ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found

[CZHanoi]

As the title, I want to convert my Seurat object (sequenced by MARs-seq) to h5ad. Howerver, it raised the bug:

Error in py_module_import(module, convert = convert) :
ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version GLIBCXX_3.4.29' not found (required by /home/data/zchen2/anaconda3/lib/python3.11/site-packages/pa ndas/_libs/window/aggregations.cpython-311-x86_64-linux-gnu.so) Run reticulate::py_last_error()` for details.
Calls: ... do.call -> -> -> py_module_import

[katosh]

Hello @CZHanoi,

Thank you for your inquiry. This error suggests that there is an issue with the version of the GNU Standard C++ Library (libstdc++) available on your system. You might be able to reproduce this error when running

python -c 'import pandas'

I am not sure how and when this incompatibility arose on your system. However, judging by the path of the uses pandas package, it seems like you are using conda in the base environment. To fix pandas and its dependencies you could run

conda update pandas --update-deps

However, I suspect, since there are already incompatibilities in this conda environment, that conda might not be able to resolve all dependencies. In that case I would recommend making a new environment, e.g., with

conda create -n new_environment_name -c conda-forge anndata
conda activate new_environment_name

Please let me know how it goes!