Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-07-31 12:05:48 -0400 (Sat, 31 Jul 2021).

CHECK results for RCy3 on nebbiolo2

To the developers/maintainers of the RCy3 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCy3.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1505/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.13.3  (landing page)
Alex Pico
Snapshot Date: 2021-07-30 14:50:06 -0400 (Fri, 30 Jul 2021)
URL: https://git.bioconductor.org/packages/RCy3
Branch: master
Last Commit: 36f52f2
Last Changed Date: 2021-06-15 21:29:56 -0400 (Tue, 15 Jun 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RCy3
Version: 2.13.3
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings RCy3_2.13.3.tar.gz
StartedAt: 2021-07-30 20:55:00 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 20:56:21 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 80.6 seconds
RetCode: 0
Status:   OK  
CheckDir: RCy3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings RCy3_2.13.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/RCy3.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* 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 ‘2.13.3’
* 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
.edgeNameToEdgeSUID: no visible binding for global variable ‘SUID’
.nodeNameToNodeSUID: no visible binding for global variable ‘SUID’
commandsGET: no visible binding for global variable ‘requester’
commandsHelp: no visible binding for global variable ‘requester’
commandsPOST: no visible binding for global variable ‘requester’
createNetworkFromDataFrames: no visible binding for global variable
  ‘SUID’
cyrestDELETE: no visible binding for global variable ‘requester’
cyrestGET: no visible binding for global variable ‘requester’
cyrestPOST: no visible binding for global variable ‘requester’
cyrestPUT: no visible binding for global variable ‘requester’
paletteColorRandom: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  SUID requester rgb
Consider adding
  importFrom("grDevices", "rgb")
to your NAMESPACE file.
* 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-3.14-bioc/meat/RCy3.Rcheck/00check.log’
for details.



Installation output

RCy3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL RCy3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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)

Tests output

RCy3.Rcheck/tests/runTests.Rout


R version 4.1.0 beta (2021-05-03 r80259) -- "Camp Pontanezen"
Copyright (C) 2021 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 
  0.159   0.019   0.165 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

nameusersystemelapsed
AddToGroup000
RemoveFromGroup000
addAnnotationText000
addCyEdges000
addCyNodes0.0000.0000.001
analyzeNetwork000
applyFilter000
bundleEdges000
checkNotebookIsRunning0.0010.0000.000
checkRunningRemote000
clearEdgeBends000
clearEdgePropertyBypass000
clearNetworkCenterBypass0.0000.0000.001
clearNetworkPropertyBypass000
clearNetworkZoomBypass000
clearNodeOpacityBypass000
clearNodePropertyBypass000
clearSelection000
cloneNetwork000
closeSession000
collapseGroup000
commandEcho000
commandOpenDialog000
commandPause000
commandQuit000
commandRunFile000
commandSleep0.0010.0000.000
commandsAPI000
commandsGET000
commandsHelp000
commandsPOST0.0000.0000.001
commandsRun000
copyVisualStyle000
createColumnFilter000
createCompositeFilter000
createDegreeFilter000
createGraphFromNetwork000
createGroup000
createGroupByColumn000
createIgraphFromNetwork000
createNetworkFromDataFrames000
createNetworkFromGraph000
createNetworkFromIgraph000
createSubnetwork000
createVisualStyle000
cybrowserClose000
cybrowserDialog000
cybrowserHide000
cybrowserList000
cybrowserSend000
cybrowserShow000
cybrowserVersion000
cyrestAPI000
cyrestDELETE000
cyrestGET0.0000.0000.001
cyrestPOST000
cyrestPUT000
cytoscapeApiVersions000
cytoscapeFreeMemory000
cytoscapeMemoryStatus000
cytoscapeNumberOfCores000
cytoscapePing000
cytoscapeVersionInfo0.0000.0000.001
deleteAllNetworks000
deleteAnnotation000
deleteDuplicateEdges000
deleteGroup0.0010.0000.000
deleteNetwork000
deleteSelectedEdges000
deleteSelectedNodes000
deleteSelfLoops0.0000.0000.001
deleteStyleMapping000
deleteTableColumn000
deleteVisualStyle000
diffusionAdvanced000
diffusionBasic000
disableApp000
doInitializeSandbox000
doRequestRemote000
doSetSandbox000
dockPanel000
dot-getDefaultSandbox0.0000.0000.001
dot-getRequester000
enableApp000
expandGroup000
exportFilters000
exportImage000
exportNetwork000
exportNetworkToNDEx000
exportVisualStyles000
findRemoteCytoscape000
fitContent000
floatPanel0.0000.0000.001
getAbsSandboxPath000
getAllEdges000
getAllNodes000
getAllStyleMappings0.0010.0000.000
getAnnotationList000
getAppInformation000
getAppStatus000
getAppUpdates0.0000.0000.001
getArrowShapes000
getAvailableApps000
getBackgroundColorDefault000
getBrowserClientChannel000
getBrowserClientJs000
getCollectionList000
getCollectionName000
getCollectionNetworks000
getCollectionSuid0.0010.0000.000
getCurrentSandbox000
getCurrentSandboxName000
getCurrentSandboxPath000
getCurrentStyle000
getDefaultSandbox000
getDefaultSandboxPath000
getDisabledApps000
getEdgeColor000
getEdgeCount000
getEdgeInfo000
getEdgeLineStyle000
getEdgeLineWidth000
getEdgeProperty0.0010.0000.000
getEdgeSelectionColorDefault000
getEdgeTargetArrowShape000
getFilterList000
getFirstNeighbors000
getGroupInfo000
getInstalledApps000
getJupyterBridgeURL000
getLayoutNameMapping000
getLayoutNames000
getLayoutPropertyNames000
getLayoutPropertyType000
getLayoutPropertyValue000
getLineStyles000
getNetworkCenter0.0000.0000.001
getNetworkCount000
getNetworkList000
getNetworkNDExId000
getNetworkName000
getNetworkProperty000
getNetworkSuid000
getNetworkViewSuid000
getNetworkViews000
getNetworkZoom000
getNodeColor000
getNodeCount000
getNodeHeight000
getNodePosition000
getNodeProperty000
getNodeSelectionColorDefault000
getNodeShapes000
getNodeSize000
getNodeWidth000
getNotebookIsRunning0.0010.0000.000
getSandboxReinitialize000
getSelectedEdgeCount000
getSelectedEdges000
getSelectedNodeCount000
getSelectedNodes000
getStyleDependencies000
getStyleMapping000
getTableColumnNames000
getTableColumnTypes0.0000.0000.001
getTableColumns000
getTableValue000
getUninstalledApps000
getVisualPropertyDefault000
getVisualPropertyNames000
getVisualStyleNames000
hideAllPanels000
hideEdges000
hideNodes000
hidePanel000
hideSelectedEdges000
hideSelectedNodes000
importFilters000
importNetworkFromFile000
importNetworkFromNDEx000
importVisualStyles000
installApp000
invertEdgeSelection000
invertNodeSelection000
layoutCopycat000
layoutNetwork000
listGroups000
lockNodeDimensions000
makeSimpleGraph0.0550.0000.055
makeSimpleIgraph0.0100.0000.009
mapTableColumn000
mapVisualProperty000
matchArrowColorToEdge000
mergeNetworks000
openAppStore000
openSession000
paletteColorBrewerAccent0.0040.0000.004
paletteColorBrewerBlues000
paletteColorBrewerBrBG000
paletteColorBrewerBuGn000
paletteColorBrewerBuPu000
paletteColorBrewerDark2000
paletteColorBrewerGnBu000
paletteColorBrewerGreens000
paletteColorBrewerGreys000
paletteColorBrewerOrRd000
paletteColorBrewerOranges000
paletteColorBrewerPRGn000
paletteColorBrewerPaired000
paletteColorBrewerPastel1000
paletteColorBrewerPastel20.0010.0000.000
paletteColorBrewerPiYG0.0000.0000.001
paletteColorBrewerPuBu0.0010.0000.000
paletteColorBrewerPuBuGn0.0000.0000.001
paletteColorBrewerPuOr0.0010.0000.000
paletteColorBrewerPuRd0.0000.0000.001
paletteColorBrewerPurples0.0010.0000.000
paletteColorBrewerRdBu0.0000.0000.001
paletteColorBrewerRdPu000
paletteColorBrewerRdYlBu0.0000.0000.001
paletteColorBrewerReds000
paletteColorBrewerSet1000
paletteColorBrewerSet2000
paletteColorBrewerSet3000
paletteColorBrewerYlGn000
paletteColorBrewerYlGnBu000
paletteColorBrewerYlOrBr000
paletteColorBrewerYlOrRd000
paletteColorRandom000
removeNodeCustomGraphics000
renameNetwork000
renameTableColumn000
resetDefaultSandbox000
runningRemoteCheck0.0010.0000.000
sandboxGetFileInfo000
sandboxGetFrom000
sandboxInitializer000
sandboxRemove000
sandboxRemoveFile000
sandboxSendTo000
sandboxSet000
sandboxUrlTo000
saveSession000
selectAllEdges000
selectAllNodes000
selectEdges000
selectEdgesAdjacentToSelectedNodes000
selectEdgesConnectingSelectedNodes000
selectFirstNeighbors000
selectNodes0.0010.0000.000
selectNodesConnectedBySelectedEdges000
setBackgroundColorDefault000
setCatchupFilterSecs000
setCatchupNetworkSecs000
setCurrentNetwork000
setCurrentSandbox000
setCurrentView0.0010.0000.000
setDefaultSandbox000
setDefaultSandboxPath000
setEdgeColorBypass000
setEdgeColorDefault000
setEdgeColorMapping000
setEdgeFontFaceBypass000
setEdgeFontFaceDefault000
setEdgeFontFaceMapping000
setEdgeFontSizeBypass000
setEdgeFontSizeDefault000
setEdgeFontSizeMapping000
setEdgeLabelBypass000
setEdgeLabelColorBypass0.0010.0000.000
setEdgeLabelColorDefault000
setEdgeLabelColorMapping000
setEdgeLabelDefault000
setEdgeLabelMapping000
setEdgeLabelOpacityBypass0.0010.0000.000
setEdgeLabelOpacityDefault000
setEdgeLabelOpacityMapping000
setEdgeLineStyleBypass000
setEdgeLineStyleDefault000
setEdgeLineStyleMapping000
setEdgeLineWidthBypass000
setEdgeLineWidthDefault000
setEdgeLineWidthMapping000
setEdgeOpacityBypass0.0000.0000.001
setEdgeOpacityDefault000
setEdgeOpacityMapping000
setEdgePropertyBypass000
setEdgeSelectionColorDefault000
setEdgeSourceArrowColorBypass000
setEdgeSourceArrowColorDefault000
setEdgeSourceArrowColorMapping000
setEdgeSourceArrowMapping000
setEdgeSourceArrowShapeBypass000
setEdgeSourceArrowShapeDefault000
setEdgeSourceArrowShapeMapping000
setEdgeTargetArrowColorBypass000
setEdgeTargetArrowColorDefault000
setEdgeTargetArrowColorMapping000
setEdgeTargetArrowMapping0.0010.0000.000
setEdgeTargetArrowShapeBypass000
setEdgeTargetArrowShapeDefault000
setEdgeTargetArrowShapeMapping000
setEdgeTooltipBypass0.0000.0000.001
setEdgeTooltipDefault000
setEdgeTooltipMapping000
setLayoutProperties000
setModelPropagationSecs0.0010.0000.000
setNetworkCenterBypass0.0000.0000.001
setNetworkPropertyBypass000
setNetworkZoomBypass000
setNodeBorderColorBypass000
setNodeBorderColorDefault000
setNodeBorderColorMapping000
setNodeBorderOpacityBypass000
setNodeBorderOpacityDefault000
setNodeBorderOpacityMapping0.0000.0000.001
setNodeBorderWidthBypass000
setNodeBorderWidthDefault000
setNodeBorderWidthMapping000
setNodeColorBypass000
setNodeColorDefault000
setNodeColorMapping000
setNodeComboOpacityMapping0.0010.0000.000
setNodeCustomBarChart000
setNodeCustomBoxChart000
setNodeCustomHeatMapChart000
setNodeCustomLineChart0.0000.0010.000
setNodeCustomLinearGradient000
setNodeCustomPieChart000
setNodeCustomPosition000
setNodeCustomRadialGradient000
setNodeCustomRingChart000
setNodeFillOpacityBypass000
setNodeFillOpacityDefault000
setNodeFillOpacityMapping000
setNodeFontFaceBypass000
setNodeFontFaceDefault000
setNodeFontFaceMapping000
setNodeFontSizeBypass0.0010.0000.000
setNodeFontSizeDefault000
setNodeFontSizeMapping000
setNodeHeightBypass000
setNodeHeightDefault000
setNodeHeightMapping000
setNodeLabelBypass000
setNodeLabelColorBypass000
setNodeLabelColorDefault000
setNodeLabelColorMapping000
setNodeLabelDefault000
setNodeLabelMapping000
setNodeLabelOpacityBypass000
setNodeLabelOpacityDefault000
setNodeLabelOpacityMapping000
setNodeOpacityBypass000
setNodePropertyBypass000
setNodeSelectionColorDefault000
setNodeShapeBypass000
setNodeShapeDefault0.0010.0000.000
setNodeShapeMapping000
setNodeSizeBypass000
setNodeSizeDefault000
setNodeSizeMapping0.0000.0000.001
setNodeTooltipBypass000
setNodeTooltipDefault000
setNodeTooltipMapping000
setNodeWidthBypass000
setNodeWidthDefault000
setNodeWidthMapping000
setNotebookIsRunning0.0010.0000.000
setSandboxReinitialize000
setStyleDependencies000
setVisualPropertyDefault000
setVisualStyle0.0000.0000.001
syncNodeCustomGraphicsSize000
toggleGraphicsDetails000
unhideAll000
unhideEdges000
unhideNodes000
uninstallApp000
updateApp0.0010.0000.000
updateNetworkInNDEx000
updateStyleDefaults000
updateStyleMapping000