Using NicheNet with OmnipathR in windows

[jv-20]

Hello there,

I would like to use NicheNet with OmnipathR. I was following this tutorial [http://www.bioconductor.org/packages/release/bioc/vignettes/OmnipathR/inst/doc/nichenet.html]

and received the following error message in

Error in parallelStart(mode = MODE_MULTICORE, cpus = cpus, level = level,  : 
  Multicore mode not supported on windows!

when running this code

nichenet_results <- nichenet_main(
    expressed_genes_transmitter = expressed_genes_transmitter,
    expressed_genes_receiver = expressed_genes_receiver,
    genes_of_interest = genes_of_interest,
    background_genes = background_genes,
    signaling_network = list(
        cpdb = NULL,
        evex = list(min_confidence = 1.0)
    ),
    gr_network = list(only_omnipath = TRUE),
    n_top_ligands = 20,
    mlrmbo_optimization_param = list(ncores = 4)
)

Could you please advise?

Thanks,
Janaki

[deeenes]

Hi Janaki,

First we should find out where this issue happened exactly. A traceback() output (right after the error happens) and an OmnipathR log (find the logfile by omnipath_logfile()) could help with this. It should originate from the call of a nichenetr function, and a subcall probably to the parallelMap package, probably via the mlr package.

As these packages are not developed by me, likely you need to ask the nichenetr developers, and maybe they too will send you to the mlr developers.

Best,

Denes