I think we're talking about the same problem. I just ran into this:
checking matlab's mex compilation flags... done
configure: error: Couldn't find mex... check your installation of matlab
The problem is with Matlab not knowing about new macOS versions. It checks certain SDK versions, but if you only have the newest version installed, then it won't find an SDK that it can work with.
The solution is to upgrade to the newest Matlab version of to manually add an entry for the new SDK version. You will have to modify the following files:
/Applications/MATLAB_R2015b.app/bin/maci64/mexopts/clang_maci64.xml
/Applications/MATLAB_R2015b.app/bin/maci64/mexopts/clang++_maci64.xml
/Applications/MATLAB_R2015b.app/bin/maci64/mexopts/gfortran_maci64.xml
In these files you will find entries like the following:
<dirExists name="$$/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk" />
<cmdReturns name="find $$ -name MacOSX10.11.sdk" />
You will need to add the appropriate entries for newer SDK versions. For version 10.12 for example you would add:
<dirExists name="$$/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk" />
<cmdReturns name="find $$ -name MacOSX10.12.sdk" />
Make sure you add both lines in the appropriate place. Also, in each file there are two places where this modification should be made.
