Package: MethylSeekR

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MethylSeekR_1.0.0.tar.gz

StartedAt: 2013-05-01 07:53:29 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 08:05:43 -0700 (Wed, 01 May 2013)

EllapsedTime: 734.0 seconds

RetCode: 0

Status:  OK

CheckDir: MethylSeekR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MethylSeekR.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MethylSeekR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethylSeekR' version '1.0.0'
* 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 'MethylSeekR' can be installed ... [23s/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 installed files from 'inst/doc' ... OK
* checking examples ... [483s/516s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
MethylSeekR-package         130.938 17.850 158.414
plotPMDSegmentation          65.982 10.071  77.527
savePMDSegments              60.562  7.405  68.459
segmentPMDs                  58.916  7.542  67.142
calculateFDRs                36.916  4.672  60.616
plotAlphaDistributionOneChr  28.237  1.478  30.230
plotFinalSegmentation        16.875  2.722  19.952
segmentUMRsLMRs               6.967  0.995   8.050
saveUMRLMRSegments            6.214  0.881   7.137
* 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
** testing if installed package can be loaded
* DONE (MethylSeekR)

name	user	system	elapsed
MethylSeekR-package	130.938	17.850	158.414
calculateFDRs	36.916	4.672	60.616
plotAlphaDistributionOneChr	28.237	1.478	30.230
plotFinalSegmentation	16.875	2.722	19.952
plotPMDSegmentation	65.982	10.071	77.527
readMethylome	1.707	0.249	2.005
readSNPTable	0.305	0.026	0.333
removeSNPs	3.951	0.410	4.387
savePMDSegments	60.562	7.405	68.459
saveUMRLMRSegments	6.214	0.881	7.137
segmentPMDs	58.916	7.542	67.142
segmentUMRsLMRs	6.967	0.995	8.050