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Prototypes suffer from several other problems, too. They can change function behavior, by forcing scalar context when evaluating arguments that might not be scalars, or by forcing list context when evaluating arguments that might not be lists.  A function's prototype is ignored when that function is invoked with the & character. Finally, according to the perlfunc manpage [Wall 2011]:

Method calls are not influenced by prototypes either, because the function to be called is indeterminate at compile time, since the exact code called depends on inheritance.

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