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Cloufield / gwaslab

A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/
GNU General Public License v3.0
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Installation error #93

Closed bsb2014 closed 4 months ago

bsb2014 commented 4 months ago

pip install gwaslab==3.4.43 ############################# ERROR: Ignored the following versions that require a different python version: 3.4.25 Requires-Python <=3.9,>=3.8; 3.4.26 Requires-Python <=3.9,>=3.8; 3.4.27 Requires-Python <=3.9,>=3.8; 3.4.28 Requires-Python <=3.9,>=3.8; 3.4.29 Requires-Python <=3.9,>=3.8; 3.4.30 Requires-Python <=3.10,>=3.8; 3.4.31 Requires-Python <=3.10,>=3.8; 3.4.32 Requires-Python <=3.10,>=3.8; 3.4.33 Requires-Python <=3.10,>=3.8; 3.4.34 Requires-Python <=3.10,>=3.8; 3.4.35 Requires-Python <=3.10,>=3.8; 3.4.36 Requires-Python <=3.10,>=3.8; 3.4.37 Requires-Python <=3.10,>=3.9; 3.4.38 Requires-Python <=3.10,>=3.9; 3.4.39 Requires-Python <=3.10,>=3.9; 3.4.40 Requires-Python <=3.10,>=3.9; 3.4.41 Requires-Python <=3.10,>=3.9; 3.4.42 Requires-Python <=3.10,>=3.9; 3.4.43 Requires-Python <=3.10,>=3.9; 3.4.44 Requires-Python <=3.10,>=3.9 ERROR: Could not find a version that satisfies the requirement gwaslab==3.4.43 (from versions: 0.0.1, 0.0.2, 0.0.3, 0.0.4, 0.0.5, 0.0.6, 1.0.0, 1.0.1, 1.0.2, 1.0.3, 1.0.4, 3.0.0, 3.0.1, 3.0.2, 3.1.0, 3.1.1, 3.1.2, 3.2.0, 3.3.0, 3.3.1, 3.3.2, 3.3.3, 3.3.4, 3.3.5, 3.3.6, 3.3.7, 3.3.8, 3.3.9, 3.3.10, 3.3.11, 3.3.12, 3.3.13, 3.3.14, 3.3.15, 3.3.16, 3.3.17, 3.3.18, 3.3.19, 3.3.20, 3.3.21, 3.3.22, 3.3.23, 3.3.24, 3.4.0, 3.4.1, 3.4.2, 3.4.3, 3.4.4, 3.4.5, 3.4.6, 3.4.7, 3.4.8, 3.4.9, 3.4.10, 3.4.11, 3.4.12, 3.4.13, 3.4.14, 3.4.15, 3.4.16, 3.4.17, 3.4.18, 3.4.19, 3.4.20, 3.4.21, 3.4.22, 3.4.23, 3.4.24) ERROR: No matching distribution found for gwaslab==3.4.43 ################################ My python version is

Python 3.10.8 | packaged by conda-forge | (main, Nov 22 2022, 08:23:14) [GCC 10.4.0] on linux Type "help", "copyright", "credits" or "license" for more information

Cloufield commented 4 months ago

Hi, Thanks for the feedback. Python 3.10 should have worked. I guess the way I set the requirements was wrong. For now, you can install it using pip install --ignore-requires-python gwaslab==3.4.43 to skip the version check for Python.

bsb2014 commented 4 months ago

Thanks for your prompt response. I have another problem. ERROR: Failed building wheel for pySAM. My pySAM version is 0.21.0

Cloufield commented 4 months ago

That would be a pysam installation issue. I also met that error several times so I restricted the version of pysam to 0.19. Would you please try 'pysam==0.19.1'?

bsb2014 commented 4 months ago

Do I need to change pysam==0.19 to pysam==0.19.1 in the environment.yml?

Cloufield commented 4 months ago

Sorry for not making it clear. There is no need to change that.

  1. If you want to install in your current environment, I think you could simply run pip install pysam==0.19.1 and then pip install --ignore-requires-python gwaslab==3.4.43.
  2. If installing by creating a new environment, you can use conda with this environment.yml (for versions >3.4.40).
bsb2014 commented 4 months ago

I tried the method 1 and failed.

ERROR: Failed building wheel for pysam.

More information: pysam/libcalignedsegment.pyx:1451:21: Invalid index type 'double'

It should be relevant to my Cython installation.

jmarshall commented 4 months ago

The Cython source code in pysam ≤0.20.0 expected to be compiled with language_level=2. You are now compiling it with a version of Cython in which that is not the default, as indicated by that “invalid index type” error message.

The sensible way to fix this is to move forward in time by using a current version of pysam (currently 0.22.1, which is fully Python/Cython 3) rather than moving backward in time by trying to use an older pysam that predates such versions of Cython.

Cloufield commented 4 months ago

The Cython source code in pysam ≤0.20.0 expected to be compiled with language_level=2. You are now compiling it with a version of Cython in which that is not the default, as indicated by that “invalid index type” error message.

The sensible way to fix this is to move forward in time by using a current version of pysam (currently 0.22.1, which is fully Python/Cython 3) rather than moving backward in time by trying to use an older pysam that predates such versions of Cython.

Thanks for your comments! I totally agree with your solution. Just tested and updated pysam requirements to the latest version v0.22.1.

Cloufield commented 4 months ago

I tried the method 1 and failed.

ERROR: Failed building wheel for pysam.

More information: pysam/libcalignedsegment.pyx:1451:21: Invalid index type 'double'

It should be relevant to my Cython installation.

@bsb2014 , Would you please try 'pip install gwaslab==3.4.45'. I updated the python and pysam version requirements and it should work now.

bsb2014 commented 4 months ago

It works!!