Package: ChIPsim

Version: 1.7.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings ChIPsim_1.7.0.tar.gz

StartedAt: 2011-05-09 15:50:26 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 15:54:54 -0700 (Mon, 09 May 2011)

EllapsedTime: 267.9 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPsim.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/ChIPsim.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChIPsim/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChIPsim' version '1.7.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ChIPsim' 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 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 'ChIPsim' ...
** R
** 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

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

* DONE (ChIPsim)

name	user	system	elapsed
ChIPsim-package	0	0	0
bindDens2readDens	4.31	0.00	6.51
decodeQuality	0	0	0
defaultControl	0	0	0
defaultErrorProb	0	0	0
defaultFunctions	0	0	0
defaultGenerator	0.14	0.00	0.14
extractQuality	0	0	0
feat2dens	1.92	0.02	1.94
featureDensity	0	0	0
makeFeatures	0.14	0.00	0.14
placeFeatures	0.21	0.00	0.20
pos2fastq	0.07	0.00	0.08
readError	0	0	0
reconcileFeatures	0.19	0.01	0.20
sampleReads	2.80	0.03	3.11
simChIP	0	0	0
simpleNames	0	0	0
stableFeature	0	0	0
writeFASTQ	0	0	0