From christos.hatzis at nuverabio.com  Wed Aug 26 05:30:48 2009
From: christos.hatzis at nuverabio.com (Christos Hatzis)
Date: Tue, 25 Aug 2009 23:30:48 -0400
Subject: [Rd] package dependencies specification
In-Reply-To: <4A949AD4.5000805@fhcrc.org>
References: <EC5E05CAC02145E7BEE087E2A3629A28@headquarters.silicoinsights>
	<4A949AD4.5000805@fhcrc.org>
Message-ID: <14704F1369354135A07D5CAF88DBF1F7@headquarters.silicoinsights>

Hi Martin,

Thanks for taking a look and for the explanation of the error message.  
The problem seems to have been the space in R (>= 2.5.0) in the Depends
statement.  Removing that space resolved the error.  The parser seems to be
quite unforgiving.

Then I got the error that packages hgu133acdf, hgu133plus2cdf cannot be
imported because they do not have a namespace.  Moving those to the Depdends
statement seems to have resolved the package dependencies issues.

Thanks again.
-Christos   

> -----Original Message-----
> From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
> Sent: Tuesday, August 25, 2009 10:16 PM
> To: christos.hatzis at nuverabio.com
> Cc: r-devel at r-project.org
> Subject: Re: [Rd] package dependencies specification
> 
> 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
Christos Hatzis