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vtraag / leidenalg

Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.
GNU General Public License v3.0
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ERROR: Failed building wheel for leidenalg in Colab Environment #105

Closed cmboye closed 1 year ago

cmboye commented 2 years ago

Hello,

I am trying to install leidenalg to ultimately run BPNet. I am using a Google Colab environment with Python 3.6. Please see below:

!sudo apt-get install build-essential autoconf automake flex bison
!sudo update-alternatives --config python3
!sudo apt install python3-pip
!python -m pip install --upgrade pip
!apt-get install -y bedtools > /dev/null
!pip install pprint -i http://pypi.douban.com/simple/ --trusted-host pypi.douban.com
!pip install git+https://github.com/kundajelab/DeepExplain.git --quiet
!pip install -U cloudpickle<1.7.0 h5py tqdm --quiet
!pip install -U pyyaml --quiet
!pip install igraph
!pip install leidenalg --no-use-pep517
!export DISABLE_BCOLZ_AVX2=true
!pip install bpnet --quiet --quiet

I get the following error: ERROR: Failed building wheel for leidenalg. Do you know what might cause this? I do not think I will be able to use a different version of Python due to errors with other dependencies. Thank you!

vtraag commented 2 years ago

When I try to run this on Google Colab, I don't get an error at leidenalg installation (although it does install version 0.8.9 instead of 0.8.10, not sure what is the problem there). However, it does error out at the installation of bpnet giving:

ERROR: Cannot install bpnet because these package versions have conflicting dependencies.
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies

So, I don't know exactly what the problem is, but it doesn't seem there is a problem with leidenalg, but with bpnet.

vtraag commented 1 year ago

I'm closing this issue for now. Feel free to re-open if necessary.