From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Add CPPFLAGS & CFLAGS

And make the build more verbose so we can confirm this.
--- proteinortho.orig/Makefile
+++ proteinortho/Makefile
@@ -152,13 +152,13 @@
 ifeq ($(USEPRECOMPILEDLAPACK),TRUE)
 ifeq ($(STATIC),TRUE)
 	@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (static linking)";
-	@$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -static -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] ) || ( \
+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -static -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] ) || ( \
 		echo "......$(ORANGE)static linking failed, now I try dynamic linking.$(NC)"; \
-		$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+		$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
 			echo "......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX).$(NC)"; \
-			$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+			$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
 				echo "......$(ORANGE)dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas.$(NC)"; \
-				$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+				$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
 					echo "......$(ORANGE)last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking.$(NC)"; \
 					echo "......[ 33%] Extracting the LAPACK library"; \
 					if [ ! -d src/lapack-3.8.0 ]; then cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi; \
@@ -168,18 +168,18 @@
 					$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) ) )
 else
 	@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)";
-	@$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
 		echo "......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX).$(NC)"; \
-		$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+		$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
 			echo "......$(ORANGE)dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas.$(NC)"; \
-			$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+			$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp  -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
 				echo "......$(ORANGE)last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking.$(NC)"; \
 				echo "......[ 33%] Extracting the LAPACK library"; \
 				if [ ! -d src/lapack-3.8.0 ]; then cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi; \
 				echo "......[ 66%] Compiling the LAPACK library (using cmake + make)"; \
 				if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then mkdir src/lapack-3.8.0/build 2> /dev/null; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi; \
 				echo "......[ 99%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"; \
-				$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) )
+				$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) )
 endif
 	@if [ ! -e $(BUILDDIR)/proteinortho_clustering ]; then echo "proteinortho_clustering compilation failed. Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes"; false; fi
 else
@@ -188,47 +188,47 @@
 	@echo "[ 18%] Compiling the LAPACK library (using cmake + make)";
 	@if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null 2>&1; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi;
 	@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)";
-	@$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran;
+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran;
 endif
 endif
 ifeq ($(USELAPACK),FALSE)
 	@echo "[ 20%] Building **proteinortho_clustering** WITHOUT(!) LAPACK";
-	@$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
 		echo "......$(ORANGE)static linking failed of proteinortho_clustering_nolapack, now i switch to dynamic linking.$(NC)"; \
-		$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) && echo "......OK dynamic linking was successful for proteinortho_clustering_nolapack!"; )
+		$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) && echo "......OK dynamic linking was successful for proteinortho_clustering_nolapack!"; )
 endif
 
 $(BUILDDIR)/proteinortho_cleanupblastgraph: src/cleanupblastgraph.cpp
 	$(dir_guard)
 	@echo "[ 50%] Building **cleanupblastgraph**"
 ifeq ($(STATIC),TRUE)
-	@$(CXX) -std=c++11 $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
+	$(CXX) -std=c++11 $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
 		echo "......$(ORANGE)static linking failed of cleanupblastgraph, now i switch to dynamic linking.$(NC)"; \
-		$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< && echo "......OK dynamic linking was successful of cleanupblastgraph!"; )
+		$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< && echo "......OK dynamic linking was successful of cleanupblastgraph!"; )
 else
-	@$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS)
+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS)
 endif
 
 $(BUILDDIR)/proteinortho_graphMinusRemovegraph: src/graphMinusRemovegraph.cpp
 	$(dir_guard)
 	@echo "[ 25%] Building **graphMinusRemovegraph**"
 ifeq ($(STATIC),TRUE)
-	@$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
 		echo "......$(ORANGE)static linking failed of graphMinusRemovegraph, now i switch to dynamic linking.$(NC)"; \
-		$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< && echo "......OK dynamic linking was successful of graphMinusRemovegraph!"; )
+		$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< && echo "......OK dynamic linking was successful of graphMinusRemovegraph!"; )
 else
-	@$(CXX) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS)
+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_PO) -o $@ $< $(LDFLAGS) $(LDLIBS)
 endif
 
 $(BUILDDIR)/proteinortho_treeBuilderCore: src/po_tree.c
 	$(dir_guard)
 	@echo "[ 75%] Building **po_tree**"
 ifeq ($(STATIC),TRUE)
-	@$(CC) $(CCFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
+	$(CC) $(CPPFLAGS) $(CCFLAGS) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
 		echo "......$(ORANGE)static linking failed of po_tree, now i switch to dynamic linking.$(NC)"; \
-		$(CC) $(CCFLAGS) -o $@ $< && echo "......OK dynamic linking was successful of po_tree!"; )
+		$(CC) $(CPPFLAGS) $(CCFLAGS) $(CFLAGS) -o $@ $< && echo "......OK dynamic linking was successful of po_tree!"; )
 else
-	@$(CC) $(CCFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)
+	$(CC) $(CPPFLAGS) $(CCFLAGS) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)
 endif
 
 .PHONY: install
