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  1.  
  2. In file included from /usr/include/c++/10.3.0/bits/locale_conv.h:41,
  3. from /usr/include/c++/10.3.0/locale:43,
  4. from /usr/include/c++/10.3.0/iomanip:43,
  5. from /usr/include/Utils/TextTools.h:50,
  6. from /usr/include/NumCalc/VectorExceptions.h:45,
  7. from /usr/include/NumCalc/VectorTools.h:43,
  8. from /usr/include/Phyl/TreeTools.h:52,
  9. from /usr/include/Phyl/TreeTemplateTools.h:45,
  10. from /usr/include/Phyl/TreeTemplate.h:45,
  11. from /usr/include/Phyl/Newick.h:44,
  12. from BCFasta.h:5,
  13. from caps.cpp:3:
  14. /usr/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here
  15. 57 | template<typename> class auto_ptr;
  16. | ^~~~~~~~
  17. caps.cpp: In function 'double getIndex(const std::vector<double>&, double)':
  18. caps.cpp:910:1: warning: control reaches end of non-void function [-Wreturn-type]
  19. 910 | }
  20. | ^
  21. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `Chi_squared(int, int, double, double&)':
  22. /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:867: undefined reference to `gsl_cdf_chisq_Pinv'
  23. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:876: undefined reference to `gsl_cdf_chisq_Pinv'
  24. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:878: undefined reference to `gsl_cdf_chisq_Pinv'
  25. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:869: undefined reference to `gsl_cdf_chisq_Pinv'
  26. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:871: undefined reference to `gsl_cdf_chisq_Pinv'
  27. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `Boot(std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, int, int, int, double)':
  28. /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:1099: undefined reference to `gsl_rng_uniform_int'
  29. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::AbstractAgglomerativeDistanceMethod::AbstractAgglomerativeDistanceMethod()':
  30. /usr/include/Phyl/AbstractAgglomerativeDistanceMethod.h:74: undefined reference to `VTT for bpp::BioNJ'
  31. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::BioNJ::BioNJ()':
  32. /usr/include/Phyl/BioNJ.h:65: undefined reference to `vtable for bpp::BioNJ'
  33. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `create_input_tree(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
  34. /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3060: undefined reference to `vtable for bpp::BioNJ'
  35. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::BioNJ::~BioNJ()':
  36. /usr/include/Phyl/BioNJ.h:78: undefined reference to `vtable for bpp::BioNJ'
  37. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::getLeavesNames[abi:cxx11]() const':
  38. /usr/include/Phyl/TreeTemplate.h:168: undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
  39. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `Remove_names(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, bpp::TreeTemplate<bpp::Node>*)':
  40. /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3150: undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
  41. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3196: undefined reference to `bpp::Newick::read(std::istream&) const'
  42. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::getLeavesNames[abi:cxx11]() const':
  43. /usr/include/Phyl/TreeTemplate.h:168: undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
  44. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `Put_distances_on_tree(bpp::TreeTemplate<bpp::Node>*, std::auto_ptr<bpp::DistanceMatrix>)':
  45. /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3440: undefined reference to `gsl_matrix_alloc'
  46. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3441: undefined reference to `gsl_vector_alloc'
  47. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3442: undefined reference to `gsl_vector_alloc'
  48. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3447: undefined reference to `gsl_matrix_set'
  49. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3449: undefined reference to `gsl_vector_set'
  50. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3452: undefined reference to `gsl_linalg_HH_solve'
  51. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3461: undefined reference to `gsl_vector_get'
  52. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3456: undefined reference to `gsl_vector_get'
  53. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3457: undefined reference to `gsl_vector_set'
  54. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3462: undefined reference to `gsl_vector_get'
  55. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3470: undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
  56. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3488: undefined reference to `gsl_vector_free'
  57. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3489: undefined reference to `gsl_vector_free'
  58. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:3490: undefined reference to `gsl_matrix_free'
  59. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `getAncestralSequences(int, char**, bpp::TreeTemplate<bpp::Node>*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::map<int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<int>, std::allocator<std::pair<int const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&)':
  60. /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2575: undefined reference to `bpp::BppApplication::BppApplication(int, char**, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  61. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2576: undefined reference to `bpp::BppApplication::startTimer()'
  62. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2577: undefined reference to `bpp::SequenceApplicationTools::getAlphabet(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool, bool)'
  63. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2578: undefined reference to `bpp::VectorSiteContainer::VectorSiteContainer(bpp::Alphabet const*)'
  64. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2580: undefined reference to `bpp::SequenceContainerTools::createContainerOfSpecifiedSize(bpp::Alphabet const*, unsigned int)'
  65. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2583: undefined reference to `bpp::Sequence::Sequence(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Alphabet const*)'
  66. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::Sequence::~Sequence()':
  67. /usr/include/Seq/Sequence.h:186: undefined reference to `vtable for bpp::Sequence'
  68. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::SymbolList::~SymbolList()':
  69. /usr/include/Seq/SymbolList.h:138: undefined reference to `VTT for bpp::Sequence'
  70. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `getAncestralSequences(int, char**, bpp::TreeTemplate<bpp::Node>*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::map<int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<int>, std::allocator<std::pair<int const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&)':
  71. /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2590: undefined reference to `bpp::SequenceApplicationTools::getSitesToAnalyse(bpp::SiteContainer const&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, bool, bool)'
  72. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2595: undefined reference to `bpp::ApplicationTools::getAFilePath(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&, bool, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)'
  73. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2597: undefined reference to `bpp::ApplicationTools::getStringParameter(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool)'
  74. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2601: undefined reference to `typeinfo for bpp::ProteicAlphabet'
  75. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2601: undefined reference to `bpp::JTT92::JTT92(bpp::ProteicAlphabet const*)'
  76. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2606: undefined reference to `bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::Alphabet const*, bool)'
  77. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2607: undefined reference to `bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  78. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2609: undefined reference to `bpp::SubstitutionModelSetTools::createHomogeneousModelSet(bpp::SubstitutionModel*, bpp::FrequenciesSet*, bpp::Tree const*)'
  79. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2610: undefined reference to `bpp::PhylogeneticsApplicationTools::getRateDistribution(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool)'
  80. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2611: undefined reference to `bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(bpp::Tree const&, bpp::SiteContainer const&, bpp::SubstitutionModelSet*, bpp::DiscreteDistribution*, bool)'
  81. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2622: undefined reference to `bpp::ApplicationTools::getBooleanParameter(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool)'
  82. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2625: undefined reference to `bpp::ApplicationTools::getAFilePath(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&, bool, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)'
  83. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2626: undefined reference to `bpp::ApplicationTools::getAFilePath(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&, bool, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)'
  84. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(int) const':
  85. /usr/include/Phyl/MarginalAncestralStateReconstruction.h:172: undefined reference to `bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(int, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >*, bool) const'
  86. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::Sequence::~Sequence()':
  87. /usr/include/Seq/Sequence.h:186: undefined reference to `vtable for bpp::Sequence'
  88. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::SymbolList::~SymbolList()':
  89. /usr/include/Seq/SymbolList.h:138: undefined reference to `VTT for bpp::Sequence'
  90. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::MarginalAncestralStateReconstruction::~MarginalAncestralStateReconstruction()':
  91. /usr/include/Phyl/MarginalAncestralStateReconstruction.h:128: undefined reference to `vtable for bpp::MarginalAncestralStateReconstruction'
  92. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `getAncestralSequences(int, char**, bpp::TreeTemplate<bpp::Node>*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::map<int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<int>, std::allocator<std::pair<int const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&)':
  93. /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:2653: undefined reference to `bpp::BppApplication::done()'
  94. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::getLeavesNames[abi:cxx11]() const':
  95. /usr/include/Phyl/TreeTemplate.h:168: undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
  96. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::getTotalLength()':
  97. /usr/include/Phyl/TreeTemplate.h:304: undefined reference to `bpp::TreeTemplateTools::getTotalLength(bpp::Node const&, bool)'
  98. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::getBranchLengths() const':
  99. /usr/include/Phyl/TreeTemplate.h:166: undefined reference to `bpp::TreeTemplateTools::getBranchLengths(bpp::Node const&)'
  100. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::getNumberOfNodes() const':
  101. /usr/include/Phyl/TreeTemplate.h:156: undefined reference to `bpp::TreeTemplateTools::getNumberOfNodes(bpp::Node const&)'
  102. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::getNumberOfLeaves() const':
  103. /usr/include/Phyl/TreeTemplate.h:154: undefined reference to `bpp::TreeTemplateTools::getNumberOfLeaves(bpp::Node const&)'
  104. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(int) const':
  105. /usr/include/Phyl/MarginalAncestralStateReconstruction.h:172: undefined reference to `bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(int, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >*, bool) const'
  106. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `virtual thunk to bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(int) const':
  107. /usr/include/Phyl/MarginalAncestralStateReconstruction.h:172: undefined reference to `bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(int, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >*, bool) const'
  108. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::getNextId()':
  109. /usr/include/Phyl/TreeTemplate.h:333: undefined reference to `bpp::TreeTools::getMPNUId(bpp::Tree const&, int)'
  110. /usr/bin/ld: /usr/include/Phyl/TreeTemplate.h:333: undefined reference to `bpp::TreeTools::getMPNUId(bpp::Tree const&, int)'
  111. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::setBranchLengths(double)':
  112. /usr/include/Phyl/TreeTemplate.h:311: undefined reference to `bpp::TreeTemplateTools::setBranchLengths(bpp::Node&, double)'
  113. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::setVoidBranchLengths(double)':
  114. /usr/include/Phyl/TreeTemplate.h:319: undefined reference to `bpp::TreeTemplateTools::setVoidBranchLengths(bpp::Node&, double)'
  115. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::scaleTree(double)':
  116. /usr/include/Phyl/TreeTemplate.h:327: undefined reference to `bpp::TreeTemplateTools::scaleTree(bpp::Node&, double)'
  117. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::isMultifurcating() const':
  118. /usr/include/Phyl/TreeTemplate.h:286: undefined reference to `bpp::TreeTemplateTools::isMultifurcating(bpp::Node const&)'
  119. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::DistanceMatrix::operator()(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
  120. /usr/include/Seq/DistanceMatrix.h:194: undefined reference to `bpp::DistanceMatrix::getNameIndex(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
  121. /usr/bin/ld: /usr/include/Seq/DistanceMatrix.h:195: undefined reference to `bpp::DistanceMatrix::getNameIndex(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
  122. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::DistanceMatrix::operator()(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
  123. /usr/include/Seq/DistanceMatrix.h:209: undefined reference to `bpp::DistanceMatrix::getNameIndex(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
  124. /usr/bin/ld: /usr/include/Seq/DistanceMatrix.h:210: undefined reference to `bpp::DistanceMatrix::getNameIndex(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
  125. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::unroot()':
  126. /usr/include/Phyl/TreeTemplate.h:230: undefined reference to `bpp::UnrootedTreeException::UnrootedTreeException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Tree const*)'
  127. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplateTools::getLeafId(bpp::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
  128. /usr/include/Phyl/TreeTemplateTools.h:150: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  129. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::IOTree::IOTree()':
  130. /usr/include/Phyl/IOTree.h:64: undefined reference to `VTT for bpp::Newick'
  131. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::Newick::Newick(bool, bool)':
  132. /usr/include/Phyl/Newick.h:109: undefined reference to `vtable for bpp::Newick'
  133. /usr/bin/ld: /usr/include/Phyl/Newick.h:109: undefined reference to `bpp::TreeTools::BOOTSTRAP[abi:cxx11]'
  134. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::Newick::~Newick()':
  135. /usr/include/Phyl/Newick.h:111: undefined reference to `vtable for bpp::Newick'
  136. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::AbstractOMultiTree::~AbstractOMultiTree()':
  137. /usr/include/Phyl/IOTree.h:269: undefined reference to `VTT for bpp::Newick'
  138. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::Sequence::~Sequence()':
  139. /usr/include/Seq/Sequence.h:186: undefined reference to `vtable for bpp::Sequence'
  140. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::SymbolList::~SymbolList()':
  141. /usr/include/Seq/SymbolList.h:138: undefined reference to `VTT for bpp::Sequence'
  142. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::VectorSiteContainer::~VectorSiteContainer()':
  143. /usr/include/Seq/VectorSiteContainer.h:124: undefined reference to `vtable for bpp::VectorSiteContainer'
  144. /usr/bin/ld: /usr/include/Seq/VectorSiteContainer.h:124: undefined reference to `bpp::VectorSiteContainer::clear()'
  145. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::AbstractSequenceContainer::~AbstractSequenceContainer()':
  146. /usr/include/Seq/AbstractSequenceContainer.h:116: undefined reference to `VTT for bpp::VectorSiteContainer'
  147. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `virtual thunk to bpp::VectorSiteContainer::~VectorSiteContainer()':
  148. /usr/include/Seq/VectorSiteContainer.h:124: undefined reference to `vtable for bpp::VectorSiteContainer'
  149. /usr/bin/ld: /usr/include/Seq/VectorSiteContainer.h:124: undefined reference to `bpp::VectorSiteContainer::clear()'
  150. /usr/bin/ld: /usr/include/Seq/VectorSiteContainer.h:124: undefined reference to `VTT for bpp::VectorSiteContainer'
  151. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::Sequence::~Sequence()':
  152. /usr/include/Seq/Sequence.h:186: undefined reference to `vtable for bpp::Sequence'
  153. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::SymbolList::~SymbolList()':
  154. /usr/include/Seq/SymbolList.h:138: undefined reference to `VTT for bpp::Sequence'
  155. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `virtual thunk to bpp::Sequence::~Sequence()':
  156. /usr/include/Seq/Sequence.h:186: undefined reference to `vtable for bpp::Sequence'
  157. /usr/bin/ld: /usr/include/Seq/Sequence.h:186: undefined reference to `VTT for bpp::Sequence'
  158. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::VectorSiteContainer::~VectorSiteContainer()':
  159. /usr/include/Seq/VectorSiteContainer.h:124: undefined reference to `vtable for bpp::VectorSiteContainer'
  160. /usr/bin/ld: /usr/include/Seq/VectorSiteContainer.h:124: undefined reference to `bpp::VectorSiteContainer::clear()'
  161. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::AbstractSequenceContainer::~AbstractSequenceContainer()':
  162. /usr/include/Seq/AbstractSequenceContainer.h:116: undefined reference to `VTT for bpp::VectorSiteContainer'
  163. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `virtual thunk to bpp::VectorSiteContainer::~VectorSiteContainer()':
  164. /usr/include/Seq/VectorSiteContainer.h:124: undefined reference to `vtable for bpp::VectorSiteContainer'
  165. /usr/bin/ld: /usr/include/Seq/VectorSiteContainer.h:124: undefined reference to `bpp::VectorSiteContainer::clear()'
  166. /usr/bin/ld: /usr/include/Seq/VectorSiteContainer.h:124: undefined reference to `VTT for bpp::VectorSiteContainer'
  167. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::MarginalAncestralStateReconstruction::~MarginalAncestralStateReconstruction()':
  168. /usr/include/Phyl/MarginalAncestralStateReconstruction.h:128: undefined reference to `vtable for bpp::MarginalAncestralStateReconstruction'
  169. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `virtual thunk to bpp::MarginalAncestralStateReconstruction::~MarginalAncestralStateReconstruction()':
  170. /usr/include/Phyl/MarginalAncestralStateReconstruction.h:128: undefined reference to `vtable for bpp::MarginalAncestralStateReconstruction'
  171. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::BioNJ::~BioNJ()':
  172. /usr/include/Phyl/BioNJ.h:78: undefined reference to `vtable for bpp::BioNJ'
  173. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::NeighborJoining::~NeighborJoining()':
  174. /usr/include/Phyl/NeighborJoining.h:78: undefined reference to `VTT for bpp::BioNJ'
  175. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `virtual thunk to bpp::BioNJ::~BioNJ()':
  176. /usr/include/Phyl/BioNJ.h:78: undefined reference to `vtable for bpp::BioNJ'
  177. /usr/bin/ld: /usr/include/Phyl/BioNJ.h:78: undefined reference to `VTT for bpp::BioNJ'
  178. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::Node* bpp::TreeTemplateTools::cloneSubtree<bpp::Node>(bpp::Node const&)':
  179. /usr/include/Phyl/TreeTemplateTools.h:580: undefined reference to `bpp::Node::Node(bpp::Node const&)'
  180. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::Node::removeSon(unsigned int)':
  181. /usr/include/Phyl/Node.h:439: undefined reference to `bpp::IndexOutOfBoundsException::IndexOutOfBoundsException(char const*, int, int, int)'
  182. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `void bpp::ApplicationTools::displayResult<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
  183. /usr/include/Utils/ApplicationTools.h:416: undefined reference to `bpp::ApplicationTools::terminalWidth'
  184. /usr/bin/ld: /usr/include/Utils/ApplicationTools.h:416: undefined reference to `bpp::ApplicationTools::terminalSplit'
  185. /usr/bin/ld: /usr/include/Utils/ApplicationTools.h:416: undefined reference to `bpp::TextTools::resizeRight(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, char)'
  186. /usr/bin/ld: /usr/include/Utils/ApplicationTools.h:416: undefined reference to `bpp::ApplicationTools::displayMessage(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  187. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::Node::Node(int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
  188. /usr/include/Phyl/Node.h:155: undefined reference to `vtable for bpp::Node'
  189. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::Node::Node(int)':
  190. /usr/include/Phyl/Node.h:129: undefined reference to `vtable for bpp::Node'
  191. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::MarginalAncestralStateReconstruction::MarginalAncestralStateReconstruction(bpp::DRTreeLikelihood const*)':
  192. /usr/include/Phyl/MarginalAncestralStateReconstruction.h:89: undefined reference to `vtable for bpp::MarginalAncestralStateReconstruction'
  193. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::SubstitutionModelSet::~SubstitutionModelSet()':
  194. /usr/include/Phyl/SubstitutionModelSet.h:206: undefined reference to `vtable for bpp::SubstitutionModelSet'
  195. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::AbstractParametrizable::~AbstractParametrizable()':
  196. /usr/include/NumCalc/AbstractParametrizable.h:72: undefined reference to `VTT for bpp::SubstitutionModelSet'
  197. /usr/bin/ld: /usr/include/NumCalc/AbstractParametrizable.h:72: undefined reference to `bpp::ParameterList::~ParameterList()'
  198. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::getBranchLengths()':
  199. /usr/include/Phyl/TreeTemplate.h:296: undefined reference to `bpp::TreeTemplateTools::getBranchLengths(bpp::Node const&)'
  200. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::getNode(int)':
  201. /usr/include/Phyl/TreeTemplate.h:372: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  202. /usr/bin/ld: /usr/include/Phyl/TreeTemplate.h:371: undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
  203. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::getNode(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
  204. /usr/include/Phyl/TreeTemplate.h:390: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  205. /usr/bin/ld: /usr/include/Phyl/TreeTemplate.h:389: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  206. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `main':
  207. /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:200: undefined reference to `gsl_rng_env_setup'
  208. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:201: undefined reference to `gsl_rng_default'
  209. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:202: undefined reference to `gsl_rng_mt19937'
  210. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:202: undefined reference to `gsl_rng_alloc'
  211. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:203: undefined reference to `gsl_rng_set'
  212. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:815: undefined reference to `gsl_cdf_chisq_Pinv'
  213. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:817: undefined reference to `gsl_cdf_chisq_Pinv'
  214. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:508: undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
  215. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:514: undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
  216. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:564: undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
  217. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:565: undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
  218. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:332: undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
  219. /usr/bin/ld: /tmp/cc1Sy5la.o:/ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:334: more undefined references to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)' follow
  220. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `main':
  221. /ports/build/caps-coev-static-2.0/src/caps2.0_src/caps.cpp:836: undefined reference to `gsl_rng_free'
  222. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::getNode(int) const':
  223. /usr/include/Phyl/TreeTemplate.h:381: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  224. /usr/bin/ld: /usr/include/Phyl/TreeTemplate.h:380: undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
  225. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::rootAt(bpp::Node*)':
  226. /usr/include/Phyl/TreeTemplate.h:407: undefined reference to `bpp::TreeTemplateTools::getPathBetweenAnyTwoNodes(bpp::Node&, bpp::Node&, bool)'
  227. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::getNextId()':
  228. /usr/include/Phyl/TreeTemplate.h:333: undefined reference to `bpp::TreeTools::getMPNUId(bpp::Tree const&, int)'
  229. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::Node::Node()':
  230. /usr/include/Phyl/Node.h:116: undefined reference to `vtable for bpp::Node'
  231. /usr/bin/ld: /tmp/cc1Sy5la.o: in function `bpp::TreeTemplate<bpp::Node>::getNode(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
  232. /usr/include/Phyl/TreeTemplate.h:399: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  233. /usr/bin/ld: /usr/include/Phyl/TreeTemplate.h:398: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  234. /usr/bin/ld: create.o: in function `create_seq(bpp::TreeTemplate<bpp::Node>*&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, unsigned int)':
  235. /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:14: undefined reference to `bpp::GammaDiscreteDistribution::GammaDiscreteDistribution(unsigned int, double, double)'
  236. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:15: undefined reference to `bpp::ProteicAlphabet::ProteicAlphabet()'
  237. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:17: undefined reference to `typeinfo for bpp::ProteicAlphabet'
  238. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:17: undefined reference to `bpp::JTT92::JTT92(bpp::ProteicAlphabet const*)'
  239. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:19: undefined reference to `bpp::FullFrequenciesSet::FullFrequenciesSet(bpp::Alphabet const*, bool)'
  240. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:20: undefined reference to `bpp::FullFrequenciesSet::setFrequencies(std::vector<double, std::allocator<double> > const&)'
  241. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:21: undefined reference to `bpp::SubstitutionModelSetTools::createHomogeneousModelSet(bpp::SubstitutionModel*, bpp::FrequenciesSet*, bpp::Tree const*)'
  242. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:22: undefined reference to `bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator(bpp::SubstitutionModelSet const*, bpp::DiscreteDistribution const*, bpp::Tree const*)'
  243. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:23: undefined reference to `bpp::NonHomogeneousSequenceSimulator::simulate(unsigned int) const'
  244. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:27: undefined reference to `bpp::Sequence::Sequence(bpp::Sequence const&)'
  245. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:28: undefined reference to `bpp::SymbolList::toString[abi:cxx11]() const'
  246. /usr/bin/ld: create.o: in function `bpp::Sequence::~Sequence()':
  247. /usr/include/Seq/Sequence.h:186: undefined reference to `vtable for bpp::Sequence'
  248. /usr/bin/ld: create.o: in function `bpp::SymbolList::~SymbolList()':
  249. /usr/include/Seq/SymbolList.h:138: undefined reference to `VTT for bpp::Sequence'
  250. /usr/bin/ld: create.o: in function `ScoreDist(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
  251. /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:54: undefined reference to `bpp::ProteicAlphabet::ProteicAlphabet()'
  252. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:55: undefined reference to `bpp::GammaDiscreteDistribution::GammaDiscreteDistribution(unsigned int, double, double)'
  253. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:56: undefined reference to `typeinfo for bpp::ProteicAlphabet'
  254. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:57: undefined reference to `bpp::JTT92::JTT92(bpp::ProteicAlphabet const*)'
  255. /usr/bin/ld: create.o: in function `bpp::SequenceContainer::SequenceContainer()':
  256. /usr/include/Seq/SequenceContainer.h:86: undefined reference to `VTT for bpp::VectorSequenceContainer'
  257. /usr/bin/ld: create.o: in function `bpp::VectorSequenceContainer::VectorSequenceContainer(bpp::Alphabet const*)':
  258. /usr/include/Seq/VectorSequenceContainer.h:96: undefined reference to `vtable for bpp::VectorSequenceContainer'
  259. /usr/bin/ld: create.o: in function `ScoreDist(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
  260. /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:65: undefined reference to `bpp::Sequence::Sequence(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Alphabet const*)'
  261. /usr/bin/ld: create.o: in function `bpp::Sequence::~Sequence()':
  262. /usr/include/Seq/Sequence.h:186: undefined reference to `vtable for bpp::Sequence'
  263. /usr/bin/ld: create.o: in function `bpp::SymbolList::~SymbolList()':
  264. /usr/include/Seq/SymbolList.h:138: undefined reference to `VTT for bpp::Sequence'
  265. /usr/bin/ld: create.o: in function `ScoreDist(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
  266. /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:68: undefined reference to `bpp::VectorSiteContainer::VectorSiteContainer(bpp::Alphabet const*)'
  267. /usr/bin/ld: /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:71: undefined reference to `bpp::Sequence::Sequence(bpp::Sequence const&)'
  268. /usr/bin/ld: create.o: in function `bpp::Sequence::~Sequence()':
  269. /usr/include/Seq/Sequence.h:186: undefined reference to `vtable for bpp::Sequence'
  270. /usr/bin/ld: create.o: in function `bpp::SymbolList::~SymbolList()':
  271. /usr/include/Seq/SymbolList.h:138: undefined reference to `VTT for bpp::Sequence'
  272. /usr/bin/ld: create.o: in function `ScoreDist(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
  273. /ports/build/caps-coev-static-2.0/src/caps2.0_src/create.cpp:78: undefined reference to `bpp::SiteContainerTools::changeGapsToUnknownCharacters(bpp::SiteContainer&)'
  274. /usr/bin/ld: create.o: in function `bpp::ParameterList::ParameterList()':
  275. /usr/include/NumCalc/ParameterList.h:75: undefined reference to `vtable for bpp::ParameterList'
  276. /usr/bin/ld: create.o: in function `bpp::DistanceEstimation::DistanceEstimation(bpp::SubstitutionModel*, bpp::DiscreteDistribution*, bpp::SiteContainer const*, unsigned int, bool)':
  277. /usr/include/Phyl/DistanceEstimation.h:347: undefined reference to `bpp::DistanceEstimation::computeMatrix()'
  278. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::removeFather()':
  279. /usr/include/Phyl/NodeTemplate.h:141: undefined reference to `typeinfo for bpp::Node'
  280. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getFather()':
  281. /usr/include/Phyl/NodeTemplate.h:139: undefined reference to `typeinfo for bpp::Node'
  282. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getFather() const':
  283. /usr/include/Phyl/NodeTemplate.h:137: undefined reference to `typeinfo for bpp::Node'
  284. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int) const':
  285. /usr/include/Phyl/NodeTemplate.h:143: undefined reference to `typeinfo for bpp::Node'
  286. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int)':
  287. /usr/include/Phyl/NodeTemplate.h:145: undefined reference to `typeinfo for bpp::Node'
  288. /usr/bin/ld: create.o: in function `bpp::LetterAlphabet::setState(unsigned int, bpp::AlphabetState const&)':
  289. /usr/include/Seq/LetterAlphabet.h:82: undefined reference to `bpp::AbstractAlphabet::setState(unsigned int, bpp::AlphabetState const&)'
  290. /usr/bin/ld: create.o: in function `bpp::LetterAlphabet::registerState(bpp::AlphabetState const&)':
  291. /usr/include/Seq/LetterAlphabet.h:76: undefined reference to `bpp::AbstractAlphabet::registerState(bpp::AlphabetState const&)'
  292. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::getTotalLength()':
  293. /usr/include/Phyl/TreeTemplate.h:304: undefined reference to `bpp::TreeTemplateTools::getTotalLength(bpp::Node const&, bool)'
  294. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::getBranchLengths() const':
  295. /usr/include/Phyl/TreeTemplate.h:166: undefined reference to `bpp::TreeTemplateTools::getBranchLengths(bpp::Node const&)'
  296. /usr/bin/ld: create.o: in function `bpp::MetaOptimizer::clone() const':
  297. /usr/include/NumCalc/MetaOptimizer.h:220: undefined reference to `bpp::MetaOptimizer::MetaOptimizer(bpp::MetaOptimizer const&)'
  298. /usr/bin/ld: create.o: in function `covariant return thunk to bpp::MetaOptimizer::clone() const':
  299. /usr/include/NumCalc/MetaOptimizer.h:220: undefined reference to `bpp::MetaOptimizer::MetaOptimizer(bpp::MetaOptimizer const&)'
  300. /usr/bin/ld: create.o: in function `covariant return thunk to bpp::MetaOptimizer::clone() const':
  301. /usr/include/NumCalc/MetaOptimizer.h:220: undefined reference to `bpp::MetaOptimizer::MetaOptimizer(bpp::MetaOptimizer const&)'
  302. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::getLeavesNames[abi:cxx11]() const':
  303. /usr/include/Phyl/TreeTemplate.h:168: undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
  304. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::getNumberOfNodes() const':
  305. /usr/include/Phyl/TreeTemplate.h:156: undefined reference to `bpp::TreeTemplateTools::getNumberOfNodes(bpp::Node const&)'
  306. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::getNumberOfLeaves() const':
  307. /usr/include/Phyl/TreeTemplate.h:154: undefined reference to `bpp::TreeTemplateTools::getNumberOfLeaves(bpp::Node const&)'
  308. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::getNextId()':
  309. /usr/include/Phyl/TreeTemplate.h:333: undefined reference to `bpp::TreeTools::getMPNUId(bpp::Tree const&, int)'
  310. /usr/bin/ld: /usr/include/Phyl/TreeTemplate.h:333: undefined reference to `bpp::TreeTools::getMPNUId(bpp::Tree const&, int)'
  311. /usr/bin/ld: create.o: in function `bpp::Node::getDistanceToFather() const':
  312. /usr/include/Phyl/Node.h:279: undefined reference to `bpp::NodeException::NodeException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Node const*)'
  313. /usr/bin/ld: create.o: in function `bpp::Node::getName[abi:cxx11]() const':
  314. /usr/include/Phyl/Node.h:232: undefined reference to `bpp::NodeException::NodeException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Node const*)'
  315. /usr/bin/ld: create.o: in function `bpp::LetterAlphabet::charToInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
  316. /usr/include/Seq/LetterAlphabet.h:70: undefined reference to `bpp::BadCharException::BadCharException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Alphabet const*)'
  317. /usr/bin/ld: /usr/include/Seq/LetterAlphabet.h:70: undefined reference to `typeinfo for bpp::BadCharException'
  318. /usr/bin/ld: create.o: in function `bpp::BadCharException::~BadCharException()':
  319. /usr/include/Seq/AlphabetExceptions.h:112: undefined reference to `vtable for bpp::BadCharException'
  320. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int)':
  321. /usr/include/Phyl/NodeTemplate.h:145: undefined reference to `typeinfo for bpp::Node'
  322. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::setBranchLengths(double)':
  323. /usr/include/Phyl/TreeTemplate.h:311: undefined reference to `bpp::TreeTemplateTools::setBranchLengths(bpp::Node&, double)'
  324. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int)':
  325. /usr/include/Phyl/NodeTemplate.h:145: undefined reference to `typeinfo for bpp::Node'
  326. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::setVoidBranchLengths(double)':
  327. /usr/include/Phyl/TreeTemplate.h:319: undefined reference to `bpp::TreeTemplateTools::setVoidBranchLengths(bpp::Node&, double)'
  328. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int)':
  329. /usr/include/Phyl/NodeTemplate.h:145: undefined reference to `typeinfo for bpp::Node'
  330. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::scaleTree(double)':
  331. /usr/include/Phyl/TreeTemplate.h:327: undefined reference to `bpp::TreeTemplateTools::scaleTree(bpp::Node&, double)'
  332. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int)':
  333. /usr/include/Phyl/NodeTemplate.h:145: undefined reference to `typeinfo for bpp::Node'
  334. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::isMultifurcating() const':
  335. /usr/include/Phyl/TreeTemplate.h:286: undefined reference to `bpp::TreeTemplateTools::isMultifurcating(bpp::Node const&)'
  336. /usr/bin/ld: create.o: in function `bpp::Node::setSon(unsigned int, bpp::Node*)':
  337. /usr/include/Phyl/Node.h:432: undefined reference to `bpp::NodeException::NodeException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Node const*)'
  338. /usr/bin/ld: /usr/include/Phyl/Node.h:427: undefined reference to `bpp::IndexOutOfBoundsException::IndexOutOfBoundsException(char const*, int, int, int)'
  339. /usr/bin/ld: create.o: in function `bpp::BadCharException::~BadCharException()':
  340. /usr/include/Seq/AlphabetExceptions.h:112: undefined reference to `vtable for bpp::BadCharException'
  341. /usr/bin/ld: create.o: in function `bpp::Node::~Node()':
  342. /usr/include/Phyl/Node.h:174: undefined reference to `vtable for bpp::Node'
  343. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::NodeTemplate(bpp::NodeTemplate<bpp::SimData> const&)':
  344. /usr/include/Phyl/NodeTemplate.h:115: undefined reference to `bpp::Node::Node(bpp::Node const&)'
  345. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int)':
  346. /usr/include/Phyl/NodeTemplate.h:145: undefined reference to `typeinfo for bpp::Node'
  347. /usr/bin/ld: create.o: in function `bpp::TreeTemplateTools::getLeafId(bpp::Node const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
  348. /usr/include/Phyl/TreeTemplateTools.h:150: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  349. /usr/bin/ld: create.o: in function `bpp::Sequence::~Sequence()':
  350. /usr/include/Seq/Sequence.h:186: undefined reference to `vtable for bpp::Sequence'
  351. /usr/bin/ld: create.o: in function `bpp::SymbolList::~SymbolList()':
  352. /usr/include/Seq/SymbolList.h:138: undefined reference to `VTT for bpp::Sequence'
  353. /usr/bin/ld: create.o: in function `virtual thunk to bpp::Sequence::~Sequence()':
  354. /usr/include/Seq/Sequence.h:186: undefined reference to `vtable for bpp::Sequence'
  355. /usr/bin/ld: /usr/include/Seq/Sequence.h:186: undefined reference to `VTT for bpp::Sequence'
  356. /usr/bin/ld: create.o: in function `bpp::VectorSequenceContainer::~VectorSequenceContainer()':
  357. /usr/include/Seq/VectorSequenceContainer.h:151: undefined reference to `vtable for bpp::VectorSequenceContainer'
  358. /usr/bin/ld: /usr/include/Seq/VectorSequenceContainer.h:151: undefined reference to `bpp::VectorSequenceContainer::clear()'
  359. /usr/bin/ld: create.o: in function `bpp::AbstractSequenceContainer::~AbstractSequenceContainer()':
  360. /usr/include/Seq/AbstractSequenceContainer.h:116: undefined reference to `VTT for bpp::VectorSequenceContainer'
  361. /usr/bin/ld: create.o: in function `virtual thunk to bpp::VectorSequenceContainer::~VectorSequenceContainer()':
  362. /usr/include/Seq/VectorSequenceContainer.h:151: undefined reference to `vtable for bpp::VectorSequenceContainer'
  363. /usr/bin/ld: /usr/include/Seq/VectorSequenceContainer.h:151: undefined reference to `bpp::VectorSequenceContainer::clear()'
  364. /usr/bin/ld: /usr/include/Seq/VectorSequenceContainer.h:151: undefined reference to `VTT for bpp::VectorSequenceContainer'
  365. /usr/bin/ld: create.o: in function `bpp::VectorSequenceContainer::~VectorSequenceContainer()':
  366. /usr/include/Seq/VectorSequenceContainer.h:151: undefined reference to `vtable for bpp::VectorSequenceContainer'
  367. /usr/bin/ld: /usr/include/Seq/VectorSequenceContainer.h:151: undefined reference to `bpp::VectorSequenceContainer::clear()'
  368. /usr/bin/ld: create.o: in function `bpp::AbstractSequenceContainer::~AbstractSequenceContainer()':
  369. /usr/include/Seq/AbstractSequenceContainer.h:116: undefined reference to `VTT for bpp::VectorSequenceContainer'
  370. /usr/bin/ld: create.o: in function `virtual thunk to bpp::VectorSequenceContainer::~VectorSequenceContainer()':
  371. /usr/include/Seq/VectorSequenceContainer.h:151: undefined reference to `vtable for bpp::VectorSequenceContainer'
  372. /usr/bin/ld: /usr/include/Seq/VectorSequenceContainer.h:151: undefined reference to `bpp::VectorSequenceContainer::clear()'
  373. /usr/bin/ld: /usr/include/Seq/VectorSequenceContainer.h:151: undefined reference to `VTT for bpp::VectorSequenceContainer'
  374. /usr/bin/ld: create.o: in function `bpp::PropertyNotFoundException::PropertyNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Node const*)':
  375. /usr/include/Phyl/TreeExceptions.h:129: undefined reference to `bpp::NodeException::NodeException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Node const*)'
  376. /usr/bin/ld: create.o: in function `bpp::DistanceEstimation::~DistanceEstimation()':
  377. /usr/include/Phyl/DistanceEstimation.h:398: undefined reference to `bpp::ParameterList::~ParameterList()'
  378. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int)':
  379. /usr/include/Phyl/NodeTemplate.h:145: undefined reference to `typeinfo for bpp::Node'
  380. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::unroot()':
  381. /usr/include/Phyl/TreeTemplate.h:230: undefined reference to `bpp::UnrootedTreeException::UnrootedTreeException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Tree const*)'
  382. /usr/bin/ld: create.o: in function `bpp::MetaOptimizer::clone() const':
  383. /usr/include/NumCalc/MetaOptimizer.h:220: undefined reference to `bpp::MetaOptimizer::MetaOptimizer(bpp::MetaOptimizer const&)'
  384. /usr/bin/ld: create.o: in function `bpp::DistanceEstimation::DistanceEstimation(bpp::DistanceEstimation const&)':
  385. /usr/include/Phyl/DistanceEstimation.h:365: undefined reference to `bpp::ParameterList::ParameterList(bpp::ParameterList const&)'
  386. /usr/bin/ld: /usr/include/Phyl/DistanceEstimation.h:365: undefined reference to `bpp::ParameterList::~ParameterList()'
  387. /usr/bin/ld: create.o: in function `covariant return thunk to bpp::DistanceEstimation::clone() const':
  388. /usr/include/NumCalc/MetaOptimizer.h:220: undefined reference to `bpp::MetaOptimizer::MetaOptimizer(bpp::MetaOptimizer const&)'
  389. /usr/bin/ld: create.o: in function `covariant return thunk to bpp::DistanceEstimation::clone() const':
  390. /usr/include/Phyl/DistanceEstimation.h:365: undefined reference to `bpp::ParameterList::ParameterList(bpp::ParameterList const&)'
  391. /usr/bin/ld: /usr/include/Phyl/DistanceEstimation.h:365: undefined reference to `bpp::ParameterList::~ParameterList()'
  392. /usr/bin/ld: create.o: in function `bpp::AbstractAlphabet::~AbstractAlphabet()':
  393. /usr/include/Seq/AbstractAlphabet.h:110: undefined reference to `vtable for bpp::AbstractAlphabet'
  394. /usr/bin/ld: create.o: in function `bpp::AbstractAlphabet::~AbstractAlphabet()':
  395. /usr/include/Seq/AbstractAlphabet.h:110: undefined reference to `vtable for bpp::AbstractAlphabet'
  396. /usr/bin/ld: /usr/include/Seq/AbstractAlphabet.h:110: undefined reference to `vtable for bpp::AbstractAlphabet'
  397. /usr/bin/ld: /usr/include/Seq/AbstractAlphabet.h:110: undefined reference to `vtable for bpp::AbstractAlphabet'
  398. /usr/bin/ld: create.o: in function `bpp::Node::addSon(bpp::Node*)':
  399. /usr/include/Phyl/Node.h:418: undefined reference to `bpp::NodeException::NodeException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Node const*)'
  400. /usr/bin/ld: create.o: in function `bpp::Node::removeSon(bpp::Node*)':
  401. /usr/include/Phyl/Node.h:459: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
  402. /usr/bin/ld: create.o: in function `bpp::NonHomogeneousSequenceSimulator::~NonHomogeneousSequenceSimulator()':
  403. /usr/include/Phyl/NonHomogeneousSequenceSimulator.h:142: undefined reference to `vtable for bpp::NonHomogeneousSequenceSimulator'
  404. /usr/bin/ld: create.o: in function `bpp::DetailedSiteSimulator::~DetailedSiteSimulator()':
  405. /usr/include/Phyl/DetailedSiteSimulator.h:216: undefined reference to `VTT for bpp::NonHomogeneousSequenceSimulator'
  406. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int)':
  407. /usr/include/Phyl/NodeTemplate.h:145: undefined reference to `typeinfo for bpp::Node'
  408. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::getBranchLengths()':
  409. /usr/include/Phyl/TreeTemplate.h:296: undefined reference to `bpp::TreeTemplateTools::getBranchLengths(bpp::Node const&)'
  410. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::NodeTemplate(bpp::Node const&)':
  411. /usr/include/Phyl/NodeTemplate.h:107: undefined reference to `bpp::Node::Node(bpp::Node const&)'
  412. /usr/bin/ld: create.o: in function `bpp::DistanceEstimation::DistanceEstimation(bpp::SubstitutionModel*, bpp::DiscreteDistribution*, bpp::SiteContainer const*, unsigned int, bool)':
  413. /usr/include/Phyl/DistanceEstimation.h:344: undefined reference to `bpp::ParameterList::~ParameterList()'
  414. /usr/bin/ld: create.o: in function `bpp::DistanceEstimation::_init()':
  415. /usr/include/Phyl/DistanceEstimation.h:417: undefined reference to `bpp::PseudoNewtonOptimizer::PseudoNewtonOptimizer(bpp::DerivableSecondOrder*)'
  416. /usr/bin/ld: /usr/include/Phyl/DistanceEstimation.h:417: undefined reference to `bpp::MetaOptimizerInfos::IT_TYPE_FULL[abi:cxx11]'
  417. /usr/bin/ld: /usr/include/Phyl/DistanceEstimation.h:418: undefined reference to `bpp::ParameterList::ParameterList(bpp::ParameterList const&)'
  418. /usr/bin/ld: /usr/include/Phyl/DistanceEstimation.h:419: undefined reference to `bpp::ParameterList::addParameters(bpp::ParameterList const&)'
  419. /usr/bin/ld: /usr/include/Phyl/DistanceEstimation.h:420: undefined reference to `bpp::ParameterList::getParameterNames[abi:cxx11]() const'
  420. /usr/bin/ld: /usr/include/Phyl/DistanceEstimation.h:420: undefined reference to `bpp::SimpleMultiDimensions::SimpleMultiDimensions(bpp::Function*)'
  421. /usr/bin/ld: /usr/include/Phyl/DistanceEstimation.h:420: undefined reference to `bpp::MetaOptimizerInfos::IT_TYPE_STEP[abi:cxx11]'
  422. /usr/bin/ld: /usr/include/Phyl/DistanceEstimation.h:421: undefined reference to `bpp::MetaOptimizer::MetaOptimizer(bpp::Function*, bpp::MetaOptimizerInfos*, unsigned int)'
  423. /usr/bin/ld: create.o: in function `bpp::MetaOptimizer::clone() const':
  424. /usr/include/NumCalc/MetaOptimizer.h:220: undefined reference to `bpp::MetaOptimizer::MetaOptimizer(bpp::MetaOptimizer const&)'
  425. /usr/bin/ld: create.o: in function `bpp::DistanceEstimation::_init()':
  426. /usr/include/Phyl/DistanceEstimation.h:418: undefined reference to `bpp::ParameterList::~ParameterList()'
  427. /usr/bin/ld: /usr/include/Phyl/DistanceEstimation.h:418: undefined reference to `bpp::ParameterList::~ParameterList()'
  428. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int) const':
  429. /usr/include/Phyl/NodeTemplate.h:143: undefined reference to `typeinfo for bpp::Node'
  430. /usr/bin/ld: /usr/include/Phyl/NodeTemplate.h:143: undefined reference to `typeinfo for bpp::Node'
  431. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::rootAt(bpp::NodeTemplate<bpp::SimData>*)':
  432. /usr/include/Phyl/TreeTemplate.h:407: undefined reference to `bpp::TreeTemplateTools::getPathBetweenAnyTwoNodes(bpp::Node&, bpp::Node&, bool)'
  433. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::getNextId()':
  434. /usr/include/Phyl/TreeTemplate.h:333: undefined reference to `bpp::TreeTools::getMPNUId(bpp::Tree const&, int)'
  435. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getFather()':
  436. /usr/include/Phyl/NodeTemplate.h:139: undefined reference to `typeinfo for bpp::Node'
  437. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int)':
  438. /usr/include/Phyl/NodeTemplate.h:145: undefined reference to `typeinfo for bpp::Node'
  439. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::getNode(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
  440. /usr/include/Phyl/TreeTemplate.h:390: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  441. /usr/bin/ld: /usr/include/Phyl/TreeTemplate.h:389: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  442. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int)':
  443. /usr/include/Phyl/NodeTemplate.h:145: undefined reference to `typeinfo for bpp::Node'
  444. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::getNode(int)':
  445. /usr/include/Phyl/TreeTemplate.h:372: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  446. /usr/bin/ld: /usr/include/Phyl/TreeTemplate.h:371: undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
  447. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int)':
  448. /usr/include/Phyl/NodeTemplate.h:145: undefined reference to `typeinfo for bpp::Node'
  449. /usr/bin/ld: /usr/include/Phyl/NodeTemplate.h:145: undefined reference to `typeinfo for bpp::Node'
  450. /usr/bin/ld: /usr/include/Phyl/NodeTemplate.h:145: undefined reference to `typeinfo for bpp::Node'
  451. /usr/bin/ld: /usr/include/Phyl/NodeTemplate.h:145: undefined reference to `typeinfo for bpp::Node'
  452. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int) const':
  453. /usr/include/Phyl/NodeTemplate.h:143: undefined reference to `typeinfo for bpp::Node'
  454. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::getNode(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
  455. /usr/include/Phyl/TreeTemplate.h:399: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  456. /usr/bin/ld: /usr/include/Phyl/TreeTemplate.h:398: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  457. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int) const':
  458. /usr/include/Phyl/NodeTemplate.h:143: undefined reference to `typeinfo for bpp::Node'
  459. /usr/bin/ld: create.o: in function `bpp::TreeTemplate<bpp::NodeTemplate<bpp::SimData> >::getNode(int) const':
  460. /usr/include/Phyl/TreeTemplate.h:381: undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
  461. /usr/bin/ld: /usr/include/Phyl/TreeTemplate.h:380: undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
  462. /usr/bin/ld: create.o: in function `bpp::NodeTemplate<bpp::SimData>::getSon(unsigned int) const':
  463. /usr/include/Phyl/NodeTemplate.h:143: undefined reference to `typeinfo for bpp::Node'
  464. /usr/bin/ld: /usr/include/Phyl/NodeTemplate.h:143: undefined reference to `typeinfo for bpp::Node'
  465. /usr/bin/ld: /usr/include/Phyl/NodeTemplate.h:143: undefined reference to `typeinfo for bpp::Node'
  466. /usr/bin/ld: /usr/include/Phyl/NodeTemplate.h:143: undefined reference to `typeinfo for bpp::Node'
  467. /usr/bin/ld: create.o:(.data.rel.ro._ZTIN3bpp14LetterAlphabetE[_ZTIN3bpp14LetterAlphabetE]+0x10): undefined reference to `typeinfo for bpp::AbstractAlphabet'
  468. /usr/bin/ld: create.o:(.data.rel.ro._ZTIN3bpp12NodeTemplateINS_7SimDataEEE[_ZTIN3bpp12NodeTemplateINS_7SimDataEEE]+0x10): undefined reference to `typeinfo for bpp::Node'
  469. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp14LetterAlphabetE[_ZTVN3bpp14LetterAlphabetE]+0x20): undefined reference to `bpp::AbstractAlphabet::getName[abi:cxx11](int) const'
  470. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp14LetterAlphabetE[_ZTVN3bpp14LetterAlphabetE]+0x28): undefined reference to `bpp::AbstractAlphabet::getName(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
  471. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp14LetterAlphabetE[_ZTVN3bpp14LetterAlphabetE]+0x30): undefined reference to `bpp::AbstractAlphabet::isIntInAlphabet(int) const'
  472. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp14LetterAlphabetE[_ZTVN3bpp14LetterAlphabetE]+0x40): undefined reference to `bpp::AbstractAlphabet::getState(int) const'
  473. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp14LetterAlphabetE[_ZTVN3bpp14LetterAlphabetE]+0x48): undefined reference to `bpp::AbstractAlphabet::getState(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
  474. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp14LetterAlphabetE[_ZTVN3bpp14LetterAlphabetE]+0x50): undefined reference to `bpp::AbstractAlphabet::intToChar[abi:cxx11](int) const'
  475. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp14LetterAlphabetE[_ZTVN3bpp14LetterAlphabetE]+0x78): undefined reference to `bpp::AbstractAlphabet::getAlias(int) const'
  476. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp14LetterAlphabetE[_ZTVN3bpp14LetterAlphabetE]+0x80): undefined reference to `bpp::AbstractAlphabet::getAlias(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
  477. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp14LetterAlphabetE[_ZTVN3bpp14LetterAlphabetE]+0x88): undefined reference to `bpp::AbstractAlphabet::getGeneric(std::vector<int, std::allocator<int> > const&) const'
  478. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp14LetterAlphabetE[_ZTVN3bpp14LetterAlphabetE]+0x90): undefined reference to `bpp::AbstractAlphabet::getGeneric(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const'
  479. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp14LetterAlphabetE[_ZTVN3bpp14LetterAlphabetE]+0x98): undefined reference to `bpp::AbstractAlphabet::getSupportedInts() const'
  480. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp14LetterAlphabetE[_ZTVN3bpp14LetterAlphabetE]+0xa0): undefined reference to `bpp::AbstractAlphabet::getSupportedChars[abi:cxx11]() const'
  481. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp14LetterAlphabetE[_ZTVN3bpp14LetterAlphabetE]+0xf8): undefined reference to `bpp::AbstractAlphabet::getStateAt(unsigned int)'
  482. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp14LetterAlphabetE[_ZTVN3bpp14LetterAlphabetE]+0x100): undefined reference to `bpp::AbstractAlphabet::getStateAt(unsigned int) const'
  483. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp12NodeTemplateINS_7SimDataEEE[_ZTVN3bpp12NodeTemplateINS_7SimDataEEE]+0x100): undefined reference to `bpp::Node::swap(unsigned int, unsigned int)'
  484. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp12NodeTemplateINS_7SimDataEEE[_ZTVN3bpp12NodeTemplateINS_7SimDataEEE]+0x108): undefined reference to `bpp::Node::getSonPosition(bpp::Node const*) const'
  485. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp12NodeTemplateINS_7SimDataEEE[_ZTVN3bpp12NodeTemplateINS_7SimDataEEE]+0x1a8): undefined reference to `bpp::Node::hasBootstrapValue() const'
  486. /usr/bin/ld: create.o:(.data.rel.ro._ZTVN3bpp12NodeTemplateINS_7SimDataEEE[_ZTVN3bpp12NodeTemplateINS_7SimDataEEE]+0x1b0): undefined reference to `bpp::Node::getBootstrapValue() const'
  487. /usr/bin/ld: create.o:(.data.rel.local.DW.ref._ZTIN3bpp16BadCharExceptionE[DW.ref._ZTIN3bpp16BadCharExceptionE]+0x0): undefined reference to `typeinfo for bpp::BadCharException'
  488. collect2: error: ld returned 1 exit status
  489. make: *** [Makefile:17: caps] Error 1
  490. =======> ERROR: Building '/ports/packages/
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