Package: methVisual

Version: 1.2.0

Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings methVisual_1.2.0.tar.gz

StartedAt: 2011-03-31 07:23:43 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 07:25:35 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 111.8 seconds

RetCode: 0

Status:  OK

CheckDir: methVisual.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/methVisual.Rcheck'
* using R version 2.12.2 (2011-02-25)
* 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 '1.2.0'
* 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 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, mapply, order, paste, pmax, pmax.int, pmin,
    pmin.int, rbind, rep.int, table

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 ...
** testing if installed package can be loaded

* DONE (methVisual)

name	user	system	elapsed
Cooccurrence	0.74	0.00	0.75
MethAlignNW	1.73	0.03	2.43
MethDataInput	0.03	0.03	0.06
MethLollipops	0.03	0.00	0.03
MethylQC	1.55	0.02	1.56
cgInAlign	0	0	0
cgMethFinder	0	0	0
coversionGenom	0	0	0
findNonAligned	0.00	0.01	0.01
heatMapMeth	0.13	0.00	0.16
makeDataMethGFF	0.34	0.02	0.48
makeLocalExpDir	0.05	0.03	0.08
makeTabFilePath	0	0	0
matrixSNP	0.29	0.02	0.31
methCA	0.03	0.00	0.10
methData	0.00	0.01	0.01
methFisherTest	0.05	0.00	0.05
methWhitneyUTest	0.02	0.00	0.02
plotAbsMethyl	0	0	0
plotMatrixSNP	0.65	0.00	0.67
readBisulfFASTA	0.07	0.02	0.08
selectRefSeq	0.03	0.03	0.06