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This page was generated on 2025-09-29 12:06 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4833
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4621
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4566
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 1716/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCX 1.13.1  (landing page)
Florian Auer
Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 Sep 2025)
git_url: https://git.bioconductor.org/packages/RCX
git_branch: devel
git_last_commit: 996b128
git_last_commit_date: 2025-09-06 08:48:09 -0400 (Sat, 06 Sep 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 RCX on kjohnson3

To the developers/maintainers of the RCX package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCX.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: RCX
Version: 1.13.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCX_1.13.1.tar.gz
StartedAt: 2025-09-28 21:10:38 -0400 (Sun, 28 Sep 2025)
EndedAt: 2025-09-28 21:10:58 -0400 (Sun, 28 Sep 2025)
EllapsedTime: 20.3 seconds
RetCode: 0
Status:   OK  
CheckDir: RCX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCX_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/RCX.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCX’ version ‘1.13.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RCX’ 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'Igraph.Rd':
  ‘[igraph:aaa-igraph-package]{igraph}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  jsonToRCX.Rd: jsonlite
  readCX.Rd: jsonlite
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'dot-format.Rd':
  ‘.log’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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/RCX.Rcheck/00check.log’
for details.


Installation output

RCX.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘RCX’ ...
** this is package ‘RCX’ version ‘1.13.1’
** 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 (RCX)

Tests output

RCX.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.

> library(testthat)
> library(RCX)
> 
> test_check("RCX")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 60 ]
> 
> proc.time()
   user  system elapsed 
  0.818   0.047   0.865 

Example timings

RCX.Rcheck/RCX-Ex.timings

nameusersystemelapsed
CartesianLayout0.0020.0010.002
Convert-Names-and-Classes000
CyGroups0.0010.0010.002
CyHiddenAttributes0.0390.0020.041
CyNetworkRelations0.0010.0000.000
CySubNetworks0.0020.0000.002
CyTableColumn0.0010.0000.001
CyVisualProperties0.0040.0010.004
CyVisualProperty0.0030.0000.004
CyVisualPropertyDependencies0.0010.0000.001
CyVisualPropertyMappings0.0010.0000.002
CyVisualPropertyProperties0.0010.0000.001
EdgeAttributes0.0050.0010.006
Edges0.0010.0000.000
Igraph0.7950.0120.807
Meta-data0.0070.0000.008
NetworkAttributes0.0030.0000.003
NodeAttributes0.0040.0010.005
Nodes0.0000.0000.001
RCX-object0.0620.0010.062
aspectClasses0.0000.0010.001
checks000
convert-data-types-and-values0.0000.0000.001
convert2json000
countElements0.0040.0000.004
custom-print0.0010.0000.002
dot-addAspectNameToJson000
dot-addAttributeData000
dot-aspectClass000
dot-convertRawList000
dot-createAttributeAspect000
dot-createCyVpPorD0.0000.0000.001
dot-filterBy000
dot-format000
dot-infer000
dot-json2RDataType000
dot-jsonL000
dot-jsonV0.0000.0000.001
dot-log0.0010.0000.000
dot-mergeAttributesAspect000
dot-mergeIdAspect0.0000.0010.000
dot-modClass0.0000.0000.001
dot-pasteC000
dot-renameDF0.0010.0000.000
dot-stop000
dot-summaryAspect000
dot-transformListLength-set0.0010.0000.001
dot-transformVLD0.0010.0010.001
getCyVisualProperty0.0020.0000.003
graphNEL0.8670.0090.876
hasIds000
idProperty0.0010.0000.000
jsonToRCX0.0000.0010.001
markAttributeColumn000
markRefColumn0.0000.0000.001
maxId0.0010.0000.000
rcxToJson000
readCX0.2240.0010.226
referredBy0.0020.0000.003
refersTo000
setExtension000
summary0.0030.0000.003
toCX0.0030.0000.003
updateCartesianLayout0.0130.0010.014
updateCyGroups0.0100.0010.011
updateCyHiddenAttributes0.0120.0000.013
updateCyNetworkRelations0.0110.0010.012
updateCySubNetworks0.0070.0000.008
updateCyTableColumn0.0140.0000.014
updateCyVisualProperties0.0670.0020.074
updateCyVisualProperty0.0170.0010.018
updateEdgeAttributes0.0140.0000.014
updateEdges0.0060.0000.006
updateMetaDataProperties0.0050.0010.006
updateNetworkAttributes0.0130.0000.013
updateNodeAttributes0.0170.0010.018
updateNodes0.0050.0000.004
validate0.0870.0020.089
visualize0.0030.0000.002
writeCX000
writeHTML0.0230.0100.035