BioC 3.5: CHECK report for RedeR on veracruz2

Package: RedeR

Version: 1.24.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RedeR_1.24.1.tar.gz

StartedAt: 2017-10-18 08:02:57 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 08:03:39 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 42.7 seconds

RetCode: 0

Status:  OK

CheckDir: RedeR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RedeR_1.24.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RedeR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RedeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RedeR’ version ‘1.24.1’
* 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 ‘RedeR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    java   4.3Mb
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 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-3.5-bioc/meat/RedeR.Rcheck/00check.log’
for details.

* installing *source* package ‘RedeR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RedeR)

name	user	system	elapsed
RedPort-class	0.003	0.000	0.004
RedPort	0.001	0.000	0.001
RedeR.data	0.463	0.022	0.498
addEdgeBetweenContainers	0.013	0.001	0.014
addEdges	0.009	0.000	0.011
addGraph	0.009	0.001	0.011
addLegend	0.012	0.001	0.013
addNodes	0.009	0.001	0.010
addSeries	0.01	0.00	0.01
addSubgraph	0.009	0.001	0.010
addSubgraph.list	0.010	0.001	0.011
att	0.481	0.011	0.501
calld	0.001	0.000	0.001
cea	0.014	0.001	0.015
deSelectEdges	0.009	0.001	0.010
deSelectGraph	0.009	0.001	0.010
deSelectNodes	0.009	0.001	0.010
deleteEdges	0.008	0.000	0.008
deleteNodes	0.009	0.000	0.010
deleteSelectedEdges	0.009	0.000	0.010
deleteSelectedNodes	0.009	0.000	0.010
duplicateGraph	0.011	0.000	0.011
exitd	0.001	0.000	0.001
getContainerComponets	0.009	0.000	0.010
getEdgeIDs	0.006	0.000	0.008
getEdges	0.009	0.001	0.009
getGraph	0.010	0.001	0.011
getNodeIDs	0.009	0.000	0.009
getNodes	0.009	0.000	0.010
getSourceEdgeIDs	0.008	0.001	0.009
getTargetEdgeIDs	0.009	0.001	0.009
gtoy.rm	0.000	0.000	0.001
isDynamicsActive	0.001	0.000	0.001
mergeNodes	0.010	0.001	0.012
mergeOutEdges	0.008	0.001	0.009
nestNodes	0.010	0.000	0.012
nesthc	1.657	0.060	1.754
ping	0.002	0.000	0.002
relax	0.012	0.000	0.013
resetd	0.001	0.000	0.002
selectAllEdges	0.012	0.001	0.012
selectAllNodes	0.012	0.001	0.014
selectEdges	0.013	0.001	0.014
selectGraph	0.012	0.001	0.014
selectNodes	0.013	0.001	0.014
setArrowDirection	0.027	0.001	0.027
subg	0.047	0.005	0.054
updateContainerSize	0.012	0.001	0.013
updateGraph	0.012	0.001	0.013
version	0.001	0.000	0.001