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biocore / biom-format

The Biological Observation Matrix (BIOM) Format Project
http://biom-format.org
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Trouble with installation using pip #941

Closed UmaJan closed 7 months ago

UmaJan commented 8 months ago

Attempting installation on cluster using pip install results in "failure to build wheel" messag repeatedly.

wasade commented 8 months ago

Hi @UmaJan, can you confirm what version of python and share the full output you're receiving?

UmaJan commented 8 months ago

I am using 3.1 and am getting these messages image image

error: command 'gcc' failed: No such file or directory [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for biom-format Failed to build biom-format ERROR: Could not build wheels for biom-format, which is required to install pyproject.toml-based projects

sfiligoi commented 8 months ago

Maybe it should be documented, but looks like the recipe expects you to have a valid compiler installed.

Can you retry after installing separately the usual compiler environment: gcc, g++, make

wasade commented 8 months ago

Hi @UmaJan, we have not verified support for Python 3.12 yet, and also do not currently provide pre-built wheels for Python 3.12. You can find the versions we test against here.

Are you required to use Python 3.12 or can you instead use 3.11?

UmaJan commented 8 months ago

I am using 3.6.8 currently I will try with some of the tested versions

wasade commented 8 months ago

Okay, but the screenshots show Python 3.12. We dropped support for 3.6 a bit ago. Please let us know how things proceed!

UmaJan commented 8 months ago

know

I switched to pyenv and used a 3.7 shell and it works, thanks!

wasade commented 7 months ago

That's great! Sorry for the issues and glad it's working now!