[Bioc-devel] parallel package generics

Martin Morgan mtmorgan at fhcrc.org
Tue Oct 23 14:20:51 CEST 2012

On 10/17/2012 05:45 AM, Hahne, Florian wrote:
> Hi all,
> I was wondering whether it would be possible to have proper generics for
> some of the functions in the parallel package, e.g. parLapply and
> clusterCall. The reason I am asking is because I want to build an S4 class
> that essentially looks like an S3 cluster object but knows how to deal
> with the SGE. That way I can abstract away all the overhead regarding job
> submission, job status and reducing the results in the parLapply method of
> that class, and would be able to supply this new cluster object to all of
> my existing functions that can be processed in parallel using a cluster
> object as input. I have played around with the BatchJobs package as an
> abstraction layer to SGE and that work nicely. As a test case I have
> created the necessary generics myself in order to supply my own SGEcluster
> object to a function that normally deals with the "regular" parallel
> package S3 cluster objects and everything just worked out of the box, but
> obviously this fails once I am in a name space and my generic is not found
> anymore. Of course what we would really want is some proper abstraction of
> parallelization in R, but for now this seem to be at least a cheap
> compromise. Any thoughts on this?

Hi Florian -- we talked about this locally, but I guess we didn't actually send 
any email!

Is there an obstacle to promoting these to generics in your own package? The 
usual motivation for inclusion in BiocGenerics has been to avoid conflicts 
between packages, but I'm not sure whether this is the case (yet)? This would 
also add a dependency fairly deep in the hierarchy.

What do you think?


> Florian

Computational Biology / Fred Hutchinson Cancer Research Center
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