In the current version of the system all public C functions of SWI-Prolog are in the symbol table. This can lead to name clashes with foreign code. Someday I should write a program to strip all these symbols from the symbol table (why does Unix not have that?). For now I can only suggest you give your function another name. You can do this using the C preprocessor. If---for example---your foreign package uses a function warning(), which happens to exist in SWI-Prolog as well, the following macro should fix the problem:
#define warning warning_
Note that shared libraries do not have this problem as the shared library loader will only look for symbols in the main executable for symbols that are not defined in the library itself.