Robustness to BiocParallel

YosefLab / scone

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Robustness to BiocParallel #24

Closed drisso closed 8 years ago

drisso commented 8 years ago

Handling an error from a normalization method (not propagated)
Handling error in the projection

drisso commented 8 years ago

@HenrikBengtsson if you want to help, this is probably the place where we need it the most!

HenrikBengtsson commented 8 years ago

Related to what we discussed over lunch:

You're looking for what I would call "early propagation of errors" or possible shorter "early stopping". It can only occur when the calling R processes checks in with the background R processes ("pools the workers for errors"), that is, if a background R process detects an error, none of the asynchronous backends I know of in R can push this to the main process such that the error occurs immediately.

drisso commented 8 years ago

We should have a look at this: https://www.bioconductor.org/packages/release/bioc/vignettes/BiocParallel/inst/doc/Errors_Logs_And_Debugging.pdf

drisso commented 8 years ago

Useful param values for debugging:

register(SerialParam(stop.on.error=TRUE, log=TRUE, threshold = "TRACE"))