gentoo-overlay/sci-biology/cd-hit/files/4.6-gentoo.patch

 Makefile |   47 ++++++++++++++++++++++-------------------------
 1 files changed, 22 insertions(+), 25 deletions(-)

diff --git a/Makefile b/Makefile
index e9796a1..97dd72b 100644
--- a/Makefile
+++ b/Makefile
@@ -1,16 +1,13 @@
-
-CC = g++ -Wall -ggdb
-CC = g++ -pg
-CC = g++
+CXX ?= g++
 
 # without OpenMP
-CCFLAGS = -DNO_OPENMP
+#CXXFLAGS = -DNO_OPENMP
 
 # with OpenMP
 # in command line: 
 # make openmp=yes
 ifeq ($(openmp),yes)
-CCFLAGS = -fopenmp
+CXXFLAGS += -fopenmp
 endif
 
 # support debugging
@@ -18,22 +15,22 @@ endif
 # make debug=yes
 # make openmp=yes debug=yes
 ifeq ($(debug),yes)
-CCFLAGS += -ggdb
+CXXFLAGS += 
 else
-CCFLAGS += -O2
+CXXFLAGS += 
 endif
 
 ifdef MAX_SEQ
-CCFLAGS += -DMAX_SEQ=$(MAX_SEQ)
+CXXFLAGS += -DMAX_SEQ=$(MAX_SEQ)
 endif
 
 #LDFLAGS = -static -o
-LDFLAGS = -o
+#LDFLAGS += -o
 
 PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
 
 .c++.o:
-	$(CC) $(CCFLAGS) -c $<
+	$(CXX) $(CXXFLAGS) -c $<
 
 all: $(PROGS)
 
@@ -43,47 +40,47 @@ clean:
 # 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) $(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) $(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) $(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) $(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) $(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) $(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) $(CXXFLAGS) cdhit-common.c++ -c
 
 cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
-	$(CC) $(CCFLAGS) cdhit-utility.c++ -c
+	$(CXX) $(CXXFLAGS) cdhit-utility.c++ -c
 
 cdhit.o: cdhit.c++ cdhit-utility.h
-	$(CC) $(CCFLAGS) cdhit.c++ -c
+	$(CXX) $(CXXFLAGS) cdhit.c++ -c
 
 cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
-	$(CC) $(CCFLAGS) cdhit-2d.c++ -c
+	$(CXX) $(CXXFLAGS) cdhit-2d.c++ -c
 
 cdhit-est.o: cdhit-est.c++ cdhit-utility.h
-	$(CC) $(CCFLAGS) cdhit-est.c++ -c
+	$(CXX) $(CXXFLAGS) cdhit-est.c++ -c
 
 cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
-	$(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
+	$(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c
 
 cdhit-div.o: cdhit-div.c++ cdhit-common.h
-	$(CC) $(CCFLAGS) cdhit-div.c++ -c
+	$(CXX) $(CXXFLAGS) cdhit-div.c++ -c
 
 cdhit-454.o: cdhit-454.c++ cdhit-common.h
-	$(CC) $(CCFLAGS) cdhit-454.c++ -c
+	$(CXX) $(CXXFLAGS) cdhit-454.c++ -c
 
 PREFIX ?= /usr/local/bin