diff options
Diffstat (limited to 'sci-biology/cd-hit/files/4.5.1-gentoo.patch')
-rw-r--r-- | sci-biology/cd-hit/files/4.5.1-gentoo.patch | 85 |
1 files changed, 85 insertions, 0 deletions
diff --git a/sci-biology/cd-hit/files/4.5.1-gentoo.patch b/sci-biology/cd-hit/files/4.5.1-gentoo.patch new file mode 100644 index 000000000000..c3eaf79cc8f2 --- /dev/null +++ b/sci-biology/cd-hit/files/4.5.1-gentoo.patch @@ -0,0 +1,85 @@ +diff --git a/Makefile b/Makefile +index f1eaa26..92d3130 100644 +--- a/Makefile ++++ b/Makefile +@@ -10,7 +10,7 @@ CCFLAGS = -O2 -DNO_OPENMP + # in command line: + # make openmp=yes + ifeq ($(openmp),yes) +-CCFLAGS = -O2 -fopenmp ++CXXFLAGS += -fopenmp + endif + + # support debugging +@@ -18,16 +18,16 @@ endif + # make debug=yes + # make openmp=yes debug=yes + ifeq ($(debug),yes) +-CCFLAGS += -ggdb ++CXXFLAGS += -ggdb + endif + + #LDFLAGS = -static -o +-LDFLAGS = -o ++LDFLAGS += -o + + PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div + + .c++.o: +- $(CC) $(CCFLAGS) -c $< ++ $(CXX) $(CXXFLAGS) -c $< + + all: $(PROGS) + +@@ -37,39 +37,39 @@ 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) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div + + # 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 + |