Package: LiquidAssociation

Version: 1.13.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings LiquidAssociation_1.13.0.tar.gz

StartedAt: 2013-01-16 03:56:24 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 03:58:32 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 128.2 seconds

RetCode: 0

Status:  OK

CheckDir: LiquidAssociation.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/LiquidAssociation.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LiquidAssociation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LiquidAssociation’ 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 ‘LiquidAssociation’ can be installed ... 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’ ... NOTE
The following files should probably not be installed:
  ‘biom.bst’, ‘biom.sty’, ‘natbib.sty’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getsGLA-methods 8.868  0.028   8.906
getsLA-methods  5.501  0.004   5.513
* 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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/LiquidAssociation.Rcheck/00check.log’
for details.

* installing *source* package ‘LiquidAssociation’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘LiquidAssociation’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘LiquidAssociation.Rnw’ 
** testing if installed package can be loaded

* DONE (LiquidAssociation)

name	user	system	elapsed
CNM-class	0.008	0.004	0.011
CNM.full-methods	0.272	0.016	0.285
CNM.simple-methods	0.048	0.000	0.049
GLA-methods	0.024	0.000	0.024
LA-methods	0.016	0.000	0.017
LiquidAssociation-package	0.044	0.000	0.049
getsGLA-methods	8.868	0.028	8.906
getsLA-methods	5.501	0.004	5.513
plotGLA-methods	0.024	0.008	1.034