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

Henrik Bengtsson hb at stat.berkeley.edu
Sun Jan 6 23:09:09 CET 2008


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



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