[Bioc-devel] R version in Bioc packages (was Re: [BioC] Package \'jmosaics\' not found)

Dan Tenenbaum dtenenba at fhcrc.org
Tue May 21 22:01:35 CEST 2013

Hi Steffen,

On Tue, May 21, 2013 at 12:40 PM, Steffen Neumann <sneumann at ipb-halle.de> wrote:
> Hi,
> On Tue, 2013-05-21 at 11:47 -0400, James W. MacDonald wrote:
>> Not that I can recall. But I do agree that it is at minimum redundant
>> and probably just wrong to have R-version requirements for BioC packages.
> I'd like to disagree. BioC *promises* that stuff works together
> at a certain point in time, simply because that stuff was green
> at the build farm at that time.

No, it's more than that. We *intend* that all packages in a given BioC
version will work with all other packages in that version. Conversely,
we pretty much guarantee problems if you start mixing and matching.

> But what should keep me as a developer from promising
> that my stuff also works on older releases ?
> (For the fun of it, I once bisected R versions to find
>  a minimal R version for xcms ...).

For one thing, dependeing on when your package was introduced, there
is an older version of it already available that will work with the
older R version. Of course it may not have the coolest new features
but it is there.
For example, xcms was introduced in BioC 1.6, a long time ago. And so
anyone running R 2.1 or earlier can simply
and the appropriate version of xcms (and all its dependencies) for
that version of BioC will be installed.

> So why shouldn't I declare that xcms still runs on R-2.14.0 ?
> I can R CMD check it there, and if someone knows what he does,
> he can bypass biocLite() and install the latest from SVN manually.

Sure....one can do a lot of things but that doesn't mean they are the
right things to do.


> If I *know* xcms won't work reliably with R-2.13 and older,
> then omitting "Depends: R (>= 2.14.0)" means that someone
> with an old cluster (which oftentimes receives fewer upgrades
> than your average laptop) with venerable R-2.10.0 fill fail
> *at some time* rather than on install time.
> Just my 2c.
> Yours,
> Steffen
> --
> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   http://msbi.bic-gh.de
> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
>                                   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

More information about the Bioc-devel mailing list