In a long-running function I am writing, I use bptry() around bplapply() so that I might re-do failed tasks (this is such a cool feature!). If any failures are detected, I want to return a custom error message to help the user re-run just the failed tasks, along with the partial results. Right now, I'm using warning() to return the error message but this feels wrong because it really is an error and not a warning.

I feel like this might be a job for the bplist_error or bperror arguments of bptry(), but I don't understand them well enough. Help doing this is much appreciated.

Here's a toy example.

suppressPackageStartupMessages(library(BiocParallel))
f <- function(x, BPPARAM, BPREDO = list()) {
    val <- bptry(bplapply(x, sqrt, BPPARAM = BPPARAM, BPREDO = BPREDO))
    if (!all(bpok(val))) {
        # Feels like this should be an error rather than a warning, but I 
        # want to return the partial results so can't use stop() (I think)
        warning("f() encountered errors: ",
                sum(!bpok(val)), " of ", length(val), " tasks failed.\n",
                "f() has returned partial results, including errors, ",
                "for debugging purposes.\n",
                "It may be possible to re-run just these failed tasks.\n", 
                "See help(\"f\")",
                call. = FALSE)
        return(val)
    }
    data.frame(x = unlist(x), val = unlist(val))
}

BPPARAM <- MulticoreParam(workers = 2, stop.on.error = FALSE)
# Good input
a <- f(list(1, 2, 3), BPPARAM = BPPARAM)
a
#>   x      val
#> 1 1 1.000000
#> 2 2 1.414214
#> 3 3 1.732051
# Bad input
b <- f(list(1, "2", 3), BPPARAM = BPPARAM)
#> Warning: f() encountered errors: 1 of 3 tasks failed.
#> f() has returned partial results, including errors, for debugging purposes.
#> It may be possible to re-run just these failed tasks.
#> See help("f")
b
#> [[1]]
#> [1] 1
#> 
#> [[2]]
#> <remote_error in FUN(...): non-numeric argument to mathematical function>
#> traceback() available as 'attr(x, "traceback")'
#> 
#> [[3]]
#> [1] 1.732051
# Re-do failed task
c <- f(list(1, 2, 3), BPPARAM = BPPARAM, BPREDO = b)
#> resuming previous calculation ...
c
#>   x      val
#> 1 1 1.000000
#> 2 2 1.414214
#> 3 3 1.732051
BiocManager::valid()
#> 
#> * sessionInfo()
#> 
#> R version 3.5.0 (2018-04-23)
#> Platform: x86_64-apple-darwin15.6.0 (64-bit)
#> Running under: macOS Sierra 10.12.6
#> 
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base
#> 
#> other attached packages:
#> [1] BiocParallel_1.15.3 repete_0.0.0.9011   devtools_1.13.5
#> 
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_0.12.17           lobstr_0.0.0.9000      XVector_0.21.1
#>  [4] magrittr_1.5           GenomicRanges_1.33.5   BiocGenerics_0.27.0
#>  [7] zlibbioc_1.27.0        IRanges_2.15.13        munsell_0.4.3
#> [10] colorspace_1.3-2       rlang_0.2.0            stringr_1.3.1
#> [13] GenomeInfoDb_1.17.1    plyr_1.8.4             tools_3.5.0
#> [16] parallel_3.5.0         withr_2.1.2            fortunes_1.5-4
#> [19] digest_0.6.15          GenomeInfoDbData_1.1.0 BiocManager_1.29.45
#> [22] pryr_0.1.4             S4Vectors_0.19.5       bitops_1.0-6
#> [25] codetools_0.2-15       RCurl_1.95-4.10        memoise_1.1.0
#> [28] stringi_1.2.2          compiler_3.5.0         scales_0.5.0
#> [31] stats4_3.5.0
#> 
#> Bioconductor version '3.8'
#> 
#>   * 0 packages out-of-date
#>   * 1 packages too new
#> 
#> create a valid installation with
#> 
#>   BiocManager::install("reprex", update = TRUE, ask = FALSE)

#> Warning message:
#> 0 packages out-of-date; 1 packages too new

Created on 2018-05-25 by the reprex package (v0.2.0).

The basic paradigm in R is that an error terminates execution, whereas a warning allows continuation. Within this paradigm, it's not possible to both signal an error and return a value. You could use bplist_error= to do something special and then signal the condition, e.g., store the value for later retrieval

handler <- function() {
    value <- NULL
    list(error = function(err) {
        value <<- attr(err, "result")
        signalCondition(err)
    }, get = function() {
        value
    })
}

used as

h <- handler()
x <- bptry(
    bplapply(list(1, "2", 3), sqrt),
    bplist_error = h$error, bperror = stop
)
h$get()

This could be achieved probably more directly by testing the return value of bptry() with bpok(), and using that to store-then-signal.

I think this would be quite confusing for your average user; it's confusing enough for me!