Package: methyAnalysis

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch methyAnalysis_1.0.0.tar.gz

StartedAt: 2013-03-25 00:22:38 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:32:54 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 616.0 seconds

RetCode: 0

Status:  OK

CheckDir: methyAnalysis.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/methyAnalysis.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'methyAnalysis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methyAnalysis' version '1.0.0'
* 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 whether package 'methyAnalysis' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... NOTE
coerce,GenoSet-MethyGenoSet: no visible global function definition for
  'estimateM'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
plotMethylationHeatmapByGene 25.555  1.773  38.135
annotateDMRInfo              22.257  1.450  24.096
export.DMRInfo               20.482  1.581  22.294
annotateGRanges              14.475  0.950  16.085
buildAnnotationTracks        14.070  0.820  26.757
heatmapByChromosome           9.507  0.625  10.329
MethyLumiM2GenoSet            8.722  0.440   9.534
plotTracksWithDataTrackInfo   8.088  0.645   9.425
createTranscriptTrack         7.005  0.499   7.595
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/methyAnalysis.Rcheck/00check.log'
for details.

* installing *source* package 'methyAnalysis' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'image' when loading 'graphics'
** help
*** installing help indices
** building package indices
** installing vignettes
   'methyAnalysis.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'image' when loading 'graphics'

* DONE (methyAnalysis)

name	user	system	elapsed
MethyGenoSet-class	0.572	0.011	0.584
MethyLumiM2GenoSet	8.722	0.440	9.534
annotateDMRInfo	22.257	1.450	24.096
annotateGRanges	14.475	0.950	16.085
buildAnnotationTracks	14.070	0.820	26.757
checkChrName	0.210	0.017	0.233
createTranscriptTrack	7.005	0.499	7.595
detectDMR.slideWin	0.896	0.091	1.016
exampleMethyGenoSet	0.405	0.018	0.424
export.DMRInfo	20.482	1.581	22.294
export.methyGenoSet	0.547	0.045	0.612
getContinuousRegion	1.157	0.124	1.295
heatmapByChromosome	9.507	0.625	10.329
identifySigDMR	1.229	0.203	1.561
plotMethylationHeatmapByGene	25.555	1.773	38.135
plotTracksWithDataTrackInfo	8.088	0.645	9.425
smoothMethyData	0.715	0.061	1.228