Multiple platform build/check report for BioC 3.8 - CHECK report for RCy3 on merida1

Package: RCy3

Version: 2.2.9

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_2.2.9.tar.gz

StartedAt: 2019-04-16 02:13:47 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:14:56 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 68.7 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_2.2.9.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/RCy3.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.2.9’
* 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-3.8-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 3.5.3 (2019-03-11) -- "Great Truth"
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 
  0.246   0.058   0.277

name	user	system	elapsed
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RemoveFromGroup	0	0	0
addCyEdges	0	0	0
addCyNodes	0	0	0
applyFilter	0	0	0
bundleEdges	0	0	0
clearEdgePropertyBypass	0	0	0
clearNetworkCenterBypass	0.000	0.000	0.001
clearNetworkPropertyBypass	0	0	0
clearNetworkZoomBypass	0	0	0
clearNodeOpacityBypass	0	0	0
clearNodePropertyBypass	0.001	0.000	0.000
clearSelection	0	0	0
cloneNetwork	0	0	0
closeSession	0.001	0.000	0.000
collapseGroup	0.000	0.001	0.001
commandEcho	0	0	0
commandOpenDialog	0	0	0
commandPause	0	0	0
commandQuit	0.000	0.001	0.001
commandRunFile	0	0	0
commandSleep	0	0	0
commandsAPI	0	0	0
commandsGET	0.000	0.000	0.001
commandsHelp	0	0	0
commandsPOST	0	0	0
commandsRun	0.000	0.000	0.001
copyVisualStyle	0.000	0.000	0.001
createColumnFilter	0	0	0
createCompositeFilter	0	0	0
createDegreeFilter	0	0	0
createGraphFromNetwork	0	0	0
createGroup	0	0	0
createIgraphFromNetwork	0.001	0.000	0.000
createNetworkFromDataFrames	0	0	0
createNetworkFromGraph	0	0	0
createNetworkFromIgraph	0	0	0
createSubnetwork	0	0	0
createVisualStyle	0	0	0
cybrowserClose	0	0	0
cybrowserDialog	0	0	0
cybrowserHide	0	0	0
cybrowserList	0	0	0
cybrowserSend	0	0	0
cybrowserShow	0.000	0.000	0.001
cybrowserVersion	0	0	0
cyrestAPI	0	0	0
cyrestDELETE	0.000	0.000	0.001
cyrestGET	0.000	0.001	0.000
cyrestPOST	0	0	0
cyrestPUT	0	0	0
cytoscapeApiVersions	0	0	0
cytoscapeFreeMemory	0	0	0
cytoscapeMemoryStatus	0	0	0
cytoscapeNumberOfCores	0	0	0
cytoscapePing	0	0	0
cytoscapeVersionInfo	0	0	0
deleteAllNetworks	0	0	0
deleteDuplicateEdges	0	0	0
deleteGroup	0	0	0
deleteNetwork	0.001	0.000	0.001
deleteSelectedEdges	0.000	0.000	0.001
deleteSelectedNodes	0.000	0.001	0.000
deleteSelfLoops	0	0	0
deleteStyleMapping	0.000	0.000	0.001
deleteTableColumn	0	0	0
deleteVisualStyle	0	0	0
diffusionAdvanced	0	0	0
diffusionBasic	0.000	0.000	0.001
disableApp	0.000	0.001	0.000
dockPanel	0	0	0
enableApp	0	0	0
expandGroup	0	0	0
exportFilters	0	0	0
exportImage	0	0	0
exportNetwork	0	0	0
exportNetworkToNDEx	0.000	0.000	0.001
exportVisualStyles	0	0	0
fitContent	0	0	0
floatPanel	0	0	0
getAllEdges	0.001	0.001	0.000
getAllNodes	0.001	0.000	0.000
getAppInformation	0.001	0.000	0.000
getAppStatus	0.001	0.000	0.000
getAppUpdates	0	0	0
getArrowShapes	0.000	0.000	0.001
getAvailableApps	0.000	0.000	0.001
getBackgroundColorDefault	0	0	0
getCollectionList	0	0	0
getCollectionName	0	0	0
getCollectionNetworks	0	0	0
getCollectionSuid	0.000	0.001	0.001
getDisabledApps	0	0	0
getEdgeColor	0	0	0
getEdgeCount	0.000	0.000	0.001
getEdgeLineStyle	0	0	0
getEdgeLineWidth	0	0	0
getEdgeProperty	0	0	0
getEdgeSelectionColorDefault	0.000	0.000	0.001
getEdgeTargetArrowShape	0	0	0
getFilterList	0	0	0
getFirstNeighbors	0.000	0.001	0.000
getGroupInfo	0	0	0
getInstalledApps	0	0	0
getLayoutNameMapping	0.000	0.000	0.001
getLayoutNames	0	0	0
getLayoutPropertyNames	0	0	0
getLayoutPropertyType	0	0	0
getLayoutPropertyValue	0.000	0.001	0.001
getLineStyles	0	0	0
getNetworkCenter	0	0	0
getNetworkCount	0.000	0.001	0.000
getNetworkList	0	0	0
getNetworkNDExId	0	0	0
getNetworkName	0.000	0.000	0.001
getNetworkProperty	0	0	0
getNetworkSuid	0	0	0
getNetworkViewSuid	0	0	0
getNetworkViews	0.000	0.001	0.000
getNetworkZoom	0	0	0
getNodeColor	0.000	0.000	0.001
getNodeCount	0	0	0
getNodeHeight	0.000	0.000	0.001
getNodeProperty	0	0	0
getNodeSelectionColorDefault	0.000	0.000	0.001
getNodeShapes	0	0	0
getNodeSize	0	0	0
getNodeWidth	0.000	0.000	0.001
getSelectedEdgeCount	0	0	0
getSelectedEdges	0	0	0
getSelectedNodeCount	0.001	0.000	0.000
getSelectedNodes	0	0	0
getStyleDependencies	0.000	0.000	0.001
getTableColumnNames	0.001	0.000	0.000
getTableColumnTypes	0	0	0
getTableColumns	0	0	0
getTableValue	0	0	0
getUninstalledApps	0	0	0
getVisualPropertyDefault	0.000	0.000	0.001
getVisualPropertyNames	0.000	0.000	0.001
getVisualStyleNames	0	0	0
hideAllPanels	0	0	0
hideEdges	0	0	0
hideNodes	0	0	0
hidePanel	0	0	0
hideSelectedEdges	0.000	0.000	0.001
hideSelectedNodes	0	0	0
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	0.001	0.001	0.001
listGroups	0.001	0.000	0.000
lockNodeDimensions	0.001	0.000	0.000
makeSimpleGraph	0.097	0.001	0.099
makeSimpleIgraph	0.018	0.001	0.019
mapTableColumn	0.000	0.000	0.001
mapVisualProperty	0	0	0
matchArrowColorToEdge	0	0	0
openAppStore	0	0	0
openSession	0	0	0
removeNodeCustomGraphics	0.000	0.000	0.001
renameNetwork	0	0	0
renameTableColumn	0	0	0
saveSession	0	0	0
selectAllEdges	0	0	0
selectAllNodes	0	0	0
selectEdges	0.000	0.000	0.001
selectEdgesAdjacentToSelectedNodes	0	0	0
selectEdgesConnectingSelectedNodes	0	0	0
selectFirstNeighbors	0	0	0
selectNodes	0	0	0
selectNodesConnectedBySelectedEdges	0	0	0
setBackgroundColorDefault	0.000	0.000	0.001
setCurrentNetwork	0	0	0
setCurrentView	0.001	0.000	0.001
setEdgeColorBypass	0.001	0.000	0.000
setEdgeColorDefault	0	0	0
setEdgeColorMapping	0	0	0
setEdgeFontFaceBypass	0	0	0
setEdgeFontSizeBypass	0	0	0
setEdgeFontSizeDefault	0	0	0
setEdgeLabelBypass	0.001	0.001	0.000
setEdgeLabelColorBypass	0	0	0
setEdgeLabelMapping	0	0	0
setEdgeLabelOpacityBypass	0.001	0.000	0.001
setEdgeLineStyleBypass	0	0	0
setEdgeLineStyleDefault	0.000	0.001	0.000
setEdgeLineStyleMapping	0.001	0.000	0.000
setEdgeLineWidthBypass	0	0	0
setEdgeLineWidthDefault	0	0	0
setEdgeLineWidthMapping	0	0	0
setEdgeOpacityBypass	0	0	0
setEdgeOpacityMapping	0.000	0.000	0.001
setEdgePropertyBypass	0.001	0.000	0.001
setEdgeSelectionColorDefault	0	0	0
setEdgeSourceArrowColorBypass	0	0	0
setEdgeSourceArrowColorDefault	0.000	0.000	0.001
setEdgeSourceArrowColorMapping	0	0	0
setEdgeSourceArrowMapping	0	0	0
setEdgeSourceArrowShapeBypass	0.000	0.000	0.001
setEdgeSourceArrowShapeDefault	0	0	0
setEdgeTargetArrowColorBypass	0.000	0.000	0.001
setEdgeTargetArrowColorDefault	0	0	0
setEdgeTargetArrowColorMapping	0	0	0
setEdgeTargetArrowMapping	0	0	0
setEdgeTargetArrowShapeBypass	0.000	0.001	0.001
setEdgeTargetArrowShapeDefault	0	0	0
setEdgeTooltipBypass	0	0	0
setEdgeTooltipMapping	0	0	0
setLayoutProperties	0.001	0.000	0.001
setNetworkCenterBypass	0	0	0
setNetworkPropertyBypass	0.000	0.001	0.001
setNetworkZoomBypass	0	0	0
setNodeBorderColorBypass	0	0	0
setNodeBorderColorDefault	0.000	0.000	0.001
setNodeBorderColorMapping	0	0	0
setNodeBorderOpacityBypass	0.000	0.000	0.001
setNodeBorderWidthBypass	0	0	0
setNodeBorderWidthDefault	0.000	0.000	0.001
setNodeBorderWidthMapping	0	0	0
setNodeColorBypass	0.000	0.000	0.001
setNodeColorDefault	0.000	0.001	0.000
setNodeColorMapping	0	0	0
setNodeComboOpacityMapping	0	0	0
setNodeCustomBarChart	0	0	0
setNodeCustomBoxChart	0	0	0
setNodeCustomHeatMapChart	0	0	0
setNodeCustomLineChart	0	0	0
setNodeCustomLinearGradient	0	0	0
setNodeCustomPieChart	0	0	0
setNodeCustomPosition	0	0	0
setNodeCustomRadialGradient	0.000	0.000	0.001
setNodeCustomRingChart	0	0	0
setNodeFillOpacityBypass	0	0	0
setNodeFontSizeBypass	0	0	0
setNodeFontSizeDefault	0	0	0
setNodeHeightBypass	0	0	0
setNodeLabelBypass	0	0	0
setNodeLabelColorBypass	0	0	0
setNodeLabelColorDefault	0	0	0
setNodeLabelMapping	0.001	0.000	0.000
setNodeLabelOpacityBypass	0.000	0.001	0.000
setNodeOpacityBypass	0.001	0.000	0.000
setNodePropertyBypass	0	0	0
setNodeSelectionColorDefault	0	0	0
setNodeShapeBypass	0.001	0.000	0.001
setNodeShapeDefault	0	0	0
setNodeShapeMapping	0	0	0
setNodeSizeBypass	0.000	0.000	0.001
setNodeSizeDefault	0.001	0.000	0.000
setNodeSizeMapping	0	0	0
setNodeTooltipMapping	0	0	0
setNodeWidthBypass	0	0	0
setStyleDependencies	0.000	0.001	0.000
setVisualPropertyDefault	0.001	0.000	0.001
setVisualStyle	0.001	0.000	0.000
syncNodeCustomGraphicsSize	0	0	0
toggleGraphicsDetails	0	0	0
unhideAll	0.000	0.000	0.001
unhideEdges	0	0	0
unhideNodes	0.000	0.000	0.001
uninstallApp	0.001	0.000	0.000
updateApp	0.001	0.000	0.000
updateNetworkInNDEx	0.001	0.000	0.001
updateStyleDefaults	0.001	0.000	0.000
updateStyleMapping	0	0	0

CHECK report for RCy3 on merida1

Summary

Command output

Installation output

Tests output

Example timings