[Bioc-devel] ‘SOCKcluster’ cluster error with bplapply() under merida2
Carmen M. Livi
carmen.livi at ifom.eu
Wed Apr 18 16:47:55 CEST 2018
Dear Martin Morgan,
ok, I will switch back to parallel then. Thank you very much for your reply.
On 18/04/2018 15:30, Martin Morgan wrote:
> 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().
>> 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
>> 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
>> 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,
>> [[alternative HTML version deleted]]
>> Bioc-devel at r-project.org mailing list
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