install doesn't work on MacOSX

[schultzm]

Hi,

This looks like a really useful program. Unfortunately I haven't been able to install it.

I have a gurobi licence, and I have done the conda installs into a python2.7 environment as per the issue submitted by @tseemann. That is:

conda install -c etetoolkit ete3
conda install -c anaconda cython 
conda install numpy scipy
conda config --add channels http://conda.anaconda.org/gurobi
conda install gurobi

Then after git cloning your repo, and I try to runpython setup.py install from the directory, I see:

python2 setup.py install
running install
running bdist_egg
running egg_info
creating Phydelity.egg-info
writing Phydelity.egg-info/PKG-INFO
writing top-level names to Phydelity.egg-info/top_level.txt
writing dependency_links to Phydelity.egg-info/dependency_links.txt
writing manifest file 'Phydelity.egg-info/SOURCES.txt'
reading manifest file 'Phydelity.egg-info/SOURCES.txt'
writing manifest file 'Phydelity.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.6-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.macosx-10.6-x86_64-2.7
creating build/lib.macosx-10.6-x86_64-2.7/phyilpd
copying phyilpd/stats_utils.py -> build/lib.macosx-10.6-x86_64-2.7/phyilpd
copying phyilpd/output_utils.py -> build/lib.macosx-10.6-x86_64-2.7/phyilpd
copying phyilpd/__init__.py -> build/lib.macosx-10.6-x86_64-2.7/phyilpd
copying phyilpd/gurobi_solver.py -> build/lib.macosx-10.6-x86_64-2.7/phyilpd
copying phyilpd/tree_utils.py -> build/lib.macosx-10.6-x86_64-2.7/phyilpd
running build_ext
building 'phyilpx' extension
creating build/temp.macosx-10.6-x86_64-2.7
creating build/temp.macosx-10.6-x86_64-2.7/phyilpx
gcc -fno-strict-aliasing -I/usr/local/Caskroom/miniconda/base/envs/phydelity_env/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/envs/phydelity_env/lib/python2.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/envs/phydelity_env/include/python2.7 -c phyilpx/phyilpx.c -o build/temp.macosx-10.6-x86_64-2.7/phyilpx/phyilpx.o
In file included from /usr/local/Caskroom/miniconda/base/envs/phydelity_env/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/syslimits.h:7:0,
                 from /usr/local/Caskroom/miniconda/base/envs/phydelity_env/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:34,
                 from /usr/local/Caskroom/miniconda/base/envs/phydelity_env/include/python2.7/Python.h:19,
                 from phyilpx/phyilpx.c:17:
/usr/local/Caskroom/miniconda/base/envs/phydelity_env/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:168:61: fatal error: limits.h: No such file or directory
 #include_next <limits.h>  /* recurse down to the real one */
                                                             ^
compilation terminated.
error: command 'gcc' failed with exit status 1

[alvinxhan]

Hi @schultzm, sorry for the late reply. Are you using macOS mojave? I recall reading about this error where you can't find header files (as well as a fix) here - https://programmer.help/blogs/how-to-resolve-pip-install-twisted-error-limits.h-no-such-file-or-directory.html

Let me know if it works!

[schultzm]

Hi @alvinxhan Thanks for your reply. Much appreciated. I am running 10.15.4 Catalina. For me, the limits.h file exists, even though it says 'No such file'. I can less the file and it's real.