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### =========================================================================
### Error handling
### -------------------------------------------------------------------------
.bpeltok <-
function(x, type = bperrorTypes())
{
!inherits(x, type)
}
bpok <-
function(x, type = bperrorTypes())
{
x <- bpresult(x)
type <- match.arg(type)
vapply(x, .bpeltok, logical(1), type)
}
.bpallok <-
function(x, type = bperrorTypes(), attrOnly = FALSE)
{
if (attrOnly)
is.null(.redo_env(x))
else
is.null(.redo_env(x)) && all(bpok(x, type))
}
bptry <-
function(expr, ..., bplist_error, bperror)
{
if (missing(bplist_error))
bplist_error <- bpresult
if (missing(bperror))
bperror <- identity
tryCatch(expr, ..., bplist_error=bplist_error, bperror=bperror)
}
bpresult <- function(x)
{
if (is(x, "bplist_error"))
x <- attr(x, "result")
x
}
.error <- function(msg, class=NULL) {
structure(list(message=msg),
class = c(class, "bperror", "error", "condition"))
}
.error_remote <- function(x, call) {
structure(x, class = c("remote_error", "bperror", "error", "condition"),
traceback = capture.output(traceback(call)))
}
.error_unevaluated <- function()
{
structure(list(message="not evaluated due to previous error"),
class=c("unevaluated_error", "bperror", "error", "condition"))
}
.error_not_available <- function(msg)
{
structure(list(message=msg),
class=c("not_available_error", "bperror", "error", "condition"))
}
.error_worker_comm <- function(error, msg) {
msg <- sprintf("%s:\n %s", msg, conditionMessage(error))
structure(list(message=msg, original_error_class=class(error)),
class=c("worker_comm_error", "bperror", "error", "condition"))
}
bperrorTypes <-
function()
{
subclasses <- paste0(
c("remote", "unevaluated", "not_available", "worker_comm"),
"_error"
)
c("bperror", subclasses)
}
.error_bplist <- function(result) {
if (is.null(attr(result, "errors"))) {
errors <- result
total_error <- sum(!bpok(errors))
remote_error <-
!bpok(errors, "remote_error") |
!bpok(errors, "worker_comm_error")
remote_idx <- which(remote_error)
if (length(remote_idx))
first_error <- errors[[remote_idx[1]]]
else
first_error <- ""
} else {
errors <- attr(result, "errors")
total_error <- length(errors)
remote_error <-
!bpok(errors, "remote_error") |
!bpok(errors, "worker_comm_error")
first_error_idx <- which(remote_error)[1]
if (!is.null(first_error_idx))
first_error <- errors[[first_error_idx]]
else
first_error <- ""
remote_idx <- as.integer(names(errors[remote_error]))
}
n_remote_error <- length(remote_idx)
n_other_error <- total_error - n_remote_error
fmt = paste(
"BiocParallel errors",
"%d remote errors, element index: %s%s",
"%d unevaluated and other errors",
"first remote error:\n%s",
sep = "\n "
)
class(first_error) <- tail(class(first_error), 2L)
first_error_msg <- as.character(first_error)
message <- sprintf(
fmt,
n_remote_error,
paste(head(remote_idx), collapse = ", "),
ifelse(length(remote_idx) > 6, ", ...", ""),
n_other_error,
first_error_msg
)
err <- structure(
list(message=message),
result=result,
class = c("bplist_error", "bperror", "error", "condition"))
}
print.remote_error <- function(x, ...) {
NextMethod(x)
cat("traceback() available as 'attr(x, \"traceback\")'\n")
}
`print.bplist_error` <- function(x, ...) {
NextMethod(x)
cat("results and errors available as 'bpresult(x)'\n")
}
|
