Tensorqtl installation

[JingjingBai2021]

Hi ,

I am installing tensorqtl on linux " pip3 install tensorqtl" and got the following error:

Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-jm0rzo5a/pandas-plink/

Best, Jingjing

[francois-a]

This is an issue with pandas-plink — please submit an issue at https://github.com/limix/pandas-plink. What version of Python are you using?

[JingjingBai2021]

Thank you for your response. I solved the issue by using conda installation. But a new error pops up.

$ python3 -m tensorqtl --help

A module that was compiled using NumPy 1.x cannot be run in NumPy 2.0.0 as it may crash. To support both 1.x and 2.x versions of NumPy, modules must be compiled with NumPy 2.0. Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to downgrade to 'numpy<2' or try to upgrade the affected module. We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last): File "", line 198, in _run_module_as_main File "", line 88, in _run_code File "/groups/umcg-weersma/tmp01/Jingjing/tools/tensorqtl/tensorqtl/tensorqtl.py", line 15, in from post import File "/groups/umcg-weersma/tmp01/Jingjing/tools/tensorqtl/tensorqtl/post.py", line 13, in import mixqtl File "/groups/umcg-weersma/tmp01/Jingjing/tools/tensorqtl/tensorqtl/mixqtl.py", line 6, in import cis File "/groups/umcg-weersma/tmp01/Jingjing/tools/tensorqtl/tensorqtl/cis.py", line 11, in import genotypeio, eigenmt File "/groups/umcg-weersma/tmp01/Jingjing/tools/tensorqtl/tensorqtl/genotypeio.py", line 17, in import pgen File "/groups/umcg-weersma/tmp01/Jingjing/tools/tensorqtl/tensorqtl/pgen.py", line 6, in import pgenlib as pg Traceback (most recent call last): File "", line 198, in _run_module_as_main File "", line 88, in _run_code File "/groups/umcg-weersma/tmp01/Jingjing/tools/tensorqtl/tensorqtl/tensorqtl.py", line 15, in from post import File "/groups/umcg-weersma/tmp01/Jingjing/tools/tensorqtl/tensorqtl/post.py", line 13, in import mixqtl File "/groups/umcg-weersma/tmp01/Jingjing/tools/tensorqtl/tensorqtl/mixqtl.py", line 6, in import cis File "/groups/umcg-weersma/tmp01/Jingjing/tools/tensorqtl/tensorqtl/cis.py", line 11, in import genotypeio, eigenmt File "/groups/umcg-weersma/tmp01/Jingjing/tools/tensorqtl/tensorqtl/genotypeio.py", line 22, in gt_to_dosage_dict = {'0/0':0, '0/1':1, '1/1':2, './.':np.NaN, ^^^^^^ File "/groups/umcg-weersma/tmp01/Jingjing/tools/tensorqtl/pip_pkgs/numpy/init.py", line 397, in getattr raise AttributeError( AttributeError: np.NaN was removed in the NumPy 2.0 release. Use np.nan instead.. Did you mean: 'nan'?

Thanks for your help in advance.

[JingjingBai2021]

Problem solved by downgrading numpy.