BioC 2.12: CHECK report for methyAnalysis on petty

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: 2013-10-08 23:02:17 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:24:02 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 1305.2 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 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file '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 ... [67s/68s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [415s/524s] 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 75.126  4.147 105.421
buildAnnotationTracks        45.687  2.062  88.633
annotateDMRInfo              41.250  1.246  42.908
plotHeatmapByGene            39.991  2.030  56.226
export.DMRInfo               31.148  1.389  40.650
plotTracksWithDataTrackInfo  28.995  1.872  31.344
heatmapByChromosome          28.480  1.855  31.718
createTranscriptTrack        26.561  2.425  30.928
annotateGRanges              26.391  0.807  38.411
MethyLumiM2GenoSet           12.432  0.425  13.337
* 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	0.196	0.025	0.220
MethyLumiM2GenoSet	12.432	0.425	13.337
annotateDMRInfo	41.250	1.246	42.908
annotateGRanges	26.391	0.807	38.411
buildAnnotationTracks	45.687	2.062	88.633
checkChrName	0.385	0.027	0.743
createTranscriptTrack	26.561	2.425	30.928
detectDMR.slideWin	1.185	0.046	1.282
exampleMethyGenoSet	0.536	0.020	0.584
export.DMRInfo	31.148	1.389	40.650
export.methyGenoSet	0.840	0.028	1.368
getContinuousRegion	1.495	0.046	2.999
heatmapByChromosome	28.480	1.855	31.718
identifySigDMR	1.628	0.036	1.672
plotHeatmapByGene	39.991	2.030	56.226
plotMethylationHeatmapByGene	75.126	4.147	105.421
plotTracksWithDataTrackInfo	28.995	1.872	31.344
smoothMethyData	0.936	0.025	0.965