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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Issue Running runSCENIC_2_createRegulons() on Windows OS #179

Open Aaron-O-Gonzalez opened 3 years ago

Aaron-O-Gonzalez commented 3 years ago

Hello:

I have been running into some issues with the SCENIC wrappers on a Windows OS. It is a 64 GB RAM OS and all previous parts of the pipeline have been successfully executed. However when I run the function, I get an error at RcisTarget: Prunning Targets:

Error in socketAccept(socket = socket, blocking = TRUE, open = "a+b", : all connections are in use

In addition: Warning messages: 1: In MulticoreParam(nCores) : MulticoreParam() not supported on Windows, use SnowParam()

There are additional warning messages unrelated to this problem. I have tried playing around with the number of cores. Starting with 10, I ran into a different error message that said something along the lines of all connections being used. This error message is using nCores = 5.

Is this a problem inherent to my OS?

Thank you!

sgh212 commented 3 years ago

hello! I also have this problem. Have you solved this problem?

Aaron-O-Gonzalez commented 3 years ago

Hi! So while I didn't really solve the problem, I did find a way to get the code to work. If you are running the default 10 cores for the nCores option, then I would recommend that you change it to 1. I saw a previous post that recommended cutting down the number of cores, but the only way to get that to work on my end was using scenicOptions@settings$nCores <- 1.