From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@redcorelinux.org>
Date: Mon, 9 Oct 2017 18:53:29 +0100
Subject: reinit the tree, so we can have metadata

---
 .../probcons/files/probcons-1.12-cxxflags.patch    | 47 ++++++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 sci-biology/probcons/files/probcons-1.12-cxxflags.patch

(limited to 'sci-biology/probcons/files/probcons-1.12-cxxflags.patch')

diff --git a/sci-biology/probcons/files/probcons-1.12-cxxflags.patch b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch
new file mode 100644
index 000000000000..e07ebe1a613f
--- /dev/null
+++ b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch
@@ -0,0 +1,47 @@
+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:
-- 
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