[Debian-med-packaging] Bug#1133629: seqan-raptor: ftbfs with GCC-16

[Emanuele Rocca]

Package: src:seqan-raptor
Version: 3.0.1+ds-11
Severity: important
Tags: sid forky ftbfs
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-16

Hi,

seqan-raptor fails to build in a test rebuild on at least amd64 and arm64 with
gcc-16/g++-16, but builds properly with gcc-15/g++-15. The severity of this
report will be raised before the forky release.

The full build log can be found at:
https://people.debian.org/~ema/gcc-16-rebuilds/output-1/seqan-raptor_arm64.build.xz

The last lines of the build log are at the end of this report.

To build with GCC 16, either set CC=gcc-16 CXX=g++-16 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures include unused (but set) variables, array subscripts
partly outside array bounds, and new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-16/porting_to.html

Please only close this issue after double-checking that the package can be
built correctly with GCC 16.

Please do not reassign this bug to another package. If a fix in another package
is required, then file a bug for the other package (or clone), and mark this
bug as blocked by the bug in the other package.

[...]


   97 |             for_each_hash(filename, callback);
      |             ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/seqan-raptor-3.0.1+ds/src/prepare/compute_minimiser.cpp:92:33:   required from ‘raptor::compute_minimiser(const prepare_arguments&)::<lambda(auto:87&&, auto:88&&)> [with auto:87 = std::ranges::take_view<std::ranges::subrange<std::ranges::zip_view<std::ranges::ref_view<const std::vector<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::allocator<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > >, std::ranges::iota_view<unsigned int, std::unreachable_sentinel_t> >::_Iterator<true>, std::ranges::zip_view<std::ranges::ref_view<const std::vector<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::allocator<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > >, std::ranges::iota_view<unsigned int, std::unreachable_sentinel_t> >::_Sentinel<true>, std::ranges::subrange_kind::unsized> >; auto:88 = raptor::call_parallel_on_bins<compute_minimiser(const prepare_arguments&)::<lambda(auto:87&&, auto:88&&)>&>(compute_minimiser(const prepare_arguments&)::<lambda(auto:87&&, auto:88&&)>&, const std::vector<std::vector<std::__cxx11::basic_string<char> > >&, uint8_t)::<lambda()>]’
   92 |             reader.for_each_hash(file_names,
      |             ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
   93 |                                  [&](auto && hash)
      |                                  ~~~~~~~~~~~~~~~~~
   94 |                                  {
      |                                  ~
   95 |                                      minimiser_table[hash] = std::min<uint8_t>(254u, minimiser_table[hash] + 1);
      |                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   96 |                                  });
      |                                  ~~
/usr/include/c++/16/type_traits:3850:7:   required from ‘constexpr const bool std::is_invocable_v<raptor::compute_minimiser(const prepare_arguments&)::<lambda(auto:87&&, auto:88&&)>, std::ranges::take_view<std::ranges::subrange<std::ranges::zip_view<std::ranges::ref_view<const std::vector<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::allocator<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > >, std::ranges::iota_view<unsigned int, std::unreachable_sentinel_t> >::_Iterator<true>, std::ranges::zip_view<std::ranges::ref_view<const std::vector<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::allocator<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > >, std::ranges::iota_view<unsigned int, std::unreachable_sentinel_t> >::_Sentinel<true>, std::ranges::subrange_kind::unsized> >, raptor::call_parallel_on_bins<compute_minimiser(const prepare_arguments&)::<lambda(auto:87&&, auto:88&&)>&>(compute_minimiser(const prepare_arguments&)::<lambda(auto:87&&, auto:88&&)>&, const std::vector<std::vector<std::__cxx11::basic_string<char> > >&, uint8_t)::<lambda()> >’
 3850 |     = __is_invocable(_Fn, _Args...);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/16/concepts:383:25:   required by substitution of ‘template<class algorithm_t, class algorithm_input_range_t, class callback_t>  requires (copy_constructible<algorithm_t>) && (input_range<algorithm_input_range_t>) && (copy_constructible<callback_t>) && (invocable<algorithm_t, decltype(*(declval<decltype(std::ranges::__access::__begin((declval<_Pattern&>)()))&>)()), callback_t>) void seqan3::detail::execution_handler_parallel::bulk_execute(algorithm_t&&, algorithm_input_range_t&&, callback_t&&) [with algorithm_t = raptor::compute_minimiser(const prepare_arguments&)::<lambda(auto:87&&, auto:88&&)>; algorithm_input_range_t = std::ranges::chunk_view<std::ranges::zip_view<std::ranges::ref_view<const std::vector<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::allocator<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > >, std::ranges::iota_view<unsigned int, std::unreachable_sentinel_t> > >; callback_t = raptor::call_parallel_on_bins<compute_minimiser(const prepare_arguments&)::<lambda(auto:87&&, auto:88&&)>&>(compute_minimiser(const prepare_arguments&)::<lambda(auto:87&&, auto:88&&)>&, const std::vector<std::vector<std::__cxx11::basic_string<char> > >&, uint8_t)::<lambda()>]’
  383 |     concept invocable = is_invocable_v<_Fn, _Args...>;
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/seqan-raptor-3.0.1+ds/include/raptor/call_parallel_on_bins.hpp:32:29:   required from ‘void raptor::call_parallel_on_bins(algorithm_t&&, const std::vector<std::vector<std::__cxx11::basic_string<char> > >&, uint8_t) [with algorithm_t = compute_minimiser(const prepare_arguments&)::<lambda(auto:87&&, auto:88&&)>&; uint8_t = unsigned char]’
   32 |     executioner.bulk_execute(std::move(worker), std::move(chunked_view), []() {});
      |     ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/seqan-raptor-3.0.1+ds/src/prepare/compute_minimiser.cpp:132:26:   required from here
  132 |     call_parallel_on_bins(worker, arguments.bin_path, arguments.threads);
      |     ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/seqan-raptor-3.0.1+ds/lib/robin-hood-hashing/src/include/robin_hood.h:2417:41: error: ‘UINT64_C’ was not declared in this scope
 2417 |             val = (val >> 1U) & UINT64_C(0x7f7f7f7f7f7f7f7f);
      |                                 ~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/seqan-raptor-3.0.1+ds/lib/robin-hood-hashing/src/include/robin_hood.h:2417:41: note: ‘UINT64_C’ is a function-like macro and might be used incorrectly
make[4]: *** [src/prepare/CMakeFiles/raptor_prepare.dir/build.make:82: src/prepare/CMakeFiles/raptor_prepare.dir/compute_minimiser.cpp.o] Error 1
make[4]: Leaving directory '/build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:669: src/prepare/CMakeFiles/raptor_prepare.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
make[4]: Leaving directory '/build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:572: src/build/hibf/CMakeFiles/raptor_build_hibf.dir/all] Error 2
[ 70%] Linking CXX static library ../../../lib/libchopper_layout_lib.a
cd /build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu/_deps/raptor_chopper_project-build/src && /usr/bin/cmake -P CMakeFiles/chopper_layout_lib.dir/cmake_clean_target.cmake
cd /build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu/_deps/raptor_chopper_project-build/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/chopper_layout_lib.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../lib/libchopper_layout_lib.a CMakeFiles/chopper_layout_lib.dir/chopper_layout.cpp.o
/usr/bin/ranlib ../../../lib/libchopper_layout_lib.a
make[4]: Leaving directory '/build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu'
[ 70%] Built target chopper_layout_lib
[ 72%] Linking CXX static library ../../lib/libraptor_search.a
cd /build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu/src/search && /usr/bin/cmake -P CMakeFiles/raptor_search.dir/cmake_clean_target.cmake
cd /build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu/src/search && /usr/bin/cmake -E cmake_link_script CMakeFiles/raptor_search.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/libraptor_search.a CMakeFiles/raptor_search.dir/raptor_search.cpp.o CMakeFiles/raptor_search.dir/search_hibf.cpp.o CMakeFiles/raptor_search.dir/search_ibf.cpp.o CMakeFiles/raptor_search.dir/search_partitioned_ibf.cpp.o
/usr/bin/ranlib ../../lib/libraptor_search.a
make[4]: Leaving directory '/build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu'
[ 72%] Built target raptor_search
[ 74%] Linking CXX static library ../../lib/libraptor_upgrade.a
cd /build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu/src/upgrade && /usr/bin/cmake -P CMakeFiles/raptor_upgrade.dir/cmake_clean_target.cmake
cd /build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu/src/upgrade && /usr/bin/cmake -E cmake_link_script CMakeFiles/raptor_upgrade.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/libraptor_upgrade.a CMakeFiles/raptor_upgrade.dir/raptor_upgrade.cpp.o
/usr/bin/ranlib ../../lib/libraptor_upgrade.a
make[4]: Leaving directory '/build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu'
[ 74%] Built target raptor_upgrade
[ 76%] Linking CXX static library ../../lib/libraptor_argument_parsing.a
cd /build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu/src/argument_parsing && /usr/bin/cmake -P CMakeFiles/raptor_argument_parsing.dir/cmake_clean_target.cmake
cd /build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu/src/argument_parsing && /usr/bin/cmake -E cmake_link_script CMakeFiles/raptor_argument_parsing.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/libraptor_argument_parsing.a CMakeFiles/raptor_argument_parsing.dir/__/build/hibf/parse_chopper_pack_line.cpp.o CMakeFiles/raptor_argument_parsing.dir/build_parsing.cpp.o CMakeFiles/raptor_argument_parsing.dir/compute_bin_size.cpp.o CMakeFiles/raptor_argument_parsing.dir/init_shared_meta.cpp.o CMakeFiles/raptor_argument_parsing.dir/parse_bin_path.cpp.o CMakeFiles/raptor_argument_parsing.dir/prepare_parsing.cpp.o CMakeFiles/raptor_argument_parsing.dir/search_parsing.cpp.o CMakeFiles/raptor_argument_parsing.dir/upgrade_parsing.cpp.o
/usr/bin/ranlib ../../lib/libraptor_argument_parsing.a
make[4]: Leaving directory '/build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu'
[ 76%] Built target raptor_argument_parsing
make[3]: Leaving directory '/build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu'
make[2]: *** [Makefile:139: all] Error 2
make[2]: Leaving directory '/build/reproducible-path/seqan-raptor-3.0.1+ds/obj-aarch64-linux-gnu'
dh_auto_build: error: cd obj-aarch64-linux-gnu && make -j128 INSTALL="install --strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:30: override_dh_auto_build-arch] Error 25
make[1]: Leaving directory '/build/reproducible-path/seqan-raptor-3.0.1+ds'
make: *** [debian/rules:13: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2