From Kurt.Hornik at wu-wien.ac.at  Thu Sep  8 10:41:15 2005
From: Kurt.Hornik at wu-wien.ac.at (Kurt Hornik)
Date: Thu, 8 Sep 2005 10:41:15 +0200
Subject: [Rd] CRAN, Bioconductor and ctv package dependency questions
In-Reply-To: <971536df05090710422229e025@mail.gmail.com>
References: <971536df05090710422229e025@mail.gmail.com>
Message-ID: <17183.63787.468382.354659@mithrandir.hornik.net>

>>>>> 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 :-)

> 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



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