I'm getting the same issue reported in message #5 with flex 2.6.1-1.3 amd64.
$ echo %% | flex ; gcc -c -Wsign-compare lex.yy.c lex.yy.c: In function ‘yy_get_next_buffer’: lex.yy.c:557:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for ( n = 0; n < max_size && \ ^ lex.yy.c:960:3: note: in expansion of macro ‘YY_INPUT’ YY_INPUT( (&YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move]), ^~~~~~~~ Downgrading to 2.6.1-1.2 did not solve the issue.