[Debian-med-packaging] Bug#1020035: seqan3: FTBFS: char_traits.h:431:56: error: ‘void* __builtin_memcpy(void, const void, long unsigned int) ’ accessing 9223372036854775810 or more bytes at offsets 4 and 3 may overlap up to 9223372036854775813 bytes at offset -3 [-Werror=restrict]

Sun Sep 18 07:22:01 BST 2022

Source: seqan3
Version: 3.2.0+ds-2
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20220917 ftbfs-bookworm

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

Relevant part (hopefully):
> /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/test/include -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/submodules/sdsl-lite/include -isystem /<<PKGBUILDDIR>>/build_unit/vendor/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Werror -Wno-interference-size -std=c++20 -MD -MT alphabet/container/CMakeFiles/container_concept_test.dir/container_concept_test.cpp.o -MF alphabet/container/CMakeFiles/container_concept_test.dir/container_concept_test.cpp.o.d -o alphabet/container/CMakeFiles/container_concept_test.dir/container_concept_test.cpp.o -c /<<PKGBUILDDIR>>/test/unit/alphabet/container/container_concept_test.cpp
> In file included from /usr/include/c++/12/ios:40,
>                  from /usr/include/c++/12/ostream:38,
>                  from /usr/include/c++/12/bits/unique_ptr.h:41,
>                  from /usr/include/c++/12/memory:76,
>                  from /usr/include/gtest/gtest.h:54,
>                  from /<<PKGBUILDDIR>>/test/unit/alphabet/container/container_concept_test.cpp:8:
> In static member function ‘static constexpr std::char_traits<char>::char_type* std::char_traits<char>::copy(char_type*, const char_type*, std::size_t)’,
>     inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/12/bits/basic_string.h:423:21,
>     inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22,
>     inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/12/bits/basic_string.h:2171:19,
>     inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::insert(size_type, const _CharT*) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/12/bits/basic_string.h:1928:22,
>     inlined from ‘virtual void container_sequence_container_former_travis_bug_Test::TestBody()’ at /<<PKGBUILDDIR>>/test/unit/alphabet/container/container_concept_test.cpp:75:13:
> /usr/include/c++/12/bits/char_traits.h:431:56: error: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets 4 and 3 may overlap up to 9223372036854775813 bytes at offset -3 [-Werror=restrict]
>   431 |         return static_cast<char_type*>(__builtin_memcpy(__s1, __s2, __n));
>       |                                        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
> In static member function ‘static constexpr std::char_traits<char>::char_type* std::char_traits<char>::copy(char_type*, const char_type*, std::size_t)’,
>     inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/12/bits/basic_string.h:423:21,
>     inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22,
>     inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/12/bits/basic_string.h:2171:19,
>     inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::insert(size_type, const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/12/bits/basic_string.h:1858:29,
>     inlined from ‘virtual void container_sequence_container_former_travis_bug_Test::TestBody()’ at /<<PKGBUILDDIR>>/test/unit/alphabet/container/container_concept_test.cpp:79:13:
> /usr/include/c++/12/bits/char_traits.h:431:56: error: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets 8 and 7 may overlap up to 9223372036854775813 bytes at offset -3 [-Werror=restrict]
>   431 |         return static_cast<char_type*>(__builtin_memcpy(__s1, __s2, __n));
>       |                                        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
> In static member function ‘static constexpr std::char_traits<char>::char_type* std::char_traits<char>::copy(char_type*, const char_type*, std::size_t)’,
>     inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/12/bits/basic_string.h:423:21,
>     inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22,
>     inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/12/bits/basic_string.h:2171:19,
>     inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::replace(__const_iterator, __const_iterator, const _CharT*, const _CharT*) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/12/bits/basic_string.h:2380:22,
>     inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::iterator std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = const char*; <template-parameter-2-2> = void; _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/12/bits/basic_string.h:1798:17,
>     inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::iterator std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::insert(const_iterator, std::initializer_list<_Tp>) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ at /usr/include/c++/12/bits/basic_string.h:1830:28,
>     inlined from ‘virtual void container_sequence_container_former_travis_bug_Test::TestBody()’ at /<<PKGBUILDDIR>>/test/unit/alphabet/container/container_concept_test.cpp:136:13:
> /usr/include/c++/12/bits/char_traits.h:431:56: error: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Werror=restrict]
>   431 |         return static_cast<char_type*>(__builtin_memcpy(__s1, __s2, __n));
>       |                                        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
> cc1plus: all warnings being treated as errors
> [200/624] /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/test/include -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/submodules/sdsl-lite/include -isystem /<<PKGBUILDDIR>>/build_unit/vendor/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Werror -Wno-interference-size -std=c++20 -MD -MT alphabet/composite/CMakeFiles/alphabet_variant_test.dir/alphabet_variant_test.cpp.o -MF alphabet/composite/CMakeFiles/alphabet_variant_test.dir/alphabet_variant_test.cpp.o.d -o alphabet/composite/CMakeFiles/alphabet_variant_test.dir/alphabet_variant_test.cpp.o -c /<<PKGBUILDDIR>>/test/unit/alphabet/composite/alphabet_variant_test.cpp
> [201/624] /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/test/include -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/submodules/sdsl-lite/include -isystem /<<PKGBUILDDIR>>/build_unit/vendor/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Werror -Wno-interference-size -std=c++20 -MD -MT alignment/pairwise/edit_distance/CMakeFiles/semi_global_edit_distance_unbanded_test.dir/semi_global_edit_distance_unbanded_test.cpp.o -MF alignment/pairwise/edit_distance/CMakeFiles/semi_global_edit_distance_unbanded_test.dir/semi_global_edit_distance_unbanded_test.cpp.o.d -o alignment/pairwise/edit_distance/CMakeFiles/semi_global_edit_distance_unbanded_test.dir/semi_global_edit_distance_unbanded_test.cpp.o -c /<<PKGBUILDDIR>>/test/unit/alignment/pairwise/edit_distance/semi_global_edit_distance_unbanded_test.cpp
> [202/624] /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/test/include -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/submodules/sdsl-lite/include -isystem /<<PKGBUILDDIR>>/build_unit/vendor/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Werror -Wno-interference-size -std=c++20 -MD -MT alphabet/container/CMakeFiles/bitpacked_sequence_test.dir/bitpacked_sequence_test.cpp.o -MF alphabet/container/CMakeFiles/bitpacked_sequence_test.dir/bitpacked_sequence_test.cpp.o.d -o alphabet/container/CMakeFiles/bitpacked_sequence_test.dir/bitpacked_sequence_test.cpp.o -c /<<PKGBUILDDIR>>/test/unit/alphabet/container/bitpacked_sequence_test.cpp
> [203/624] /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/test/include -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/submodules/sdsl-lite/include -isystem /<<PKGBUILDDIR>>/build_unit/vendor/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Werror -Wno-interference-size -std=c++20 -MD -MT alignment/pairwise/edit_distance/CMakeFiles/global_edit_distance_max_errors_unbanded_test.dir/global_edit_distance_max_errors_unbanded_test.cpp.o -MF alignment/pairwise/edit_distance/CMakeFiles/global_edit_distance_max_errors_unbanded_test.dir/global_edit_distance_max_errors_unbanded_test.cpp.o.d -o alignment/pairwise/edit_distance/CMakeFiles/global_edit_distance_max_errors_unbanded_test.dir/global_edit_distance_max_errors_unbanded_test.cpp.o -c /<<PKGBUILDDIR>>/test/unit/alignment/pairwise/edit_distance/global_edit_distance_max_errors_unbanded_test.cpp
> [204/624] /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/test/include -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/submodules/sdsl-lite/include -isystem /<<PKGBUILDDIR>>/build_unit/vendor/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Werror -Wno-interference-size -std=c++20 -MD -MT alphabet/composite/CMakeFiles/composite_integration_test.dir/composite_integration_test.cpp.o -MF alphabet/composite/CMakeFiles/composite_integration_test.dir/composite_integration_test.cpp.o.d -o alphabet/composite/CMakeFiles/composite_integration_test.dir/composite_integration_test.cpp.o -c /<<PKGBUILDDIR>>/test/unit/alphabet/composite/composite_integration_test.cpp
> [205/624] /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/test/include -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/submodules/sdsl-lite/include -isystem /<<PKGBUILDDIR>>/build_unit/vendor/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Werror -Wno-interference-size -std=c++20 -MD -MT alphabet/container/CMakeFiles/container_of_container_test.dir/container_of_container_test.cpp.o -MF alphabet/container/CMakeFiles/container_of_container_test.dir/container_of_container_test.cpp.o.d -o alphabet/container/CMakeFiles/container_of_container_test.dir/container_of_container_test.cpp.o -c /<<PKGBUILDDIR>>/test/unit/alphabet/container/container_of_container_test.cpp
> [206/624] /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/test/include -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/submodules/sdsl-lite/include -isystem /<<PKGBUILDDIR>>/build_unit/vendor/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Werror -Wno-interference-size -std=c++20 -MD -MT alignment/pairwise/edit_distance/CMakeFiles/semi_global_edit_distance_max_errors_unbanded_test.dir/semi_global_edit_distance_max_errors_unbanded_test.cpp.o -MF alignment/pairwise/edit_distance/CMakeFiles/semi_global_edit_distance_max_errors_unbanded_test.dir/semi_global_edit_distance_max_errors_unbanded_test.cpp.o.d -o alignment/pairwise/edit_distance/CMakeFiles/semi_global_edit_distance_max_errors_unbanded_test.dir/semi_global_edit_distance_max_errors_unbanded_test.cpp.o -c /<<PKGBUILDDIR>>/test/unit/alignment/pairwise/edit_distance/semi_global_edit_distance_max_errors_unbanded_test.cpp
> ninja: build stopped: subcommand failed.
> dh_auto_build: error: cd build_unit && LC_ALL=C.UTF-8 ninja -j8 -v returned exit code 1
> make[1]: *** [debian/rules:42: override_dh_auto_build] Error 25

The full build log is available from:
http://qa-logs.debian.net/2022/09/17/seqan3_3.2.0+ds-2_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20220917;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220917&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.

[Debian-med-packaging] Bug#1020035: seqan3: FTBFS: char_traits.h:431:56: error: ‘void* __builtin_memcpy(void*, const void*, long unsigned int) ’ accessing 9223372036854775810 or more bytes at offsets 4 and 3 may overlap up to 9223372036854775813 bytes at offset -3 [-Werror=restrict]

[Debian-med-packaging] Bug#1020035: seqan3: FTBFS: char_traits.h:431:56: error: ‘void* __builtin_memcpy(void, const void, long unsigned int) ’ accessing 9223372036854775810 or more bytes at offsets 4 and 3 may overlap up to 9223372036854775813 bytes at offset -3 [-Werror=restrict]