Package: methyAnalysis

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch methyAnalysis_1.2.0.tar.gz

StartedAt: 2013-05-01 07:52:15 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 08:11:25 -0700 (Wed, 01 May 2013)

EllapsedTime: 1149.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: methyAnalysis.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/methyAnalysis.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 'methyAnalysis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methyAnalysis' version '1.2.0'
* 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 'methyAnalysis' can be installed ... [59s/60s] 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [469s/568s] WARNING
Found the following significant warnings:

  Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                               user system elapsed
plotMethylationHeatmapByGene 93.278  4.720 132.097
buildAnnotationTracks        54.348  2.591  93.484
plotHeatmapByGene            47.784  2.397  71.440
plotTracksWithDataTrackInfo  40.300  2.211  43.907
heatmapByChromosome          38.482  2.042  41.442
createTranscriptTrack        37.534  2.739  41.394
annotateDMRInfo              36.640  1.673  39.537
export.DMRInfo               27.817  1.805  30.149
annotateGRanges              22.760  1.018  24.199
MethyLumiM2GenoSet           12.249  0.489  13.157
* 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

WARNING: There was 1 warning.
See
  '/Users/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'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'image' when loading 'graphics'
Warning: replacing previous import 'nleqslv' when loading 'nleqslv'
* DONE (methyAnalysis)

name	user	system	elapsed
MethyGenoSet-class	0.169	0.025	0.197
MethyLumiM2GenoSet	12.249	0.489	13.157
annotateDMRInfo	36.640	1.673	39.537
annotateGRanges	22.760	1.018	24.199
buildAnnotationTracks	54.348	2.591	93.484
checkChrName	0.280	0.020	0.304
createTranscriptTrack	37.534	2.739	41.394
detectDMR.slideWin	1.018	0.046	1.069
exampleMethyGenoSet	0.511	0.027	0.547
export.DMRInfo	27.817	1.805	30.149
export.methyGenoSet	0.806	0.032	0.842
getContinuousRegion	1.156	0.051	1.313
heatmapByChromosome	38.482	2.042	41.442
identifySigDMR	1.555	0.049	1.638
plotHeatmapByGene	47.784	2.397	71.440
plotMethylationHeatmapByGene	93.278	4.720	132.097
plotTracksWithDataTrackInfo	40.300	2.211	43.907
smoothMethyData	0.781	0.032	0.859