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

[Andreas Tille]

Hi Julien,

On Fri, Feb 09, 2018 at 09:34:58AM +0100, Julien Yann Dutheil wrote:
> I have committed a patch. But there are other errors like:

Thanks for the quick response.  For future pushes can you please make
sure two things:

   1. Add DEP3 headers to the patch - at least Author, Last-Updated and
  Description, if applicable Bug-Debian.
   2. Close fixed bugs in changelog

I've pushed my changes in case you have no idea what I mean.

Kind regards

   Andreas.

-- 
http://fam-tille.de

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

[Adrian Bunk]

On Fri, Feb 09, 2018 at 09:34:58AM +0100, Julien Yann Dutheil wrote:
> Hi,
> 
> I have committed a patch.

Thanks.

> But there are other errors like:
>...
> /usr/include/c++/7/bits/stl_iterator.h:1241:5: note: parameter passing for
> argument of type 'std::move_iterator' changed in GCC 7.1
>  __miter_base(move_iterator<_Iterator> __it)
>  ^~~~
> 
> which I am unsure how to handle...

This is not an error, this is a warning.

libbpp-phyl in unstable already has a different so-name than libbpp-phyl
in stable, so any potential stretch -> buster upgrade issues are already
covered.

> Julien.

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

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
/<>/src/Bpp/Phyl/Io/BppORateDistributionFormat.h:43,
 from
/<>/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' 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  wrote:

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

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

[Adrian Bunk]

Source: libbpp-phyl
Version: 2.3.2-1
Severity: serious

https://buildd.debian.org/status/package.php?p=libbpp-phyl=sid

...
In file included from 
/<>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:113:0:
/<>/src/Bpp/Phyl/Io/../Model/RegisterRatesSubstitutionModel.h:154:36:
 error: invalid covariant return type for 'virtual std::vector bpp::RegisterRatesSubstitutionModel::getModelStates(int) const'
 std::vector getModelStates(int i) const
^~
In file included from 
/<>/src/Bpp/Phyl/Io/../Model/Codon/../AbstractBiblioSubstitutionModel.h:44:0,
 from /<>/src/Bpp/Phyl/Io/../Model/Codon/MG94.h:43,
 from 
/<>/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:50:
/<>/src/Bpp/Phyl/Io/../Model/Codon/../AbstractWrappedModel.h:77:25:
 error:   overriding 'virtual std::vector 
bpp::AbstractWrappedModel::getModelStates(int) const'
 std::vector getModelStates(int code) const { return 
getModel().getModelStates(code); }
 ^~