Package: spotSegmentation

Version: 1.7.0

Command: /loc/biocbuild/2.0d/R/bin/R CMD check spotSegmentation_1.7.0.tar.gz

RetCode: 1

Time: 46.7 seconds

Status: ERROR

CheckDir: spotSegmentation.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/2.0d/Rpacks/spotSegmentation.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'spotSegmentation/DESCRIPTION' ... OK
* this is package 'spotSegmentation' version '1.7.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'spotSegmentation' can be installed ... 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 syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating spotSegmentation-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'spotSegmentation-Ex.R' failed.
The error most likely occurred in:

> ### * plot.spotseg
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: plot.spotseg
> ### Title: Microarray Spot Segmentation Plot
> ### Aliases: plot.spotseg
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(spotSegTest)
> 
> # columns of spotSegTest:
> #  1 intensities from the Cy3 (green) channel
> #  2 intensities from the Cy5 (red) channel
> 
> dataTransformation <- function(x) (256*256-1-x)^2*4.71542407E-05 
> 
> chan1 <- matrix(dataTransformation(spotSegTest[,1]), 144, 199)
> chan2 <- matrix(dataTransformation(spotSegTest[,2]), 144, 199)
> 
> hivGrid <- spotgrid( chan1, chan2, rows = 4, cols = 6, show = TRUE)
> 
> library(mclust)
> 
> hivSeg <- spotseg( chan1, chan2, hivGrid$rowcut, hivGrid$colcut)
Error in estepV(data = c(985.911474259757, 974.51915116936, 962.074769814704,  : 
	argument "parameters" is missing, with no default
Execution halted

* Installing *source* package 'spotSegmentation' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: mclust
** help
 >>> Building/Updating help pages for package 'spotSegmentation'
     Formats: text html latex example 
  plot.spotseg                      text    html    latex   example
  plotBlockImage                    text    html    latex   example
  spotSegTest                       text    html    latex
  spotgrid                          text    html    latex   example
  spotseg                           text    html    latex   example
  summary.spotseg                   text    html    latex   example
** building package indices ...
* DONE (spotSegmentation)