BioC 2.12: CHECK report for methyAnalysis on george2

Package: methyAnalysis

Version: 1.2.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings methyAnalysis_1.2.0.tar.gz

StartedAt: 2013-10-09 03:11:01 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:34:55 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 1433.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: methyAnalysis.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/methyAnalysis.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.2.0’
* 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 ... [81s/82s] 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 ... [8m/11m] 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 70.749  1.220 128.381
annotateDMRInfo              57.972  0.208  58.583
buildAnnotationTracks        50.639  0.788  78.343
export.DMRInfo               48.407  0.088  74.637
plotHeatmapByGene            44.703  0.736  90.930
annotateGRanges              37.282  0.080  37.390
heatmapByChromosome          31.958  0.716  61.150
createTranscriptTrack        30.206  0.516  37.319
plotTracksWithDataTrackInfo  27.149  0.492  29.570
MethyLumiM2GenoSet           17.881  0.324  18.472
* 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
  ‘/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’
** 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	0.160	0.004	0.165
MethyLumiM2GenoSet	17.881	0.324	18.472
annotateDMRInfo	57.972	0.208	58.583
annotateGRanges	37.282	0.080	37.390
buildAnnotationTracks	50.639	0.788	78.343
checkChrName	0.284	0.004	0.290
createTranscriptTrack	30.206	0.516	37.319
detectDMR.slideWin	1.432	0.000	2.775
exampleMethyGenoSet	0.624	0.008	0.959
export.DMRInfo	48.407	0.088	74.637
export.methyGenoSet	0.992	0.004	1.961
getContinuousRegion	1.308	0.020	1.859
heatmapByChromosome	31.958	0.716	61.150
identifySigDMR	1.948	0.008	3.283
plotHeatmapByGene	44.703	0.736	90.930
plotMethylationHeatmapByGene	70.749	1.220	128.381
plotTracksWithDataTrackInfo	27.149	0.492	29.570
smoothMethyData	0.936	0.000	1.222