Package: topGO

Version: 2.3.1

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch topGO_2.3.1.tar.gz

StartedAt: 2011-02-24 21:43:32 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 21:45:56 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 143.8 seconds

RetCode: 0

Status:  OK

CheckDir: topGO.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/topGO.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘topGO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘topGO’ version ‘2.3.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘topGO’ can be installed ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
GOSumTest,classicScore: no visible binding for global variable
  ‘.PERMSUM.MAT’
GOSumTest,classicScore: no visible binding for global variable
  ‘.PERMSUM.LOOKUP’
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘topGO’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: AnnotationDbi
Loading required package: DBI
Package SparseM (0.86) loaded.
	   To cite, see citation("SparseM")


Attaching package: 'SparseM'

The following object(s) are masked from 'package:base':

    backsolve

Creating a new generic function for "print" in "topGO"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

* DONE (topGO)

name	user	system	elapsed
GOdata	0.191	0.004	0.198
annFUN	1.848	0.165	2.076
classicCount-class	0	0	0
classicExpr-class	0.002	0.000	0.003
classicScore-class	0.009	0.000	0.009
dagFunctions	0.001	0.000	0.001
diagnosticMethods	0.815	0.012	0.829
elimExpr-class	0.002	0.001	0.002
elimScore-class	0.000	0.000	0.001
geneList	0.006	0.001	0.007
getPvalues	5.728	0.362	6.200
getSigGroups	8.248	0.050	8.340
groupGOTerms	0.628	0.022	0.655
inducedGraph	0.097	0.002	0.101
parentChild-class	0.004	0.001	0.004
printGraph-methods	0.001	0.000	0.000
topGOdata-class	8.964	0.558	9.617
topGOresult-class	0.072	0.002	0.075