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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.
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
!!
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
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