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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 1722/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCy3 2.28.1  (landing page)
Alex Pico
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/RCy3
git_branch: RELEASE_3_21
git_last_commit: 2dbd87a
git_last_commit_date: 2025-05-28 03:01:28 -0400 (Wed, 28 May 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for RCy3 on merida1

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: 2.28.1
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_2.28.1.tar.gz
StartedAt: 2025-10-14 08:54:28 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 08:57:38 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 189.6 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_2.28.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RCy3.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘2.28.1’
* 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-3.21-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 ‘2.28.1’
** 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 RC (2025-06-05 r88288) -- "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 
  0.342   0.114   0.440 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

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clearNetworkCenterBypass0.0010.0000.000
clearNetworkPropertyBypass0.0000.0000.001
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clearNodeOpacityBypass0.0000.0010.009
clearNodePropertyBypass0.0000.0000.001
clearSelection0.0000.0010.001
cloneNetwork0.0000.0010.003
closeSession0.0000.0000.002
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commandQuit0.0000.0010.001
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copyVisualStyle0.0010.0000.001
createColumnFilter000
createCompositeFilter0.0000.0010.001
createCytoscapejsFromNetwork0.0000.0010.001
createDegreeFilter0.0000.0000.002
createGraphFromNetwork0.0010.0010.000
createGroup000
createGroupByColumn0.0000.0010.000
createIgraphFromNetwork0.0000.0000.001
createNetworkFromCytoscapejs0.0010.0000.000
createNetworkFromDataFrames0.0000.0010.001
createNetworkFromGraph0.0000.0000.001
createNetworkFromIgraph0.0000.0000.001
createSubnetwork0.0000.0000.001
createView0.0000.0000.001
createVisualStyle0.0010.0000.001
cybrowserClose000
cybrowserDialog0.0000.0010.000
cybrowserHide000
cybrowserList0.0000.0010.001
cybrowserSend0.0000.0000.001
cybrowserShow0.0010.0010.001
cybrowserVersion0.0010.0000.001
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cyrestGET0.0000.0010.001
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cyrestPUT0.0000.0010.001
cytoscapeApiVersions0.0000.0010.000
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cytoscapeMemoryStatus0.0000.0010.001
cytoscapeNumberOfCores0.0000.0010.001
cytoscapePing000
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deleteAllNetworks0.0000.0010.001
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deleteGroup0.0000.0000.001
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deleteSelfLoops0.0000.0010.000
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deleteTableColumn000
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diffusionAdvanced0.0000.0000.001
diffusionBasic0.0000.0010.001
disableApp0.0010.0000.001
doInitializeSandbox0.0000.0010.000
doRequestRemote0.0000.0010.001
doSetSandbox000
dockPanel0.0000.0010.000
dot-exportShowImage0.0000.0000.001
dot-getDefaultSandbox0.0000.0010.001
dot-getRequester0.0010.0000.001
enableApp0.0010.0000.000
expandGroup0.0000.0000.001
exportFilters0.0000.0010.001
exportImage0.0000.0010.000
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exportPDF0.0000.0000.001
exportPNG0.0000.0000.001
exportPS0.0000.0000.001
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exportVisualStyles0.0000.0010.001
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fitContent0.0000.0010.001
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getAnnotationList0.0010.0000.001
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getAppStatus0.0010.0000.001
getAppUpdates0.0010.0010.001
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getAvailableApps0.0000.0010.001
getBackgroundColorDefault0.0000.0000.001
getBrowserClientChannel0.0000.0010.001
getBrowserClientJs000
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getCollectionSuid0.0000.0010.001
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getEdgeInfo0.0010.0000.002
getEdgeLineStyle0.0000.0010.005
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getEdgeProperty0.0000.0010.003
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getNetworkCount000
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getNetworkSuid000
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getNetworkViews000
getNetworkZoom000
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getNodeSelectionColorDefault0.0010.0010.002
getNodeShapes0.0000.0000.001
getNodeSize0.0000.0000.001
getNodeWidth0.0000.0010.001
getNotebookIsRunning000
getSandboxReinitialize0.0000.0010.000
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getSelectedEdges000
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getSelectedNodes0.0000.0000.002
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getStyleMapping0.0000.0000.004
getTableColumnNames0.0010.0000.000
getTableColumnTypes0.0000.0010.004
getTableColumns0.0000.0000.001
getTableValue0.0000.0000.001
getUninstalledApps0.0000.0010.002
getVisualPropertyDefault0.0010.0000.004
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getVisualStyleJSON0.0000.0010.000
getVisualStyleNames0.0000.0000.001
groupAnnotation000
hideAllPanels0.0000.0000.001
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hidePanel0.0000.0010.000
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hideSelectedNodes000
importFileFromUrl0.0000.0010.003
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installApp0.0000.0010.001
invertEdgeSelection0.0000.0000.001
invertNodeSelection0.0010.0000.001
layoutCopycat0.0000.0000.001
layoutNetwork0.0000.0010.001
listGroups0.0000.0010.000
lockNodeDimensions0.0000.0010.001
makeSimpleGraph0.1370.0030.154
makeSimpleIgraph0.1510.0150.190
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mergeNetworks0.0000.0000.001
notebookExportShowImage0.0000.0010.000
notebookShowImage0.0010.0000.001
openAppStore0.0000.0000.001
openSession0.0000.0000.001
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paletteColorBrewerBrBG0.0010.0010.001
paletteColorBrewerBuGn0.0000.0010.001
paletteColorBrewerBuPu0.0010.0010.001
paletteColorBrewerDark20.0000.0000.001
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updateNetworkInNDEx000
updateStyleDefaults0.0000.0010.001
updateStyleMapping000