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Kukuster / SumStatsRehab

GWAS summary statistics files QC tool
https://doi.org/10.1186/s12859-022-04920-7
MIT License
33 stars 6 forks source link

AttributeError: /usr/lib64/libmagic.so.1: undefined symbol: magic_list #8

Open jingydz opened 3 months ago

jingydz commented 3 months ago

Comman

git clone https://github.com/Kukuster/SumStatsRehab.git && cd SumStatsRehab pip install -r requirements.txt python3 setup.py build python3 setup.py install SumStatsRehab --help

Bug

SumStatsRehab]$ SumStatsRehab --help Traceback (most recent call last): File "/xxx/software/miniconda3/bin/SumStatsRehab", line 33, in sys.exit(load_entry_point('SumStatsRehab==1.2.1', 'console_scripts', 'SumStatsRehab')()) File "/xxx/software/miniconda3/bin/SumStatsRehab", line 25, in importlib_load_entry_point return next(matches).load() File "/xxx/software/miniconda3/lib/python3.9/importlib/metadata.py", line 77, in load module = import_module(match.group('module')) File "/xxx/software/miniconda3/lib/python3.9/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1030, in _gcd_import File "", line 1007, in _find_and_load File "", line 986, in _find_and_load_unlocked File "", line 680, in _load_unlocked File "", line 850, in exec_module File "", line 228, in _call_with_frames_removed File "/xxx/software/miniconda3/lib/python3.9/site-packages/SumStatsRehab-1.2.1-py3.9.egg/SumStatsRehab.py", line 14, in from lib.prepare_GWASSS_columns import prepare_GWASSS_columns File "/xxx/software/miniconda3/lib/python3.9/site-packages/SumStatsRehab-1.2.1-py3.9.egg/lib/prepare_GWASSS_columns.py", line 10, in from lib.file import resolve_bare_text_file File "/xxx/software/miniconda3/lib/python3.9/site-packages/SumStatsRehab-1.2.1-py3.9.egg/lib/file.py", line 10, in import magic File "/xxx/software/miniconda3/lib/python3.9/site-packages/magic/init.py", line 452, in _add_compat(globals()) File "/xxx/software/miniconda3/lib/python3.9/site-packages/magic/init.py", line 416, in _add_compat from magic import compat File "/xxx/software/miniconda3/lib/python3.9/site-packages/magic/compat.py", line 98, in _list = _libraries['magic'].magic_list File "/xxx/software/miniconda3/lib/python3.9/ctypes/init.py", line 395, in getattr func = self.getitem(name) File "/xxx/software/miniconda3/lib/python3.9/ctypes/init.py", line 400, in getitem func = self._FuncPtr((name_or_ordinal, self)) AttributeError: /usr/lib64/libmagic.so.1: undefined symbol: magic_list

Kukuster commented 3 months ago

I reproduced the issue on fresh Ubuntu 20.04.1 Docker image, with miniconda 24.3.0, python 3.10.12.

We will have to make an update. But for now, I recommend the following steps to fix your issue:

1) Manually change the requirements for scipy version in both requirements.txt and setup.py files

from: scipy==1.6.1 to: scipy==1.10.1

2) Install system package libmagic and/or reinstall python package python-magic. Depending on your system [R], run:

Debian-based Linux

pip uninstall python-magic
apt install libmagic1 -y
pip install -r requirements.txt # will reinstall python-magic and scipy

MacOS

pip uninstall python-magic
brew install libmagic
pip install -r requirements.txt # will reinstall python-magic and scipy

Windows

pip uninstall python-magic
pip install -r requirements.txt # will reinstall python-magic and scipy 
pip install python-magic-bin

3) Reinstall SumStatsRehab:

python3 setup.py build
python3 setup.py install

After this SumStatsRehab --help should work.

scipy update will not affect the functionality: we rely only on normal distribution (scipy.stats.norm), and it was not changed between these versions according to the scipy release notes.