Specify %option prefix="glcpp_" in the source code, not the Makefile.
diff --git a/glcpp/glcpp-lex.l b/glcpp/glcpp-lex.l
index 0d9a754..cc5f28f 100644
--- a/glcpp/glcpp-lex.l
+++ b/glcpp/glcpp-lex.l
@@ -31,6 +31,7 @@
 
 %option reentrant noyywrap
 %option extra-type="glcpp_parser_t *"
+%option prefix="glcpp_"
 
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