issue running setup.py install

[angelajmcd]

Hi Paul,

I've been attempting to use HyDe with both python 2 and python 3 (at different times, of course) and I've gotten this error while running setup.py:

AngJMcD:HyDe angelarein$ python3 setup.py install Compiling phyde/core/data.pyx because it depends on /Users/angelarein/miniconda3/lib/python3.7/site-packages/Cython/Includes/numpy/init.pxd. [1/1] Cythonizing phyde/core/data.pyx /Users/angelarein/miniconda3/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Applications/HyDe/phyde/core/data.pyx tree = Parsing.p_module(s, pxd, full_module_name) running install running bdist_egg running egg_info writing phyde.egg-info/PKG-INFO writing dependency_links to phyde.egg-info/dependency_links.txt writing top-level names to phyde.egg-info/top_level.txt reading manifest file 'phyde.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'phyde.egg-info/SOURCES.txt' installing library code to build/bdist.macosx-10.7-x86_64/egg running install_lib running build_py creating build/lib.macosx-10.7-x86_64-3.7 creating build/lib.macosx-10.7-x86_64-3.7/phyde copying phyde/init.py -> build/lib.macosx-10.7-x86_64-3.7/phyde creating build/lib.macosx-10.7-x86_64-3.7/phyde/core copying phyde/core/bootstrap.py -> build/lib.macosx-10.7-x86_64-3.7/phyde/core copying phyde/core/init.py -> build/lib.macosx-10.7-x86_64-3.7/phyde/core copying phyde/core/result.py -> build/lib.macosx-10.7-x86_64-3.7/phyde/core copying phyde/core/utils.py -> build/lib.macosx-10.7-x86_64-3.7/phyde/core creating build/lib.macosx-10.7-x86_64-3.7/phyde/visualize copying phyde/visualize/init.py -> build/lib.macosx-10.7-x86_64-3.7/phyde/visualize copying phyde/visualize/viz.py -> build/lib.macosx-10.7-x86_64-3.7/phyde/visualize running build_ext building 'phyde.core.data' extension creating build/temp.macosx-10.7-x86_64-3.7 creating build/temp.macosx-10.7-x86_64-3.7/phyde creating build/temp.macosx-10.7-x86_64-3.7/phyde/core gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/angelarein/miniconda3/include -arch x86_64 -I/Users/angelarein/miniconda3/include -arch x86_64 -I/Users/angelarein/miniconda3/lib/python3.7/site-packages/numpy/core/include -I/Users/angelarein/miniconda3/include/python3.7m -c phyde/core/data.cpp -o build/temp.macosx-10.7-x86_64-3.7/phyde/core/data.o warning: include path for stdlibc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found] In file included from phyde/core/data.cpp:632: In file included from /Users/angelarein/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /Users/angelarein/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /Users/angelarein/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830: /Users/angelarein/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

warning "Using deprecated NumPy API, disable it with " \

^ phyde/core/data.cpp:635:10: fatal error: 'ios' file not found

include "ios"

     ^~~~~

2 warnings and 1 error generated. error: command 'gcc' failed with exit status 1

Any recommendations about how to work around this? I've completed software updates and ensured numpy is up to date... I'm not sure at all about what to do about missing stdlibc++ headers... (or even what that means, really!)

Let me know what you think, Angela

[angelajmcd]

An update: I think I might have fixed the issue, for now.

I think I found/installed headers using this: open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

I then still kept getting the gcc failed error, so I ran the following: export MACOSX_DEPLOYMENT_TARGET=10.10 CFLAGS='-stdlib=libc++' python setup.py install

It looks like it is running now. The files it's making are still 0 bytes, so not 100% sure yet.

[pblischak]

Hi Angela,

I've gotten this error before too and it is a weird one that is associated with using macOS Mojave and the version of Xcode that you have (at least I'm pretty sure). It looks like you are using Python 3.7, which is the one I used as well, and I used the CFLAGS='--stdlib=c++' python setup.py install command as well. I didn't set the MACOSX_DEPLOYMENT_TARGET=10.10 command though. You might try seeing if the tests run correctly. You can run them by going into the HyDe folder that you cloned from GitHub and typing make. If the tests work then everything should be good. Let me know how everything goes though.

Paul

[angelajmcd]

Hey Paul,

I ran it through the test dataset successfully. It is still chugging through the 10k+ triples for a real analysis; the files it's making there are still at 0 kb. Probably just running slow.

Thanks!