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CHECK report for RCyjs on merida1

This page was generated on 2021-05-06 12:36:20 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the RCyjs package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1476/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCyjs 2.12.0  (landing page)
Paul Shannon
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/RCyjs
Branch: RELEASE_3_12
Last Commit: bc3444a
Last Changed Date: 2020-10-27 11:04:38 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: RCyjs
Version: 2.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCyjs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCyjs_2.12.0.tar.gz
StartedAt: 2021-05-06 05:14:24 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:15:17 -0400 (Thu, 06 May 2021)
EllapsedTime: 52.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RCyjs.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCyjs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCyjs_2.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/RCyjs.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCyjs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCyjs’ version ‘2.12.0’
* 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 ‘RCyjs’ 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 ... OK
* 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 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 ... WARNING
Undocumented arguments in documentation object 'hideNodes,RCyjs-method'
  ‘nodeIDs’

Undocumented arguments in documentation object 'readAndStandardizeJSONNetworkFile'
  ‘filename’
Documented arguments not in \usage in documentation object 'readAndStandardizeJSONNetworkFile':
  ‘file’

Undocumented arguments in documentation object 'readAndStandardizeJSONStyleFile'
  ‘filename’
Documented arguments not in \usage in documentation object 'readAndStandardizeJSONStyleFile':
  ‘file’

Undocumented arguments in documentation object 'showNodes,RCyjs-method'
  ‘nodeIDs’

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 include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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 WARNING
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/RCyjs.Rcheck/00check.log’
for details.



Installation output

RCyjs.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RCyjs
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘RCyjs’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘layout’ in package ‘RCyjs’
** 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 (RCyjs)

Tests output

RCyjs.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> # disabled: the bioc build system no longer supports browser use.
> # BiocGenerics:::testPackage("RCyjs")
> 
> proc.time()
   user  system elapsed 
  0.249   0.057   0.286 

Example timings

RCyjs.Rcheck/RCyjs-Ex.timings

nameusersystemelapsed
RCyjs-class0.0010.0000.001
addGraph0.0010.0000.001
addGraphFromFile0.0000.0010.000
clearSelection0.0010.0010.001
createTestGaph0.0080.0010.008
deleteGraph000
deleteSelectedNodes0.0010.0000.001
eda0.0000.0010.001
edaNames0.0010.0000.001
fit000
fitSelection0.0000.0000.001
getEdgeCount0.0010.0000.001
getJSON000
getLayoutStrategies0.0010.0000.001
getNodeCount0.0000.0010.001
getNodes0.0000.0000.001
getPosition0.0010.0000.001
getSelectedNodes0.0000.0010.001
getSupportedEdgeDecoratorShapes000
getSupportedNodeShapes000
getZoom0.0010.0010.002
graphNELtoJSON.string0.0000.0000.001
hAlign0.0010.0000.002
hideAllEdges0.0010.0000.002
hideEdges0.0010.0000.001
hideNodes0.0010.0010.001
hideSelectedNodes0.0010.0010.002
invertNodeSelection0.0000.0010.001
layout0.0000.0010.001
layoutSelectionInGrid0.0010.0000.001
layoutSelectionInGridInferAnchorm0.0010.0000.001
loadStyleFile0.0010.0010.001
noa0.0010.0000.000
noaNames0.0000.0000.001
redraw0.0000.0000.001
restoreLayout0.0000.0000.001
saveJPG0.0010.0010.001
saveLayout000
savePNG0.0010.0010.001
selectFirstNeighborsOfSelectedNodes0.0010.0000.001
selectNodes000
setBackgroundColor0.0010.0010.000
setDefaultEdgeColor0.0000.0000.001
setDefaultEdgeLineColor0.0010.0000.001
setDefaultEdgeLineStyle0.0000.0010.001
setDefaultEdgeSourceArrowColor0.0000.0000.001
setDefaultEdgeSourceArrowShape0.0010.0000.001
setDefaultEdgeTargetArrowColor0.0010.0010.000
setDefaultEdgeTargetArrowShape0.0010.0000.001
setDefaultEdgeWidth0.0010.0010.000
setDefaultNodeBorderColor0.0000.0000.001
setDefaultNodeBorderWidth0.0010.0000.001
setDefaultNodeColor0.0000.0000.001
setDefaultNodeFontColor0.0010.0000.001
setDefaultNodeFontSize0.0010.0000.000
setDefaultNodeHeight0.0010.0000.001
setDefaultNodeShape0.0010.0000.000
setDefaultNodeSize0.0010.0000.001
setDefaultNodeWidth0.0010.0010.000
setDefaultStyle0.0010.0000.001
setEdgeStyle0.0010.0000.001
setGraph0.0010.0010.001
setNodeAttributes0.0000.0000.001
setNodeBorderColor000
setNodeBorderWidth0.0000.0010.001
setNodeColor000
setNodeColorRule0.0010.0000.001
setNodeFontColor0.0000.0000.001
setNodeFontSize000
setNodeHeight0.0000.0000.001
setNodeLabelRule0.0000.0000.001
setNodeShape0.0010.0010.001
setNodeSize0.0010.0000.001
setNodeSizeRule0.0010.0000.001
setNodeWidth0.0010.0000.000
setPosition0.0000.0010.001
setZoom0.0000.0010.001
sfn0.0010.0000.001
showAll0.0010.0000.001
showEdges0.0000.0010.000
showNodes0.0000.0000.001
simpleDemoGraph0.0620.0010.063
vAlign0.0010.0000.000