bpok {BiocParallel} | R Documentation |
Resume computation with partial results
Description
Identifies unsuccessful results returned from bplapply
,
bpmapply
, bpvec
, bpaggregate
or bpvectorize
.
Usage
bpok(x, type = bperrorTypes())
bperrorTypes()
bpresult(x)
Arguments
x |
Results returned from a call to |
type |
A character(1) error type, from the vector returned by
|
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
.
bperrorTypes()
returns a character() vector of possible error
types generated during parallel evaluation. Types are:
bperror
: Any of the following errors. This is the default value forbpok()
.remote_error
: An R error occurring while evaluatingFUN()
, e.g., taking the square root of a character vector,sqrt("One")
.unevaluated_error
: When*Param(stop.on.error = TRUE)
(default), a remote error halts evaluation of other tasks assigned to the same worker. The return value for these unevaluated elements is an error of typeunevaluated_error
.not_available_error
: Only produced byDoparParam()
when a remote error occurs during evaluation of an element ofX
–DoparParam()
sets all values after the remote error to this class.worker_comm_error
: An error occurring while trying to communicate with workers, e.g., when a worker quits unexpectedly. when this type of error occurs, the length of the result may differ from the length of the inputX
.
bpresult()
when applied to an object with a class of one of the
error types returns the list of tasks results.
Author(s)
Michel Lang, Martin Morgan, Valerie Obenchain, and Jiefei Wang
See Also
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)
result <- tryCatch({
bplapply(list(1, "two", 3), sqrt, BPPARAM = param)
}, error=identity)
result
class(result)
bpresult(result)
## 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)