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commit 2bfb7c7abf508d7619c6c6ba23f5ebe577e0f5ff Author: Julien Y. Dutheil <[email protected]> Date: Mon Feb 5 17:36:50 2018 +0100 Version 2.3.2. --- debian/changelog | 7 + debian/control | 6 +- .../rm_VectorProbabilisticSiteContainer.patch | 322 --------------------- debian/patches/series | 1 - debian/rules | 1 - 5 files changed, 10 insertions(+), 327 deletions(-) diff --git a/debian/changelog b/debian/changelog index ed75da8..cd96451 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +libbpp-seq (2.3.2-1) UNRELEASED; urgency=medium + + * Rebuild with gcc-7 + * Standards-Version: 4.0.1 + + -- Julien Dutheil <[email protected]> Mon, 05 Feb 2018 17:36:38 +0200 + libbpp-seq (2.3.1-8) unstable; urgency=medium * Rebuild with gcc-7 diff --git a/debian/control b/debian/control index 313aff8..b4e076f 100644 --- a/debian/control +++ b/debian/control @@ -7,7 +7,7 @@ Priority: optional Build-Depends: debhelper (>= 10), cmake, d-shlibs (>= 0.80), - libbpp-core-dev (>= 2.3.1) + libbpp-core-dev (>= 2.3.2) Standards-Version: 4.0.1 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbpp-seq.git Vcs-Git: https://anonscm.debian.org/git/debian-med/libbpp-seq.git @@ -18,7 +18,7 @@ Architecture: any Section: libdevel Depends: libbpp-seq11 (= ${binary:Version}), ${misc:Depends}, - libbpp-core-dev (>= 2.3.1) + libbpp-core-dev (>= 2.3.2) Description: Bio++ Sequence library development files Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. @@ -36,7 +36,7 @@ Pre-Depends: ${misc:Pre-Depends} Multi-Arch: same Depends: ${shlibs:Depends}, ${misc:Depends}, - libbpp-core3 (>= 2.3.1) + libbpp-core3 (>= 2.3.2) Description: Bio++ Sequence library Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. diff --git a/debian/patches/rm_VectorProbabilisticSiteContainer.patch b/debian/patches/rm_VectorProbabilisticSiteContainer.patch deleted file mode 100644 index a869f0a..0000000 --- a/debian/patches/rm_VectorProbabilisticSiteContainer.patch +++ /dev/null @@ -1,322 +0,0 @@ -Author: Julien Dutheil <[email protected]> -Last-Update: Wed, 12 Jul 2017 13:21:07 +0000 -Description: Removed unused class VectorProbabilisticSiteContainer - This class was moved to a dedicated branch but these files were left on - the master branch. Yet they were not listed by cmake for compilation. - ---- a/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.cpp -+++ /dev/null -@@ -1,187 +0,0 @@ --// --// File: VectorProbabilisticSiteContainer.cpp --// Created by: Murray Patterson --// Created on: Mon Oct 19 2015 --// -- --/* -- Copyright or © or Copr. Bio++ Development Team, (November 17, 2004) -- -- This software is a computer program whose purpose is to provide classes -- for sequences analysis. -- -- This software is governed by the CeCILL license under French law and -- abiding by the rules of distribution of free software. You can use, -- modify and/ or redistribute the software under the terms of the CeCILL -- license as circulated by CEA, CNRS and INRIA at the following URL -- "http://www.cecill.info";. -- -- As a counterpart to the access to the source code and rights to copy, -- modify and redistribute granted by the license, users are provided only -- with a limited warranty and the software's author, the holder of the -- economic rights, and the successive licensors have only limited -- liability. -- -- In this respect, the user's attention is drawn to the risks associated -- with loading, using, modifying and/or developing or reproducing the -- software by the user in light of its specific status of free software, -- that may mean that it is complicated to manipulate, and that also -- therefore means that it is reserved for developers and experienced -- professionals having in-depth computer knowledge. Users are therefore -- encouraged to load and test the software's suitability as regards their -- requirements in conditions enabling the security of their systems and/or -- data to be ensured and, more generally, to use and operate it in the -- same conditions as regards security. -- -- The fact that you are presently reading this means that you have had -- knowledge of the CeCILL license and that you accept its terms. --*/ -- --#include "VectorProbabilisticSiteContainer.h" -- --#include <Bpp/Text/TextTools.h> --#include <Bpp/Numeric/DataTable.h> -- --using namespace bpp; -- --/********************************************************************************/ -- --VectorProbabilisticSiteContainer::VectorProbabilisticSiteContainer(const Alphabet * alpha) : -- VectorSiteContainer(alpha), -- p_sites_(0), -- p_sequences_(0) --{} -- --/********************************************************************************/ -- --const ProbabilisticSite & VectorProbabilisticSiteContainer::getProbabilisticSite(std::size_t i) const throw (IndexOutOfBoundsException) --{ -- if(i >= getNumberOfProbabilisticSites()) -- throw IndexOutOfBoundsException("VectorProbabilisticSiteContainer::getProbabilisticSite.", i, 0, getNumberOfProbabilisticSites() - 1); -- -- return *p_sites_[i]; --} -- --/********************************************************************************/ -- --void VectorProbabilisticSiteContainer::addSite(const ProbabilisticSite & site, bool checkPosition) throw (Exception) --{ -- // check size : -- if(site.size() != getNumberOfProbabilisticSequences()) -- throw Exception("VectorProbabilisticSiteContainer::addSite. Site does not have the appropriate length: " + TextTools::toString(site.size()) + ", should be " + TextTools::toString(getNumberOfProbabilisticSequences()) + "."); -- -- // new site's alphabet and site container's alphabet must match : -- if(site.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType()) -- throw AlphabetMismatchException("VectorProbabilisticSiteContainer::addSite.", getAlphabet(), site.getAlphabet()); -- -- // check position : -- if(checkPosition) { -- -- int position = site.getPosition(); -- // for all positions in vector : throw exception if position already exists -- for(std::size_t i = 0; i < p_sites_.size(); ++i) -- if(p_sites_[i]->getPosition() == position) -- throw Exception("VectorSiteContainer::addSite. Site position: " + TextTools::toString(position) + ", already exists in container."); -- } -- -- p_sites_.push_back(dynamic_cast<ProbabilisticSite *>(site.clone())); --} -- --/********************************************************************************/ -- --const ProbabilisticSequence & VectorProbabilisticSiteContainer::getProbabilisticSequence(std::size_t i) const throw (IndexOutOfBoundsException) --{ -- -- if(i >= getNumberOfProbabilisticSequences()) -- throw IndexOutOfBoundsException("VectorProbabilisticSiteContainer::getProbabilisticSequence.", i, 0, getNumberOfProbabilisticSequences() - 1); -- -- // main loop : for all sites -- std::size_t n = getNumberOfProbabilisticSites(); -- DataTable sequence(getAlphabet()->getResolvedChars()); -- for(std::size_t j = 0; j < n; ++j) -- sequence.addRow(p_sites_[j]->getContent().getRow(i)); -- -- if(p_sequences_[i]) -- delete p_sequences_[i]; -- -- p_sequences_[i] = new BasicProbabilisticSequence(names_[i], sequence, *comments_[i], getAlphabet()); -- -- return *p_sequences_[i]; --} -- --/********************************************************************************/ -- --void VectorProbabilisticSiteContainer::addSequence(const ProbabilisticSequence & sequence, bool checkName) throw (Exception) --{ -- -- // if the container has no sequence, we set the size to the size of this sequence : -- if(getNumberOfProbabilisticSequences() == 0) -- pRealloc(sequence.size()); -- -- // new sequence's alphabet and site container's alphabet must match : -- if(sequence.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType()) -- throw AlphabetMismatchException("VectorProbabilisticSiteContainer::addSequence.", getAlphabet(), sequence.getAlphabet()); -- -- if(sequence.size() != p_sites_.size()) -- throw Exception("VectorProbabilisticSiteContainer::addSequence. Sequence does not have the appropriate length: " + TextTools::toString(sequence.size()) + ", should be " + TextTools::toString(p_sites_.size()) + "."); -- -- // check name : -- if(checkName) -- for(std::size_t i = 0; i < names_.size(); ++i) -- if(sequence.getName() == names_[i]) -- throw Exception("VectorProbabilisticSiteContainer::addSequence. Name: " + sequence.getName() + ", already exists in the container."); -- -- // append name : -- names_.push_back(sequence.getName()); -- -- // append elements at each site : -- for(size_t i = 0; i < p_sites_.size(); ++i) -- p_sites_[i]->addElement(sequence.getContent().getRow(i)); -- -- // append comments : -- comments_.push_back(new Comments(sequence.getComments())); -- -- // sequence pointers : -- p_sequences_.push_back(0); --} -- --/********************************************************************************/ -- --void VectorProbabilisticSiteContainer::pClear() --{ -- clear(); // call VectorSiteContainer clear -- -- // now clear all probabilistic sites / sequences -- for(std::size_t i = 0; i < p_sites_.size(); ++i) -- delete p_sites_[i]; -- -- for(std::size_t i = 0; i < p_sequences_.size(); ++i) -- delete p_sequences_[i]; -- -- // and delete the corresponding pointers -- p_sites_.clear(); -- p_sequences_.clear(); --} -- --/********************************************************************************/ -- --void VectorProbabilisticSiteContainer::reindexpSites() --{ -- int pos = 1; // start at position 1 -- std::vector<ProbabilisticSite *>::iterator i = p_sites_.begin(); -- for(; i != p_sites_.end(); ++i) -- (*i)->setPosition(++pos); --} -- --/********************************************************************************/ -- --void VectorProbabilisticSiteContainer::pRealloc(std::size_t n) --{ -- pClear(); -- p_sites_.resize(n); -- -- for(std::size_t i = 0; i < n; ++i) -- p_sites_[i] = new BasicProbabilisticSite(getAlphabet()); -- -- reindexpSites(); --} ---- a/src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h -+++ /dev/null -@@ -1,123 +0,0 @@ --// --// File: VectorProbabilisticSiteContainer.h --// Created by: Murray Patterson --// Created on: Mon Oct 19 2015 --// -- --/* -- Copyright or © or Copr. CNRS, (November 17, 2004) -- -- This software is a computer program whose purpose is to provide classes -- for sequences analysis. -- -- This software is governed by the CeCILL license under French law and -- abiding by the rules of distribution of free software. You can use, -- modify and/ or redistribute the software under the terms of the CeCILL -- license as circulated by CEA, CNRS and INRIA at the following URL -- "http://www.cecill.info";. -- -- As a counterpart to the access to the source code and rights to copy, -- modify and redistribute granted by the license, users are provided only -- with a limited warranty and the software's author, the holder of the -- economic rights, and the successive licensors have only limited -- liability. -- -- In this respect, the user's attention is drawn to the risks associated -- with loading, using, modifying and/or developing or reproducing the -- software by the user in light of its specific status of free software, -- that may mean that it is complicated to manipulate, and that also -- therefore means that it is reserved for developers and experienced -- professionals having in-depth computer knowledge. Users are therefore -- encouraged to load and test the software's suitability as regards their -- requirements in conditions enabling the security of their systems and/or -- data to be ensured and, more generally, to use and operate it in the -- same conditions as regards security. -- -- The fact that you are presently reading this means that you have had -- knowledge of the CeCILL license and that you accept its terms. --*/ -- --#ifndef _VECTORPROBABILISTICSITECONTAINER_H_ --#define _VECTORPROBABILISTICSITECONTAINER_H_ -- --#include "VectorSiteContainer.h" -- --#include "../ProbabilisticSite.h" --#include "../ProbabilisticSequence.h" -- --// From the STL : --#include <vector> -- --namespace bpp --{ -- --/** -- * @brief The VectorProbabilisticSiteContainer class. -- * -- * ProbabilisticSites are stored in a std::vector of pointers. -- * ProbabilisticSite access is hence in \f$O(1)\f$, and sequence -- * access in \f$O(l)\f$, where \f$l\f$ is the number of sites in the -- * container. -- * -- * This is a modified copy of VectorSiteContainer with the minimum -- * changes necessary for it to work with bppML and bppAncestor -- * -- * @see ProbabilisticSequence, ProbabilisticSite, VectorSiteContainer -- */ --class VectorProbabilisticSiteContainer : -- public VectorSiteContainer --{ -- -- protected : -- -- std::vector<ProbabilisticSite *> p_sites_; -- mutable std::vector<ProbabilisticSequence *> p_sequences_; -- -- public : -- -- /** -- * @brief Build a new emtpy container. -- * -- * @param alpha The alphabet for this container. -- */ -- VectorProbabilisticSiteContainer(const Alphabet * alpha); -- -- /** -- * @name The Clonable interface. -- * -- * @{ -- */ -- VectorSiteContainer* clone() const { return new VectorSiteContainer(*this); } -- -- /** -- * @} -- */ -- -- // class destructor -- virtual ~VectorProbabilisticSiteContainer() { pClear(); } -- -- public : -- -- const ProbabilisticSite & getProbabilisticSite(std::size_t i) const throw (IndexOutOfBoundsException); -- -- void addSite(const ProbabilisticSite & site, bool checkPosition = true) throw (Exception); -- -- const ProbabilisticSequence & getProbabilisticSequence(std::size_t i) const throw (IndexOutOfBoundsException); -- -- void addSequence(const ProbabilisticSequence & sequence, bool checkName = true) throw (Exception); -- -- std::size_t getNumberOfProbabilisticSites() const { return p_sites_.size(); } -- std::size_t getNumberOfProbabilisticSequences() const { return p_sequences_.size(); } -- -- void pClear(); -- void reindexpSites(); -- -- protected : -- -- // create n void probabilistic sites : -- void pRealloc(std::size_t n); --}; -- --} // end of namespace bpp -- --#endif // _VECTORPROBABILISTICSITECONTAINER_H_ diff --git a/debian/patches/series b/debian/patches/series index 1704a6b..4ff7e79 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,2 @@ unforce-cxxflags.patch -rm_VectorProbabilisticSiteContainer.patch relax_test_timeout.patch diff --git a/debian/rules b/debian/rules index aa1cdb9..ecd2fa6 100755 --- a/debian/rules +++ b/debian/rules @@ -12,7 +12,6 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all override_dh_install: # Broken header, don't install (if we do, the postinst will pull it # into generic include files) - rm -f debian/tmp/usr/include/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h dh_install d-shlibmove --commit \ --multiarch \ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libbpp-seq.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
