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BatchtoolsParam fails to propagate errors in bpiterate

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#257 2 comentarios 0 reacciones 0 asignados Ver en GitHub

Nadie ha tomado este issue todavía.

Evaluación

Dificultad
4/5
Tiempo estimado
3-5 días
Aptitud para principiantes
35/100
Tipo de issue
Error
Claridad
Bastante claro
Estado de actividad
Estancado
Stack tecnológico
r
Área
backend

Línea de trabajo

Start by reproducing the reprex at bpiterate with BatchtoolsParam, then compare its error handling with SerialParam, MulticoreParam, and SnowParam. Done means the failing callback propagates as an error rather than returning NULL results with an errors attribute, and bpok reports the failure consistently.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

I've discovered a case where BatchtoolsParam behaves differently from other backends. Consider the following reprex:

library(BiocParallel)
library(iterators)
library(assertthat)
library(testthat)
## Convert a foreach iterator into a BiocParallel iterator
makeIter <- function(it) {
  f <- function() {
    tryCatch(it$nextElem(), error = function(e) {
      if (e$message == "StopIteration") {
        NULL
      } else {
        stop(e)
      }
    })
  }
  f
}

## Example non-error usage of makeIter
bpiterate(
  makeIter(icount(10)),
  sqrt,
  BPPARAM = SerialParam()
)
#> [[1]]
#> [1] 1
#> 
#> [[2]]
#> [1] 1.414214
#> 
#> [[3]]
#> [1] 1.732051
#> 
#> [[4]]
#> [1] 2
#> 
#> [[5]]
#> [1] 2.236068
#> 
#> [[6]]
#> [1] 2.44949
#> 
#> [[7]]
#> [1] 2.645751
#> 
#> [[8]]
#> [1] 2.828427
#> 
#> [[9]]
#> [1] 3
#> 
#> [[10]]
#> [1] 3.162278

## Correctly throws the error
expect_error(bpiterate(
  makeIter(iterators::icount(10)),
  function(x) stop("This function always throws an error"),
  BPPARAM = SerialParam()
))

## Correctly throws the error
expect_error(bpiterate(
  makeIter(iterators::icount(10)),
  function(x) stop("This function always throws an error"),
  BPPARAM = MulticoreParam(workers = 2)
))

## Correctly throws the error
expect_error(bpiterate(
  makeIter(iterators::icount(10)),
  function(x) stop("This function always throws an error"),
  BPPARAM = SnowParam(workers = 2)
))

## Does not throw the error, but collects in attr(,"errors")
resList <- bpiterate(
  makeIter(iterators::icount(10)),
  function(x) stop("This function always throws an error"),
  BPPARAM = BatchtoolsParam(cluster = "socket", workers = 2)
)
#> Submitting 10 jobs in 2 chunks using cluster functions 'Socket' ...

print(resList)
#> [[1]]
#> NULL
#> 
#> [[2]]
#> NULL
#> 
#> [[3]]
#> NULL
#> 
#> [[4]]
#> NULL
#> 
#> [[5]]
#> NULL
#> 
#> [[6]]
#> NULL
#> 
#> [[7]]
#> NULL
#> 
#> [[8]]
#> NULL
#> 
#> [[9]]
#> NULL
#> 
#> [[10]]
#> NULL
#> 
#> attr(,"errors")
#> attr(,"errors")$`10`
#> <unevaluated_error: not evaluated due to previous error>
#> 
#> attr(,"errors")$`1`
#> <remote_error in FUN(...): This function always throws an error>
#> traceback() available as 'attr(x, "traceback")'
#> 
#> attr(,"errors")$`2`
#> <unevaluated_error: not evaluated due to previous error>
#> 
#> attr(,"errors")$`3`
#> <unevaluated_error: not evaluated due to previous error>
#> 
#> attr(,"errors")$`4`
#> <unevaluated_error: not evaluated due to previous error>
#> 
#> attr(,"errors")$`5`
#> <remote_error in FUN(...): This function always throws an error>
#> traceback() available as 'attr(x, "traceback")'
#> 
#> attr(,"errors")$`6`
#> <unevaluated_error: not evaluated due to previous error>
#> 
#> attr(,"errors")$`7`
#> <unevaluated_error: not evaluated due to previous error>
#> 
#> attr(,"errors")$`8`
#> <unevaluated_error: not evaluated due to previous error>
#> 
#> attr(,"errors")$`9`
#> <unevaluated_error: not evaluated due to previous error>

## This assertion fails
assert_that(!any(bpok(resList)))
#> Error: !any(bpok(resList)) is not TRUE
## This assertion passes
assert_that(!any(bpok(attr(resList, "errors"))))
#> [1] TRUE

Created on 2023-07-07 with reprex v2.0.2

With any other backend (SerialParam, MulticoreParam, SnowParam), the bpiterate call throws an error (verified here by calling expect_error). However, BatchtoolsParam does not throw an error and instead returns a list with all NULL elements and an attribute "errors" containing the errors thrown during iteration. Furthermore, bpok says this object is totally fine. I would expect BatchtoolsParam to behave the same as the other backends here.

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