Package: MethylSeekR

Version: 0.99.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MethylSeekR_0.99.1.tar.gz

StartedAt: 2013-03-25 03:30:50 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:39:44 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 533.7 seconds

RetCode: 0

Status:  OK

CheckDir: MethylSeekR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MethylSeekR.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 'MethylSeekR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethylSeekR' version '0.99.1'
* 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 'MethylSeekR' can be installed ... [19s/19s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [331s/346s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
MethylSeekR-package         89.682 17.794 113.575
plotPMDSegmentation         39.685  8.159  48.158
savePMDSegments             36.907  7.247  44.560
segmentPMDs                 37.227  6.877  44.600
calculateFDRs               19.322  6.323  33.151
plotAlphaDistributionOneChr 16.012  1.786  17.831
plotFinalSegmentation       12.566  2.251  14.881
saveUMRLMRSegments           6.544  0.814   7.383
segmentUMRsLMRs              5.406  0.737   6.198
* 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 'MethylSeekR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'MethylSeekR.Rnw' 
** testing if installed package can be loaded
* DONE (MethylSeekR)

name	user	system	elapsed
MethylSeekR-package	89.682	17.794	113.575
calculateFDRs	19.322	6.323	33.151
plotAlphaDistributionOneChr	16.012	1.786	17.831
plotFinalSegmentation	12.566	2.251	14.881
plotPMDSegmentation	39.685	8.159	48.158
readMethylome	1.843	0.206	2.061
readSNPTable	0.226	0.054	0.286
removeSNPs	3.470	0.424	3.911
savePMDSegments	36.907	7.247	44.560
saveUMRLMRSegments	6.544	0.814	7.383
segmentPMDs	37.227	6.877	44.600
segmentUMRsLMRs	5.406	0.737	6.198