I have been trying to compile the mirnylib onto a new Mac running Sierra (10.12.6); I have all the dependencies installed correctly (through Anaconda), and when I run the install_linux.py program, I get this error message:
cent234-mac1:mirnylab-mirnylib aklocko$ python install_linux.py The PYTHONPATH is already set in /Users/aklocko/.bash_profile The PYTHONPATH is already set in /Users/aklocko/.bashrc Building cython modules.. If it does not work, check cython version (need 0.16+) running build_ext cythoning mirnylib/numutils_new.pyx to mirnylib/numutils_new.cpp building 'mirnylib.numutils_new' extension gcc -fno-strict-aliasing -I/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda/lib/python2.7/site-packages/numpy/core/include -I/anaconda/include/python2.7 -c mirnylib/numutils_new.cpp -o build/temp.macosx-10.7-x86_64-2.7/mirnylib/numutils_new.o cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default] In file included from /anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0, from /anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from mirnylib/numutils_new.cpp:499: /anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] mirnylib/numutils_new.cpp: In function 'PyObject* __pyx_pf_8mirnylib_12numutils_new_18observedOverExpected(PyObject*, PyObject*)': mirnylib/numutils_new.cpp:15398:38: error: 'isnan' was not declared in this scope mirnylib/numutils_new.cpp:15398:38: note: suggested alternative: In file included from /opt/local/include/gcc47/c++/complex:44:0, from mirnylib/numutils_new.cpp:722: /opt/local/include/gcc47/c++/cmath:839:5: note: 'std::isnan' error: command 'gcc' failed with exit status 1
I think it might be an issue with the compiler; I am using gcc.4.7 (installed through macports), but perhaps I am using the wrong one. Before I tried switching compilers, I was using the default compilers with Xcode (clang), which I think would be if I selected compilers through this code (and selecting "none"):
$ port select --list gcc Available versions for gcc: mp-gcc47 (active) none
I had successfully compiled the mirnylib and hiclib on an older iMac at my previous position (I am not sure what version; maybe 10.9?), so I am thinking it is something with this new software.
Any help would be most appreciated! Thank you in advance.