BioC 2.12: CHECK report for minfi on petty

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: 2013-10-08 23:04:14 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:19:27 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 912.9 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 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file '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 ... [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 ... [342s/462s] OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
preprocessSwan                    100.451 15.623 142.593
plotBetasByType                    55.155  8.782 133.959
densityBeanPlot                    25.428  1.524  26.984
detectionP                         18.303  2.626  20.973
preprocessIllumina                 18.839  1.652  35.930
read.450k.exp                      16.486  1.332  18.457
densityPlot                        14.480  1.579  16.106
read.450k                          12.928  1.193  14.841
preprocessRaw                      10.750  1.404  17.483
IlluminaMethylationManifest-class   6.794  0.418   7.343
controlStripPlot                    5.747  0.345   6.306
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [165s/197s]
 [166s/198s] 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	0.011	0.003	0.015
GenomicRatioSet-class	0.005	0.001	0.007
IlluminaMethylationManifest-class	6.794	0.418	7.343
MethylSet-class	0.005	0.006	0.011
RGChannelSet-class	0.004	0.005	0.009
controlStripPlot	5.747	0.345	6.306
densityBeanPlot	25.428	1.524	26.984
densityPlot	14.480	1.579	16.106
detectionP	18.303	2.626	20.973
dmpFinder	2.151	0.527	2.866
logit2	0.001	0.003	0.004
mdsPlot	2.752	0.410	3.167
plotBetasByType	55.155	8.782	133.959
plotCpg	0.761	0.112	1.510
preprocessIllumina	18.839	1.652	35.930
preprocessRaw	10.750	1.404	17.483
preprocessSwan	100.451	15.623	142.593
qcReport	0.149	0.012	0.177
read.450k	12.928	1.193	14.841
read.450k.exp	16.486	1.332	18.457
read.450k.sheet	0.156	0.015	0.220