Rosetta 3.9 is a bit on the older side. I think if you get the most recent version of Rosetta, this should be fixed.
If you do need to use Rosetta 3.9, see try removing the `using namespace boost;` line from source/src/protocols/antibody/database/CDRSetOptionsParser.cc — If you subsequently get compilation errors about not recognizing symbols in that file, you can try prepending `boost::` to them and see if that fixes the compilation. (cf. https://www.rosettacommons.org/node/10731)
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