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: 2013-03-24 07:32:08 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 07:42:58 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 649.9 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 beta (2013-03-21 r62346)
* 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 '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 ... [23s/23s] 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 ... [409s/433s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
MethylSeekR-package         108.352 18.047 139.082
plotPMDSegmentation          54.461  9.801  65.050
savePMDSegments              49.687  7.270  57.803
segmentPMDs                  45.031  7.231  52.547
calculateFDRs                24.001  5.365  38.067
plotAlphaDistributionOneChr  20.735  1.541  22.726
plotFinalSegmentation        17.331  2.753  20.156
segmentUMRsLMRs               7.346  0.840   8.190
saveUMRLMRSegments            7.276  0.905   8.217
removeSNPs                    5.379  0.367   5.859
* 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	108.352	18.047	139.082
calculateFDRs	24.001	5.365	38.067
plotAlphaDistributionOneChr	20.735	1.541	22.726
plotFinalSegmentation	17.331	2.753	20.156
plotPMDSegmentation	54.461	9.801	65.050
readMethylome	2.849	0.213	3.082
readSNPTable	0.307	0.032	0.342
removeSNPs	5.379	0.367	5.859
savePMDSegments	49.687	7.270	57.803
saveUMRLMRSegments	7.276	0.905	8.217
segmentPMDs	45.031	7.231	52.547
segmentUMRsLMRs	7.346	0.840	8.190