[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.

Kind regards,

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.
> 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
>> //
>>     [[alternative HTML version deleted]]
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