Merge branch 'Jiefei-Wang-user_null' into devel

- Closes #267. Closes #269.

Author: mtmorgan

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: BiocParallel
 Type: Package
 Title: Bioconductor facilities for parallel evaluation
-Version: 1.43.0
+Version: 1.43.1
 Authors@R: c(
     person("Martin", "Morgan",
         email = "mtmorgan.bioc@gmail.com",

NEWS

@@ -1,3 +1,12 @@
+CHANGES IN VERSION 1.44
+-----------------------
+
+NEW FEATURES
+
+    o (1.43.1) Support NULL return value from bplapply. see
+    <https://github.com/Bioconductor/BiocParallel/issues/267>
+    <https://github.com/Bioconductor/BiocParallel/pull/269>
+
 CHANGES IN VERSION 1.42
 -----------------------
 

R/bploop.R

@@ -1,3 +1,16 @@
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+### utils
+
+## a reserved value to represent a NULL value in X in bplapply
+.bp_null <- function(){
+    structure(list(), class = "bp_null")
+}
+
+.is_bp_null <- function(x){
+    inherits(x, "bp_null")
+}
+
+
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### Manager loop used by SOCK, MPI and FORK
 
@@ -81,6 +94,12 @@
 .bploop_lapply_iter <-
     function(X, redo_index, elements_per_task)
 {
+    ## replace the user-provided NULL with a reserved NULL
+    null_indices <- which(vapply(X, is.null, logical(1)))
+    for (null_index in null_indices) {
+        X[[null_index]] <- .bp_null()
+    }
+
     redo_n <- length(redo_index)
     redo_i <- 1L
     x_n <- length(X)
@@ -270,6 +289,13 @@
                     warning("first invocation of 'ITER()' returned NULL")
                 break
             }
+
+            ## Replace the reserved NULL value with a real NULL
+            null_indices <- which(vapply(value, .is_bp_null, logical(1)))
+            for (null_index in null_indices) {
+                value[null_index] <- list(NULL)
+            }
+
             args <- ARGFUN(value, seed)
             task <- .EXEC(
                 total + 1L, .workerLapply,

inst/unitTests/test_bplapply.R

@@ -150,3 +150,12 @@ test_bplapply_auto_export <- function(){
     bpexportvariables(p) <- FALSE
     checkException(bplapply(1:2, fun2, BPPARAM = p), silent = TRUE)
 }
+
+
+test_bplapply_null_value_in_input <- function(){
+    p <- SerialParam()
+    FUN <- function(x) x
+    X <- list(a = 1, b = 2, c = NULL, d = 4)
+    result <- bptry(bplapply(X, FUN, BPPARAM = p))
+    checkIdentical(X, result)
+}