From Kurt.Hornik at wu-wien.ac.at  Thu Sep  8 11:50:38 2005
From: Kurt.Hornik at wu-wien.ac.at (Kurt Hornik)
Date: Thu, 8 Sep 2005 11:50:38 +0200
Subject: [Rd] CRAN, Bioconductor and ctv package dependency questions
In-Reply-To: <20050908112117.444612da.Achim.Zeileis@wu-wien.ac.at>
References: <971536df05090710422229e025@mail.gmail.com>
	<17183.63787.468382.354659@mithrandir.hornik.net>
	<20050908112117.444612da.Achim.Zeileis@wu-wien.ac.at>
Message-ID: <17184.2414.260320.121790@mithrandir.hornik.net>

>>>>> Achim Zeileis writes:

> 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.

Ah yes.  We want to provide repository-side metadata in the style of
Debian's 'Release' files, and take advantage of them.  Which has been on
my TODO pile for quite some time now ... how hard can it be to write a
DCF file containing three or four lines ...

-k



[Rd] CRAN, Bioconductor and ctv package dependency questions
Kurt Hornik