Bug#825443: marked as done (bppsuite: FTBFS against c++v5 transitioned libraries)

[Debian Bug Tracking System]

Your message dated Sat, 10 Sep 2016 11:53:14 +0000
with message-id <e1bigqq-0006df...@franck.debian.org>
and subject line Bug#825443: fixed in bppsuite 2.2.0-0.1
has caused the Debian Bug report #825443,
regarding bppsuite: FTBFS against c++v5 transitioned libraries
to be marked as done.

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

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


-- 
825443: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=825443
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

Source: bppsuite
Version: 0.8.0-1+build1
Severity: serious
Justification: fails to build from source

Hi,

bppsuite FTBFS with GCC 5 building against the C++v5 transitioned bpp
libraries:

https://buildd.debian.org/status/fetch.php?pkg=bppsuite&arch=amd64&ver=0.8.0-1%2Bbuild1%2Bb1&stamp=1464293213

make[3]: Entering directory '/«PKGBUILDDIR»'
[ 37%] Building CXX object bppSuite/CMakeFiles/bppseqgen.dir/bppSeqGen.cpp.o
/«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp: In function 'int main(int, char**)':
/«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:204:118: error: no matching function for 
call to 
'bpp::PhylogeneticsApplicationTools::getSubstitutionModel(bpp::Alphabet*&, int, 
std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&)'
     SubstitutionModel* model = 
PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, 0, 
bppseqgen.getParams());
                                                                                
                                      ^
In file included from /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:63:0:
/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:158:31: note: 
candidate: static bpp::SubstitutionModel* 
bpp::PhylogeneticsApplicationTools::getSubstitutionModel(const bpp::Alphabet*, 
const bpp::GeneticCode*, const bpp::SiteContainer*, 
std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, 
const string&, bool, bool, int)
     static SubstitutionModel* getSubstitutionModel(
                               ^
/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:158:31: note:   
candidate expects 8 arguments, 3 provided
/«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:205:97: error: no matching function for 
call to 'bpp::FixedFrequenciesSet::FixedFrequenciesSet(const bpp::Alphabet*, 
const Vdouble&)'
     FrequenciesSet* fSet = new FixedFrequenciesSet(model->getAlphabet(), 
model->getFrequencies());
                                                                                
                 ^
In file included from /usr/include/Bpp/Phyl/Model/SubstitutionModel.h:43:0,
                 from 
/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:45,
                 from /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:63:
/usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:332:3: note: 
candidate: bpp::FixedFrequenciesSet::FixedFrequenciesSet(bpp::StateMap*, const 
string&)
   FixedFrequenciesSet(StateMap* stateMap, const std::string& name = "Fixed");
   ^
/usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:332:3: note:   no 
known conversion for argument 1 from 'const bpp::Alphabet*' to 'bpp::StateMap*'
/usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:324:3: note: 
candidate: bpp::FixedFrequenciesSet::FixedFrequenciesSet(bpp::StateMap*, const 
std::vector<double, std::allocator<double> >&, const string&)
   FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& 
initFreqs, const std::string& name = "Fixed") throw (Exception);
   ^
/usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:324:3: note:   no 
known conversion for argument 1 from 'const bpp::Alphabet*' to 'bpp::StateMap*'
/usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:311:7: note: 
candidate: bpp::FixedFrequenciesSet::FixedFrequenciesSet(const 
bpp::FixedFrequenciesSet&)
 class FixedFrequenciesSet :
       ^
/usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:311:7: note:   
candidate expects 1 argument, 2 provided
/«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:216:101: error: no matching function for 
call to 
'bpp::PhylogeneticsApplicationTools::getSubstitutionModel(bpp::Alphabet*&, int, 
std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&)'
       model = PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, 0, 
bppseqgen.getParams());
                                                                                
                     ^
In file included from /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:63:0:
/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:158:31: note: 
candidate: static bpp::SubstitutionModel* 
bpp::PhylogeneticsApplicationTools::getSubstitutionModel(const bpp::Alphabet*, 
const bpp::GeneticCode*, const bpp::SiteContainer*, 
std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, 
const string&, bool, bool, int)
     static SubstitutionModel* getSubstitutionModel(
                               ^
/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:158:31: note:   
candidate expects 8 arguments, 3 provided
/«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:222:111: error: no matching function for 
call to 
'bpp::PhylogeneticsApplicationTools::getSubstitutionModel(bpp::Alphabet*&, 
bpp::VectorSiteContainer*&, std::map<std::__cxx11::basic_string<char>, 
std::__cxx11::basic_string<char> >&)'
       model = PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, 
allSitesAln, bppseqgen.getParams());
                                                                                
                               ^
In file included from /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:63:0:
/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:158:31: note: 
candidate: static bpp::SubstitutionModel* 
bpp::PhylogeneticsApplicationTools::getSubstitutionModel(const bpp::Alphabet*, 
const bpp::GeneticCode*, const bpp::SiteContainer*, 
std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, 
const string&, bool, bool, int)
     static SubstitutionModel* getSubstitutionModel(
                               ^
/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:158:31: note:   
candidate expects 8 arguments, 3 provided
/«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:234:131: error: no matching function for 
call to 
'bpp::PhylogeneticsApplicationTools::getRootFrequenciesSet(bpp::Alphabet*&, 
int, std::map<std::__cxx11::basic_string<char>, 
std::__cxx11::basic_string<char> >&, std::vector<double, std::allocator<double> 
>&)'
     FrequenciesSet* rootFreqs = 
PhylogeneticsApplicationTools::getRootFrequenciesSet(alphabet, 0, 
bppseqgen.getParams(), rateFreqs);
                                                                                
                                                   ^
In file included from /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:63:0:
/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:218:28: note: 
candidate: static bpp::FrequenciesSet* 
bpp::PhylogeneticsApplicationTools::getRootFrequenciesSet(const bpp::Alphabet*, 
const bpp::GeneticCode*, const bpp::SiteContainer*, 
std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, 
const std::vector<double, std::allocator<double> >&, const string&, bool, bool, 
int)
     static FrequenciesSet* getRootFrequenciesSet(
                            ^
/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:218:28: note:   
candidate expects 9 arguments, 4 provided
/«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:250:106: error: no matching function for 
call to 
'bpp::PhylogeneticsApplicationTools::getSubstitutionModelSet(bpp::Alphabet*&, 
int, std::map<std::__cxx11::basic_string<char>, 
std::__cxx11::basic_string<char> >&)'
      modelSet = 
PhylogeneticsApplicationTools::getSubstitutionModelSet(alphabet, 0, 
bppseqgen.getParams());
                                                                                
                          ^
In file included from /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:63:0:
/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:263:35: note: 
candidate: static bpp::SubstitutionModelSet* 
bpp::PhylogeneticsApplicationTools::getSubstitutionModelSet(const 
bpp::Alphabet*, const bpp::GeneticCode*, const bpp::SiteContainer*, 
std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, 
const string&, bool, bool, int)
      static SubstitutionModelSet* getSubstitutionModelSet(
                                   ^
/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:263:35: note:   
candidate expects 8 arguments, 3 provided
/«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:256:117: error: no matching function for 
call to 
'bpp::PhylogeneticsApplicationTools::getSubstitutionModelSet(bpp::Alphabet*&, 
bpp::VectorSiteContainer*&, std::map<std::__cxx11::basic_string<char>, 
std::__cxx11::basic_string<char> >&)'
       modelSet = 
PhylogeneticsApplicationTools::getSubstitutionModelSet(alphabet, allSitesAln, 
bppseqgen.getParams());
                                                                                
                                     ^
In file included from /«PKGBUILDDIR»/bppSuite/bppSeqGen.cpp:63:0:
/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:263:35: note: 
candidate: static bpp::SubstitutionModelSet* 
bpp::PhylogeneticsApplicationTools::getSubstitutionModelSet(const 
bpp::Alphabet*, const bpp::GeneticCode*, const bpp::SiteContainer*, 
std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, 
const string&, bool, bool, int)
      static SubstitutionModelSet* getSubstitutionModelSet(
                                   ^
/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:263:35: note:   
candidate expects 8 arguments, 3 provided
bppSuite/CMakeFiles/bppseqgen.dir/build.make:62: recipe for target 
'bppSuite/CMakeFiles/bppseqgen.dir/bppSeqGen.cpp.o' failed
make[3]: *** [bppSuite/CMakeFiles/bppseqgen.dir/bppSeqGen.cpp.o] Error 1
make[3]: Leaving directory '/«PKGBUILDDIR»'


Andreas

--- End Message ---

--- Begin Message ---

Source: bppsuite
Source-Version: 2.2.0-0.1

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

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

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 825...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Beckmann <a...@debian.org> (supplier of updated bppsuite package)

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


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

Format: 1.8
Date: Sat, 10 Sep 2016 13:35:04 +0200
Source: bppsuite
Binary: bppsuite
Architecture: source
Version: 2.2.0-0.1
Distribution: unstable
Urgency: low
Maintainer: Loic Dachary <l...@dachary.org>
Changed-By: Andreas Beckmann <a...@debian.org>
Description:
 bppsuite   - Bio++ program suite
Closes: 708457 776111 811271 825443
Changes:
 bppsuite (2.2.0-0.1) unstable; urgency=low
 .
   [ Andreas Beckmann ]
   * Non-maintainer upload.
   * New upstream release 2.2.0 (git commit 7890d12).
     (Closes: #776111, #825443, #708457)
   * Remove hardcoded library dependencies.  (Closes: #811271)
 .
   [ Julien Dutheil ]
   * Compatibility update. Bio++ Program Suite version number is now indexed
     on Bio++'s version.
   * Programs support the --seed argument for setting the random seed.
   * bppSeqGen support generic characters as input.
   * bppPhySamp outputs sampled trees.
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Checksums-Sha256:
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bppsuite_2.2.0-0.1.dsc
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Files:
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 ab322a3d64c3097177ee0a536adc9278 193790 science optional 
bppsuite_2.2.0.orig.tar.gz
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bppsuite_2.2.0-0.1.debian.tar.xz

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