Merge pull request #1604 from RosettaCommons/roccomoretti/fix_cxx11_dep
Fix some issues with modern compilers.
The C++11 update revealed some issues with modern compilers, mainly with deprecated constructs. This pull request should fix many of them.
In particular, it fixes issues with gcc 6.2.0, clang 3.9.0, and ICC 14.0 on my Linux machine.
This doesn't necessarily fix all issues: most notably Vikram is still experiencing issues on the Baker Lab machines. But those issues there can be addressed in a future pull request. (The fixes here are not contingent on fixing ICC 16.0.)