Package: spotSegmentation

Version: 1.7.0

Command: D:\biocbld\2.0d\R\bin\R.exe CMD check spotSegmentation_1.7.0.tar.gz

RetCode: 1

Time: 30.5 seconds

Status: ERROR

CheckDir: spotSegmentation.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory 'D:/biocbld/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 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 R.css in D:/biocbld/2.0d/Rpacks/spotSegmentation.Rcheck


---------- Making package spotSegmentation ------------
  adding build stamp to DESCRIPTION
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'spotSegmentation'
     Formats: text html latex example chm 
  plot.spotseg                      text    html    latex   example chm
  plotBlockImage                    text    html    latex   example chm
  spotSegTest                       text    html    latex           chm
  spotgrid                          text    html    latex   example chm
  spotseg                           text    html    latex   example chm
  summary.spotseg                   text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\2.0d\Rpacks\spotSegmentation.Rcheck\00_pkg_src\spotSegmentation\chm\spotSegmentation.chm


Compile time: 0 minutes, 0 seconds
7	Topics
19	Local links
1	Internet link
1	Graphic


Created d:\biocbld\2.0d\Rpacks\spotSegmentation.Rcheck\00_pkg_src\spotSegmentation\chm\spotSegmentation.chm, 24,031 bytes
Compression decreased file by 413 bytes.
  preparing package spotSegmentation for lazy loading
Loading required package: mclust
  adding MD5 sums

* DONE (spotSegmentation)