Failed to load celloracle

[YuchenXiangEMBL]

I have tried to install celloracle conda create -n celloracle_env python=3.8 conda activate celloracle_env conda install -c bioconda pybedtools The installation was successful, however, when I try to import it, import celloracle as co it reports error >>> import celloracle as co //miniconda3/envs/celloracle_pybedtools/lib/python3.8/site-packages/loompy/bus_file.py:68: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_to_dna(twobit: int, size: int) -> str: //miniconda3/envs/celloracle_pybedtools/lib/python3.8/site-packages/loompy/bus_file.py:85: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def dna_to_twobit(dna: str) -> int: //miniconda3/envs/celloracle_pybedtools/lib/python3.8/site-packages/loompy/bus_file.py:102: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details. def twobit_1hamming(twobit: int, size: int) -> List[int]: which: no R in (//miniconda3/envs/celloracle_pybedtools/bin://miniforge3/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin://.local/bin://bin) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/miniconda3/envs/celloracle_pybedtools/lib/python3.8/site-packages/celloracle/__init__.py", line 8, in <module> from . import utility, network, network_analysis, go_analysis, data, data_conversion, oracle_utility File "/miniconda3/envs/celloracle_pybedtools/lib/python3.8/site-packages/celloracle/utility/__init__.py", line 18, in <module> from .load_hdf5 import load_hdf5 File "/miniconda3/envs/celloracle_pybedtools/lib/python3.8/site-packages/celloracle/utility/load_hdf5.py", line 8, in <module> from ..motif_analysis.tfinfo_core import load_TFinfo File "/miniconda3/envs/celloracle_pybedtools/lib/python3.8/site-packages/celloracle/motif_analysis/__init__.py", line 11, in <module> from .motif_analysis_utility import is_genome_installed File "/miniconda3/envs/celloracle_pybedtools/lib/python3.8/site-packages/celloracle/motif_analysis/motif_analysis_utility.py", line 25, in <module> from gimmemotifs.scanner import Scanner File "/miniconda3/envs/celloracle_pybedtools/lib/python3.8/site-packages/gimmemotifs/__init__.py", line 58, in <module> from . import background # noqa: F401 File "/miniconda3/envs/celloracle_pybedtools/lib/python3.8/site-packages/gimmemotifs/background.py", line 27, in <module> import pybedtools File "/miniconda3/envs/celloracle_pybedtools/lib/python3.8/site-packages/pybedtools/__init__.py", line 8, in <module> from .cbedtools import ( ImportError: /lib64/libstdc++.so.6: versionGLIBCXX_3.4.29' not found (required by //miniconda3/envs/celloracle_pybedtools/lib/python3.8/site-packages/pybedtools/cbedtools.cpython-38-x86_64-linux-gnu.so) And I tried to import pybedtools first and then import celloracle >>> import pybedtools

import celloracle as co` I am not sure what's going on and why the pybedtools need to use the system GLIBCXX

[KenjiKamimoto-ac]

It seems your pybedtools installation is broken because of some random reasons. Can you uninstall and reinstall pybedtools? And please make sure you can import pybedtools without problem by running just import pybedtools. And then, please try celloracle.

[PauBadiaM]

It seems like the new version 0.9.1 of pybedtools has issues with gcc. After downgrading to 0.9.0 it worked for me.

pip install pybedtools==0.9.0