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CHECK report for RCyjs on merida1

This page was generated on 2019-04-16 11:58:34 -0400 (Tue, 16 Apr 2019).

Package 1270/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCyjs 2.4.0
Paul Shannon
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/RCyjs
Branch: RELEASE_3_8
Last Commit: 205545f
Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RCyjs
Version: 2.4.0
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_2.4.0.tar.gz
StartedAt: 2019-04-16 02:14:06 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:14:52 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 45.8 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_2.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/RCyjs.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.4.0’
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking include directives in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... 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’ ... WARNING
Package vignette without corresponding PDF/HTML:
   ‘RCyjs.Rmd’

* 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-3.8-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/3.5/Resources/library’
* installing *source* package ‘RCyjs’ ...
** 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
* DONE (RCyjs)

Tests output

RCyjs.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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 
  0.221   0.055   0.245 

Example timings

RCyjs.Rcheck/RCyjs-Ex.timings

nameusersystemelapsed
RCyjs-class0.0000.0000.001
addGraph0.0010.0000.001
addGraphFromFile0.0000.0000.001
clearSelection0.0010.0000.000
createTestGaph0.0100.0000.012
deleteGraph0.0010.0000.000
deleteSelectedNodes0.0010.0010.001
eda0.0010.0000.001
edaNames000
fit0.0010.0000.001
fitSelection0.0000.0000.001
getEdgeCount0.0010.0010.000
getJSON0.0000.0000.001
getLayoutStrategies0.0000.0000.001
getNodeCount0.0010.0000.001
getNodes0.0000.0000.001
getPosition0.0010.0010.001
getSelectedNodes0.0010.0000.000
getSupportedEdgeDecoratorShapes000
getSupportedNodeShapes0.0010.0000.001
getZoom0.0010.0000.001
hAlign0.0010.0000.000
hideAllEdges0.0000.0000.001
hideEdges0.0010.0010.001
hideSelectedNodes0.0010.0000.002
invertNodeSelection0.0000.0010.001
layout0.0020.0000.001
layoutSelectionInGrid0.0010.0000.002
layoutSelectionInGridInferAnchorm0.0010.0000.001
loadStyleFile0.0000.0000.001
noa0.0010.0000.000
noaNames0.0000.0000.001
redraw000
restoreLayout0.0010.0000.001
saveJPG0.0010.0000.002
saveLayout000
savePNG0.0010.0010.002
selectFirstNeighborsOfSelectedNodes0.0010.0000.001
selectNodes0.0000.0000.001
setBackgroundColor0.0010.0000.001
setDefaultEdgeColor000
setDefaultEdgeLineColor0.0010.0000.000
setDefaultEdgeLineStyle0.0010.0000.000
setDefaultEdgeSourceArrowColor000
setDefaultEdgeSourceArrowShape0.0010.0000.000
setDefaultEdgeTargetArrowColor000
setDefaultEdgeTargetArrowShape0.0010.0000.001
setDefaultEdgeWidth0.0010.0000.001
setDefaultNodeBorderColor0.0000.0000.001
setDefaultNodeBorderWidth0.0000.0000.001
setDefaultNodeColor0.0010.0000.001
setDefaultNodeFontColor0.0010.0010.001
setDefaultNodeFontSize0.0000.0000.001
setDefaultNodeHeight0.0000.0000.001
setDefaultNodeShape000
setDefaultNodeSize000
setDefaultNodeWidth0.0000.0000.001
setDefaultStyle0.0000.0000.001
setEdgeStyle0.0010.0000.000
setGraph0.0010.0000.001
setNodeAttributes0.0010.0000.001
setNodeBorderColor0.0010.0000.000
setNodeBorderWidth0.0010.0000.001
setNodeColor0.0010.0000.001
setNodeColorRule0.0010.0000.001
setNodeFontColor000
setNodeFontSize0.0010.0000.001
setNodeHeight0.0010.0010.001
setNodeLabelRule0.0010.0000.001
setNodeShape000
setNodeSize0.0000.0000.001
setNodeSizeRule0.0010.0000.001
setNodeWidth0.0010.0000.001
setPosition0.0010.0000.001
setZoom0.0000.0000.001
sfn0.0010.0000.001
showAll0.0010.0000.001
showEdges0.0010.0000.001
simpleDemoGraph0.0870.0000.090
vAlign0.0000.0010.001