gentoo-overlay/sci-biology/cd-hit/files/cd-hit-4.6.6-fix-build-system.patch

Fix build system, in order to honour user variables

--- a/makefile
+++ b/makefile
@@ -1,7 +1,4 @@
-
-CC = g++ -Wall -ggdb
-CC = g++ -pg
-CC = g++
+CXX ?= g++
 
 # without OpenMP
 
@@ -9,35 +6,19 @@
 # in command line: 
 # make openmp=yes
 ifeq ($(openmp),no)
-  CCFLAGS = -DNO_OPENMP
-else
-  CCFLAGS = -fopenmp
-endif
-
-# support debugging
-# in command line:
-# make debug=yes
-# make openmp=yes debug=yes
-ifeq ($(debug),yes)
-CCFLAGS += -ggdb
+  my_CPPFLAGS = -DNO_OPENMP
 else
-CCFLAGS += -O2
+  my_CXXFLAGS = -fopenmp
 endif
 
 ifdef MAX_SEQ
-CCFLAGS += -DMAX_SEQ=$(MAX_SEQ)
+my_CPPFLAGS += -DMAX_SEQ=$(MAX_SEQ)
 endif
 
-#LDFLAGS = -static -o
-LDFLAGS += -o
-
 PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
 
-# Propagate hardening flags
-CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS)
-
 .c++.o:
-	$(CC) $(CCFLAGS) -c $<
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) -c $<
 
 all: $(PROGS)
 
@@ -47,52 +28,52 @@
 # programs
 
 cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
-	$(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit
 
 cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
-	$(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d
 
 cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
-	$(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est
 
 cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
-	$(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d
 
 cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
-	$(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div
 
 cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o
-	$(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454
 
 # objects
 cdhit-common.o: cdhit-common.c++ cdhit-common.h
-	$(CC) $(CCFLAGS) cdhit-common.c++ -c
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-common.c++ -c
 
 cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
-	$(CC) $(CCFLAGS) cdhit-utility.c++ -c
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-utility.c++ -c
 
 cdhit.o: cdhit.c++ cdhit-utility.h
-	$(CC) $(CCFLAGS) cdhit.c++ -c
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit.c++ -c
 
 cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
-	$(CC) $(CCFLAGS) cdhit-2d.c++ -c
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-2d.c++ -c
 
 cdhit-est.o: cdhit-est.c++ cdhit-utility.h
-	$(CC) $(CCFLAGS) cdhit-est.c++ -c
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-est.c++ -c
 
 cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
-	$(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-est-2d.c++ -c
 
 cdhit-div.o: cdhit-div.c++ cdhit-common.h
-	$(CC) $(CCFLAGS) cdhit-div.c++ -c
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-div.c++ -c
 
 cdhit-454.o: cdhit-454.c++ cdhit-common.h
-	$(CC) $(CCFLAGS) cdhit-454.c++ -c
+	$(CXX) $(my_CXXFLAGS) $(CXXFLAGS) $(my_CPPFLAGS) $(CPPFLAGS) cdhit-454.c++ -c
 
 PREFIX ?= /usr/local/bin
 
 install:
 	for prog in $(PROGS); do \
-		install -m 0755 $$prog $(PREFIX); \
+		install -m 0755 $$prog $(DESTDIR)$(PREFIX); \
 	done
-	install -m 0755 *.pl $(PREFIX);
+	install -m 0755 *.pl $(DESTDIR)$(PREFIX);