Resume computation with partial results
Identifies unsuccessful results returned from bplapply
,
bpmapply
, bpvec
, bpaggregate
or bpvectorize
.
bpok(x)
x |
Results returned from a call to |
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
.
Michel Lang, Martin Morgan and Valerie Obenchain
## ----------------------------------------------------------------------- ## 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)
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.