CMakeLists.txt

@@ -95,10 +95,10 @@ ENDIF(NO_DEP_CHECK)
 # Packager
 SET(CPACK_PACKAGE_NAME "libbpp-phyl")
 SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
 SET(CPACK_PACKAGE_VERSION_MAJOR "2")
 SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
 SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Phylogenetics library")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
 SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")

Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = bpp-phyl
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 2.4.0
+PROJECT_NUMBER         = 2.4.1
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

bpp-phyl.spec

@@ -3,7 +3,7 @@
 URL: https://github.com/BioPP/bpp-phyl
 
 Name: bpp-phyl
-Version: 1.4.0
+Version: 2.4.1
 Release: 1%{?dist}
 License: CECILL-2.0
 Vendor: The Bio++ Project
@@ -85,6 +85,8 @@ rm -rf $RPM_BUILD_ROOT
 %{_prefix}/include/*
 
 %changelog
+* Mon Aug 13 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.1-1
+- Compatibility update gcc8
 * Mon Mar 12 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1
 - Increased interface number
 - Removed dynamic exceptions specifications.

debian/changelog

+libbpp-phyl (2.4.1-1) UNRELEASED; urgency=medium
+
+  * New upstream update.
+  * Ref: #906478 
+
+ -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Sun, 19 Aug 2018 21:36:23 +0200
+
 libbpp-phyl (2.4.0-2) unstable; urgency=medium
 
   [ Julien Dutheil ]

debian/control

@@ -7,7 +7,7 @@ Priority: optional
 Build-Depends: debhelper (>= 11~),
                cmake,
                d-shlibs (>= 0.82),
-               libbpp-seq-dev (>= 2.4.0)
+               libbpp-seq-dev (>= 2.4.1)
 Standards-Version: 4.1.4
 Vcs-Browser: https://salsa.debian.org/med-team/libbpp-phyl
 Vcs-Git: https://salsa.debian.org/med-team/libbpp-phyl.git
@@ -18,7 +18,7 @@ Architecture: any
 Section: libdevel
 Depends: libbpp-phyl12 (= ${binary:Version}),
          ${misc:Depends},
-         libbpp-seq-dev (>= 2.4.0)
+         libbpp-seq-dev (>= 2.4.1)
 Description: Bio++ Phylogenetic library development files
  Bio++ is a set of C++ libraries for Bioinformatics, including sequence
  analysis, phylogenetics, molecular evolution and population genetics.

debian/patches/increase_test_tolerance.patch

@@ -25,34 +25,3 @@ index b4cd485..c38a277 100644
      throw Exception("Incorrect final value.");
  }
  
-@@ -89,14 +89,14 @@ int main() {
-   DiscreteDistribution* rdist = new GammaDiscreteRateDistribution(4, 1.0);
- 
-   size_t nsites = 1000;
--  unsigned int nrep = 20;
-+  unsigned int nrep = 5;
-   size_t nmodels = modelSet->getNumberOfModels();
-   vector<double> thetas(nmodels);
-   vector<double> thetasEst1(nmodels);
-   vector<double> thetasEst2(nmodels);
- 
-   for (size_t i = 0; i < nmodels; ++i) {
--    double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.99) + 0.005;
-+    double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.9) + 0.05;
-     cout << "Theta" << i << " set to " << theta << endl; 
-     modelSet->setParameterValue("T92.theta_" + TextTools::toString(i + 1), theta);
-     thetas[i] = theta;
-@@ -119,11 +119,11 @@ int main() {
-     tl2.initialize();
-    
-     unsigned int c1 = OptimizationTools::optimizeNumericalParameters2(
--        &tl, tl.getParameters(), 0,
-+        &tl, tl.getSubstitutionModelParameters(), 0,
-         0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
- 
-     unsigned int c2 = OptimizationTools::optimizeNumericalParameters2(
--        &tl2, tl2.getParameters(), 0,
-+        &tl2, tl2.getSubstitutionModelParameters(), 0,
-         0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
- 
-     cout << c1 << ": " << tl.getValue() << "\t" << c2 << ": " << tl2.getValue() << endl;

src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp

@@ -138,13 +138,14 @@ TransitionModel* BppOTransitionModelFormat::readTransitionModel(
     }
 
     delete nestedModel;
-  }
-  else
-    model.reset(BppOSubstitutionModelFormat::read(alphabet, modelDescription, data, parseArguments));
 
+    // update only for transition models
     updateParameters_(model.get(), args);
     if (parseArguments)
       initialize_(*model, data);
+  }
+  else
+    model.reset(BppOSubstitutionModelFormat::read(alphabet, modelDescription, data, parseArguments));
 
   return model.release();
 }

src/Bpp/Phyl/Io/IoTree.h

@@ -5,7 +5,7 @@
 //
 
 /*
-Copyright or © or Copr. CNRS, (November 16, 2004)
+Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
 
 This software is a computer program whose purpose is to provide classes
 for phylogenetic data analysis.
@@ -170,7 +170,7 @@ class AbstractOTree:
         write(tree, output);
         output.close();
       }
-      catch (IOException e)
+      catch (IOException& e)
         {
           std::stringstream ss ;
           ss << e.what() <<"\nProblem writing tree to file "<< path <<"\n Is the file path correct and do \

src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp

@@ -138,7 +138,7 @@ void DRASRTreeLikelihoodData::initLikelihoods(const Node* node, const SiteContai
     {
       seq = &sequences.getSequence(node->getName());
     }
-    catch (SequenceNotFoundException snfe)
+    catch (SequenceNotFoundException& snfe)
     {
       throw SequenceNotFoundException("DRASRTreeLikelihoodData::initTreelikelihoods. Leaf name in tree not found in site conainer: ", (node->getName()));
     }
@@ -241,7 +241,7 @@ SitePatterns* DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(const Node* n
     {
       seq = &subSequences->getSequence(node->getName());
     }
-    catch (SequenceNotFoundException snfe)
+    catch (SequenceNotFoundException& snfe)
     {
       throw SequenceNotFoundException("HomogeneousTreeLikelihood::initTreelikelihoodsWithPatterns. Leaf name in tree not found in site conainer: ", (node->getName()));
     }

src/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp

@@ -37,18 +37,22 @@
 */
 
 #include "AbstractCodonAAFitnessSubstitutionModel.h"
+
+#include <Bpp/Seq/Alphabet/AlphabetTools.h>
+
 using namespace bpp;
 using namespace std;
+
 /****************************************************************************************/
+
 AbstractCodonAAFitnessSubstitutionModel::AbstractCodonAAFitnessSubstitutionModel(FrequenciesSet* pfitset, const GeneticCode* pgencode, const string& prefix):
-  AbstractParameterAliasable(prefix), pfitset_(pfitset), pgencode_(pgencode), fitName_("")
+  AbstractParameterAliasable(prefix), pfitset_(pfitset), pgencode_(pgencode), fitName_(""), stateMap_(&pfitset->getStateMap())
 {
-  if (pfitset_->getAlphabet()->getAlphabetType()!="Proteic")
+  if (!AlphabetTools::isProteicAlphabet(pfitset_->getAlphabet()))
     throw Exception("AbstractCodonAAFitnessSubstitutionModel::AbstractCodonAAFitnessSubstitutionModel need Proteic Fitness.");
   
   fitName_ = "fit_" + pfitset_->getNamespace();
   pfitset_->setNamespace(prefix + fitName_);
-  stateMap_=&pfitset_->getStateMap();
   
   addParameters_(pfitset_->getParameters());
 }

src/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.h

@@ -90,7 +90,6 @@ namespace bpp
      * @param pmodel shared_ptr to an amino_acid generator
      * @param pgencode the genetic code
      * @param prefix the Namespace
-     * @param statemap the statemap
      * @param paramSynRate is true iff synonymous rate is parameterised
      *       (default=false).
      */

src/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.h

@@ -93,7 +93,6 @@ namespace bpp
      *
      * @param pgencode the genetic code
      * @param prefix the Namespace
-     * @param statemap the statemap
      */
     AbstractCodonBGCSubstitutionModel(
       const GeneticCode* pgencode,

src/Bpp/Phyl/Model/SubstitutionModelSet.h

@@ -269,7 +269,7 @@ public:
   {
     try
     {
-      return dynamic_cast<const SubstitutionModel*>(getModel(i));
+      return &dynamic_cast<const SubstitutionModel&>(*getModel(i));
     }
     catch (std::bad_cast& bc)
     {
@@ -282,7 +282,7 @@ public:
   {
     try
     {
-      return dynamic_cast<SubstitutionModel*>(getModel(i));
+      return &dynamic_cast<SubstitutionModel&>(*getModel(i));
     }
     catch (std::bad_cast& bc)
     {

src/Bpp/Phyl/TreeTemplateTools.cpp

@@ -241,7 +241,7 @@ TreeTemplateTools::Element TreeTemplateTools::getElement(const string& elt)
       }
     }
   }
-  catch (exception e)
+  catch (exception& e)
   {
     throw IOException("Bad tree description: " + elt);
   }

test/test_likelihood_nh.cpp

@@ -89,14 +89,14 @@ int main() {
   DiscreteDistribution* rdist = new GammaDiscreteRateDistribution(4, 1.0);
 
   size_t nsites = 1000;
-  unsigned int nrep = 20;
+  unsigned int nrep = 3;
   size_t nmodels = modelSet->getNumberOfModels();
   vector<double> thetas(nmodels);
   vector<double> thetasEst1(nmodels);
   vector<double> thetasEst2(nmodels);
 
   for (size_t i = 0; i < nmodels; ++i) {
-    double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.99) + 0.005;
+    double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.9) + 0.05;
     cout << "Theta" << i << " set to " << theta << endl; 
     modelSet->setParameterValue("T92.theta_" + TextTools::toString(i + 1), theta);
     thetas[i] = theta;
@@ -119,11 +119,11 @@ int main() {
     tl2.initialize();
    
     unsigned int c1 = OptimizationTools::optimizeNumericalParameters2(
-        &tl, tl.getParameters(), 0,
+        &tl, tl.getSubstitutionModelParameters(), 0,
         0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
 
     unsigned int c2 = OptimizationTools::optimizeNumericalParameters2(
-        &tl2, tl2.getParameters(), 0,
+        &tl2, tl2.getSubstitutionModelParameters(), 0,
         0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
 
     cout << c1 << ": " << tl.getValue() << "\t" << c2 << ": " << tl2.getValue() << endl;