Probelm bpp in installation Phyldog: undefined reference to `bpp

[Victoria Moris]

Hello,

I am trying to install Phyldog. For that I needed to install bio ++.
Howe ever I have these error messages "undefined reference to `bpp..."
I do not know if bio++ can cause that.
Let me know.

Thank you for your help.
Best,
Victoria



make
[  2%] Building CXX object src/CMakeFiles/phyldog.dir/Phyldog.cpp.o
[  4%] Building CXX object src/CMakeFiles/phyldog.dir/SpeciesTreeLikelihood.cpp.o
[  7%] Building CXX object src/CMakeFiles/phyldog.dir/SpeciesTreeExploration.cpp.o
[  9%] Building CXX object src/CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o
[ 11%] Building CXX object src/CMakeFiles/phyldog.dir/DLGeneTreeLikelihood.cpp.o
[ 14%] Building CXX object src/CMakeFiles/phyldog.dir/COALGeneTreeLikelihood.cpp.o
[ 16%] Building CXX object src/CMakeFiles/phyldog.dir/GeneTreeLikelihood.cpp.o
[ 19%] Building CXX object src/CMakeFiles/phyldog.dir/COALTools.cpp.o
[ 21%] Building CXX object src/CMakeFiles/phyldog.dir/GenericTreeExplorationAlgorithms.cpp.o
[ 23%] Building CXX object src/CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o
[ 26%] Building CXX object src/CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o
[ 28%] Building CXX object src/CMakeFiles/phyldog.dir/ClientComputingGeneLikelihoods.cpp.o
[ 30%] Building CXX object src/CMakeFiles/phyldog.dir/LikelihoodEvaluator.cpp.o
[ 33%] Linking CXX executable ../bin/phyldog
CMakeFiles/phyldog.dir/Phyldog.cpp.o: In function `bpp::TreeTemplate<bpp::Node>::getLeavesNames() const':
Phyldog.cpp:(.text._ZNK3bpp12TreeTemplateINS_4NodeEE14getLeavesNamesEv[_ZNK3bpp12TreeTemplateINS_4NodeEE14getLeavesNamesEv]+0x1d): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
CMakeFiles/phyldog.dir/Phyldog.cpp.o: In function `bpp::AbstractParametrizable::setParameterValue(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, double)':
Phyldog.cpp:(.text._ZN3bpp22AbstractParametrizable17setParameterValueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd[_ZN3bpp22AbstractParametrizable17setParameterValueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd]+0x4f): undefined reference to `bpp::ParameterList::setParameterValue(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, double)'
Phyldog.cpp:(.text._ZN3bpp22AbstractParametrizable17setParameterValueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd[_ZN3bpp22AbstractParametrizable17setParameterValueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd]+0x8c): undefined reference to `bpp::ParameterList::subList(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/Phyldog.cpp.o: In function `bpp::AbstractParametrizable::getParameter(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
Phyldog.cpp:(.text._ZNK3bpp22AbstractParametrizable12getParameterERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNK3bpp22AbstractParametrizable12getParameterERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x30): undefined reference to `bpp::ParameterList::getParameter(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/Phyldog.cpp.o: In function `bpp::AbstractParametrizable::hasParameter(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
Phyldog.cpp:(.text._ZNK3bpp22AbstractParametrizable12hasParameterERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNK3bpp22AbstractParametrizable12hasParameterERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x2f): undefined reference to `bpp::ParameterList::hasParameter(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/Phyldog.cpp.o: In function `bpp::TreeTemplate<bpp::Node>::getLeafId(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
Phyldog.cpp:(.text._ZNK3bpp12TreeTemplateINS_4NodeEE9getLeafIdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNK3bpp12TreeTemplateINS_4NodeEE9getLeafIdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x86): 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&)'
CMakeFiles/phyldog.dir/Phyldog.cpp.o: In function `bpp::TreeTemplate<bpp::Node>::unroot()':
Phyldog.cpp:(.text._ZN3bpp12TreeTemplateINS_4NodeEE6unrootEv[_ZN3bpp12TreeTemplateINS_4NodeEE6unrootEv]+0x2c7): undefined reference to `bpp::UnrootedTreeException::UnrootedTreeException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Tree const*)'
CMakeFiles/phyldog.dir/Phyldog.cpp.o: In function `main':
Phyldog.cpp:(.text.startup+0xcf): undefined reference to `bpp::AttributesTools::parseOptions[abi:cxx11](int, char**)'
Phyldog.cpp:(.text.startup+0x129): 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, int)'
Phyldog.cpp:(.text.startup+0x1c7): 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, int)'
Phyldog.cpp:(.text.startup+0xa7e): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
Phyldog.cpp:(.text.startup+0x10e0): undefined reference to `bpp::ApplicationTools::displayTime(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/Phyldog.cpp.o: In function `bpp::TreeTemplate<bpp::Node>::getNode(int, bool) const':
Phyldog.cpp:(.text._ZNK3bpp12TreeTemplateINS_4NodeEE7getNodeEib[_ZNK3bpp12TreeTemplateINS_4NodeEE7getNodeEib]+0xc8): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
Phyldog.cpp:(.text._ZNK3bpp12TreeTemplateINS_4NodeEE7getNodeEib[_ZNK3bpp12TreeTemplateINS_4NodeEE7getNodeEib]+0x167): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
Phyldog.cpp:(.text._ZNK3bpp12TreeTemplateINS_4NodeEE7getNodeEib[_ZNK3bpp12TreeTemplateINS_4NodeEE7getNodeEib]+0x191): 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&)'
Phyldog.cpp:(.text._ZNK3bpp12TreeTemplateINS_4NodeEE7getNodeEib[_ZNK3bpp12TreeTemplateINS_4NodeEE7getNodeEib]+0x20b): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
Phyldog.cpp:(.text._ZNK3bpp12TreeTemplateINS_4NodeEE7getNodeEib[_ZNK3bpp12TreeTemplateINS_4NodeEE7getNodeEib]+0x235): 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&)'
CMakeFiles/phyldog.dir/Phyldog.cpp.o: In function `bpp::TreeTemplate<bpp::Node>::getNode(int, bool)':
Phyldog.cpp:(.text._ZN3bpp12TreeTemplateINS_4NodeEE7getNodeEib[_ZN3bpp12TreeTemplateINS_4NodeEE7getNodeEib]+0xc8): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
Phyldog.cpp:(.text._ZN3bpp12TreeTemplateINS_4NodeEE7getNodeEib[_ZN3bpp12TreeTemplateINS_4NodeEE7getNodeEib]+0x167): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
Phyldog.cpp:(.text._ZN3bpp12TreeTemplateINS_4NodeEE7getNodeEib[_ZN3bpp12TreeTemplateINS_4NodeEE7getNodeEib]+0x191): 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&)'
Phyldog.cpp:(.text._ZN3bpp12TreeTemplateINS_4NodeEE7getNodeEib[_ZN3bpp12TreeTemplateINS_4NodeEE7getNodeEib]+0x20b): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
Phyldog.cpp:(.text._ZN3bpp12TreeTemplateINS_4NodeEE7getNodeEib[_ZN3bpp12TreeTemplateINS_4NodeEE7getNodeEib]+0x235): 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&)'
CMakeFiles/phyldog.dir/Phyldog.cpp.o: In function `bpp::TreeTemplate<bpp::Node>::getNode(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
Phyldog.cpp:(.text._ZN3bpp12TreeTemplateINS_4NodeEE7getNodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN3bpp12TreeTemplateINS_4NodeEE7getNodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0xd0): 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&)'
Phyldog.cpp:(.text._ZN3bpp12TreeTemplateINS_4NodeEE7getNodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN3bpp12TreeTemplateINS_4NodeEE7getNodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x160): 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&)'
CMakeFiles/phyldog.dir/Phyldog.cpp.o: In function `bpp::TreeTemplate<bpp::Node>::getNode(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
Phyldog.cpp:(.text._ZNK3bpp12TreeTemplateINS_4NodeEE7getNodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNK3bpp12TreeTemplateINS_4NodeEE7getNodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0xd0): 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&)'
Phyldog.cpp:(.text._ZNK3bpp12TreeTemplateINS_4NodeEE7getNodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNK3bpp12TreeTemplateINS_4NodeEE7getNodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x160): 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&)'
CMakeFiles/phyldog.dir/Phyldog.cpp.o:(.rodata._ZTCN3bpp21SpeciesTreeLikelihoodE8_NS_22AbstractParametrizableE[_ZTVN3bpp21SpeciesTreeLikelihoodE]+0xf0): undefined reference to `bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/Phyldog.cpp.o:(.rodata._ZTCN3bpp21SpeciesTreeLikelihoodE8_NS_22AbstractParametrizableE[_ZTVN3bpp21SpeciesTreeLikelihoodE]+0x100): undefined reference to `bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/Phyldog.cpp.o:(.rodata._ZTCN3bpp21SpeciesTreeLikelihoodE8_NS_22AbstractParametrizableE[_ZTVN3bpp21SpeciesTreeLikelihoodE]+0x1f8): undefined reference to `virtual thunk to bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/Phyldog.cpp.o:(.rodata._ZTCN3bpp21SpeciesTreeLikelihoodE8_NS_22AbstractParametrizableE[_ZTVN3bpp21SpeciesTreeLikelihoodE]+0x208): undefined reference to `virtual thunk to bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/Phyldog.cpp.o:(.rodata._ZTVN3bpp21SpeciesTreeLikelihoodE[_ZTVN3bpp21SpeciesTreeLikelihoodE]+0xf0): undefined reference to `virtual thunk to bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/Phyldog.cpp.o:(.rodata._ZTVN3bpp21SpeciesTreeLikelihoodE[_ZTVN3bpp21SpeciesTreeLikelihoodE]+0x100): undefined reference to `virtual thunk to bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/Phyldog.cpp.o:(.rodata._ZTVN3bpp21SpeciesTreeLikelihoodE[_ZTVN3bpp21SpeciesTreeLikelihoodE]+0x220): undefined reference to `bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/Phyldog.cpp.o:(.rodata._ZTVN3bpp21SpeciesTreeLikelihoodE[_ZTVN3bpp21SpeciesTreeLikelihoodE]+0x230): undefined reference to `bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/SpeciesTreeLikelihood.cpp.o: In function `bpp::TreeTemplate<bpp::Node>::getNode(int, bool) [clone .constprop.1154]':
SpeciesTreeLikelihood.cpp:(.text+0x80b): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
SpeciesTreeLikelihood.cpp:(.text+0x828): 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&)'
CMakeFiles/phyldog.dir/SpeciesTreeLikelihood.cpp.o: In function `bpp::SpeciesTreeLikelihood::initialize()':
SpeciesTreeLikelihood.cpp:(.text+0xae9): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0xbc8): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0xc87): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0xdf3): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0xe90): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0xedc): undefined reference to `bpp::ApplicationTools::displayMessage(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
SpeciesTreeLikelihood.cpp:(.text+0x11b2): undefined reference to `bpp::ApplicationTools::displayTime(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/SpeciesTreeLikelihood.cpp.o: In function `bpp::SpeciesTreeLikelihood::parseOptions()':
SpeciesTreeLikelihood.cpp:(.text+0x1ab8): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x1bd3): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x1cf9): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x1f76): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x20db): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
SpeciesTreeLikelihood.cpp:(.text+0x21ff): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x22cd): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x2498): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x2633): undefined reference to `bpp::TreeTemplateTools::getRandomTree(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> > > >&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x267e): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x2772): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x288d): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x298f): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x2a34): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x2b54): undefined reference to `bpp::ApplicationTools::getIntParameter(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> > > > >&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, int)'
SpeciesTreeLikelihood.cpp:(.text+0x2bf9): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x2d9f): undefined reference to `bpp::ApplicationTools::getIntParameter(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> > > > >&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, int)'
SpeciesTreeLikelihood.cpp:(.text+0x2e83): undefined reference to `bpp::ApplicationTools::getIntParameter(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> > > > >&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, int)'
SpeciesTreeLikelihood.cpp:(.text+0x32d0): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x3468): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x379d): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x3a7f): undefined reference to `bpp::StringTokenizer::StringTokenizer(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)'
SpeciesTreeLikelihood.cpp:(.text+0x3bb7): undefined reference to `bpp::TextTools::toDouble(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char, char)'
SpeciesTreeLikelihood.cpp:(.text+0x3e58): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
SpeciesTreeLikelihood.cpp:(.text+0x4ae7): undefined reference to `bpp::TreeTemplateTools::getRandomTree(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> > > >&, bool)'
CMakeFiles/phyldog.dir/SpeciesTreeLikelihood.cpp.o: In function `bpp::SpeciesTreeLikelihood::outputEndResults()':
SpeciesTreeLikelihood.cpp:(.text+0x4f33): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x520f): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x52e0): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x5357): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x55db): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x568e): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x5705): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x57f0): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x58d8): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x59a7): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x5a5c): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis(bpp::TreeTemplate<bpp::Node> const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
SpeciesTreeLikelihood.cpp:(.text+0x5b11): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x5dd9): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x5e9d): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x5f14): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
CMakeFiles/phyldog.dir/SpeciesTreeLikelihood.cpp.o: In function `bpp::SpeciesTreeLikelihood::MLSearchButNotOptimizeTopology()':
SpeciesTreeLikelihood.cpp:(.text+0x65a5): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x67e0): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x684e): undefined reference to `bpp::ApplicationTools::displayTime(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
SpeciesTreeLikelihood.cpp:(.text+0x6978): undefined reference to `bpp::ApplicationTools::displayTime(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/SpeciesTreeLikelihood.cpp.o: In function `bpp::SpeciesTreeLikelihood::outputALRTTree()':
SpeciesTreeLikelihood.cpp:(.text+0x6e4e): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
CMakeFiles/phyldog.dir/SpeciesTreeLikelihood.cpp.o: In function `bpp::SpeciesTreeLikelihood::MLSearchAndOptimizeTopology()':
SpeciesTreeLikelihood.cpp:(.text+0x71f5): 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, int)'
SpeciesTreeLikelihood.cpp:(.text+0x72b2): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x75bf): undefined reference to `bpp::ApplicationTools::displayTime(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
SpeciesTreeLikelihood.cpp:(.text+0x7660): undefined reference to `bpp::ApplicationTools::displayTime(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
SpeciesTreeLikelihood.cpp:(.text+0x78e0): undefined reference to `bpp::ApplicationTools::displayTime(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
SpeciesTreeLikelihood.cpp:(.text+0x794d): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x7d48): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x7f92): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x8012): undefined reference to `bpp::ApplicationTools::displayTime(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
SpeciesTreeLikelihood.cpp:(.text+0x8345): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeLikelihood.cpp:(.text+0x8410): undefined reference to `bpp::ApplicationTools::displayTime(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
SpeciesTreeLikelihood.cpp:(.text+0x85a2): undefined reference to `bpp::ApplicationTools::displayTime(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
SpeciesTreeLikelihood.cpp:(.text+0x88de): undefined reference to `bpp::ApplicationTools::displayTime(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
SpeciesTreeLikelihood.cpp:(.text+0x8b34): undefined reference to `bpp::ApplicationTools::displayTime(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/SpeciesTreeLikelihood.cpp.o: In function `bpp::Number<double>::toString() const':
SpeciesTreeLikelihood.cpp:(.text._ZNK3bpp6NumberIdE8toStringEv[_ZNK3bpp6NumberIdE8toStringEv]+0x23): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
CMakeFiles/phyldog.dir/SpeciesTreeLikelihood.cpp.o: In function `bpp::Newick::Newick(bool, bool)':
SpeciesTreeLikelihood.cpp:(.text._ZN3bpp6NewickC1Ebb[_ZN3bpp6NewickC1Ebb]+0x1f5): undefined reference to `bpp::TreeTools::BOOTSTRAP[abi:cxx11]'
SpeciesTreeLikelihood.cpp:(.text._ZN3bpp6NewickC1Ebb[_ZN3bpp6NewickC1Ebb]+0x221): undefined reference to `bpp::TreeTools::BOOTSTRAP[abi:cxx11]'
CMakeFiles/phyldog.dir/SpeciesTreeLikelihood.cpp.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&)':
SpeciesTreeLikelihood.cpp:(.text._ZN3bpp16ApplicationTools13displayResultINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RKT_[_ZN3bpp16ApplicationTools13displayResultINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RKT_]+0x153): undefined reference to `bpp::TextTools::resizeRight(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, char)'
SpeciesTreeLikelihood.cpp:(.text._ZN3bpp16ApplicationTools13displayResultINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RKT_[_ZN3bpp16ApplicationTools13displayResultINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RKT_]+0x189): undefined reference to `bpp::ApplicationTools::displayMessage(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/SpeciesTreeExploration.cpp.o: In function `outputNNIAndRootLks(std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, 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> >&)':
SpeciesTreeExploration.cpp:(.text+0x2dc): 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, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
SpeciesTreeExploration.cpp:(.text+0x3bd): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
SpeciesTreeExploration.cpp:(.text+0x3dd): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
CMakeFiles/phyldog.dir/SpeciesTreeExploration.cpp.o: In function `inputNNIAndRootLks(std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, 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> >&)':
SpeciesTreeExploration.cpp:(.text+0x60c): 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, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
SpeciesTreeExploration.cpp:(.text+0x805): undefined reference to `bpp::StringTokenizer::StringTokenizer(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)'
SpeciesTreeExploration.cpp:(.text+0x908): undefined reference to `bpp::TextTools::toDouble(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char, char)'
SpeciesTreeExploration.cpp:(.text+0x97f): undefined reference to `bpp::TextTools::toDouble(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char, char)'
CMakeFiles/phyldog.dir/SpeciesTreeExploration.cpp.o: In function `computeSpeciesTreeLikelihood(boost::mpi::communicator const&, unsigned int&, bool, double&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<double, std::allocator<double> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, bool, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, 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, int> > >, bpp::TreeTemplate<bpp::Node>&, unsigned int)':
SpeciesTreeExploration.cpp:(.text+0x1fce): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
CMakeFiles/phyldog.dir/SpeciesTreeExploration.cpp.o: In function `computeSpeciesTreeLikelihoodWhileOptimizingDuplicationAndLossRates(boost::mpi::communicator const&, unsigned int&, bool, double&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<double, std::allocator<double> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, bool, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, 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, int> > >, bpp::TreeTemplate<bpp::Node>&, double&, unsigned int)':
SpeciesTreeExploration.cpp:(.text+0x2573): undefined reference to `bpp::ApplicationTools::displayTime(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/SpeciesTreeExploration.cpp.o: In function `fastTryAllPossibleReRootingsAndMakeBestOne(boost::mpi::communicator const&, bpp::TreeTemplate<bpp::Node>*&, bpp::TreeTemplate<bpp::Node>*&, unsigned int&, unsigned int&, bool, int, double&, double&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<double, std::allocator<double> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, bool, unsigned int&, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, 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, int> > >, bool, unsigned int)':
SpeciesTreeExploration.cpp:(.text+0x2eb0): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeExploration.cpp:(.text+0x3381): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeExploration.cpp:(.text+0x33c9): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
CMakeFiles/phyldog.dir/SpeciesTreeExploration.cpp.o: In function `fastTryAllPossibleSPRs(boost::mpi::communicator const&, bpp::TreeTemplate<bpp::Node>*&, bpp::TreeTemplate<bpp::Node>*&, unsigned int&, unsigned int&, bool, int, double&, double&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<double, std::allocator<double> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, bool, unsigned int&, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, 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, int> > >, int, bool, unsigned int, bool, 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> > > >)':
SpeciesTreeExploration.cpp:(.text+0x3dd3): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeExploration.cpp:(.text+0x4308): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeExploration.cpp:(.text+0x4427): undefined reference to `bpp::ApplicationTools::displayTime(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/SpeciesTreeExploration.cpp.o: In function `localOptimizationWithNNIsAndReRootings(boost::mpi::communicator const&, bpp::TreeTemplate<bpp::Node>*&, bpp::TreeTemplate<bpp::Node>*&, unsigned int&, unsigned int&, bool&, int, double&, double&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<unsigned int, std::allocator<unsigned int> >&, std::vector<double, std::allocator<double> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, bool, unsigned int&, unsigned int, unsigned long&, unsigned long&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, 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, double> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, 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, int> > >, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, unsigned int, bool, 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> > > >)':
SpeciesTreeExploration.cpp:(.text+0x53fe): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
SpeciesTreeExploration.cpp:(.text+0x5634): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `bpp::Node::getSon(unsigned long) [clone .constprop.1380]':
ReconciliationTools.cpp:(.text+0x50b): undefined reference to `bpp::IndexOutOfBoundsException::IndexOutOfBoundsException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, unsigned long, unsigned long)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `bpp::Node::getSon(unsigned long) [clone .constprop.1381]':
ReconciliationTools.cpp:(.text+0x606): undefined reference to `bpp::IndexOutOfBoundsException::IndexOutOfBoundsException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, unsigned long, unsigned long)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `getModelFromOptions(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> > > > >, bpp::Alphabet*, bpp::VectorSiteContainer*, bool&)':
ReconciliationTools.cpp:(.text+0x2811): undefined reference to `bpp::PhylogeneticsApplicationTools::getSubstitutionModel(bpp::Alphabet const*, bpp::GeneticCode const*, 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> > const&, bool, bool, int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `getRateDistributionFromOptions(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> > > > >, bpp::SubstitutionModel*, bool&)':
ReconciliationTools.cpp:(.text+0x2952): 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)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `getAlphabetFromOptions(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&)':
ReconciliationTools.cpp:(.text+0x29f0): 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, int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `cleanVectorOfOptions(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> > > >&, bool)':
ReconciliationTools.cpp:(.text+0x3ee0): undefined reference to `bpp::TextTools::removeWhiteSpaces(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `getSequencesFromOptions(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> > > > >, bpp::Alphabet*, bool&)':
ReconciliationTools.cpp:(.text+0x4896): 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, int)'
ReconciliationTools.cpp:(.text+0x48f8): undefined reference to `bpp::FileTools::fileExists(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ReconciliationTools.cpp:(.text+0x49d0): undefined reference to `bpp::SequenceApplicationTools::getSiteContainer(bpp::Alphabet 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&, bool, bool, int)'
ReconciliationTools.cpp:(.text+0x4a45): undefined reference to `bpp::TextTools::removeSurroundingWhiteSpaces(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ReconciliationTools.cpp:(.text+0x4d08): undefined reference to `bpp::ApplicationTools::getIntParameter(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> > > > >&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, int)'
ReconciliationTools.cpp:(.text+0x51df): 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, int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `removeUselessSequencesFromAlignment(bpp::TreeTemplate<bpp::Node> const*, bpp::VectorSiteContainer*, bool&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::deque<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::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::deque<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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
ReconciliationTools.cpp:(.text+0x55f6): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `getCorrespondanceSequenceSpeciesFromOptions(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::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::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::deque<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::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::deque<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> > > > > > >&)':
ReconciliationTools.cpp:(.text+0x6377): 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, int)'
ReconciliationTools.cpp:(.text+0x645f): undefined reference to `bpp::FileTools::fileExists(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ReconciliationTools.cpp:(.text+0x658c): undefined reference to `bpp::StringTokenizer::StringTokenizer(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)'
ReconciliationTools.cpp:(.text+0x6671): undefined reference to `bpp::StringTokenizer::StringTokenizer(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)'
ReconciliationTools.cpp:(.text+0x67f2): undefined reference to `bpp::TextTools::removeSurroundingWhiteSpaces(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ReconciliationTools.cpp:(.text+0x6845): undefined reference to `bpp::TextTools::removeSurroundingWhiteSpaces(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ReconciliationTools.cpp:(.text+0x6f3c): undefined reference to `bpp::TextTools::removeSurroundingWhiteSpaces(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ReconciliationTools.cpp:(.text+0x70c3): undefined reference to `bpp::TextTools::removeSurroundingWhiteSpaces(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `bpp::TreeTemplate<bpp::Node>::getNode(int, bool) [clone .constprop.1340]':
ReconciliationTools.cpp:(.text+0x76eb): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
ReconciliationTools.cpp:(.text+0x7708): 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&)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `annotateGeneTreeWithDuplicationEvents(bpp::TreeTemplate<bpp::Node>&, bpp::TreeTemplate<bpp::Node>&, bpp::Node*, 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::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, 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, int> > >)':
ReconciliationTools.cpp:(.text+0x782d): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
ReconciliationTools.cpp:(.text+0x7aad): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
ReconciliationTools.cpp:(.text+0x7b2e): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
ReconciliationTools.cpp:(.text+0x7c3b): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
ReconciliationTools.cpp:(.text+0x7d2f): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
ReconciliationTools.cpp:(.text+0x7e1d): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `resetLossesAndDuplications(bpp::TreeTemplate<bpp::Node>&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)':
ReconciliationTools.cpp:(.text+0x84ab): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `resetLossesDuplicationsSpeciations(bpp::TreeTemplate<bpp::Node>&, std::vector<int, std::allocator<int> >&, std::vector<double, std::allocator<double> >&, std::vector<int, std::allocator<int> >&, std::vector<double, std::allocator<double> >&, std::vector<int, std::allocator<int> >&)':
ReconciliationTools.cpp:(.text+0x8d9a): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o:ReconciliationTools.cpp:(.text+0x97ce): more undefined references to `bpp::TextTools::toString[abi:cxx11](int)' follow
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `annotateGeneTreeWithScoredDuplicationEvents(bpp::TreeTemplate<bpp::Node>&, bpp::TreeTemplate<bpp::Node>&, bpp::Node*, 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::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, 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, int> > >)':
ReconciliationTools.cpp:(.text+0xd3fa): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
ReconciliationTools.cpp:(.text+0xd47b): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
ReconciliationTools.cpp:(.text+0xd58b): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
ReconciliationTools.cpp:(.text+0xd67f): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
ReconciliationTools.cpp:(.text+0xd76e): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `qualityControlGeneTree(bpp::TreeTemplate<bpp::Node>*, bpp::VectorSiteContainer*, bool&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
ReconciliationTools.cpp:(.text+0xed2e): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `setNDProperty(bpp::TreeTemplate<bpp::Node>*)':
ReconciliationTools.cpp:(.text+0xf3e9): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `recoverDuplicationsAndLosses(bpp::TreeTemplate<bpp::Node>*, bpp::TreeTemplate<bpp::Node>*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
ReconciliationTools.cpp:(.text+0xf8ca): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
ReconciliationTools.cpp:(.text+0xf971): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
ReconciliationTools.cpp:(.text+0xf9f4): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
ReconciliationTools.cpp:(.text+0xfb2e): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
ReconciliationTools.cpp:(.text+0xfdb9): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
ReconciliationTools.cpp:(.text+0x10166): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
ReconciliationTools.cpp:(.text+0x1030e): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
ReconciliationTools.cpp:(.text+0x104cb): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `recoverOrthologsAndParalogs(bpp::TreeTemplate<bpp::Node>*, bpp::TreeTemplate<bpp::Node>*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
ReconciliationTools.cpp:(.text+0x110fa): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
ReconciliationTools.cpp:(.text+0x111a1): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
ReconciliationTools.cpp:(.text+0x11224): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
ReconciliationTools.cpp:(.text+0x114ce): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
ReconciliationTools.cpp:(.text+0x11650): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
ReconciliationTools.cpp:(.text+0x11a76): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
ReconciliationTools.cpp:(.text+0x11bf8): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `getTreeFromOptions(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> > > > >, bpp::Alphabet*, bpp::VectorSiteContainer*, bpp::SubstitutionModel*, bpp::DiscreteDistribution*, bool&)':
ReconciliationTools.cpp:(.text+0x12c72): 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, int)'
ReconciliationTools.cpp:(.text+0x12d24): 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, int)'
ReconciliationTools.cpp:(.text+0x12e42): 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, int)'
ReconciliationTools.cpp:(.text+0x12ecd): undefined reference to `bpp::FileTools::fileExists(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `findMLReconciliationDR(bpp::TreeTemplate<bpp::Node>*, bpp::TreeTemplate<bpp::Node>*, 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::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, 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, int> > >, std::vector<double, std::allocator<double> >, std::vector<double, std::allocator<double> >, int&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::set<int, std::less<int>, std::allocator<int> >&, bool)':
ReconciliationTools.cpp:(.text+0x181f3): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `writeReconciledGeneTree(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> > > > >, bpp::TreeTemplate<bpp::Node>*, bpp::TreeTemplate<bpp::Node>*, 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)':
ReconciliationTools.cpp:(.text+0x1893a): 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, int)'
ReconciliationTools.cpp:(.text+0x189f0): 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, int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `outputNumbersOfEventsPerFamilyPerSpecies(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> > > > >, bpp::TreeTemplate<bpp::Node>*, bpp::TreeTemplate<bpp::Node>*, 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)':
ReconciliationTools.cpp:(.text+0x18f01): 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, int)'
ReconciliationTools.cpp:(.text+0x18fb7): 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, int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `outputOrthologousAndParalogousGenes(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> > > > >, bpp::TreeTemplate<bpp::Node>*, bpp::TreeTemplate<bpp::Node>*, 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)':
ReconciliationTools.cpp:(.text+0x19541): 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, int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o:ReconciliationTools.cpp:(.text+0x195f7): more undefined references 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, int)' follow
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `extractSubVectorsWithCompletelySequencedLineages(std::vector<int, std::allocator<int> > const&, std::vector<int, std::allocator<int> > const&, std::vector<int, std::allocator<int> > const&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, 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, int> > > const&, bpp::TreeTemplate<bpp::Node> const&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&)':
ReconciliationTools.cpp:(.text+0x1a097): 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&)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `alterLineageCountsWithCoverages(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, 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, int> > > const&, bpp::TreeTemplate<bpp::Node> const&, bool)':
ReconciliationTools.cpp:(.text+0x1b1a4): 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&)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `generateListOfOptionsPerClient(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> > > >, int, std::vector<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::allocator<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<unsigned int, std::allocator<unsigned int> >&)':
ReconciliationTools.cpp:(.text+0x1b671): undefined reference to `bpp::TextTools::hasSubstring(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&)'
ReconciliationTools.cpp:(.text+0x1b718): undefined reference to `bpp::TextTools::toDouble(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char, char)'
ReconciliationTools.cpp:(.text+0x1b889): undefined reference to `bpp::StringTokenizer::StringTokenizer(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)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `nodeToParenthesisWithIntNodeValues(bpp::Tree const&, int, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
ReconciliationTools.cpp:(.text+0x1e3a7): undefined reference to `bpp::TreeTools::BOOTSTRAP[abi:cxx11]'
ReconciliationTools.cpp:(.text+0x1e43f): undefined reference to `bpp::TreeTools::BOOTSTRAP[abi:cxx11]'
ReconciliationTools.cpp:(.text+0x1e501): undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `treeToParenthesisWithIntNodeValues(bpp::Tree const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
ReconciliationTools.cpp:(.text+0x1e78e): undefined reference to `bpp::TreeTools::BOOTSTRAP[abi:cxx11]'
ReconciliationTools.cpp:(.text+0x1e9ae): undefined reference to `bpp::TreeTools::BOOTSTRAP[abi:cxx11]'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `nodeToParenthesisWithDoubleNodeValues(bpp::Tree const&, int, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
ReconciliationTools.cpp:(.text+0x1ed7f): undefined reference to `bpp::TreeTools::BOOTSTRAP[abi:cxx11]'
ReconciliationTools.cpp:(.text+0x1edf2): undefined reference to `bpp::TreeTools::BOOTSTRAP[abi:cxx11]'
ReconciliationTools.cpp:(.text+0x1eeeb): undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `treeToParenthesisWithDoubleNodeValues(bpp::Tree const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
ReconciliationTools.cpp:(.text+0x1f13e): undefined reference to `bpp::TreeTools::BOOTSTRAP[abi:cxx11]'
ReconciliationTools.cpp:(.text+0x1f35e): undefined reference to `bpp::TreeTools::BOOTSTRAP[abi:cxx11]'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `bpp::Number<int>::toString() const':
ReconciliationTools.cpp:(.text._ZNK3bpp6NumberIiE8toStringEv[_ZNK3bpp6NumberIiE8toStringEv]+0x1c): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.o: In function `bpp::Node::getSon(unsigned long)':
ReconciliationTools.cpp:(.text._ZN3bpp4Node6getSonEm[_ZN3bpp4Node6getSonEm]+0x8b): undefined reference to `bpp::IndexOutOfBoundsException::IndexOutOfBoundsException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, unsigned long, unsigned long)'
CMakeFiles/phyldog.dir/ReconciliationTools.cpp.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*)':
ReconciliationTools.cpp:(.text._ZN3bpp25PropertyNotFoundExceptionC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_PKNS_4NodeE[_ZN3bpp25PropertyNotFoundExceptionC5ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_PKNS_4NodeE]+0x63): undefined reference to `bpp::NodePException::NodePException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Node const*)'
CMakeFiles/phyldog.dir/DLGeneTreeLikelihood.cpp.o: In function `DLGeneTreeLikelihood::print() const':
DLGeneTreeLikelihood.cpp:(.text+0x471): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
DLGeneTreeLikelihood.cpp:(.text+0x4cd): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
DLGeneTreeLikelihood.cpp:(.text+0x531): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
CMakeFiles/phyldog.dir/DLGeneTreeLikelihood.cpp.o: In function `bpp::TreeTemplate<bpp::Node>::getNode(int, bool) [clone .constprop.1227]':
DLGeneTreeLikelihood.cpp:(.text+0x281b): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
DLGeneTreeLikelihood.cpp:(.text+0x2838): 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&)'
CMakeFiles/phyldog.dir/DLGeneTreeLikelihood.cpp.o: In function `DLGeneTreeLikelihood::refineGeneTreeNNIs(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> > > > >, unsigned int)':
DLGeneTreeLikelihood.cpp:(.text+0x3101): 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, int)'
DLGeneTreeLikelihood.cpp:(.text+0x336e): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
DLGeneTreeLikelihood.cpp:(.text+0x33a9): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
DLGeneTreeLikelihood.cpp:(.text+0x33c9): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
DLGeneTreeLikelihood.cpp:(.text+0x34e0): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
DLGeneTreeLikelihood.cpp:(.text+0x351b): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
DLGeneTreeLikelihood.cpp:(.text+0x353e): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
DLGeneTreeLikelihood.cpp:(.text+0x36bb): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
CMakeFiles/phyldog.dir/DLGeneTreeLikelihood.cpp.o: In function `DLGeneTreeLikelihood::refineGeneTreeSPRsFast2(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> > > > >)':
DLGeneTreeLikelihood.cpp:(.text+0x3b80): 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, int)'
DLGeneTreeLikelihood.cpp:(.text+0x3cfe): 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, int)'
CMakeFiles/phyldog.dir/DLGeneTreeLikelihood.cpp.o: In function `DLGeneTreeLikelihood::refineGeneTreeMuffato(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> > > > >)':
DLGeneTreeLikelihood.cpp:(.text+0x4e78): 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, int)'
DLGeneTreeLikelihood.cpp:(.text+0x4fe3): 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, int)'
DLGeneTreeLikelihood.cpp:(.text+0x520c): undefined reference to `bpp::ApplicationTools::getDoubleParameter(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> > > > >&, double, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, int)'
CMakeFiles/phyldog.dir/DLGeneTreeLikelihood.cpp.o: In function `DLGeneTreeLikelihood::initParameters()':
DLGeneTreeLikelihood.cpp:(.text+0x5c3a): 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, int)'
DLGeneTreeLikelihood.cpp:(.text+0x5d99): 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, int)'
CMakeFiles/phyldog.dir/DLGeneTreeLikelihood.cpp.o: In function `DLGeneTreeLikelihood::refineGeneTreeSPRsFast3(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> > > > >)':
DLGeneTreeLikelihood.cpp:(.text+0x6363): 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, int)'
DLGeneTreeLikelihood.cpp:(.text+0x6517): 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, int)'
CMakeFiles/phyldog.dir/DLGeneTreeLikelihood.cpp.o: In function `DLGeneTreeLikelihood::isSingleCopy()':
DLGeneTreeLikelihood.cpp:(.text+0x79c9): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
CMakeFiles/phyldog.dir/DLGeneTreeLikelihood.cpp.o: In function `bpp::NodeException::NodeException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)':
DLGeneTreeLikelihood.cpp:(.text._ZN3bpp13NodeExceptionC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEi[_ZN3bpp13NodeExceptionC5ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEi]+0x31): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
CMakeFiles/phyldog.dir/COALGeneTreeLikelihood.cpp.o: In function `COALGeneTreeLikelihood::print() const':
COALGeneTreeLikelihood.cpp:(.text+0x459): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
COALGeneTreeLikelihood.cpp:(.text+0x4bb): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
COALGeneTreeLikelihood.cpp:(.text+0x525): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
CMakeFiles/phyldog.dir/COALGeneTreeLikelihood.cpp.o: In function `bpp::TreeTemplate<bpp::Node>::getNode(int, bool) [clone .constprop.1288]':
COALGeneTreeLikelihood.cpp:(.text+0xe0b): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
COALGeneTreeLikelihood.cpp:(.text+0xe28): 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&)'
CMakeFiles/phyldog.dir/COALGeneTreeLikelihood.cpp.o: In function `COALGeneTreeLikelihood::refineGeneTreeSPRsFast(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> > > > >)':
COALGeneTreeLikelihood.cpp:(.text+0x1e0c): 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, int)'
COALGeneTreeLikelihood.cpp:(.text+0x1f5e): 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, int)'
CMakeFiles/phyldog.dir/COALGeneTreeLikelihood.cpp.o: In function `COALGeneTreeLikelihood::refineGeneTreeNNIs(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> > > > >, unsigned int)':
COALGeneTreeLikelihood.cpp:(.text+0x3d42): 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, int)'
COALGeneTreeLikelihood.cpp:(.text+0x3f8e): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
COALGeneTreeLikelihood.cpp:(.text+0x3fc9): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
COALGeneTreeLikelihood.cpp:(.text+0x3fe9): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
COALGeneTreeLikelihood.cpp:(.text+0x4101): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
COALGeneTreeLikelihood.cpp:(.text+0x413c): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
COALGeneTreeLikelihood.cpp:(.text+0x415f): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
COALGeneTreeLikelihood.cpp:(.text+0x42c0): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
CMakeFiles/phyldog.dir/COALGeneTreeLikelihood.cpp.o: In function `COALGeneTreeLikelihood::isSingleCopy()':
COALGeneTreeLikelihood.cpp:(.text+0x4b59): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
CMakeFiles/phyldog.dir/GeneTreeLikelihood.cpp.o: In function `GeneTreeLikelihood::GeneTreeLikelihood(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, 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> > > > >, bpp::TreeTemplate<bpp::Node>&)':
GeneTreeLikelihood.cpp:(.text+0x10e8): 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, int)'
GeneTreeLikelihood.cpp:(.text+0x116b): undefined reference to `bpp::ApplicationTools::getDoubleParameter(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> > > > >&, double, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, int)'
GeneTreeLikelihood.cpp:(.text+0x1333): 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, int)'
GeneTreeLikelihood.cpp:(.text+0x1610): undefined reference to `bpp::TextTools::removeSurroundingWhiteSpaces(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
GeneTreeLikelihood.cpp:(.text+0x17fc): undefined reference to `bpp::TreeTools::BOOTSTRAP[abi:cxx11]'
GeneTreeLikelihood.cpp:(.text+0x18bd): 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, int)'
GeneTreeLikelihood.cpp:(.text+0x1a8c): 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, int)'
GeneTreeLikelihood.cpp:(.text+0x1b29): undefined reference to `bpp::ApplicationTools::getIntParameter(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> > > > >&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, int)'
CMakeFiles/phyldog.dir/COALTools.cpp.o: In function `resizeSpeciesTreeAndComputeSubtreeCoalCountsPostorder(bpp::TreeTemplate<bpp::Node>&, bpp::TreeTemplate<bpp::Node>&, bpp::Node*, 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::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, 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, int> > >&, std::vector<std::vector<std::vector<std::vector<unsigned int, std::allocator<unsigned int> >, std::allocator<std::vector<unsigned int, std::allocator<unsigned int> > > >, std::allocator<std::vector<std::vector<unsigned int, std::allocator<unsigned int> >, std::allocator<std::vector<unsigned int, std::allocator<unsigned int> > > > > >, std::allocator<std::vector<std::vector<std::vector<unsigned int, std::allocator<unsigned int> >, std::allocator<std::vector<unsigned int, std::allocator<unsigned int> > > >, std::allocator<std::vector<std::vector<unsigned int, std::allocator<unsigned int> >, std::allocator<std::vector<unsigned int, std::allocator<unsigned int> > > > > > > >&, std::vector<std::vector<unsigned int, std::allocator<unsigned int> >, std::allocator<std::vector<unsigned int, std::allocator<unsigned int> > > >&)':
COALTools.cpp:(.text+0x1052): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
CMakeFiles/phyldog.dir/COALTools.cpp.o: In function `computeCoalBls(std::vector<std::vector<std::vector<unsigned int, std::allocator<unsigned int> >, std::allocator<std::vector<unsigned int, std::allocator<unsigned int> > > >, std::allocator<std::vector<std::vector<unsigned int, std::allocator<unsigned int> >, std::allocator<std::vector<unsigned int, std::allocator<unsigned int> > > > > >&, std::vector<double, std::allocator<double> >&)':
COALTools.cpp:(.text+0x1e4f): undefined reference to `bpp::Parameter::Parameter(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, double, bpp::Constraint const*, double)'
CMakeFiles/phyldog.dir/COALTools.cpp.o: In function `findMLCoalReconciliationDR(bpp::TreeTemplate<bpp::Node>*, bpp::TreeTemplate<bpp::Node>*, 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::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, 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, int> > >, std::vector<double, std::allocator<double> >, int&, std::vector<std::vector<std::vector<std::vector<unsigned int, std::allocator<unsigned int> >, std::allocator<std::vector<unsigned int, std::allocator<unsigned int> > > >, std::allocator<std::vector<std::vector<unsigned int, std::allocator<unsigned int> >, std::allocator<std::vector<unsigned int, std::allocator<unsigned int> > > > > >, std::allocator<std::vector<std::vector<std::vector<unsigned int, std::allocator<unsigned int> >, std::allocator<std::vector<unsigned int, std::allocator<unsigned int> > > >, std::allocator<std::vector<std::vector<unsigned int, std::allocator<unsigned int> >, std::allocator<std::vector<unsigned int, std::allocator<unsigned int> > > > > > > >&, std::set<int, std::less<int>, std::allocator<int> >&, bool)':
COALTools.cpp:(.text+0x4c83): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
COALTools.cpp:(.text+0x4dbc): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
CMakeFiles/phyldog.dir/COALTools.cpp.o:(.rodata._ZTC20CoalBranchLikelihood8_N3bpp22AbstractParametrizableE[_ZTV20CoalBranchLikelihood]+0xf0): undefined reference to `bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/COALTools.cpp.o:(.rodata._ZTC20CoalBranchLikelihood8_N3bpp22AbstractParametrizableE[_ZTV20CoalBranchLikelihood]+0x100): undefined reference to `bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/COALTools.cpp.o:(.rodata._ZTC20CoalBranchLikelihood8_N3bpp22AbstractParametrizableE[_ZTV20CoalBranchLikelihood]+0x1f8): undefined reference to `virtual thunk to bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/COALTools.cpp.o:(.rodata._ZTC20CoalBranchLikelihood8_N3bpp22AbstractParametrizableE[_ZTV20CoalBranchLikelihood]+0x208): undefined reference to `virtual thunk to bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/COALTools.cpp.o:(.rodata._ZTV20CoalBranchLikelihood[_ZTV20CoalBranchLikelihood]+0xf0): undefined reference to `virtual thunk to bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/COALTools.cpp.o:(.rodata._ZTV20CoalBranchLikelihood[_ZTV20CoalBranchLikelihood]+0x100): undefined reference to `virtual thunk to bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/COALTools.cpp.o:(.rodata._ZTV20CoalBranchLikelihood[_ZTV20CoalBranchLikelihood]+0x220): undefined reference to `bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/COALTools.cpp.o:(.rodata._ZTV20CoalBranchLikelihood[_ZTV20CoalBranchLikelihood]+0x230): undefined reference to `bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/GenericTreeExplorationAlgorithms.cpp.o: In function `checkChangeHasNotBeenDone(bpp::TreeTemplate<bpp::Node>&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, 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, double> > >)':
GenericTreeExplorationAlgorithms.cpp:(.text+0xa1a): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
CMakeFiles/phyldog.dir/GenericTreeExplorationAlgorithms.cpp.o: In function `nodeToParenthesisBIS[abi:cxx11](bpp::Tree const&, int, bool)':
GenericTreeExplorationAlgorithms.cpp:(.text+0x1173): undefined reference to `bpp::NodeNotFoundException::NodeNotFoundException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
CMakeFiles/phyldog.dir/GenericTreeExplorationAlgorithms.cpp.o: In function `bpp::TreeTemplate<bpp::Node>::getNode(int, bool) [clone .constprop.1029]':
GenericTreeExplorationAlgorithms.cpp:(.text+0x123b): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
GenericTreeExplorationAlgorithms.cpp:(.text+0x1258): 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&)'
CMakeFiles/phyldog.dir/GenericTreeExplorationAlgorithms.cpp.o: In function `rootTreeWithOutgroup(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> > > >)':
GenericTreeExplorationAlgorithms.cpp:(.text+0x4eca): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
GenericTreeExplorationAlgorithms.cpp:(.text+0x4f2d): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
GenericTreeExplorationAlgorithms.cpp:(.text+0x4f65): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
GenericTreeExplorationAlgorithms.cpp:(.text+0x509b): undefined reference to `bpp::TreeException::TreeException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Tree const*)'
CMakeFiles/phyldog.dir/GenericTreeExplorationAlgorithms.cpp.o: In function `isTreeRootedWithOutgroup(bpp::TreeTemplate<bpp::Node> const&, 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> > > >)':
GenericTreeExplorationAlgorithms.cpp:(.text+0x51c3): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
GenericTreeExplorationAlgorithms.cpp:(.text+0x51f0): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
CMakeFiles/phyldog.dir/GenericTreeExplorationAlgorithms.cpp.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&)':
GenericTreeExplorationAlgorithms.cpp:(.text._ZN3bpp14DistanceMatrixclERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_[_ZN3bpp14DistanceMatrixclERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_]+0xb): undefined reference to `bpp::DistanceMatrix::getNameIndex(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
GenericTreeExplorationAlgorithms.cpp:(.text._ZN3bpp14DistanceMatrixclERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_[_ZN3bpp14DistanceMatrixclERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_]+0x19): undefined reference to `bpp::DistanceMatrix::getNameIndex(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/GenericTreeExplorationAlgorithms.cpp.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':
GenericTreeExplorationAlgorithms.cpp:(.text._ZNK3bpp14DistanceMatrixclERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_[_ZNK3bpp14DistanceMatrixclERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_]+0xb): undefined reference to `bpp::DistanceMatrix::getNameIndex(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
GenericTreeExplorationAlgorithms.cpp:(.text._ZNK3bpp14DistanceMatrixclERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_[_ZNK3bpp14DistanceMatrixclERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_]+0x19): undefined reference to `bpp::DistanceMatrix::getNameIndex(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/GenericTreeExplorationAlgorithms.cpp.o: In function `bpp::DistanceEstimation::init_()':
GenericTreeExplorationAlgorithms.cpp:(.text._ZN3bpp18DistanceEstimation5init_Ev[_ZN3bpp18DistanceEstimation5init_Ev]+0x13e): undefined reference to `bpp::MetaOptimizerInfos::IT_TYPE_FULL[abi:cxx11]'
GenericTreeExplorationAlgorithms.cpp:(.text._ZN3bpp18DistanceEstimation5init_Ev[_ZN3bpp18DistanceEstimation5init_Ev]+0x1cc): undefined reference to `bpp::ParameterList::getParameterNames[abi:cxx11]() const'
GenericTreeExplorationAlgorithms.cpp:(.text._ZN3bpp18DistanceEstimation5init_Ev[_ZN3bpp18DistanceEstimation5init_Ev]+0x206): undefined reference to `bpp::MetaOptimizerInfos::IT_TYPE_STEP[abi:cxx11]'
CMakeFiles/phyldog.dir/GenericTreeExplorationAlgorithms.cpp.o: In function `bpp::Node::addSon(bpp::Node*)':
GenericTreeExplorationAlgorithms.cpp:(.text._ZN3bpp4Node6addSonEPS0_[_ZN3bpp4Node6addSonEPS0_]+0xd7): undefined reference to `bpp::NodePException::NodePException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bpp::Node const*)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `refineGeneTreeBranchLengthsUsingSequenceLikelihoodOnly(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> > > > >&, bpp::TreeTemplate<bpp::Node>*&, bpp::VectorSiteContainer*, bpp::SubstitutionModel*, bpp::DiscreteDistribution*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bpp::Alphabet*, bool)':
GeneTreeAlgorithms.cpp:(.text+0x1042): undefined reference to `bpp::PhylogeneticsApplicationTools::optimizeParameters(bpp::TreeLikelihood*, bpp::ParameterList 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&, bool, bool, int)'
GeneTreeAlgorithms.cpp:(.text+0x118f): undefined reference to `bpp::PhylogeneticsApplicationTools::optimizeParameters(bpp::TreeLikelihood*, bpp::ParameterList 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&, bool, bool, int)'
GeneTreeAlgorithms.cpp:(.text+0x11b8): undefined reference to `bpp::ApplicationTools::displayWarning(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
GeneTreeAlgorithms.cpp:(.text+0x11e5): undefined reference to `bpp::ApplicationTools::displayWarning(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
GeneTreeAlgorithms.cpp:(.text+0x1212): undefined reference to `bpp::ApplicationTools::displayWarning(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
GeneTreeAlgorithms.cpp:(.text+0x1358): undefined reference to `bpp::ApplicationTools::displayError(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
GeneTreeAlgorithms.cpp:(.text+0x1588): undefined reference to `bpp::ApplicationTools::displayError(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
GeneTreeAlgorithms.cpp:(.text+0x1690): undefined reference to `bpp::ApplicationTools::displayError(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `optimizeBranchLengthsParameters(bpp::DiscreteRatesAcrossSitesTreeLikelihood*, bpp::ParameterList const&, double, bpp::OptimizationListener*, double, unsigned int, bpp::OutputStream*, bpp::OutputStream*, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
GeneTreeAlgorithms.cpp:(.text+0x2934): undefined reference to `bpp::OptimizationTools::OPTIMIZATION_GRADIENT[abi:cxx11]'
GeneTreeAlgorithms.cpp:(.text+0x2986): undefined reference to `bpp::OptimizationTools::OPTIMIZATION_NEWTON[abi:cxx11]'
GeneTreeAlgorithms.cpp:(.text+0x299b): undefined reference to `bpp::OptimizationTools::OPTIMIZATION_BFGS[abi:cxx11]'
GeneTreeAlgorithms.cpp:(.text+0x2aec): undefined reference to `bpp::AutoParameter::CONSTRAINTS_AUTO[abi:cxx11]'
GeneTreeAlgorithms.cpp:(.text+0x2cea): undefined reference to `bpp::ApplicationTools::displayMessage(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
GeneTreeAlgorithms.cpp:(.text+0x2f3e): undefined reference to `bpp::AutoParameter::CONSTRAINTS_AUTO[abi:cxx11]'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `bpp::TreeTemplate<bpp::Node>::getNode(int, bool) [clone .constprop.1144]':
GeneTreeAlgorithms.cpp:(.text+0x311b): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
GeneTreeAlgorithms.cpp:(.text+0x3138): 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&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `buildASequenceTreeFromASpeciesTreeAndCorrespondanceMap(bpp::TreeTemplate<bpp::Node>&, 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> > > > >&)':
GeneTreeAlgorithms.cpp:(.text+0x3230): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `geneTreeToParenthesisWithSpeciesNames(bpp::TreeTemplate<bpp::Node>*, 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> > > > >)':
GeneTreeAlgorithms.cpp:(.text+0x3eb9): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `geneTreeToParenthesisPlusSpeciesNames(bpp::TreeTemplate<bpp::Node>*, 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> > > > >)':
GeneTreeAlgorithms.cpp:(.text+0x4286): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `optimizeBLForSPRs(bpp::DRTreeLikelihood*, double, 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> > > > >)':
GeneTreeAlgorithms.cpp:(.text+0x44b5): undefined reference to `bpp::ApplicationTools::getIntParameter(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> > > > >&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, int)'
GeneTreeAlgorithms.cpp:(.text+0x457c): undefined reference to `bpp::PhylogeneticsApplicationTools::optimizeParameters(bpp::TreeLikelihood*, bpp::ParameterList 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&, bool, bool, int)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `buildBioNJTree(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> > > > >&, bpp::SiteContainer*, bpp::SubstitutionModel*, bpp::DiscreteDistribution*, bpp::Alphabet*)':
GeneTreeAlgorithms.cpp:(.text+0x4ac5): undefined reference to `bpp::MetaOptimizerInfos::IT_TYPE_FULL[abi:cxx11]'
GeneTreeAlgorithms.cpp:(.text+0x4bce): undefined reference to `bpp::AutoParameter::CONSTRAINTS_AUTO[abi:cxx11]'
GeneTreeAlgorithms.cpp:(.text+0x50cb): undefined reference to `bpp::TwoTreeLikelihood::TwoTreeLikelihood(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::SiteContainer const&, bpp::SubstitutionModel*, bpp::DiscreteDistribution*, bool)'
GeneTreeAlgorithms.cpp:(.text+0x54bb): undefined reference to `bpp::TwoTreeLikelihood::TwoTreeLikelihood(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::SiteContainer const&, bpp::SubstitutionModel*, bpp::DiscreteDistribution*, bool)'
GeneTreeAlgorithms.cpp:(.text+0x5c02): undefined reference to `bpp::AutoParameter::CONSTRAINTS_AUTO[abi:cxx11]'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `parenthesisPlusSpeciesNamesToGeneTree(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
GeneTreeAlgorithms.cpp:(.text+0x5cbb): undefined reference to `bpp::TreeTools::BOOTSTRAP[abi:cxx11]'
GeneTreeAlgorithms.cpp:(.text+0x5ce1): undefined reference to `bpp::TreeTemplateTools::parenthesisToTree(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)'
GeneTreeAlgorithms.cpp:(.text+0x5f2c): undefined reference to `bpp::StringTokenizer::StringTokenizer(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)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `recoverSAndSpPresentInSubtree(bpp::TreeTemplate<bpp::Node>&, bpp::Node*)':
GeneTreeAlgorithms.cpp:(.text+0x67a6): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
GeneTreeAlgorithms.cpp:(.text+0x6825): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
GeneTreeAlgorithms.cpp:(.text+0x6920): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
GeneTreeAlgorithms.cpp:(.text+0x6a06): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
GeneTreeAlgorithms.cpp:(.text+0x6ae1): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
GeneTreeAlgorithms.cpp:(.text+0x6bce): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `optimizeBranchLengthsFast(bpp::DRHomogeneousTreeLikelihood*, bpp::ParameterList const&, double)':
GeneTreeAlgorithms.cpp:(.text+0x7314): undefined reference to `bpp::Parameter::Parameter(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, double, bpp::Constraint const*, double)'
GeneTreeAlgorithms.cpp:(.text+0x776c): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `editDuplicationNodesMuffato(bpp::TreeTemplate<bpp::Node>&, bpp::TreeTemplate<bpp::Node>&, bpp::Node*, double, bool&)':
GeneTreeAlgorithms.cpp:(.text+0x8000): undefined reference to `bpp::TextTools::toDouble(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char, char)'
GeneTreeAlgorithms.cpp:(.text+0x808f): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
GeneTreeAlgorithms.cpp:(.text+0x8118): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
GeneTreeAlgorithms.cpp:(.text+0x81a4): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
GeneTreeAlgorithms.cpp:(.text+0x8493): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
GeneTreeAlgorithms.cpp:(.text+0x8863): undefined reference to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:GeneTreeAlgorithms.cpp:(.text+0x8b5a): more undefined references to `bpp::TextTools::toInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char)' follow
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `editDuplicationNodesMuffato(bpp::TreeTemplate<bpp::Node>&, bpp::TreeTemplate<bpp::Node>&, double)':
GeneTreeAlgorithms.cpp:(.text+0xa25a): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis(bpp::TreeTemplate<bpp::Node> const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `refineGeneTreeUsingSequenceLikelihoodOnly(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> > > > >&, bpp::TreeTemplate<bpp::Node>*&, bpp::VectorSiteContainer*, bpp::SubstitutionModel*, bpp::DiscreteDistribution*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bpp::Alphabet*)':
GeneTreeAlgorithms.cpp:(.text+0xb8c8): undefined reference to `bpp::PhylogeneticsApplicationTools::optimizeParameters(bpp::TreeLikelihood*, bpp::ParameterList 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&, bool, bool, int)'
GeneTreeAlgorithms.cpp:(.text+0xbb6e): undefined reference to `bpp::ApplicationTools::displayWarning(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
GeneTreeAlgorithms.cpp:(.text+0xbba7): undefined reference to `bpp::ApplicationTools::displayWarning(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
GeneTreeAlgorithms.cpp:(.text+0xbbe0): undefined reference to `bpp::ApplicationTools::displayWarning(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
GeneTreeAlgorithms.cpp:(.text+0xbd1a): undefined reference to `bpp::ApplicationTools::displayError(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
GeneTreeAlgorithms.cpp:(.text+0xbf4e): undefined reference to `bpp::ApplicationTools::displayError(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
GeneTreeAlgorithms.cpp:(.text+0xc054): undefined reference to `bpp::ApplicationTools::displayError(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `bpp::GeneticCode::isStart(int) const':
GeneTreeAlgorithms.cpp:(.text._ZNK3bpp11GeneticCode7isStartEi[_ZNK3bpp11GeneticCode7isStartEi]+0x21): undefined reference to `bpp::AbstractAlphabet::intToChar[abi:cxx11](int) const'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `bpp::StandardGeneticCode::isAltStart(int) const':
GeneTreeAlgorithms.cpp:(.text._ZNK3bpp19StandardGeneticCode10isAltStartEi[_ZNK3bpp19StandardGeneticCode10isAltStartEi]+0x28): undefined reference to `bpp::AbstractAlphabet::intToChar[abi:cxx11](int) const'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `bpp::StandardGeneticCode::isStop(int) const':
GeneTreeAlgorithms.cpp:(.text._ZNK3bpp19StandardGeneticCode6isStopEi[_ZNK3bpp19StandardGeneticCode6isStopEi]+0x28): undefined reference to `bpp::AbstractAlphabet::intToChar[abi:cxx11](int) const'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `bpp::WordAlphabet::charToInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
GeneTreeAlgorithms.cpp:(.text._ZNK3bpp12WordAlphabet9charToIntERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNK3bpp12WordAlphabet9charToIntERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x3b): undefined reference to `bpp::WordAlphabet::containsUnresolved(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
GeneTreeAlgorithms.cpp:(.text._ZNK3bpp12WordAlphabet9charToIntERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNK3bpp12WordAlphabet9charToIntERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x4a): undefined reference to `bpp::WordAlphabet::containsGap(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
GeneTreeAlgorithms.cpp:(.text._ZNK3bpp12WordAlphabet9charToIntERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNK3bpp12WordAlphabet9charToIntERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x59): undefined reference to `bpp::AbstractAlphabet::charToInt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
GeneTreeAlgorithms.cpp:(.text._ZNK3bpp12WordAlphabet9charToIntERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNK3bpp12WordAlphabet9charToIntERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0xfe): 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*)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o: In function `bpp::GeneticCode::isStart(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
GeneTreeAlgorithms.cpp:(.text._ZNK3bpp11GeneticCode7isStartERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZNK3bpp11GeneticCode7isStartERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x44): undefined reference to `bpp::AbstractAlphabet::intToChar[abi:cxx11](int) const'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTCN3bpp4SiteE0_NS_15BasicSymbolListE[_ZTVN3bpp4SiteE]+0x108): undefined reference to `bpp::BasicSymbolList::setContent(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&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTCN3bpp4SiteE0_NS_15BasicSymbolListE[_ZTVN3bpp4SiteE]+0x110): undefined reference to `bpp::BasicSymbolList::toString[abi:cxx11]() const'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTCN3bpp4SiteE0_NS_15BasicSymbolListE[_ZTVN3bpp4SiteE]+0x118): undefined reference to `bpp::BasicSymbolList::addElement(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTCN3bpp4SiteE0_NS_15BasicSymbolListE[_ZTVN3bpp4SiteE]+0x120): undefined reference to `bpp::BasicSymbolList::addElement(unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTCN3bpp4SiteE0_NS_15BasicSymbolListE[_ZTVN3bpp4SiteE]+0x128): undefined reference to `bpp::BasicSymbolList::setElement(unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTCN3bpp4SiteE0_NS_15BasicSymbolListE[_ZTVN3bpp4SiteE]+0x140): undefined reference to `bpp::BasicSymbolList::getChar[abi:cxx11](unsigned long) const'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTVN3bpp4SiteE[_ZTVN3bpp4SiteE]+0x108): undefined reference to `bpp::BasicSymbolList::setContent(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&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTVN3bpp4SiteE[_ZTVN3bpp4SiteE]+0x110): undefined reference to `bpp::BasicSymbolList::toString[abi:cxx11]() const'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTVN3bpp4SiteE[_ZTVN3bpp4SiteE]+0x118): undefined reference to `bpp::BasicSymbolList::addElement(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTVN3bpp4SiteE[_ZTVN3bpp4SiteE]+0x120): undefined reference to `bpp::BasicSymbolList::addElement(unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTVN3bpp4SiteE[_ZTVN3bpp4SiteE]+0x128): undefined reference to `bpp::BasicSymbolList::setElement(unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTVN3bpp4SiteE[_ZTVN3bpp4SiteE]+0x140): undefined reference to `bpp::BasicSymbolList::getChar[abi:cxx11](unsigned long) const'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTCN3bpp16BranchLikelihoodE8_NS_22AbstractParametrizableE[_ZTVN3bpp16BranchLikelihoodE]+0xf0): undefined reference to `bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTCN3bpp16BranchLikelihoodE8_NS_22AbstractParametrizableE[_ZTVN3bpp16BranchLikelihoodE]+0x100): undefined reference to `bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTCN3bpp16BranchLikelihoodE8_NS_22AbstractParametrizableE[_ZTVN3bpp16BranchLikelihoodE]+0x1f8): undefined reference to `virtual thunk to bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTCN3bpp16BranchLikelihoodE8_NS_22AbstractParametrizableE[_ZTVN3bpp16BranchLikelihoodE]+0x208): undefined reference to `virtual thunk to bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTVN3bpp16BranchLikelihoodE[_ZTVN3bpp16BranchLikelihoodE]+0xf0): undefined reference to `virtual thunk to bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTVN3bpp16BranchLikelihoodE[_ZTVN3bpp16BranchLikelihoodE]+0x100): undefined reference to `virtual thunk to bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTVN3bpp16BranchLikelihoodE[_ZTVN3bpp16BranchLikelihoodE]+0x220): undefined reference to `bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTVN3bpp16BranchLikelihoodE[_ZTVN3bpp16BranchLikelihoodE]+0x230): undefined reference to `bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTCN3bpp19StandardGeneticCodeE8_NS_11GeneticCodeE[_ZTVN3bpp19StandardGeneticCodeE]+0x78): undefined reference to `bpp::GeneticCode::translate(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/GeneTreeAlgorithms.cpp.o:(.rodata._ZTVN3bpp19StandardGeneticCodeE[_ZTVN3bpp19StandardGeneticCodeE]+0x158): undefined reference to `bpp::GeneticCode::translate(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o: In function `FastRHomogeneousTreeLikelihood::setData(bpp::SiteContainer const&)':
FastRHomogeneousTreeLikelihood.cpp:(.text+0x81b): undefined reference to `bpp::ApplicationTools::displayTask(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o: In function `FastRHomogeneousTreeLikelihood::getFirstOrderDerivative(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
FastRHomogeneousTreeLikelihood.cpp:(.text+0x54e9): undefined reference to `bpp::ParameterList::hasParameter(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
FastRHomogeneousTreeLikelihood.cpp:(.text+0x551b): undefined reference to `bpp::ParameterList::hasParameter(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
FastRHomogeneousTreeLikelihood.cpp:(.text+0x55af): undefined reference to `bpp::ParameterNotFoundException::ParameterNotFoundException(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&)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o: In function `FastRHomogeneousTreeLikelihood::getSecondOrderDerivative(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
FastRHomogeneousTreeLikelihood.cpp:(.text+0x572e): undefined reference to `bpp::ParameterList::hasParameter(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
FastRHomogeneousTreeLikelihood.cpp:(.text+0x5760): undefined reference to `bpp::ParameterList::hasParameter(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
FastRHomogeneousTreeLikelihood.cpp:(.text+0x5898): undefined reference to `bpp::ParameterNotFoundException::ParameterNotFoundException(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&)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o: In function `bpp::Node::getSon(unsigned long) const':
FastRHomogeneousTreeLikelihood.cpp:(.text._ZNK3bpp4Node6getSonEm[_ZNK3bpp4Node6getSonEm]+0x8b): undefined reference to `bpp::IndexOutOfBoundsException::IndexOutOfBoundsException(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, unsigned long, unsigned long)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o: In function `bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength(double)':
FastRHomogeneousTreeLikelihood.cpp:(.text._ZN3bpp33AbstractHomogeneousTreeLikelihood22setMaximumBranchLengthEd[_ZN3bpp33AbstractHomogeneousTreeLikelihood22setMaximumBranchLengthEd]+0x107): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o: In function `bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength(double)':
FastRHomogeneousTreeLikelihood.cpp:(.text._ZN3bpp33AbstractHomogeneousTreeLikelihood22setMinimumBranchLengthEd[_ZN3bpp33AbstractHomogeneousTreeLikelihood22setMinimumBranchLengthEd]+0x107): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o: In function `bpp::IntervalConstraint::getDescription[abi:cxx11]() const':
FastRHomogeneousTreeLikelihood.cpp:(.text._ZNK3bpp18IntervalConstraint14getDescriptionB5cxx11Ev[_ZNK3bpp18IntervalConstraint14getDescriptionB5cxx11Ev]+0x7c): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
FastRHomogeneousTreeLikelihood.cpp:(.text._ZNK3bpp18IntervalConstraint14getDescriptionB5cxx11Ev[_ZNK3bpp18IntervalConstraint14getDescriptionB5cxx11Ev]+0xbb): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp22AbstractParametrizableE[_ZTV30FastRHomogeneousTreeLikelihood]+0xf0): undefined reference to `bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp22AbstractParametrizableE[_ZTV30FastRHomogeneousTreeLikelihood]+0x100): undefined reference to `bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp22AbstractParametrizableE[_ZTV30FastRHomogeneousTreeLikelihood]+0x1f8): undefined reference to `virtual thunk to bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp22AbstractParametrizableE[_ZTV30FastRHomogeneousTreeLikelihood]+0x208): undefined reference to `virtual thunk to bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp22AbstractTreeLikelihoodE[_ZTV30FastRHomogeneousTreeLikelihood]+0x110): undefined reference to `bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp22AbstractTreeLikelihoodE[_ZTV30FastRHomogeneousTreeLikelihood]+0x120): undefined reference to `bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp22AbstractTreeLikelihoodE[_ZTV30FastRHomogeneousTreeLikelihood]+0x430): undefined reference to `virtual thunk to bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp22AbstractTreeLikelihoodE[_ZTV30FastRHomogeneousTreeLikelihood]+0x440): undefined reference to `virtual thunk to bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp46AbstractDiscreteRatesAcrossSitesTreeLikelihoodE[_ZTV30FastRHomogeneousTreeLikelihood]+0x118): undefined reference to `bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp46AbstractDiscreteRatesAcrossSitesTreeLikelihoodE[_ZTV30FastRHomogeneousTreeLikelihood]+0x128): undefined reference to `bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp46AbstractDiscreteRatesAcrossSitesTreeLikelihoodE[_ZTV30FastRHomogeneousTreeLikelihood]+0x4c0): undefined reference to `virtual thunk to bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp46AbstractDiscreteRatesAcrossSitesTreeLikelihoodE[_ZTV30FastRHomogeneousTreeLikelihood]+0x4d0): undefined reference to `virtual thunk to bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp46AbstractDiscreteRatesAcrossSitesTreeLikelihoodE[_ZTV30FastRHomogeneousTreeLikelihood]+0x988): undefined reference to `virtual thunk to bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp46AbstractDiscreteRatesAcrossSitesTreeLikelihoodE[_ZTV30FastRHomogeneousTreeLikelihood]+0x998): undefined reference to `virtual thunk to bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp33AbstractHomogeneousTreeLikelihoodE[_ZTV30FastRHomogeneousTreeLikelihood]+0x120): undefined reference to `bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp33AbstractHomogeneousTreeLikelihoodE[_ZTV30FastRHomogeneousTreeLikelihood]+0x130): undefined reference to `bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp33AbstractHomogeneousTreeLikelihoodE[_ZTV30FastRHomogeneousTreeLikelihood]+0x5a8): undefined reference to `virtual thunk to bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTC30FastRHomogeneousTreeLikelihood0_N3bpp33AbstractHomogeneousTreeLikelihoodE[_ZTV30FastRHomogeneousTreeLikelihood]+0x5b8): undefined reference to `virtual thunk to bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTV30FastRHomogeneousTreeLikelihood[_ZTV30FastRHomogeneousTreeLikelihood]+0x120): undefined reference to `bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTV30FastRHomogeneousTreeLikelihood[_ZTV30FastRHomogeneousTreeLikelihood]+0x130): undefined reference to `bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTV30FastRHomogeneousTreeLikelihood[_ZTV30FastRHomogeneousTreeLikelihood]+0x6a8): undefined reference to `virtual thunk to bpp::AbstractParametrizable::setNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/FastRHomogeneousTreeLikelihood.cpp.o:(.rodata._ZTV30FastRHomogeneousTreeLikelihood[_ZTV30FastRHomogeneousTreeLikelihood]+0x6b8): undefined reference to `virtual thunk to bpp::AbstractParametrizable::getParameterNameWithoutNamespace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/phyldog.dir/ClientComputingGeneLikelihoods.cpp.o: In function `bpp::ClientComputingGeneLikelihoods::outputGeneTrees(unsigned int&)':
ClientComputingGeneLikelihoods.cpp:(.text+0xb1a): undefined reference to `bpp::TreeTools::BOOTSTRAP[abi:cxx11]'
ClientComputingGeneLikelihoods.cpp:(.text+0xb24): undefined reference to `bpp::TreeTemplateTools::parenthesisToTree(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)'
CMakeFiles/phyldog.dir/ClientComputingGeneLikelihoods.cpp.o: In function `bpp::ClientComputingGeneLikelihoods::parseAssignedGeneFamilies()':
ClientComputingGeneLikelihoods.cpp:(.text+0x1627): undefined reference to `bpp::FileTools::fileExists(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x165a): undefined reference to `bpp::AttributesTools::getAttributesMapFromFile(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&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x16ac): undefined reference to `bpp::AttributesTools::resolveVariables(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> > > > >&, char, char, char)'
ClientComputingGeneLikelihoods.cpp:(.text+0x16bf): undefined reference to `bpp::AttributesTools::actualizeAttributesMap(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::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> > > > > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x1722): 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, int)'
ClientComputingGeneLikelihoods.cpp:(.text+0x20b2): 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, int)'
ClientComputingGeneLikelihoods.cpp:(.text+0x2265): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
ClientComputingGeneLikelihoods.cpp:(.text+0x2355): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&, bool)'
ClientComputingGeneLikelihoods.cpp:(.text+0x24db): undefined reference to `bpp::TreeTemplateTools::parenthesisToTree(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)'
ClientComputingGeneLikelihoods.cpp:(.text+0x26fd): undefined reference to `bpp::ApplicationTools::displayWarning(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x2736): undefined reference to `bpp::ApplicationTools::displayWarning(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x276f): undefined reference to `bpp::ApplicationTools::displayWarning(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x295e): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
ClientComputingGeneLikelihoods.cpp:(.text+0x2b69): undefined reference to `bpp::ApplicationTools::displayWarning(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x2ba2): undefined reference to `bpp::ApplicationTools::displayWarning(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x2bdb): undefined reference to `bpp::ApplicationTools::displayWarning(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x2dd8): undefined reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
ClientComputingGeneLikelihoods.cpp:(.text+0x2e6d): undefined reference to `bpp::ApplicationTools::displayError(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x2ea5): undefined reference to `bpp::ApplicationTools::displayError(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x2ed6): undefined reference to `bpp::ApplicationTools::displayError(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x391b): undefined reference to `bpp::ApplicationTools::displayError(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x3954): undefined reference to `bpp::ApplicationTools::displayError(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/phyldog.dir/ClientComputingGeneLikelihoods.cpp.o:ClientComputingGeneLikelihoods.cpp:(.text+0x398d): more undefined references to `bpp::ApplicationTools::displayError(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' follow
CMakeFiles/phyldog.dir/ClientComputingGeneLikelihoods.cpp.o: In function `bpp::ClientComputingGeneLikelihoods::parseOptions()':
ClientComputingGeneLikelihoods.cpp:(.text+0x3d15): undefined reference to `bpp::TreeTemplateTools::parenthesisToTree(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)'
ClientComputingGeneLikelihoods.cpp:(.text+0x3dc5): undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
ClientComputingGeneLikelihoods.cpp:(.text+0x3ff8): 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, int)'
ClientComputingGeneLikelihoods.cpp:(.text+0x4089): undefined reference to `bpp::ApplicationTools::getIntParameter(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> > > > >&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, int)'
ClientComputingGeneLikelihoods.cpp:(.text+0x426d): 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, int)'
ClientComputingGeneLikelihoods.cpp:(.text+0x44af): undefined reference to `bpp::TreeTemplateTools::parenthesisToTree(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)'
CMakeFiles/phyldog.dir/ClientComputingGeneLikelihoods.cpp.o: In function `bpp::ClientComputingGeneLikelihoods::MLSearch()':
ClientComputingGeneLikelihoods.cpp:(.text+0x4dc8): 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, int)'
ClientComputingGeneLikelihoods.cpp:(.text+0x55d1): undefined reference to `bpp::TreeTemplateTools::parenthesisToTree(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)'
ClientComputingGeneLikelihoods.cpp:(.text+0x59a8): 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, int)'
ClientComputingGeneLikelihoods.cpp:(.text+0x5df3): undefined reference to `bpp::Nhx::treeToParenthesis[abi:cxx11](bpp::TreeTemplate<bpp::Node> const&) const'
ClientComputingGeneLikelihoods.cpp:(.text+0x5e60): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis(bpp::TreeTemplate<bpp::Node> const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x5ea9): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis(bpp::TreeTemplate<bpp::Node> const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x616b): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis(bpp::TreeTemplate<bpp::Node> const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x61be): undefined reference to `bpp::TreeTemplateTools::treeToParenthesis(bpp::TreeTemplate<bpp::Node> const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ClientComputingGeneLikelihoods.cpp:(.text+0x64d7): 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, int)'
CMakeFiles/phyldog.dir/LikelihoodEvaluator.cpp.o: In function `LikelihoodEvaluator::loadDataFromParams()':
LikelihoodEvaluator.cpp:(.text+0xa0a): 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, int)'
LikelihoodEvaluator.cpp:(.text+0xbb7): 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, int)'
LikelihoodEvaluator.cpp:(.text+0xdb2): undefined reference to `bpp::TreeTemplateTools::getRandomTree(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> > > >&, bool)'
LikelihoodEvaluator.cpp:(.text+0xdfe): undefined reference to `bpp::ApplicationTools::getDoubleParameter(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> > > > >&, double, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, int)'
CMakeFiles/phyldog.dir/LikelihoodEvaluator.cpp.o: In function `LikelihoodEvaluator::PLL_evaluate(bpp::TreeTemplate<bpp::Node>**)':
LikelihoodEvaluator.cpp:(.text+0x1da3): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
LikelihoodEvaluator.cpp:(.text+0x1db2): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
LikelihoodEvaluator.cpp:(.text+0x20cf): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
LikelihoodEvaluator.cpp:(.text+0x2227): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
CMakeFiles/phyldog.dir/LikelihoodEvaluator.cpp.o: In function `LikelihoodEvaluator::writeAlignmentFilesForPLL()':
LikelihoodEvaluator.cpp:(.text+0x29aa): undefined reference to `bpp::BasicSymbolList::toString[abi:cxx11]() const'
LikelihoodEvaluator.cpp:(.text+0x2dbd): 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, int)'
CMakeFiles/phyldog.dir/LikelihoodEvaluator.cpp.o: In function `LikelihoodEvaluator::BPP_evaluate(bpp::TreeTemplate<bpp::Node>**)':
LikelihoodEvaluator.cpp:(.text+0x3583): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
LikelihoodEvaluator.cpp:(.text+0x358f): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
LikelihoodEvaluator.cpp:(.text+0x3717): undefined reference to `bpp::OptimizationTools::OPTIMIZATION_NEWTON[abi:cxx11]'
LikelihoodEvaluator.cpp:(.text+0x3728): undefined reference to `bpp::OptimizationTools::optimizeBranchLengthsParameters(bpp::DiscreteRatesAcrossSitesTreeLikelihood*, bpp::ParameterList const&, bpp::OptimizationListener*, double, unsigned int, bpp::OutputStream*, bpp::OutputStream*, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
LikelihoodEvaluator.cpp:(.text+0x3807): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
LikelihoodEvaluator.cpp:(.text+0x3947): undefined reference to `bpp::TreeTemplateTools::getLeavesNames[abi:cxx11](bpp::Node const&)'
CMakeFiles/phyldog.dir/LikelihoodEvaluator.cpp.o: In function `LikelihoodEvaluator::LikelihoodEvaluator(bpp::Tree const*, bpp::SiteContainer const*, bpp::SubstitutionModel*, bpp::DiscreteDistribution*, 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)':
LikelihoodEvaluator.cpp:(.text+0x45c8): 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, int)'
collect2: error: ld returned 1 exit status
src/CMakeFiles/phyldog.dir/build.make:414: recipe for target 'bin/phyldog' failed
make[2]: *** [bin/phyldog] Error 1
CMakeFiles/Makefile2:117: recipe for target 'src/CMakeFiles/phyldog.dir/all' failed
make[1]: *** [src/CMakeFiles/phyldog.dir/all] Error 2
Makefile:149: recipe for target 'all' failed
make: *** [all] Error 2