BioC 3.5: CHECK report for RedeR on malbec2

Package: RedeR

Version: 1.24.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RedeR_1.24.1.tar.gz

StartedAt: 2017-08-16 01:43:28 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:44:00 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 32.0 seconds

RetCode: 0

Status:  OK

CheckDir: RedeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RedeR_1.24.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/RedeR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 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
  ‘/home/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	0.004	0.000	0.003
RedPort	0	0	0
RedeR.data	0.464	0.008	0.471
addEdgeBetweenContainers	0.012	0.000	0.011
addEdges	0.004	0.004	0.008
addGraph	0.008	0.000	0.008
addLegend	0.012	0.000	0.011
addNodes	0.008	0.000	0.008
addSeries	0.008	0.000	0.008
addSubgraph	0.008	0.000	0.008
addSubgraph.list	0.008	0.000	0.008
att	0.372	0.000	0.371
calld	0.000	0.000	0.001
cea	0.012	0.000	0.013
deSelectEdges	0.008	0.000	0.009
deSelectGraph	0.008	0.000	0.008
deSelectNodes	0.008	0.000	0.008
deleteEdges	0.012	0.000	0.011
deleteNodes	0.008	0.000	0.008
deleteSelectedEdges	0.008	0.000	0.008
deleteSelectedNodes	0.008	0.000	0.008
duplicateGraph	0.008	0.000	0.009
exitd	0.000	0.000	0.001
getContainerComponets	0.008	0.000	0.009
getEdgeIDs	0.008	0.000	0.008
getEdges	0.008	0.000	0.008
getGraph	0.008	0.000	0.008
getNodeIDs	0.008	0.000	0.008
getNodes	0.008	0.000	0.008
getSourceEdgeIDs	0.008	0.000	0.009
getTargetEdgeIDs	0.008	0.000	0.009
gtoy.rm	0	0	0
isDynamicsActive	0.004	0.000	0.001
mergeNodes	0.008	0.000	0.008
mergeOutEdges	0.012	0.000	0.010
nestNodes	0.008	0.000	0.008
nesthc	1.352	0.020	1.373
ping	0.000	0.000	0.001
relax	0.012	0.000	0.010
resetd	0	0	0
selectAllEdges	0.012	0.000	0.010
selectAllNodes	0.008	0.000	0.009
selectEdges	0.008	0.000	0.009
selectGraph	0.008	0.000	0.010
selectNodes	0.012	0.000	0.010
setArrowDirection	0.152	0.000	0.151
subg	0.040	0.004	0.043
updateContainerSize	0.008	0.000	0.009
updateGraph	0.012	0.000	0.009
version	0.000	0.000	0.001