Package: ChIPsim

Version: 1.7.2

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings ChIPsim_1.7.2.tar.gz

StartedAt: 2011-07-07 00:01:28 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 00:04:15 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 167.8 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPsim.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/ChIPsim.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-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 ‘1.7.2’
* 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 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	5.684	0.036	5.775
decodeQuality	0.000	0.000	0.001
defaultControl	0.000	0.000	0.002
defaultErrorProb	0	0	0
defaultFunctions	0.000	0.000	0.003
defaultGenerator	0.360	0.008	0.364
extractQuality	0	0	0
feat2dens	2.140	0.008	2.152
featureDensity	0.004	0.000	0.001
makeFeatures	0.120	0.000	0.121
placeFeatures	0.204	0.000	0.206
pos2fastq	0.076	0.000	0.073
readError	0.000	0.000	0.002
reconcileFeatures	0.205	0.000	0.207
sampleReads	3.424	0.032	3.540
simChIP	0	0	0
simpleNames	0.000	0.000	0.001
stableFeature	0.004	0.000	0.001
writeFASTQ	0.000	0.000	0.001