Package: methVisual

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch methVisual_1.3.0.tar.gz

StartedAt: 2011-02-24 16:15:27 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 16:16:53 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 85.4 seconds

RetCode: 0

Status:  OK

CheckDir: methVisual.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/methVisual.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'methVisual/DESCRIPTION' ... OK
* this is package 'methVisual' version '1.3.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'methVisual' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'methVisual' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: proto
Loading required package: DBI
Loading required package: RSQLite
Loading required package: RSQLite.extfuns
Loading required package: chron
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(...) : error in rgl_init
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (methVisual)

name	user	system	elapsed
Cooccurrence	0.633	0.008	0.643
MethAlignNW	1.830	0.026	1.969
MethDataInput	0.043	0.010	0.053
MethLollipops	0.012	0.000	0.013
MethylQC	1.564	0.014	1.578
cgInAlign	0.003	0.000	0.003
cgMethFinder	0.000	0.000	0.001
coversionGenom	0	0	0
findNonAligned	0.003	0.001	0.004
heatMapMeth	0.091	0.001	0.093
makeDataMethGFF	0.342	0.018	0.526
makeLocalExpDir	0.034	0.009	0.043
makeTabFilePath	0.005	0.001	0.006
matrixSNP	0.351	0.009	0.361
methCA	0.016	0.002	0.017
methData	0.002	0.000	0.002
methFisherTest	0.042	0.002	0.043
methWhitneyUTest	0.005	0.001	0.006
plotAbsMethyl	0.004	0.000	0.004
plotMatrixSNP	0.805	0.013	0.819
readBisulfFASTA	0.038	0.010	0.047
selectRefSeq	0.033	0.009	0.042