Package: topGO

Version: 1.16.2

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings topGO_1.16.2.tar.gz

StartedAt: 2010-10-04 18:59:07 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 19:02:11 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 184.0 seconds

RetCode: 0

Status:  OK

CheckDir: topGO.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/topGO.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'topGO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'topGO' version '1.16.2'
* 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 ... 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

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

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. 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	0.080	0.006	0.086
annFUN	1.793	0.151	1.994
classicCount-class	0	0	0
classicExpr-class	0.003	0.000	0.004
classicScore-class	0.011	0.000	0.012
dagFunctions	0	0	0
diagnosticMethods	1.106	0.017	1.131
elimExpr-class	0.003	0.000	0.002
elimScore-class	0.001	0.000	0.001
geneList	0.005	0.001	0.006
getPvalues	5.847	0.326	6.254
getSigGroups	9.007	0.067	9.202
groupGOTerms	0.635	0.025	0.669
inducedGraph	0.123	0.002	0.128
parentChild-class	0.003	0.000	0.004
printGraph-methods	0	0	0
topGOdata-class	9.342	0.607	10.427
topGOresult-class	0.067	0.002	0.069