Source: libbpp-phyl
Version: 2.3.1-9
Severity: serious
Tags: buster sid
User: debian...@lists.debian.org
Usertags: qa-ftbfs-20170805 qa-ftbfs
Justification: FTBFS on amd64
Hi,
During a rebuild of all packages in sid, your package failed to build on
amd64.
Relevant part (hopefully):
> /usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -Wl,-z,relro
> -Wl,-z,now -rdynamic CMakeFiles/test_nhx.dir/test_nhx.cpp.o -o test_nhx
> -Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src
> ../src/libbpp-phyl.so.11.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.11.0.0
> /usr/lib/x86_64-linux-gnu/libbpp-core.so.3.0.0
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43:0,
> from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:44:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void init_(const SiteContainer& data, bool verbose) throw (Exception);
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
> from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:95:7:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:118:7:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:136:18:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void init_() throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:147:47:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void setData(const SiteContainer & sites) throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:152:44:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException)
> { return likelihoodData_->getRootArrayPosition(site); }
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
> from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:180:58:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void setParameters(const ParameterList & parameters) throw
> (ParameterNotFoundException, ConstraintException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:185:29:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getValue() const throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:192:71:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getFirstOrderDerivative(const std::string& variable) const throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:200:72:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getSecondOrderDerivative(const std::string& variable) const throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:201:103:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getSecondOrderDerivative(const std::string& variable1, const
> std::string& variable2) const throw (Exception) { return 0; } // Not
> implemented for now.
>
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:62:0,
> from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43,
> from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:46:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:221:36:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> size_t getNumberOfStates() const throw (Exception)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:250:53:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> const SubstitutionModel* getModel(size_t i) const throw
> (IndexOutOfBoundsException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:257:41:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> SubstitutionModel* getModel(size_t i) throw (IndexOutOfBoundsException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:264:61:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> const TransitionModel* getTransitionModel(size_t i) const throw
> (IndexOutOfBoundsException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:270:49:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> TransitionModel* getTransitionModel(size_t i) throw
> (IndexOutOfBoundsException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:281:65:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> const SubstitutionModel* getSubstitutionModel(size_t i) const throw
> (IndexOutOfBoundsException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:294:53:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> SubstitutionModel* getSubstitutionModel(size_t i) throw
> (IndexOutOfBoundsException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:327:49:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> size_t getModelIndexForNode(int nodeId) const throw (Exception)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:342:60:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> const TransitionModel* getModelForNode(int nodeId) const throw (Exception)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:349:48:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> TransitionModel* getModelForNode(int nodeId) throw (Exception)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:357:74:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> const SubstitutionModel* getSubstitutionModelForNode(int nodeId) const
> throw (Exception)
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:362:62:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> SubstitutionModel* getSubstitutionModelForNode(int nodeId) throw
> (Exception)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:374:61:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> const std::vector<int>& getNodesWithModel(size_t i) const throw
> (IndexOutOfBoundsException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:386:73:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> std::vector<int> getNodesWithParameter(const std::string& name) const
> throw (ParameterNotFoundException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:416:64:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void replaceModel(size_t modelIndex, TransitionModel* model) throw
> (Exception);
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
> from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void init(const SiteContainer& sites, const StateMap& stateMap) throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void reInit() throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:528:69:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> bool isFullySetUpFor(const Tree& tree, bool throwEx = true) const throw
> (Exception)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:551:46:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> bool checkOrphanModels(bool throwEx) const throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:553:63:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> bool checkOrphanNodes(const Tree& tree, bool throwEx) const throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/../Model/SubstitutionModelSet.h:555:64:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> bool checkUnknownNodes(const Tree& tree, bool throwEx) const throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void init(const Node* node, const SiteContainer& sites, const StateMap&
> stateMap) throw (Exception);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void reInit(const Node* node) throw (Exception);
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:143:3:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> throw (ParameterNotFoundException, ConstraintException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:148:27:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getValue() const throw (Exception) { return lnL_; }
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:46:0,
> from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
> from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../TopologySearch.h:142:25: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual void search() throw (Exception) = 0;
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:44:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44,
> from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:120:44: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual double testNNI(int nodeId) const throw (NodeException) = 0;
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:128:34: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual void doNNI(int nodeId) throw (NodeException) = 0;
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/../NNISearchable.h:142:45: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual double getTopologyValue() const throw (Exception) = 0;
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getTopologyValue() const throw (Exception) { return getScore(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double testNNI(int nodeId) const throw (NodeException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void doNNI(int nodeId) throw (NodeException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:201:3:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:222:3:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:236:44:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void setData(const SiteContainer& sites) throw (Exception)
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:256:35:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getTopologyValue() const throw (Exception) { return getValue(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:258:36:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double testNNI(int nodeId) const throw (NodeException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:260:26:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void doNNI(int nodeId) throw (NodeException);
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:47:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49,
> from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getFunctionValue() const throw (NullPointerException) { return
> currentValue_; }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void doInit(const ParameterList& params) throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double doStep() throw (Exception);
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h:43:0,
> from /<<PKGBUILDDIR>>/test/test_detailed_simulations.cpp:46:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h:136:7:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> ) throw (Exception);
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:46:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:116:17: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void search() throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:150:23: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void searchFast() throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:151:23: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void searchBetter() throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:152:23: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void searchPhyML() throw (Exception);
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:143:3:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> throw (ParameterNotFoundException, ConstraintException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:148:27:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getValue() const throw (Exception) { return lnL_; }
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
> from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void init_(const SiteContainer& data, bool verbose) throw (Exception);
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
> from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:44:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void init(const SiteContainer& sites, const StateMap& stateMap) throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void reInit() throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void init(const Node* node, const SiteContainer& sites, const StateMap&
> stateMap) throw (Exception);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void reInit(const Node* node) throw (Exception);
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:124:22: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> bool verbose) throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:151:45: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:155:57: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> const TreeLikelihoodData* getLikelihoodData() const throw
> (NotImplementedException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:165:73: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex)
> throw (NodeNotFoundException) { return model_; }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:166:85: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> const TransitionModel* getSubstitutionModel(int nodeId, size_t
> siteIndex) const throw (NodeNotFoundException) { return model_; }
>
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:168:44: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException)
> { return rootPatternLinks_[site]; }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:173:46: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> void setData(const SiteContainer& sites) throw (Exception) {}
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:174:23: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> void initialize() throw(Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:202:75: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const
> throw (NotImplementedException)
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:207:77: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const
> throw (NotImplementedException)
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:227:57: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> void setParameters(const ParameterList& parameters) throw
> (ParameterNotFoundException, ConstraintException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:228:29: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> double getValue() const throw(Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:235:71: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> double getFirstOrderDerivative(const std::string& variable) const throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:243:72: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> double getSecondOrderDerivative(const std::string& variable) const throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:244:103: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> double getSecondOrderDerivative(const std::string& variable1, const
> std::string& variable2) const throw (Exception) { return 0; } // Not
> implemented for now.
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:275:75: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual void initTreeLikelihoods(const SequenceContainer & sequences)
> throw (Exception);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:201:3:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:293:36: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual void applyParameters() throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:222:3:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:236:44:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void setData(const SiteContainer& sites) throw (Exception)
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:44:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:256:35:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getTopologyValue() const throw (Exception) { return getValue(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:258:36:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double testNNI(int nodeId) const throw (NodeException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:260:26:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void doNNI(int nodeId) throw (NodeException);
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:46:0,
> from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:45,
> from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:44:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../TopologySearch.h:142:25: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual void search() throw (Exception) = 0;
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:45:0,
> from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:44:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:120:44: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual double testNNI(int nodeId) const throw (NodeException) = 0;
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:128:34: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual void doNNI(int nodeId) throw (NodeException) = 0;
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/../NNISearchable.h:142:45: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual double getTopologyValue() const throw (Exception) = 0;
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/test/test_parsimony.cpp:44:0:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getTopologyValue() const throw (Exception) { return getScore(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double testNNI(int nodeId) const throw (NodeException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void doNNI(int nodeId) throw (NodeException);
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:43:0,
> from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
> from /<<PKGBUILDDIR>>/test/test_models.cpp:40:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../FrequenciesSet/FrequenciesSet.h:368:118:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>&
> initFreqs, const std::string& name = "Fixed") throw (Exception);
>
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:46:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:116:17: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void search() throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:150:23: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void searchFast() throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:151:23: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void searchBetter() throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/NNITopologySearch.h:152:23: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void searchPhyML() throw (Exception);
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:43:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
> from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:70:3:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:77:3:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h:108:55:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void init_(const SiteContainer& data, bool verbose) throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:473:26: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> void computeMatrix() throw (NullPointerException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:484:57: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> const TransitionModel& getSubstitutionModel() const throw (Exception) {
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:495:61: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> const DiscreteDistribution& getRateDistribution() const throw
> (Exception) {
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
> from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void init(const SiteContainer& sites, const StateMap& stateMap) throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void reInit() throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void init(const Node* node, const SiteContainer& sites, const StateMap&
> stateMap) throw (Exception);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void reInit(const Node* node) throw (Exception);
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:50:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceMethod.h:75:64: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual void setDistanceMatrix(const DistanceMatrix& matrix) throw
> (Exception) = 0;
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
> from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:88:71: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static std::vector<int> getLeavesId(const Tree& tree, int nodeId) throw
> (NodeNotFoundException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:98:85: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static void getLeavesId(const Tree& tree, int nodeId, std::vector<int>&
> leaves) throw (NodeNotFoundException);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:107:67: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static size_t getNumberOfLeaves(const Tree& tree, int nodeId) throw
> (NodeNotFoundException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:118:81: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static int getLeafId(const Tree& tree, int nodeId, const std::string&
> name) throw (NodeNotFoundException);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:129:93: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static void searchLeaf(const Tree& tree, int nodeId, const std::string&
> name, int*& id) throw (NodeNotFoundException);
>
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:45:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45,
> from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:141:128: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static std::vector<int> getPathBetweenAnyTwoNodes(const Tree& tree, int
> nodeId1, int nodeId2, bool includeAncestor = true) throw
> (NodeNotFoundException);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:151:72: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static std::vector<int> getAncestors(const Tree& tree, int nodeId) throw
> (NodeNotFoundException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:163:89: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static int getLastCommonAncestor(const Tree& tree, const
> std::vector<int>& nodeIds) throw (NodeNotFoundException, Exception);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:186:58: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static size_t getDepth(const Tree& tree, int nodeId) throw
> (NodeNotFoundException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:210:90: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static size_t getDepths(const Tree& tree, int nodeId, std::map<int,
> size_t>& depths) throw (NodeNotFoundException);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:225:59: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static double getHeight(const Tree& tree, int nodeId) throw
> (NodeNotFoundException,NodeException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:240:92: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static double getHeights(const Tree& tree, int nodeId, std::map<int,
> double>& heights) throw (NodeNotFoundException,NodeException);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:259:67: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static Vdouble getBranchLengths(const Tree& tree, int nodeId) throw
> (NodeNotFoundException,NodeException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:272:93: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static double getTotalLength(const Tree& tree, int nodeId, bool
> includeAncestor = true) throw (NodeNotFoundException,NodeException);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:282:72: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static void setBranchLengths(Tree& tree, int nodeId, double brLen) throw
> (NodeNotFoundException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:292:76: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static void setVoidBranchLengths(Tree& tree, int nodeId, double brLen)
> throw (NodeNotFoundException);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:305:66: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static void scaleTree(Tree& tree, int nodeId, double factor) throw
> (NodeNotFoundException,NodeException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:337:92: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static void computeBranchLengthsGrafen(Tree& tree, double power = 1,
> bool init = true) throw (NodeException);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:340:67: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static size_t initBranchLengthsGrafen(Tree& tree, int nodeId) throw
> (NodeNotFoundException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:341:134: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static void computeBranchLengthsGrafen(Tree& tree, int nodeId, double
> power, double total, double& height, double& heightRaised) throw
> (NodeNotFoundException,NodeException);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:443:94: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool
> writeId = false) throw (NodeNotFoundException);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:459:121: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static std::string nodeToParenthesis(const Tree& tree, int nodeId, bool
> bootstrap, const std::string& propertyName) throw (NodeNotFoundException);
>
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:0:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:85:68: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void optimizationStepPerformed(const OptimizationEvent &event) throw
> (Exception)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:502:70: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static std::vector<int> getNodesId(const Tree& tree, int nodeId) throw
> (NodeNotFoundException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:512:83: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static void getNodesId(const Tree& tree, int nodeId, std::vector<int>&
> nodes) throw (NodeNotFoundException);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:545:65: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static bool checkIds(const Tree& tree, bool throwException) throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:600:153: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static int robinsonFouldsDistance(const Tree& tr1, const Tree& tr2, bool
> checkNames = true, int* missing_in_tr2 = NULL, int* missing_in_tr1 = NULL)
> throw (Exception);
>
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTools.h:628:126: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> static TreeTemplate<Node>* thresholdConsensus(const std::vector<Tree*>&
> vecTr, double threshold, bool checkNames = true) throw (Exception);
>
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getTopologyValue() const throw (Exception) { return getScore(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double testNNI(int nodeId) const throw (NodeException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void doNNI(int nodeId) throw (NodeException);
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
> from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:165:67: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> static int getLeafId(const Node& node, const std::string& name) throw
> (NodeNotFoundException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:186:79: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> static void searchLeaf(const Node& node, const std::string& name, int*&
> id) throw (NodeNotFoundException)
>
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:47:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49,
> from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getFunctionValue() const throw (NullPointerException) { return
> currentValue_; }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:210:76: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName)
> throw (NodeNotFoundException, Exception)
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:267:65: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> static void dropSubtree(TreeTemplate<N>& tree, Node* subtree) throw
> (Exception)
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:43:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
> from /<<PKGBUILDDIR>>/test/test_models.cpp:40:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../SubstitutionModel.h:259:60:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> virtual double getInitValue(size_t i, int state) const throw
> (IndexOutOfBoundsException, BadIntException) = 0;
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void doInit(const ParameterList& params) throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double doStep() throw (Exception);
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:45:0,
> from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:832:53: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> static Vdouble getBranchLengths(const Node& node) throw (NodePException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:843:79: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> static double getTotalLength(const Node& node, bool includeAncestor =
> true) throw (NodePException);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:877:52: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> static void scaleTree(Node& node, double factor) throw (NodePException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:952:53: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> static Element getElement(const std::string& elt) throw (IOException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplateTools.h:982:201: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> static TreeTemplate<Node>* parenthesisToTree(const std::string&
> description, bool bootstrap = true, const std::string& propertyName =
> TreeTools::BOOTSTRAP, bool withId = false, bool verbose = true) throw
> (Exception);
>
>
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/test/test_likelihood_nh.cpp:50:0:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:351:3: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:387:3: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:420:3: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:458:3: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:490:3: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:523:53: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void setParameters(const ParameterList& lambda) throw
> (ParameterNotFoundException, ConstraintException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:524:29: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> double getValue() const throw (ParameterException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:525:48: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> const ParameterList& getParameters() const throw (Exception) { return
> lambda_; }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:526:66: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> const Parameter& getParameter(const std::string& name) const throw
> (ParameterNotFoundException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:531:61: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> double getParameterValue(const std::string& name) const throw
> (ParameterNotFoundException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:569:3: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:625:3: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:679:3: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:719:31: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> unsigned int verbose = 0) throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:755:31: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> unsigned int verbose = 0) throw (Exception);
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h:44:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/GTR.h:43,
> from /<<PKGBUILDDIR>>/test/test_models.cpp:40:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Nucleotide/../AbstractSubstitutionModel.h:288:50:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getInitValue(size_t i, int state) const throw
> (IndexOutOfBoundsException, BadIntException);
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:0:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:170:48: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> int getLeafId(const std::string& name) const throw (NodeNotFoundException)
> { return TreeTemplateTools::getLeafId(*root_, name); }
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/test/test_tree.cpp:40:0:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:184:50: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> std::vector<int> getSonsId(int parentId) const throw
> (NodeNotFoundException) { return getNode(parentId)->getSonsId(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:186:53: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> std::vector<int> getAncestorsId(int nodeId) const throw
> (NodeNotFoundException) { return
> TreeTemplateTools::getAncestorsId(*getNode(nodeId)); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:188:39: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> int getFatherId(int parentId) const throw (NodeNotFoundException) { return
> getNode(parentId)->getFatherId(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:190:36: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> bool hasFather(int nodeId) const throw (NodeNotFoundException) { return
> getNode(nodeId)->hasFather(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:192:45: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> std::string getNodeName(int nodeId) const throw (NodeNotFoundException) {
> return getNode(nodeId)->getName(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:194:38: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> bool hasNodeName(int nodeId) const throw (NodeNotFoundException) { return
> getNode(nodeId)->hasName(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:196:57: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void setNodeName(int nodeId, const std::string& name) throw
> (NodeNotFoundException) { getNode(nodeId)->setName(name); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:198:35: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void deleteNodeName(int nodeId) throw (NodeNotFoundException) { return
> getNode(nodeId)->deleteName(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:202:33: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> bool isLeaf(int nodeId) const throw (NodeNotFoundException) { return
> getNode(nodeId)->isLeaf(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:204:33: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> bool isRoot(int nodeId) const throw (NodeNotFoundException) { return
> TreeTemplateTools::isRoot(*getNode(nodeId)); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:214:67: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> bool hasNodeProperty(int nodeId, const std::string& name) const throw
> (NodeNotFoundException) { return getNode(nodeId)->hasNodeProperty(name); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:216:87: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void setNodeProperty(int nodeId, const std::string& name, const Clonable&
> property) throw (NodeNotFoundException) {
> getNode(nodeId)->setNodeProperty(name, property); }
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:218:66: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> Clonable* getNodeProperty(int nodeId, const std::string& name) throw
> (NodeNotFoundException) { return getNode(nodeId)->getNodeProperty(name); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:220:78: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> const Clonable* getNodeProperty(int nodeId, const std::string& name) const
> throw (NodeNotFoundException) { return
> getNode(nodeId)->getNodeProperty(name); }
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:222:69: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> Clonable* removeNodeProperty(int nodeId, const std::string& name) throw
> (NodeNotFoundException) { return getNode(nodeId)->removeNodeProperty(name); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:224:67: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> std::vector<std::string> getNodePropertyNames(int nodeId) const throw
> (NodeNotFoundException) { return getNode(nodeId)->getNodePropertyNames(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:226:69: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> bool hasBranchProperty(int nodeId, const std::string& name) const throw
> (NodeNotFoundException) { return getNode(nodeId)->hasBranchProperty(name); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:228:89: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void setBranchProperty(int nodeId, const std::string& name, const
> Clonable& property) throw (NodeNotFoundException) {
> getNode(nodeId)->setBranchProperty(name, property); }
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:230:68: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> Clonable* getBranchProperty(int nodeId, const std::string& name) throw
> (NodeNotFoundException) { return getNode(nodeId)->getBranchProperty(name); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:232:80: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> const Clonable* getBranchProperty(int nodeId, const std::string& name)
> const throw (NodeNotFoundException) { return
> getNode(nodeId)->getBranchProperty(name); }
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:234:71: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> Clonable* removeBranchProperty(int nodeId, const std::string& name) throw
> (NodeNotFoundException) { return getNode(nodeId)->removeBranchProperty(name);
> }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:236:69: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> std::vector<std::string> getBranchPropertyNames(int nodeId) const throw
> (NodeNotFoundException) { return getNode(nodeId)->getBranchPropertyNames(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:238:27: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void rootAt(int nodeId) throw (NodeNotFoundException) {
> rootAt(getNode(nodeId)); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:240:32: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void newOutGroup(int nodeId) throw (NodeNotFoundException) {
> newOutGroup(getNode(nodeId)); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:244:17: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> bool unroot() throw (UnrootedTreeException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:345:42: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> std::vector<double> getBranchLengths() throw (NodeException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:356:27: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> double getTotalLength() throw (NodeException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:377:33: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void scaleTree(double factor) throw (NodeException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:390:54: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> void swapNodes(int parentId, size_t i1, size_t i2) throw
> (NodeNotFoundException, IndexOutOfBoundsException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:421:52: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual N* getNode(int id, bool checkId = false) throw
> (NodeNotFoundException, Exception)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:438:64: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual const N* getNode(int id, bool checkId = false) const throw
> (NodeNotFoundException, Exception)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:455:47: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual N* getNode(const std::string& name) throw (NodeNotFoundException,
> Exception)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/TreeTemplate.h:464:59: warning: dynamic
> exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual const N* getNode(const std::string& name) const throw
> (NodeNotFoundException, Exception)
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:44:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47,
> from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:307:67:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void init(const SiteContainer& sites, const StateMap& stateMap) throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:308:17:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void reInit() throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:311:85:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void init(const Node* node, const SiteContainer& sites, const StateMap&
> stateMap) throw (Exception);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h:312:33:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void reInit(const Node* node) throw (Exception);
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:43:0,
> from /<<PKGBUILDDIR>>/test/test_tree.cpp:42:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:89:55: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> virtual Tree* read(const std::string& path) const throw (Exception) = 0;
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:97:48: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> virtual Tree* read(std::istream& in) const throw (Exception) = 0;
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:124:22: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> bool verbose) throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:151:45: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:120:89: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> virtual void write(const Tree& tree, const std::string& path, bool
> overwrite) const throw (Exception) = 0;
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:128:67: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> virtual void write(const Tree& tree, std::ostream& out) const throw
> (Exception) = 0;
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:155:57: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> const TreeLikelihoodData* getLikelihoodData() const throw
> (NotImplementedException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:165:73: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> TransitionModel* getSubstitutionModel(int nodeId, size_t siteIndex)
> throw (NodeNotFoundException) { return model_; }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:142:48: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> virtual Tree* read(std::istream& in) const throw (Exception) = 0;
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:166:85: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> const TransitionModel* getSubstitutionModel(int nodeId, size_t
> siteIndex) const throw (NodeNotFoundException) { return model_; }
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:143:55: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> virtual Tree* read(const std::string& path) const throw (Exception)
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:168:44: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException)
> { return rootPatternLinks_[site]; }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:173:46: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> void setData(const SiteContainer& sites) throw (Exception) {}
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:174:23: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> void initialize() throw(Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:202:75: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> ConstBranchModelIterator* getNewBranchModelIterator(int nodeId) const
> throw (NotImplementedException)
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:207:77: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> ConstSiteModelIterator* getNewSiteModelIterator(size_t siteIndex) const
> throw (NotImplementedException)
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:227:57: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> void setParameters(const ParameterList& parameters) throw
> (ParameterNotFoundException, ConstraintException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:228:29: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> double getValue() const throw(Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:235:71: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> double getFirstOrderDerivative(const std::string& variable) const throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:243:72: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> double getSecondOrderDerivative(const std::string& variable) const throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:164:59: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> void write(const Tree& tree, std::ostream& out) const throw (Exception)
> = 0;
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:244:103: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> double getSecondOrderDerivative(const std::string& variable1, const
> std::string& variable2) const throw (Exception) { return 0; } // Not
> implemented for now.
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:275:75: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual void initTreeLikelihoods(const SequenceContainer & sequences)
> throw (Exception);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:293:36: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> virtual void applyParameters() throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:165:89: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> virtual void write(const Tree& tree, const std::string& path, bool
> overwrite) const throw (Exception)
>
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:47:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:69:3: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:76:3: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:169:35:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getTopologyValue() const throw (Exception) { return getScore(); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:171:36:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double testNNI(int nodeId) const throw (NodeException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h:173:26:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void doNNI(int nodeId) throw (NodeException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:208:81: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> virtual void read(const std::string& path, std::vector<Tree*>& trees)
> const throw (Exception) = 0;
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:216:74: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> virtual void read(std::istream& in, std::vector<Tree*>& trees) const
> throw (Exception) = 0;
>
> ^~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:47:0,
> from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49,
> from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:116:37:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getFunctionValue() const throw (NullPointerException) { return
> currentValue_; }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:119:46:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> void doInit(const ParameterList& params) throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:239:104: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> virtual void write(const std::vector<Tree*>& trees, const std::string&
> path, bool overwrite) const throw (Exception) = 0;
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:247:82: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> virtual void write(const std::vector<Tree*>& trees, std::ostream& out)
> const throw (Exception) = 0;
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/../Likelihood/PseudoNewtonOptimizer.h:121:21:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double doStep() throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:261:74: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> virtual void read(std::istream& in, std::vector<Tree*>& trees) const
> throw (Exception) = 0;
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:262:81: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> virtual void read(const std::string& path, std::vector<Tree*>& trees)
> const throw (Exception)
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:282:74: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> void write(const std::vector<Tree*>& trees, std::ostream& out) const
> throw (Exception) = 0;
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/IoTree.h:283:104: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> virtual void write(const std::vector<Tree*>& trees, const std::string&
> path, bool overwrite) const throw (Exception)
>
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/test/test_tree.cpp:42:0:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:143:61: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> TreeTemplate<Node>* read(const std::string& path) const throw (Exception)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:148:54: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> TreeTemplate<Node>* read(std::istream& in) const throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:156:88: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> void write(const Tree& tree, const std::string& path, bool overwrite =
> true) const throw (Exception)
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:161:59: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> void write(const Tree& tree, std::ostream& out) const throw (Exception)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:172:73: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> void read(const std::string& path, std::vector<Tree*>& trees) const
> throw (Exception)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:176:66: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> void read(std::istream& in, std::vector<Tree*>& trees) const throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:184:103: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> void write(const std::vector<Tree*>& trees, const std::string& path,
> bool overwrite = true) const throw (Exception)
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:188:74: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> void write(const std::vector<Tree*>& trees, std::ostream& out) const
> throw (Exception)
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:195:60: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> void write_(const Tree& tree, std::ostream& out) const throw (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:198:71: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> void write_(const TreeTemplate<N>& tree, std::ostream& out) const throw
> (Exception);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:200:75: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> void write_(const std::vector<Tree*>& trees, std::ostream& out) const
> throw (Exception);
>
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/Newick.h:203:86: warning: dynamic exception
> specifications are deprecated in C++11 [-Wdeprecated]
> void write_(const std::vector<TreeTemplate<N>*>& trees, std::ostream&
> out) const throw (Exception);
>
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/YN98.h:43:0,
> from /<<PKGBUILDDIR>>/test/test_models.cpp:41:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Model/Codon/../AbstractBiblioSubstitutionModel.h:171:52:
> warning: dynamic exception specifications are deprecated in C++11
> [-Wdeprecated]
> double getInitValue(size_t i, int state) const throw (BadIntException) {
> return getModel().getInitValue(i, state); }
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:473:26: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> void computeMatrix() throw (NullPointerException);
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:484:57: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> const TransitionModel& getSubstitutionModel() const throw (Exception) {
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:495:61: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> const DiscreteDistribution& getRateDistribution() const throw
> (Exception) {
> ^~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/OptimizationTools.h:49:0,
> from /<<PKGBUILDDIR>>/test/test_likelihood_clock.cpp:48:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:124:22: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> bool verbose) throw (Exception);
> ^~~~~
> ../src/libbpp-phyl.so.11.0.0: undefined reference to `virtual thunk to
> bpp::AbstractParameterAliasable::getAliases[abi:cxx11]() const'
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:151:45: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> TreeLikelihoodData* getLikelihoodData() throw (NotImplementedException)
> ^~~~~
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Distance/DistanceEstimation.h:155:57: warning:
> dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
> const TreeLikelihoodData* getLikelihoodData() const throw
> (NotImplementedException)
> ^~~~~
> collect2: error: ld returned 1 exit status
The full build log is available from:
http://aws-logs.debian.net/2017/08/05/libbpp-phyl_2.3.1-9_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
