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

Carmen M. Livi carmen.livi at ifom.eu
Mon Apr 16 20:43:37 CEST 2018

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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