It was not clear from any of the documentation that Xcode 5.0.1 for 10.8 and for 10.9 use (by default) essentially separate C++ toolchains. Both are based on clang++ "3.3svn" which is Apple parlance for 'some version less than 3.3 and lacking some 3.2 features'. But they have different headers and C++ libraries. - 10.8 is using those from g++ 4.2.1 - 10.9 is using those from libcxx. This means that they are not completely ABI-compatible, and any package with C++ linkage (e.g. packages rgdal and rzmq) may need the external software recompiled. [NB: clang++ vs g++ were ABI compatible in 10.8. And 'may' not 'will'.] 10.9 contains a back-compatibility libstdc++, and most binary packages using C++ still work. However, at least for me JAGS (and hence packages rjags and runjags) and BioC package mzR segfault. I successfully re-compiled JAGS and rjags from their sources, but mzR will not compile. There are about 35 C++-based CRAN packages which do not compile using clang++ plus libcxx. The usual issues: g++ headers include other headers not required by the standards which other implementations do not, g++ uses 'tr1' for headers where libcxx does not, and more comprehensive implementations result in ambiguous matches.
Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595