Bug#871085: marked as done (libbpp-phyl: FTBFS: collect2: error: ld returned 1 exit status)

[Debian Bug Tracking System]

Your message dated Fri, 25 Aug 2017 12:19:13 +0000
with message-id <e1dldzx-000d67...@fasolo.debian.org>
and subject line Bug#871085: fixed in libbpp-phyl 2.3.1-10
has caused the Debian Bug report #871085,
regarding libbpp-phyl: FTBFS: collect2: error: ld returned 1 exit status
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
871085: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=871085
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

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.

--- End Message ---

--- Begin Message ---

Source: libbpp-phyl
Source-Version: 2.3.1-10

We believe that the bug you reported is fixed in the latest version of
libbpp-phyl, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 871...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated libbpp-phyl package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Wed, 23 Aug 2017 23:32:26 +0200
Source: libbpp-phyl
Binary: libbpp-phyl-dev libbpp-phyl11
Architecture: source amd64
Version: 2.3.1-10
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
 libbpp-phyl-dev - Bio++ Phylogenetic library development files
 libbpp-phyl11 - Bio++ Phylogenetic library
Closes: 871085
Changes:
 libbpp-phyl (2.3.1-10) unstable; urgency=medium
 .
   [ Julien Dutheil ]
   * Does not override debian cxx flags anymore.
 .
   [ Andreas Tille ]
   * Rebuild with gcc-7
     Closes: #871085
   * Standards-Version: 4.0.1
   * Fix d-shlibs override
Checksums-Sha1:
 255334cedafe18cd00948f8d98dfb2659bf931ee 2174 libbpp-phyl_2.3.1-10.dsc
 e01c89f0a606982bd1cd8d8b3bebd9b8f1527642 8312 
libbpp-phyl_2.3.1-10.debian.tar.xz
 7b9a853423c30e377b1f52d4986a7d2d184a8b65 2770522 
libbpp-phyl-dev_2.3.1-10_amd64.deb
 90f818118f1b7958c25f718e1507ecf1ccd2b27f 30384372 
libbpp-phyl11-dbgsym_2.3.1-10_amd64.deb
 2d89943c53c0523e65640dcc42302226d534c1d9 1458418 
libbpp-phyl11_2.3.1-10_amd64.deb
 cadfd4ea60b9e7c9a977a7226c3878a9c36aa24a 7255 
libbpp-phyl_2.3.1-10_amd64.buildinfo
Checksums-Sha256:
 30eae1cafd494f96cd34b65c7378c9cb4821f76881a20ab993284971c555b7ed 2174 
libbpp-phyl_2.3.1-10.dsc
 51056dc79438de8a31573a1ccfcfd439f1c88920920e4ab59368f172f12baeae 8312 
libbpp-phyl_2.3.1-10.debian.tar.xz
 d5c3ee21bfc4058997a0a8654607ee3a86ea01ba10641d0ff987f24907af1385 2770522 
libbpp-phyl-dev_2.3.1-10_amd64.deb
 d64f5f4b1323934c58b69fd8ea9425f065c5f4bea8d037ae7046ae672bed9555 30384372 
libbpp-phyl11-dbgsym_2.3.1-10_amd64.deb
 30ec86b92b838157361b4d84287ab106637718efe65d89ed3390e306965e9759 1458418 
libbpp-phyl11_2.3.1-10_amd64.deb
 13e2aaaa4216926642192605de36906b87a43bc253dcbb73e421c48869cb8fe3 7255 
libbpp-phyl_2.3.1-10_amd64.buildinfo
Files:
 f6b4d9eebe1557e22374de3ef198e23b 2174 science optional libbpp-phyl_2.3.1-10.dsc
 e2e022f080adba7a9e9ce9ba4ab4f05b 8312 science optional 
libbpp-phyl_2.3.1-10.debian.tar.xz
 311ae9ce422b946dbed5940744bda9f1 2770522 libdevel optional 
libbpp-phyl-dev_2.3.1-10_amd64.deb
 15580284a6b79e7620d81064f9d2e98b 30384372 debug extra 
libbpp-phyl11-dbgsym_2.3.1-10_amd64.deb
 bf70fd8d3f877794f7ac0045edb4f5a5 1458418 libs optional 
libbpp-phyl11_2.3.1-10_amd64.deb
 2a0d6726206d2ac9a5ed44c4cc2463e9 7255 science optional 
libbpp-phyl_2.3.1-10_amd64.buildinfo

-----BEGIN PGP SIGNATURE-----
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=2bQ8
-----END PGP SIGNATURE-----

--- End Message ---