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This page was generated on 2025-10-02 12:05 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4844
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4576
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1719/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.29.1  (landing page)
Alex Pico
Snapshot Date: 2025-10-01 13:45 -0400 (Wed, 01 Oct 2025)
git_url: https://git.bioconductor.org/packages/RCy3
git_branch: devel
git_last_commit: 1b82e1c
git_last_commit_date: 2025-06-11 19:27:12 -0400 (Wed, 11 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for RCy3 on lconway

To the developers/maintainers of the RCy3 package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RCy3
Version: 2.29.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCy3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCy3_2.29.1.tar.gz
StartedAt: 2025-10-01 23:47:45 -0400 (Wed, 01 Oct 2025)
EndedAt: 2025-10-01 23:49:27 -0400 (Wed, 01 Oct 2025)
EllapsedTime: 102.0 seconds
RetCode: 0
Status:   OK  
CheckDir: RCy3.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCy3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCy3_2.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/RCy3.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCy3/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCy3’ version ‘2.29.1’
* package encoding: UTF-8
* 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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
.checkHexColor: no visible global function definition for ‘colors’
.edgeNameToEdgeSUID: no visible binding for global variable ‘SUID’
.nodeNameToNodeSUID: no visible binding for global variable ‘SUID’
createNetworkFromDataFrames: no visible binding for global variable
  ‘SUID’
Undefined global functions or variables:
  SUID colors
Consider adding
  importFrom("grDevices", "colors")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) importFileFromUrl.Rd:24: Lost braces; missing escapes or markup?
    24 | dict: {'filePath': <new file's absolute path in Cytoscape workstation>, 'fileByteCount': number of bytes read}
       |       ^
checkRd: (-1) sandboxGetFileInfo.Rd:17: Lost braces; missing escapes or markup?
    17 | dict: {'filePath': <full path on Cytoscape workstation>, 'modifiedTime': <last changed time, '' if file doesn't exist>, 'isFile': <True if file, False if directory>}
       |       ^
checkRd: (-1) sandboxRemove.Rd:15: Lost braces; missing escapes or markup?
    15 | dict: {'sandboxPath': <directory on Cytoscape workstation>, 'existed': <True if sandbox existed>}
       |       ^
checkRd: (-1) sandboxRemoveFile.Rd:17: Lost braces; missing escapes or markup?
    17 | dict: {'filePath': <file's absolute path in Cytoscape workstation>, 'existed': True if file existed before being deleted}
       |       ^
checkRd: (-1) sandboxUrlTo.Rd:27: Lost braces; missing escapes or markup?
    27 | dict: {'filePath': <new file's absolute path in Cytoscape workstation>, 'fileByteCount': number of bytes read}
       |       ^
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/RCy3.Rcheck/00check.log’
for details.


Installation output

RCy3.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RCy3
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘RCy3’ ...
** this is package ‘RCy3’ version ‘2.29.1’
** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  0.204   0.088   0.269 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

nameusersystemelapsed
AddToGroup000
RemoveFromGroup000
UpdateAnnotationBoundedText000
addAnnotationBoundedText0.0010.0000.000
addAnnotationImage0.0000.0000.001
addAnnotationShape000
addAnnotationText000
addCyEdges000
addCyNodes000
analyzeNetwork0.0000.0010.000
applyFilter000
bundleEdges000
checkNotebookIsRunning000
checkRunningRemote000
clearEdgeBends000
clearEdgePropertyBypass0.0000.0000.001
clearNetworkCenterBypass000
clearNetworkPropertyBypass000
clearNetworkZoomBypass000
clearNodeOpacityBypass000
clearNodePropertyBypass000
clearSelection0.0010.0000.000
cloneNetwork000
closeSession0.0010.0000.000
collapseGroup000
commandEcho0.0000.0010.001
commandOpenDialog0.0000.0000.001
commandPause0.0000.0000.001
commandQuit0.0000.0000.001
commandRunFile000
commandSleep0.0000.0000.001
commandsAPI000
commandsGET000
commandsHelp000
commandsPOST000
commandsRun000
copyVisualStyle0.0000.0000.001
createColumnFilter0.0000.0000.001
createCompositeFilter0.0000.0000.001
createCytoscapejsFromNetwork0.0000.0000.001
createDegreeFilter000
createGraphFromNetwork000
createGroup000
createGroupByColumn000
createIgraphFromNetwork000
createNetworkFromCytoscapejs000
createNetworkFromDataFrames000
createNetworkFromGraph0.0000.0010.001
createNetworkFromIgraph0.0000.0000.001
createSubnetwork0.0000.0010.000
createView000
createVisualStyle0.0010.0000.001
cybrowserClose000
cybrowserDialog000
cybrowserHide000
cybrowserList000
cybrowserSend0.0000.0000.001
cybrowserShow0.0000.0000.001
cybrowserVersion0.0000.0000.001
cyrestAPI000
cyrestDELETE000
cyrestGET0.0000.0010.000
cyrestPOST000
cyrestPUT000
cytoscapeApiVersions000
cytoscapeFreeMemory000
cytoscapeMemoryStatus000
cytoscapeNumberOfCores000
cytoscapePing000
cytoscapeVersionInfo000
deleteAllNetworks000
deleteAllVisualStyle000
deleteAnnotation000
deleteDuplicateEdges000
deleteGroup000
deleteNetwork000
deleteSelectedEdges000
deleteSelectedNodes000
deleteSelfLoops000
deleteStyleMapping000
deleteTableColumn000
deleteVisualStyle0.0000.0010.000
diffusionAdvanced0.0000.0000.001
diffusionBasic000
disableApp000
doInitializeSandbox0.0010.0000.000
doRequestRemote0.0000.0010.000
doSetSandbox000
dockPanel000
dot-exportShowImage000
dot-getDefaultSandbox000
dot-getRequester0.0000.0000.001
enableApp000
expandGroup0.0000.0000.001
exportFilters000
exportImage000
exportJPG000
exportNetwork0.0010.0000.000
exportNetworkToNDEx0.0000.0000.001
exportPDF0.0010.0000.001
exportPNG000
exportPS000
exportSVG000
exportVisualStyles000
findRemoteCytoscape000
fitContent000
floatPanel000
getAbsSandboxPath000
getAllEdges000
getAllNodes0.0000.0010.000
getAllStyleMappings000
getAnnotationList0.0000.0000.001
getAppInformation000
getAppStatus000
getAppUpdates000
getArrowShapes0.0000.0000.001
getAvailableApps000
getBackgroundColorDefault0.0010.0000.000
getBrowserClientChannel000
getBrowserClientJs0.0000.0010.000
getCollectionList000
getCollectionName000
getCollectionNetworks000
getCollectionSuid0.0000.0000.001
getCurrentSandbox000
getCurrentSandboxName000
getCurrentSandboxPath000
getCurrentStyle000
getDefaultSandbox000
getDefaultSandboxPath0.0000.0000.001
getDisabledApps000
getEdgeColor000
getEdgeCount000
getEdgeInfo000
getEdgeLineStyle000
getEdgeLineWidth000
getEdgeProperty000
getEdgeSelectionColorDefault000
getEdgeTargetArrowShape000
getFilterList000
getFirstNeighbors000
getGroupInfo000
getInstalledApps000
getJupyterBridgeURL000
getLayoutNameMapping000
getLayoutNames000
getLayoutPropertyNames000
getLayoutPropertyType000
getLayoutPropertyValue000
getLineStyles000
getNetworkCenter000
getNetworkCount000
getNetworkList000
getNetworkNDExId000
getNetworkName000
getNetworkProperty000
getNetworkSuid000
getNetworkViewSuid000
getNetworkViews000
getNetworkZoom000
getNodeColor0.0000.0000.001
getNodeCount000
getNodeHeight000
getNodeLabelPosition000
getNodeLabelPositionDefault0.0010.0000.000
getNodePosition0.0000.0010.000
getNodeProperty000
getNodeSelectionColorDefault000
getNodeShapes000
getNodeSize000
getNodeWidth000
getNotebookIsRunning000
getSandboxReinitialize0.0010.0000.000
getSelectedEdgeCount000
getSelectedEdges000
getSelectedNodeCount000
getSelectedNodes000
getStyleDependencies000
getStyleMapping0.0010.0000.000
getTableColumnNames000
getTableColumnTypes0.0010.0000.000
getTableColumns000
getTableValue000
getUninstalledApps000
getVisualPropertyDefault0.0000.0000.001
getVisualPropertyNames000
getVisualStyleJSON000
getVisualStyleNames000
groupAnnotation000
hideAllPanels000
hideEdges000
hideNodes000
hidePanel0.0000.0010.000
hideSelectedEdges0.0000.0000.001
hideSelectedNodes0.0010.0000.000
importFileFromUrl000
importFilters000
importNetworkFromFile000
importNetworkFromNDEx000
importVisualStyles000
installApp000
invertEdgeSelection0.0000.0000.001
invertNodeSelection000
layoutCopycat000
layoutNetwork000
listGroups000
lockNodeDimensions000
makeSimpleGraph0.0680.0020.070
makeSimpleIgraph0.0760.0080.084
mapTableColumn000
mapVisualProperty000
matchArrowColorToEdge000
mergeNetworks0.0000.0010.000
notebookExportShowImage000
notebookShowImage0.0000.0010.000
openAppStore000
openSession0.0000.0000.001
paletteColorBrewerAccent0.0050.0000.006
paletteColorBrewerBlues000
paletteColorBrewerBrBG0.0010.0000.001
paletteColorBrewerBuGn000
paletteColorBrewerBuPu0.0010.0000.000
paletteColorBrewerDark2000
paletteColorBrewerGnBu0.0000.0000.001
paletteColorBrewerGreens0.0000.0010.000
paletteColorBrewerGreys000
paletteColorBrewerOrRd000
paletteColorBrewerOranges0.0010.0010.001
paletteColorBrewerPRGn000
paletteColorBrewerPaired000
paletteColorBrewerPastel10.0000.0010.001
paletteColorBrewerPastel2000
paletteColorBrewerPiYG000
paletteColorBrewerPuBu0.0000.0000.001
paletteColorBrewerPuBuGn000
paletteColorBrewerPuOr0.0000.0010.000
paletteColorBrewerPuRd000
paletteColorBrewerPurples0.0000.0010.000
paletteColorBrewerRdBu0.0000.0000.001
paletteColorBrewerRdPu0.0000.0010.000
paletteColorBrewerRdYlBu000
paletteColorBrewerReds0.0000.0000.001
paletteColorBrewerSet1000
paletteColorBrewerSet20.0010.0000.000
paletteColorBrewerSet3000
paletteColorBrewerYlGn0.0010.0000.001
paletteColorBrewerYlGnBu000
paletteColorBrewerYlOrBr0.0010.0000.000
paletteColorBrewerYlOrRd0.0000.0000.001
paletteColorRandom000
paletteColorVirdis000
removeNodeCustomGraphics000
renameNetwork000
renameTableColumn000
resetDefaultSandbox000
rotateLayout000
runningRemoteCheck000
sandboxGetFileInfo000
sandboxGetFrom000
sandboxInitializer000
sandboxRemove0.0010.0010.000
sandboxRemoveFile000
sandboxSendTo0.0000.0010.000
sandboxSet000
sandboxUrlTo0.0010.0000.001
saveSession000
scaleLayout0.0000.0010.000
selectAll000
selectAllEdges0.0000.0000.001
selectAllNodes0.0000.0000.001
selectEdges000
selectEdgesAdjacentToNodes000
selectEdgesAdjacentToSelectedNodes0.0000.0010.000
selectEdgesConnectingSelectedNodes000
selectFirstNeighbors000
selectNodes0.0010.0000.000
selectNodesConnectedBySelectedEdges000
setBackgroundColorDefault0.0000.0000.001
setCatchupFilterSecs000
setCatchupNetworkSecs0.0000.0010.000
setCollectionName000
setCurrentNetwork0.0000.0010.000
setCurrentSandbox000
setCurrentView000
setDefaultSandbox000
setDefaultSandboxPath000
setEdgeColorBypass0.0010.0000.000
setEdgeColorDefault000
setEdgeColorMapping0.0000.0000.001
setEdgeFontFaceBypass000
setEdgeFontFaceDefault000
setEdgeFontFaceMapping000
setEdgeFontSizeBypass000
setEdgeFontSizeDefault000
setEdgeFontSizeMapping000
setEdgeLabelBypass000
setEdgeLabelColorBypass000
setEdgeLabelColorDefault000
setEdgeLabelColorMapping000
setEdgeLabelDefault000
setEdgeLabelMapping0.0000.0010.000
setEdgeLabelOpacityBypass000
setEdgeLabelOpacityDefault000
setEdgeLabelOpacityMapping000
setEdgeLineStyleBypass0.0000.0000.001
setEdgeLineStyleDefault0.0000.0000.001
setEdgeLineStyleMapping000
setEdgeLineWidthBypass000
setEdgeLineWidthDefault000
setEdgeLineWidthMapping000
setEdgeOpacityBypass000
setEdgeOpacityDefault0.0010.0000.000
setEdgeOpacityMapping000
setEdgePropertyBypass0.0010.0010.000
setEdgeSelectionColorDefault0.0000.0000.001
setEdgeSourceArrowColorBypass0.0000.0000.001
setEdgeSourceArrowColorDefault000
setEdgeSourceArrowColorMapping000
setEdgeSourceArrowMapping000
setEdgeSourceArrowShapeBypass000
setEdgeSourceArrowShapeDefault000
setEdgeSourceArrowShapeMapping000
setEdgeTargetArrowColorBypass0.0000.0000.001
setEdgeTargetArrowColorDefault000
setEdgeTargetArrowColorMapping0.0000.0010.000
setEdgeTargetArrowMapping000
setEdgeTargetArrowShapeBypass000
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setEdgeTargetArrowShapeMapping000
setEdgeTooltipBypass000
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setEdgeTooltipMapping000
setLayoutProperties000
setModelPropagationSecs0.0000.0000.001
setNetworkCenterBypass000
setNetworkPropertyBypass000
setNetworkZoomBypass0.0000.0010.000
setNodeBorderColorBypass000
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setNodeBorderOpacityBypass000
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setNodeComboOpacityMapping0.0000.0010.000
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setNodeSizeDefault0.0000.0010.000
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setNotebookIsRunning000
setSandboxReinitialize0.0000.0000.001
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toggleGraphicsDetails0.0000.0000.001
ungroupAnnotation000
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updateStyleDefaults0.0000.0010.001
updateStyleMapping000