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arzwa / wgd

Python package and CLI for whole-genome duplication related analyses. This package is deprecated in favor of https://github.com/heche-psb/wgd.
http://wgd.readthedocs.io/en/latest/
GNU General Public License v3.0
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Installation stuck at pandas wheel #52

Closed Cecilia-Sensalari closed 3 years ago

Cecilia-Sensalari commented 3 years ago

Hi, I've been trying to install wgd on my Linux computer through pip3 and Python 3.8.5 (3.8 is default in Ubuntu 20.04). However, it has troubles when building the pandas wheel. I've read online that this may be caused by some incompatibility between pandas 0.24 and Python 3.8 (on stackoverflow). Here is how the installation log looked like, it got stuck for some time and I cancelled it (perhaps it just takes 20 minutes as the post says).

csensa@Data:~/Documents/wgd-1.1.1$ pip3 install .
Processing /home/csensa/Documents/wgd-1.1.1
Requirement already satisfied: click>=7.0 in /usr/lib/python3/dist-packages (from wgd==1.1) (7.0)
Requirement already satisfied: biopython>=1.75 in /home/csensa/.local/lib/python3.8/site-packages (from wgd==1.1) (1.78)
Requirement already satisfied: seaborn>=0.9.0 in /usr/lib/python3/dist-packages (from wgd==1.1) (0.10.0)
Requirement already satisfied: coloredlogs>=10.0 in /home/csensa/.local/lib/python3.8/site-packages (from wgd==1.1) (14.0)
Requirement already satisfied: fastcluster==1.1.25 in /home/csensa/.local/lib/python3.8/site-packages (from wgd==1.1) (1.1.25)
Requirement already satisfied: numpy>=1.16 in /usr/lib/python3/dist-packages (from wgd==1.1) (1.17.4)
Requirement already satisfied: sklearn in /home/csensa/.local/lib/python3.8/site-packages (from wgd==1.1) (0.0)
Requirement already satisfied: scipy>=1.2 in /usr/lib/python3/dist-packages (from wgd==1.1) (1.3.3)
Requirement already satisfied: matplotlib>=3.0.2 in /usr/lib/python3/dist-packages (from wgd==1.1) (3.1.2)
Requirement already satisfied: plumbum>=1.6.7 in /home/csensa/.local/lib/python3.8/site-packages (from wgd==1.1) (1.6.9)
Collecting pandas==0.24.1
  Using cached pandas-0.24.1.tar.gz (11.8 MB)
Requirement already satisfied: progressbar2>=3.39 in /home/csensa/.local/lib/python3.8/site-packages (from wgd==1.1) (3.53.1)
Requirement already satisfied: joblib==0.11 in /home/csensa/.local/lib/python3.8/site-packages (from wgd==1.1) (0.11)
Requirement already satisfied: ete3>=3.1 in /home/csensa/.local/lib/python3.8/site-packages (from wgd==1.1) (3.1.2)
Requirement already satisfied: bokeh>=1.0.4 in /home/csensa/.local/lib/python3.8/site-packages (from wgd==1.1) (1.4.0)
Requirement already satisfied: humanfriendly>=7.1 in /home/csensa/.local/lib/python3.8/site-packages (from coloredlogs>=10.0->wgd==1.1) (8.2)
Requirement already satisfied: scikit-learn in /home/csensa/.local/lib/python3.8/site-packages (from sklearn->wgd==1.1) (0.23.2)
Requirement already satisfied: python-dateutil>=2.5.0 in /usr/lib/python3/dist-packages (from pandas==0.24.1->wgd==1.1) (2.7.3)
Requirement already satisfied: pytz>=2011k in /usr/lib/python3/dist-packages (from pandas==0.24.1->wgd==1.1) (2019.3)
Requirement already satisfied: six in /usr/lib/python3/dist-packages (from progressbar2>=3.39->wgd==1.1) (1.14.0)
Requirement already satisfied: python-utils>=2.3.0 in /home/csensa/.local/lib/python3.8/site-packages (from progressbar2>=3.39->wgd==1.1) (2.4.0)
Requirement already satisfied: Jinja2>=2.7 in /home/csensa/.local/lib/python3.8/site-packages (from bokeh>=1.0.4->wgd==1.1) (2.11.2)
Requirement already satisfied: tornado>=4.3 in /home/csensa/.local/lib/python3.8/site-packages (from bokeh>=1.0.4->wgd==1.1) (6.0.4)
Requirement already satisfied: pillow>=4.0 in /home/csensa/.local/lib/python3.8/site-packages (from bokeh>=1.0.4->wgd==1.1) (7.2.0)
Requirement already satisfied: packaging>=16.8 in /usr/lib/python3/dist-packages (from bokeh>=1.0.4->wgd==1.1) (20.3)
Requirement already satisfied: PyYAML>=3.10 in /usr/lib/python3/dist-packages (from bokeh>=1.0.4->wgd==1.1) (5.3.1)
Requirement already satisfied: threadpoolctl>=2.0.0 in /home/csensa/.local/lib/python3.8/site-packages (from scikit-learn->sklearn->wgd==1.1) (2.1.0)
Requirement already satisfied: MarkupSafe>=0.23 in /usr/lib/python3/dist-packages (from Jinja2>=2.7->bokeh>=1.0.4->wgd==1.1) (1.1.0)
Building wheels for collected packages: wgd, pandas
  Building wheel for wgd (setup.py) ... done
  Created wheel for wgd: filename=wgd-1.1-py3-none-any.whl size=74849 sha256=5d5701b55793be0d34affd7b74af9757878a2550c9fcfb1eeb6a204731b4b173
  Stored in directory: /home/csensa/.cache/pip/wheels/c5/17/a8/ba6431f85d4761f80672f2de7c246331f429c6dd10a843c5df
  Building wheel for pandas (setup.py) ... |^canceled

For a comparison I edited the setup.py asking for the latest pandas version (1.2.0) and the installation could reach immediately the end. I tried the example A.thaliana dataset with mcl and ksd commands and they worked.

arzwa commented 3 years ago

Thanks for reporting, I've noticed similar issues with python 3.9 on the dev branch , we should check whether bumping the pandas version doesn't mess up other things (or breaks wgd on python3.6). Feel free to make a PR with the changes to the setup.py file.