New upstream version 2.4.0 (37e12ef4) · Commits · Debian Med / libbpp-phyl-omics

CMakeLists.txt

+8 −6

Original line number	Diff line number	Diff line
		@@ -35,7 +35,7 @@ ELSE(NO_DEP_CHECK)
		# library implements.
		# In other words, the library implements all the interface numbers in the
		# range from number current - age to current.
		SET(${PROJECT_NAME}_VERSION_CURRENT "2")
		SET(${PROJECT_NAME}_VERSION_CURRENT "3")
		SET(${PROJECT_NAME}_VERSION_REVISION "0")
		SET(${PROJECT_NAME}_VERSION_AGE "0")

		@@ -53,8 +53,8 @@ if (CMAKE_INSTALL_PREFIX)
		endif (CMAKE_INSTALL_PREFIX)

		include (GNUInstallDirs)
		find_package (bpp-seq-omics 2.0.0 REQUIRED)
		find_package (bpp-phyl 11.0.0 REQUIRED)
		find_package (bpp-seq-omics 3.0.0 REQUIRED)
		find_package (bpp-phyl 12.0.0 REQUIRED)

		# CMake package
		set (cmake-package-location ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
		@@ -96,10 +96,10 @@ ENDIF(NO_DEP_CHECK)
		# Packager
		SET(CPACK_PACKAGE_NAME "libbpp-phyl-omics")
		SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
		SET(CPACK_PACKAGE_VERSION "2.3.1")
		SET(CPACK_PACKAGE_VERSION "2.4.0")
		SET(CPACK_PACKAGE_VERSION_MAJOR "2")
		SET(CPACK_PACKAGE_VERSION_MINOR "3")
		SET(CPACK_PACKAGE_VERSION_PATCH "1")
		SET(CPACK_PACKAGE_VERSION_MINOR "4")
		SET(CPACK_PACKAGE_VERSION_PATCH "0")
		SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Phylogen-Omics library")
		SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
		SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
		@@ -108,6 +108,8 @@ SET(CPACK_SOURCE_GENERATOR "TGZ")
		# /!\ This assumes that an external build is used
		SET(CPACK_SOURCE_IGNORE_FILES
		"/build/"
		"/html/"
		"/BppPhylOmics.tag"
		"/\\\\.git/"
		"/\\\\.gitignore"
		${CPACK_SOURCE_IGNORE_FILES}

ChangeLog

+6 −0

Original line number	Diff line number	Diff line
		09/03/18 -- Version 2.4.0 --

		09/03/18 Julien Dutheil
		* Removed all dynamic exception specifications
		* Increased interface number.

		10/12/17 -- Version 2.3.2 --

		10/05/17 -- Version 2.3.0. --

Doxyfile

+1 −1

Original line number	Diff line number	Diff line
		@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-phyl-omics
		# could be handy for archiving the generated documentation or if some version
		# control system is used.

		PROJECT_NUMBER = 2.3.0
		PROJECT_NUMBER = 2.4.0

		# 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-omics.spec

+36 −36

Original line number	Diff line number	Diff line
		%define _basename bpp-phyl-omics
		%define _version 2.3.1
		%define _release 1
		%define _prefix /usr

		URL: http://biopp.univ-montp2.fr/
		URL: https://github.com/BioPP/bpp-phyl-omics

		Name: %{_basename}
		Version: %{_version}
		Release: %{_release}
		Name: bpp-phyl-omics
		Version: 2.4.0
		Release: 1%{?dist}
		License: CECILL-2.0
		Vendor: The Bio++ Project
		Source: http://biopp.univ-montp2.fr/repos/sources/%{_basename}-%{_version}.tar.gz
		Source: %{name}-%{version}.tar.gz
		Summary: Bio++ Sequence library: genomics components
		Group: Development/Libraries/C and C++
		Requires: bpp-core = %{_version}
		Requires: bpp-seq = %{_version}
		Requires: bpp-phyl = %{_version}
		Requires: bpp-seq-omics = %{_version}
		Requires: bpp-core = %{version}
		Requires: bpp-seq = %{version}
		Requires: bpp-phyl = %{version}
		Requires: bpp-seq-omics = %{version}

		BuildRoot: %{_builddir}/%{_basename}-root
		BuildRoot: %{_builddir}/%{name}-root
		BuildRequires: cmake >= 2.8.11
		BuildRequires: gcc-c++ >= 4.7.0
		BuildRequires: libbpp-core3 = %{_version}
		BuildRequires: libbpp-core-devel = %{_version}
		BuildRequires: libbpp-seq11 = %{_version}
		BuildRequires: libbpp-seq-devel = %{_version}
		BuildRequires: libbpp-phyl11 = %{_version}
		BuildRequires: libbpp-phyl-devel = %{_version}
		BuildRequires: libbpp-seq-omics2 = %{_version}
		BuildRequires: libbpp-seq-omics-devel = %{_version}
		BuildRequires: libbpp-core4 = %{version}
		BuildRequires: libbpp-core-devel = %{version}
		BuildRequires: libbpp-seq12 = %{version}
		BuildRequires: libbpp-seq-devel = %{version}
		BuildRequires: libbpp-phyl12 = %{version}
		BuildRequires: libbpp-phyl-devel = %{version}
		BuildRequires: libbpp-seq-omics3 = %{version}
		BuildRequires: libbpp-seq-omics-devel = %{version}

		AutoReq: yes
		AutoProv: yes
		@@ -37,30 +34,30 @@ AutoProv: yes
		This library contains the genomics components of the Bio++ phylogenetics library.
		It is part of the Bio++ project.

		%package -n libbpp-phyl-omics2
		%package -n libbpp-phyl-omics3
		Summary: Bio++ Phylogenetics library: genomics components
		Group: Development/Libraries/C and C++

		%description -n libbpp-phyl-omics2
		%description -n libbpp-phyl-omics3
		This library contains the genomics components of the Bio++ phylogenetics library.
		It is part of the Bio++ project.

		%package -n libbpp-phyl-omics-devel
		Summary: Bio++ Phylogenetics library: genomics components
		Group: Development/Libraries/C and C++
		Requires: libbpp-phyl-omics2 = %{_version}
		Requires: libbpp-seq11 = %{_version}
		Requires: libbpp-seq-devel = %{_version}
		Requires: libbpp-core3 = %{_version}
		Requires: libbpp-core-devel = %{_version}
		Requires: libbpp-phyl11 = %{_version}
		Requires: libbpp-phyl-devel = %{_version}
		Requires: libbpp-seq-omics2 = %{_version}
		Requires: libbpp-seq-omics-devel = %{_version}
		Requires: libbpp-phyl-omics3 = %{version}
		Requires: libbpp-seq12 = %{version}
		Requires: libbpp-seq-devel = %{version}
		Requires: libbpp-core4 = %{version}
		Requires: libbpp-core-devel = %{version}
		Requires: libbpp-phyl12 = %{version}
		Requires: libbpp-phyl-devel = %{version}
		Requires: libbpp-seq-omics3 = %{version}
		Requires: libbpp-seq-omics-devel = %{version}

		%description -n libbpp-phyl-omics-devel
		The libbpp-phyl-omics-devel package contains the header files and static libraries for
		building applications which use %{_basename}.
		building applications which use %{name}.

		%prep
		%setup -q
		@@ -77,11 +74,11 @@ make DESTDIR=$RPM_BUILD_ROOT install
		%clean
		rm -rf $RPM_BUILD_ROOT

		%post -n libbpp-phyl-omics2 -p /sbin/ldconfig
		%post -n libbpp-phyl-omics3 -p /sbin/ldconfig

		%postun -n libbpp-phyl-omics2 -p /sbin/ldconfig
		%postun -n libbpp-phyl-omics3 -p /sbin/ldconfig

		%files -n libbpp-phyl-omics2
		%files -n libbpp-phyl-omics3
		%defattr(-,root,root)
		%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
		%{_prefix}/%{_lib}/lib.so.
		@@ -97,6 +94,9 @@ rm -rf $RPM_BUILD_ROOT
		%{_prefix}/include/*

		%changelog
		* Mon Mar 12 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1
		- Increased interface number
		- Removed dynamic exceptions specifications.
		* Tue Jun 06 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.1-1
		- Increased interface number
		* Wed May 10 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.0-1

src/Bpp/Seq/Io/Maf/AbstractDistanceEstimationMafIterator.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -69,7 +69,7 @@ class AbstractDistanceEstimationMafIterator:
		{}

		private:
		MafBlock* analyseCurrentBlock_() throw (Exception)
		MafBlock* analyseCurrentBlock_()
		{
		MafBlock* block = iterator_->nextBlock();
		if (!block) return 0;