Package: minfi

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch minfi_1.6.0.tar.gz

StartedAt: 2013-05-01 08:02:53 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 08:15:38 -0700 (Wed, 01 May 2013)

EllapsedTime: 765.5 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/minfi.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 'minfi/DESCRIPTION' ... OK
* this is package 'minfi' version '1.6.0'
* 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 'minfi' 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 ... [377s/385s] OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
preprocessSwan                    113.047 18.477 135.160
plotBetasByType                    55.203  8.408  64.247
detectionP                         31.612  3.136  35.112
densityBeanPlot                    28.603  1.672  30.843
preprocessIllumina                 19.561  1.573  21.228
read.450k.exp                      16.569  1.420  18.746
densityPlot                        15.488  1.898  17.447
read.450k                          13.024  1.258  14.855
preprocessRaw                      12.674  1.407  14.217
IlluminaMethylationManifest-class   6.376  0.437   6.994
controlStripPlot                    6.324  0.397   6.988
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [163s/166s]
 [164s/167s] 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
** testing if installed package can be loaded
* DONE (minfi)

name	user	system	elapsed
GenomicMethylSet-class	0.007	0.003	0.010
GenomicRatioSet-class	0.007	0.003	0.009
IlluminaMethylationManifest-class	6.376	0.437	6.994
MethylSet-class	0.004	0.008	0.012
RGChannelSet-class	0.005	0.009	0.013
controlStripPlot	6.324	0.397	6.988
densityBeanPlot	28.603	1.672	30.843
densityPlot	15.488	1.898	17.447
detectionP	31.612	3.136	35.112
dmpFinder	2.038	0.449	2.656
logit2	0.002	0.003	0.006
mdsPlot	1.813	0.409	2.237
plotBetasByType	55.203	8.408	64.247
plotCpg	0.670	0.053	0.733
preprocessIllumina	19.561	1.573	21.228
preprocessRaw	12.674	1.407	14.217
preprocessSwan	113.047	18.477	135.160
qcReport	0.089	0.011	0.117
read.450k	13.024	1.258	14.855
read.450k.exp	16.569	1.420	18.746
read.450k.sheet	0.733	0.096	0.900