search

Russel88 / DAtest

Compare different differential abundance and expression methods
GNU General Public License v3.0
49 stars 9 forks source link

Parallelization does not work in R 4.0 + Rstudio #13

Closed askerdb closed 4 years ago

askerdb commented 4 years ago

There is a work-around in this thread, maybe it should be the default for now?

https://github.com/rstudio/rstudio/issues/6692

Russel88 commented 4 years ago

Thanks for reporting this Asker.

It seems that Henriks solution should work without breaking things:

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

Can you confirm, because then I will include it

askerdb commented 4 years ago

It seemingly worked for me, but I can't find documentation on what changes.

Russel88 commented 4 years ago

All that is changed is that the workers are not set up in parallel, but sequentially, and only on macOS Darwin, R 4.0 in Rstudio.

Since it works, I'll include it

Russel88 commented 4 years ago

Should be fixed in 2.7.16