[Debian-med-packaging] Bug#1097838: salmon: ftbfs with GCC-15

[Matthias Klose]

Package: src:salmon
Version: 1.10.2+ds1-1
Severity: important
Tags: sid forky
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-15

[This bug is NOT targeted to the upcoming trixie release]

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-15/g++-15, but succeeds to build with gcc-14/g++-14. The
severity of this report will be raised before the forky release.

The full build log can be found at:
http://qa-logs.debian.net/2025/02/16/amd64exp/salmon_1.10.2+ds1-1_unstable_gccexp.log.gz
The last lines of the build log are at the end of this report.

To build with GCC 15, either set CC=gcc-15 CXX=g++-15 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

GCC 15 now defaults to the C23/C++23 standards, exposing many FTBFS.
Other 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-15/porting_to.html

[...]
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’
[ 73%] Linking CXX executable unitTests
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitTests.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/unitTests.dir/link.d CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -o unitTests   -L/build/reproducible-path/salmon-1.10.2+ds1/lib  -L/build/reproducible-path/salmon-1.10.2+ds1/external/install/lib  -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex libsalmon_core.a libalevin_core.a -lgff libUnitTestsMain.a /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_timer.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libstaden-read.so /usr/lib/x86_64-linux-gnu/libhtscodecs.so /usr/lib/x86_64-linux-gnu/libcurl.so -lz -lm -llzma -lbz2 -ltbb -ltbbmalloc -lgomp -lrt -ldl /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0
Copying unitTests
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E copy /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src/unitTests /build/reproducible-path/salmon-1.10.2+ds1/tests/unitTests
make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[ 73%] Built target unitTests
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/sha2.hpp:9,
                 from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/digestpp.hpp:6,
                 from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:27:
In member function ‘void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]’,
    inlined from ‘digestpp::detail::sha2_provider<long unsigned int, 0>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
    inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<long unsigned int, 0>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
    inlined from ‘void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
    inlined from ‘digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<long unsigned int, 0>; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
    inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:537:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript ‘const long unsigned int[0]’ is partly outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=]
  208 |                                 M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
      |                                        ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/digestpp.hpp:5:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: object ‘byte’ of size 1
  169 |                         unsigned char byte = *begin++;
      |                                       ^~~~
In member function ‘void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’,
    inlined from ‘digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
    inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
    inlined from ‘void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
    inlined from ‘digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
    inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript ‘const unsigned int[0]’ is partly outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=]
  208 |                                 M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
      |                                        ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: object ‘byte’ of size 1
  169 |                         unsigned char byte = *begin++;
      |                                       ^~~~
In member function ‘void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’,
    inlined from ‘digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
    inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
    inlined from ‘void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
    inlined from ‘digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<const char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
    inlined from ‘fixFasta(single_parser*, spp::sparse_hash_set<std::__cxx11::basic_string<char> >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr<spdlog::logger>, std::string, std::vector<unsigned int>&, std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&)::<lambda(bool, const std::string&)>’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26,
    inlined from ‘bool fixFasta(single_parser*, spp::sparse_hash_set<std::__cxx11::basic_string<char> >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr<spdlog::logger>, std::string, std::vector<unsigned int>&, std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript ‘const unsigned int[0]’ is partly outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=]
  208 |                                 M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
      |                                        ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool fixFasta(single_parser*, spp::sparse_hash_set<std::__cxx11::basic_string<char> >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr<spdlog::logger>, std::string, std::vector<unsigned int>&, std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&)’:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: object ‘byte’ of size 1
  169 |                         unsigned char byte = *begin++;
      |                                       ^~~~
make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:522: external/pufferfish/src/CMakeFiles/puffer.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
[ 74%] Linking CXX static library libtwopaco.a
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -P CMakeFiles/twopaco.dir/cmake_clean_target.cmake
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -E cmake_link_script CMakeFiles/twopaco.dir/link.txt --verbose=1
/usr/bin/ar qc libtwopaco.a CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o CMakeFiles/twopaco.dir/constructor.cpp.o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o CMakeFiles/twopaco.dir/compressedstring.cpp.o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o CMakeFiles/twopaco.dir/test.cpp.o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o CMakeFiles/twopaco.dir/common.cpp.o
/usr/bin/ranlib libtwopaco.a
make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[ 74%] Built target twopaco
make[3]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:169: all] Error 2
make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:37: override_dh_auto_build] Error 25
make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1'
make: *** [debian/rules:26: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2