This is already tracked in https://trac.sagemath.org/ticket/31539


On Monday, June 28, 2021 at 2:35:54 PM UTC-7 vdelecroix wrote:

> Hello,
>
> I am trying to build sage in a conda environment. I did install a lot
> of things in it (including Python 3.9). However, the configure
> scripts does choose a strange solution
>
> configure:34331: result: no, this is a misconfigured Python whose 
> sysconfig compiler/linker flags contain -I or -L options, which may 
> cause wrong versions of libraries to leak into the build
> of Python packages - see https://trac.sagemath.org/ticket/31132; to use 
> it anyway, use ./configure 
> --with-python=/home/vincent/miniconda3/envs/sage-build/bin/python3
> configure:33784: checking ... whether /usr/bin/python3 is good
>
> Instead of using the conda Python3 it succeeds in using the system
> one. Which would better be avoided here.
>
> Vincent
>

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