Package: ChIPsim

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChIPsim_1.7.0.tar.gz

StartedAt: 2011-05-09 13:55:17 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 13:58:49 -0700 (Mon, 09 May 2011)

EllapsedTime: 211.8 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPsim.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/ChIPsim.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* 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 ‘1.7.0’
* 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 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘ChIPsimIntro.pdf’ from 2214Kb to 499Kb
  consider running tools::compactPDF() on these files
* 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	5.127	0.996	6.497
decodeQuality	0.002	0.000	0.002
defaultControl	0.006	0.000	0.006
defaultErrorProb	0.001	0.000	0.001
defaultFunctions	0.009	0.001	0.010
defaultGenerator	0.170	0.003	0.180
extractQuality	0.000	0.000	0.001
feat2dens	3.091	1.051	4.475
featureDensity	0.002	0.000	0.002
makeFeatures	0.177	0.002	0.180
placeFeatures	0.284	0.014	0.304
pos2fastq	0.102	0.005	0.108
readError	0.003	0.000	0.004
reconcileFeatures	0.281	0.004	0.286
sampleReads	4.176	1.135	5.373
simChIP	0.001	0.000	0.001
simpleNames	0.000	0.001	0.001
stableFeature	0.001	0.000	0.001
writeFASTQ	0.002	0.000	0.003