Multiple platform build/check report for BioC 3.11 - CHECK report for RCy3 on celaya2

Package: RCy3

Version: 2.7.3

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_2.7.3.tar.gz

StartedAt: 2020-01-16 08:00:57 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 08:02:36 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 98.9 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_2.7.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/RCy3.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.7.3’
* 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-3.11-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
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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) (2019-12-14 r77572) -- "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 
  0.415   0.155   0.513

name	user	system	elapsed
AddToGroup	0.000	0.001	0.000
RemoveFromGroup	0	0	0
addCyEdges	0.000	0.000	0.001
addCyNodes	0.000	0.000	0.001
applyFilter	0.001	0.000	0.001
bundleEdges	0	0	0
clearEdgeBends	0	0	0
clearEdgePropertyBypass	0.000	0.000	0.001
clearNetworkCenterBypass	0.000	0.000	0.001
clearNetworkPropertyBypass	0	0	0
clearNetworkZoomBypass	0	0	0
clearNodeOpacityBypass	0	0	0
clearNodePropertyBypass	0.000	0.000	0.001
clearSelection	0	0	0
cloneNetwork	0	0	0
closeSession	0	0	0
collapseGroup	0	0	0
commandEcho	0	0	0
commandOpenDialog	0.000	0.001	0.001
commandPause	0	0	0
commandQuit	0.001	0.000	0.000
commandRunFile	0	0	0
commandSleep	0.000	0.001	0.001
commandsAPI	0.001	0.000	0.001
commandsGET	0.000	0.000	0.001
commandsHelp	0.001	0.001	0.000
commandsPOST	0	0	0
commandsRun	0	0	0
copyVisualStyle	0	0	0
createColumnFilter	0.000	0.000	0.001
createCompositeFilter	0	0	0
createDegreeFilter	0.000	0.000	0.001
createGraphFromNetwork	0.000	0.000	0.001
createGroup	0.000	0.000	0.001
createGroupByColumn	0	0	0
createIgraphFromNetwork	0	0	0
createNetworkFromDataFrames	0	0	0
createNetworkFromGraph	0	0	0
createNetworkFromIgraph	0.001	0.001	0.001
createSubnetwork	0	0	0
createVisualStyle	0.000	0.000	0.001
cybrowserClose	0	0	0
cybrowserDialog	0.000	0.000	0.001
cybrowserHide	0.000	0.001	0.001
cybrowserList	0.000	0.000	0.001
cybrowserSend	0	0	0
cybrowserShow	0.000	0.000	0.001
cybrowserVersion	0	0	0
cyrestAPI	0.001	0.000	0.000
cyrestDELETE	0	0	0
cyrestGET	0	0	0
cyrestPOST	0.001	0.000	0.001
cyrestPUT	0.000	0.000	0.001
cytoscapeApiVersions	0.000	0.001	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	0.000	0.000
deleteAllNetworks	0.001	0.000	0.001
deleteDuplicateEdges	0.000	0.000	0.001
deleteGroup	0.000	0.000	0.001
deleteNetwork	0	0	0
deleteSelectedEdges	0.001	0.000	0.000
deleteSelectedNodes	0.000	0.001	0.000
deleteSelfLoops	0.001	0.000	0.001
deleteStyleMapping	0	0	0
deleteTableColumn	0.001	0.001	0.000
deleteVisualStyle	0	0	0
diffusionAdvanced	0.001	0.000	0.000
diffusionBasic	0.000	0.001	0.001
disableApp	0.001	0.000	0.000
dockPanel	0.000	0.001	0.000
enableApp	0.000	0.000	0.001
expandGroup	0.000	0.000	0.001
exportFilters	0.000	0.001	0.001
exportImage	0	0	0
exportNetwork	0	0	0
exportNetworkToNDEx	0	0	0
exportVisualStyles	0	0	0
fitContent	0	0	0
floatPanel	0	0	0
getAllEdges	0.000	0.000	0.001
getAllNodes	0.000	0.000	0.001
getAppInformation	0.000	0.000	0.001
getAppStatus	0.000	0.000	0.001
getAppUpdates	0.001	0.001	0.000
getArrowShapes	0	0	0
getAvailableApps	0.001	0.000	0.000
getBackgroundColorDefault	0.000	0.001	0.001
getCollectionList	0.001	0.000	0.001
getCollectionName	0	0	0
getCollectionNetworks	0.000	0.000	0.001
getCollectionSuid	0.000	0.001	0.000
getDisabledApps	0	0	0
getEdgeColor	0.000	0.001	0.000
getEdgeCount	0.001	0.000	0.001
getEdgeInfo	0.000	0.000	0.001
getEdgeLineStyle	0	0	0
getEdgeLineWidth	0	0	0
getEdgeProperty	0.001	0.000	0.001
getEdgeSelectionColorDefault	0	0	0
getEdgeTargetArrowShape	0	0	0
getFilterList	0.000	0.001	0.001
getFirstNeighbors	0.000	0.000	0.001
getGroupInfo	0	0	0
getInstalledApps	0.000	0.000	0.001
getLayoutNameMapping	0.000	0.000	0.001
getLayoutNames	0.000	0.000	0.001
getLayoutPropertyNames	0	0	0
getLayoutPropertyType	0	0	0
getLayoutPropertyValue	0	0	0
getLineStyles	0	0	0
getNetworkCenter	0.000	0.001	0.001
getNetworkCount	0.000	0.001	0.000
getNetworkList	0.001	0.000	0.001
getNetworkNDExId	0	0	0
getNetworkName	0.001	0.000	0.000
getNetworkProperty	0.000	0.000	0.001
getNetworkSuid	0	0	0
getNetworkViewSuid	0.001	0.000	0.001
getNetworkViews	0	0	0
getNetworkZoom	0	0	0
getNodeColor	0.001	0.000	0.000
getNodeCount	0.000	0.000	0.001
getNodeHeight	0	0	0
getNodePosition	0.001	0.000	0.000
getNodeProperty	0.000	0.000	0.001
getNodeSelectionColorDefault	0.000	0.000	0.001
getNodeShapes	0.000	0.000	0.001
getNodeSize	0.000	0.000	0.001
getNodeWidth	0.001	0.000	0.001
getSelectedEdgeCount	0	0	0
getSelectedEdges	0.000	0.000	0.001
getSelectedNodeCount	0.000	0.000	0.001
getSelectedNodes	0	0	0
getStyleDependencies	0	0	0
getTableColumnNames	0	0	0
getTableColumnTypes	0	0	0
getTableColumns	0.000	0.000	0.001
getTableValue	0	0	0
getUninstalledApps	0.000	0.000	0.001
getVisualPropertyDefault	0	0	0
getVisualPropertyNames	0	0	0
getVisualStyleNames	0.000	0.001	0.001
hideAllPanels	0	0	0
hideEdges	0.000	0.000	0.001
hideNodes	0	0	0
hidePanel	0.000	0.001	0.000
hideSelectedEdges	0.000	0.000	0.001
hideSelectedNodes	0	0	0
importFilters	0.000	0.000	0.001
importNetworkFromFile	0.000	0.001	0.001
importNetworkFromNDEx	0	0	0
importVisualStyles	0.000	0.001	0.001
installApp	0.000	0.000	0.001
invertEdgeSelection	0	0	0
invertNodeSelection	0	0	0
layoutCopycat	0.000	0.000	0.001
layoutNetwork	0.000	0.001	0.001
listGroups	0	0	0
lockNodeDimensions	0.001	0.000	0.000
makeSimpleGraph	0.134	0.003	0.138
makeSimpleIgraph	0.016	0.001	0.016
mapTableColumn	0	0	0
mapVisualProperty	0.000	0.000	0.001
matchArrowColorToEdge	0.001	0.000	0.001
openAppStore	0	0	0
openSession	0.000	0.001	0.001
removeNodeCustomGraphics	0	0	0
renameNetwork	0.000	0.000	0.001
renameTableColumn	0	0	0
saveSession	0.001	0.000	0.000
selectAllEdges	0.000	0.001	0.001
selectAllNodes	0.001	0.000	0.001
selectEdges	0.001	0.000	0.000
selectEdgesAdjacentToSelectedNodes	0	0	0
selectEdgesConnectingSelectedNodes	0.000	0.000	0.001
selectFirstNeighbors	0	0	0
selectNodes	0	0	0
selectNodesConnectedBySelectedEdges	0.001	0.000	0.000
setBackgroundColorDefault	0.000	0.000	0.001
setCurrentNetwork	0	0	0
setCurrentView	0.000	0.001	0.000
setEdgeColorBypass	0.000	0.000	0.001
setEdgeColorDefault	0.000	0.000	0.001
setEdgeColorMapping	0.000	0.000	0.001
setEdgeFontFaceBypass	0	0	0
setEdgeFontFaceDefault	0.001	0.000	0.000
setEdgeFontFaceMapping	0.001	0.000	0.001
setEdgeFontSizeBypass	0	0	0
setEdgeFontSizeDefault	0.000	0.000	0.001
setEdgeFontSizeMapping	0	0	0
setEdgeLabelBypass	0.000	0.001	0.000
setEdgeLabelColorBypass	0	0	0
setEdgeLabelColorDefault	0.000	0.000	0.001
setEdgeLabelColorMapping	0.000	0.001	0.000
setEdgeLabelDefault	0	0	0
setEdgeLabelMapping	0.000	0.001	0.001
setEdgeLabelOpacityBypass	0.001	0.000	0.001
setEdgeLabelOpacityDefault	0.000	0.001	0.000
setEdgeLabelOpacityMapping	0	0	0
setEdgeLineStyleBypass	0.001	0.000	0.000
setEdgeLineStyleDefault	0.000	0.001	0.001
setEdgeLineStyleMapping	0	0	0
setEdgeLineWidthBypass	0	0	0
setEdgeLineWidthDefault	0.001	0.001	0.000
setEdgeLineWidthMapping	0	0	0
setEdgeOpacityBypass	0	0	0
setEdgeOpacityDefault	0	0	0
setEdgeOpacityMapping	0	0	0
setEdgePropertyBypass	0.000	0.000	0.001
setEdgeSelectionColorDefault	0	0	0
setEdgeSourceArrowColorBypass	0	0	0
setEdgeSourceArrowColorDefault	0	0	0
setEdgeSourceArrowColorMapping	0.001	0.000	0.000
setEdgeSourceArrowMapping	0.000	0.001	0.001
setEdgeSourceArrowShapeBypass	0.001	0.000	0.001
setEdgeSourceArrowShapeDefault	0	0	0
setEdgeSourceArrowShapeMapping	0.001	0.000	0.001
setEdgeTargetArrowColorBypass	0.001	0.001	0.000
setEdgeTargetArrowColorDefault	0	0	0
setEdgeTargetArrowColorMapping	0	0	0
setEdgeTargetArrowMapping	0	0	0
setEdgeTargetArrowShapeBypass	0	0	0
setEdgeTargetArrowShapeDefault	0.000	0.000	0.001
setEdgeTargetArrowShapeMapping	0	0	0
setEdgeTooltipBypass	0	0	0
setEdgeTooltipDefault	0.000	0.000	0.001
setEdgeTooltipMapping	0.001	0.000	0.000
setLayoutProperties	0	0	0
setNetworkCenterBypass	0	0	0
setNetworkPropertyBypass	0.000	0.000	0.001
setNetworkZoomBypass	0	0	0
setNodeBorderColorBypass	0	0	0
setNodeBorderColorDefault	0.000	0.000	0.001
setNodeBorderColorMapping	0	0	0
setNodeBorderOpacityBypass	0.000	0.001	0.000
setNodeBorderOpacityDefault	0	0	0
setNodeBorderOpacityMapping	0.001	0.000	0.000
setNodeBorderWidthBypass	0	0	0
setNodeBorderWidthDefault	0	0	0
setNodeBorderWidthMapping	0.000	0.000	0.001
setNodeColorBypass	0	0	0
setNodeColorDefault	0	0	0
setNodeColorMapping	0.000	0.000	0.001
setNodeComboOpacityMapping	0	0	0
setNodeCustomBarChart	0.000	0.001	0.000
setNodeCustomBoxChart	0.001	0.000	0.000
setNodeCustomHeatMapChart	0.000	0.000	0.001
setNodeCustomLineChart	0	0	0
setNodeCustomLinearGradient	0.001	0.000	0.001
setNodeCustomPieChart	0	0	0
setNodeCustomPosition	0.001	0.000	0.000
setNodeCustomRadialGradient	0	0	0
setNodeCustomRingChart	0.001	0.000	0.000
setNodeFillOpacityBypass	0.000	0.001	0.001
setNodeFillOpacityDefault	0.001	0.000	0.001
setNodeFillOpacityMapping	0	0	0
setNodeFontFaceBypass	0.001	0.001	0.000
setNodeFontFaceDefault	0	0	0
setNodeFontFaceMapping	0.001	0.000	0.001
setNodeFontSizeBypass	0.000	0.001	0.000
setNodeFontSizeDefault	0	0	0
setNodeFontSizeMapping	0.000	0.000	0.001
setNodeHeightBypass	0.000	0.001	0.001
setNodeHeightDefault	0	0	0
setNodeHeightMapping	0.001	0.000	0.000
setNodeLabelBypass	0.000	0.000	0.001
setNodeLabelColorBypass	0.001	0.000	0.001
setNodeLabelColorDefault	0	0	0
setNodeLabelColorMapping	0.001	0.000	0.000
setNodeLabelDefault	0	0	0
setNodeLabelMapping	0.001	0.000	0.000
setNodeLabelOpacityBypass	0.000	0.000	0.001
setNodeLabelOpacityDefault	0.001	0.000	0.000
setNodeLabelOpacityMapping	0.000	0.000	0.001
setNodeOpacityBypass	0.000	0.000	0.001
setNodePropertyBypass	0.001	0.001	0.000
setNodeSelectionColorDefault	0	0	0
setNodeShapeBypass	0.000	0.000	0.001
setNodeShapeDefault	0.001	0.000	0.001
setNodeShapeMapping	0	0	0
setNodeSizeBypass	0	0	0
setNodeSizeDefault	0.001	0.000	0.000
setNodeSizeMapping	0	0	0
setNodeTooltipBypass	0	0	0
setNodeTooltipDefault	0	0	0
setNodeTooltipMapping	0.001	0.000	0.001
setNodeWidthBypass	0.000	0.000	0.001
setNodeWidthDefault	0.001	0.000	0.000
setNodeWidthMapping	0	0	0
setStyleDependencies	0.000	0.001	0.001
setVisualPropertyDefault	0.001	0.000	0.001
setVisualStyle	0.000	0.000	0.001
syncNodeCustomGraphicsSize	0	0	0
toggleGraphicsDetails	0	0	0
unhideAll	0	0	0
unhideEdges	0	0	0
unhideNodes	0.001	0.000	0.000
uninstallApp	0	0	0
updateApp	0	0	0
updateNetworkInNDEx	0.000	0.000	0.001
updateStyleDefaults	0	0	0
updateStyleMapping	0.000	0.001	0.000

CHECK report for RCy3 on celaya2

Summary

Command output

Installation output

Tests output

Example timings