bplapply does not handle NULL values

[RonanDaly]

It's not clear to me what the correct behaviour should be, but bplapply stops with
an error whenever it encounters a NULL in X

bplapply(list(NULL), function(x) {
     42
})
Error: BiocParallel errors
  0 remote errors, element index: 
  1 unevaluated and other errors
  first remote error:
In addition: Warning message:
In .bploop_impl(ITER = ITER, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM,  :
  first invocation of 'ITER()' returned NULL

> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.6.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

time zone: Europe/London
tzcode source: internal

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

other attached packages:
[1] BiocParallel_1.39.0

loaded via a namespace (and not attached):
[1] compiler_4.4.2   parallel_4.4.2   codetools_0.2-20

I tried this on an earlier version, which works

> bplapply(list(NULL), function(x) {
+      42
+ })
[[1]]
[1] 42

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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_1.18.0

loaded via a namespace (and not attached):
[1] compiler_3.6.3 parallel_3.6.3

[Jiefei-Wang]

This is because BiocParallel uses an iterator internally to handle the list object, and the iterator uses NULL value to determine the end of the sequence. Here is a better example. Unlike the example from @RonanDaly , this time BiocParallel does not end gracefully. There is no error message at all.

> bplapply(list(1,2,NULL,4), function(x) {
+     x
+ })
Error: BiocParallel errors
  0 remote errors, element index:
  1 unevaluated and other errors
  first remote error:

I think we should wrap the user-given NULL value so it would not terminate the iterator. What do you think? @mtmorgan . I can make a pull request for it.

[mtmorgan]

PR sounds great