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

[Julien Yann Dutheil]

Dear Andreas, Adrian,

Just to be sure I get everything right:
- The error you found before was due to building against a previous version
of bpp-core
- 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?

Best,

Julien.

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/debian-med-packaging/attachments/20170606/9c296725/attachment.html>