Package: ChIPsim

Version: 1.13.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ChIPsim_1.13.0.tar.gz

StartedAt: 2013-03-25 00:43:39 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:48:57 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 317.8 seconds

RetCode: 0

Status:  OK

CheckDir: ChIPsim.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ChIPsim.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.13.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChIPsim’ can be installed ... [28s/29s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [29s/30s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
bindDens2readDens 6.677  0.032   6.741
* 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
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘ChIPsimIntro.Rnw’ 
** testing if installed package can be loaded
* DONE (ChIPsim)

name	user	system	elapsed
ChIPsim-package	0.008	0.004	0.012
bindDens2readDens	6.677	0.032	6.741
decodeQuality	0.020	0.000	0.021
defaultControl	0.008	0.000	0.011
defaultErrorProb	0.008	0.000	0.007
defaultFunctions	0.012	0.000	0.010
defaultGenerator	0.152	0.000	0.157
extractQuality	0.004	0.004	0.011
feat2dens	2.680	0.000	2.692
featureDensity	0.020	0.000	0.022
makeFeatures	0.160	0.000	0.159
placeFeatures	0.260	0.000	0.262
pos2fastq	0.116	0.008	0.121
readError	0.020	0.000	0.019
reconcileFeatures	0.284	0.000	0.283
sampleReads	4.612	0.008	4.774
simChIP	0.008	0.000	0.009
simpleNames	0.004	0.000	0.004
stableFeature	0.004	0.000	0.004
writeFASTQ	0.012	0.000	0.015