bpok: Resume computation with partial results

In BiocParallel: Bioconductor facilities for parallel evaluation

Description

Identifies unsuccessful results returned from bplapply, bpmapply, bpvec, bpaggregate or bpvectorize.

Usage

  bpok(x)

Arguments

x	Results returned from a call to bp*apply.

Details

• bpok Returns a logical() vector: FALSE for any jobs that resulted in an error. x is the result list output by bplapply, bpmapply, bpvec, bpaggregate or bpvectorize.

Author(s)

Michel Lang, Martin Morgan and Valerie Obenchain

Examples

## -----------------------------------------------------------------------
## Catch errors: 
## -----------------------------------------------------------------------

## By default 'stop.on.error' is TRUE in BiocParallelParam objects.  If
## 'stop.on.error' is TRUE an ill-fated bplapply() simply stops,
## displaying the error message.
param <- SnowParam(workers = 2, stop.on.error = TRUE)
tryCatch({
    bplapply(list(1, "two", 3), sqrt, BPPARAM = param)
}, error=identity)

## If 'stop.on.error' is FALSE then the computation continues. Errors
## are signalled but the full evaluation can be retrieved
param <- SnowParam(workers = 2, stop.on.error = FALSE)
X <- list(1, "two", 3)
result <- bptry(bplapply(X, sqrt, BPPARAM = param))
result

## Check for errors:
fail <- !bpok(result)
fail

## Access the traceback with attr():
tail(attr(result[[2]], "traceback"), 5)

## -----------------------------------------------------------------------
## Resume calculations: 
## -----------------------------------------------------------------------

## The 'resume' mechanism is triggered by supplying a list of partial
## results as 'BPREDO'. Data elements that failed are rerun and merged
## with previous results.

## A call of sqrt() on the character "2" returns an error. Fix the input
## data by changing the character "2" to a numeric 2:
X_mod <- list(1, 2, 3)
bplapply(X_mod, sqrt, BPPARAM = param , BPREDO = result)

BiocParallel documentation built on Nov. 8, 2020, 5:46 p.m.