BioC 2.12: CHECK report for LiquidAssociation on george2

Package: LiquidAssociation

Version: 1.14.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings LiquidAssociation_1.14.0.tar.gz

StartedAt: 2013-10-09 02:54:29 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:57:23 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 173.1 seconds

RetCode: 0

Status:  OK

CheckDir: LiquidAssociation.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/LiquidAssociation.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.14.0’
* 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/14s] 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 ... [25s/27s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getsGLA-methods 10.037  0.012  10.610
getsLA-methods   7.292  0.012   7.354
* 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
  ‘/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
** testing if installed package can be loaded
* DONE (LiquidAssociation)

name	user	system	elapsed
CNM-class	0.008	0.004	0.015
CNM.full-methods	0.444	0.000	0.445
CNM.simple-methods	0.052	0.000	0.050
GLA-methods	0.040	0.004	0.044
LA-methods	0.020	0.016	0.035
LiquidAssociation-package	0.036	0.016	0.054
getsGLA-methods	10.037	0.012	10.610
getsLA-methods	7.292	0.012	7.354
plotGLA-methods	0.044	0.012	1.060