SQLite3-autoconf builds shell utility by default (shell.c -> sqlite3[.exe]).
It uses system() call that was deprecated in iOS 8:
'system' is deprecated: first deprecated in iOS 8.0 - Use posix_spawn APIs instead.
In iOS 11 system() was disabled:
__swift_unavailable_on("Use posix_spawn APIs or NSTask instead.", "Process spawning is unavailable")
__API_AVAILABLE(macos(10.0)) __IOS_PROHIBITED
__WATCHOS_PROHIBITED __TVOS_PROHIBITED
int system(const char *) __DARWIN_ALIAS_C(system);
#undef __swift_unavailable_on
sqlite3 configure does not have option to exclude shell utility from makefile
So you need to modify makefile or replace "make clean install" command with targets excluding shell utility.