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
>
> ______________________________________________
> 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
