[Debian-med-packaging] Bug#897837: prime-phylo: ftbfs with GCC-8

Fri May 4 13:23:11 BST 2018

Package: src:prime-phylo
Version: 1.0.11-4
Severity: normal
Tags: sid buster
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-8

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-8/g++-8, but succeeds to build with gcc-7/g++-7. The
severity of this report will be raised before the buster release.

The full build log can be found at:
http://aws-logs.debian.net/2018/05/01/gcc8/prime-phylo_1.0.11-4_unstable_gcc8.log.gz
The last lines of the build log are at the end of this report.

To build with GCC 8, either set CC=gcc-8 CXX=g++-8 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-8/porting_to.html

[...]
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.hh:162:33: error: 'std::ostream& beep::operator<<(std::ostream&, const beep::PrimeOptionMap&)' should have been declared inside 'beep'
        const PrimeOptionMap& pom);
                                 ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.hh:164:29: error: 'std::ostream& beep::operator<<(std::ostream&, const beep::PrimeOption&)' should have been declared inside 'beep'
        const PrimeOption& po);
                             ^
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.cc:3:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOption.hh: In member function 'void beep::UserSubstitutionMatrixOption::parseParams(std::__cxx11::string&, unsigned int, std::vector<beep::UserSubstMatrixParams>&)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOption.hh:405:23: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
  catch(std::exception e)
                       ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOption.hh:423:23: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
  catch(std::exception e)
                       ^
make[3]: *** [src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make:221: src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** Waiting for unfinished jobs....
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Tokenizer.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TimeEstimator.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/ODESolver.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscreteGamma.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ProbabilityModel.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/Probability.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Probability.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/BeepOption.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepOption.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:137: src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/all] Error 2
make[1]: *** [Makefile:155: all] Error 2
dh_auto_build: cd obj-x86_64-linux-gnu && make -j8 -Oline returned exit code 2
make: *** [debian/rules:10: build-arch] Error 25
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2