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 03:12:51 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:14:00 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 69.0 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) (2018-11-27 r75683)
* 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’ ...
** 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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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 
  0.274   0.071   0.310 

name	user	system	elapsed
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applyFilter	0.001	0.000	0.001
bundleEdges	0	0	0
clearEdgePropertyBypass	0	0	0
clearNetworkCenterBypass	0	0	0
clearNetworkPropertyBypass	0	0	0
clearNetworkZoomBypass	0.000	0.000	0.001
clearNodeOpacityBypass	0	0	0
clearNodePropertyBypass	0	0	0
clearSelection	0.000	0.000	0.001
cloneNetwork	0	0	0
closeSession	0.001	0.000	0.001
collapseGroup	0.001	0.000	0.000
commandEcho	0.001	0.000	0.000
commandOpenDialog	0.001	0.000	0.000
commandPause	0.001	0.001	0.001
commandQuit	0.001	0.000	0.000
commandRunFile	0.001	0.000	0.001
commandSleep	0.000	0.001	0.000
commandsAPI	0	0	0
commandsGET	0	0	0
commandsHelp	0.001	0.000	0.001
commandsPOST	0	0	0
commandsRun	0.000	0.000	0.001
copyVisualStyle	0	0	0
createColumnFilter	0	0	0
createCompositeFilter	0.000	0.000	0.001
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createGraphFromNetwork	0	0	0
createGroup	0	0	0
createIgraphFromNetwork	0	0	0
createNetworkFromDataFrames	0.001	0.000	0.001
createNetworkFromGraph	0.000	0.001	0.001
createNetworkFromIgraph	0	0	0
createSubnetwork	0	0	0
createVisualStyle	0	0	0
cybrowserClose	0.000	0.000	0.001
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cybrowserHide	0	0	0
cybrowserList	0	0	0
cybrowserSend	0.000	0.000	0.001
cybrowserShow	0	0	0
cybrowserVersion	0	0	0
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cyrestPUT	0	0	0
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cytoscapeNumberOfCores	0	0	0
cytoscapePing	0	0	0
cytoscapeVersionInfo	0	0	0
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deleteSelectedNodes	0.001	0.000	0.000
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diffusionBasic	0	0	0
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getTableColumnTypes	0.001	0.000	0.000
getTableColumns	0.001	0.000	0.001
getTableValue	0.001	0.000	0.000
getUninstalledApps	0	0	0
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getVisualStyleNames	0	0	0
hideAllPanels	0	0	0
hideEdges	0.001	0.000	0.000
hideNodes	0	0	0
hidePanel	0.000	0.000	0.001
hideSelectedEdges	0	0	0
hideSelectedNodes	0.000	0.001	0.000
importFilters	0	0	0
importNetworkFromFile	0	0	0
importNetworkFromNDEx	0	0	0
importVisualStyles	0	0	0
installApp	0.000	0.000	0.001
invertEdgeSelection	0	0	0
invertNodeSelection	0	0	0
layoutCopycat	0	0	0
layoutNetwork	0	0	0
listGroups	0.000	0.000	0.001
lockNodeDimensions	0	0	0
makeSimpleGraph	0.093	0.001	0.094
makeSimpleIgraph	0.011	0.000	0.011
mapTableColumn	0	0	0
mapVisualProperty	0.001	0.000	0.000
matchArrowColorToEdge	0	0	0
openAppStore	0	0	0
openSession	0.001	0.000	0.000
removeNodeCustomGraphics	0	0	0
renameNetwork	0	0	0
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saveSession	0.000	0.000	0.001
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selectAllNodes	0	0	0
selectEdges	0	0	0
selectEdgesAdjacentToSelectedNodes	0	0	0
selectEdgesConnectingSelectedNodes	0	0	0
selectFirstNeighbors	0.000	0.001	0.000
selectNodes	0	0	0
selectNodesConnectedBySelectedEdges	0	0	0
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setEdgeOpacityBypass	0.001	0.000	0.001
setEdgeOpacityMapping	0	0	0
setEdgePropertyBypass	0	0	0
setEdgeSelectionColorDefault	0.001	0.000	0.000
setEdgeSourceArrowColorBypass	0	0	0
setEdgeSourceArrowColorDefault	0	0	0
setEdgeSourceArrowColorMapping	0	0	0
setEdgeSourceArrowMapping	0	0	0
setEdgeSourceArrowShapeBypass	0.000	0.000	0.001
setEdgeSourceArrowShapeDefault	0	0	0
setEdgeTargetArrowColorBypass	0.000	0.001	0.000
setEdgeTargetArrowColorDefault	0	0	0
setEdgeTargetArrowColorMapping	0	0	0
setEdgeTargetArrowMapping	0.000	0.000	0.001
setEdgeTargetArrowShapeBypass	0	0	0
setEdgeTargetArrowShapeDefault	0	0	0
setEdgeTooltipBypass	0.000	0.000	0.001
setEdgeTooltipMapping	0	0	0
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setNetworkZoomBypass	0	0	0
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