Package: Neve2006

Version: 0.1.3

Command: D:\biocbld\bbs-2.0-bioc\R\bin\R.exe CMD check Neve2006_0.1.3.tar.gz

RetCode: 1

Time: 62.6 seconds

Status: ERROR

CheckDir: Neve2006.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.0-data-experiment/meat/Neve2006.Rcheck'
* using R version 2.5.1 (2007-06-27)
* checking for file 'Neve2006/DESCRIPTION' ... OK
* this is package 'Neve2006' version '0.1.3'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Neve2006' can be installed ... WARNING
Found the following significant warnings:
       missing link(s):  eSet-class VersionedBiobase-class Versioned-class
See 'D:/biocbld/bbs-2.0-data-experiment/meat/Neve2006.Rcheck/00install.out' for details.
* 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 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 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 cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  cloneMeta cloneNames make_cghExSet
Undocumented data sets:
  neveExCGH
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... WARNING
Data sets with usage in documentation object 'neveCGHmatch' but not in code:
  neveCels

* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... WARNING
  Warning: found non-ASCII string(s)
  '37<a1>c, 5% CO2'  '37<a1>c, no CO2'
Portable packages use only ASCII characters in their datasets.
* creating Neve2006-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'Neve2006-Ex.R' failed.
The error most likely occurred in:

> ### * cghExSet-class
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: cghExSet-class
> ### Title: Class "cghExSet" for combining CGH and expression data
> ### Aliases: cghExSet-class cloneMeta,cghExSet-method
> ###   cloneNames,cghExSet-method exprs,cghExSet-method
> ###   initialize,cghExSet-method logRatios,cghExSet-method
> ###   show,cghExSet-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("cghExSet")

Slots:
                                                               
Name:           cghAssays          cloneMeta          assayData
Class:          AssayData AnnotatedDataFrame          AssayData
                                                               
Name:           phenoData        featureData     experimentData
Class: AnnotatedDataFrame AnnotatedDataFrame              MIAME
                                            
Name:          annotation  .__classVersion__
Class:          character           Versions

Extends: 
Class "eSet", directly
Class "VersionedBiobase", by class "eSet", distance 2
Class "Versioned", by class "eSet", distance 3
> data(neveExCGH)
> logRatios(neveExCGH)[1:4,]
Error in function (classes, fdef, mtable)  : 
	unable to find an inherited method for function "assayData", for signature "environment"
Execution halted

installing R.css in D:/biocbld/bbs-2.0-data-experiment/meat/Neve2006.Rcheck


---------- Making package Neve2006 ------------
  adding build stamp to DESCRIPTION
  installing R files
  installing inst files
  installing data files
  preparing package Neve2006 for lazy loading
Loading required package: tools
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: hgu133a
Loading required package: annotate
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'Neve2006'
     Formats: text html latex example chm 
  cghExSet-class                    text    html    latex   example chm
     missing link(s):  eSet-class VersionedBiobase-class Versioned-class
  logRatios                         text    html    latex   example chm
  neveCGHmatch                      text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.0-data-experiment\meat\Neve2006.Rcheck\00_pkg_src\Neve2006\chm\Neve2006.chm


Compile time: 0 minutes, 0 seconds
4	Topics
16	Local links
0	Internet links
1	Graphic


Created d:\biocbld\bbs-2.0-data-experiment\meat\Neve2006.Rcheck\00_pkg_src\Neve2006\chm\Neve2006.chm, 18,795 bytes
Compression increased file by 3,093 bytes.
  adding MD5 sums

* DONE (Neve2006)