Global option for parallel processing

[zkamvar]

Right now for anything dealing with genlight objects, parallel processing is dependent on whether or not the package parallel is installed:

glSim(..., parallel = require("parallel"))

It can be a pain to specify parallel = FALSE for all the functions when dealing with genlight. I propose to add a global option adegenet.parallel to be set when the package is loaded in a similar fashion to dplyr: https://github.com/hadley/dplyr/blob/master/R/zzz.r

This way, the checking could be done with the option, as opposed to loading the parallel package:

options(adegenet.parallel = FALSE)
glSim(..., parallel = getOption("adegenet.parallel"))

I'm just putting this here so I can open a pull request later 😄

[thibautjombart]

Great idea :)

[thierrygosselin]

I thought parallel was installed automatically now with R ?

[romunov]

@thierrygosselin it's not a matter of installing the package but passing parameters to various functions.

[zkamvar]

@thierrygosselin, there have been a history of problems with parallel on windows, but the main issue this would fix is testing on clusters (as was brought up in #128).

[thierrygosselin]

Ha ! ok great!

[thibautjombart]

I can't remember: has this been implemented - shall I close the issue?

[zkamvar]

No, it has not.

Sent from my iPhone

On Jan 9, 2017, at 04:16, Thibaut Jombart [email protected] wrote:

I can't remember: has this been implemented - shall I close the issue?

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