Bug: pip install error: subprocess-exited-with-error

[ferygood]

Describe the bug
After creating a virtual environment using python -m venv myEnv and install MACS3 from pip, I get this subprocess-exited-with-error.

To Reproduce

1. Create a virtual environment using venv, i.e. python -m venv macs3
2. Run pip install MACS3

Expected behavior
I expect the software can be installed

Screenshots
Last lines in error message (see full file in attachement
macs_install_error_log.txt
):

       note: This error originates from a subprocess, and is likely not a problem with pip.
        ERROR: Failed building wheel for cykhash
      Failed to build cykhash
      ERROR: Could not build wheels for cykhash, which is required to install pyproject.toml-based projects
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

System (please complete the following information):

• OS: Debian12 (bookworm)
• Python version 3.9.12
• Numpy version No Numpy yet (due to fail installation of MACS3)
• MACS Version MACS3

Thank you for your time and help!

[taoliu]

I read through your log, and it seems that you created a virtual python environment under your anaconda environment /home/yaochung41/anaconda3/ and while compiling cykash which is the khash implemented by Cython, the compiler is also looking for C library files under the system root directory /lib/x86_64-linux-gnu/libc.so.6. It's like three or four different systems mixed together. I suggest you use your anaconda environment to create a dedicated conda environment through conda env create... then activate the conda environment and then install MACS3 there.

[ferygood]

Thank you, taoliu, for your response and explanation. It helps a lot and I have successfully installed MACS3 with conda.

solution shared:

# 1. create a conda environment with python 3.9
conda create -n macs3 python=3.9  

# 2. install macs3 from pypi
pip install macs3