Comments (3)
ACEnglish
commented on July 4, 2024
This appears to be a problem upstream from Truvari. Best I can tell from google searches is that there's something going on with python 3.11 and/or cython (example)? Alternatively, you could try asking the edlib developers or look for help from python/cython user groups. I don't believe there's anything I can change in truvari to fix this issue.
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Overcraft90
commented on July 4, 2024
I see thanks @ACEnglish for the prompt reply, I will look into that and hopefully find a solution. For the time being maybe I keep this open, so once I've some news I can post here. Thanks again!
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ACEnglish
commented on July 4, 2024
I'm testing a new Truvari release and ran into the same problem. I able to install edlib without the wheel by performing the following steps:
git clone https://github.com/Martinsos/edlib.git
cd edlib/bindings/python
make sdist
python3 -m pip install dist/edlib-1.3.9.tar.gz
I believe the problem is that edlib wheel needs to be updated to be pip-installable for python 3.11. But after the manual installation above, Truvari's installation no longer ran in to edlib's problem:
DEPRECATION: edlib is being installed using the legacy 'setup.py install' method, because it does not have a 'pyproject.toml' and the 'wheel' package is not installed. pip 23.1 will enforce this behaviour change. A possible replacement is to enable the '--use-pep517' option. Discussion can be found at https://github.com/pypa/pip/issues/8559
Running setup.py install for edlib ... error
error: subprocess-exited-with-error
× Running setup.py install for edlib did not run successfully.
│ exit code: 1
╰─> [16 lines of output]
running install
/Users/english/temp/test_truvari/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_ext
building 'edlib' extension
creating build
creating build/temp.macosx-13-x86_64-cpython-311
creating build/temp.macosx-13-x86_64-cpython-311/edlib
creating build/temp.macosx-13-x86_64-cpython-311/edlib/src
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Iedlib/include -I/Users/english/temp/test_truvari/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.11/include/python3.11 -c edlib.bycython.cpp -o build/temp.macosx-13-x86_64-cpython-311/edlib.bycython.o -O3 -std=c++11
edlib.bycython.cpp:198:12: fatal error: 'longintrepr.h' file not found
#include "longintrepr.h"
^~~~~~~~~~~~~~~
1 error generated.
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
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