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This page was generated on 2025-08-21 11:40 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1721/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCX 1.12.0  (landing page)
Florian Auer
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/RCX
git_branch: RELEASE_3_21
git_last_commit: 546c3df
git_last_commit_date: 2025-04-15 12:44:41 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for RCX on merida1

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: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2025-08-19 09:46:14 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 09:48:11 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 117.6 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RCX.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 ‘RCX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCX’ version ‘1.12.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
graphNEL 7.319  0.054   8.047
Igraph   6.876  0.091   7.674
* 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-3.21-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-x86_64/Resources/library’
* installing *source* package ‘RCX’ ...
** this is package ‘RCX’ version ‘1.12.0’
** 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 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.

> library(testthat)
> library(RCX)
> 
> test_check("RCX")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 60 ]
> 
> proc.time()
   user  system elapsed 
  6.184   0.275   7.015 

Example timings

RCX.Rcheck/RCX-Ex.timings

nameusersystemelapsed
CartesianLayout0.0090.0030.014
Convert-Names-and-Classes0.0010.0020.003
CyGroups0.0090.0010.013
CyHiddenAttributes0.2540.0120.286
CyNetworkRelations0.0030.0010.003
CySubNetworks0.0100.0010.012
CyTableColumn0.0120.0010.015
CyVisualProperties0.0330.0040.040
CyVisualProperty0.0250.0040.031
CyVisualPropertyDependencies0.0080.0020.009
CyVisualPropertyMappings0.0090.0020.012
CyVisualPropertyProperties0.0070.0020.008
EdgeAttributes0.0370.0030.041
Edges0.0040.0000.003
Igraph6.8760.0917.674
Meta-data0.0650.0040.077
NetworkAttributes0.0240.0030.029
NodeAttributes0.0350.0040.042
Nodes0.0040.0010.006
RCX-object0.5970.0100.674
aspectClasses0.0020.0030.005
checks0.0000.0000.001
convert-data-types-and-values0.0030.0010.014
convert2json000
countElements0.0280.0010.033
custom-print0.0130.0010.018
dot-addAspectNameToJson0.0010.0000.001
dot-addAttributeData0.0000.0000.001
dot-aspectClass0.0000.0010.002
dot-convertRawList0.0010.0000.001
dot-createAttributeAspect0.0000.0000.001
dot-createCyVpPorD0.0000.0000.001
dot-filterBy0.0010.0010.001
dot-format0.0000.0010.002
dot-infer0.0000.0010.001
dot-json2RDataType0.0010.0010.001
dot-jsonL0.0000.0010.001
dot-jsonV0.0020.0010.003
dot-log0.0000.0010.001
dot-mergeAttributesAspect0.0000.0010.001
dot-mergeIdAspect0.0000.0010.001
dot-modClass0.0000.0010.001
dot-pasteC0.0010.0000.001
dot-renameDF0.0040.0010.005
dot-stop0.0000.0000.001
dot-summaryAspect0.0030.0010.005
dot-transformListLength-set0.0040.0000.005
dot-transformVLD0.0080.0020.012
getCyVisualProperty0.0210.0030.030
graphNEL7.3190.0548.047
hasIds0.0010.0010.003
idProperty0.0020.0010.002
jsonToRCX0.0050.0010.006
markAttributeColumn0.0030.0010.005
markRefColumn0.0030.0010.003
maxId0.0010.0010.003
rcxToJson0.0040.0000.004
readCX1.6010.0081.748
referredBy0.0200.0000.024
refersTo0.0020.0010.002
setExtension0.0000.0010.001
summary0.0280.0030.034
toCX0.0260.0020.032
updateCartesianLayout0.1110.0080.131
updateCyGroups0.0780.0080.093
updateCyHiddenAttributes0.1140.0030.128
updateCyNetworkRelations0.0940.0040.106
updateCySubNetworks0.0680.0030.075
updateCyTableColumn0.1190.0030.134
updateCyVisualProperties0.5770.0230.648
updateCyVisualProperty0.1510.0070.167
updateEdgeAttributes0.1140.0040.130
updateEdges0.0480.0020.055
updateMetaDataProperties0.0500.0050.058
updateNetworkAttributes0.1130.0040.128
updateNodeAttributes0.1440.0030.160
updateNodes0.0350.0010.038
validate0.7480.0170.836
visualize0.0210.0000.023
writeCX0.0000.0010.001
writeHTML0.1270.1210.279