[Debian-med-packaging] Bug#1097770: rapmap: ftbfs with GCC-15
Matthias Klose
doko at debian.org
Mon Feb 17 17:49:49 GMT 2025
Package: src:rapmap
Version: 0.15.0+dfsg-4
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/rapmap_0.15.0+dfsg-4_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
[...]
| ~~~~~~~~~~~~~~
768 | &iomutex,
| ~~~~~~~~~
769 | outQueue,
| ~~~~~~~~~
770 | std::ref(hctr),
| ~~~~~~~~~~~~~~~
771 | mopts);
| ~~~~~~
/build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:872:31: required from ‘bool mapReads(RapMapIndexT&, std::shared_ptr<spdlog::logger>, MappingOpts*) [with RapMapIndexT = RapMapSAIndex<int, FrugalBooMap<long unsigned int, rapmap::utils::SAInterval<int> > >]’
872 | spawnProcessReadsThreads(nthread, pairParserPtr.get(), rmi, iomutex,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
873 | outLog, hctrs, mopts);
| ~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:1232:31: required from here
1232 | success = mapReads(rmi, consoleLog, &mopts);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup<std::pair<const int, int>, spp::libc_allocator<std::pair<const int, int> > >::value_type’ {aka ‘std::pair<const int, int>’} to ‘spp::sparsegroup<std::pair<const int, int>, spp::libc_allocator<std::pair<const int, int> > >::mutable_reference’ {aka ‘std::pair<int, int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const int; _U2 = int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = int; _T2 = int]’ [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics
make[4]: *** [src/CMakeFiles/rapmap.dir/build.make:152: src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o] Error 1
make[4]: *** Waiting for unfinished jobs....
cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics
cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics
cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics
In file included from /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/algorithm/sha2.hpp:9,
from /build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/digestpp.hpp:6,
from /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:73:
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/rapmap-0.15.0+dfsg/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/rapmap-0.15.0+dfsg/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/rapmap-0.15.0+dfsg/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/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:170:19,
inlined from ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set<std::__cxx11::basic_string<char> >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr<spdlog::logger>) [with ParserT = fastx_parser::FastxParser<fastx_parser::ReadSeq>]’ at /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:581:30:
/build/reproducible-path/rapmap-0.15.0+dfsg/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/rapmap-0.15.0+dfsg/include/digestpp/digestpp.hpp:5:
/build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp: In function ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set<std::__cxx11::basic_string<char> >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr<spdlog::logger>) [with ParserT = fastx_parser::FastxParser<fastx_parser::ReadSeq>]’:
/build/reproducible-path/rapmap-0.15.0+dfsg/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 = 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/rapmap-0.15.0+dfsg/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/rapmap-0.15.0+dfsg/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/rapmap-0.15.0+dfsg/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/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:170:19,
inlined from ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set<std::__cxx11::basic_string<char> >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr<spdlog::logger>) [with ParserT = fastx_parser::FastxParser<fastx_parser::ReadSeq>]’ at /build/reproducible-path/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:671:33:
/build/reproducible-path/rapmap-0.15.0+dfsg/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]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp: In function ‘void indexTranscriptsSA(ParserT*, std::string&, spp::sparse_hash_set<std::__cxx11::basic_string<char> >&, bool, bool, uint32_t, bool, std::string&, std::mutex&, std::shared_ptr<spdlog::logger>) [with ParserT = fastx_parser::FastxParser<fastx_parser::ReadSeq>]’:
/build/reproducible-path/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:169:39: note: object ‘byte’ of size 1
169 | unsigned char byte = *begin++;
| ^~~~
At global scope:
cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics
At global scope:
cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics
make[4]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:154: src/CMakeFiles/rapmap.dir/all] Error 2
make[3]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:169: all] Error 2
make[2]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg/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:23: override_dh_auto_build] Error 25
make[1]: Leaving directory '/build/reproducible-path/rapmap-0.15.0+dfsg'
make: *** [debian/rules:17: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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