[Bioc-devel] Wish: BioC devel on R stable for more frequent package updates

Wolfgang Huber huber at ebi.ac.uk
Mon Jan 7 19:00:29 CET 2008

Dear all,

I like the suggestion a lot but...:

I guess the main problem is that the daily checks in Seattle are run on 
R-devel and there is no easy way to make sure that a package also runs 
on a different version of R. Basically Henrik's proposal shifts the 
burden of testing that packages pass R CMD check and R CMD INSTALL on 
all the possible versions of R that their "Depends" field allows (and 
all platforms) to the individual maintainer. And I am not sure whether 
everybody is ready for that, or whether it is an efficient use of our time.

Best wishes

Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

Henrik Bengtsson wrote:
> Hi,
> I'm quite sure something similar to the below has been discussed
> before.  I've got aroma.affymetrix
> (http://www.braju.com/R/aroma.affymetrix/) and I am thinking of making
> it available on Bioconductor trying to meet the following:
> 1) The package is designed to work with the release version of R
> (v2.6.x) in order to be more user friendly (and more stable).
> 2) The package is frequently updated (a few times a month).
> 3) Users should be able to run it on R release (or R devel, if they
> are in that league).
> 4) Users should be able to use other BioC release package (or BioC
> devel packages,
> if they are in that league).
> I'm currently providing the above via my own repository using standard
> R installation mechanisms.  However, the BioC release/devel repository
> system does not support the above, because:
> A) BioC release should not be updated beyond bug fixes and minor updates.
> B) The BioC devel branch requires R devel.
> What are the objectives for strictly enforcing R devel on BioC devel?
> Couldn't the latter requirement, which is mostly an installation
> script requirement, instead be taken care of by the regular package
> dependencies?  That is, you can put a package in BioC devel that
> depends on R stable and as long as other package dependencies install
> on R stable, then everything should be fine (relying on the standard R
> installation mechanisms).  For example, if Biobase requires R devel,
> then all packages depending on it will also need R devel, but
> non-Biobase packages will not "inherit" that dependency on R devel.
> Nightly builds and checks can still be done on R devel, meaning a BioC
> devel package should install on R devel, but may also install on R
> stable.
> Best,

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