[BioC] doParallel with Bumphunter gives Error in mcfork()

Steve Lianoglou lianoglou.steve at gene.com
Mon Apr 14 07:23:07 CEST 2014


Not related to the methylation analysis at all, but:

On Sun, Apr 13, 2014 at 4:31 PM, Tim Triche, Jr. <tim.triche at gmail.com> wrote:
> Send your sessionInfo().
> While you're doing that, here are some suggestions:
> 1) use fewer processes.  minfi will kill a machine with 64GB of RAM using
> as few as 4 processes for bumphunting. Plus, you probably want to use
> doMC() instead of doParallel().  Try setting options("mc.cores") to
> something like 4 and gradually increasing it as you successfully run
> analyses on this machine/cluster/whatever.

I'm curious why you'd suggest that? I thought the general consensus
was that the `multicore` package has "passed the baton" to the
`parallel` package, so people who want to use "it" via `foreach`
should then prefer doParallel ... no?


Steve Lianoglou
Computational Biologist

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