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This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 1703/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCX 1.13.0  (landing page)
Florian Auer
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/RCX
git_branch: devel
git_last_commit: 76430ca
git_last_commit_date: 2025-04-15 12:44:41 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2025-08-08 21:07:15 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 21:07:38 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 23.4 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/RCX.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCX’ version ‘1.13.0’
* 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 ‘1.13.0’
** 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 (2025-06-14 r88325) -- "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 
  0.837   0.050   0.926 

Example timings

RCX.Rcheck/RCX-Ex.timings

nameusersystemelapsed
CartesianLayout0.0020.0010.005
Convert-Names-and-Classes0.0000.0010.007
CyGroups0.0020.0000.002
CyHiddenAttributes0.0410.0020.048
CyNetworkRelations0.0000.0000.001
CySubNetworks0.0020.0000.004
CyTableColumn0.0010.0010.002
CyVisualProperties0.0050.0010.005
CyVisualProperty0.0030.0010.005
CyVisualPropertyDependencies0.0010.0000.002
CyVisualPropertyMappings0.0010.0000.005
CyVisualPropertyProperties0.0010.0000.002
EdgeAttributes0.0050.0010.006
Edges0.0010.0000.001
Igraph0.8370.0130.871
Meta-data0.0080.0010.010
NetworkAttributes0.0030.0010.005
NodeAttributes0.0050.0010.011
Nodes0.0000.0000.001
RCX-object0.0680.0020.085
aspectClasses000
checks000
convert-data-types-and-values0.0000.0000.001
convert2json000
countElements0.0040.0000.006
custom-print0.0020.0000.002
dot-addAspectNameToJson000
dot-addAttributeData000
dot-aspectClass000
dot-convertRawList0.0010.0000.000
dot-createAttributeAspect000
dot-createCyVpPorD000
dot-filterBy0.0000.0000.001
dot-format000
dot-infer0.0000.0010.001
dot-json2RDataType0.0010.0000.000
dot-jsonL000
dot-jsonV0.0000.0000.001
dot-log000
dot-mergeAttributesAspect000
dot-mergeIdAspect000
dot-modClass000
dot-pasteC000
dot-renameDF0.0000.0000.001
dot-stop000
dot-summaryAspect000
dot-transformListLength-set0.0010.0010.001
dot-transformVLD0.0010.0000.001
getCyVisualProperty0.0030.0010.005
graphNEL0.8990.0100.937
hasIds0.0010.0000.001
idProperty000
jsonToRCX0.0010.0000.001
markAttributeColumn0.0000.0000.001
markRefColumn0.0010.0000.001
maxId000
rcxToJson0.0010.0000.000
readCX0.2270.0020.231
referredBy0.0020.0000.004
refersTo0.0010.0000.001
setExtension000
summary0.0030.0000.006
toCX0.0030.0000.005
updateCartesianLayout0.0130.0010.021
updateCyGroups0.0100.0010.012
updateCyHiddenAttributes0.0130.0000.015
updateCyNetworkRelations0.0110.0010.017
updateCySubNetworks0.0070.0000.009
updateCyTableColumn0.0150.0010.018
updateCyVisualProperties0.0690.0050.091
updateCyVisualProperty0.0180.0020.026
updateEdgeAttributes0.0150.0000.016
updateEdges0.0060.0000.007
updateMetaDataProperties0.0060.0010.008
updateNetworkAttributes0.0140.0010.020
updateNodeAttributes0.0190.0010.030
updateNodes0.0050.0000.006
validate0.0860.0030.091
visualize0.0020.0000.002
writeCX0.0000.0000.001
writeHTML0.0240.0240.063