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.
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.