On Wed, Nov 14, 2012 at 12:23 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> Interested developers -- I added the start of a BiocParallel package to
> the Bioconductor subversion repository and build system.
>
> The package is mirrored on github to allow for social coding; I encourage
> people to contribute via that mechanism.
>
>   https://github.com/**Bioconductor/BiocParallel<https://github.com/Bioconductor/BiocParallel>
>
> The purpose is to help focus our efforts at developing appropriate
> parallel paradigms. Currently the package Imports: parallel and implements
> pvec and mclapply in a way that allows for operation on any vector or list
> supporting length(), [, and [[ (the latter for mclapply). pvec in
> particular seems to be appropriate for GRanges-like objects, where we don't
> necessarily want to extract many thousands of S4 instances of individual
> ranges with [[.
>

Makes sense. Besides, [[ does not even work on GRanges. One limitation of
pvec is that it does not support a chunk size; it just uses length(x) /
ncores. It would be nice to be able to restrict that, which would then
require multiple jobs per core. Unless I'm missing something.


>
> Hopefully the ideas in the package can be folded back in to parallel as
> they mature.
>
> Martin
> --
> Dr. Martin Morgan, PhD
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
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