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

Seth Falcon seth at userprimary.net
Fri Jan 11 15:38:35 CET 2008

"Henrik Bengtsson" <hb at stat.berkeley.edu> writes:
> Yes, this basically comes down to the problem of installing a
> BioC-devel package on R release.  I've wrote my own hack allowing to
> "fool" biocLite() et al. about the real R version, e.g. biocLite(pkg,
> rver="2.7.0") can be used on R v2.6.1 but biocLite() thinks it runs R
> v2.7.0.  This is of course a hack.  It is probably better to have a
> biocLite(pkg, repos="auto") where 'repos' defaults to BioC release and
> devel depending on R version, but can be also be specified explicitly
> as biocLite(pkgm repos="devel") to force installation of a BioC-devel
> package.

And how should dependencies be handled in such a mixed case?  I think
doing this in general is harder than you may realize given how the
underlying tools (install.packages) work.

>>   I would sooner see you put some new functionality in BioC-release and
>> maintain the synchronization of R-release - BioC-release or R-devel and
>> BioC-devel.

This has the advantage that the BioC release build system will check
the package against release dependencies, if any, as well as check
release version packages that depend on the given package.  The risk
is destabalizing the release, but I suspect this is largely mitigated
by the strong user response that would follow ;-)

> What I am suggesting that it should be possible to provide a BioC v2.2
> (devel) package as:
> Package: FooBar
> Version: 1.2.3
> Date: 2008-01-10
> Title: A Package
> Depends: R (>= 2.6.0), Biobase (>= 1.16.2)

Isn't this already possible?

> and provide an easy way to install it on R v2.6.0 (release) as well.

Again, because of dependencies it isn't clear what this means.  And
past experience shows that having users mix release and devel makes
support more difficult and often results in confusion.

And there _is_ a way to easily install a single package from the BioC
devel repository; use install.packages and specify the URL for the
devel repo.

+ seth

Seth Falcon | seth at userprimary.net | blog: http://userprimary.net/user/

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