[Debian-med-packaging] C++ issue in latest unanimity (packaging refreshed, but may be tiny stumbling C++ stone for me)

[Olivier Sallou]

On 10/10/2018 09:45 AM, Andreas Tille wrote:
> Hi,
>
> I have updated the unanimity packaging[1] but I'm running into
>
> ...
> /usr/bin/c++  -g -O2 -fdebug-prefix-map=/build/unanimity-3.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-  variable -Wno-unused-local-typedefs  -lpthread  -rdynamic CMakeFiles/ccs.dir/main/ccs.cpp.o  -o ../ccs -ldl libunanimity.a libcc2.a -lpbbam -Wl,-Bstatic -lpbcopper -Wl,-Bdynamic
> /usr/bin/ld: CMakeFiles/ccs.dir/main/ccs.cpp.o: in function `Runner(PacBio::CLI::Results const&)':
> ./build/src/./src/main/ccs.cpp:361: undefined reference to `PacBio::CCS::ConsensusSettings::ConsensusSettings(PacBio::CLI::Results const&)'
PacBio lib (pbbam) seems to not have the ConsensusSettings defined,
maybe this lib has been modified.. I see you uploaded a new version this
month (and a new upstream in september)

Olivier

> /usr/bin/ld: CMakeFiles/ccs.dir/main/ccs.cpp.o: in function `main':
> ./build/src/./src/main/ccs.cpp:600: undefined reference to `PacBio::CCS::ConsensusSettings::CreateCLI(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&)'
> collect2: error: ld returned 1 exit status
>
>
> I've checked upstream Git but there are no changes to src/main/ccs.cpp
> since the release.
>
> Any help would be appreciated
>
>       Andreas.
>
>
> [1] https://salsa.debian.org/med-team/unanimity
>

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438