I have did some reading on "Merging Makefiles", one suggest I should leave the two Makefiles separate in different folders [1]. For me this look counter intuitive, because I have the following situation: I have 3 source files (main.cpp flexibility.cpp constraints.cpp) one of them (flexibility.cpp) is making use of the COIN-OR Linear Programming library (Clp) When installing this library on my computer it makes sample Makefiles, which I have adjust the Makefile and it currently makes a good working binary. # Copyright (C) 2006 International Business Machines and others. # All Rights Reserved. # This file is distributed under the Eclipse Public License. # $Id: Makefile.in 726 2006-04-17 04:16:00Z andreasw $ ########################################################################## # You can modify this example makefile to fit for your own program. # # Usually, you only need to change the five CHANGEME entries below. # ########################################################################## # To compile other examples, either changed the following line, or # add the argument DRIVER=problem_name to make DRIVER = main # CHANGEME: This should be the name of your executable EXE = clp # CHANGEME: Here is the name of all object files corresponding to the source # code that you wrote in order to define the problem statement OBJS = $(DRIVER).o constraints.o flexibility.o # CHANGEME: Additional libraries ADDLIBS = # CHANGEME: Additional flags for compilation (e.g., include flags) ADDINCFLAGS = # CHANGEME: Directory to the sources for the (example) problem definition # files SRCDIR = . ########################################################################## # Usually, you don't have to change anything below. Note that if you # # change certain compiler options, you might have to recompile the # # COIN package. # ########################################################################## COIN_HAS_PKGCONFIG = TRUE COIN_CXX_IS_CL = #TRUE COIN_HAS_SAMPLE = TRUE COIN_HAS_NETLIB = #TRUE # C++ Compiler command CXX = g++ # C++ Compiler options CXXFLAGS = -O3 -pipe -DNDEBUG -pedantic-errors -Wparentheses -Wreturn-type -Wcast-qual -Wall -Wpointer-arith -Wwrite-strings -Wconversion -Wno-unknown-pragmas -Wno-long-long -DCLP_BUILD # additional C++ Compiler options for linking CXXLINKFLAGS = -Wl,--rpath -Wl,/home/martijn/Downloads/COIN/coin-Clp/lib # C Compiler command CC = gcc # C Compiler options CFLAGS = -O3 -pipe -DNDEBUG -pedantic-errors -Wimplicit -Wparentheses -Wsequence-point -Wreturn-type -Wcast-qual -Wall -Wno-unknown-pragmas -Wno-long-long -DCLP_BUILD # Sample data directory ifeq ($(COIN_HAS_SAMPLE), TRUE) ifeq ($(COIN_HAS_PKGCONFIG), TRUE) CXXFLAGS += -DSAMPLEDIR=\"`PKG_CONFIG_PATH=/home/martijn/Downloads/COIN/coin-Clp/lib64/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/lib/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/share/pkgconfig: pkg-config --variable=datadir coindatasample`\" CFLAGS += -DSAMPLEDIR=\"`PKG_CONFIG_PATH=/home/martijn/Downloads/COIN/coin-Clp/lib64/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/lib/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/share/pkgconfig: pkg-config --variable=datadir coindatasample`\" else CXXFLAGS += -DSAMPLEDIR=\"\" CFLAGS += -DSAMPLEDIR=\"\" endif endif # Netlib data directory ifeq ($(COIN_HAS_NETLIB), TRUE) ifeq ($(COIN_HAS_PKGCONFIG), TRUE) CXXFLAGS += -DNETLIBDIR=\"`PKG_CONFIG_PATH=/home/martijn/Downloads/COIN/coin-Clp/lib64/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/lib/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/share/pkgconfig: pkg-config --variable=datadir coindatanetlib`\" CFLAGS += -DNETLIBDIR=\"`PKG_CONFIG_PATH=/home/martijn/Downloads/COIN/coin-Clp/lib64/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/lib/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/share/pkgconfig: pkg-config --variable=datadir coindatanetlib`\" else CXXFLAGS += -DNETLIBDIR=\"\" CFLAGS += -DNETLIBDIR=\"\" endif endif # Include directories (we use the CYGPATH_W variables to allow compilation with Windows compilers) ifeq ($(COIN_HAS_PKGCONFIG), TRUE) INCL = `PKG_CONFIG_PATH=/home/martijn/Downloads/COIN/coin-Clp/lib64/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/lib/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/share/pkgconfig: pkg-config --cflags clp` else INCL = endif INCL += $(ADDINCFLAGS) # Linker flags ifeq ($(COIN_HAS_PKGCONFIG), TRUE) LIBS = `PKG_CONFIG_PATH=/home/martijn/Downloads/COIN/coin-Clp/lib64/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/lib/pkgconfig:/home/martijn/Downloads/COIN/coin-Clp/share/pkgconfig: pkg-config --libs clp` else ifeq ($(COIN_CXX_IS_CL), TRUE) LIBS = -link -libpath:`$(CYGPATH_W) /home/martijn/Downloads/COIN/coin-Clp/lib` libClp.lib else LIBS = -L/home/martijn/Downloads/COIN/coin-Clp/lib -lClp endif endif # The following is necessary under cygwin, if native compilers are used CYGPATH_W = echo # Here we list all possible generated objects or executables to delete them CLEANFILES = clp \ main.o \ flexibility.o \ constraints.o \ all: $(EXE) .SUFFIXES: .cpp .c .o .obj $(EXE): $(OBJS) bla=;\ for file in $(OBJS); do bla="$$bla `$(CYGPATH_W) $$file`"; done; \ $(CXX) $(CXXLINKFLAGS) $(CXXFLAGS) -o $@ $$bla $(LIBS) $(ADDLIBS) clean: rm -rf $(CLEANFILES) .cpp.o: $(CXX) $(CXXFLAGS) $(INCL) -c -o $@ `test -f '$<' || echo '$(SRCDIR)/'`$< .cpp.obj: $(CXX) $(CXXFLAGS) $(INCL) -c -o $@ `if test -f '$<'; then $(CYGPATH_W) '$<'; else $(CYGPATH_W) '$(SRCDIR)/$<'; fi` .c.o: $(CC) $(CFLAGS) $(INCL) -c -o $@ `test -f '$<' || echo '$(SRCDIR)/'`$< .c.obj: $(CC) $(CFLAGS) $(INCL) -c -o $@ `if test -f '$<'; then $(CYGPATH_W) '$<'; else $(CYGPATH_W) '$(SRCDIR)/$<'; fi` The other Makefile compiles a lot of code and makes use of bison and flex. This one is also made by someone else. I am able to alter this Makefile when I want to add some code. This Makefile also makes a binary. CFLAGS=-Wall LDLIBS=-LC:/GnuWin32/lib -lfl -lm LSOURCES=lex.l YSOURCES=grammar.ypp CSOURCES=debug.cpp esta_plus.cpp heap.cpp main.cpp stjn.cpp timing.cpp tmsp.cpp token.cpp chaining.cpp flexibility.cpp exceptions.cpp HSOURCES=$(CSOURCES:.cpp=.h) includes.h OBJECTS=$(LSOURCES:.l=.o) $(YSOURCES:.ypp=.tab.o) $(CSOURCES:.cpp=.o) all: solver solver: CFLAGS+=-g -O0 -DDEBUG solver: $(OBJECTS) main.o debug.o g++ $(CFLAGS) -o $@ $^ $(LDLIBS) solver.release: CFLAGS+=-O5 solver.release: $(OBJECTS) main.o g++ $(CFLAGS) -o $@ $^ $(LDLIBS) %.o: %.cpp g++ -c $(CFLAGS) -o $@ $< lex.cpp: lex.l grammar.tab.cpp grammar.tab.hpp flex -o$@ $< %.tab.cpp %.tab.hpp: %.ypp bison --verbose -d $< ifneq ($(LSOURCES),) $(LSOURCES:.l=.cpp): $(YSOURCES:.y=.tab.h) endif -include $(OBJECTS:.o=.d) clean: rm -f $(OBJECTS) $(OBJECTS:.o=.d) $(YSOURCES:.ypp=.tab.cpp) $(YSOURCES:.ypp=.tab.hpp) $(YSOURCES:.ypp=.output) $(LSOURCES:.l=.cpp) solver solver.release 2>/dev/null .PHONY: all clean debug release Both of these Makefiles are, for me, hard to understand. I don't know what they exactly do. What I want is to merge the two of them so I get only one binary. The code compiled in the second Makefile should be the result. I want to add flexibility.cpp and constraints.cpp to the second Makefile, but when I do. I get the problem following problem: flexibility.h:4:26: fatal error: ClpSimplex.hpp: No such file or directory #include "ClpSimplex.hpp" So the compiler can't find the Clp library. I also tried to copy-paste more code from the first Makefile into the second, but it still gives me that same error. Q: Can you please help me with merging the two makefiles or pointing out a more elegant way? Q: In this case is it indeed better to merge the two Makefiles? I also tried to use cmake, but I gave upon that one quickly, because I don't know much about flex and bison.