Package: ChIPsim

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChIPsim_1.5.0.tar.gz

StartedAt: 2011-02-24 18:46:46 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 18:49:16 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 149.8 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPsim.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/ChIPsim.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: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPsim/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPsim’ 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 ‘ChIPsim’ 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 examples ... OK
* checking package vignettes in ‘inst/doc’ ... 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 ...
** testing if installed package can be loaded

* DONE (ChIPsim)

name	user	system	elapsed
ChIPsim-package	0	0	0
bindDens2readDens	5.459	1.114	6.633
decodeQuality	0.002	0.000	0.003
defaultControl	0.006	0.001	0.006
defaultErrorProb	0.000	0.000	0.001
defaultFunctions	0.009	0.000	0.010
defaultGenerator	0.330	0.005	0.335
extractQuality	0.000	0.001	0.001
feat2dens	3.155	1.010	4.209
featureDensity	0.002	0.000	0.003
makeFeatures	0.192	0.016	0.209
placeFeatures	0.301	0.017	0.321
pos2fastq	0.094	0.003	0.098
readError	0.004	0.000	0.005
reconcileFeatures	0.291	0.001	0.293
sampleReads	4.186	1.167	5.381
simChIP	0.000	0.000	0.001
simpleNames	0.001	0.000	0.001
stableFeature	0.001	0.001	0.001
writeFASTQ	0.003	0.000	0.003