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This page was generated on 2025-10-25 12:05 -0400 (Sat, 25 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4658
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 1738/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.29.2  (landing page)
Alex Pico
Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 2025)
git_url: https://git.bioconductor.org/packages/RCy3
git_branch: devel
git_last_commit: b195f53
git_last_commit_date: 2025-10-13 20:16:19 -0400 (Mon, 13 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 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    NA    NA  


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: 2.29.2
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_2.29.2.tar.gz
StartedAt: 2025-10-24 23:38:26 -0400 (Fri, 24 Oct 2025)
EndedAt: 2025-10-24 23:40:08 -0400 (Fri, 24 Oct 2025)
EllapsedTime: 101.8 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_2.29.2.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 ‘2.29.2’
* 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 ‘2.29.2’
** 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 
  0.200   0.073   0.271 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

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analyzeNetwork000
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cloneNetwork000
closeSession000
collapseGroup000
commandEcho0.0000.0010.000
commandOpenDialog000
commandPause000
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commandRunFile0.0000.0000.001
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commandsHelp000
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createDegreeFilter0.0000.0010.000
createGraphFromNetwork0.0000.0000.001
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createGroupByColumn0.0000.0000.001
createIgraphFromNetwork000
createNetworkFromCytoscapejs000
createNetworkFromDataFrames000
createNetworkFromGraph0.0010.0000.000
createNetworkFromIgraph000
createSubnetwork0.0000.0000.001
createView000
createVisualStyle000
cybrowserClose0.0000.0010.000
cybrowserDialog000
cybrowserHide000
cybrowserList000
cybrowserSend000
cybrowserShow000
cybrowserVersion000
cyrestAPI0.0000.0000.001
cyrestDELETE0.0000.0000.001
cyrestGET0.0000.0010.000
cyrestPOST0.0000.0000.001
cyrestPUT0.0000.0000.001
cytoscapeApiVersions0.0010.0000.001
cytoscapeFreeMemory000
cytoscapeMemoryStatus000
cytoscapeNumberOfCores000
cytoscapePing000
cytoscapeVersionInfo000
deleteAllNetworks000
deleteAllVisualStyle000
deleteAnnotation000
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deleteGroup000
deleteNetwork000
deleteSelectedEdges0.0010.0000.000
deleteSelectedNodes000
deleteSelfLoops0.0010.0000.000
deleteStyleMapping000
deleteTableColumn0.0000.0000.001
deleteVisualStyle0.0000.0010.001
diffusionAdvanced000
diffusionBasic0.0000.0010.000
disableApp000
doInitializeSandbox000
doRequestRemote0.0000.0010.001
doSetSandbox000
dockPanel0.0010.0000.000
dot-exportShowImage000
dot-getDefaultSandbox000
dot-getRequester000
enableApp000
expandGroup000
exportFilters0.0000.0000.001
exportImage000
exportJPG0.0010.0000.000
exportNetwork000
exportNetworkToNDEx0.0010.0000.000
exportPDF0.0000.0010.000
exportPNG0.0010.0000.000
exportPS000
exportSVG000
exportVisualStyles000
findRemoteCytoscape000
fitContent000
floatPanel000
getAbsSandboxPath000
getAllEdges000
getAllNodes000
getAllStyleMappings000
getAnnotationList000
getAppInformation000
getAppStatus000
getAppUpdates000
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getAvailableApps000
getBackgroundColorDefault000
getBrowserClientChannel000
getBrowserClientJs000
getCollectionList000
getCollectionName0.0000.0000.001
getCollectionNetworks000
getCollectionSuid0.0010.0000.000
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getCurrentSandboxName000
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getCurrentStyle000
getDefaultSandbox0.0000.0000.001
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getDisabledApps0.0000.0000.001
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getEdgeLineStyle000
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getEdgeProperty000
getEdgeSelectionColorDefault000
getEdgeTargetArrowShape000
getFilterList000
getFirstNeighbors000
getGroupInfo0.0010.0010.000
getInstalledApps000
getJupyterBridgeURL000
getLayoutNameMapping000
getLayoutNames000
getLayoutPropertyNames000
getLayoutPropertyType0.0010.0010.000
getLayoutPropertyValue000
getLineStyles0.0000.0000.001
getNetworkCenter000
getNetworkCount000
getNetworkList000
getNetworkNDExId000
getNetworkName000
getNetworkProperty000
getNetworkSuid000
getNetworkViewSuid0.0000.0000.001
getNetworkViews000
getNetworkZoom000
getNodeColor000
getNodeCount0.0000.0000.001
getNodeHeight000
getNodeLabelPosition000
getNodeLabelPositionDefault000
getNodePosition000
getNodeProperty000
getNodeSelectionColorDefault000
getNodeShapes000
getNodeSize000
getNodeWidth000
getNotebookIsRunning000
getSandboxReinitialize000
getSelectedEdgeCount0.0010.0000.000
getSelectedEdges000
getSelectedNodeCount0.0010.0000.000
getSelectedNodes000
getStyleDependencies000
getStyleMapping000
getTableColumnNames000
getTableColumnTypes000
getTableColumns000
getTableValue000
getUninstalledApps000
getVisualPropertyDefault000
getVisualPropertyNames000
getVisualStyleJSON000
getVisualStyleNames000
groupAnnotation000
hideAllPanels000
hideEdges000
hideNodes000
hidePanel000
hideSelectedEdges000
hideSelectedNodes000
importFileFromUrl000
importFilters000
importNetworkFromFile000
importNetworkFromNDEx000
importVisualStyles0.0000.0000.001
installApp0.0000.0010.000
invertEdgeSelection0.0000.0000.001
invertNodeSelection0.0000.0000.001
layoutCopycat0.0000.0000.001
layoutNetwork000
listGroups000
lockNodeDimensions0.0000.0010.000
makeSimpleGraph0.0630.0010.063
makeSimpleIgraph0.0760.0070.084
mapTableColumn000
mapVisualProperty0.0000.0000.001
matchArrowColorToEdge0.0000.0000.001
mergeNetworks0.0000.0000.001
notebookExportShowImage000
notebookShowImage000
openAppStore0.0000.0010.000
openSession000
paletteColorBrewerAccent0.0030.0010.003
paletteColorBrewerBlues000
paletteColorBrewerBrBG0.0000.0010.000
paletteColorBrewerBuGn000
paletteColorBrewerBuPu000
paletteColorBrewerDark2000
paletteColorBrewerGnBu000
paletteColorBrewerGreens000
paletteColorBrewerGreys0.0010.0000.000
paletteColorBrewerOrRd000
paletteColorBrewerOranges0.0010.0000.000
paletteColorBrewerPRGn000
paletteColorBrewerPaired0.0000.0000.001
paletteColorBrewerPastel10.0000.0000.001
paletteColorBrewerPastel20.0000.0000.001
paletteColorBrewerPiYG000
paletteColorBrewerPuBu000
paletteColorBrewerPuBuGn000
paletteColorBrewerPuOr0.0000.0010.001
paletteColorBrewerPuRd0.0000.0000.001
paletteColorBrewerPurples000
paletteColorBrewerRdBu000
paletteColorBrewerRdPu0.0000.0000.001
paletteColorBrewerRdYlBu0.0000.0000.001
paletteColorBrewerReds0.0000.0010.000
paletteColorBrewerSet10.0010.0000.000
paletteColorBrewerSet20.0000.0000.001
paletteColorBrewerSet30.0000.0000.001
paletteColorBrewerYlGn0.0000.0000.001
paletteColorBrewerYlGnBu000
paletteColorBrewerYlOrBr000
paletteColorBrewerYlOrRd0.0000.0000.001
paletteColorRandom0.0010.0010.001
paletteColorVirdis000
removeNodeCustomGraphics0.0010.0000.001
renameNetwork000
renameTableColumn000
resetDefaultSandbox0.0000.0010.000
rotateLayout0.0000.0000.001
runningRemoteCheck000
sandboxGetFileInfo000
sandboxGetFrom000
sandboxInitializer000
sandboxRemove000
sandboxRemoveFile000
sandboxSendTo0.0010.0000.001
sandboxSet000
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selectNodesConnectedBySelectedEdges0.0000.0000.001
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setEdgeSourceArrowColorDefault0.0000.0010.000
setEdgeSourceArrowColorMapping000
setEdgeSourceArrowMapping000
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setEdgeSourceArrowShapeMapping0.0000.0000.001
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