[Debian-med-packaging] Bug#864188: libbpp-core2v5: symbols removed without soname bump

Tue Jun 6 10:47:38 UTC 2017

Dear Adrian,

These functions are now inline in the corresponding .h files, but their
interfaces have not changed as far as I know. Does making a function inline
break the interface??

J.

---------- Forwarded message ----------
From: Adrian Bunk <bunk at debian.org>
Date: Tue, Jun 6, 2017 at 11:48 AM
Subject: Re: Bug#864188: libbpp-core2v5: symbols removed without soname bump
To: Julien Yann Dutheil <dutheil at evolbio.mpg.de>
Cc: Andreas Tille <tille at debian.org>, 864188 at bugs.debian.org, GINDRAUD
FRANCOIS <francois.gindraud at univ-lyon1.fr>

On Tue, Jun 06, 2017 at 11:35:57AM +0200, Julien Yann Dutheil wrote:
> Dear Andreas, Adrian,
>...
> - This error actually revealed an interface breakdown (essentially due to
> our upgrade to c++11), and your suggestion is to reflect this change by
> increasing the interface number (which would result in a change in package
> name, such as libbpp-core2 -> libbpp-core3), am I correct?

This ABI breakage is unrelated to the C++ version used.

RandomTools::lnGamma() was removed from src/Bpp/Numeric/Random/
RandomTools.cpp
TextTools::startsWith() was removed from src/Bpp/Text/TextTools.cpp
ApplicationTools::parameterExists() was removed from
src/Bpp/App/ApplicationTools.cpp
...

Removing any such function breaks the ABI in an incompatible way,
and therefore requires a soname bump.

> Best,
>
> Julien.

cu
Adrian

> On Mon, Jun 5, 2017 at 9:50 AM, Andreas Tille <tille at debian.org> wrote:
>
> > Hi Julien,
> >
> > while I made a mistake to upload libbpp-core to unstable rather than
> > experimental as it was planed this has probably lead to spot a bug
> > earlier.  The problem is that the soversion needs to be bumped due to
> > the ABI change.
> >
> >    $ objdump -p ./libbpp-core.so.2.0.4   | sed -n 's/^.*SONAME *//p'
> >    libbpp-core.so.2
> >
> > I think you should bump the SOVERSION to reflect that change.
> >
> > Kind regards
> >
> >      Andreas.
> >
> > On Mon, Jun 05, 2017 at 02:42:58AM +0300, Adrian Bunk wrote:
> > > Package: libbpp-core2v5
> > > Version: 2.3.0-1~exp1
> > > Severity: serious
> > > Control: affects -1 libbpp-seq9v5 src:libbpp-phyl
> > >
> > > 2.3.0-1~exp1 in unstable (sic) removes symbols without changing
soname,
> > > causing the following FTBFS in libbpp-phyl:
> > >
> > > https://tests.reproducible-builds.org/debian/rb-pkg/
> > unstable/amd64/libbpp-phyl.html
> > >
> > > ...
> > > [ 93%] Linking CXX executable test_bowker
> > > cd /build/1st/libbpp-phyl-2.2.0/obj-x86_64-linux-gnu/test &&
> > /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.dir/link.txt
> > --verbose=1
> > > /usr/bin/c++   -Wall -Wshadow -Weffc++ -Wconversion  -Wl,-z,relro
> > CMakeFiles/test_bowker.dir/test_bowker.cpp.o  -o test_bowker -rdynamic
> > -lbpp-seq -lbpp-core -L../src -lbpp-phyl
> > > /usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/
libbpp-seq.so:
> > undefined reference to `bpp::RandomTools::lnGamma(double)'
> > > /usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/
libbpp-seq.so:
> > undefined reference to `bpp::TextTools::startsWith(
> > 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&)'
> > > /usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/
libbpp-seq.so:
> > undefined reference to `bpp::ApplicationTools::
> > parameterExists(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> > > > >&)'
> > > /usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/
libbpp-seq.so:
> > 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
> > > test/CMakeFiles/test_bowker.dir/build.make:99: recipe for target
> > 'test/test_bowker' failed
> > > make[3]: *** [test/test_bowker] Error 1
> >
> > --
> > http://fam-tille.de
> >
>
>
>
> --
> 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

-- 
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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