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This page was generated on 2025-08-12 12:10 -0400 (Tue, 12 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
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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: 2025-08-11 13:45 -0400 (Mon, 11 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for RCX on lconway

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: 2025-08-11 23:34:09 -0400 (Mon, 11 Aug 2025)
EndedAt: 2025-08-11 23:35:16 -0400 (Mon, 11 Aug 2025)
EllapsedTime: 67.2 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 (2025-06-13)
* 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 ‘1.13.0’
* 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-x86_64/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 (2025-06-13) -- "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 
  3.040   0.185   3.288 

Example timings

RCX.Rcheck/RCX-Ex.timings

nameusersystemelapsed
CartesianLayout0.0040.0020.006
Convert-Names-and-Classes0.0000.0010.002
CyGroups0.0060.0010.005
CyHiddenAttributes0.1420.0090.154
CyNetworkRelations0.0010.0000.002
CySubNetworks0.0070.0000.007
CyTableColumn0.0070.0000.007
CyVisualProperties0.0190.0020.022
CyVisualProperty0.0150.0010.017
CyVisualPropertyDependencies0.0040.0010.005
CyVisualPropertyMappings0.0050.0010.006
CyVisualPropertyProperties0.0040.0000.005
EdgeAttributes0.0200.0010.021
Edges0.0020.0000.002
Igraph2.8320.0572.910
Meta-data0.0300.0020.032
NetworkAttributes0.0130.0010.015
NodeAttributes0.0160.0010.018
Nodes0.0020.0000.002
RCX-object0.2630.0040.269
aspectClasses0.0010.0010.002
checks0.0010.0000.000
convert-data-types-and-values0.0010.0010.002
convert2json0.0000.0000.001
countElements0.0130.0000.013
custom-print0.0050.0000.006
dot-addAspectNameToJson0.0000.0000.001
dot-addAttributeData0.0010.0000.000
dot-aspectClass0.0000.0000.001
dot-convertRawList0.0000.0010.001
dot-createAttributeAspect000
dot-createCyVpPorD000
dot-filterBy0.0000.0010.001
dot-format000
dot-infer0.0000.0000.001
dot-json2RDataType0.0000.0010.001
dot-jsonL0.0000.0000.001
dot-jsonV0.0010.0000.001
dot-log0.0000.0010.000
dot-mergeAttributesAspect000
dot-mergeIdAspect000
dot-modClass0.0000.0000.001
dot-pasteC000
dot-renameDF0.0010.0010.003
dot-stop0.0000.0000.001
dot-summaryAspect0.0020.0000.002
dot-transformListLength-set0.0030.0010.003
dot-transformVLD0.0050.0010.005
getCyVisualProperty0.0110.0010.012
graphNEL3.0450.0403.109
hasIds0.0010.0000.001
idProperty0.0010.0000.001
jsonToRCX0.0030.0000.003
markAttributeColumn0.0010.0010.002
markRefColumn0.0010.0000.001
maxId0.0010.0000.001
rcxToJson0.0020.0010.002
readCX0.7990.0070.812
referredBy0.0110.0010.011
refersTo0.0010.0010.001
setExtension0.0000.0000.001
summary0.0140.0010.015
toCX0.0100.0010.011
updateCartesianLayout0.0500.0050.055
updateCyGroups0.0380.0030.042
updateCyHiddenAttributes0.0530.0010.055
updateCyNetworkRelations0.0440.0010.046
updateCySubNetworks0.0320.0010.035
updateCyTableColumn0.0590.0020.061
updateCyVisualProperties0.2950.0110.307
updateCyVisualProperty0.0860.0040.092
updateEdgeAttributes0.0670.0010.069
updateEdges0.0260.0010.027
updateMetaDataProperties0.0220.0020.024
updateNetworkAttributes0.0550.0020.058
updateNodeAttributes0.0780.0010.081
updateNodes0.020.000.02
validate0.3350.0070.344
visualize0.0090.0000.009
writeCX0.0000.0010.000
writeHTML0.0790.0670.151