Package: LiquidAssociation

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch LiquidAssociation_1.14.0.tar.gz

StartedAt: 2013-05-01 07:28:12 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 07:30:50 -0700 (Wed, 01 May 2013)

EllapsedTime: 158.4 seconds

RetCode: 0

Status:  OK

CheckDir: LiquidAssociation.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/LiquidAssociation.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'LiquidAssociation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LiquidAssociation' version '1.14.0'
* 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 ... [14s/15s] 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 ... [24s/26s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getsGLA-methods 9.520  0.119   9.898
getsLA-methods  6.768  0.087   7.272
* 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
  '/Users/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
** testing if installed package can be loaded
* DONE (LiquidAssociation)

name	user	system	elapsed
CNM-class	0.007	0.001	0.009
CNM.full-methods	0.326	0.005	0.331
CNM.simple-methods	0.083	0.002	0.093
GLA-methods	0.021	0.001	0.023
LA-methods	0.025	0.001	0.027
LiquidAssociation-package	0.096	0.003	0.101
getsGLA-methods	9.520	0.119	9.898
getsLA-methods	6.768	0.087	7.272
plotGLA-methods	0.032	0.004	1.035