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KIT-MBS / distruct

MIT License
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Error in installation #1

Closed drewaight closed 1 year ago

drewaight commented 3 years ago

Hi I have tried to install distruct in every way I know how (conda, pip, building from source with networkit) but I cant get test programs to run.

I have installed with biopython 1.77 because Bio.Alphabet is removed in 1.78

Traceback (most recent call last): File "/SFS/user/ry/waight/anaconda3/envs/distruct/lib/python3.7/site-packages/distruct/__init__.py", line 30, in <module> from _diSTruct import Distructure ImportError: /SFS/user/ry/waight/anaconda3/envs/distruct/lib/python3.7/site-packages/_diSTruct.cpython-37m-x86_64-linux-gnu.so: undefined symbol: _ZN9NetworKit6VectordVERKd

Do you have any advice on how to get distruct running? Thanks for your help!

oskar-taubert commented 3 years ago

Hi @drewaight, sorry the response took me a while. I tested it again for Python >= 3.7 it should work with:

`

python -m venv dsvenv source dsvenv/bin/activate pip install --upgrade pip git clone https://github.com/KIT-MBS/distruct.git cd distruct pip install cython pip install networkit==7.0 pip install -e . pip install pytest python -m pytest distruct/tests/ `

Your error looks like it might have to do with the way anaconda does things. I've set the biopython version for now, but I'll streamline the installation process and the dependency handling in the next update and fix the Bio.Alphabet deprecation issue.

If this doesn't help I would have to do testing with Anaconda.