Package: epigenomix

Version: 0.99.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings epigenomix_0.99.0.tar.gz

StartedAt: 2013-03-25 01:25:50 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:33:05 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 434.7 seconds

RetCode: 0

Status:  OK

CheckDir: epigenomix.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/epigenomix.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epigenomix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epigenomix’ version ‘0.99.0’
* 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 ‘epigenomix’ can be installed ... [24s/24s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 examples ... [186s/188s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotChains    76.213  0.016  76.997
bayesMixModel 56.208  0.092  56.705
mlMixModel    38.458  0.068  39.366
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

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

name	user	system	elapsed
ChIPseqSet-class	0.012	0.000	0.011
MixModel-class	0.016	0.000	0.013
MixModelBayes-class	0.012	0.000	0.014
MixModelML-class	0.016	0.000	0.015
MixtureComponent-class	0.012	0.000	0.014
bayesMixModel	56.208	0.092	56.705
eSet	0.104	0.008	0.110
integrateData	0.760	0.004	0.764
mappedReads	0.144	0.004	0.150
matchProbeToPromoter	0.720	0.000	0.721
mlMixModel	38.458	0.068	39.366
normalizeChIP	0.08	0.00	0.08
plotChains	76.213	0.016	76.997
plotClassification	0.092	0.000	0.094
plotComponents	0.140	0.004	0.145
summarizeReads	0.632	0.004	0.634
transToTSS	0.024	0.000	0.022