Package: methVisual

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings methVisual_1.0.1.tar.gz

StartedAt: 2010-10-04 17:52:35 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 17:54:49 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 133.7 seconds

RetCode: 0

Status:  OK

CheckDir: methVisual.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/methVisual.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'methVisual/DESCRIPTION' ... OK
* this is package 'methVisual' version '1.0.1'
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* 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, 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	0.811	0.028	0.876
MethAlignNW	4.418	0.126	4.824
MethDataInput	0.065	0.018	0.096
MethLollipops	0.021	0.002	0.023
MethylQC	3.564	0.057	3.713
cgInAlign	0.003	0.001	0.003
cgMethFinder	0.001	0.000	0.001
coversionGenom	0.000	0.001	0.001
findNonAligned	0.004	0.002	0.005
heatMapMeth	0.132	0.008	0.213
makeDataMethGFF	0.549	0.064	0.654
makeLocalExpDir	0.049	0.017	0.082
makeTabFilePath	0.053	0.005	0.087
matrixSNP	0.506	0.014	0.549
methCA	0.022	0.004	0.029
methData	0.002	0.001	0.003
methFisherTest	0.059	0.002	0.066
methWhitneyUTest	0.007	0.001	0.008
plotAbsMethyl	0.005	0.001	0.006
plotMatrixSNP	1.070	0.020	1.169
readBisulfFASTA	0.055	0.017	0.091
selectRefSeq	0.051	0.018	0.078