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Gentoo's Bugzilla – Attachment 199528 Details for
Bug 278571
sci-biology/mafft-6.707: new version request
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Makefile2
Makefile2 (text/plain), 4.24 KB, created by
Martin Mokrejš
on 2009-07-29 10:02:52 UTC
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Description:
Makefile2
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MIME Type:
Creator:
Martin Mokrejš
Created:
2009-07-29 10:02:52 UTC
Size:
4.24 KB
patch
obsolete
>################################################################################ ># Makefile for probcons >################################################################################ > >################################################################################ ># 1) Choose C++ compiler. >################################################################################ > >CXX = g++ > >################################################################################ ># 2) Set C++ flags. ># a) DEBUG mode -- no optimizations, enable SafeVector checking, no inlining ># b) PROFILE mode -- for gprof ># c) RELEASE mode >################################################################################ >BIG_INLINE_LIMIT = 20000 >OTHERFLAGS = -DNumInsertStates=1 -DVERSION="2.0" > >PROBCONS = ./probconsRNA >VIENNA = ./vienna > ># debug mode >#CXXFLAGS = -g -W -Wall -DENABLE_CHECKS $(OTHERFLAGS) -I./rfold-0.1/src/ -I./rfold-0.1/src/vienna -L./rfold-0.1/src/ $(CFLAGS) $(CFLAGS1) -finline-limit=$(BIG_INLINE_LIMIT) -I$(PROBCONS) -L$(PROBCONS) -I$(VIENNA) -L$(VIENNA) -I./ -L./ ># profile mode >#CXXFLAGS = -pg -W -Wall -pedantic $(OTHERFLAGS) $(CFLAGS1) -I$(PROBCONS) -L$(PROBCONS) -I$(VIENNA) -L$(VIENNA) -I./ -L./ > ># release mode >#CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer -I$(PROBCONS) -L$(PROBCONS) -I$(VIENNA) -L$(VIENNA) -I./ -L./ >#CXXFLAGS = -O3 -W -Wasll -DNDEBUG -static $(OTHERFLAGS) -funroll-loops $(CFLAGS1) -finline-limit=$(BIG_INLINE_LIMIT) -I$(PROBCONS) -L$(PROBCONS) -I$(VIENNA) -L$(VIENNA) -I./ -L./ > ># no -Wall option for warning >CXXFLAGS = -O3 -funroll-loops $(CFLAGS1) -finline-limit=$(BIG_INLINE_LIMIT) >LIBDIR = -L$(PROBCONS) -L./ >INCDIR = -I$(PROBCONS) -I$(VIENNA) -I./ >OFLAGS = -DNDEBUG $(OTHERFLAGS) > >################################################################################ ># 3) Dependencies >################################################################################ > >TARGETS = mxscarna > >OBJS = Main.o McCaskill.o vienna/energy_param.o seq2scs.o Globaldp.o postProcessings.o AlifoldMEA.o > >.PHONY : all >all : $(TARGETS) > >mxscarna : $(OBJS) > $(CXX) $(CXXFLAGS) $(LIBDIR) $(INCDIR) $(OFLAGS) -lm -o $@ $(OBJS) > >rfold: > cd $(RFOLD); \ > make; \ > cd .. \ > cd .. >probcons: > cd $(PROBCONS); \ > make; \ > cd .. > >#.cpp.cc.o: ># $(CXX) $(CXXFLAGS) $(LIBDIR) $(INCDIR) $(OFLAGS) -c $< > >#probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc ># $(CXX) $(CXXFLAGS) -lm -o probcons $(OBJS) >#Main.cc > >Main.o : $(PROBCONS)/SafeVector.h $(PROBCONS)/FileBuffer.h $(PROBCONS)/Sequence.h $(PROBCONS)/MultiSequence.h $(PROBCONS)/EvolutionaryTree.h scarna.hpp BPPMatrix.hpp StemCandidate.hpp Globaldp.hpp AlifoldMEA.h Main.cc > $(CXX) $(CXXFLAGS) $(LIBDIR) $(INCDIR) $(OFLAGS) -c Main.cc -o Main.o >McCaskill.o: McCaskill.hpp $(VIENNA)/energy_param.hpp Util.hpp Beta.hpp ScoreType.hpp McCaskill.cpp > $(CXX) $(CXXFLAGS) $(LIBDIR) $(INCDIR) $(OFLAGS) -c McCaskill.cpp -o McCaskill.o >$(VIENNA)/energy_param.o: $(VIENNA)/energy_param.hpp $(VIENNA)/energy_param.cpp > $(CXX) $(CXXFLAGS) $(LIBDIR) $(INCDIR) $(OFLAGS) -c $(VIENNA)/energy_param.cpp -o $(VIENNA)/energy_param.o >seq2scs.o: $(PROBCONS)/SafeVector.h StemCandidate.hpp $(PROBCONS)/Sequence.h $(PROBCONS)/MultiSequence.h BPPMatrix.hpp nrutil.h seq2scs.cpp > $(CXX) $(CXXFLAGS) $(LIBDIR) $(INCDIR) $(OFLAGS) -c seq2scs.cpp -o seq2scs.o >Globaldp.o: Globaldp.hpp nrutil.h Util.hpp Beta.hpp scarna.hpp StemCandidate.hpp $(PROBCONS)/MultiSequence.h $(PROBCONS)/Sequence.h BPPMatrix.hpp > $(CXX) $(CXXFLAGS) $(LIBDIR) $(INCDIR) $(OFLAGS) -c Globaldp.cpp -o Globaldp.o >GlobalParameters.o: scarna.hpp > $(CXX) $(CXXFLAGS) $(LIBDIR) $(INCDIR) $(OFLAGS) -c GlobalParameters.cpp -o GlobalParameters.o >postProcessings.o: StemCandidate.hpp scarna.hpp > $(CXX) $(CXXFLAGS) $(LIBDIR) $(INCDIR) $(OFLAGS) -c postProcessings.cpp -o postProcessings.o >AlifoldMEA.o: nrutil.h Util.hpp Beta.hpp BPPMatrix.hpp $(PROBCONS)/MultiSequence.h $(PROBCONS)/Sequence.h $(PROBCONS)/SafeVector.h > $(CXX) $(CXXFLAGS) $(LIBDIR) $(INCDIR) $(OFLAGS) -c AlifoldMEA.cpp -o AlifoldMEA.o > >.PHONY : clean >clean: > rm -f $(TARGETS) *.o *.h~ *.hpp~ *.cpp~ *.cc~ $(VIENNA)/*.o > $(MAKE) -C $(PROBCONS) clean
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bug 278571
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198705
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198943
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199524
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199526
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199528
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200249
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200250
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201591