Package: RSVSim

Version: 0.99.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RSVSim_0.99.3.tar.gz

StartedAt: 2013-03-24 10:00:41 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 10:05:28 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 286.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RSVSim.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/RSVSim.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RSVSim/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RSVSim' version '0.99.3'
* 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 'RSVSim' can be installed ... [24s/28s] 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 ... WARNING
Undocumented data sets:
  'weightsMechanisms' 'weightsRepeats'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [37s/38s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
simulateSV 17.412  0.118  17.719
compareSVs  7.359  0.063   7.758
* 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

WARNING: There was 1 warning.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/RSVSim.Rcheck/00check.log'
for details.

* installing *source* package 'RSVSim' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'vignette.Rnw' 
** testing if installed package can be loaded
* DONE (RSVSim)

name	user	system	elapsed
compareSVs	7.359	0.063	7.758
estimateSVSizes	0.102	0.010	0.113
segmentalDuplications	0.240	0.022	0.262
simulateSV	17.412	0.118	17.719
weightsMechanism	0.016	0.003	0.019
weightsRepeat	0.011	0.004	0.014