`Makefile` incorrectly includes header files (`*.h`) as compilation sources

[taejun-song]

I encountered a build error when compiling RIsearch1 due to the inclusion of *.h files in the Makefile's targets. The default rule:

RIsearch: *.c *.h
	$(CC) $(CFLAGS) -O3 $^ -DRISVERSION=1 -lm -o $@

causes the compiler to fail with:

clang: error: cannot specify -o when generating multiple output files
make: *** [RIsearch] Error 1

This happens because header files (e.g., fasta.h) are not valid input files for the linker, yet they are included via the *.h glob and expanded into $^.

✅ Suggested Fix

A more portable and correct Makefile would explicitly list only the source files (*.c) as dependencies:

CFLAGS += -Wall -pedantic
SRC := dsm.c fasta.c risearch.c weights.c

all: RIsearch RIsearch.dbg

RIsearch: $(SRC)
	$(CC) $(CFLAGS) -O3 $(SRC) -DRISVERSION=1 -lm -o RIsearch

RIsearch.dbg: $(SRC)
	$(CC) $(CFLAGS) -g -O0 -DRISVERSION=1 -DDEBUG -DVERBOSE=2 $(SRC) -lm -o RIsearch.dbg

.PHONY: clean

clean:
	rm -f RIsearch RIsearch.dbg *.o

This avoids passing headers to the linker and allows the build to complete cleanly.