Package: methVisual

Version: 1.5.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings methVisual_1.5.0.tar.gz

StartedAt: 2011-05-09 14:34:33 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:36:15 -0700 (Mon, 09 May 2011)

EllapsedTime: 102.5 seconds

RetCode: 0

Status:  OK

CheckDir: methVisual.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/methVisual.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methVisual/DESCRIPTION' ... OK
* this is package 'methVisual' version '1.5.0'
* 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 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 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* 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

* 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
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'methVisual.Rnw' 
** testing if installed package can be loaded

* DONE (methVisual)

name	user	system	elapsed
Cooccurrence	0.58	0.00	0.59
MethAlignNW	1.61	0.01	2.52
MethDataInput	0.06	0.02	0.07
MethLollipops	0.02	0.00	0.02
MethylQC	1.48	0.00	1.59
cgInAlign	0	0	0
cgMethFinder	0	0	0
coversionGenom	0	0	0
findNonAligned	0	0	0
heatMapMeth	0.10	0.00	0.11
makeDataMethGFF	0.25	0.01	0.38
makeLocalExpDir	0.03	0.03	0.06
makeTabFilePath	0	0	0
matrixSNP	0.28	0.00	0.28
methCA	0.02	0.00	0.06
methData	0	0	0
methFisherTest	0.03	0.00	0.04
methWhitneyUTest	0.01	0.00	0.01
plotAbsMethyl	0	0	0
plotMatrixSNP	0.63	0.00	0.63
readBisulfFASTA	0.08	0.00	0.09
selectRefSeq	0.04	0.04	0.08