[med-svn] [Git][med-team/libbpp-popgen][upstream] New upstream version 2.4.1
Julien Y. Dutheil
gitlab at salsa.debian.org
Wed Aug 22 15:34:01 BST 2018
Julien Y. Dutheil pushed to branch upstream at Debian Med / libbpp-popgen
Commits:
d9174eb5 by Julien Y. Dutheil at 2018-08-20T10:34:18Z
New upstream version 2.4.1
- - - - -
8 changed files:
- CMakeLists.txt
- Doxyfile
- bpp-popgen.spec
- src/Bpp/PopGen/DataSet/DataSet.cpp
- src/Bpp/PopGen/DataSet/Group.cpp
- src/Bpp/PopGen/DataSet/Individual.cpp
- src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp
- src/Bpp/PopGen/DataSet/MultiSeqIndividual.cpp
Changes:
=====================================
CMakeLists.txt
=====================================
--- a/CMakeLists.txt
+++ b/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
=====================================
--- a/Doxyfile
+++ b/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
=====================================
--- a/bpp-popgen.spec
+++ b/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 at univ-montp2.fr> 2.4.1-1
+- Compatibility update gcc8.
* Mon Mar 12 2018 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.4.0-1
- Remove deprecated dynamic exception specifications
- Increased interface number
=====================================
src/Bpp/PopGen/DataSet/DataSet.cpp
=====================================
--- a/src/Bpp/PopGen/DataSet/DataSet.cpp
+++ b/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
=====================================
--- a/src/Bpp/PopGen/DataSet/Group.cpp
+++ b/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
=====================================
--- a/src/Bpp/PopGen/DataSet/Individual.cpp
+++ b/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
=====================================
--- a/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp
+++ b/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
=====================================
--- a/src/Bpp/PopGen/DataSet/MultiSeqIndividual.cpp
+++ b/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;
}
View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/commit/d9174eb5a24d62350e103229fcb4626dad7ca9d1
--
View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/commit/d9174eb5a24d62350e103229fcb4626dad7ca9d1
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