BioC 2.12: CHECK report for MethylSeekR on george2

Package: MethylSeekR

Version: 1.0.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings MethylSeekR_1.0.1.tar.gz

StartedAt: 2013-10-09 03:11:05 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:26:32 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 926.7 seconds

RetCode: 0

Status:  OK

CheckDir: MethylSeekR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/MethylSeekR.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [30s/30s] 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 ... [11m/11m] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
MethylSeekR-package         194.229  1.720 203.166
plotPMDSegmentation         112.631  0.756 114.460
savePMDSegments             111.911  0.604 113.764
segmentPMDs                 106.846  0.504 107.686
calculateFDRs                28.849  0.048  35.463
plotAlphaDistributionOneChr  22.414  0.108  22.724
plotFinalSegmentation        16.669  0.200  17.432
saveUMRLMRSegments            6.889  0.168   7.091
segmentUMRsLMRs               5.973  0.104   6.162
* 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	194.229	1.720	203.166
calculateFDRs	28.849	0.048	35.463
plotAlphaDistributionOneChr	22.414	0.108	22.724
plotFinalSegmentation	16.669	0.200	17.432
plotPMDSegmentation	112.631	0.756	114.460
readMethylome	0.888	0.012	0.905
readSNPTable	0.296	0.012	0.314
removeSNPs	3.512	0.008	3.533
savePMDSegments	111.911	0.604	113.764
saveUMRLMRSegments	6.889	0.168	7.091
segmentPMDs	106.846	0.504	107.686
segmentUMRsLMRs	5.973	0.104	6.162