[Bioc-devel] " Error in serialize(data, node$con, xdr = FALSE)" during Vignette build (ChIC)

Obenchain, Valerie Valerie.Obenchain at RoswellPark.org
Tue Apr 24 22:00:00 CEST 2018


What is the name of your package?


On 04/16/2018 11:42 AM, Carmen M. Livi wrote:

Hi all,

my package recently got accepted and moved to the Bioconductor repository.

Suddenly I get an error during the package build for Linux and OS (the
INSTALL is working). The error occurs during the creation of the
vignette in a chunk. The error was not there before and I can't
reproduce it on my local machine:

" Error in serialize(data, node$con, xdr = FALSE) :
error writing to connection
Execution halted "

Interestingly I get the same error in totally different points for Linux
and OS.

I am using BiocParallel with BPPARAM =
BiocParallel::MulticoreParam(workers = 5) and requested 5 CPUs.
Can it be that I am not supposed to use that many CPUs? Did anyone
encounter a similar issue?
Should I avoid parallelization in the vignette or should I just reduce
the number?
The dataset I use in the vignette is a small one, so I suppose it is not
a memory issue.

Thanks for any suggestion,


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