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This page was generated on 2024-05-04 11:39:49 -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 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: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2024-05-04 00:18:46 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 00:19:51 -0400 (Sat, 04 May 2024)
EllapsedTime: 64.7 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/RCX.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* 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 12.7.1
* 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 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-3.19-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 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
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 
  3.281   0.215   3.528 

Example timings

RCX.Rcheck/RCX-Ex.timings

nameusersystemelapsed
CartesianLayout0.0050.0020.007
Convert-Names-and-Classes0.0010.0010.002
CyGroups0.0050.0000.005
CyHiddenAttributes0.1420.0090.153
CyNetworkRelations0.0050.0000.006
CySubNetworks0.0030.0010.004
CyTableColumn0.0060.0010.007
CyVisualProperties0.0180.0020.019
CyVisualProperty0.0120.0010.014
CyVisualPropertyDependencies0.0040.0000.005
CyVisualPropertyMappings0.0050.0010.006
CyVisualPropertyProperties0.0070.0000.007
EdgeAttributes0.0190.0010.021
Edges0.0020.0000.002
Igraph2.9650.0813.087
Meta-data0.0320.0030.035
NetworkAttributes0.0140.0030.017
NodeAttributes0.0230.0020.024
Nodes0.0020.0000.003
RCX-object0.2770.0060.286
aspectClasses0.0000.0010.001
checks000
convert-data-types-and-values0.0010.0010.002
convert2json0.0000.0000.001
countElements0.010.000.01
custom-print0.0050.0000.006
dot-addAspectNameToJson0.0000.0010.000
dot-addAttributeData000
dot-aspectClass0.0000.0010.000
dot-convertRawList0.0000.0000.001
dot-createAttributeAspect000
dot-createCyVpPorD0.0000.0010.001
dot-filterBy0.0010.0010.001
dot-format000
dot-infer000
dot-json2RDataType0.0000.0010.001
dot-jsonL0.0000.0000.001
dot-jsonV0.0010.0000.001
dot-log000
dot-mergeAttributesAspect0.0000.0000.001
dot-mergeIdAspect0.0010.0000.001
dot-modClass0.0000.0010.000
dot-pasteC0.0000.0000.001
dot-renameDF0.0020.0000.002
dot-stop000
dot-summaryAspect0.0020.0010.003
dot-transformListLength-set0.0030.0010.003
dot-transformVLD0.0050.0010.007
getCyVisualProperty0.0080.0010.009
graphNEL3.1820.0623.285
hasIds0.0010.0000.002
idProperty0.0010.0000.001
jsonToRCX0.0030.0010.004
markAttributeColumn0.0010.0010.002
markRefColumn0.0010.0010.001
maxId0.0010.0000.001
rcxToJson0.0020.0000.003
readCX0.6520.0110.674
referredBy0.0100.0000.011
refersTo0.0010.0000.001
setExtension000
summary0.1110.0020.115
toCX0.0100.0010.010
updateCartesianLayout0.0460.0010.049
updateCyGroups0.0260.0020.029
updateCyHiddenAttributes0.0540.0050.060
updateCyNetworkRelations0.0410.0030.045
updateCySubNetworks0.0270.0020.029
updateCyTableColumn0.0450.0010.046
updateCyVisualProperties0.2770.0110.290
updateCyVisualProperty0.0780.0040.082
updateEdgeAttributes0.0630.0020.064
updateEdges0.0340.0010.035
updateMetaDataProperties0.0210.0010.021
updateNetworkAttributes0.0530.0030.058
updateNodeAttributes0.0710.0030.074
updateNodes0.0230.0010.023
validate0.2870.0080.297
visualize0.0080.0000.007
writeCX0.0000.0010.000
writeHTML0.0710.0640.139