[Bioc-devel] as.list.List (was Re: parallel package generics)

[Martin Morgan]

On 10/25/2012 07:53 PM, Cook, Malcolm wrote:
> Namely, base::Reduce coerces X to a list using as.list  if it is an object
> whereas BiocGenerics::Reduce does not.  Otherwise they are identical.
>
> As a result, base::Reduce(myGRangesList) fails with "no method for coercing
> this S4 class to a vector".

Well, so when you put it this way... I was wondering why there is no

   as.list.List

i.e., an S3 method for List on the generic as.list? This seems to be consistent 
with the recommendation on ?Methods under 'Methods for S3 Generic Functions' 
(and this little hack seems to allow both Reduce and mclapply to 'work').

Index: NAMESPACE
===================================================================
--- NAMESPACE	(revision 70700)
+++ NAMESPACE	(working copy)
@@ -332,3 +332,4 @@
      expand
  )

+S3method(as.list, List)
Index: R/List-class.R
===================================================================
--- R/List-class.R	(revision 70700)
+++ R/List-class.R	(working copy)
@@ -442,10 +442,11 @@
  ### Coercion.
  ###

+as.list.List <-
+    function(x, ...) lapply(x, identity)
+
  setAs("List", "list", function(from) as.list(from))

-setMethod("as.list", "List", function(x, ...) lapply(x, identity))
-
  setGeneric("as.env", function(x, ...) standardGeneric("as.env"))

  setMethod("as.env", "List",

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