Try as I may I was unable to reproduce the issue that you where experiencing but I did a little digging and this is what I found, hopefully it will lead to some sort of resolution:
The error you are describing is emitted as an exception of the PHP_Depend_Code_ASTFieldDeclaration:::setModifiers
method call, it is thrown as a result of not having any modifiers for the method/class/property in question.
If I had to take a guess on what your issue was then I would say I might be because a version mismatch between PDepend and PHPMD. I would try uninstalling and reinstalling (I sourced mine from the pear repo if that makes any difference).
Good Luck.