[Bioc-devel] parallel package generics

Hahne, Florian florian.hahne at novartis.com
Wed Oct 17 14:45:44 CEST 2012

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?


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