[Debian-med-packaging] Bug#889953: libbpp-phyl FTBFS on 32bit: RegisterRatesSubstitutionModel.h:154:36: error: invalid covariant return type

[Julien Yann Dutheil]

Hi,

I have committed a patch. But there are other errors like:

In file included from /usr/include/c++/7/bits/stl_algobase.h:67:0,
                 from /usr/include/c++/7/bits/char_traits.h:39,
                 from /usr/include/c++/7/string:40,
                 from /usr/include/Bpp/Numeric/VectorExceptions.h:46,
                 from /usr/include/Bpp/Numeric/VectorTools.h:43,
                 from
/usr/include/Bpp/Numeric/Prob/DiscreteDistribution.h:43,
                 from
/usr/include/Bpp/Io/IoDiscreteDistributionFactory.h:43,
                 from
/usr/include/Bpp/Io/BppODiscreteDistributionFormat.h:43,
                 from
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppORateDistributionFormat.h:43,
                 from
/<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp:40:
/usr/include/c++/7/bits/stl_iterator.h: In function 'decltype
(std::__miter_base(__it.base()))
std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator =
double*]':
/usr/include/c++/7/bits/stl_iterator.h:1241:5: note: parameter passing for
argument of type 'std::move_iterator<double*>' changed in GCC 7.1
     __miter_base(move_iterator<_Iterator> __it)
     ^~~~~~~~~~~~

which I am unsure how to handle...

Julien.

On Fri, Feb 9, 2018 at 8:41 AM, Adrian Bunk <bunk at debian.org> wrote:

> Source: libbpp-phyl
> Version: 2.3.2-1
> Severity: serious
>
> https://buildd.debian.org/status/package.php?p=libbpp-phyl&suite=sid
>
> ...
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/
> BppOSubstitutionModelFormat.cpp:113:0:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/RegisterRatesSubstitutionModel.h:154:36:
> error: invalid covariant return type for 'virtual std::vector<long unsigned
> int> bpp::RegisterRatesSubstitutionModel::getModelStates(int) const'
>      std::vector<long unsigned int> getModelStates(int i) const
>                                     ^~~~~~~~~~~~~~
> In file included from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/Codon/../
> AbstractBiblioSubstitutionModel.h:44:0,
>                  from /<<PKGBUILDDIR>>/src/Bpp/Phyl/
> Io/../Model/Codon/MG94.h:43,
>                  from /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/
> BppOSubstitutionModelFormat.cpp:50:
> /<<PKGBUILDDIR>>/src/Bpp/Phyl/Io/../Model/Codon/../AbstractWrappedModel.h:77:25:
> error:   overriding 'virtual std::vector<unsigned int>
> bpp::AbstractWrappedModel::getModelStates(int) const'
>      std::vector<size_t> getModelStates(int code) const { return
> getModel().getModelStates(code); }
>                          ^~~~~~~~~~~~~~
>
>


-- 
Julien Y. Dutheil, Ph-D
0 (+49) 4522 763 298

§ Max Planck Institute for Evolutionary Biology
Molecular Systems Evolution
Department of Evolutionary Genetics
Plön -- GERMANY

§ Institute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE
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