Package: edd

Version: 1.11.1

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check edd_1.11.1.tar.gz

RetCode: 1

Time: 52.8 seconds

Status: ERROR

CheckDir: edd.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/Users/biocbuild/1.9d/Rpacks/edd.Rcheck'
* using R version 2.4.0 alpha (2006-09-07 r39185)
* checking for file 'edd/DESCRIPTION' ... OK
* this is package 'edd' version '1.11.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'edd' 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 whether the name space 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 edd-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'edd-Ex.R' failed.
The error most likely occurred in:

> ### * edd
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: edd
> ### Title: new expression density diagnostics interface
> ### Aliases: edd
> ### Keywords: models
> 
> ### ** Examples
> 
> require(Biobase)
[1] TRUE
> data(sample.exprSet.1)
> # should filter to genes with reasonable variation
> table( edd(sample.exprSet.1, meth="nnet", size=10, decay=.2) )
# weights:  369
initial  value 2592.827806 
iter  10 value 1911.028756
iter  20 value 1713.980314
iter  30 value 1461.436970
iter  40 value 1124.092000
iter  50 value 884.864786
iter  60 value 745.397518
iter  70 value 703.559622
iter  80 value 681.230220
iter  90 value 657.842068
iter 100 value 631.747806
final  value 631.747806 
stopped after 100 iterations

.25N(0,1)+.75N(4,1) .75N(0,1)+.25N(4,1)              B(2,8)              B(8,2) 
                  9                  76                  74                  20 
             N(0,1)              U(0,1)              X^2(1)           logN(0,1) 
                116                  19                   6                  34 
               t(3) 
                146 
> library(golubEsets)
> data(Golub_Merge)
> madvec <- apply(exprs(Golub_Merge),1,mad)
> minvec <- apply(exprs(Golub_Merge),1,min)
> keep <- (madvec > median(madvec)) & (minvec > 300)
> gmfilt <- Golub_Merge[keep==TRUE,]
Error in featureData(x) : no slot of name "featureData" for this object of class "ExpressionSet"
Execution halted

* Installing *source* package 'edd' ...
** R
** inst
** save image
Loading required package: golubEsets
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: class
Loading required package: nnet
Loading required package: xtable
** help
 >>> Building/Updating help pages for package 'edd'
     Formats: text html latex example 
  centerScale                       text    html    latex   example
  edd                               text    html    latex   example
  eddDist-class                     text    html    latex   example
  eddObsolete                       text    html    latex   example
  flatQQNorm                        text    html    latex   example
  latEDtable                        text    html    latex   example
  makeCandmat.raw                   text    html    latex   example
  maxKSp                            text    html    latex   example
  plotED                            text    html    latex   example
** building package indices ...
* DONE (edd)