BioC 2.12: CHECK report for topGO on george2

Package: topGO

Version: 2.12.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings topGO_2.12.0.tar.gz

StartedAt: 2013-10-09 05:18:38 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 05:23:40 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 302.3 seconds

RetCode: 0

Status:  OK

CheckDir: topGO.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/topGO.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘2.12.0’
* 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 ... [23s/24s] 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [49s/51s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
topGOdata-class 13.037  0.160  13.743
getPvalues       9.508  0.232   9.777
getSigGroups     8.141  0.040   8.729
* 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
  ‘/home/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
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (topGO)

name	user	system	elapsed
GOdata	0.684	0.000	0.689
annFUN	2.648	0.112	2.842
classicCount-class	0.088	0.000	0.088
classicExpr-class	0.056	0.000	0.053
classicScore-class	0.072	0.000	0.073
dagFunctions	0.028	0.000	0.029
diagnosticMethods	0.945	0.016	0.964
elimExpr-class	0.060	0.012	0.071
elimScore-class	0.056	0.012	0.067
geneList	0.056	0.004	0.060
getPvalues	9.508	0.232	9.777
getSigGroups	8.141	0.040	8.729
groupGOTerms	0.772	0.020	0.792
inducedGraph	0.104	0.000	0.103
parentChild-class	0.008	0.012	0.018
printGraph-methods	0.040	0.012	0.054
topGOdata-class	13.037	0.160	13.743
topGOresult-class	0.104	0.032	0.150