[BioC] mcmapply with edgeR?

[Martin Morgan]

On 08/13/2012 10:07 AM, Aaron Mackey wrote:
> I have mcmapply (and related parallel library functions) working fine with
> example code, but when I try to run my own function (which makes calls to
> estimateGLMCommonDisp, etc) in parallel, only one core remains engaged, no
> forking happens.  The only thing I can imagine is that the parallel library
> has detected my use of a dynamically loaded .so, and has reverted to serial
> behavior?  Or is edgeR preventing it's functions from being fork'ed somehow?

using a shared object shouldn't be a problem with mclapply (rather than 
mcmapply, which is not from the parallel library?); maybe you can create 
a short script that has the essentials for someone else to evaluate, 
maybe using small simulated data, perhaps from one of the help pages of 
edgeR?

Martin

>
> Thanks in advance,
> -Aaron
>
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