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Ubuntu – undefined symbol: sqlite3_deserialize in Jupyter notebook – Visual Studio Code

I use remote development plug-in in visual studio because I run code on server. When I try to run any line of code in interactive window the following error occurs:

ImportError: /home/user/anaconda3/envs/geo/lib/python3.12/lib-dynload/_sqlite3.cpython-312-x86_64-linux-gnu.so: undefined symbol: sqlite3_deserialize.

I have already intalled Ipykernel and Jupyter plug in.

I use Ubuntu 22.04, python 3.12.2

Am I missing something?

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2

Answers


  1. Chosen as BEST ANSWER
    0

    By inspecting the version of sqlite3 installed on my conda environment using sqlite3 --version I found out that the version was 3.22. My ultimate goal was to install gdal, but as it turned out there some incompatibilities between them.

    I fix it by using:

    - sqlite 2.6.0
- gdal 3.9.2
- python 3.12.6

    on ubuntu 24.04


  2. 0

    I run into the same error in Python3.11.9. I noticed when I installed rapids my Python was downgraded to 3.11.8 as well as sqlite. Tried upgrading python again to 3.11.9, but that didn’t work. Any way to reinstall sqlite maybe?

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