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CHECK report for RCyjs on celaya2

This page was generated on 2020-01-16 13:42:13 -0500 (Thu, 16 Jan 2020).

Package 1388/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCyjs 2.9.0
Paul Shannon
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/RCyjs
Branch: master
Last Commit: 7b2f222
Last Changed Date: 2019-10-29 13:39:17 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RCyjs
Version: 2.9.0
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_2.9.0.tar.gz
StartedAt: 2020-01-16 08:02:00 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 08:03:07 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 67.3 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_2.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/RCyjs.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.9.0’
* 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 '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-3.11-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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 
  0.428   0.160   0.526 

Example timings

RCyjs.Rcheck/RCyjs-Ex.timings

nameusersystemelapsed
RCyjs-class0.0020.0010.002
addGraph0.0010.0000.001
addGraphFromFile0.0010.0010.002
clearSelection0.0010.0000.002
createTestGaph0.0130.0000.013
deleteGraph0.0010.0000.001
deleteSelectedNodes0.0010.0000.002
eda0.0010.0000.001
edaNames0.0010.0000.001
fit0.0010.0010.001
fitSelection0.0010.0000.001
getEdgeCount0.0010.0000.001
getJSON0.0010.0000.001
getLayoutStrategies0.0010.0000.001
getNodeCount0.0010.0000.001
getNodes0.0000.0010.000
getPosition0.0000.0010.002
getSelectedNodes0.0000.0000.001
getSupportedEdgeDecoratorShapes0.0000.0000.001
getSupportedNodeShapes0.0010.0000.001
getZoom0.0010.0010.001
hAlign0.0010.0010.001
hideAllEdges0.0010.0000.001
hideEdges0.0020.0000.001
hideNodes0.0010.0000.002
hideSelectedNodes0.0010.0000.002
invertNodeSelection0.0010.0000.001
layout0.0020.0000.001
layoutSelectionInGrid0.0010.0000.001
layoutSelectionInGridInferAnchorm0.0010.0000.001
loadStyleFile0.0000.0000.001
noa0.0000.0010.000
noaNames0.0010.0000.000
redraw0.0010.0000.000
restoreLayout0.0010.0010.001
saveJPG0.0020.0000.002
saveLayout0.0010.0000.001
savePNG0.0010.0000.001
selectFirstNeighborsOfSelectedNodes0.0010.0000.002
selectNodes0.0010.0000.001
setBackgroundColor0.0010.0000.001
setDefaultEdgeColor0.0010.0000.001
setDefaultEdgeLineColor0.0010.0000.001
setDefaultEdgeLineStyle0.0000.0000.001
setDefaultEdgeSourceArrowColor0.0000.0000.001
setDefaultEdgeSourceArrowShape0.0010.0000.002
setDefaultEdgeTargetArrowColor0.0000.0010.001
setDefaultEdgeTargetArrowShape0.0000.0000.001
setDefaultEdgeWidth0.0010.0000.001
setDefaultNodeBorderColor0.0010.0000.001
setDefaultNodeBorderWidth0.0010.0000.001
setDefaultNodeColor0.0000.0000.001
setDefaultNodeFontColor0.0000.0010.001
setDefaultNodeFontSize000
setDefaultNodeHeight0.0010.0000.000
setDefaultNodeShape0.0010.0010.001
setDefaultNodeSize000
setDefaultNodeWidth0.0010.0000.001
setDefaultStyle0.0000.0010.002
setEdgeStyle0.0010.0010.002
setGraph0.0000.0000.001
setNodeAttributes0.0010.0000.002
setNodeBorderColor0.0010.0000.001
setNodeBorderWidth0.0010.0000.001
setNodeColor0.0000.0010.001
setNodeColorRule0.0010.0010.002
setNodeFontColor0.0010.0010.001
setNodeFontSize0.0000.0000.001
setNodeHeight0.0000.0000.001
setNodeLabelRule0.0010.0000.001
setNodeShape0.0010.0010.001
setNodeSize0.0000.0010.001
setNodeSizeRule0.0010.0000.002
setNodeWidth0.0010.0000.001
setPosition0.0020.0000.001
setZoom0.0010.0000.001
sfn0.0000.0000.002
showAll0.0010.0000.002
showEdges0.0010.0000.001
showNodes0.0010.0010.002
simpleDemoGraph0.1180.0010.118
vAlign0.0000.0000.001