Package: clusterProfiler

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clusterProfiler_1.7.1.tar.gz

StartedAt: 2013-03-24 03:51:25 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 03:54:32 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 187.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clusterProfiler.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/clusterProfiler.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'clusterProfiler/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'clusterProfiler' version '1.7.1'
* 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 'clusterProfiler' can be installed ... [16s/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 ... 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 ... WARNING
Codoc mismatches from documentation object 'Gff2GeneTable':
Gff2GeneTable
  Code: function(gffFile, compress = TRUE)
  Docs: function(gffFile)
  Argument names in code not in docs:
    compress

* 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 ... [21s/26s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
groupGO 7.603  1.153  13.169
* 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

WARNING: There was 1 warning.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/clusterProfiler.Rcheck/00check.log'
for details.

* installing *source* package 'clusterProfiler' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'clusterProfiler.Rnw' 
** testing if installed package can be loaded
* DONE (clusterProfiler)

name	user	system	elapsed
compareCluster	3.181	0.197	3.684
enrichGO	0.244	0.003	0.249
enrichKEGG	0.455	0.025	0.483
groupGO	7.603	1.153	13.169