[Bioc-devel] ‘SOCKcluster’ cluster error with bplapply() under merida2

Martin Morgan martin.morgan at roswellpark.org
Wed Apr 18 15:30:02 CEST 2018

I'm sorry not to respond to your first email. This is a problem in 
BiocParallel that I am working on. In your particular case, where you 
are relying on a third-party package that uses parallel::mclapply, I 
think you should revert to using that.


On 04/18/2018 09:22 AM, Carmen M. Livi wrote:
> Hi all,
> I was using parallel::mclapply() but have been encouraged to substitute
> it with BiocParallel::bplapply().
> BiocParallel::bplapply(data,
>       BPPARAM = BiocParallel::MulticoreParam(workers =x ),
>       FUN  =...)....
> I never had problems with the code. Now the package got accepted and
> moved to the bioconductor-repository and suddenly I am getting errors in
> the vignette build when asking for 5 workers:
> "Error in serialize(data, node$con, xdr = FALSE) : error writing to
> connection"
> After reducing the number of requested workers to 3 my package passed
> under linux (malbec2 and malbec1) but still fails under OS X (merida2):
> "Error : failed to stop ‘SOCKcluster’ cluster: error writing to connection"
> https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/ChIC/merida2-buildsrc.html
> Does anyone have an idea what is going on? Am I not supposed to ask for
> more then 1 worker in the vignette?
> What if I just switch back to parallel::mclapply?
> Thank you,
> Carmen
> //
> 	[[alternative HTML version deleted]]
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