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This page was generated on 2024-12-02 12:04 -0500 (Mon, 02 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4739
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4482
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4510
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4462
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 1690/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCX 1.10.0  (landing page)
Florian Auer
Snapshot Date: 2024-11-28 13:00 -0500 (Thu, 28 Nov 2024)
git_url: https://git.bioconductor.org/packages/RCX
git_branch: RELEASE_3_20
git_last_commit: df064cb
git_last_commit_date: 2024-10-29 11:07:45 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
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


CHECK results for RCX on nebbiolo2

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: 1.10.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RCX.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RCX_1.10.0.tar.gz
StartedAt: 2024-11-29 05:13:21 -0500 (Fri, 29 Nov 2024)
EndedAt: 2024-11-29 05:17:56 -0500 (Fri, 29 Nov 2024)
EllapsedTime: 275.3 seconds
RetCode: 0
Status:   OK  
CheckDir: RCX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RCX.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RCX_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RCX.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RCX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCX’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 loading without being on the library search path ... 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 ... OK
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/RCX.Rcheck/00check.log’
for details.


Installation output

RCX.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL RCX
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘RCX’ ...
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  2.105   0.090   2.183 

Example timings

RCX.Rcheck/RCX-Ex.timings

nameusersystemelapsed
CartesianLayout0.0020.0020.004
Convert-Names-and-Classes0.0010.0010.000
CyGroups0.0030.0000.004
CyHiddenAttributes0.0980.0000.099
CyNetworkRelations0.0010.0000.001
CySubNetworks0.0020.0000.002
CyTableColumn0.0040.0000.004
CyVisualProperties0.0130.0000.012
CyVisualProperty0.0080.0000.008
CyVisualPropertyDependencies0.0020.0000.002
CyVisualPropertyMappings0.0050.0000.006
CyVisualPropertyProperties0.0030.0000.003
EdgeAttributes0.0120.0000.012
Edges0.0020.0000.001
Igraph2.0820.0412.124
Meta-data0.0210.0000.021
NetworkAttributes0.0120.0000.011
NodeAttributes0.0120.0000.011
Nodes0.0010.0000.002
RCX-object0.1890.0000.190
aspectClasses000
checks000
convert-data-types-and-values0.0010.0000.001
convert2json000
countElements0.0060.0000.007
custom-print0.0040.0010.004
dot-addAspectNameToJson000
dot-addAttributeData000
dot-aspectClass0.0000.0000.001
dot-convertRawList0.0010.0000.000
dot-createAttributeAspect000
dot-createCyVpPorD000
dot-filterBy000
dot-format000
dot-infer000
dot-json2RDataType000
dot-jsonL000
dot-jsonV0.0010.0000.000
dot-log000
dot-mergeAttributesAspect000
dot-mergeIdAspect000
dot-modClass000
dot-pasteC000
dot-renameDF0.0010.0000.001
dot-stop000
dot-summaryAspect0.0010.0000.001
dot-transformListLength-set0.0020.0000.001
dot-transformVLD0.0040.0000.003
getCyVisualProperty0.0080.0000.007
graphNEL2.2450.0062.250
hasIds0.0010.0000.001
idProperty0.0010.0000.001
jsonToRCX0.0010.0010.002
markAttributeColumn0.0010.0000.001
markRefColumn0.0010.0000.001
maxId0.0000.0000.001
rcxToJson0.0010.0000.002
readCX0.5170.0030.521
referredBy0.0060.0000.007
refersTo0.0000.0000.001
setExtension000
summary0.0090.0000.009
toCX0.0090.0000.008
updateCartesianLayout0.0340.0010.034
updateCyGroups0.0250.0020.027
updateCyHiddenAttributes0.0410.0030.044
updateCyNetworkRelations0.0290.0000.030
updateCySubNetworks0.0210.0000.022
updateCyTableColumn0.0350.0010.037
updateCyVisualProperties0.1950.0020.198
updateCyVisualProperty0.050.000.05
updateEdgeAttributes0.0450.0120.058
updateEdges0.0150.0030.019
updateMetaDataProperties0.0160.0020.018
updateNetworkAttributes0.0380.0030.041
updateNodeAttributes0.0530.0010.053
updateNodes0.0120.0000.012
validate0.2160.0040.219
visualize0.0070.0000.006
writeCX000
writeHTML0.0430.0140.063