Successfully solved! Thanks! feedback for others facing the same problem: * compile last version of sqlite3 * backup the file /usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6 * from the compilation directory copy the file ~/sqlite-autoconf-3310100/.libs/libsqlite3.so.0.8.6 to the /usr/lib/x86_64-linux-gnu/ * install compiled version (sudo make install ) Finally python and system have the same version of sqlite3