Package: topGO

Version: 2.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch topGO_2.11.0.tar.gz

StartedAt: 2013-03-25 05:00:40 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:04:18 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 218.0 seconds

RetCode: 0

Status:  OK

CheckDir: topGO.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/topGO.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '2.11.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'topGO' can be installed ... [19s/19s] OK
* checking installed package size ... OK
* checking package directory ... 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 ... [38s/38s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
topGOdata-class 10.668  0.835  11.559
getSigGroups     6.448  0.072   6.522
getPvalues       5.358  0.279   5.695
* 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-2.12-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	0.120	0.014	0.135
annFUN	2.852	0.259	3.131
classicCount-class	0.027	0.006	0.032
classicExpr-class	0.028	0.007	0.036
classicScore-class	0.030	0.008	0.039
dagFunctions	0.017	0.006	0.023
diagnosticMethods	0.697	0.039	0.742
elimExpr-class	0.025	0.008	0.033
elimScore-class	0.026	0.009	0.036
geneList	0.029	0.009	0.038
getPvalues	5.358	0.279	5.695
getSigGroups	6.448	0.072	6.522
groupGOTerms	0.708	0.031	0.739
inducedGraph	0.091	0.011	0.103
parentChild-class	0.030	0.011	0.041
printGraph-methods	0.012	0.007	0.020
topGOdata-class	10.668	0.835	11.559
topGOresult-class	0.099	0.025	0.125