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CHECK report for RCy3 on merida1

This page was generated on 2021-05-06 12:36:20 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the RCy3 package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1475/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.10.2  (landing page)
Alex Pico
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/RCy3
Branch: RELEASE_3_12
Last Commit: 85dc193
Last Changed Date: 2020-11-18 15:46:50 -0400 (Wed, 18 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: RCy3
Version: 2.10.2
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_2.10.2.tar.gz
StartedAt: 2021-05-06 05:13:45 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:15:06 -0400 (Thu, 06 May 2021)
EllapsedTime: 81.7 seconds
RetCode: 0
Status:   OK  
CheckDir: RCy3.Rcheck
Warnings: 0

Command output

##############################################################################
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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_2.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/RCy3.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.10.2’
* 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-3.12-bioc/meat/RCy3.Rcheck/00check.log’
for details.



Installation output

RCy3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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)

Tests output

RCy3.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  0.258   0.062   0.299 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

nameusersystemelapsed
AddToGroup000
RemoveFromGroup000
addCyEdges000
addCyNodes000
analyzeNetwork000
applyFilter000
bundleEdges0.0000.0010.000
clearEdgeBends0.0000.0000.001
clearEdgePropertyBypass000
clearNetworkCenterBypass000
clearNetworkPropertyBypass0.0010.0000.000
clearNetworkZoomBypass000
clearNodeOpacityBypass0.0000.0010.001
clearNodePropertyBypass0.0010.0000.001
clearSelection000
cloneNetwork0.0000.0000.001
closeSession0.0010.0000.000
collapseGroup0.0000.0010.000
commandEcho000
commandOpenDialog000
commandPause000
commandQuit0.0010.0000.001
commandRunFile0.0000.0000.001
commandSleep0.0000.0010.001
commandsAPI000
commandsGET000
commandsHelp000
commandsPOST0.0010.0000.001
commandsRun000
copyVisualStyle0.0000.0000.001
createColumnFilter0.0010.0000.000
createCompositeFilter0.0010.0000.000
createDegreeFilter0.0010.0000.001
createGraphFromNetwork0.0010.0010.000
createGroup0.0000.0000.001
createGroupByColumn000
createIgraphFromNetwork000
createNetworkFromDataFrames000
createNetworkFromGraph000
createNetworkFromIgraph000
createSubnetwork0.0000.0010.000
createVisualStyle000
cybrowserClose000
cybrowserDialog0.0010.0000.001
cybrowserHide0.0000.0010.001
cybrowserList000
cybrowserSend000
cybrowserShow000
cybrowserVersion000
cyrestAPI000
cyrestDELETE0.0010.0000.001
cyrestGET000
cyrestPOST000
cyrestPUT0.0010.0010.000
cytoscapeApiVersions000
cytoscapeFreeMemory0.0000.0000.001
cytoscapeMemoryStatus0.0000.0000.001
cytoscapeNumberOfCores000
cytoscapePing000
cytoscapeVersionInfo000
deleteAllNetworks000
deleteDuplicateEdges0.0000.0000.001
deleteGroup000
deleteNetwork0.0010.0000.000
deleteSelectedEdges0.0000.0010.000
deleteSelectedNodes000
deleteSelfLoops0.0010.0000.000
deleteStyleMapping000
deleteTableColumn000
deleteVisualStyle0.0010.0000.000
diffusionAdvanced000
diffusionBasic000
disableApp000
dockPanel0.0000.0000.001
enableApp0.0000.0010.000
expandGroup0.0010.0000.000
exportFilters000
exportImage0.0000.0000.001
exportNetwork0.0000.0010.001
exportNetworkToNDEx000
exportVisualStyles000
fitContent000
floatPanel0.0000.0010.000
getAllEdges000
getAllNodes000
getAppInformation0.0000.0010.000
getAppStatus0.0000.0000.001
getAppUpdates0.0000.0000.001
getArrowShapes0.0010.0000.000
getAvailableApps000
getBackgroundColorDefault000
getCollectionList0.0000.0000.001
getCollectionName000
getCollectionNetworks000
getCollectionSuid000
getCurrentStyle000
getDisabledApps0.0010.0010.000
getEdgeColor000
getEdgeCount000
getEdgeInfo0.0000.0010.001
getEdgeLineStyle0.0010.0010.000
getEdgeLineWidth0.0000.0010.000
getEdgeProperty0.0000.0000.001
getEdgeSelectionColorDefault0.0000.0010.000
getEdgeTargetArrowShape000
getFilterList000
getFirstNeighbors000
getGroupInfo000
getInstalledApps000
getLayoutNameMapping000
getLayoutNames0.0000.0010.001
getLayoutPropertyNames0.0000.0000.001
getLayoutPropertyType0.0000.0000.001
getLayoutPropertyValue000
getLineStyles000
getNetworkCenter0.0010.0010.000
getNetworkCount000
getNetworkList0.0000.0000.001
getNetworkNDExId000
getNetworkName000
getNetworkProperty000
getNetworkSuid0.0000.0010.000
getNetworkViewSuid0.0000.0000.001
getNetworkViews0.0000.0010.000
getNetworkZoom0.0000.0000.001
getNodeColor000
getNodeCount000
getNodeHeight0.0000.0000.001
getNodePosition0.0010.0000.001
getNodeProperty0.0010.0000.000
getNodeSelectionColorDefault0.0010.0000.000
getNodeShapes0.0000.0000.001
getNodeSize0.0000.0000.001
getNodeWidth000
getSelectedEdgeCount000
getSelectedEdges0.0000.0010.000
getSelectedNodeCount0.0010.0000.000
getSelectedNodes000
getStyleDependencies000
getTableColumnNames0.0000.0010.000
getTableColumnTypes000
getTableColumns000
getTableValue000
getUninstalledApps0.0000.0000.001
getVisualPropertyDefault0.0000.0000.001
getVisualPropertyNames000
getVisualStyleNames0.0000.0000.001
hideAllPanels000
hideEdges000
hideNodes000
hidePanel000
hideSelectedEdges000
hideSelectedNodes000
importFilters000
importNetworkFromFile0.0000.0000.001
importNetworkFromNDEx000
importVisualStyles0.0000.0000.001
installApp0.0000.0000.001
invertEdgeSelection0.0000.0000.001
invertNodeSelection000
layoutCopycat0.0000.0010.000
layoutNetwork0.0000.0000.001
listGroups0.0000.0000.001
lockNodeDimensions000
makeSimpleGraph0.0970.0000.098
makeSimpleIgraph0.0170.0010.019
mapTableColumn0.0000.0000.001
mapVisualProperty0.0010.0000.000
matchArrowColorToEdge0.0010.0000.000
mergeNetworks000
openAppStore0.0000.0000.001
openSession0.0000.0000.001
removeNodeCustomGraphics0.0000.0000.001
renameNetwork0.0000.0010.001
renameTableColumn0.0010.0000.001
saveSession0.0000.0000.001
selectAllEdges0.0000.0000.001
selectAllNodes000
selectEdges0.0000.0000.001
selectEdgesAdjacentToSelectedNodes000
selectEdgesConnectingSelectedNodes000
selectFirstNeighbors000
selectNodes0.0000.0010.000
selectNodesConnectedBySelectedEdges000
setBackgroundColorDefault0.0010.0000.000
setCurrentNetwork0.0000.0010.000
setCurrentView0.0000.0000.001
setEdgeColorBypass0.0000.0000.001
setEdgeColorDefault0.0000.0000.001
setEdgeColorMapping0.0000.0010.001
setEdgeFontFaceBypass000
setEdgeFontFaceDefault0.0000.0010.000
setEdgeFontFaceMapping000
setEdgeFontSizeBypass0.0000.0000.001
setEdgeFontSizeDefault000
setEdgeFontSizeMapping0.0000.0000.001
setEdgeLabelBypass0.0000.0000.001
setEdgeLabelColorBypass000
setEdgeLabelColorDefault0.0000.0010.000
setEdgeLabelColorMapping0.0000.0000.001
setEdgeLabelDefault0.0000.0000.001
setEdgeLabelMapping000
setEdgeLabelOpacityBypass000
setEdgeLabelOpacityDefault0.0000.0010.000
setEdgeLabelOpacityMapping000
setEdgeLineStyleBypass0.0010.0000.001
setEdgeLineStyleDefault000
setEdgeLineStyleMapping000
setEdgeLineWidthBypass0.0010.0000.000
setEdgeLineWidthDefault000
setEdgeLineWidthMapping0.0000.0010.000
setEdgeOpacityBypass0.0000.0000.001
setEdgeOpacityDefault0.0000.0000.001
setEdgeOpacityMapping0.0000.0000.001
setEdgePropertyBypass0.0010.0010.001
setEdgeSelectionColorDefault0.0000.0000.001
setEdgeSourceArrowColorBypass0.0000.0000.001
setEdgeSourceArrowColorDefault0.0000.0000.001
setEdgeSourceArrowColorMapping000
setEdgeSourceArrowMapping000
setEdgeSourceArrowShapeBypass0.0000.0000.001
setEdgeSourceArrowShapeDefault000
setEdgeSourceArrowShapeMapping000
setEdgeTargetArrowColorBypass000
setEdgeTargetArrowColorDefault0.0000.0010.001
setEdgeTargetArrowColorMapping000
setEdgeTargetArrowMapping0.0010.0000.001
setEdgeTargetArrowShapeBypass000
setEdgeTargetArrowShapeDefault000
setEdgeTargetArrowShapeMapping0.0000.0000.001
setEdgeTooltipBypass0.0000.0000.001
setEdgeTooltipDefault000
setEdgeTooltipMapping000
setLayoutProperties000
setNetworkCenterBypass000
setNetworkPropertyBypass0.0000.0010.001
setNetworkZoomBypass000
setNodeBorderColorBypass0.0000.0000.001
setNodeBorderColorDefault000
setNodeBorderColorMapping000
setNodeBorderOpacityBypass000
setNodeBorderOpacityDefault0.0000.0010.000
setNodeBorderOpacityMapping000
setNodeBorderWidthBypass0.0000.0010.000
setNodeBorderWidthDefault000
setNodeBorderWidthMapping000
setNodeColorBypass0.0010.0000.000
setNodeColorDefault0.0000.0000.001
setNodeColorMapping0.0000.0000.001
setNodeComboOpacityMapping0.0000.0010.001
setNodeCustomBarChart000
setNodeCustomBoxChart000
setNodeCustomHeatMapChart0.0000.0000.001
setNodeCustomLineChart0.0000.0000.001
setNodeCustomLinearGradient0.0010.0000.000
setNodeCustomPieChart000
setNodeCustomPosition000
setNodeCustomRadialGradient0.0000.0010.000
setNodeCustomRingChart0.0000.0000.001
setNodeFillOpacityBypass000
setNodeFillOpacityDefault0.0000.0010.000
setNodeFillOpacityMapping000
setNodeFontFaceBypass0.0000.0010.000
setNodeFontFaceDefault000
setNodeFontFaceMapping0.0010.0000.001
setNodeFontSizeBypass000
setNodeFontSizeDefault000
setNodeFontSizeMapping0.0000.0000.001
setNodeHeightBypass0.0010.0000.000
setNodeHeightDefault000
setNodeHeightMapping0.0000.0000.001
setNodeLabelBypass000
setNodeLabelColorBypass000
setNodeLabelColorDefault000
setNodeLabelColorMapping000
setNodeLabelDefault000
setNodeLabelMapping0.0000.0010.000
setNodeLabelOpacityBypass000
setNodeLabelOpacityDefault0.0000.0000.001
setNodeLabelOpacityMapping0.0000.0000.001
setNodeOpacityBypass0.0000.0000.001
setNodePropertyBypass0.0000.0010.000
setNodeSelectionColorDefault000
setNodeShapeBypass0.0000.0000.001
setNodeShapeDefault0.0000.0010.001
setNodeShapeMapping0.0010.0000.000
setNodeSizeBypass000
setNodeSizeDefault000
setNodeSizeMapping0.0000.0000.001
setNodeTooltipBypass000
setNodeTooltipDefault000
setNodeTooltipMapping0.0000.0010.000
setNodeWidthBypass000
setNodeWidthDefault0.0010.0000.000
setNodeWidthMapping000
setStyleDependencies0.0000.0000.001
setVisualPropertyDefault000
setVisualStyle000
syncNodeCustomGraphicsSize0.0000.0000.001
toggleGraphicsDetails000
unhideAll000
unhideEdges0.0000.0000.001
unhideNodes000
uninstallApp000
updateApp000
updateNetworkInNDEx0.0000.0010.000
updateStyleDefaults0.0000.0000.001
updateStyleMapping000