another (different?) installation issue

[a-e-cole]

Hi! I'm trying to install on macOS Mojave and running into issues. Not sure whether they're related to problems others are having. When I attempt via pip:

Alex-Mac:ripser.py-master alex$ pip3 install ripser
Collecting ripser
  Using cached https://files.pythonhosted.org/packages/20/59/302dab2f1be85f32c57bdf8d4595d0437db76131b13504025abfc8373b03/ripser-0.3.0.tar.gz
Requirement already satisfied: Cython in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from ripser) (0.29.3)
Requirement already satisfied: numpy in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from ripser) (1.16.0)
Requirement already satisfied: scipy in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from ripser) (1.2.0)
Requirement already satisfied: matplotlib in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from ripser) (3.0.2)
Requirement already satisfied: scikit-learn in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from ripser) (0.20.2)
Requirement already satisfied: python-dateutil>=2.1 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from matplotlib->ripser) (2.7.5)
Requirement already satisfied: cycler>=0.10 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from matplotlib->ripser) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from matplotlib->ripser) (2.3.1)
Requirement already satisfied: kiwisolver>=1.0.1 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from matplotlib->ripser) (1.0.1)
Requirement already satisfied: six>=1.5 in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from python-dateutil>=2.1->matplotlib->ripser) (1.12.0)
Requirement already satisfied: setuptools in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib->ripser) (40.6.2)
Building wheels for collected packages: ripser
  Building wheel for ripser (setup.py) ... error
  Complete output from command /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/sr/kj8trxfd57sc9c_bwvwxl8nh0000gn/T/pip-install-wqfcvtit/ripser/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /private/var/folders/sr/kj8trxfd57sc9c_bwvwxl8nh0000gn/T/pip-wheel-i8piv9uu --python-tag cp37:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.9-x86_64-3.7
  creating build/lib.macosx-10.9-x86_64-3.7/ripser
  copying ripser/_version.py -> build/lib.macosx-10.9-x86_64-3.7/ripser
  copying ripser/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/ripser
  copying ripser/ripser.py -> build/lib.macosx-10.9-x86_64-3.7/ripser
  running build_ext
  building 'pyRipser' extension
  creating build/temp.macosx-10.9-x86_64-3.7
  creating build/temp.macosx-10.9-x86_64-3.7/ripser
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -DUSE_COEFFICIENTS=1 -DNDEBUG=1 -DASSEMBLE_REDUCTION_MATRIX=1 -I./ripser -I/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/core/include -c ripser/pyRipser.cpp -o build/temp.macosx-10.9-x86_64-3.7/ripser/pyRipser.o -std=c++11 -Ofast -D_hypot=hypot
  In file included from /usr/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/include-fixed/syslimits.h:7:0,
                   from /usr/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/include-fixed/limits.h:34,
                   from /Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m/Python.h:11,
                   from ripser/pyRipser.cpp:42:
  /usr/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/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
  
  ----------------------------------------
  Failed building wheel for ripser
  Running setup.py clean for ripser
Failed to build ripser
Installing collected packages: ripser
  Running setup.py install for ripser ... error
    Complete output from command /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/sr/kj8trxfd57sc9c_bwvwxl8nh0000gn/T/pip-install-wqfcvtit/ripser/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/sr/kj8trxfd57sc9c_bwvwxl8nh0000gn/T/pip-record-mn9lirpo/install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.9-x86_64-3.7
    creating build/lib.macosx-10.9-x86_64-3.7/ripser
    copying ripser/_version.py -> build/lib.macosx-10.9-x86_64-3.7/ripser
    copying ripser/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/ripser
    copying ripser/ripser.py -> build/lib.macosx-10.9-x86_64-3.7/ripser
    running build_ext
    building 'pyRipser' extension
    creating build/temp.macosx-10.9-x86_64-3.7
    creating build/temp.macosx-10.9-x86_64-3.7/ripser
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -DUSE_COEFFICIENTS=1 -DNDEBUG=1 -DASSEMBLE_REDUCTION_MATRIX=1 -I./ripser -I/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/core/include -c ripser/pyRipser.cpp -o build/temp.macosx-10.9-x86_64-3.7/ripser/pyRipser.o -std=c++11 -Ofast -D_hypot=hypot
    In file included from /usr/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/include-fixed/syslimits.h:7:0,
                     from /usr/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/include-fixed/limits.h:34,
                     from /Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m/Python.h:11,
                     from ripser/pyRipser.cpp:42:
    /usr/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/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`
    
    ----------------------------------------
`Command "/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/sr/kj8trxfd57sc9c_bwvwxl8nh0000gn/T/pip-install-wqfcvtit/ripser/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/sr/kj8trxfd57sc9c_bwvwxl8nh0000gn/T/pip-record-mn9lirpo/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/sr/kj8trxfd57sc9c_bwvwxl8nh0000gn/T/pip-install-wqfcvtit/ripser/

and when I try directly from the master branch:

Alex-Mac:ripser.py-master alex$ python3 setup.py install
Add compile flag macs
running install
running bdist_egg
running egg_info
writing ripser.egg-info/PKG-INFO
writing dependency_links to ripser.egg-info/dependency_links.txt
writing requirements to ripser.egg-info/requires.txt
writing top-level names to ripser.egg-info/top_level.txt
reading manifest file 'ripser.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'ripser.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.9-x86_64/egg
running install_lib
running build_py
running build_ext
building 'pyRipser' extension
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -DUSE_COEFFICIENTS=1 -DNDEBUG=1 -DASSEMBLE_REDUCTION_MATRIX=1 -I./ripser -I/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/core/include -c ripser/pyRipser.cpp -o build/temp.macosx-10.9-x86_64-3.7/ripser/pyRipser.o -std=c++11 -Ofast -D_hypot=hypot -stdlib=libc++
gcc: error: unrecognized command line option ‘-stdlib=libc++’
error: command 'gcc' failed with exit status 1

Any advice would be much appreciated!

[sauln]

This is a different issue and I'm not sure exactly what's wrong. How did you install your Python? Could you try installing python-dev as well to see if that helps.

[a-e-cole]

This is with Python 3.7.2 installed from https://www.python.org/downloads/.

I haven't tried with python-dev yet but using homebrew to install Python 3 has given me a successful install! Either with pip or by the master branch download. Strange!

[sauln]

Great! I'm glad the home-brew install worked. I'll play around with the versions from python.org and see if I can get it to break also.