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This page was generated on 2024-05-04 11:40:59 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1705/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCX 1.8.0  (landing page)
Florian Auer
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/RCX
git_branch: RELEASE_3_19
git_last_commit: d46f370
git_last_commit_date: 2024-04-30 11:39:53 -0400 (Tue, 30 Apr 2024)
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  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 1.8.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:RCX.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings RCX_1.8.0.tar.gz
StartedAt: 2024-05-04 11:03:32 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 11:04:28 -0000 (Sat, 04 May 2024)
EllapsedTime: 56.1 seconds
RetCode: 0
Status:   OK  
CheckDir: RCX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:RCX.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings RCX_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RCX.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* 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 ‘1.8.0’
* 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-beta-2024-04-15_r86425/bin/R CMD INSTALL RCX
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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 
  3.689   0.082   3.767 

Example timings

RCX.Rcheck/RCX-Ex.timings

nameusersystemelapsed
CartesianLayout0.0060.0000.006
Convert-Names-and-Classes000
CyGroups0.0050.0000.005
CyHiddenAttributes0.1520.0040.157
CyNetworkRelations0.0020.0000.002
CySubNetworks0.0030.0000.003
CyTableColumn0.0060.0000.006
CyVisualProperties0.0190.0000.019
CyVisualProperty0.0130.0000.014
CyVisualPropertyDependencies0.0040.0000.004
CyVisualPropertyMappings0.0100.0000.009
CyVisualPropertyProperties0.0040.0000.004
EdgeAttributes0.0190.0000.020
Edges0.0020.0000.001
Igraph3.7600.0243.794
Meta-data0.0340.0000.033
NetworkAttributes0.0180.0000.019
NodeAttributes0.020.000.02
Nodes0.0020.0000.003
RCX-object0.3200.0040.326
aspectClasses0.0000.0010.001
checks000
convert-data-types-and-values0.0000.0020.002
convert2json0.0000.0000.001
countElements0.0110.0010.012
custom-print0.0040.0030.007
dot-addAspectNameToJson0.0000.0000.001
dot-addAttributeData000
dot-aspectClass000
dot-convertRawList0.0000.0000.001
dot-createAttributeAspect000
dot-createCyVpPorD000
dot-filterBy0.0000.0000.001
dot-format000
dot-infer000
dot-json2RDataType0.0000.0000.001
dot-jsonL000
dot-jsonV0.0010.0000.000
dot-log000
dot-mergeAttributesAspect000
dot-mergeIdAspect000
dot-modClass0.0010.0000.000
dot-pasteC000
dot-renameDF0.0020.0000.002
dot-stop000
dot-summaryAspect0.0020.0000.002
dot-transformListLength-set0.0030.0000.003
dot-transformVLD0.0060.0000.006
getCyVisualProperty0.0120.0000.012
graphNEL4.0210.0234.052
hasIds0.0010.0000.001
idProperty0.0010.0000.001
jsonToRCX0.0000.0030.003
markAttributeColumn0.0020.0000.001
markRefColumn0.0010.0000.002
maxId0.0010.0000.001
rcxToJson0.0030.0000.002
readCX0.8920.0120.905
referredBy0.0110.0000.011
refersTo0.0010.0000.001
setExtension000
summary0.0150.0000.015
toCX0.0130.0000.014
updateCartesianLayout0.0550.0000.055
updateCyGroups0.0290.0080.038
updateCyHiddenAttributes0.0690.0000.069
updateCyNetworkRelations0.0480.0000.048
updateCySubNetworks0.0360.0000.035
updateCyTableColumn0.0610.0000.061
updateCyVisualProperties0.3220.0000.322
updateCyVisualProperty0.0760.0040.080
updateEdgeAttributes0.0690.0000.070
updateEdges0.0270.0000.027
updateMetaDataProperties0.0230.0040.026
updateNetworkAttributes0.0610.0000.061
updateNodeAttributes0.0780.0000.079
updateNodes0.0250.0000.025
validate0.3900.0000.391
visualize0.0110.0000.011
writeCX000
writeHTML0.0850.0120.102