BioC 3.0: CHECK report for RedeR on oaxaca

Package: RedeR

Version: 1.14.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RedeR_1.14.10.tar.gz

StartedAt: 2015-04-10 02:42:27 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:43:25 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 57.7 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 --no-multiarch RedeR_1.14.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/RedeR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.14.10’
* 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 ... [4s/4s] OK
* checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    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 ... [2s/3s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.002	0.000	0.003
RedPort	0.001	0.000	0.001
RedeR.data	0.713	0.050	0.846
addEdgeBetweenContainers	0.003	0.001	0.004
addEdges	0.001	0.000	0.001
addGraph	0.003	0.001	0.003
addLegend	0.002	0.000	0.002
addNodes	0.001	0.000	0.001
addSeries	0.001	0.000	0.001
addSubgraph	0.002	0.000	0.002
addSubgraph.list	0.001	0.000	0.002
att	0.083	0.011	0.103
calld	0.001	0.000	0.002
cea	0.114	0.011	0.136
deSelectEdges	0.001	0.000	0.002
deSelectGraph	0.001	0.001	0.002
deSelectNodes	0.001	0.000	0.001
deleteEdges	0.002	0.000	0.003
deleteNodes	0.002	0.001	0.001
deleteSelectedEdges	0.001	0.000	0.001
deleteSelectedNodes	0.001	0.000	0.002
duplicateGraph	0.001	0.001	0.002
exitd	0.001	0.000	0.002
getContainerComponets	0.003	0.000	0.005
getEdgeIDs	0.002	0.000	0.002
getEdges	0.002	0.000	0.001
getGraph	0.001	0.000	0.005
getNodeIDs	0.001	0.000	0.002
getNodes	0.001	0.000	0.001
getSourceEdgeIDs	0.001	0.000	0.002
getTargetEdgeIDs	0.002	0.000	0.002
gtoy.rm	0.001	0.000	0.001
isDynamicsActive	0.002	0.001	0.001
mergeNodes	0.002	0.000	0.002
mergeOutEdges	0.002	0.000	0.002
nestNodes	0.001	0.000	0.003
nesthc	0.000	0.000	0.001
ping	0.001	0.000	0.002
relax	0.002	0.001	0.005
resetd	0.002	0.000	0.001
selectAllEdges	0.001	0.000	0.001
selectAllNodes	0.001	0.000	0.002
selectEdges	0.001	0.001	0.002
selectGraph	0.002	0.000	0.002
selectNodes	0.002	0.001	0.002
setArrowDirection	0.001	0.000	0.002
subg	0.095	0.019	0.126
updateContainerSize	0.002	0.000	0.001
updateGraph	0.001	0.000	0.002
version	0.001	0.000	0.002