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This page was generated on 2025-09-30 12:05 -0400 (Tue, 30 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
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" 4575
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: 2025-09-29 13:45 -0400 (Mon, 29 Sep 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: 2025-09-29 23:40:55 -0400 (Mon, 29 Sep 2025)
EndedAt: 2025-09-29 23:42:38 -0400 (Mon, 29 Sep 2025)
EllapsedTime: 103.0 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   0.081   0.276 

Example timings

RCy3.Rcheck/RCy3-Ex.timings

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createNetworkFromIgraph0.0000.0000.001
createSubnetwork0.0000.0000.001
createView0.0000.0000.001
createVisualStyle0.0010.0000.000
cybrowserClose0.0000.0000.001
cybrowserDialog000
cybrowserHide000
cybrowserList000
cybrowserSend000
cybrowserShow000
cybrowserVersion000
cyrestAPI000
cyrestDELETE000
cyrestGET000
cyrestPOST000
cyrestPUT000
cytoscapeApiVersions0.0000.0010.000
cytoscapeFreeMemory000
cytoscapeMemoryStatus000
cytoscapeNumberOfCores000
cytoscapePing000
cytoscapeVersionInfo0.0000.0010.001
deleteAllNetworks000
deleteAllVisualStyle000
deleteAnnotation000
deleteDuplicateEdges000
deleteGroup000
deleteNetwork000
deleteSelectedEdges000
deleteSelectedNodes000
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deleteStyleMapping000
deleteTableColumn000
deleteVisualStyle000
diffusionAdvanced000
diffusionBasic0.0000.0010.000
disableApp000
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doRequestRemote0.0000.0000.001
doSetSandbox000
dockPanel000
dot-exportShowImage000
dot-getDefaultSandbox000
dot-getRequester000
enableApp0.0000.0000.001
expandGroup000
exportFilters000
exportImage000
exportJPG000
exportNetwork000
exportNetworkToNDEx000
exportPDF000
exportPNG0.0000.0000.001
exportPS0.0000.0000.001
exportSVG000
exportVisualStyles0.0000.0010.000
findRemoteCytoscape0.0000.0000.001
fitContent000
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getAnnotationList0.0000.0000.001
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getAppStatus000
getAppUpdates000
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getFilterList000
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getInstalledApps000
getJupyterBridgeURL0.0010.0000.000
getLayoutNameMapping0.0000.0000.001
getLayoutNames000
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getLayoutPropertyValue000
getLineStyles000
getNetworkCenter000
getNetworkCount0.0000.0010.001
getNetworkList000
getNetworkNDExId000
getNetworkName000
getNetworkProperty000
getNetworkSuid0.0000.0000.001
getNetworkViewSuid0.0000.0010.000
getNetworkViews000
getNetworkZoom000
getNodeColor0.0010.0000.000
getNodeCount000
getNodeHeight000
getNodeLabelPosition000
getNodeLabelPositionDefault0.0000.0000.001
getNodePosition000
getNodeProperty000
getNodeSelectionColorDefault000
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getNodeSize0.0010.0000.000
getNodeWidth000
getNotebookIsRunning000
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getSelectedEdgeCount0.0000.0000.001
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getTableValue0.0010.0000.000
getUninstalledApps000
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getVisualStyleJSON0.0010.0000.000
getVisualStyleNames0.0000.0010.000
groupAnnotation000
hideAllPanels0.0000.0010.000
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hideNodes0.0000.0000.001
hidePanel000
hideSelectedEdges0.0000.0000.001
hideSelectedNodes0.0000.0000.001
importFileFromUrl000
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importNetworkFromNDEx0.0000.0000.001
importVisualStyles0.0000.0010.000
installApp000
invertEdgeSelection000
invertNodeSelection000
layoutCopycat0.0000.0010.000
layoutNetwork000
listGroups000
lockNodeDimensions000
makeSimpleGraph0.0640.0010.066
makeSimpleIgraph0.0790.0080.087
mapTableColumn0.0000.0010.000
mapVisualProperty000
matchArrowColorToEdge000
mergeNetworks000
notebookExportShowImage000
notebookShowImage000
openAppStore000
openSession0.0000.0000.001
paletteColorBrewerAccent0.0030.0000.004
paletteColorBrewerBlues000
paletteColorBrewerBrBG0.0000.0010.001
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paletteColorBrewerDark20.0000.0000.001
paletteColorBrewerGnBu0.0010.0000.000
paletteColorBrewerGreens0.0000.0000.001
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paletteColorBrewerPRGn000
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paletteColorBrewerPastel1000
paletteColorBrewerPastel2000
paletteColorBrewerPiYG0.0000.0000.001
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paletteColorBrewerPuBuGn000
paletteColorBrewerPuOr0.0010.0000.000
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paletteColorBrewerRdBu000
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paletteColorBrewerReds000
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paletteColorVirdis0.0010.0000.001
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renameNetwork0.0000.0010.000
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