[med-svn] r20771 - in trunk/packages/probcons/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-12-15 20:25:59 +0000 (Tue, 15 Dec 2015)
New Revision: 20771

Added:
   trunk/packages/probcons/trunk/debian/patches/hardening.patch
   trunk/packages/probcons/trunk/debian/patches/mayhem.patch
Modified:
   trunk/packages/probcons/trunk/debian/changelog
   trunk/packages/probcons/trunk/debian/patches/series
Log:
Fix Mayhem issues


Modified: trunk/packages/probcons/trunk/debian/changelog
===================================================================
--- trunk/packages/probcons/trunk/debian/changelog	2015-12-15 12:11:54 UTC (rev 20770)
+++ trunk/packages/probcons/trunk/debian/changelog	2015-12-15 20:25:59 UTC (rev 20771)
@@ -1,4 +1,4 @@
-probcons (1.12-10) UNRELEASED; urgency=medium
+probcons (1.12-10) unstable; urgency=medium
 
   * Moved debian/upstream to debian/upstream/metadata
   * cme fix dpkg-control
@@ -6,8 +6,10 @@
   * DEP3 fix
   * Propagate hardening options
   * spelling in manpage
+  * Fix Mayhem bugs
+    Closes: #716581, #716505
 
- -- Andreas Tille <tille at debian.org>  Tue, 15 Dec 2015 11:35:22 +0100
+ -- Andreas Tille <tille at debian.org>  Tue, 15 Dec 2015 21:23:03 +0100
 
 probcons (1.12-9) unstable; urgency=low
 

Added: trunk/packages/probcons/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/hardening.patch	                        (rev 0)
+++ trunk/packages/probcons/trunk/debian/patches/hardening.patch	2015-12-15 20:25:59 UTC (rev 20771)
@@ -0,0 +1,46 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 15 Dec 2015 11:35:22 +0100
+Description: Propagate hardening options
+
+--- a/Makefile
++++ b/Makefile
+@@ -27,8 +27,8 @@ OTHERFLAGS-RNA = -DNumInsertStates=1 -DV
+ # 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-RNA = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS-RNA) -funroll-loops
++CXXFLAGS-RNA := -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS-RNA) -funroll-loops $(CXXFLAGS)
++CXXFLAGS := -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops $(CXXFLAGS)
+ 
+ 
+ ################################################################################
+@@ -41,22 +41,22 @@ TARGETS = probcons probcons-RNA pc-compa
+ 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) $(CXXFLAGS) -lm -o probcons Main.cc $(LDFLAGS)
+ 
+ pc-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
+-	$(CXX) $(CXXFLAGS) -o pc-compare CompareToRef.cc
++	$(CXX) $(CXXFLAGS) -o pc-compare CompareToRef.cc $(LDFLAGS)
+ 
+ probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
+-	$(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc 
++	$(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc $(LDFLAGS)
+ 
+ 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) $(CXXFLAGS) -o fixref FixRef.cc $(LDFLAGS)
+ 
+ pc-project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
+-	$(CXX) $(CXXFLAGS) -o pc-project ProjectPairwise.cc
++	$(CXX) $(CXXFLAGS) -o pc-project ProjectPairwise.cc $(LDFLAGS)
+ 
+ pc-makegnuplot : MakeGnuPlot.cc
+-	$(CXX) $(CXXFLAGS) -o pc-makegnuplot MakeGnuPlot.cc
++	$(CXX) $(CXXFLAGS) -o pc-makegnuplot MakeGnuPlot.cc $(LDFLAGS)
+ 
+ .PHONY : clean
+ clean:

Added: trunk/packages/probcons/trunk/debian/patches/mayhem.patch
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/mayhem.patch	                        (rev 0)
+++ trunk/packages/probcons/trunk/debian/patches/mayhem.patch	2015-12-15 20:25:59 UTC (rev 20771)
@@ -0,0 +1,38 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 15 Dec 2015 11:35:22 +0100
+Bug-Debian: https://bugs.debian.org/716581
+            https://bugs.debian.org/716505
+Description: Fix Mayhem issues
+
+--- a/Main.cc
++++ b/Main.cc
+@@ -210,11 +210,13 @@ int main (int argc, char **argv){
+                                         ProbabilisticModel (initDistrib, gapOpen, gapExtend,  emitPairs, emitSingle),
+                                         initDistrib, gapOpen, gapExtend, emitPairs, emitSingle);
+     
+-    if (!enableAllPairs){
+-      if (enableClustalWOutput)
+-	alignment->WriteALN (cout);
+-      else
+-	alignment->WriteMFA (cout);
++    if (alignment) {
++      if (!enableAllPairs){
++        if (enableClustalWOutput)
++	  alignment->WriteALN (cout);
++        else
++	  alignment->WriteMFA (cout);
++      }
+     }
+     delete alignment;
+     delete sequences;
+@@ -307,6 +309,10 @@ MultiSequence *DoAlign (MultiSequence *s
+   assert (sequences);
+ 
+   const int numSeqs = sequences->GetNumSequences();
++  if (numSeqs == 0) {
++    fprintf(stderr, "Zero sequences delivered to function DoAlign()\n");
++    return NULL;
++  }
+   VVF distances (numSeqs, VF (numSeqs, 0));
+   SafeVector<SafeVector<SparseMatrix *> > sparseMatrices (numSeqs, SafeVector<SparseMatrix *>(numSeqs, NULL));
+ 

Modified: trunk/packages/probcons/trunk/debian/patches/series
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/series	2015-12-15 12:11:54 UTC (rev 20770)
+++ trunk/packages/probcons/trunk/debian/patches/series	2015-12-15 20:25:59 UTC (rev 20771)
@@ -3,3 +3,4 @@
 fix-gcc-4.5-headers
 fix-gcc-4.6.patch
 hardening.patch
+mayhem.patch