Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-28 11:41:11 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1683/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCX 1.7.0  (landing page)
Florian Auer
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/RCX
git_branch: devel
git_last_commit: ff4762f
git_last_commit_date: 2023-10-24 11:39:07 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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 kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: RCX
Version: 1.7.0
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:RCX.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings RCX_1.7.0.tar.gz
StartedAt: 2024-03-28 08:45:29 -0000 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 08:46:23 -0000 (Thu, 28 Mar 2024)
EllapsedTime: 54.1 seconds
RetCode: 0
Status:   OK  
CheckDir: RCX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:RCX.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings RCX_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RCX.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCX’ version ‘1.7.0’
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/RCX.Rcheck/00check.log’
for details.


Installation output

RCX.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL RCX
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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 Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
  3.617   0.100   3.715 

Example timings

RCX.Rcheck/RCX-Ex.timings

nameusersystemelapsed
CartesianLayout0.0050.0000.005
Convert-Names-and-Classes000
CyGroups0.0050.0000.006
CyHiddenAttributes0.1650.0030.168
CyNetworkRelations0.0000.0010.001
CySubNetworks0.0030.0000.003
CyTableColumn0.0070.0000.007
CyVisualProperties0.020.000.02
CyVisualProperty0.0140.0000.014
CyVisualPropertyDependencies0.0050.0000.004
CyVisualPropertyMappings0.0110.0000.011
CyVisualPropertyProperties0.0050.0000.004
EdgeAttributes0.0220.0000.022
Edges0.0020.0000.002
Igraph3.8160.0603.889
Meta-data0.0340.0000.035
NetworkAttributes0.0130.0000.013
NodeAttributes0.0200.0000.019
Nodes0.0030.0000.002
RCX-object0.3250.0000.326
aspectClasses0.0010.0000.000
checks000
convert-data-types-and-values0.0020.0000.002
convert2json000
countElements0.0130.0000.012
custom-print0.0080.0000.008
dot-addAspectNameToJson000
dot-addAttributeData000
dot-aspectClass000
dot-convertRawList0.0010.0000.000
dot-createAttributeAspect000
dot-createCyVpPorD000
dot-filterBy0.0010.0000.000
dot-format000
dot-infer000
dot-json2RDataType0.0010.0000.000
dot-jsonL000
dot-jsonV0.0010.0000.001
dot-log000
dot-mergeAttributesAspect000
dot-mergeIdAspect000
dot-modClass000
dot-pasteC0.0000.0000.001
dot-renameDF0.0030.0000.002
dot-stop000
dot-summaryAspect0.0020.0000.002
dot-transformListLength-set0.0030.0000.003
dot-transformVLD0.0060.0000.006
getCyVisualProperty0.0120.0000.013
graphNEL4.0100.0364.058
hasIds0.0020.0000.001
idProperty0.0010.0000.001
jsonToRCX0.0040.0000.003
markAttributeColumn0.0020.0000.001
markRefColumn0.0010.0000.001
maxId0.0010.0000.001
rcxToJson0.0030.0000.002
readCX0.9120.0120.927
referredBy0.0110.0000.011
refersTo0.0010.0000.001
setExtension000
summary0.0130.0030.015
toCX0.0110.0040.015
updateCartesianLayout0.0600.0000.061
updateCyGroups0.0440.0000.044
updateCyHiddenAttributes0.0610.0000.061
updateCyNetworkRelations0.0520.0000.052
updateCySubNetworks0.0360.0000.036
updateCyTableColumn0.0640.0000.064
updateCyVisualProperties0.3090.0000.310
updateCyVisualProperty0.0840.0000.084
updateEdgeAttributes0.0620.0000.063
updateEdges0.0270.0000.027
updateMetaDataProperties0.0260.0000.026
updateNetworkAttributes0.0560.0040.060
updateNodeAttributes0.0820.0000.082
updateNodes0.0150.0040.019
validate0.3860.0000.387
visualize0.0110.0000.010
writeCX000
writeHTML0.0630.0240.091