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CHECK report for RCyjs on merida2

This page was generated on 2018-10-17 08:54:41 -0400 (Wed, 17 Oct 2018).

Package 1202/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCyjs 2.2.2
Paul Shannon
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/RCyjs
Branch: RELEASE_3_7
Last Commit: 694250d
Last Changed Date: 2018-07-03 09:37:28 -0400 (Tue, 03 Jul 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RCyjs
Version: 2.2.2
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_2.2.2.tar.gz
StartedAt: 2018-10-16 23:34:02 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:34:50 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 47.7 seconds
RetCode: 0
Status:  OK 
CheckDir: RCyjs.Rcheck
Warnings: 0

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_2.2.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/RCyjs.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.2.2’
* 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’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

RCyjs.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RCyjs
###
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* 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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 
  0.222   0.049   0.243 

Example timings

RCyjs.Rcheck/RCyjs-Ex.timings

nameusersystemelapsed
RCyjs-class0.0020.0000.002
addGraph0.0010.0000.001
addGraphFromFile0.0020.0010.002
clearSelection0.0020.0000.002
createTestGaph0.010.000.01
deleteGraph0.0010.0000.002
deleteSelectedNodes0.0020.0000.003
eda0.0030.0000.003
edaNames0.0020.0000.003
fit0.0010.0000.001
fitSelection0.0020.0000.002
getEdgeCount0.0020.0010.002
getJSON0.0030.0000.002
getLayoutStrategies0.0020.0010.002
getNodeCount0.0010.0000.002
getNodes0.0020.0000.002
getPosition0.0020.0000.002
getSelectedNodes0.0010.0000.001
getSupportedEdgeDecoratorShapes0.0010.0010.001
getSupportedNodeShapes0.0010.0000.001
getZoom0.0020.0000.001
hAlign0.0020.0010.003
hideAllEdges0.0020.0000.003
hideEdges0.0020.0000.003
hideSelectedNodes0.0020.0000.002
invertNodeSelection0.0020.0000.003
layout0.0020.0000.003
layoutSelectionInGrid0.0030.0000.004
layoutSelectionInGridInferAnchorm0.0020.0000.002
loadStyleFile0.0020.0000.003
noa0.0010.0010.002
noaNames0.0010.0000.002
redraw0.0020.0000.003
restoreLayout0.0020.0000.003
saveJPG0.0030.0010.003
saveLayout0.0030.0000.003
savePNG0.0040.0010.004
selectFirstNeighborsOfSelectedNodes0.0030.0000.003
selectNodes0.0020.0010.001
setBackgroundColor0.0010.0000.001
setDefaultEdgeColor0.0010.0000.001
setDefaultEdgeLineColor0.0020.0010.002
setDefaultEdgeLineStyle0.0010.0000.002
setDefaultEdgeSourceArrowColor0.0030.0000.003
setDefaultEdgeSourceArrowShape0.0010.0000.002
setDefaultEdgeTargetArrowColor0.0020.0000.002
setDefaultEdgeTargetArrowShape0.0020.0010.001
setDefaultEdgeWidth0.0020.0000.001
setDefaultNodeBorderColor0.0010.0000.002
setDefaultNodeBorderWidth0.0010.0010.002
setDefaultNodeColor0.0020.0000.002
setDefaultNodeFontColor0.0020.0000.001
setDefaultNodeFontSize0.0020.0000.003
setDefaultNodeHeight0.0020.0000.002
setDefaultNodeShape0.0020.0000.002
setDefaultNodeSize0.0010.0000.001
setDefaultNodeWidth0.0020.0000.002
setDefaultStyle0.0020.0000.002
setEdgeStyle0.0030.0000.003
setGraph0.0020.0000.002
setNodeAttributes0.0020.0000.001
setNodeBorderColor0.0020.0000.002
setNodeBorderWidth0.0010.0010.002
setNodeColor0.0020.0000.002
setNodeColorRule0.0010.0000.002
setNodeFontColor0.0020.0000.003
setNodeFontSize0.0020.0000.003
setNodeHeight0.0020.0000.002
setNodeLabelRule0.0020.0000.002
setNodeShape0.0020.0010.003
setNodeSize0.0030.0000.002
setNodeSizeRule0.0030.0000.003
setNodeWidth0.0020.0000.003
setPosition0.0030.0000.003
setZoom0.0020.0000.002
sfn0.0020.0000.002
showAll0.0020.0000.003
showEdges0.0030.0000.003
simpleDemoGraph0.070.000.07
vAlign0.0030.0000.002