Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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: 2024-11-19 13:40 -0500 (Tue, 19 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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2024-11-20 01:41:43 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 01:46:18 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 275.5 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RCX.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.10.0’
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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 
  1.947   0.130   2.541 

Example timings

RCX.Rcheck/RCX-Ex.timings

nameusersystemelapsed
CartesianLayout0.0040.0010.004
Convert-Names-and-Classes0.0000.0000.001
CyGroups0.0030.0000.004
CyHiddenAttributes0.0880.0040.094
CyNetworkRelations0.0030.0000.004
CySubNetworks0.0020.0000.002
CyTableColumn0.0040.0000.005
CyVisualProperties0.0110.0010.012
CyVisualProperty0.0080.0010.009
CyVisualPropertyDependencies0.0030.0000.003
CyVisualPropertyMappings0.0040.0000.004
CyVisualPropertyProperties0.0050.0000.005
EdgeAttributes0.0110.0010.012
Edges0.0010.0000.002
Igraph1.7970.0341.938
Meta-data0.0190.0020.021
NetworkAttributes0.0080.0010.010
NodeAttributes0.0120.0020.013
Nodes0.0010.0010.002
RCX-object0.1720.0020.174
aspectClasses0.0000.0010.001
checks000
convert-data-types-and-values0.0010.0000.002
convert2json0.0000.0010.001
countElements0.0070.0000.007
custom-print0.0040.0000.004
dot-addAspectNameToJson0.0010.0010.000
dot-addAttributeData000
dot-aspectClass0.0000.0010.000
dot-convertRawList0.0010.0000.001
dot-createAttributeAspect000
dot-createCyVpPorD0.0000.0000.001
dot-filterBy0.0000.0000.001
dot-format0.0000.0010.001
dot-infer000
dot-json2RDataType000
dot-jsonL000
dot-jsonV0.0010.0000.001
dot-log0.0010.0010.000
dot-mergeAttributesAspect0.0000.0000.001
dot-mergeIdAspect000
dot-modClass0.0000.0000.001
dot-pasteC000
dot-renameDF0.0020.0000.002
dot-stop000
dot-summaryAspect0.0010.0010.002
dot-transformListLength-set0.0020.0000.002
dot-transformVLD0.0030.0000.003
getCyVisualProperty0.0090.0010.010
graphNEL1.9270.0221.950
hasIds0.0010.0000.000
idProperty0.0010.0000.001
jsonToRCX0.0020.0000.001
markAttributeColumn0.0010.0010.001
markRefColumn0.0010.0000.001
maxId0.0010.0000.001
rcxToJson0.0020.0000.002
readCX0.4480.0010.449
referredBy0.0060.0000.007
refersTo0.0010.0010.000
setExtension000
summary0.0090.0010.009
toCX0.0070.0010.007
updateCartesianLayout0.0300.0010.031
updateCyGroups0.0210.0030.024
updateCyHiddenAttributes0.0390.0040.043
updateCyNetworkRelations0.0270.0010.027
updateCySubNetworks0.0200.0010.020
updateCyTableColumn0.0340.0010.035
updateCyVisualProperties0.1760.0060.182
updateCyVisualProperty0.0450.0020.047
updateEdgeAttributes0.0380.0010.040
updateEdges0.0190.0000.019
updateMetaDataProperties0.0140.0020.015
updateNetworkAttributes0.0350.0010.036
updateNodeAttributes0.0430.0010.044
updateNodes0.0130.0000.014
validate0.1940.0040.198
visualize0.0060.0000.007
writeCX0.0000.0000.001
writeHTML0.0530.0480.219