Fail to install demuxEM

[jiananwehi]

The following shows the error:
gcc -std=gnu11 -pthread -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -I/stornext/Bioinf/data/lab_speed/wang.j/python_package/myenv/include -I/stornext/System/data/apps/python/python-3.12.0/include/python3.12 -c ext_modules/fast_funcs.c -o build/temp.linux-x86_64-cpython-312/ext_modules/fast_funcs.o
ext_modules/fast_funcs.c:1517:27: fatal error: stdatomic.h: No such file or directory
#include <stdatomic.h>
^
compilation terminated.
error: command '/usr/bin/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 pegasusio
Failed to build pegasusio
ERROR: Could not build wheels for pegasusio, which is required to install pyproject.toml-based projects

[yihming]

Hi @jiananwehi . This looks like an issue with pegasusio (https://github.com/lilab-bcb/pegasusio), a dependency package, as it does not support Python 3.12 yet.

I'll see if I could make that package support Python 3.12. Will keep you posted.

[yihming]

I was able to install demuxEM (as well as pegasusio) in Python 3.12.

May I ask the version of your GCC compiler? Based on https://stackoverflow.com/questions/20326604/stdatomic-h-in-gcc-4-8, it seems the issue with "stdatomic.h" file missing was fixed for GCC v4.9+.