BioC 2.12: CHECK report for MethylSeekR on petty

Package: MethylSeekR

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MethylSeekR_1.0.1.tar.gz

StartedAt: 2013-10-08 23:02:19 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:19:12 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 1012.9 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 3.0.1 (2013-05-16)
* 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 '1.0.1'
* 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 ... [26s/27s] 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 ... [10m/13m] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
MethylSeekR-package         166.586 14.516 193.130
plotPMDSegmentation         103.008  8.387 147.633
savePMDSegments              93.604  5.902 108.361
segmentPMDs                  90.686  5.840 127.192
calculateFDRs                21.644  4.981  68.196
plotFinalSegmentation        19.601  2.598  41.093
plotAlphaDistributionOneChr  18.443  1.429  45.610
saveUMRLMRSegments            7.690  0.726   8.526
segmentUMRsLMRs               7.266  0.692   8.040
removeSNPs                    4.582  0.289   5.111
* 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	166.586	14.516	193.130
calculateFDRs	21.644	4.981	68.196
plotAlphaDistributionOneChr	18.443	1.429	45.610
plotFinalSegmentation	19.601	2.598	41.093
plotPMDSegmentation	103.008	8.387	147.633
readMethylome	1.754	0.152	2.115
readSNPTable	0.354	0.024	0.388
removeSNPs	4.582	0.289	5.111
savePMDSegments	93.604	5.902	108.361
saveUMRLMRSegments	7.690	0.726	8.526
segmentPMDs	90.686	5.840	127.192
segmentUMRsLMRs	7.266	0.692	8.040