Package: RSVSim

Version: 0.99.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RSVSim_0.99.3.tar.gz

StartedAt: 2013-03-25 04:30:59 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:36:25 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 326.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RSVSim.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/RSVSim.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 ‘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 ... [29s/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 ... 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 ... [43s/44s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
simulateSV 19.161  0.044  19.640
compareSVs  9.121  0.072   9.505
* 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
  ‘/home/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	9.121	0.072	9.505
estimateSVSizes	0.100	0.004	0.104
segmentalDuplications	0.216	0.012	0.228
simulateSV	19.161	0.044	19.640
weightsMechanism	0.02	0.00	0.02
weightsRepeat	0.004	0.012	0.016