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:mtmor...@fhcrc.org] > Sent: Tuesday, August 25, 2009 10:16 PM > To: christos.hat...@nuverabio.com > Cc: r-devel@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@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
