Open biobirds9 opened 5 months ago
zhouyiqi91
commented
5 months ago I think you can downgrade numpy to 1.26
pip install numpy==1.26
https://stackoverflow.com/questions/78634235/numpy-dtype-size-changed-may-indicate-binary-incompatibility-expected-96-from
Besides, I recommend using nf-celescope instead of celescope.
Khillo81
commented
4 months ago Just to add that downgrading pandas also helps. We helped someone out by suggesting to downgrade pandas to 1.4.2
biobirds9
commented
4 months ago I think you can downgrade numpy to 1.26
pip install numpy==1.26https://stackoverflow.com/questions/78634235/numpy-dtype-size-changed-may-indicate-binary-incompatibility-expected-96-fromBesides, I recommend using nf-celescope instead of celescope.
Thank you very much for your reply, this suggestion worked, thanks again for your work!
RubTalha
Hello! Thank you for such an excellent software.
I am trying to run CeleScope to test , but it throws me the following error.
============================= test session starts ============================== platform linux -- Python 3.9.19, pytest-8.2.2, pluggy-1.5.0 rootdir: /public/home/hpc236503011/Celescope/test_dir/celescope_test_script collected 0 items / 1 error
==================================== ERRORS ==================================== ____ ERROR collecting test_multi.py ____ test_multi.py:9: in
import celescope.tools.utils as utils
../../../.conda/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py:18: in
import pandas as pd
../../../.conda/envs/celescope/lib/python3.9/site-packages/pandas/init.py:22: in
from pandas.compat import is_numpy_dev as _is_numpy_dev
../../../.conda/envs/celescope/lib/python3.9/site-packages/pandas/compat/init.py:15: in
from pandas.compat.numpy import (
../../../.conda/envs/celescope/lib/python3.9/site-packages/pandas/compat/numpy/init.py:4: in
from pandas.util.version import Version
../../../.conda/envs/celescope/lib/python3.9/site-packages/pandas/util/init.py:1: in
from pandas.util._decorators import ( # noqa:F401
../../../.conda/envs/celescope/lib/python3.9/site-packages/pandas/util/_decorators.py:14: in
from pandas._libs.properties import cache_readonly # noqa:F401
../../../.conda/envs/celescope/lib/python3.9/site-packages/pandas/_libs/init.py:13: in
from pandas._libs.interval import Interval
pandas/_libs/interval.pyx:1: in init pandas._libs.interval
???
E ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
=========================== short test summary info ============================
ERROR test_multi.py - ValueError: numpy.dtype size changed, may indicate bina...
!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!
=============================== 1 error in 8.74s ===============================
I found out that it's because the numpy package version is too high, but it's not possible to install a lower version of numpy. What can I do to fix it?