Can I ask what version of the cctbx are you attempting to build? For some time (at least several months) it has been possible to build the cctbx (and the whole of Phenix) using the default clang on the latest Mac OS X. Most of the Phenix developers here in Berkeley are now using clang on the latest OS X, so someone would almost certainly notice immediately if something wasn't building correctly. The latest "released" build of the cctbx (dating from May 2012!) does not build with clang as I recall. Unfortunately we do not have an official release mechanism for the cctbx, beyond Nat deciding when to mark one of the nightly builds as a release. Clearly the current "released" version is rather old and we should replace it with a more recent version. For now I would recommend trying with one of the more recent nightly builds (e.g.
http://cci.lbl.gov/cctbx_build/show_results.cgi?build_tag=2013_03_22_0005), or checking the code out directly from svn.