Package: edd

Version: 1.11.1

Command: D:\biocbld\1.9d\R\bin\R.exe CMD check edd_1.11.1.tar.gz

RetCode: 1

Time: 61.7 seconds

Status: ERROR

CheckDir: edd.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory 'D:/biocbld/1.9d/Rpacks/edd.Rcheck'
* using R version 2.4.0 alpha (2006-09-10 r39242)
* 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 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 2482.023737 
iter  10 value 1547.317056
iter  20 value 1318.614271
iter  30 value 1168.755985
iter  40 value 1047.752571
iter  50 value 946.356849
iter  60 value 871.610448
iter  70 value 820.021395
iter  80 value 791.139396
iter  90 value 758.529361
iter 100 value 727.622942
final  value 727.622942 
stopped after 100 iterations

.25N(0,1)+.75N(4,1) .75N(0,1)+.25N(4,1)              B(2,8)              B(8,2) 
                 10                  80                  75                  28 
          logN(0,1)              N(0,1)                t(3)              U(0,1) 
                 34                 104                 146                  16 
             X^2(1) 
                  7 
> 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 R.css in D:/biocbld/1.9d/Rpacks/edd.Rcheck


---------- Making package edd ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  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

  installing inst files
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'edd'
     Formats: text html latex example chm 
  centerScale                       text    html    latex   example chm
  edd                               text    html    latex   example chm
  eddDist-class                     text    html    latex   example chm
  eddObsolete                       text    html    latex   example chm
  flatQQNorm                        text    html    latex   example chm
  latEDtable                        text    html    latex   example chm
  makeCandmat.raw                   text    html    latex   example chm
  maxKSp                            text    html    latex   example chm
  plotED                            text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\1.9d\Rpacks\edd.Rcheck\00_pkg_src\edd\chm\edd.chm


Compile time: 0 minutes, 0 seconds
10	Topics
72	Local links
0	Internet links
1	Graphic


Created d:\biocbld\1.9d\Rpacks\edd.Rcheck\00_pkg_src\edd\chm\edd.chm, 30,328 bytes
Compression decreased file by 15,871 bytes.
  adding MD5 sums

* DONE (edd)