I stumbled across some strange behaviour of bplapply when a large data object is passed to FUN and an error is also raised within FUN:

library(BiocParallel)
bigmat <- matrix(rnorm(1e7), nrow=50)

.recount_cells <- function(x, incoming)
{
    stop("YAY")
    return(x)
}

system.time(bplapply(1:2, FUN=.recount_cells, incoming=bigmat, 
    BPPARAM=SerialParam())) # Finishes instantly
system.time(bplapply(1:2, FUN=.recount_cells, incoming=bigmat, 
    BPPARAM=MulticoreParam(2))) # Killed after several minutes

This doesn't happen if I set bigmat <- 1, nor if I remove the stop call in .recount_cells. In those situations, both of the bplapply calls above execute in a timely manner.

I have encountered related problems with bplapply stalling even when there is no error being raised in FUN, but the above example is the simplest to reproduce on my system (Ubuntu, below). The same behaviour is observed with BiocParallel 1.7.5 and on a Mac OSX.

Anyway, here's my sessionInfo():

R version 3.3.0 Patched (2016-05-03 r70580)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocParallel_1.6.3

loaded via a namespace (and not attached):
[1] parallel_3.3.0

The problem is that on error R creates a variable .Traceback that contains a text version of the call stack. Each element of the call stack has a text representation of the entire bigmat object. Fixing this requires a change to R (after svn revision r71040) and an updated BiocParallel (version 1.6.4 / 1.7.6).