NumPy and system’s floating-point number support,

Technical Support
1

When I type the following commend:
qiime feature-table filter-features
--i-table ASV_table.qza
--m-metadata-file annotated_feature_ids.txt
--o-filtered-table filtered_ASV_table.qza
The following error message is displayed that
/home/vk1602/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)

I asked gpt what the reason was and it gave me the following answer that
The warning you're seeing is related to a compatibility issue between NumPy and your system’s floating-point number support, specifically for the longdouble type. This warning isn't critical and likely won't affect the functionality

How do I resolve this warning message

2

While this is only a harmless warning, not an error.

EDIT: It's an issue with Numpy and WSL. Using WSL 2 fixes it.

Old response

It should be resolved in the newest version of Qiime2, so a fresh install should fix it.

Try this!

conda remove -n qiime2-amplicon-2024.5 --all
conda update conda
conda clean --all
wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml
conda env create -n qiime2-amplicon-2024.5 --file qiime2-amplicon-2024.5-py39-linux-conda.yml
2 Likes
3

I ran this command to reinstall qiime2, but there is still a warning message that --o-filtered-table filtered_ASV_table.qza
/home/vk1602/anaconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)

7

Hello @vk1602

I'm investigating this more. I have been able to replicate this error on a WSL 1 install

It looks like upgrading to WSL 2 may address this warning. I'll try it and let you know if it works.

8

Try this: Upgrade WSL 1 to WSL 2

WSL 2 does real virtualization of the real Linux kernel, improving compatibility and stability.

I followed this upgrade guide. Sort of like this:

# List all VMs and their versions
wsl.exe -l -v

# Close connections to that VM so it shows as stopped
>  NAME      STATE           VERSION
>* Ubuntu    Stopped         1

# Then upgrade it
wsl --set-version UbuntuNameSeenAbove 2
1 Like