[Bioc-devel] parallel package generics

Hahne, Florian florian.hahne at novartis.com
Tue Oct 23 16:38:10 CEST 2012

Hi Martin,
I could define the generics in my own package, but that would mean that
those will only be available there, or in the global environment assuming
that I also export them, or in all additional packages that explicitly
import them from my name space. Now there already are a whole bunch of
packages around that all allow for parallelization via a cluster object.
Obviously those all import the parLapply function from the parallel
package. That means that I can't simply supply my own modified cluster
object, because the code that calls parLapply will not know about the
generic in my package, even if it is attached. Ideally parLapply would be
a generic function already in the parallel package. Not sure who needs to
be convinced in order for this to happen, but my gut feeling was that it
could be easier to have the generic in BiocGenerics.
Maybe I am missing something obvious here, but imo there is no way to
overwrite parLapply globally for my own class unless the generic is
imported by everyone who wants to make use of the special method.

On 10/23/12 2:20 PM, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:

>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
>> 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
>> submission, job status and reducing the results in the parLapply method
>> that class, and would be able to supply this new cluster object to all
>> 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
>> object to a function that normally deals with the "regular" parallel
>> package S3 cluster objects and everything just worked out of the box,
>> obviously this fails once I am in a name space and my generic is not
>> anymore. Of course what we would really want is some proper abstraction
>> 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?
>usual motivation for inclusion in BiocGenerics has been to avoid
>between packages, but I'm not sure whether this is the case (yet)? This
>also add a dependency fairly deep in the hierarchy.
>What do you think?
>> Florian
>Computational Biology / Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N.
>PO Box 19024 Seattle, WA 98109
>Location: Arnold Building M1 B861
>Phone: (206) 667-2793

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