From: alexg@... (Alex Gutteridge)
Date: 2004-02-13T02:34:57+09:00
Subject: Marshal.dump - anonymous module

Hi,

I'm new to Ruby and am having difficulty getting a deep_copy method
working. I think I'm just doing something stupid with namespaces, but
I'm not sure eactly what. Here's what I've got:

module Bio
   module PDBUtils

        [snip!]

        def deep_copy
            puts "Trying to copy #{self.class}"
            Marshal.load(Marshal.dump(self))
        end

   end

   class PDB
      include PDBUtils
      [snip!]
   end
end

I get a new PDB object fine:

   structure = Bio::PDB.new()

but when I try and use deep_copy I get an error:

   structure2 = structure.deep_copy

   Trying to copy Bio::PDB
   in 'dump': can't dump anonymous module #<Module:0x403738c>
(TypeError)

Googling for this error reveals that Marshal.dump was fixed in 1.8 to
not allow dumping of anonymous modules. Unfortunately I'm not sure I
understand why it's saying I'm giving it an anonymous module. Doesn't
the 'Trying to copy Bio::PDB' output mean that I'm giving it a
Bio::PDB object to dump?

If somone could explain exactly what an anonymous module is, and why
I've got one here I'd really appreciate it.

Thanks for your time.

Alex Gutteridge
alexg@ebi.ac.uk