[Bioc-devel] clarification of the BiocParallel vignette for SnowParam() usage

Aaron Lun alun at wehi.edu.au
Tue Oct 10 10:56:00 CEST 2017

Dear list;

Currently the vignette for the BiocParallel package states that the functions to be executed should contain the necessary library() calls if bplapply is used with SnowParam(). Now, I use bplapply in several of my packages with internal helper/wrapper functions, and that piece of advice caused me to worry whether I should have library() calls in all of these functions.

After some testing and contemplation, I realised that the internal functions would pass along the package namespace to each worker, and so no extra loading was required. Perhaps it would be a good idea to mention this in the vignette, to soothe the hearts of package developers like me.

Some mention of the memory consumption behaviour of MulticoreParam would also be useful (as discussed in https://support.bioconductor.org/p/70196/#70509), especially if people are choosing between MulticoreParam and SnowParam.



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