[Debian-med-packaging] Bug#1075435: rapmap: ftbfs with GCC-14
Matthias Klose
doko at debian.org
Wed Jul 3 13:41:48 BST 2024
Package: src:rapmap
Version: 0.15.0+dfsg-4
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/rapmap_0.15.0+dfsg-4_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
[...]
/<<PKGBUILDDIR>>/include/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const int, int>; T = std::pair<const int, int>; Alloc = spp::libc_allocator<std::pair<const int, int> >; allocator_type = spp::libc_allocator<std::pair<const int, int> >; size_type = unsigned char]’
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const int, int>; T = std::pair<const int, int>; Alloc = spp::libc_allocator<std::pair<const int, int> >; pointer = std::pair<const int, int>*; allocator_type = spp::libc_allocator<std::pair<const int, int> >; size_type = unsigned char]’
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/sparsepp/spp.h:2241:28: required from ‘spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const int, int>; T = std::pair<const int, int>; Alloc = spp::libc_allocator<std::pair<const int, int> >; reference = std::pair<const int, int>&; size_type = long unsigned int]’
2241 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/sparsepp/spp.h:3171:25: required from ‘spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const int, int>; Value = std::pair<const int, int>; Key = int; HashFcn = spp::spp_hash<int>; ExtractKey = spp::sparse_hash_map<int, int, spp::spp_hash<int>, std::equal_to<int>, spp::libc_allocator<std::pair<const int, int> > >::SelectKey; SetKey = spp::sparse_hash_map<int, int, spp::spp_hash<int>, std::equal_to<int>, spp::libc_allocator<std::pair<const int, int> > >::SetKey; EqualKey = std::equal_to<int>; Alloc = spp::libc_allocator<std::pair<const int, int> >; reference = std::pair<const int, int>&; size_type = long unsigned int]’
3171 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/<<PKGBUILDDIR>>/include/sparsepp/spp.h:3288:38: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/<<PKGBUILDDIR>>/include/FrugalBooMap.hpp:162:30: required from ‘FrugalBooMap<KeyT, ValT>::IteratorT FrugalBooMap<KeyT, ValT>::find(const KeyT&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval<int>; IteratorT = KVProxy<__gnu_cxx::__normal_iterator<int*, std::vector<int> >, rapmap::utils::SAInterval<int> >]’
162 | l = overflow_[ind];
| ~~~~~~~~~^
/<<PKGBUILDDIR>>/include/SACollector.hpp:196:25: required from ‘bool SACollector<RapMapIndexT>::operator()(std::string&, SASearcher<RapMapIndexT>&, rapmap::hit_manager::HitCollectorInfo<rapmap::utils::SAIntervalHit<typename RapMapIndexT::IndexType> >&) [with RapMapIndexT = RapMapSAIndex<int, FrugalBooMap<long unsigned int, rapmap::utils::SAInterval<int> > >; std::string = std::__cxx11::basic_string<char>; typename RapMapIndexT::IndexType = int]’
196 | merIt = khash.find(mer.word(0));//get_bits(0, 2 * k));
| ~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/RapMapSAMapper.cpp:472:35: required from ‘void processReadsPairSA(paired_parser*, RapMapIndexT&, MutexT*, std::shared_ptr<spdlog::logger>, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex<int, FrugalBooMap<long unsigned int, rapmap::utils::SAInterval<int> > >; MutexT = std::mutex; paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; HitCounters = rapmap::utils::HitCounters]’
472 | bool lh = hitCollector(rpair.first.seq,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
473 | saSearcher,
| ~~~~~~~~~~~
474 | leftHCInfo);
| ~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/RapMapSAMapper.cpp:765:37: required from ‘bool spawnProcessReadsThreads(uint32_t, paired_parser*, RapMapIndexT&, MutexT&, std::shared_ptr<spdlog::logger>, HitCounters&, MappingOpts*) [with RapMapIndexT = RapMapSAIndex<int, FrugalBooMap<long unsigned int, rapmap::utils::SAInterval<int> > >; MutexT = std::mutex; uint32_t = unsigned int; paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; HitCounters = rapmap::utils::HitCounters]’
765 | threads.emplace_back(processReadsPairSA<RapMapIndexT, MutexT>,
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
766 | parser,
| ~~~~~~~
767 | std::ref(rmi),
| ~~~~~~~~~~~~~~
768 | &iomutex,
| ~~~~~~~~~
769 | outQueue,
| ~~~~~~~~~
770 | std::ref(hctr),
| ~~~~~~~~~~~~~~~
771 | mopts);
| ~~~~~~
/<<PKGBUILDDIR>>/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);
| ~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/RapMapSAMapper.cpp:1232:31: required from here
1232 | success = mapReads(rmi, consoleLog, &mopts);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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));
| ^~~~~~~~~~~~~~~~~~~~~~
make[4]: *** [src/CMakeFiles/rapmap.dir/build.make:149: src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o] Error 1
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:93: src/CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o] Error 1
At global scope:
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:121: src/CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o] Error 1
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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:136: src/CMakeFiles/rapmap.dir/all] Error 2
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:23: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:17: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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