Package: topGO

Version: 2.8.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings topGO_2.8.0.tar.gz

StartedAt: 2012-04-01 03:44:47 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 03:47:02 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 135.0 seconds

RetCode: 0

Status:  OK

CheckDir: topGO.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/topGO.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'topGO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'topGO' version '2.8.0'
* 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 whether package 'topGO' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... NOTE
getPvalues: warning in pt(t.stats, df = length(classlabel) - 2, lower =
  FALSE): partial argument match of 'lower' to 'lower.tail'
* 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 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 ... OK
* 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/hpages/test-puck5/bbs-2.10-bioc/meat/topGO.Rcheck/00check.log'
for details.

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

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

* DONE (topGO)

name	user	system	elapsed
GOdata	0.044	0.000	0.063
annFUN	1.464	0.024	1.536
classicCount-class	0	0	0
classicExpr-class	0.000	0.000	0.001
classicScore-class	0.004	0.000	0.005
dagFunctions	0	0	0
diagnosticMethods	0.544	0.004	0.569
elimExpr-class	0.000	0.000	0.001
elimScore-class	0	0	0
geneList	0.000	0.004	0.013
getPvalues	3.296	0.084	3.436
getSigGroups	3.812	0.008	3.834
groupGOTerms	0.308	0.000	0.308
inducedGraph	0.068	0.000	0.080
parentChild-class	0.000	0.000	0.001
printGraph-methods	0	0	0
topGOdata-class	5.613	0.052	5.708
topGOresult-class	0.032	0.000	0.043