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

Henrik Bengtsson hb at stat.berkeley.edu
Mon Jan 7 21:07:36 CET 2008


On 07/01/2008, Wolfgang Huber <huber at ebi.ac.uk> wrote:
> 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.

I would like to clarify that the package should still pass the daily
builds/checks on the BioC servers which still run R devel.  This is
the only reasonable alternative.  So far nothing changed.  Same
requirement as before.

Yes, if the package also pass checks on R release and that is set in
"Depends", then the BioC servers cannot test that as well.  It will be
something the maintainer has to verify.  However, since it pass the
checks on R devel the package still meets the requirement for BioC
devel (on R devel).  The downside is that there is a risk for a
package to be broken on R stable but not R devel, which happens in
case the developer makes a commit without checking it on R stable.
(Indeed, we have the devel version of affxparser depending on R stable
as we speak)

The burden of checking a package is only on those developers who have
R stable in "Depends" in their BioC devel packages.  Anyone who don't
want to do that and stick with the current approach, just have to make
sure R devel is in "Depends".  ...or did I miss something?



> Best wishes
>    Wolfgang
> ------------------------------------------------------------------
> 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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