[Rd] package dependencies specification
Martin Morgan
mtmorgan at fhcrc.org
Wed Aug 26 04:15:48 CEST 2009
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.
>
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