error during install: `python setup.py bdist_wheel did not run sucessfully`

[nl835]

When installing deeptools, it seems to keep failing due to py2bit, so I attempted installing py2bit alone first to see if it was the one causing problems.

when running pip install py2bit, it throws the following error:

Collecting py2bit Using cached py2bit-0.3.0.tar.gz (16 kB) Preparing metadata (setup.py) ... done Building wheels for collected packages: py2bit Building wheel for py2bit (setup.py) ... error error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [45 lines of output] /home/nickylauw/anaconda3/lib/python3.12/site-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options !!

          ********************************************************************************
          Usage of dash-separated 'description-file' will not be supported in future
          versions. Please use the underscore name 'description_file' instead.
  
          By 2024-Sep-26, you need to update your project and remove deprecated calls
          or your builds will no longer be supported.
  
          See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
          ********************************************************************************
  
  !!
    opt = self.warn_dash_deprecation(opt, section)
  /home/nickylauw/anaconda3/lib/python3.12/site-packages/setuptools/_distutils/dist.py:260: UserWarning: Unknown distribution option: 'classifier'
    warnings.warn(msg)
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-cpython-312
  creating build/lib.linux-x86_64-cpython-312/py2bitTest
  copying py2bitTest/__init__.py -> build/lib.linux-x86_64-cpython-312/py2bitTest
  copying py2bitTest/test.py -> build/lib.linux-x86_64-cpython-312/py2bitTest
  running egg_info
  writing py2bit.egg-info/PKG-INFO
  writing dependency_links to py2bit.egg-info/dependency_links.txt
  writing top-level names to py2bit.egg-info/top_level.txt
  reading manifest file 'py2bit.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE.txt'
  writing manifest file 'py2bit.egg-info/SOURCES.txt'
  copying py2bitTest/foo.2bit -> build/lib.linux-x86_64-cpython-312/py2bitTest
  running build_ext
  building 'py2bit' extension
  creating build/temp.linux-x86_64-cpython-312
  creating build/temp.linux-x86_64-cpython-312/lib2bit
  gcc -pthread -B /home/nickylauw/anaconda3/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/nickylauw/anaconda3/include -fPIC -O2 -isystem /home/nickylauw/anaconda3/include -fPIC -Ilib2bit -I/home/nickylauw/anaconda3/include/python3.12 -I/home/nickylauw/anaconda3/include/python3.12 -c lib2bit/2bit.c -o build/temp.linux-x86_64-cpython-312/lib2bit/2bit.o
  gcc -pthread -B /home/nickylauw/anaconda3/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/nickylauw/anaconda3/include -fPIC -O2 -isystem /home/nickylauw/anaconda3/include -fPIC -Ilib2bit -I/home/nickylauw/anaconda3/include/python3.12 -I/home/nickylauw/anaconda3/include/python3.12 -c py2bit.c -o build/temp.linux-x86_64-cpython-312/py2bit.o
  py2bit.c: In function ‘py2bitEnter’:
  py2bit.c:35:24: error: initialization of ‘pyTwoBit_t *’ from incompatible pointer type ‘TwoBit *’ [-Wincompatible-pointer-types]
     35 |     pyTwoBit_t *pytb = self->tb;
        |                        ^~~~
  error: command '/sbin/gcc' failed with exit code 1
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for py2bit Running setup.py clean for py2bit Failed to build py2bit ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (py2bit)

Installing with pip install git+https://github.com/dpryan79/py2bit returns the same error.

Installing with conda install bioconda::py2bit is stuck for very long with the following message until I interrupt with ctrl + C

Collecting package metadata (current_repodata.json): - WARNING conda.models.version:get_matcher(563): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1., but conda is ignoring the . and treating it as 1.7.1 done Solving environment: - unsuccessful initial attempt using frozen solve. Retrying with flexible solve.

OS: Arch linux Python version: 3.12.2 pip version: 24.2 conda version: 24.7.1