Package: methyAnalysis

Version: 1.1.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings methyAnalysis_1.1.3.tar.gz

StartedAt: 2013-01-16 04:16:36 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 04:37:28 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 1251.9 seconds

RetCode: 0

Status:  OK

CheckDir: methyAnalysis.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/methyAnalysis.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methyAnalysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methyAnalysis’ version ‘1.1.3’
* 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 ‘methyAnalysis’ can be installed ... 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 ... 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 ... NOTE
  No methods found in "IRanges" for requests: nlevels
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
plotMethylationHeatmapByGene 33.966 18.349 498.350
buildAnnotationTracks        19.317  7.816 147.212
annotateDMRInfo              23.921  0.100  24.275
annotateGRanges              16.453  0.024  16.578
export.DMRInfo               13.301  0.304  17.514
MethyLumiM2GenoSet           10.397  0.184  10.691
heatmapByChromosome           7.524  0.228   8.489
plotTracksWithDataTrackInfo   6.925  0.164   9.370
createTranscriptTrack         5.525  0.236   9.286
* 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 were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-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’
Warning: replacing previous import ‘nleqslv’ when loading ‘nleqslv’
No methods found in "IRanges" for requests: nlevels
** 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’
Warning: replacing previous import ‘nleqslv’ when loading ‘nleqslv’
No methods found in "IRanges" for requests: nlevels

* DONE (methyAnalysis)

name	user	system	elapsed
MethyGenoSet-class	0.108	0.000	0.110
MethyLumiM2GenoSet	10.397	0.184	10.691
annotateDMRInfo	23.921	0.100	24.275
annotateGRanges	16.453	0.024	16.578
buildAnnotationTracks	19.317	7.816	147.212
checkChrName	0.188	0.012	0.429
createTranscriptTrack	5.525	0.236	9.286
detectDMR.slideWin	0.932	0.024	3.262
exampleMethyGenoSet	0.372	0.004	0.933
export.DMRInfo	13.301	0.304	17.514
export.methyGenoSet	0.588	0.004	0.713
getContinuousRegion	0.932	0.000	0.957
heatmapByChromosome	7.524	0.228	8.489
identifySigDMR	1.140	0.000	1.143
plotMethylationHeatmapByGene	33.966	18.349	498.350
plotTracksWithDataTrackInfo	6.925	0.164	9.370
smoothMethyData	0.764	0.004	1.058