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

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.

Martin

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
//

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