[Debian-med-packaging] Bug#1075503: seqan-raptor: ftbfs with GCC-14
Matthias Klose
doko at debian.org
Wed Jul 3 13:43:54 BST 2024
Package: src:seqan-raptor
Version: 3.0.1+ds-5
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/seqan-raptor_3.0.1+ds-5_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
[...]
from /usr/include/seqan3/submodules/sdsl-lite/include/sdsl/cereal.hpp:17,
from /usr/include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vector_il.hpp:21,
from /usr/include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vectors.hpp:13,
from /usr/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp:18,
from /<<PKGBUILDDIR>>/include/raptor/hierarchical_interleaved_bloom_filter.hpp:17,
from /<<PKGBUILDDIR>>/include/raptor/index.hpp:18,
from /<<PKGBUILDDIR>>/include/raptor/search/load_index.hpp:18,
from /<<PKGBUILDDIR>>/include/raptor/search/search_singular_ibf.hpp:20,
from /<<PKGBUILDDIR>>/src/search/search_ibf.cpp:14:
/usr/include/rapidjson/document.h: In member function ‘rapidjson::GenericStringRef<CharType>& rapidjson::GenericStringRef<CharType>::operator=(const rapidjson::GenericStringRef<CharType>&)’:
/usr/include/rapidjson/document.h:319:82: error: assignment of read-only member ‘rapidjson::GenericStringRef<CharType>::length’
319 | GenericStringRef& operator=(const GenericStringRef& rhs) { s = rhs.s; length = rhs.length; }
| ~~~~~~~^~~~~~~~~~~~
make[4]: *** [_deps/raptor_chopper_project-build/src/CMakeFiles/chopper_layout_lib.dir/build.make:79: _deps/raptor_chopper_project-build/src/CMakeFiles/chopper_layout_lib.dir/chopper_layout.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:341: _deps/raptor_chopper_project-build/src/CMakeFiles/chopper_layout_lib.dir/all] Error 2
[ 47%] Building CXX object src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/prepare_parsing.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/argument_parsing && /usr/bin/c++ -DRAPTOR_DATE=\"Unavailable\" -DRAPTOR_VERSION="\"3.0.1 (commit unavailable)\"" -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -DSHARG_HAS_BZIP2=1 -DSHARG_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -isystem /<<PKGBUILDDIR>>/lib/tool_description_lib/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/sharg-parser/include/ -I/<<PKGBUILDDIR>>/lib/submodules/lemon/include/ -pedantic -Wall -Wextra -std=c++20 -fopenmp -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -mpopcnt -flto=auto -fno-fat-lto-objects -MD -MT src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/prepare_parsing.cpp.o -MF CMakeFiles/raptor_argument_parsing.dir/prepare_parsing.cpp.o.d -o CMakeFiles/raptor_argument_parsing.dir/prepare_parsing.cpp.o -c /<<PKGBUILDDIR>>/src/argument_parsing/prepare_parsing.cpp
make[4]: *** [src/search/CMakeFiles/raptor_search.dir/build.make:93: src/search/CMakeFiles/raptor_search.dir/search_hibf.cpp.o] Error 1
make[4]: *** Waiting for unfinished jobs....
[ 49%] Building CXX object src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/search_parsing.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/argument_parsing && /usr/bin/c++ -DRAPTOR_DATE=\"Unavailable\" -DRAPTOR_VERSION="\"3.0.1 (commit unavailable)\"" -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -DSHARG_HAS_BZIP2=1 -DSHARG_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -isystem /<<PKGBUILDDIR>>/lib/tool_description_lib/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/sharg-parser/include/ -I/<<PKGBUILDDIR>>/lib/submodules/lemon/include/ -pedantic -Wall -Wextra -std=c++20 -fopenmp -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -mpopcnt -flto=auto -fno-fat-lto-objects -MD -MT src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/search_parsing.cpp.o -MF CMakeFiles/raptor_argument_parsing.dir/search_parsing.cpp.o.d -o CMakeFiles/raptor_argument_parsing.dir/search_parsing.cpp.o -c /<<PKGBUILDDIR>>/src/argument_parsing/search_parsing.cpp
In file included from /usr/include/seqan3/core/detail/iterator_traits.hpp:18,
from /usr/include/seqan3/core/range/type_traits.hpp:19,
from /usr/include/seqan3/contrib/parallel/buffer_queue.hpp:29,
from /usr/include/seqan3/io/views/async_input_buffer.hpp:21,
from /<<PKGBUILDDIR>>/src/argument_parsing/search_parsing.cpp:13:
/usr/include/seqan3/core/platform.hpp:85:17: note: ‘#pragma message: Your compiler is newer than the latest supported compiler of this SeqAn version (gcc-13). It might be that SeqAn does not compile due to this. You can disable this warning by setting -DSEQAN3_DISABLE_NEWER_COMPILER_DIAGNOSTIC.’
85 | "Your compiler is newer than the latest supported compiler of this SeqAn version (gcc-13). It might be that SeqAn does not compile due to this. You can disable this warning by setting -DSEQAN3_DISABLE_NEWER_COMPILER_DIAGNOSTIC."
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: *** [src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/build.make:93: src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/build_parsing.cpp.o] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: *** [src/upgrade/CMakeFiles/raptor_upgrade.dir/build.make:79: src/upgrade/CMakeFiles/raptor_upgrade.dir/raptor_upgrade.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:603: src/upgrade/CMakeFiles/raptor_upgrade.dir/all] Error 2
In file included from /usr/include/seqan3/core/concept/cereal.hpp:17,
from /usr/include/seqan3/utility/container/dynamic_bitset.hpp:17,
from /usr/include/seqan3/search/kmer_index/shape.hpp:16,
from /<<PKGBUILDDIR>>/include/raptor/argument_parsing/build_arguments.hpp:18,
from /<<PKGBUILDDIR>>/include/raptor/argument_parsing/parse_bin_path.hpp:15,
from /<<PKGBUILDDIR>>/src/argument_parsing/prepare_parsing.cpp:14:
/usr/include/seqan3/core/platform.hpp:85:17: note: ‘#pragma message: Your compiler is newer than the latest supported compiler of this SeqAn version (gcc-13). It might be that SeqAn does not compile due to this. You can disable this warning by setting -DSEQAN3_DISABLE_NEWER_COMPILER_DIAGNOSTIC.’
85 | "Your compiler is newer than the latest supported compiler of this SeqAn version (gcc-13). It might be that SeqAn does not compile due to this. You can disable this warning by setting -DSEQAN3_DISABLE_NEWER_COMPILER_DIAGNOSTIC."
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: *** [src/search/CMakeFiles/raptor_search.dir/build.make:107: src/search/CMakeFiles/raptor_search.dir/search_ibf.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:525: src/search/CMakeFiles/raptor_search.dir/all] Error 2
In file included from /usr/include/cereal/archives/json.hpp:67,
from /usr/include/seqan3/submodules/sdsl-lite/include/sdsl/cereal.hpp:17,
from /usr/include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vector_il.hpp:21,
from /usr/include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vectors.hpp:13,
from /usr/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp:18,
from /<<PKGBUILDDIR>>/include/raptor/hierarchical_interleaved_bloom_filter.hpp:17,
from /<<PKGBUILDDIR>>/include/raptor/index.hpp:18,
from /<<PKGBUILDDIR>>/src/argument_parsing/search_parsing.cpp:19:
/usr/include/rapidjson/document.h: In member function ‘rapidjson::GenericStringRef<CharType>& rapidjson::GenericStringRef<CharType>::operator=(const rapidjson::GenericStringRef<CharType>&)’:
/usr/include/rapidjson/document.h:319:82: error: assignment of read-only member ‘rapidjson::GenericStringRef<CharType>::length’
319 | GenericStringRef& operator=(const GenericStringRef& rhs) { s = rhs.s; length = rhs.length; }
| ~~~~~~~^~~~~~~~~~~~
make[4]: *** [src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/build.make:163: src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/search_parsing.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:420: src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/all] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:139: 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:30: override_dh_auto_build-arch] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:13: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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