Merge branch 'Jiefei-Wang-force_load' into devel

- Closes #262. Closes #270

Author: mtmorgan

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: BiocParallel
 Type: Package
 Title: Bioconductor facilities for parallel evaluation
-Version: 1.43.1
+Version: 1.43.2
 Authors@R: c(
     person("Martin", "Morgan",
         email = "[email protected]",

NEWS

@@ -3,7 +3,11 @@ CHANGES IN VERSION 1.44
 
 NEW FEATURES
 
-    o (1.43.1) Support NULL return value from bplapply. see
+    o (1.43.2) Lazy-load S4 classes in workers; see
+    <https://github.com/Bioconductor/BiocParallel/issues/262>
+    <https://github.com/Bioconductor/BiocParallel/pull/270>
+
+    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>
 

R/utilities.R

@@ -129,3 +129,26 @@
         timeout <- Inf
     timeout
 }
+
+## This function walks through a nested list and attempts to trigger
+## loading of any encountered S4 class definitions using getClassDef().
+## 
+## Limitations:
+## - It does NOT guarantee that all required packages will be loaded,
+##   because S4 objects may be hidden in attributes, environments, or other
+##   non-list structures that are not traversed here.
+.autoload_s4_classes <- function(obj) {
+    seen <- character()
+    recurse <- function(x) {
+        if (isS4(x)) {
+            cl <- class(x)
+            if (!cl %in% seen) {
+                seen <<- c(seen, cl)
+                methods::getClassDef(cl)
+            }
+        } else if (is.list(x)) {
+            lapply(x, recurse)
+        }
+    }
+    recurse(obj)
+}

R/worker.R

@@ -311,6 +311,9 @@
 
     t1 <- proc.time()
     value <- tryCatch({
+        ## Lazy loading causes some packages fail to load in the worker
+        ## environment. This works in 99% cases (see function comments).
+        .autoload_s4_classes(msg$data$args$X)
         do.call(msg$data$fun, msg$data$args)
     }, error=function(e) {
         ## return as 'list()' because msg$fun has lapply semantics