[Rd] package dependencies specification
Christos Hatzis
christos.hatzis at nuverabio.com
Wed Aug 26 05:30:48 CEST 2009
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
>
>
>
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