Multiple platform build/check report for BioC 3.9 - CHECK report for RCy3 on malbec2

Package: RCy3

Version: 2.4.6

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RCy3_2.4.6.tar.gz

StartedAt: 2019-10-16 04:22:54 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:24:02 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 68.1 seconds

RetCode: 0

Status: OK

CheckDir: RCy3.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RCy3_2.4.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/RCy3.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/RCy3.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL RCy3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-pc-linux-gnu (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 
  0.208   0.027   0.256

name	user	system	elapsed
AddToGroup	0	0	0
RemoveFromGroup	0	0	0
addCyEdges	0	0	0
addCyNodes	0.001	0.000	0.000
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	0	0
clearSelection	0	0	0
cloneNetwork	0	0	0
closeSession	0	0	0
collapseGroup	0.000	0.000	0.001
commandEcho	0	0	0
commandOpenDialog	0	0	0
commandPause	0.001	0.000	0.000
commandQuit	0	0	0
commandRunFile	0	0	0
commandSleep	0	0	0
commandsAPI	0.000	0.000	0.001
commandsGET	0	0	0
commandsHelp	0	0	0
commandsPOST	0.001	0.000	0.000
commandsRun	0	0	0
copyVisualStyle	0	0	0
createColumnFilter	0	0	0
createCompositeFilter	0	0	0
createDegreeFilter	0	0	0
createGraphFromNetwork	0	0	0
createGroup	0	0	0
createIgraphFromNetwork	0	0	0
createNetworkFromDataFrames	0	0	0
createNetworkFromGraph	0	0	0
createNetworkFromIgraph	0	0	0
createSubnetwork	0.001	0.000	0.000
createVisualStyle	0	0	0
cybrowserClose	0.000	0.000	0.001
cybrowserDialog	0	0	0
cybrowserHide	0	0	0
cybrowserList	0	0	0
cybrowserSend	0	0	0
cybrowserShow	0	0	0
cybrowserVersion	0	0	0
cyrestAPI	0	0	0
cyrestDELETE	0.001	0.000	0.000
cyrestGET	0	0	0
cyrestPOST	0	0	0
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	0.000	0.000	0.001
deleteNetwork	0	0	0
deleteSelectedEdges	0	0	0
deleteSelectedNodes	0	0	0
deleteSelfLoops	0	0	0
deleteStyleMapping	0.001	0.000	0.000
deleteTableColumn	0	0	0
deleteVisualStyle	0	0	0
diffusionAdvanced	0	0	0
diffusionBasic	0	0	0
disableApp	0.000	0.000	0.001
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	0	0
exportVisualStyles	0.000	0.001	0.000
fitContent	0	0	0
floatPanel	0.000	0.000	0.001
getAllEdges	0	0	0
getAllNodes	0	0	0
getAppInformation	0	0	0
getAppStatus	0	0	0
getAppUpdates	0.001	0.000	0.000
getArrowShapes	0	0	0
getAvailableApps	0	0	0
getBackgroundColorDefault	0.001	0.000	0.000
getCollectionList	0	0	0
getCollectionName	0	0	0
getCollectionNetworks	0	0	0
getCollectionSuid	0	0	0
getDisabledApps	0.000	0.000	0.001
getEdgeColor	0	0	0
getEdgeCount	0	0	0
getEdgeInfo	0	0	0
getEdgeLineStyle	0	0	0
getEdgeLineWidth	0.001	0.000	0.000
getEdgeProperty	0	0	0
getEdgeSelectionColorDefault	0	0	0
getEdgeTargetArrowShape	0	0	0
getFilterList	0	0	0
getFirstNeighbors	0.000	0.000	0.001
getGroupInfo	0	0	0
getInstalledApps	0	0	0
getLayoutNameMapping	0	0	0
getLayoutNames	0	0	0
getLayoutPropertyNames	0	0	0
getLayoutPropertyType	0	0	0
getLayoutPropertyValue	0.000	0.000	0.001
getLineStyles	0	0	0
getNetworkCenter	0	0	0
getNetworkCount	0	0	0
getNetworkList	0	0	0
getNetworkNDExId	0.001	0.000	0.000
getNetworkName	0	0	0
getNetworkProperty	0	0	0
getNetworkSuid	0	0	0
getNetworkViewSuid	0.000	0.000	0.001
getNetworkViews	0	0	0
getNetworkZoom	0	0	0
getNodeColor	0	0	0
getNodeCount	0	0	0
getNodeHeight	0	0	0
getNodeProperty	0	0	0
getNodeSelectionColorDefault	0	0	0
getNodeShapes	0.001	0.000	0.000
getNodeSize	0	0	0
getNodeWidth	0.000	0.000	0.001
getSelectedEdgeCount	0	0	0
getSelectedEdges	0	0	0
getSelectedNodeCount	0	0	0
getSelectedNodes	0	0	0
getStyleDependencies	0	0	0
getTableColumnNames	0	0	0
getTableColumnTypes	0	0	0
getTableColumns	0.001	0.000	0.000
getTableValue	0	0	0
getUninstalledApps	0	0	0
getVisualPropertyDefault	0	0	0
getVisualPropertyNames	0	0	0
getVisualStyleNames	0	0	0
hideAllPanels	0.001	0.000	0.000
hideEdges	0	0	0
hideNodes	0	0	0
hidePanel	0	0	0
hideSelectedEdges	0	0	0
hideSelectedNodes	0.001	0.000	0.000
importFilters	0	0	0
importNetworkFromFile	0	0	0
importNetworkFromNDEx	0.000	0.000	0.001
importVisualStyles	0	0	0
installApp	0	0	0
invertEdgeSelection	0.001	0.000	0.000
invertNodeSelection	0	0	0
layoutCopycat	0	0	0
layoutNetwork	0	0	0
listGroups	0	0	0
lockNodeDimensions	0	0	0
makeSimpleGraph	0.087	0.000	0.088
makeSimpleIgraph	0.015	0.000	0.016
mapTableColumn	0.000	0.000	0.001
mapVisualProperty	0	0	0
matchArrowColorToEdge	0.001	0.000	0.000
openAppStore	0	0	0
openSession	0	0	0
removeNodeCustomGraphics	0	0	0
renameNetwork	0.000	0.000	0.001
renameTableColumn	0.001	0.000	0.000
saveSession	0	0	0
selectAllEdges	0	0	0
selectAllNodes	0	0	0
selectEdges	0	0	0
selectEdgesAdjacentToSelectedNodes	0	0	0
selectEdgesConnectingSelectedNodes	0.000	0.000	0.001
selectFirstNeighbors	0	0	0
selectNodes	0.001	0.000	0.000
selectNodesConnectedBySelectedEdges	0	0	0
setBackgroundColorDefault	0	0	0
setCurrentNetwork	0	0	0
setCurrentView	0	0	0
setEdgeColorBypass	0	0	0
setEdgeColorDefault	0.001	0.000	0.000
setEdgeColorMapping	0	0	0
setEdgeFontFaceBypass	0	0	0
setEdgeFontFaceDefault	0	0	0
setEdgeFontFaceMapping	0.000	0.000	0.001
setEdgeFontSizeBypass	0	0	0
setEdgeFontSizeDefault	0.001	0.000	0.000
setEdgeFontSizeMapping	0	0	0
setEdgeLabelBypass	0	0	0
setEdgeLabelColorBypass	0	0	0
setEdgeLabelColorDefault	0	0	0
setEdgeLabelColorMapping	0	0	0
setEdgeLabelDefault	0	0	0
setEdgeLabelMapping	0	0	0
setEdgeLabelOpacityBypass	0	0	0
setEdgeLabelOpacityDefault	0	0	0
setEdgeLabelOpacityMapping	0	0	0
setEdgeLineStyleBypass	0	0	0
setEdgeLineStyleDefault	0	0	0
setEdgeLineStyleMapping	0	0	0
setEdgeLineWidthBypass	0	0	0
setEdgeLineWidthDefault	0.000	0.000	0.001
setEdgeLineWidthMapping	0	0	0
setEdgeOpacityBypass	0.000	0.001	0.000
setEdgeOpacityDefault	0	0	0
setEdgeOpacityMapping	0	0	0
setEdgePropertyBypass	0.000	0.000	0.001
setEdgeSelectionColorDefault	0	0	0
setEdgeSourceArrowColorBypass	0.001	0.000	0.000
setEdgeSourceArrowColorDefault	0	0	0
setEdgeSourceArrowColorMapping	0	0	0
setEdgeSourceArrowMapping	0.000	0.000	0.001
setEdgeSourceArrowShapeBypass	0	0	0
setEdgeSourceArrowShapeDefault	0.001	0.000	0.000
setEdgeSourceArrowShapeMapping	0	0	0
setEdgeTargetArrowColorBypass	0	0	0
setEdgeTargetArrowColorDefault	0	0	0
setEdgeTargetArrowColorMapping	0.000	0.000	0.001
setEdgeTargetArrowMapping	0	0	0
setEdgeTargetArrowShapeBypass	0.000	0.001	0.000
setEdgeTargetArrowShapeDefault	0	0	0
setEdgeTargetArrowShapeMapping	0	0	0
setEdgeTooltipBypass	0.000	0.000	0.001
setEdgeTooltipDefault	0	0	0
setEdgeTooltipMapping	0.001	0.000	0.000
setLayoutProperties	0	0	0
setNetworkCenterBypass	0	0	0
setNetworkPropertyBypass	0	0	0
setNetworkZoomBypass	0	0	0
setNodeBorderColorBypass	0	0	0
setNodeBorderColorDefault	0.000	0.001	0.000
setNodeBorderColorMapping	0	0	0
setNodeBorderOpacityBypass	0	0	0
setNodeBorderOpacityDefault	0.000	0.000	0.001
setNodeBorderOpacityMapping	0	0	0
setNodeBorderWidthBypass	0	0	0
setNodeBorderWidthDefault	0.001	0.000	0.000
setNodeBorderWidthMapping	0	0	0
setNodeColorBypass	0	0	0
setNodeColorDefault	0	0	0
setNodeColorMapping	0.000	0.000	0.001
setNodeComboOpacityMapping	0.000	0.000	0.001
setNodeCustomBarChart	0	0	0
setNodeCustomBoxChart	0.001	0.000	0.000
setNodeCustomHeatMapChart	0	0	0
setNodeCustomLineChart	0	0	0
setNodeCustomLinearGradient	0.000	0.000	0.001
setNodeCustomPieChart	0	0	0
setNodeCustomPosition	0.000	0.001	0.000
setNodeCustomRadialGradient	0	0	0
setNodeCustomRingChart	0	0	0
setNodeFillOpacityBypass	0.000	0.000	0.001
setNodeFillOpacityDefault	0	0	0
setNodeFillOpacityMapping	0.001	0.000	0.000
setNodeFontFaceBypass	0	0	0
setNodeFontFaceDefault	0	0	0
setNodeFontFaceMapping	0	0	0
setNodeFontSizeBypass	0	0	0
setNodeFontSizeDefault	0	0	0
setNodeFontSizeMapping	0	0	0
setNodeHeightBypass	0	0	0
setNodeHeightDefault	0.001	0.000	0.000
setNodeHeightMapping	0	0	0
setNodeLabelBypass	0.000	0.000	0.001
setNodeLabelColorBypass	0.001	0.000	0.000
setNodeLabelColorDefault	0	0	0
setNodeLabelColorMapping	0.001	0.000	0.000
setNodeLabelDefault	0	0	0
setNodeLabelMapping	0	0	0
setNodeLabelOpacityBypass	0.001	0.000	0.000
setNodeLabelOpacityDefault	0	0	0
setNodeLabelOpacityMapping	0	0	0
setNodeOpacityBypass	0	0	0
setNodePropertyBypass	0	0	0
setNodeSelectionColorDefault	0	0	0
setNodeShapeBypass	0	0	0
setNodeShapeDefault	0	0	0
setNodeShapeMapping	0.000	0.000	0.001
setNodeSizeBypass	0	0	0
setNodeSizeDefault	0	0	0
setNodeSizeMapping	0	0	0
setNodeTooltipBypass	0.000	0.000	0.001
setNodeTooltipDefault	0	0	0
setNodeTooltipMapping	0	0	0
setNodeWidthBypass	0.001	0.000	0.000
setNodeWidthDefault	0	0	0
setNodeWidthMapping	0	0	0
setStyleDependencies	0	0	0
setVisualPropertyDefault	0	0	0
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	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 malbec2

Summary

Command output

Installation output

Tests output

Example timings