[Rd] CRAN, Bioconductor and ctv package dependency questions
Kurt.Hornik at wu-wien.ac.at
Thu Sep 8 10:41:15 CEST 2005
>>>>> 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
> 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
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)?
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
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