Pyenv - WARNING: The Python sqlite3 extension was not compiled

 

zzh@ZZHPC:~/.pyenv/bin$ ./pyenv install 3.13.5
Downloading Python-3.13.5.tar.xz...
-> https://www.python.org/ftp/python/3.13.5/Python-3.13.5.tar.xz
Installing Python-3.13.5...
Traceback (most recent call last):
  File "<string>", line 1, in <module>
    import sqlite3
  File "/home/zzh/.pyenv/versions/3.13.5/lib/python3.13/sqlite3/__init__.py", line 57, in <module>
    from sqlite3.dbapi2 import *
  File "/home/zzh/.pyenv/versions/3.13.5/lib/python3.13/sqlite3/dbapi2.py", line 27, in <module>
    from _sqlite3 import *
ModuleNotFoundError: No module named '_sqlite3'
WARNING: The Python sqlite3 extension was not compiled. Missing the SQLite3 lib?
Installed Python-3.13.5 to /home/zzh/.pyenv/versions/3.13.5

 

✅ Root Cause

When building Python from source (as pyenv does), it needs the development headers and libraries of dependencies like SQLite, zlib, OpenSSL, etc.

In your case, Python found the sqlite3 Python wrapper, but could not find the native _sqlite3 C extension, because the SQLite C library and its headers were missing.

 

zzh@ZZHPC:~/.pyenv/bin$ ./pyenv uninstall 3.13.5
pyenv: remove /home/zzh/.pyenv/versions/3.13.5? (y/N) y
pyenv: 3.13.5 uninstalled

 

zzh@ZZHPC:~/.pyenv/bin$ sudo apt install libsqlite3-dev

 

zzh@ZZHPC:~/.pyenv/bin$ ./pyenv install 3.13.5
Downloading Python-3.13.5.tar.xz...
-> https://www.python.org/ftp/python/3.13.5/Python-3.13.5.tar.xz
Installing Python-3.13.5...
Installed Python-3.13.5 to /home/zzh/.pyenv/versions/3.13.5