Package: topGO

Version: 2.4.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch topGO_2.4.0.tar.gz

StartedAt: 2011-10-20 17:47:27 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 17:50:02 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 154.9 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 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'topGO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'topGO' version '2.4.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'topGO.pdf' from 2768Kb to 920Kb
  consider running tools::compactPDF() on these files
* 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

* installing *source* package 'topGO' ...
** R
** data
** inst
** preparing package for lazy loading
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	0.083	0.007	0.095
annFUN	2.257	0.180	2.724
classicCount-class	0.001	0.000	0.001
classicExpr-class	0.002	0.000	0.003
classicScore-class	0.008	0.000	0.009
dagFunctions	0.000	0.000	0.001
diagnosticMethods	0.645	0.017	0.665
elimExpr-class	0.011	0.001	0.013
elimScore-class	0	0	0
geneList	0.005	0.001	0.005
getPvalues	5.452	0.317	5.860
getSigGroups	7.728	0.060	7.945
groupGOTerms	0.651	0.028	0.700
inducedGraph	0.098	0.003	0.103
parentChild-class	0.002	0.001	0.003
printGraph-methods	0.001	0.000	0.001
topGOdata-class	9.657	0.753	11.047
topGOresult-class	0.055	0.002	0.057