3 files changed, 106 insertions, 0 deletions
diff --git a/sci-biology/probcons/files/gcc-4.3.patch b/sci-biology/probcons/files/gcc-4.3.patch
new file mode 100644
index 000000000000..37c45c03a98f
--- /dev/null
+++ b/sci-biology/probcons/files/gcc-4.3.patch
@@ -0,0 +1,44 @@
+diff -u probcons.orig/CompareToRef.cc probcons/CompareToRef.cc
+--- probcons.orig/CompareToRef.cc	2008-04-08 16:38:46.000000000 -0700
++++ probcons/CompareToRef.cc	2008-04-08 16:39:41.000000000 -0700
+@@ -16,6 +16,7 @@
+ #include <limits>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+ 
+diff -u probcons.orig/FixRef.cc probcons/FixRef.cc
+--- probcons.orig/FixRef.cc	2008-04-08 16:38:46.000000000 -0700
++++ probcons/FixRef.cc	2008-04-08 16:39:33.000000000 -0700
+@@ -17,6 +17,7 @@
+ #include <algorithm>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+ 
+diff -u probcons.orig/Main.cc probcons/Main.cc
+--- probcons.orig/Main.cc	2008-04-08 16:38:46.000000000 -0700
++++ probcons/Main.cc	2008-04-08 16:39:14.000000000 -0700
+@@ -21,6 +21,7 @@
+ #include <climits>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+ 
+diff -u probcons.orig/ProjectPairwise.cc probcons/ProjectPairwise.cc
+--- probcons.orig/ProjectPairwise.cc	2008-04-08 16:38:46.000000000 -0700
++++ probcons/ProjectPairwise.cc	2008-04-08 16:39:25.000000000 -0700
+@@ -16,6 +16,7 @@
+ #include <limits>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+ 
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:
diff --git a/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch b/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch
new file mode 100644
index 000000000000..1596f3b31916
--- /dev/null
+++ b/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch
@@ -0,0 +1,15 @@
+ SafeVector.h |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/SafeVector.h b/SafeVector.h
+index abf4b64..9c3292e 100644
+--- a/SafeVector.h
++++ b/SafeVector.h
+@@ -8,6 +8,7 @@
+ #ifndef SAFEVECTOR_H
+ #define SAFEVECTOR_H
+ 
++#include <cstddef>
+ #include <cassert>
+ #include <vector>
+