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pblischak / HyDe

Hybridization detection using phylogenetic invariants
http://hybridization-detection.readthedocs.io
MIT License
41 stars 14 forks source link

Installation error - seaborn missing #7

Closed ethering closed 5 years ago

ethering commented 5 years ago

Hi, I've tried this on Linux and Mac and get the same error. I've used pip install to install dependencies

$ pip install cython numpy matplotlib seaborn multiprocess

Looks like everything worked OK

Installing collected packages: cython, numpy, matplotlib, seaborn, multiprocess
Successfully installed cython-0.29.4 matplotlib-3.0.2 multiprocess-0.70.7 numpy-1.16.1 seaborn-0.9.0

Now install phyde

$ pip install phyde
Collecting phyde
  Downloading https://files.pythonhosted.org/packages/fc/20/4d9bc5157ad9f099db673f752d32191005a01429a0eab831d7d09a41e533/phyde-0.4.2.tar.gz (659kB)
    100% |████████████████████████████████| 665kB 5.2MB/s 
    Complete output from command python setup.py egg_info:
    ERROR:
      You are missing the following required modules:
         seaborn

    ERROR:
      Unable to install phyde.
      Please see the documentation at http://hybridization-detection.rtfd.io/.

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 255 in /private/var/folders/nn/mky1r73s295cp1qbt_z8pls0ppkbr7/T/pip-install-2j_9yzs6/phyde/

The same thing happens when I try to git clone and install. I've reinstall seaborn independently, both through pip and git (installations finish successfully), but I get the same 'seaborn missing' error when I try to install phyde. Have you seen this problem before or do you have any suggestions? Many thanks, Graham

pblischak commented 5 years ago

Hi, Graham!

I've gone through to try and see if I can replicate this error on my system by reinstalling seaborn and phyde but things seem to be working for me so I'm not exactly sure what is going on. Can you import seaborn in a Python session on its own? My only guess would be that it is installed in a place that Python can't find it (I don't know why that would be though).

As a potential 'hacky' solution, you can try commenting out the part in the setup.py file (in the main HyDe folder you cloned from here) that tries to test importing the seaborn module (lines 25-28). You can then try installing it with python setup.py install.

ethering commented 5 years ago

Hi Paul, Thanks for the advice. I tried again on Mac, using a virtualenv. I initially ran into a problem during phyde installation with matplotlib: RuntimeError: Python is not installed as a framework.....

but found the following fix: echo "backend: TkAgg" >> ~/.matplotlib/matplotlibrc

phyde then installed successfully and everything now runs fine. Many thanks, Graham

pblischak commented 5 years ago

Ok cool -- glad things are working for you! I'm going to go ahead and close this, but please feel free to reopen it if any other issues arise