Can I have a pure virtual function in a class for which I am generating a dictionary. I did not define the pure virtual function in my .cpp file (since it is pure). Yet I get an error that there is an undefined reference when the dictionary is being generated.
Yes, you can. We have plenty of examples in ROOT itself.
For example we build the dictionaries in base/src/G__Base1.cxx, G__Base2.cxx with the interfaces classes TVirtualxxxx.
See for example class TVirtualFitter.