[Debian-med-packaging] Bug#1075486: salmon: ftbfs with GCC-14

[Matthias Klose]

Package: src:salmon
Version: 1.10.2+ds1-1
Severity: important
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-14

[This bug is 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-14/g++-14, but succeeds to build with gcc-13/g++-13. The
severity of this report will be raised before the trixie release.

The full build log can be found at:
http://qa-logs.debian.net/2024/07/01/salmon_1.10.2+ds1-1_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 14, either set CC=gcc-14 CXX=g++-14 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-14/porting_to.html

[...]
    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 /<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/hasher.hpp:170:19,
    inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /<<PKGBUILDDIR>>/external/pufferfish/src/FixFasta.cpp:536:26:
/<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [12, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=]
  208 |                                 M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
      |                                        ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’:
/<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 48 into 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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/hasher.hpp:170:19,
    inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /<<PKGBUILDDIR>>/external/pufferfish/src/FixFasta.cpp:536:26:
/<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [13, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=]
  208 |                                 M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
      |                                        ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’:
/<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 52 into 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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/hasher.hpp:170:19,
    inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /<<PKGBUILDDIR>>/external/pufferfish/src/FixFasta.cpp:536:26:
/<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [14, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=]
  208 |                                 M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
      |                                        ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’:
/<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 56 into 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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/hasher.hpp:170:19,
    inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /<<PKGBUILDDIR>>/external/pufferfish/src/FixFasta.cpp:536:26:
/<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [15, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=]
  208 |                                 M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
      |                                        ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’:
/<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 60 into object ‘byte’ of size 1
  169 |                         unsigned char byte = *begin++;
      |                                       ^~~~
[ 67%] Linking CXX static library libpuffer.a
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/puffer.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/puffer.dir/link.txt --verbose=1
/usr/bin/ar qc libpuffer.a CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o CMakeFiles/puffer.dir/edlib.cpp.o CMakeFiles/puffer.dir/Util.cpp.o CMakeFiles/puffer.dir/rank9sel.cpp.o CMakeFiles/puffer.dir/rank9b.cpp.o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o CMakeFiles/puffer.dir/PufferfishStats.cpp.o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o CMakeFiles/puffer.dir/FastxParser.cpp.o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o CMakeFiles/puffer.dir/PufferFS.cpp.o CMakeFiles/puffer.dir/xxhash.c.o CMakeFiles/puffer.dir/FixFasta.cpp.o CMakeFiles/puffer.dir/MemCollector.cpp.o CMakeFiles/puffer.dir/MemChainer.cpp.o CMakeFiles/puffer.dir/PuffAligner.cpp.o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o
/usr/bin/ranlib libpuffer.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 67%] Built target puffer
[ 68%] Linking CXX static library libtwopaco.a
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -P CMakeFiles/twopaco.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 68%] Built target twopaco
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:169: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>'
make: *** [debian/rules:26: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2