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sr #2372: CoMap does not compile with latest Bpp library

Submitted by:  None
Submitted on:  Fri 26 Jun 2009 07:14:34 AM UTC  
 
Category: NonePriority: 5 - Normal
Severity: 3 - NormalStatus: None
Privacy: PublicAssigned to: None
Originator Email: -unavailable-Open/Closed: Open
Operating System: GNU/Linux

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Fri 26 Jun 2009 07:14:34 AM UTC, original submission:

I've attempted to build CoMap with the following version of the bpp library:

bpp-numcalc-1.7.0
bpp-phyl-1.8.0
bpp-seq-1.6.0
bpp-utils-1.4.0

which seem to be the latest.
My compiler is:
g++ (Debian 4.3.3-10) 4.3.3

And I get the following error:

make[1]: Entering directory `/home/sf/devel/bioinfo/CoMap/CoMap-1.3.0/CoMap'
g++ -DPACKAGE_NAME=\"CoMap\" -DPACKAGE_TARNAME=\"CoMap\" -DPACKAGE_VERSION=\"1.3.0\" -DPACKAGE_STRING=\"CoMap\ 1.3.0\" -DPACKAGE_BUGREPORT=\"Julien.Dutheil@univ-montp2.fr\" -DPACKAGE=\"CoMap\" -DVERSION=\"1.3.0\" -DHAVE_LIBBPP_UTILS=1 -DHAVE_LIBBPP_NUMCALC=1 -DHAVE_LIBBPP_SEQ=1 -DHAVE_LIBBPP_PHYL=1 -I. -g -O2 -MT CoETools.o -MD -MP -MF .deps/CoETools.Tpo -c -o CoETools.o CoETools.cpp
CoETools.cpp: In static member function ‘static void CoETools::readData(bpp::TreeTemplate<bpp::Node>*, bpp::Alphabet*&, bpp::VectorSiteContainer*&, bpp::VectorSiteContainer*&, bpp::SubstitutionModel*&, bpp::SubstitutionModelSet*&, bpp::DiscreteDistribution*&, bpp::DRTreeLikelihood*&, std::map<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<const std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&, const std::string&)’:
CoETools.cpp:193: error: no matching function for call to ‘bpp::PhylogeneticsApplicationTools::optimizeParameters(bpp::DRTreeLikelihood*&, std::map<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<const std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&, const std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, bool, bool)’
/home/sf/devel/bioinfo/bpp/install/include/Phyl/PhylogeneticsApplicationTools.h:462: note: candidates are: static bpp::TreeLikelihood* bpp::PhylogeneticsApplicationTools::optimizeParameters(bpp::TreeLikelihood*, const bpp::ParameterList&, std::map<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<const std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&, const std::string&, bool, bool)
/home/sf/devel/bioinfo/bpp/install/include/Phyl/PhylogeneticsApplicationTools.h:499: note: static void bpp::PhylogeneticsApplicationTools::optimizeParameters(bpp::DiscreteRatesAcrossSitesClockTreeLikelihood*, const bpp::ParameterList&, std::map<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<const std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&, const std::string&, bool, bool)
make[1]: *** [CoETools.o] Error 1
make[1]: Leaving directory `/home/sf/devel/bioinfo/CoMap/CoMap-1.3.0/CoMap'
make: *** [all-recursive] Error 1

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