Fix the original problem of gh-5736

theano/compile/function.py

@@ -289,13 +289,6 @@ def function(inputs, outputs=None, mode=None, updates=None, givens=None,
     uses_updates = bool(updates)
     uses_givens = bool(givens)
 
-    # See if we have any mutable / borrow inputs
-    check_for_aliased_inputs = False
-    for i in inputs:
-        if (isinstance(i, In) and ((hasattr(i, 'borrow') and i.borrow) or
-                                   (hasattr(i, 'mutable') and i.mutable))):
-            check_for_aliased_inputs = True
-
     if uses_tuple:
         # we must use old semantics in this case.
         if profile:
@@ -323,7 +316,4 @@ def function(inputs, outputs=None, mode=None, updates=None, givens=None,
                    on_unused_input=on_unused_input,
                    profile=profile,
                    output_keys=output_keys)
-    # We need to add the flag check_aliased inputs if we have any mutable or
-    # borrowed used defined inputs
-    fn._check_for_aliased_inputs = check_for_aliased_inputs
     return fn

theano/compile/function_module.py

@@ -375,6 +375,15 @@ class Function(object):
         self.nodes_with_inner_function = []
         self.output_keys = output_keys
 
+        # See if we have any mutable / borrow inputs
+        # TODO: this only need to be set if there is more then 1 input
+        self._check_for_aliased_inputs = False
+        for i in maker.inputs:
+            if (isinstance(i, In) and ((hasattr(i, 'borrow') and i.borrow) or
+                                       (hasattr(i, 'mutable') and i.mutable))):
+                self._check_for_aliased_inputs = True
+                break
+
         # We will be popping stuff off this `containers` object.  It is a copy.
         containers = list(self.input_storage)
         finder = {}
@@ -821,6 +830,7 @@ class Function(object):
                 self[k] = arg
 
         if (not self.trust_input and
+            # The getattr is only needed for old pickle
                 getattr(self, '_check_for_aliased_inputs', True)):
             # Collect aliased inputs among the storage space
             args_share_memory = []

theano/compile/tests/test_function_module.py

@@ -609,6 +609,7 @@ class T_picklefunction(unittest.TestCase):
         self.assertFalse(x in g.container)
         self.assertFalse(x in g.value)
         self.assertTrue(len(f.defaults) == len(g.defaults))
+        self.assertTrue(f._check_for_aliased_inputs is g._check_for_aliased_inputs)
         # print 'f.defaults = %s' % (f.defaults, )
         # print 'g.defaults = %s' % (g.defaults, )
         self.assertTrue(all([f_req == g_req and f_feed == g_feed and