Package: topGO

Version: 2.10.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch topGO_2.10.0.tar.gz

StartedAt: 2013-03-25 01:31:34 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:34:47 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 192.8 seconds

RetCode: 0

Status:  OK

CheckDir: topGO.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/topGO.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '2.10.0'
* 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 for left-over 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'
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 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' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
topGOdata-class 8.718  0.850   9.843
getSigGroups    5.094  0.058   5.202
* 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
  '/Users/biocbuild/bbs-2.11-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	0.057	0.004	0.061
annFUN	2.064	0.186	2.305
classicCount-class	0.000	0.001	0.001
classicExpr-class	0.002	0.000	0.002
classicScore-class	0.007	0.000	0.007
dagFunctions	0	0	0
diagnosticMethods	0.690	0.027	0.723
elimExpr-class	0.001	0.000	0.001
elimScore-class	0	0	0
geneList	0.003	0.001	0.003
getPvalues	4.497	0.283	4.972
getSigGroups	5.094	0.058	5.202
groupGOTerms	0.817	0.042	0.878
inducedGraph	0.072	0.001	0.075
parentChild-class	0.001	0.000	0.002
printGraph-methods	0.000	0.000	0.001
topGOdata-class	8.718	0.850	9.843
topGOresult-class	0.046	0.002	0.048