Package: topGO

Version: 2.6.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings topGO_2.6.0.tar.gz

StartedAt: 2012-03-24 03:03:13 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:06:06 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 173.0 seconds

RetCode: 0

Status:  OK

CheckDir: topGO.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/topGO.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-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 ‘2.6.0’
* 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 ... 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 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
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class “connection” in package ‘IRanges’ seems equivalent to one from package ‘graph’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class “file” in package ‘IRanges’ seems equivalent to one from package ‘graph’ and is not turning on duplicate class definitions for this class
Creating a generic function for ‘print’ from package ‘base’ in package ‘topGO’
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘topGO.Rnw’ 
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

* DONE (topGO)

name	user	system	elapsed
GOdata	0.040	0.004	0.046
annFUN	1.980	0.080	2.363
classicCount-class	0	0	0
classicExpr-class	0.004	0.000	0.003
classicScore-class	0.008	0.000	0.008
dagFunctions	0	0	0
diagnosticMethods	0.352	0.012	0.411
elimExpr-class	0.004	0.000	0.001
elimScore-class	0	0	0
geneList	0.004	0.000	0.004
getPvalues	5.912	0.200	6.610
getSigGroups	5.589	0.020	5.749
groupGOTerms	0.472	0.004	0.474
inducedGraph	0.06	0.00	0.06
parentChild-class	0.000	0.000	0.001
printGraph-methods	0	0	0
topGOdata-class	7.352	0.064	7.506
topGOresult-class	0.032	0.000	0.033