Multiple platform build/check report for BioC 3.10 - CHECK report for RCy3 on merida1

Package: RCy3

Version: 2.6.3

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_2.6.3.tar.gz

StartedAt: 2020-04-15 05:01:25 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:02:38 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 73.9 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_2.6.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/RCy3.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.6.3’
* 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-3.10-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/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 
  0.241   0.068   0.281

name	user	system	elapsed
AddToGroup	0	0	0
RemoveFromGroup	0.000	0.000	0.001
addCyEdges	0	0	0
addCyNodes	0	0	0
applyFilter	0.000	0.000	0.001
bundleEdges	0.000	0.000	0.001
clearEdgeBends	0.000	0.000	0.001
clearEdgePropertyBypass	0	0	0
clearNetworkCenterBypass	0.000	0.000	0.001
clearNetworkPropertyBypass	0	0	0
clearNetworkZoomBypass	0	0	0
clearNodeOpacityBypass	0.001	0.000	0.000
clearNodePropertyBypass	0	0	0
clearSelection	0.000	0.001	0.000
cloneNetwork	0.000	0.000	0.001
closeSession	0	0	0
collapseGroup	0.000	0.000	0.001
commandEcho	0	0	0
commandOpenDialog	0	0	0
commandPause	0.000	0.001	0.000
commandQuit	0.000	0.000	0.001
commandRunFile	0	0	0
commandSleep	0.000	0.001	0.001
commandsAPI	0.001	0.000	0.000
commandsGET	0.000	0.000	0.001
commandsHelp	0	0	0
commandsPOST	0	0	0
commandsRun	0	0	0
copyVisualStyle	0.000	0.000	0.001
createColumnFilter	0.000	0.000	0.001
createCompositeFilter	0.000	0.000	0.001
createDegreeFilter	0	0	0
createGraphFromNetwork	0.001	0.000	0.001
createGroup	0	0	0
createGroupByColumn	0.000	0.000	0.001
createIgraphFromNetwork	0	0	0
createNetworkFromDataFrames	0.000	0.000	0.001
createNetworkFromGraph	0	0	0
createNetworkFromIgraph	0	0	0
createSubnetwork	0	0	0
createVisualStyle	0.000	0.000	0.001
cybrowserClose	0	0	0
cybrowserDialog	0.000	0.001	0.001
cybrowserHide	0	0	0
cybrowserList	0.001	0.000	0.000
cybrowserSend	0.001	0.000	0.001
cybrowserShow	0	0	0
cybrowserVersion	0.001	0.000	0.000
cyrestAPI	0.001	0.000	0.001
cyrestDELETE	0	0	0
cyrestGET	0	0	0
cyrestPOST	0.001	0.000	0.000
cyrestPUT	0	0	0
cytoscapeApiVersions	0	0	0
cytoscapeFreeMemory	0.000	0.000	0.001
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	0.000	0.000	0.001
deleteSelectedEdges	0	0	0
deleteSelectedNodes	0.001	0.000	0.001
deleteSelfLoops	0	0	0
deleteStyleMapping	0	0	0
deleteTableColumn	0	0	0
deleteVisualStyle	0.001	0.001	0.000
diffusionAdvanced	0.001	0.000	0.000
diffusionBasic	0	0	0
disableApp	0.000	0.001	0.000
dockPanel	0.000	0.000	0.001
enableApp	0	0	0
expandGroup	0	0	0
exportFilters	0.000	0.000	0.001
exportImage	0	0	0
exportNetwork	0	0	0
exportNetworkToNDEx	0.001	0.000	0.000
exportVisualStyles	0	0	0
fitContent	0.000	0.000	0.001
floatPanel	0	0	0
getAllEdges	0.000	0.000	0.001
getAllNodes	0	0	0
getAppInformation	0	0	0
getAppStatus	0.001	0.000	0.000
getAppUpdates	0.000	0.000	0.001
getArrowShapes	0	0	0
getAvailableApps	0	0	0
getBackgroundColorDefault	0.000	0.000	0.001
getCollectionList	0	0	0
getCollectionName	0.000	0.001	0.000
getCollectionNetworks	0.000	0.000	0.001
getCollectionSuid	0	0	0
getDisabledApps	0	0	0
getEdgeColor	0	0	0
getEdgeCount	0	0	0
getEdgeInfo	0	0	0
getEdgeLineStyle	0.000	0.000	0.001
getEdgeLineWidth	0	0	0
getEdgeProperty	0	0	0
getEdgeSelectionColorDefault	0.001	0.000	0.000
getEdgeTargetArrowShape	0.000	0.001	0.001
getFilterList	0.000	0.000	0.001
getFirstNeighbors	0	0	0
getGroupInfo	0	0	0
getInstalledApps	0.000	0.001	0.000
getLayoutNameMapping	0.000	0.000	0.001
getLayoutNames	0	0	0
getLayoutPropertyNames	0.000	0.001	0.001
getLayoutPropertyType	0	0	0
getLayoutPropertyValue	0	0	0
getLineStyles	0.000	0.001	0.000
getNetworkCenter	0.001	0.000	0.000
getNetworkCount	0.000	0.000	0.001
getNetworkList	0.000	0.001	0.000
getNetworkNDExId	0.000	0.000	0.001
getNetworkName	0	0	0
getNetworkProperty	0.000	0.001	0.001
getNetworkSuid	0	0	0
getNetworkViewSuid	0	0	0
getNetworkViews	0.001	0.000	0.000
getNetworkZoom	0.001	0.000	0.000
getNodeColor	0	0	0
getNodeCount	0	0	0
getNodeHeight	0.000	0.000	0.001
getNodePosition	0	0	0
getNodeProperty	0.000	0.000	0.001
getNodeSelectionColorDefault	0	0	0
getNodeShapes	0	0	0
getNodeSize	0	0	0
getNodeWidth	0	0	0
getSelectedEdgeCount	0	0	0
getSelectedEdges	0.000	0.000	0.001
getSelectedNodeCount	0.001	0.001	0.000
getSelectedNodes	0.001	0.000	0.000
getStyleDependencies	0.001	0.000	0.001
getTableColumnNames	0.001	0.000	0.000
getTableColumnTypes	0	0	0
getTableColumns	0	0	0
getTableValue	0	0	0
getUninstalledApps	0.000	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	0	0
hideNodes	0	0	0
hidePanel	0	0	0
hideSelectedEdges	0	0	0
hideSelectedNodes	0.000	0.000	0.001
importFilters	0.000	0.001	0.000
importNetworkFromFile	0	0	0
importNetworkFromNDEx	0.001	0.000	0.001
importVisualStyles	0.001	0.001	0.000
installApp	0.000	0.000	0.001
invertEdgeSelection	0	0	0
invertNodeSelection	0.001	0.000	0.000
layoutCopycat	0	0	0
layoutNetwork	0	0	0
listGroups	0	0	0
lockNodeDimensions	0.000	0.000	0.001
makeSimpleGraph	0.094	0.001	0.096
makeSimpleIgraph	0.014	0.002	0.016
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	0	0
renameNetwork	0.000	0.000	0.001
renameTableColumn	0	0	0
saveSession	0	0	0
selectAllEdges	0.000	0.000	0.001
selectAllNodes	0	0	0
selectEdges	0	0	0
selectEdgesAdjacentToSelectedNodes	0	0	0
selectEdgesConnectingSelectedNodes	0	0	0
selectFirstNeighbors	0	0	0
selectNodes	0.000	0.001	0.000
selectNodesConnectedBySelectedEdges	0.001	0.000	0.000
setBackgroundColorDefault	0	0	0
setCurrentNetwork	0.000	0.001	0.000
setCurrentView	0	0	0
setEdgeColorBypass	0	0	0
setEdgeColorDefault	0.000	0.000	0.001
setEdgeColorMapping	0	0	0
setEdgeFontFaceBypass	0.001	0.000	0.000
setEdgeFontFaceDefault	0	0	0
setEdgeFontFaceMapping	0	0	0
setEdgeFontSizeBypass	0.000	0.000	0.001
setEdgeFontSizeDefault	0	0	0
setEdgeFontSizeMapping	0	0	0
setEdgeLabelBypass	0	0	0
setEdgeLabelColorBypass	0.000	0.000	0.001
setEdgeLabelColorDefault	0	0	0
setEdgeLabelColorMapping	0	0	0
setEdgeLabelDefault	0	0	0
setEdgeLabelMapping	0.000	0.000	0.001
setEdgeLabelOpacityBypass	0	0	0
setEdgeLabelOpacityDefault	0	0	0
setEdgeLabelOpacityMapping	0	0	0
setEdgeLineStyleBypass	0.000	0.000	0.001
setEdgeLineStyleDefault	0	0	0
setEdgeLineStyleMapping	0.001	0.000	0.001
setEdgeLineWidthBypass	0.001	0.000	0.000
setEdgeLineWidthDefault	0.001	0.000	0.000
setEdgeLineWidthMapping	0.000	0.000	0.001
setEdgeOpacityBypass	0	0	0
setEdgeOpacityDefault	0	0	0
setEdgeOpacityMapping	0.000	0.000	0.001
setEdgePropertyBypass	0	0	0
setEdgeSelectionColorDefault	0.000	0.000	0.001
setEdgeSourceArrowColorBypass	0	0	0
setEdgeSourceArrowColorDefault	0.000	0.000	0.001
setEdgeSourceArrowColorMapping	0	0	0
setEdgeSourceArrowMapping	0	0	0
setEdgeSourceArrowShapeBypass	0	0	0
setEdgeSourceArrowShapeDefault	0	0	0
setEdgeSourceArrowShapeMapping	0.001	0.000	0.000
setEdgeTargetArrowColorBypass	0	0	0
setEdgeTargetArrowColorDefault	0	0	0
setEdgeTargetArrowColorMapping	0.001	0.000	0.000
setEdgeTargetArrowMapping	0	0	0
setEdgeTargetArrowShapeBypass	0	0	0
setEdgeTargetArrowShapeDefault	0	0	0
setEdgeTargetArrowShapeMapping	0	0	0
setEdgeTooltipBypass	0.000	0.001	0.000
setEdgeTooltipDefault	0	0	0
setEdgeTooltipMapping	0	0	0
setLayoutProperties	0.000	0.001	0.000
setNetworkCenterBypass	0.001	0.000	0.000
setNetworkPropertyBypass	0.001	0.000	0.001
setNetworkZoomBypass	0.000	0.000	0.001
setNodeBorderColorBypass	0	0	0
setNodeBorderColorDefault	0	0	0
setNodeBorderColorMapping	0	0	0
setNodeBorderOpacityBypass	0.000	0.000	0.001
setNodeBorderOpacityDefault	0	0	0
setNodeBorderOpacityMapping	0	0	0
setNodeBorderWidthBypass	0	0	0
setNodeBorderWidthDefault	0	0	0
setNodeBorderWidthMapping	0	0	0
setNodeColorBypass	0.000	0.000	0.001
setNodeColorDefault	0.001	0.000	0.001
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	0.000	0.001	0.000
setNodeCustomPieChart	0	0	0
setNodeCustomPosition	0.000	0.000	0.001
setNodeCustomRadialGradient	0.001	0.000	0.001
setNodeCustomRingChart	0	0	0
setNodeFillOpacityBypass	0.000	0.001	0.001
setNodeFillOpacityDefault	0	0	0
setNodeFillOpacityMapping	0.000	0.000	0.001
setNodeFontFaceBypass	0	0	0
setNodeFontFaceDefault	0.001	0.000	0.001
setNodeFontFaceMapping	0	0	0
setNodeFontSizeBypass	0	0	0
setNodeFontSizeDefault	0	0	0
setNodeFontSizeMapping	0	0	0
setNodeHeightBypass	0	0	0
setNodeHeightDefault	0	0	0
setNodeHeightMapping	0	0	0
setNodeLabelBypass	0	0	0
setNodeLabelColorBypass	0	0	0
setNodeLabelColorDefault	0	0	0
setNodeLabelColorMapping	0	0	0
setNodeLabelDefault	0.000	0.000	0.001
setNodeLabelMapping	0	0	0
setNodeLabelOpacityBypass	0.000	0.001	0.000
setNodeLabelOpacityDefault	0	0	0
setNodeLabelOpacityMapping	0	0	0
setNodeOpacityBypass	0.000	0.001	0.001
setNodePropertyBypass	0	0	0
setNodeSelectionColorDefault	0	0	0
setNodeShapeBypass	0	0	0
setNodeShapeDefault	0.000	0.000	0.001
setNodeShapeMapping	0	0	0
setNodeSizeBypass	0	0	0
setNodeSizeDefault	0.000	0.001	0.000
setNodeSizeMapping	0	0	0
setNodeTooltipBypass	0	0	0
setNodeTooltipDefault	0.001	0.001	0.000
setNodeTooltipMapping	0	0	0
setNodeWidthBypass	0	0	0
setNodeWidthDefault	0.000	0.001	0.001
setNodeWidthMapping	0	0	0
setStyleDependencies	0.001	0.000	0.001
setVisualPropertyDefault	0.000	0.001	0.000
setVisualStyle	0	0	0
syncNodeCustomGraphicsSize	0	0	0
toggleGraphicsDetails	0	0	0
unhideAll	0	0	0
unhideEdges	0.001	0.000	0.000
unhideNodes	0	0	0
uninstallApp	0	0	0
updateApp	0	0	0
updateNetworkInNDEx	0	0	0
updateStyleDefaults	0	0	0
updateStyleMapping	0.000	0.000	0.001

CHECK report for RCy3 on merida1

Summary

Command output

Installation output

Tests output

Example timings