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pblischak / HyDe

Hybridization detection using phylogenetic invariants
http://hybridization-detection.readthedocs.io
GNU General Public License v3.0
41 stars 15 forks source link

Installation error #1

Closed slambert-git closed 7 years ago

slambert-git commented 7 years ago

Hi,

I'm getting the folllowing error when I try "pip install phyde" or "python setup.py install". I installed the dependencies also using pip. Python 2.7.12, Xubuntu 16.04.

Collecting phyde Using cached phyde-0.2.0.tar.gz Complete output from command python setup.py egg_info: make: Nothing to be done for 'all'. Testing hyde_cpp compilation... Traceback (most recent call last): File "", line 1, in File "/tmp/pip-build-_022s5/phyde/setup.py", line 78, in ext_modules=cythonize("phyde/*/.pyx", compiler_directives={'--cplus': True}), File "/usr/local/lib/python2.7/dist-packages/Cython/Build/Dependencies.py", line 886, in cythonize c_options = CompilationOptions(**options) File "/usr/local/lib/python2.7/dist-packages/Cython/Compiler/Main.py", line 568, in init raise ValueError(message) ValueError: got unknown compiler directive: --cplus

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-_022s5/phyde/

pblischak commented 7 years ago

This looks like an issue with the Cython compilation of the data.pyx module. Do you have the latest version of Cython? Also, are you running python setup.py install using a clone of the repo from GitHub?

slambert-git commented 7 years ago

Hi Paul,

I'm using an up-to-date clone of the github repo. Pip says that my Cython installation is up-to-date as well. I should mention that I'm also having this issue on our University HPC.

pblischak commented 7 years ago

I just changed the setup.py file to build and compile the data.pyx module in a different way. If you pull these changes into your clone of the repo and give python setup.py install another try hopefully it will work. Let me know if you get the same error though.

slambert-git commented 7 years ago

That seems to have fixed it! Many thanks. I will close the issue.

Shea