R devel - Sep 2005 - CRAN, Bioconductor and ctv package dependency questions

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?

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?

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?

4. Are there any considerations in the above cases related to 
CRAN Task Views (ctv package)?
http://cran.r-project.org/src/contrib/Views/

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.

Thanks.

>>>>> 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