From Achim.Zeileis at wu-wien.ac.at  Thu Sep  8 11:21:17 2005
From: Achim.Zeileis at wu-wien.ac.at (Achim Zeileis)
Date: Thu, 8 Sep 2005 11:21:17 +0200
Subject: [Rd] CRAN, Bioconductor and ctv package dependency questions
In-Reply-To: <17183.63787.468382.354659@mithrandir.hornik.net>
References: <971536df05090710422229e025@mail.gmail.com>
	<17183.63787.468382.354659@mithrandir.hornik.net>
Message-ID: <20050908112117.444612da.Achim.Zeileis@wu-wien.ac.at>

On Thu, 8 Sep 2005 10:41:15 +0200 Kurt Hornik wrote:

> >>>>> Gabor Grothendieck writes:
> 
> > 1. Can CRAN packages depend on Bioconductor packages and still pass
> > R CMD check?  That is can Suggests: and Depends: in the DESCRIPTION
> > file contain Bioconductor packages or only other CRAN packages?
> > Is there an example?
> 
> Yes, yes, yes.  (E.g., LMGene, limma, ...)
> 
> The only catch is that in the current setup of daily CRAN package
> checking, packages with non-CRAN dependencies are checked using fake
> or no installs.
> 
> > 2. If a package depends on a Bioconductor package does one just list
> > the package its dependent on or also all packages that that package
> > recursively depends on?  Is this the same as for CRAN packages that
> > a package is dependent on?
> 
> Yes.  There is a difference between "CRAN style package repositories",
> as handled by the base R Package Management system, and the main CRAN
> repository (which of course happens to be a CRAN style one).
> 
> > 3. Suppose that the output of package A is typically processed by
> > package B.  Thus strictly speaking no function in A depends on any
> > function in B; however, the output of A is not very usable without
> > post processing it by B.  Would one list A as being dependent on B
> > anyways?
> 
> I think this would fall into a third "dependency" category which we
> currently do not have.
> 
> > 4. Are there any considerations in the above cases related to 
> > CRAN Task Views (ctv package)?
> > http://cran.r-project.org/src/contrib/Views/
> 
> You would need to talk to the CRAN Task View (ctv) maintainer :-)

Yes, there are considerations that I have discusses with several people
including Kurt :-)
We're thinking about a way that CRAN style repositories can know what
their name is (CRAN, BioConductor, etc.) and then we could query whether
the repositories in getOption("repos") include a CRAN or a BioC
repository and then have views that include packages from both CRAN and
BioC and potentially other repositories.

Best,
Z

> > 5. Are the above discussed anywhere?  I looked up the Depends and
> > Suggests field in 1.1 of the R Extensions manual but none of the
> > above is addressed there.
> 
> Re 1/2: This is because R-exts tells you what to do and not what not
> to do.
> 
> Hth
> 
> -k
> 
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[Rd] CRAN, Bioconductor and ctv package dependency questions
Achim Zeileis