Package: epigenomix

Version: 0.99.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch epigenomix_0.99.0.tar.gz

StartedAt: 2013-03-25 02:18:30 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:23:55 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 325.1 seconds

RetCode: 0

Status:  OK

CheckDir: epigenomix.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/epigenomix.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 ... [15s/16s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [158s/159s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotChains    66.303  5.530  72.085
bayesMixModel 44.618  2.964  47.719
mlMixModel    27.809  2.297  30.205
* 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	0.006	0.004	0.010
MixModel-class	0.007	0.005	0.012
MixModelBayes-class	0.005	0.003	0.008
MixModelML-class	0.004	0.003	0.008
MixtureComponent-class	0.004	0.004	0.008
bayesMixModel	44.618	2.964	47.719
eSet	0.044	0.010	0.054
integrateData	0.161	0.012	0.172
mappedReads	0.083	0.008	0.091
matchProbeToPromoter	0.455	0.009	0.463
mlMixModel	27.809	2.297	30.205
normalizeChIP	0.052	0.008	0.059
plotChains	66.303	5.530	72.085
plotClassification	0.080	0.012	0.093
plotComponents	0.103	0.010	0.113
summarizeReads	0.497	0.015	0.512
transToTSS	0.015	0.008	0.022