issue with pip install bagel

[romainVala]

Is there an existing issue for this?

• I have searched the existing issues

Expected behavior

I work within a conda env
with
python --version
Python 3.13.3

I'll attache the errors

Current behavior

No response

Error message

No response

Environment

• OS:
• Python/Node version: Python 3.13
• Docker version:
• Docker Compose version:

How to reproduce

No response

Anything else?

No response

[romainVala]

nnn.txt

[alyssadai]

Hi @romainVala, could you let us know which version of pip you have in nipoppy_env? Thanks!

[alyssadai]

Some notes from trying to reproduce this:

This seems to be happening because pip can't find a compatible prebuilt wheel for pyarrow in the env, so it falls back to building from source using cmake, creating issues if the cmake version is too old or not installed.

In the following environments:

• Python 3.13.3 Conda env, pip 25.3
• Python 3.11.0 Python venv, pip 22.3

I can reproduce the error using: pip install --no-binary=pyarrow --force-reinstall pyarrow.
I cannot reproduce the error using: pip install pyarrow.

Still unclear:

• Under what contexts can pip/conda not find the prebuilt wheel?

[romainVala]

pip --version
pip 25.1.1 from /data/romain/prog/conda-forge/envs/nipoppy_env/lib/python3.13/site-packages/pip (python 3.13)

(I reproduce the error with pip install pyarrow)

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