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lilab-bcb / demuxEM

Demultiplexing cell/nucleus hashing data for single-cell genomics
https://demuxem.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Fail to install demuxEM #17

Open jiananwehi opened 8 months ago

jiananwehi commented 8 months ago

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 

                             ^
  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 commented 8 months ago

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 commented 8 months ago

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+.