BioC 2.11: CHECK report for methyAnalysis on moscato1

Package: methyAnalysis

Version: 1.0.0

Command: rm -rf methyAnalysis.buildbin-libdir && mkdir methyAnalysis.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methyAnalysis.buildbin-libdir methyAnalysis_1.0.0.tar.gz >methyAnalysis-install.out 2>&1 && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD check --library=methyAnalysis.buildbin-libdir --install="check:methyAnalysis-install.out" --force-multiarch --no-vignettes --timings methyAnalysis_1.0.0.tar.gz && mv methyAnalysis.buildbin-libdir/* methyAnalysis.Rcheck/ && rmdir methyAnalysis.buildbin-libdir

StartedAt: 2013-03-25 02:00:00 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:12:17 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 736.6 seconds

RetCode: 0

Status: OK

CheckDir: methyAnalysis.Rcheck

Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/methyAnalysis.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
plotMethylationHeatmapByGene 19.41   0.47   31.79
annotateDMRInfo              15.05   0.20   15.26
export.DMRInfo               13.62   0.11   13.74
buildAnnotationTracks        11.73   0.25   22.56
annotateGRanges              10.67   0.22   10.89
heatmapByChromosome           6.74   0.18    6.92
plotTracksWithDataTrackInfo   6.31   0.22    6.54
MethyLumiM2GenoSet            5.66   0.06    6.54
createTranscriptTrack         5.41   0.19    5.60
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
plotMethylationHeatmapByGene 24.35   0.63   38.86
annotateDMRInfo              20.09   0.24   20.33
export.DMRInfo               17.77   0.09   17.88
buildAnnotationTracks        16.02   0.51   27.88
annotateGRanges              10.88   0.20   11.07
heatmapByChromosome           9.44   0.32    9.77
MethyLumiM2GenoSet            9.09   0.09    9.19
createTranscriptTrack         8.08   0.31    8.44
plotTracksWithDataTrackInfo   8.08   0.31    8.57
* 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
  'D:/biocbld/bbs-2.11-bioc/meat/methyAnalysis.Rcheck/00check.log'
for details.


install for i386

* 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'

install for x64

* installing *source* package 'methyAnalysis' ...
** testing if installed package can be loaded
Warning: replacing previous import 'image' when loading 'graphics'
* MD5 sums
packaged installation of 'methyAnalysis' as methyAnalysis_1.0.0.zip

* DONE (methyAnalysis)

Summary

Command output