not sure whether that helps, but I tried to compile r-3-2-1 outside galaxy on the same machine:

1.straight ./configure yields error: "cannot compile a simple Fortran program."

To remedie this, I installed gfortran (=gf) 5.2 for OS X (10.11) from https://gcc.gnu.org/wiki/GFortranBinaries

and with gf installed, ./configure now completes, but make fails with "dyld: Symbol not found: _libiconv_open"

2. I then installed libiconv-1.4 as suggested in this tip for R-on-OS X: http://blog.qiubio.com:8080/archives/3897

and put /usr/local/lib into $PATH

now make finishes …

I made mistakes running ./configure and make/install

first omitting the epxort LD_LIBRARY_PATH= command … and I don’t have proper records ;-)

Not sure how to clean this up - but I wanted to let you know my findings with respect to compiling r-3-2-1

Cheers,

Hans