gentoo-overlay/sci-biology/probcons/files/probcons-1.12-cxxflags.patch

diff --git a/Makefile b/Makefile
index 75fc47a..4a19140 100644
--- a/Makefile
+++ b/Makefile
@@ -15,6 +15,8 @@ CXX = g++
 #    c) RELEASE mode
 ################################################################################
 
+OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops
+
 OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
 
 # debug mode    
@@ -25,7 +27,7 @@ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
 
 # release mode
 #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer 
-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
+CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS)
 
 ################################################################################
 # 3) Dependencies
@@ -37,19 +39,19 @@ TARGETS = probcons compare project makegnuplot
 all : $(TARGETS)
 
 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 Main.cc 
+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o probcons Main.cc -lm
 
 compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
-	$(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o compare CompareToRef.cc
 
 fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
-	$(CXX) $(CXXFLAGS) -o fixref FixRef.cc
+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o fixref FixRef.cc
 
 project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
-	$(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc
+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o project ProjectPairwise.cc
 
 makegnuplot : MakeGnuPlot.cc
-	$(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
 
 .PHONY : clean
 clean: