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This page was generated on 2023-10-20 09:38:10 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1655/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCX 1.4.0  (landing page)
Florian Auer
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/RCX
git_branch: RELEASE_3_17
git_last_commit: 6d4b6ea
git_last_commit_date: 2023-04-25 11:35:30 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for RCX on kjohnson2


To the developers/maintainers of the RCX package:
- 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: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2023-10-18 17:44:45 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 17:46:12 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 86.7 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/RCX.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCX’ version ‘1.4.0’
* 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 ... OK
* 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 R 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 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 ... OK
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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 
  2.887   0.154   4.666 

Example timings

RCX.Rcheck/RCX-Ex.timings

nameusersystemelapsed
CartesianLayout0.0040.0010.008
Convert-Names-and-Classes0.0000.0000.001
CyGroups0.0050.0010.011
CyHiddenAttributes0.1410.0070.223
CyNetworkRelations0.0010.0010.002
CySubNetworks0.0030.0010.004
CyTableColumn0.0060.0010.008
CyVisualProperties0.0190.0030.031
CyVisualProperty0.0110.0020.022
CyVisualPropertyDependencies0.0080.0010.013
CyVisualPropertyMappings0.0050.0010.008
CyVisualPropertyProperties0.0040.0000.005
EdgeAttributes0.0170.0010.029
Edges0.0020.0000.002
Igraph2.7140.0514.281
Meta-data0.0360.0020.052
NetworkAttributes0.0100.0010.017
NodeAttributes0.0200.0020.030
Nodes0.0020.0010.005
RCX-object0.2690.0060.419
aspectClasses0.0010.0010.002
checks0.0000.0010.000
convert-data-types-and-values0.0020.0000.002
convert2json000
countElements0.0100.0010.013
custom-print0.0060.0010.008
dot-addAspectNameToJson0.0000.0000.001
dot-addAttributeData000
dot-aspectClass0.0010.0010.001
dot-convertRawList000
dot-createAttributeAspect000
dot-createCyVpPorD0.0010.0000.001
dot-filterBy0.0000.0000.001
dot-format000
dot-infer000
dot-json2RDataType0.0000.0000.001
dot-jsonL0.0000.0010.001
dot-jsonV0.0000.0000.001
dot-log0.0000.0010.000
dot-mergeAttributesAspect000
dot-mergeIdAspect0.0000.0000.001
dot-modClass000
dot-pasteC000
dot-renameDF0.0020.0010.002
dot-stop0.0010.0010.000
dot-summaryAspect0.0020.0000.001
dot-transformListLength-set0.0030.0000.003
dot-transformVLD0.0050.0000.007
getCyVisualProperty0.0120.0010.018
graphNEL2.9960.0364.552
hasIds0.0080.0010.012
idProperty0.0010.0000.001
jsonToRCX0.0030.0000.005
markAttributeColumn0.0010.0000.005
markRefColumn0.0010.0000.001
maxId0.0010.0000.002
rcxToJson0.0020.0010.006
readCX0.6590.0081.020
referredBy0.0100.0000.016
refersTo0.0010.0000.001
setExtension000
summary0.0140.0010.022
toCX0.0130.0010.019
updateCartesianLayout0.0530.0030.090
updateCyGroups0.0320.0010.050
updateCyHiddenAttributes0.0510.0020.084
updateCyNetworkRelations0.0420.0020.068
updateCySubNetworks0.0360.0020.059
updateCyTableColumn0.0490.0020.079
updateCyVisualProperties0.2770.0150.443
updateCyVisualProperty0.0760.0040.122
updateEdgeAttributes0.0560.0020.085
updateEdges0.0250.0010.041
updateMetaDataProperties0.0270.0020.044
updateNetworkAttributes0.0500.0020.082
updateNodeAttributes0.0660.0020.101
updateNodes0.0170.0010.030
validate0.2890.0080.449
visualize0.0090.0010.016
writeCX000
writeHTML0.0710.0520.188