Package: RDRToolbox

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RDRToolbox_1.1.0.tar.gz

StartedAt: 2011-03-17 17:16:33 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 17:17:02 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 28.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: RDRToolbox.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/RDRToolbox.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RDRToolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RDRToolbox' version '1.1.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'RDRToolbox' 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 ... 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... ERROR
Running examples in 'RDRToolbox-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotDR
> ### Title: Plotting tool for two and three dimensional data
> ### Aliases: plotDR
> 
> ### ** Examples
> 
> ## plot a two dimensional LLE embedding of a 1.000 dimensional dataset
> d = generateData(samples=20, genes=1000, diffgenes=100, blocksize=10)
> d_low = LLE(data=d[[1]], dim=2, k=5)
Computing distance matrix ... done
Computing low dimensional emmbedding (using 5 nearest neighbours)... done
> plotDR(data=d_low, labels=d[[2]])
legend:
  class colour
1    -1  black
2     1    red
> 
> ## plot a three dimensional LLE embedding of a 1.000 dimensional dataset
> d = generateData(samples=20, genes=1000, diffgenes=100, blocksize=10)
> d_low = LLE(data=d[[1]], dim=3, k=5)
Computing distance matrix ... done
Computing low dimensional emmbedding (using 5 nearest neighbours)... done
> plotDR(data=d_low, labels=d[[2]])
Error in rgl.cur() : rgl_dev_getcurrent
Calls: plotDR ... plot3d -> plot3d.default -> clear3d -> .check3d -> rgl.cur
Execution halted

* installing *source* package 'RDRToolbox' ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(...) : error in rgl_init
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Warning messages:
1: In rgl.init(initValue) : RGL: GLX extension missing on server
2: In fun(...) : error in rgl_init

* DONE (RDRToolbox)

name	user	system	elapsed
DBIndex	0.004	0.001	0.005
Isomap	4.598	0.129	4.727
LLE	2.314	0.065	2.379
SwissRoll	0.000	0.000	0.001
generateData	2.343	0.065	2.408