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aertslab / GENIE3

GENIE3 (GEne Network Inference with Ensemble of trees) R-package
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verbose does not work with multiple cores #17

Open NicGamb opened 5 months ago

NicGamb commented 5 months ago

Hello,

weightMat <- GENIE3(as.matrix(ltpm), nCores = 1, verbose=TRUE)

returns:

################ Tree method: RF K: sqrt Number of trees: 1000 Using 1 core. Computing gene 1/24174: ENSG00000000003.15 ... ################

However,

weightMat <- GENIE3(as.matrix(ltpm), nCores = 2, verbose=TRUE)

returns:

################ Tree method: RF K: sqrt Number of trees: 1000

Using 2 core. ################

And that's it. I do not know if GENIE3 actually works or has stalled. Note the space between the number of trees and the cores. Tiny but odd details.

The verbose mode is very useful to monitor the progress of GENIE3 on very big tasks.

Best regards,

NicGamb commented 5 months ago

Indeed, I checked the code and nothing is returned when nCores >1

:-( very unfortunate.