Package: minfi

Version: 1.5.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch minfi_1.5.6.tar.gz

StartedAt: 2013-03-25 03:33:43 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:42:31 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 527.6 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/minfi.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 'minfi/DESCRIPTION' ... OK
* this is package 'minfi' version '1.5.6'
* 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 'minfi' can be installed ... [21s/21s] 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 ... [231s/232s] OK
Examples with CPU or elapsed time > 5s
                                    user system elapsed
preprocessSwan                    72.038 12.640  85.282
plotBetasByType                   30.755  5.620  36.656
densityBeanPlot                   15.836  1.215  17.081
detectionP                        13.789  2.075  15.950
read.450k.exp                     12.682  1.149  13.943
densityPlot                        9.758  1.531  11.370
preprocessIllumina                 9.916  1.137  11.094
read.450k                          7.922  0.741   8.848
preprocessRaw                      6.816  0.900   7.757
IlluminaMethylationManifest-class  4.641  0.376   5.234
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [105s/105s]
 [105s/106s] OK
* 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 'minfi' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'minfi.Rnw' 
** testing if installed package can be loaded
* DONE (minfi)

name	user	system	elapsed
GenomicMethylSet-class	0.011	0.008	0.018
GenomicRatioSet-class	0.007	0.005	0.012
IlluminaMethylationManifest-class	4.641	0.376	5.234
MethylSet-class	0.004	0.007	0.011
RGChannelSet-class	0.004	0.006	0.010
controlStripPlot	4.052	0.288	4.361
densityBeanPlot	15.836	1.215	17.081
densityPlot	9.758	1.531	11.370
detectionP	13.789	2.075	15.950
dmpFinder	2.073	0.383	2.514
logit2	0.002	0.004	0.006
mdsPlot	2.524	0.497	3.036
plotBetasByType	30.755	5.620	36.656
plotCpg	0.256	0.037	0.294
preprocessIllumina	9.916	1.137	11.094
preprocessRaw	6.816	0.900	7.757
preprocessSwan	72.038	12.640	85.282
qcReport	0.104	0.019	0.123
read.450k	7.922	0.741	8.848
read.450k.exp	12.682	1.149	13.943
read.450k.sheet	0.080	0.016	0.104