[Debian-med-packaging] Bug#1075502: seqan-needle: ftbfs with GCC-14
Matthias Klose
doko at debian.org
Wed Jul 3 13:43:53 BST 2024
Package: src:seqan-needle
Version: 1.0.2+ds-2
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-needle_1.0.2+ds-2_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
[...]
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f src/CMakeFiles/needle_lib.dir/build.make src/CMakeFiles/needle_lib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/CMakeFiles/needle_lib.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f src/CMakeFiles/needle_lib.dir/build.make src/CMakeFiles/needle_lib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 20%] Building CXX object src/CMakeFiles/needle_lib.dir/ibf.cpp.o
[ 40%] Building CXX object src/CMakeFiles/needle_lib.dir/estimate.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/src/../include -I/<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /usr/include/seqan3/submodules/sdsl-lite/include -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 -std=c++20 -fopenmp -MD -MT src/CMakeFiles/needle_lib.dir/estimate.cpp.o -MF CMakeFiles/needle_lib.dir/estimate.cpp.o.d -o CMakeFiles/needle_lib.dir/estimate.cpp.o -c /<<PKGBUILDDIR>>/src/estimate.cpp
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/src/../include -I/<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /usr/include/seqan3/submodules/sdsl-lite/include -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 -std=c++20 -fopenmp -MD -MT src/CMakeFiles/needle_lib.dir/ibf.cpp.o -MF CMakeFiles/needle_lib.dir/ibf.cpp.o.d -o CMakeFiles/needle_lib.dir/ibf.cpp.o -c /<<PKGBUILDDIR>>/src/ibf.cpp
In file included from /usr/include/seqan3/core/concept/cereal.hpp:17,
from /usr/include/seqan3/alphabet/container/concatenated_sequences.hpp:20,
from /<<PKGBUILDDIR>>/src/estimate.cpp:24:
/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."
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/seqan3/core/concept/cereal.hpp:17,
from /usr/include/seqan3/alphabet/container/concatenated_sequences.hpp:20,
from /<<PKGBUILDDIR>>/src/ibf.cpp:28:
/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."
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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>>/src/../include/shared.h:14,
from /<<PKGBUILDDIR>>/src/../include/estimate.h:12,
from /<<PKGBUILDDIR>>/src/estimate.cpp:29:
/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; }
| ~~~~~~~^~~~~~~~~~~~
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>>/src/../include/shared.h:14,
from /<<PKGBUILDDIR>>/src/../include/ibf.h:19,
from /<<PKGBUILDDIR>>/src/ibf.cpp:37:
/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; }
| ~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ibf.cpp: In function ‘void fill_hash_table_parallel(const min_arguments&, seqan3::sequence_file_input<my_traits, seqan3::fields<seqan3::field::seq> >&, robin_hood::unordered_node_map<long unsigned int, short unsigned int>&, robin_hood::unordered_node_map<long unsigned int, unsigned char>&, robin_hood::unordered_set<long unsigned int>&, robin_hood::unordered_set<long unsigned int>&, bool, uint8_t)’:
/<<PKGBUILDDIR>>/src/ibf.cpp:242:38: warning: narrowing conversion of ‘thread_count’ from ‘size_t’ {aka ‘long unsigned int’} to ‘ptrdiff_t’ {aka ‘long int’} [-Wnarrowing]
242 | seqan3::detail::latch sync_point{thread_count};
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ibf.cpp:243:40: warning: narrowing conversion of ‘thread_count’ from ‘size_t’ {aka ‘long unsigned int’} to ‘ptrdiff_t’ {aka ‘long int’} [-Wnarrowing]
243 | seqan3::detail::latch sync_point_2{thread_count};
| ^~~~~~~~~~~~
make[4]: *** [src/CMakeFiles/needle_lib.dir/build.make:93: src/CMakeFiles/needle_lib.dir/estimate.cpp.o] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: *** [src/CMakeFiles/needle_lib.dir/build.make:79: src/CMakeFiles/needle_lib.dir/ibf.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:245: src/CMakeFiles/needle_lib.dir/all] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:124: 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:19: override_dh_auto_build-arch] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:12: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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