From mtmorgan at fhcrc.org  Wed Aug 26 04:15:48 2009
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Tue, 25 Aug 2009 19:15:48 -0700
Subject: [Rd] package dependencies specification
In-Reply-To: <EC5E05CAC02145E7BEE087E2A3629A28@headquarters.silicoinsights>
References: <EC5E05CAC02145E7BEE087E2A3629A28@headquarters.silicoinsights>
Message-ID: <4A949AD4.5000805@fhcrc.org>

Hi Christos --

Christos Hatzis wrote:
>  
> Hello,
> 
> After running R CMD check on my package I received the following error on
> package dependencies:
> 
> * using log directory 'C:/z-zBackup/Nuvera Bio on
> Iatros01/Development/RPackages/nvNormalize/nvNormalize.Rcheck'
> * using R version 2.9.1 (2009-06-26)
> * using session charset: ISO8859-1
> * checking for file 'nvNormalize/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'nvNormalize' version '1.0'
> * checking package name space information ... OK
> * checking package dependencies ... ERROR
> Namespace dependencies not required:
>   affy affyio hgu133acdf hgu133plus2cdf simpleaffy

this confusingly worded message is saying that these packages are
import'ed by NAMESPACE, but not listed in Imports: or Depends: in
DESCRIPTION, but...

> 
> See the information on DESCRIPTION files in the chapter 'Creating R
> packages' of the 'Writing R Extensions' manual.
> 
> I've looked at the manual but cannot figure out if the problem is in the way
> I have specified dependencies in NAMESPACE or DESCRIPTION.  It appears that
> dependecies need to be specified in both. 
> These two files are shown below.
> 
> ------------------------------
> NAMESPACE
> 
> export(nv.batch.normalize, norm.options, combine.norm.esets,
> subset.norm.eset, update.sampleNames)
> 
> import(affy, simpleaffy, hgu133acdf, hgu133plus2cdf) 
> importFrom(affyio, read.celfile, read.celfile.header) 
>  
> DESCRIPTION
> ...
> Depends: R (>= 2.5.0), Biobase
> Imports: affy, affyio, simpleaffy, hgu133acdf, hgu133plus2cdf

I don't see anything wrong with what you list here. Perhaps the file is
malformed, or contains non-ASCII characters (tools::showNonASCII might
help) or is otherwise not processed properly (base::read.dcf)? In
addition I am not sure of the consequences of using charset ISO8859-1.

Martin

> --------------------------------
> 
> I'd appreciate any help.
> Thank you.
> 
> -Christos
> 
> Christos Hatzis, Ph.D.
> Nuvera Biosciences, Inc.
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] package dependencies specification
Martin Morgan