Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-09-30 11:37:31 -0400 (Sat, 30 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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: 2023-09-29 14:00:14 -0400 (Fri, 29 Sep 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)
nebbiolo1Linux (Ubuntu 22.04.2 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
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for RCX on merida1


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: 1.4.0
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: 2023-09-30 05:58:13 -0400 (Sat, 30 Sep 2023)
EndedAt: 2023-09-30 06:00:19 -0400 (Sat, 30 Sep 2023)
EllapsedTime: 126.0 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/meat/RCX.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* 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
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
graphNEL 6.902  0.054   8.934
Igraph   6.570  0.116   8.901
* 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/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-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-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 
  6.141   0.275   7.948 

Example timings

RCX.Rcheck/RCX-Ex.timings

nameusersystemelapsed
CartesianLayout0.0090.0030.014
Convert-Names-and-Classes0.0010.0020.004
CyGroups0.0100.0010.016
CyHiddenAttributes0.2630.0140.373
CyNetworkRelations0.0020.0010.003
CySubNetworks0.0050.0010.008
CyTableColumn0.0120.0010.018
CyVisualProperties0.0350.0040.053
CyVisualProperty0.0260.0030.038
CyVisualPropertyDependencies0.0120.0010.018
CyVisualPropertyMappings0.0090.0010.015
CyVisualPropertyProperties0.0080.0010.011
EdgeAttributes0.0340.0030.049
Edges0.0040.0010.005
Igraph6.5700.1168.901
Meta-data0.0660.0020.081
NetworkAttributes0.0220.0020.024
NodeAttributes0.0350.0030.048
Nodes0.0030.0000.005
RCX-object0.5690.0070.731
aspectClasses0.0010.0020.006
checks0.0000.0010.000
convert-data-types-and-values0.0040.0010.008
convert2json0.0010.0010.000
countElements0.0200.0010.032
custom-print0.0130.0010.016
dot-addAspectNameToJson000
dot-addAttributeData0.0010.0000.001
dot-aspectClass0.0010.0010.001
dot-convertRawList0.0000.0010.001
dot-createAttributeAspect0.0010.0000.000
dot-createCyVpPorD0.0010.0000.001
dot-filterBy0.0010.0010.005
dot-format0.0000.0010.002
dot-infer0.0000.0000.001
dot-json2RDataType0.0010.0010.001
dot-jsonL0.0000.0000.001
dot-jsonV0.0010.0000.002
dot-log0.0000.0010.000
dot-mergeAttributesAspect0.0010.0010.002
dot-mergeIdAspect0.0010.0010.000
dot-modClass0.0000.0010.001
dot-pasteC0.0000.0010.001
dot-renameDF0.0030.0010.005
dot-stop000
dot-summaryAspect0.0030.0000.003
dot-transformListLength-set0.0040.0010.005
dot-transformVLD0.0080.0010.012
getCyVisualProperty0.0210.0020.034
graphNEL6.9020.0548.934
hasIds0.0020.0000.002
idProperty0.0020.0000.002
jsonToRCX0.0040.0010.007
markAttributeColumn0.0020.0000.003
markRefColumn0.0020.0010.002
maxId0.0020.0000.002
rcxToJson0.0030.0000.004
readCX1.4220.0101.864
referredBy0.0200.0010.047
refersTo0.0020.0000.004
setExtension0.0000.0000.001
summary0.0270.0030.045
toCX0.0260.0030.050
updateCartesianLayout0.1010.0040.130
updateCyGroups0.0630.0030.080
updateCyHiddenAttributes0.1060.0040.137
updateCyNetworkRelations0.0880.0040.115
updateCySubNetworks0.0680.0030.115
updateCyTableColumn0.1050.0040.145
updateCyVisualProperties0.5500.0320.773
updateCyVisualProperty0.1440.0100.191
updateEdgeAttributes0.1130.0050.145
updateEdges0.0470.0030.063
updateMetaDataProperties0.0510.0060.070
updateNetworkAttributes0.1050.0040.133
updateNodeAttributes0.1370.0040.180
updateNodes0.0340.0010.042
validate0.6900.0160.916
visualize0.0190.0010.027
writeCX0.0000.0000.001
writeHTML0.1250.1160.322