BiocParallel (version 1.2.22)

bpok: Resume computation with partial results

Description

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

bpresume and bplaterror have been deprecated.

Usage

bpok(x)
  ## Deprected: bpresume(expr) bplasterror()

Arguments

x

Results returned from a call to bp*lapply.

expr

A expression to be re-evaluated. If the original error was due to input error, X should be modified. If hardware limitations or failure caused the error this expression may be the same as the original.

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.
• bpresume THIS FUNCTION IS DEPRECATED. The resume mechanism allows computations with errors to be re-attempted and is triggered when the argument catch.errors is TRUE. Unsuccessful results returned from bp*lapply can be identified with bpok. Failure may have been due to faulty input or hardware error. Incomplete portions of the job can be reattempted with bpresume. New results are merged with the previous and returned to the user.
• bplasterror THIS FUNCTION IS DEPRECATED. Use attr on the output of bp*apply to see traceback. See examples.

Examples

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

## By default 'catch.errors' is TRUE in BiocParallelParam objects.
SnowParam(workers = 2)

## If 'catch.errors' is FALSE an ill-fated bplapply() simply stops
## displaying the error message.
param <- SnowParam(workers = 2, catch.errors = FALSE)
## Not run: 
# > res <- bplapply(list(1, "two", 3), sqrt, BPPARAM = param)
# Error in checkForRemoteErrors(val) : 
#   one node produced an error: non-numeric argument to mathematical function
# ## End(Not run)

## When 'catch.errors' is TRUE partial results are returned with 
## the error.
param <- SnowParam(workers = 2)
X <- list(1, "two", 3)
res <- bplapply(X, sqrt, BPPARAM = param)
res

## Check if the results contain any errors:
fail <- !bpok(res)
fail

## Access the traceback with attr():
tail(attr(res[[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.
param <- SnowParam(workers = 2)
X <- list(1, "two", 3)
res <- bplapply(X, sqrt, BPPARAM = param)
res

## Fix the input data by changing the character "2" to a numeric 2:
X_mod <- list(1, 2, 3)

## Repeat the original call to bplapply() with the partial results as 'BPREDO':
bplapply(X_mod, sqrt, BPPARAM = param , BPREDO = res)