CMakeLists.txt

@@ -95,10 +95,10 @@ ENDIF(NO_DEP_CHECK)
 # Packager
 SET(CPACK_PACKAGE_NAME "libbpp-popgen")
 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++ Population Genetics 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-popgen
 # 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-popgen.spec

@@ -3,7 +3,7 @@
 URL: https://github.com/BioPP/bpp-seq
 
 Name: bpp-popgen
-Version: 2.4.0
+Version: 2.4.1
 Release: 1%{?dist}
 License: CECILL-2.0
 Vendor: The Bio++ Project
@@ -84,6 +84,8 @@ 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
 - Remove deprecated dynamic exception specifications
 - Increased interface number

debian/changelog

+libbpp-popgen (2.4.1-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * Addresses: #897782 
+
+ -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Mon, 20 Aug 2018 12:34:26 +0200
+
 libbpp-popgen (2.4.0-2) unstable; urgency=medium
 
   [ Julien Dutheil ]

debian/control

@@ -7,8 +7,8 @@ Priority: optional
 Build-Depends: debhelper (>= 11~),
                cmake,
                d-shlibs (>= 0.80),
-               libbpp-core-dev (>= 2.4.0),
-               libbpp-seq-dev (>= 2.4.0)
+               libbpp-core-dev (>= 2.4.1),
+               libbpp-seq-dev (>= 2.4.1)
 Standards-Version: 4.1.3
 Vcs-Browser: https://salsa.debian.org/med-team/libbpp-popgen
 Vcs-Git: https://salsa.debian.org/med-team/libbpp-popgen.git
@@ -19,8 +19,8 @@ Architecture: any
 Section: libdevel
 Depends: libbpp-popgen8 (= ${binary:Version}),
          ${misc:Depends},
-         libbpp-core-dev (>= 2.4.0),
-         libbpp-seq-dev (>= 2.4.0)
+         libbpp-core-dev (>= 2.4.1),
+         libbpp-seq-dev (>= 2.4.1)
 Description: Bio++ Population Genetics library development files
  Bio++ is a set of C++ libraries for Bioinformatics, including sequence
  analysis, phylogenetics, molecular evolution and population genetics.

src/Bpp/PopGen/DataSet/DataSet.cpp

@@ -6,7 +6,7 @@
 //
 
 /*
-   Copyright or © or Copr. CNRS, (November 17, 2004)
+   Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
 
    This software is a computer program whose purpose is to provide classes
    for population genetics analysis.
@@ -453,7 +453,7 @@ size_t DataSet::getIndividualPositionInGroup(size_t group_position, const std::s
   {
     return groups_[group_position]->getIndividualPosition(individual_id);
   }
-  catch (IndividualNotFoundException infe)
+  catch (IndividualNotFoundException& infe)
   {
     throw IndividualNotFoundException("DataSet::getIndividualPositionFromGroup: individual_id not found.", infe.getIdentifier());
   }
@@ -469,7 +469,7 @@ const Individual* DataSet::getIndividualAtPositionFromGroup(size_t group_positio
   {
     return &groups_[group_position]->getIndividualAtPosition(individual_position);
   }
-  catch (IndexOutOfBoundsException ioobe)
+  catch (IndexOutOfBoundsException& ioobe)
   {
     throw IndexOutOfBoundsException("DataSet::getIndividualAtPositionFromGroup: individual_position out of bouds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
@@ -485,7 +485,7 @@ const Individual* DataSet::getIndividualByIdFromGroup(size_t group_position, con
   {
     return &groups_[group_position]->getIndividualById(individual_id);
   }
-  catch (IndividualNotFoundException infe)
+  catch (IndividualNotFoundException& infe)
   {
     throw IndividualNotFoundException("DataSet::getIndividualByIdFromGroup: individual_id not found.", infe.getIdentifier());
   }
@@ -501,7 +501,7 @@ void DataSet::deleteIndividualAtPositionFromGroup(size_t group_position, size_t
   {
     groups_[group_position]->deleteIndividualAtPosition(individual_position);
   }
-  catch (IndexOutOfBoundsException ioobe)
+  catch (IndexOutOfBoundsException& ioobe)
   {
     throw IndexOutOfBoundsException("DataSet::deleteIndividualAtPositionFromGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
@@ -517,7 +517,7 @@ void DataSet::deleteIndividualByIdFromGroup(size_t group_position, const std::st
   {
     groups_[group_position]->deleteIndividualById(individual_id);
   }
-  catch (IndividualNotFoundException infe)
+  catch (IndividualNotFoundException& infe)
   {
     throw IndividualNotFoundException("DataSet::deleteIndividualByIdFromGroup: individual_id not found.", infe.getIdentifier());
   }
@@ -585,7 +585,7 @@ const Date* DataSet::getIndividualDateInGroup(size_t group_position, size_t indi
   {
     throw IndexOutOfBoundsException("DataSet::getIndividualDateInGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::getIndividualDateInGroup: individual has no date.");
   }
@@ -621,7 +621,7 @@ const Point2D<double>* DataSet::getIndividualCoordInGroup(size_t group_position,
   {
     throw IndexOutOfBoundsException("DataSet::getIndividualCoordAtPosition: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::getIndividualCoordInGroup: individual has no coordinate.");
   }
@@ -661,7 +661,7 @@ const Locality<double>* DataSet::getIndividualLocalityInGroup(size_t group_posit
   {
     throw IndexOutOfBoundsException("DataSet::getIndividualLocalityInGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::getIndividualLocalityInGroup: individual has no locality.");
   }
@@ -710,7 +710,7 @@ const Sequence& DataSet::getIndividualSequenceByNameInGroup(size_t group_positio
   {
     throw IndexOutOfBoundsException("DataSet::getIndividualSequenceByNameInGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::getIndividualSequenceByNameInGroup: individual has no sequences.");
   }
@@ -738,7 +738,7 @@ const Sequence& DataSet::getIndividualSequenceAtPositionInGroup(size_t group_pos
     else
       throw IndexOutOfBoundsException("DataSet::getIndividualSequenceAtPositionInGroup: sequence_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::getIndividualSequenceAtPositionInGroup: individual has no sequences.");
   }
@@ -758,7 +758,7 @@ void DataSet::deleteIndividualSequenceByNameInGroup(size_t group_position, size_
   {
     throw IndexOutOfBoundsException("DataSet::deleteIndividualSequenceByNameInGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::deleteIndividualSequenceByNameInGroup: individual has no sequences.");
   }
@@ -786,7 +786,7 @@ void DataSet::deleteIndividualSequenceAtPositionInGroup(size_t group_position, s
     else
       throw IndexOutOfBoundsException("DataSet::deleteIndividualSequenceAtPositionInGroup: sequence_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::deleteIndividualSequenceAtPositionInGroup: individual has no sequences.");
   }
@@ -806,7 +806,7 @@ std::vector<std::string> DataSet::getIndividualSequencesNamesInGroup(size_t grou
   {
     throw IndexOutOfBoundsException("DataSet::getIndividualSequencesNamesInGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::getIndividualSequencesNamesInGroup: individual has no sequences.");
   }
@@ -826,7 +826,7 @@ size_t DataSet::getIndividualSequencePositionInGroup(size_t group_position, size
   {
     throw IndexOutOfBoundsException("DataSet::getIndividualSequencePositionInGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::getIndividualSequencePositionInGroup: individual has no sequences.");
   }
@@ -850,7 +850,7 @@ size_t DataSet::getIndividualNumberOfSequencesInGroup(size_t group_position, siz
   {
     throw IndexOutOfBoundsException("DataSet::getIndividualNumberOfSequencesInGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::getIndividualNumberOfSequencesInGroup: individual has no sequences.");
   }
@@ -890,11 +890,11 @@ void DataSet::initIndividualGenotypeInGroup(size_t group_position, size_t indivi
   {
     throw BadIntegerException("DataSet::initIndividualGenotypeInGroup: number of loci must be > 0.", bie.getBadInteger());
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::initIndividualGenotypeInGroup: analyzed_loci is NULL.");
   }
-  catch (Exception)
+  catch (Exception&)
   {
     throw Exception("DataSet::initIndividualGenotypeInGroup: individual already has a genotype.");
   }
@@ -934,7 +934,7 @@ void DataSet::setIndividualMonolocusGenotypeInGroup(size_t group_position, size_
     else
       throw IndexOutOfBoundsException("DataSet::setIndividualMonolocusGenotypeInGroup: locus_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::setIndividualMonolocusGenotypeInGroup: individual has no genotype.");
   }
@@ -958,11 +958,11 @@ void DataSet::setIndividualMonolocusGenotypeByAlleleKeyInGroup(size_t group_posi
     else
       throw IndexOutOfBoundsException("DataSet::setIndividualMonolocusGenotypeByAlleleKeyInGroup: locus_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::setIndividualMonolocusGenotypeByAlleleKeyInGroup: individual has no genotype.");
   }
-  catch (Exception)
+  catch (Exception&)
   {
     throw Exception("DataSet::setIndividualMonolocusGenotypeByAlleleKeyInGroup: no key in allele_keys.");
   }
@@ -987,7 +987,7 @@ void DataSet::setIndividualMonolocusGenotypeByAlleleIdInGroup(size_t group_posit
     else
       throw IndexOutOfBoundsException("DataSet::setIndividualMonolocusGenotypeByAlleleIdInGroup: locus_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::setIndividualMonolocusGenotypeByAlleleIdInGroup: individual has no genotype.");
   }
@@ -1015,7 +1015,7 @@ const MonolocusGenotype* DataSet::getIndividualMonolocusGenotypeInGroup(size_t g
     else
       throw IndexOutOfBoundsException("DataSet::getIndividualMonolocusGenotypeInGroup: locus_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     throw NullPointerException("DataSet::getIndividualMonolocusGenotypeInGroup: individual has no genotype.");
   }

src/Bpp/PopGen/DataSet/Group.cpp

@@ -5,7 +5,7 @@
 //
 
 /*
-   Copyright or © or Copr. CNRS, (November 17, 2004)
+   Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
 
 
    This software is a computer program whose purpose is to provide classes
@@ -473,7 +473,7 @@ void Group::initIndividualGenotype(size_t individual_position, size_t loci_numbe
   {
     throw BadIntegerException("Group::initIndividualGenotype: loci_number must be > 0.", bie.getBadInteger());
   }
-  catch (Exception)
+  catch (Exception&)
   {
     throw Exception("Group::initIndividualGenotype: individual already has a genotype.");
   }
@@ -527,7 +527,7 @@ void Group::setIndividualMonolocusGenotypeByAlleleKey(size_t individual_position
   {
     throw IndexOutOfBoundsException("Group::setIndividualMonolocusGenotypeByAlleleKey: locus_position excedes the number of locus.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (Exception)
+  catch (Exception&)
   {
     throw Exception("Group::setIndividualMonolocusGenotypeByAlleleKey: no key in allele_keys.");
   }

src/Bpp/PopGen/DataSet/Individual.cpp

@@ -5,7 +5,7 @@
 //
 
 /*
-   Copyright or © or Copr. CNRS, (November 17, 2004)
+   Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
 
    This software is a computer program whose purpose is to provide classes
    for population genetics analysis.
@@ -122,7 +122,7 @@ Individual& Individual::operator=(const Individual& ind)
   {
     setDate(ind.getDate());
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     date_.reset();
   }
@@ -130,7 +130,7 @@ Individual& Individual::operator=(const Individual& ind)
   {
     setCoord(ind.getCoord());
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     coord_.reset();
   }
@@ -138,7 +138,7 @@ Individual& Individual::operator=(const Individual& ind)
   {
     setLocality(ind.getLocality());
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     locality_ = 0;
   }
@@ -146,7 +146,7 @@ Individual& Individual::operator=(const Individual& ind)
   {
     setSequences(dynamic_cast<const MapSequenceContainer&>(ind.getSequences()));
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     sequences_.reset();
   }
@@ -556,7 +556,7 @@ void Individual::setMonolocusGenotypeByAlleleKey(size_t locus_position, const st
   {
     throw IndexOutOfBoundsException("Individual::setMonolocusGenotypeByAlleleKey: locus_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
   }
-  catch (Exception)
+  catch (Exception&)
   {
     throw Exception("Individual::setMonolocusGenotypeByAlleleKey: no key in allele_keys.");
   }

src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp

@@ -630,7 +630,7 @@ void PopgenlibIO::write(std::ostream& os, const DataSet& data_set) const
             tmp_ind->getSequenceAtPosition(k);
             os << TextTools::toString(seqcpt++);
           }
-          catch (SequenceNotFoundException)
+          catch (SequenceNotFoundException&)
           {
             os << getMissingDataChar();
           }

src/Bpp/PopGen/DataSet/MultiSeqIndividual.cpp

@@ -86,7 +86,7 @@ MultiSeqIndividual::MultiSeqIndividual(const MultiSeqIndividual& ind) : id_(ind.
   {
     setDate(*ind.getDate());
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     date_ = 0;
   }
@@ -94,7 +94,7 @@ MultiSeqIndividual::MultiSeqIndividual(const MultiSeqIndividual& ind) : id_(ind.
   {
     setCoord(*ind.getCoord());
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     coord_ = 0;
   }
@@ -102,7 +102,7 @@ MultiSeqIndividual::MultiSeqIndividual(const MultiSeqIndividual& ind) : id_(ind.
   {
     setLocality(ind.getLocality());
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     locality_ = 0;
   }
@@ -135,7 +135,7 @@ MultiSeqIndividual& MultiSeqIndividual::operator=(const MultiSeqIndividual& ind)
   {
     setDate(*ind.getDate());
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     date_ = 0;
   }
@@ -143,7 +143,7 @@ MultiSeqIndividual& MultiSeqIndividual::operator=(const MultiSeqIndividual& ind)
   {
     setCoord(*ind.getCoord());
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     coord_ = 0;
   }
@@ -151,7 +151,7 @@ MultiSeqIndividual& MultiSeqIndividual::operator=(const MultiSeqIndividual& ind)
   {
     setLocality(ind.getLocality());
   }
-  catch (NullPointerException)
+  catch (NullPointerException&)
   {
     locality_ = 0;
   }