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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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Cluster setup failed. #45

Closed heesters closed 4 years ago

heesters commented 4 years ago

This is more a bug report for parallel, but I have a (temp) solution that works.

On OSX with R4.0.0 I get the following error with pathfindR:

Cluster setup failed. 7 of 7 workers failed to connect. Called from: makePSOCKcluster

A temporal solution is to put this in your .Rprofile:

Revert to 'sequential' setup of PSOCK cluster in RStudio Console on macOS and R 4.0.0

if (Sys.getenv("RSTUDIO") == "1" && !nzchar(Sys.getenv("RSTUDIO_TERM")) && Sys.info()["sysname"] == "Darwin" && getRversion() == "4.0.0") { parallel:::setDefaultClusterOptions(setup_strategy = "sequential") }

I don't know if this is the right place to post this...

egeulgen commented 4 years ago

I'll look into this and try to find a permanent solution.

Update: As you suggest as well, I'll add setup_strategy = "sequential" in the call as suggested here: https://github.com/rstudio/rstudio/issues/6692#issuecomment-619645114