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Well, I can't find this message in my version so I'm not sure what methods you're talking about.
Now if these are the vars related ones, the solution is in front of you

This one is deprecated:
function uid()
{
return $this->getVar("uid");
}
So don't use $myobj->uid();
but $myobj->getVar('uid');
instead....

And this generally applies to all the deprecated methods: the "old one" has been kept for compatibility reasons, but the alternate way of doing things is in the function body.
Skalpa.>