Package: clusterProfiler

Version: 1.1.3

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clusterProfiler_1.1.3.tar.gz

StartedAt: 2011-05-09 14:01:44 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:04:41 -0700 (Mon, 09 May 2011)

EllapsedTime: 176.7 seconds

RetCode: 0

Status:  OK

CheckDir: clusterProfiler.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/clusterProfiler.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clusterProfiler/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clusterProfiler’ version ‘1.1.3’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘clusterProfiler’ 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
.PlotClusterProfInternal: no visible binding for global variable
  ‘Description’
.PlotClusterProfInternal: no visible binding for global variable
  ‘Percentage’
.PlotClusterProfInternal: no visible binding for global variable
  ‘Cluster’
.PlotClusterProfInternal: no visible binding for global variable
  ‘Count’
.PlotClusterProfInternal: no visible binding for global variable
  ‘Pvalue’
.PlotClusterProfInternal: no visible binding for global variable
  ‘pvalue’
.barplotInternal: no visible binding for global variable ‘Description’
.barplotInternal: no visible binding for global variable ‘Count’
.compareClusterResultReshape: no visible binding for global variable
  ‘Description’
.compareClusterResultReshape: no visible binding for global variable
  ‘Count’
.compareClusterResultTopN: no visible binding for global variable
  ‘Cluster’
* 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 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 ‘clusterProfiler’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: reshape
Loading required package: plyr

Attaching package: ‘reshape’

The following object(s) are masked from ‘package:plyr’:

    rename, round_any

Loading required package: grid
Loading required package: proto
Loading required package: DBI




** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘clusterProfiler.Rnw’ 
** testing if installed package can be loaded

* DONE (clusterProfiler)

name	user	system	elapsed
compareCluster	8.261	0.374	8.879
enrichGO	0	0	0
enrichKEGG	1.318	0.062	1.387
groupGO	2.606	0.383	3.067