Source code documentation with Doxygen http://www.Doxygen.org isn't limited to C/C#/C++ or Java. Using the FILTERS feature http://www.doxygen.org/config.html#cfg_filter_patterns a filter program can convert the programming language you are using into something like C and that would be used by DoxyGen.
GNU-R can be converted to look like C code. A dot in the name is converted to and underscore.
There are no facilities to track classes or packages.