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Symptom: In my Django app, when I call from pysqlite2._sqlite import * I get the traceback Symbol not found: _sqlite3_enable_load_extension when

Background:

  • I've installed python using homebrew (python 2.7.13), which auto installed sqlite
  • I am running macOS 10.12.3 with Command Line Tools macOS 10.12, Xcode 8.2.1
  • I've installed pysqlite using pip (pysqlite 2.8.3)

I have tried

  • brew uninstall sqlite and brew uninstall python and reinstalling

  • Adding these to my .bash_profile 

    export PATH="$(brew --prefix sqlite)/bin:$PATH"
LDFLAGS="-L/usr/local/opt/sqlite/lib"
CPPFLAGS="-I/usr/local/opt/sqlite/include"
export PKG_CONFIG_PATH=“/usr/local/opt/sqlite/lib/pkgconfig”

  • python -c "import sqlite3" doesn't return any errors

Gist of traceback: https://gist.github.com/xwchen/e9704fa34f0463d2117fe9fbb37922a1

Xiao Wei Chen
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  • I have now the same `Symbol not found: _sqlite3_enable_load_extension` error. I reinstalled python2, python3 and sqlite without any success and I cant find a google page anymore which helps me. I also added several environment variables. Like `LDFLAGS`, `CPPFLAGS`, `PKG_CONFIG_PATH`, `DYLD_LIBRARY_PATH` I am using python 2.7 in <- virtual environment with Mac OS 10.15.6 please help. – Yuna Braska Jul 21 '20 at 09:45

3 Answers3

14

Copied answer from here (https://github.com/Homebrew/homebrew-core/pull/3134). If you're like me, you probably installed sqlite after you install python3. Anyway, if anyone stumbles upon this question and needs an answer...

First remove SQLite, python and python3 if installed via homebrew

brew uninstall --force python
brew uninstall --force python3
brew uninstall --force sqlite

This removes all copies.

Then make sure Xcode 8 or later is installed

Important

Re-install command line tools via 

xcode-select --install
sudo xcode-select --reset

and finally install command line tools via pkg file found here.

Look for command line tools in search. (I've downloaded "Command Line Tools (macOS 10.12) for Xcode 8.dmg") Then open DMG and install the pkg found there.

Now install SQLite and then python and python 3 if needed:

brew install sqlite
brew install python
brew install python3

Run brew install python --verbose and make sure there are no warnings, if none then issues should be resolved.

Don't forget to do 

pip install setuptools --upgrade && pip3 install setuptools --upgrade
Paul Kertscher
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jaxon737
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  • This didn't worked for me. I am trying since months to get up an oder project running with python 2.7 on virtual environment. but I keep getting the error message *Symbol not found: _sqlite3_enable_load_extension.* Can some one help me? – Yuna Braska Aug 06 '20 at 13:52
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    You should avoid using system python and any homebrew versions of python for development. Use `pyenv` instead. Run `brew install pyenv`. `pyenv install 2.7.18` and you can set the local python in your shell env as `pyenv shell 2.7.18` – jaxon737 Aug 07 '20 at 14:08
6

It may happen because it's not able to locate the .so library. As explained here:

On OS X, homebrew installs sqlite3 as “keg-only” because otherwise it interferes with the system sqlite3. This means that libsqlite3.dylib ends up in /usr/local/opt/sqlite/lib, not in /usr/local/lib

So you can simply do this:

export DYLD_LIBRARY_PATH=/usr/local/opt/sqlite/lib:/usr/lib

Then you should be able to import sqlite3.

jtate
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Lei Z
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  • +1 I was having this issue with python@3.9. Solved it without reinstalling, just: `export DYLD_LIBRARY_PATH="/opt/homebrew/Cellar/sqlite/3.35.5/lib:/usr/local/lib:/usr/local/include:/usr/lib:/usr/include"` – ssanch Jul 20 '21 at 18:29
  • none of these worked for me on M1 with python@3.9. – user1255933 Sep 15 '22 at 15:31
  • I was getting `Symbol not found: _sqlite3_aggregate_context` error. Without much understanding, I tried this method, and it just worked and now I can launch Jupyter. – Kouichi C. Nakamura Nov 07 '22 at 20:28
  • Using the same conda environment, I can run Jupyter by `jupyer notebook` but I still cannot use Jupyter on VScode and am still having the same error `Symbol not found: _sqlite3_aggregate_context` – Kouichi C. Nakamura Nov 07 '22 at 21:17
1

In my conda environment simply running conda install sqlite fixed it.

Matteo Ferla
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