Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:50 -0400 (Fri, 15 Oct 2021).

CHECK results for RCy3 on nebbiolo1

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 1526/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.12.4  (landing page)
Alex Pico
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/RCy3
git_branch: RELEASE_3_13
git_last_commit: 5bb5011
git_last_commit_date: 2021-08-09 14:24:15 -0400 (Mon, 09 Aug 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RCy3
Version: 2.12.4
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RCy3_2.12.4.tar.gz
StartedAt: 2021-10-14 11:15:15 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:16:33 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 77.8 seconds
RetCode: 0
Status:   OK  
CheckDir: RCy3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RCy3.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RCy3_2.12.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/RCy3.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.12.4’
* 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-3.13-bioc/meat/RCy3.Rcheck/00check.log’
for details.



Installation output

RCy3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL RCy3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
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 
  0.208   0.053   0.247 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

nameusersystemelapsed
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RemoveFromGroup000
addAnnotationText000
addCyEdges000
addCyNodes000
analyzeNetwork000
applyFilter0.0000.0010.000
bundleEdges000
checkNotebookIsRunning0.0000.0000.001
checkRunningRemote000
clearEdgeBends000
clearEdgePropertyBypass000
clearNetworkCenterBypass000
clearNetworkPropertyBypass0.0010.0000.000
clearNetworkZoomBypass000
clearNodeOpacityBypass000
clearNodePropertyBypass0.0010.0000.000
clearSelection000
cloneNetwork000
closeSession0.0000.0000.001
collapseGroup000
commandEcho000
commandOpenDialog000
commandPause000
commandQuit0.0010.0000.000
commandRunFile000
commandSleep000
commandsAPI0.0000.0000.001
commandsGET000
commandsHelp000
commandsPOST0.0000.0000.001
commandsRun000
copyVisualStyle0.0010.0000.000
createColumnFilter000
createCompositeFilter000
createDegreeFilter000
createGraphFromNetwork0.0000.0010.000
createGroup000
createGroupByColumn000
createIgraphFromNetwork000
createNetworkFromDataFrames0.0010.0000.000
createNetworkFromGraph000
createNetworkFromIgraph000
createSubnetwork000
createVisualStyle0.0000.0010.000
cybrowserClose000
cybrowserDialog0.0000.0000.001
cybrowserHide000
cybrowserList0.0010.0000.000
cybrowserSend000
cybrowserShow000
cybrowserVersion0.0010.0000.000
cyrestAPI000
cyrestDELETE000
cyrestGET000
cyrestPOST0.0000.0010.000
cyrestPUT000
cytoscapeApiVersions0.0000.0000.001
cytoscapeFreeMemory000
cytoscapeMemoryStatus000
cytoscapeNumberOfCores0.0000.0000.001
cytoscapePing000
cytoscapeVersionInfo000
deleteAllNetworks000
deleteAnnotation000
deleteDuplicateEdges000
deleteGroup0.0000.0010.000
deleteNetwork000
deleteSelectedEdges0.0000.0000.001
deleteSelectedNodes000
deleteSelfLoops000
deleteStyleMapping0.0000.0000.001
deleteTableColumn000
deleteVisualStyle0.0010.0000.000
diffusionAdvanced0.0000.0000.001
diffusionBasic000
disableApp0.0010.0000.000
doInitializeSandbox000
doRequestRemote000
doSetSandbox000
dockPanel0.0000.0010.000
dot-getDefaultSandbox000
dot-getRequester000
enableApp000
expandGroup000
exportFilters0.0000.0000.001
exportImage000
exportNetwork000
exportNetworkToNDEx0.0000.0000.001
exportVisualStyles000
findRemoteCytoscape000
fitContent0.0000.0010.000
floatPanel000
getAbsSandboxPath000
getAllEdges0.0000.0010.000
getAllNodes000
getAllStyleMappings0.0000.0000.001
getAnnotationList000
getAppInformation000
getAppStatus0.0000.0000.001
getAppUpdates000
getArrowShapes000
getAvailableApps000
getBackgroundColorDefault000
getBrowserClientChannel000
getBrowserClientJs000
getCollectionList000
getCollectionName000
getCollectionNetworks0.0000.0010.000
getCollectionSuid000
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getCurrentSandboxName0.0000.0010.000
getCurrentSandboxPath000
getCurrentStyle0.0000.0000.001
getDefaultSandbox000
getDefaultSandboxPath000
getDisabledApps0.0000.0000.001
getEdgeColor000
getEdgeCount000
getEdgeInfo000
getEdgeLineStyle000
getEdgeLineWidth000
getEdgeProperty000
getEdgeSelectionColorDefault000
getEdgeTargetArrowShape0.0000.0000.001
getFilterList0.0000.0010.000
getFirstNeighbors000
getGroupInfo000
getInstalledApps000
getJupyterBridgeURL000
getLayoutNameMapping000
getLayoutNames000
getLayoutPropertyNames0.0000.0000.001
getLayoutPropertyType000
getLayoutPropertyValue0.0010.0000.000
getLineStyles0.0000.0000.001
getNetworkCenter000
getNetworkCount000
getNetworkList000
getNetworkNDExId000
getNetworkName000
getNetworkProperty0.0000.0010.000
getNetworkSuid000
getNetworkViewSuid0.0000.0000.001
getNetworkViews000
getNetworkZoom000
getNodeColor0.0000.0000.001
getNodeCount000
getNodeHeight0.0010.0000.000
getNodePosition000
getNodeProperty000
getNodeSelectionColorDefault000
getNodeShapes000
getNodeSize000
getNodeWidth0.0000.0000.001
getNotebookIsRunning000
getSandboxReinitialize000
getSelectedEdgeCount000
getSelectedEdges000
getSelectedNodeCount000
getSelectedNodes0.0000.0010.000
getStyleDependencies000
getStyleMapping0.0000.0000.001
getTableColumnNames000
getTableColumnTypes0.0010.0000.000
getTableColumns000
getTableValue000
getUninstalledApps0.0010.0000.000
getVisualPropertyDefault0.0000.0000.001
getVisualPropertyNames000
getVisualStyleNames0.0010.0000.000
hideAllPanels000
hideEdges000
hideNodes000
hidePanel0.0000.0010.000
hideSelectedEdges000
hideSelectedNodes0.0000.0000.001
importFilters000
importNetworkFromFile000
importNetworkFromNDEx0.0000.0010.000
importVisualStyles000
installApp0.0010.0000.000
invertEdgeSelection000
invertNodeSelection000
layoutCopycat000
layoutNetwork000
listGroups000
lockNodeDimensions0.0000.0000.001
makeSimpleGraph0.0490.0000.049
makeSimpleIgraph0.0100.0000.009
mapTableColumn0.0010.0000.000
mapVisualProperty000
matchArrowColorToEdge000
mergeNetworks0.0010.0000.000
openAppStore000
openSession000
paletteColorBrewerAccent0.0020.0030.004
paletteColorBrewerBlues0.0000.0000.001
paletteColorBrewerBrBG0.0000.0000.001
paletteColorBrewerBuGn0.0000.0000.001
paletteColorBrewerBuPu000
paletteColorBrewerDark2000
paletteColorBrewerGnBu000
paletteColorBrewerGreens000
paletteColorBrewerGreys0.0000.0000.001
paletteColorBrewerOrRd0.0000.0010.000
paletteColorBrewerOranges000
paletteColorBrewerPRGn0.0010.0000.000
paletteColorBrewerPaired0.0010.0000.000
paletteColorBrewerPastel10.0000.0000.001
paletteColorBrewerPastel2000
paletteColorBrewerPiYG000
paletteColorBrewerPuBu000
paletteColorBrewerPuBuGn0.0010.0000.000
paletteColorBrewerPuOr0.0010.0000.001
paletteColorBrewerPuRd0.0000.0000.001
paletteColorBrewerPurples000
paletteColorBrewerRdBu000
paletteColorBrewerRdPu000
paletteColorBrewerRdYlBu0.0010.0000.000
paletteColorBrewerReds0.0000.0000.001
paletteColorBrewerSet1000
paletteColorBrewerSet2000
paletteColorBrewerSet30.0010.0000.000
paletteColorBrewerYlGn0.0010.0000.000
paletteColorBrewerYlGnBu0.0000.0000.001
paletteColorBrewerYlOrBr000
paletteColorBrewerYlOrRd000
paletteColorRandom0.0010.0000.000
removeNodeCustomGraphics000
renameNetwork000
renameTableColumn000
resetDefaultSandbox0.0000.0000.001
runningRemoteCheck0.0000.0010.000
sandboxGetFileInfo000
sandboxGetFrom0.0000.0000.001
sandboxInitializer0.0000.0010.000
sandboxRemove0.0010.0000.000
sandboxRemoveFile000
sandboxSendTo000
sandboxSet0.0010.0000.000
sandboxUrlTo000
saveSession000
selectAllEdges000
selectAllNodes000
selectEdges000
selectEdgesAdjacentToSelectedNodes000
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selectFirstNeighbors000
selectNodes000
selectNodesConnectedBySelectedEdges000
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setCurrentView000
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setDefaultSandboxPath0.0000.0010.000
setEdgeColorBypass000
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setEdgeColorMapping000
setEdgeFontFaceBypass000
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setEdgeLabelBypass000
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setEdgeLabelColorMapping0.0000.0000.001
setEdgeLabelDefault000
setEdgeLabelMapping0.0010.0000.000
setEdgeLabelOpacityBypass0.0000.0000.001
setEdgeLabelOpacityDefault000
setEdgeLabelOpacityMapping0.0010.0000.000
setEdgeLineStyleBypass000
setEdgeLineStyleDefault000
setEdgeLineStyleMapping000
setEdgeLineWidthBypass000
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setEdgeLineWidthMapping000
setEdgeOpacityBypass0.0000.0010.000
setEdgeOpacityDefault000
setEdgeOpacityMapping0.0000.0000.001
setEdgePropertyBypass0.0000.0010.000
setEdgeSelectionColorDefault000
setEdgeSourceArrowColorBypass0.0000.0000.001
setEdgeSourceArrowColorDefault000
setEdgeSourceArrowColorMapping000
setEdgeSourceArrowMapping000
setEdgeSourceArrowShapeBypass000
setEdgeSourceArrowShapeDefault000
setEdgeSourceArrowShapeMapping000
setEdgeTargetArrowColorBypass000
setEdgeTargetArrowColorDefault000
setEdgeTargetArrowColorMapping0.0000.0010.000
setEdgeTargetArrowMapping000
setEdgeTargetArrowShapeBypass000
setEdgeTargetArrowShapeDefault000
setEdgeTargetArrowShapeMapping000
setEdgeTooltipBypass000
setEdgeTooltipDefault000
setEdgeTooltipMapping000
setLayoutProperties0.0000.0000.001
setModelPropagationSecs000
setNetworkCenterBypass000
setNetworkPropertyBypass000
setNetworkZoomBypass000
setNodeBorderColorBypass000
setNodeBorderColorDefault0.0010.0000.000
setNodeBorderColorMapping0.0000.0000.001
setNodeBorderOpacityBypass000
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setNodeBorderOpacityMapping0.0000.0000.001
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