	0.000	0.000	0.001
commandQuit	0.001	0.001	0.001
commandRunFile	0.000	0.000	0.001
commandSleep	0	0	0
commandsAPI	0.001	0.000	0.000
commandsGET	0	0	0
commandsHelp	0	0	0
commandsPOST	0.000	0.000	0.001
commandsRun	0.000	0.000	0.001
copyVisualStyle	0.000	0.000	0.001
createColumnFilter	0.001	0.000	0.001
createCompositeFilter	0.000	0.000	0.001
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createGraphFromNetwork	0.001	0.000	0.000
createGroup	0	0	0
createIgraphFromNetwork	0	0	0
createNetworkFromDataFrames	0.000	0.000	0.001
createNetworkFromGraph	0.000	0.000	0.001
createNetworkFromIgraph	0	0	0
createSubnetwork	0	0	0
createVisualStyle	0	0	0
cybrowserClose	0.001	0.000	0.000
cybrowserDialog	0	0	0
cybrowserHide	0	0	0
cybrowserList	0	0	0
cybrowserSend	0.000	0.001	0.000
cybrowserShow	0.001	0.000	0.000
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getNodeSize	0.000	0.000	0.001
getNodeWidth	0.000	0.000	0.001
getSelectedEdgeCount	0	0	0
getSelectedEdges	0	0	0
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getSelectedNodes	0.000	0.001	0.000
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getTableColumnTypes	0.000	0.000	0.001
getTableColumns	0.000	0.001	0.000
getTableValue	0.001	0.000	0.000
getUninstalledApps	0	0	0
getVisualPropertyDefault	0	0	0
getVisualPropertyNames	0	0	0
getVisualStyleNames	0.000	0.001	0.000
hideAllPanels	0.001	0.000	0.001
hideEdges	0.000	0.000	0.001
hideNodes	0.001	0.000	0.000
hidePanel	0	0	0
hideSelectedEdges	0	0	0
hideSelectedNodes	0.001	0.001	0.001
importFilters	0	0	0
importNetworkFromFile	0.001	0.000	0.000
importNetworkFromNDEx	0	0	0
importVisualStyles	0	0	0
installApp	0.001	0.000	0.000
invertEdgeSelection	0.000	0.001	0.000
invertNodeSelection	0	0	0
layoutCopycat	0.000	0.001	0.000
layoutNetwork	0	0	0
listGroups	0.000	0.000	0.001
lockNodeDimensions	0.001	0.000	0.000
makeSimpleGraph	0.107	0.001	0.109
makeSimpleIgraph	0.018	0.002	0.020
mapTableColumn	0.001	0.000	0.000
mapVisualProperty	0.000	0.001	0.000
matchArrowColorToEdge	0.001	0.000	0.001
openAppStore	0.000	0.000	0.001
openSession	0.001	0.001	0.000
removeNodeCustomGraphics	0	0	0
renameNetwork	0.000	0.000	0.001
renameTableColumn	0	0	0
saveSession	0.000	0.001	0.001
selectAllEdges	0.000	0.000	0.001
selectAllNodes	0	0	0
selectEdges	0	0	0
selectEdgesAdjacentToSelectedNodes	0	0	0
selectEdgesConnectingSelectedNodes	0.001	0.000	0.001
selectFirstNeighbors	0.000	0.000	0.001
selectNodes	0.000	0.000	0.001
selectNodesConnectedBySelectedEdges	0	0	0
setBackgroundColorDefault	0.001	0.000	0.000
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setCurrentView	0	0	0
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setEdgeColorDefault	0	0	0
setEdgeColorMapping	0.000	0.001	0.000
setEdgeFontFaceBypass	0	0	0
setEdgeFontFaceDefault	0	0	0
setEdgeFontFaceMapping	0	0	0
setEdgeFontSizeBypass	0	0	0
setEdgeFontSizeDefault	0.001	0.000	0.001
setEdgeFontSizeMapping	0.000	0.000	0.001
setEdgeLabelBypass	0.000	0.001	0.001
setEdgeLabelColorBypass	0.000	0.000	0.001
setEdgeLabelColorDefault	0	0	0
setEdgeLabelColorMapping	0.000	0.001	0.000
setEdgeLabelDefault	0	0	0
setEdgeLabelMapping	0.000	0.001	0.000
setEdgeLabelOpacityBypass	0.000	0.000	0.001
setEdgeLabelOpacityDefault	0	0	0
setEdgeLabelOpacityMapping	0	0	0
setEdgeLineStyleBypass	0	0	0
setEdgeLineStyleDefault	0.000	0.000	0.001
setEdgeLineStyleMapping	0	0	0
setEdgeLineWidthBypass	0.000	0.001	0.000
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setEdgeOpacityBypass	0	0	0
setEdgeOpacityDefault	0.000	0.001	0.001
setEdgeOpacityMapping	0.000	0.000	0.001
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setNetworkPropertyBypass	0	0	0
setNetworkZoomBypass	0.001	0.000	0.000
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