[Debian-med-packaging] Bug#1049768: seqan-raptor: Fails to build binary packages again after successful build
Lucas Nussbaum
lucas at debian.org
Wed Aug 16 09:26:38 BST 2023
Source: seqan-raptor
Version: 3.0.0+ds-2
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild
Hi,
This package fails to do build a binary-only build (not source) after a
successful build (dpkg-buildpackage ; dpkg-buildpackage -b).
This is probably a clear violation of Debian Policy section 4.9 (clean target),
but this is filed as severity:minor for now, because a discussion on
debian-devel showed that we might want to revisit the requirement of a working
'clean' target.
More information about this class of issues, included common problems and
solutions, is available at
https://wiki.debian.org/qa.debian.org/FTBFS/DoubleBuild
Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b
> ----------------------------------------------------------------------------------------------------------------------------------
>
> dpkg-buildpackage: info: source package seqan-raptor
> dpkg-buildpackage: info: source version 3.0.0+ds-2
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe at debian.org>
> dpkg-source --before-build .
> dpkg-buildpackage: info: host architecture amd64
> debian/rules clean
> dh clean
> dh_auto_clean
> dh_clean
> debian/rules binary
> dh binary
> dh_update_autotools_config
> dh_autoreconf
> debian/rules override_dh_auto_configure-arch
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_configure -- -DRAPTOR_NATIVE_BUILD=OFF -DRAPTOR_SUBMODULES_DIR=/<<PKGBUILDDIR>>/lib
> cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DRAPTOR_NATIVE_BUILD=OFF -DRAPTOR_SUBMODULES_DIR=/<<BUILDDIR>>/seqan-raptor-3.0.0\+ds/lib ..
> -- The CXX compiler identification is GNU 13.2.0
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Check for working CXX compiler: /usr/bin/c++ - skipped
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- [1mFinding RAPTOR and checking requirements:[m
> -- RAPTOR include dir found: /<<PKGBUILDDIR>>/include
> -- Detected as running from a repository checkout…
> -- …adding submodule include: /<<PKGBUILDDIR>>/lib/chopper/include
> -- …adding submodule include: /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include
> -- …adding submodule include: /<<PKGBUILDDIR>>/lib/sharg-parser/include
> -- …adding submodule include: /<<PKGBUILDDIR>>/lib/sharg-parser/test/include
> -- …adding submodule include: /<<PKGBUILDDIR>>/lib/submodules/lemon/include
> -- C++ Standard-20 support: via -std=c++20
> -- OpenMP Support: via -fopenmp
> -- SIMD-OpenMP Support: via -fopenmp-simd
> -- Suppressing GCC 4 warnings: via -Wno-psabi
> -- Optimize build: via -mpopcnt
> -- Link-time optimization: via -flto=auto
> -- Binary-stripping: via -s
> -- Thread support: builtin
> -- Optional dependency: ZLIB-1.2.13 found
> -- Optional dependency: BZip2-1.0.8 found
> -- Optional dependency: libexecinfo found
> -- Found Raptor: /<<PKGBUILDDIR>>/include
> -- Finding program ccache
> -- Finding program ccache - Failed
> -- The C compiler identification is GNU 13.2.0
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Check for working C compiler: /usr/bin/cc - skipped
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- [1mYou can run `make` to build the application.[m
> -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1")
> -- Checking for module 'libxxhash'
> -- Found libxxhash, version 0.8.1
> -- Configuring done (4.9s)
> -- Generating done (0.0s)
> CMake Warning:
> Manually-specified variables were not used by the project:
>
> CMAKE_EXPORT_NO_PACKAGE_REGISTRY
> CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
> CMAKE_INSTALL_LOCALSTATEDIR
> CMAKE_INSTALL_RUNSTATEDIR
> CMAKE_INSTALL_SYSCONFDIR
>
>
> -- Build files have been written to: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_auto_configure -Nseqan-raptor
> cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu ..
> -- [1mFinding RAPTOR and checking requirements:[m
> -- RAPTOR include dir found: /<<PKGBUILDDIR>>/include
> -- Detected as running from a repository checkout…
> -- …adding submodule include: /<<PKGBUILDDIR>>/lib/chopper/include
> -- …adding submodule include: /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include
> -- …adding submodule include: /<<PKGBUILDDIR>>/lib/sharg-parser/include
> -- …adding submodule include: /<<PKGBUILDDIR>>/lib/sharg-parser/test/include
> -- …adding submodule include: /<<PKGBUILDDIR>>/lib/submodules/lemon/include
> -- C++ Standard-20 support: via -std=c++20
> -- OpenMP Support: via -fopenmp
> -- SIMD-OpenMP Support: via -fopenmp-simd
> -- Suppressing GCC 4 warnings: via -Wno-psabi
> -- Optimize build: via -mpopcnt
> -- Link-time optimization: via -flto=auto
> -- Binary-stripping: via -s
> -- Thread support: builtin
> -- Optional dependency: ZLIB-1.2.13 found
> -- Optional dependency: BZip2-1.0.8 found
> -- Optional dependency: libexecinfo found
> -- [1mYou can run `make` to build the application.[m
> -- Configuring done (1.0s)
> -- Generating done (0.0s)
> -- Build files have been written to: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
> debian/rules override_dh_auto_build-arch
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_build --arch
> cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1
> make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> /usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
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> make -f CMakeFiles/Makefile2 all
> make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> make -f src/upgrade/CMakeFiles/raptor_upgrade.dir/build.make src/upgrade/CMakeFiles/raptor_upgrade.dir/depend
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> make -f src/search/CMakeFiles/raptor_search.dir/build.make src/search/CMakeFiles/raptor_search.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/upgrade /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/upgrade /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/upgrade/CMakeFiles/raptor_upgrade.dir/DependInfo.cmake "--color="
> make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> make -f src/threshold/CMakeFiles/raptor_threshold.dir/build.make src/threshold/CMakeFiles/raptor_threshold.dir/depend
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/lib/chopper /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build/CMakeFiles/xxhash_project.dir/DependInfo.cmake "--color="
> make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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> make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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> make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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> make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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> make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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> make -f src/upgrade/CMakeFiles/raptor_upgrade.dir/build.make src/upgrade/CMakeFiles/raptor_upgrade.dir/build
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> [ 5%] Built target xxhash_project
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/search && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/search/CMakeFiles/raptor_search.dir/raptor_search.cpp.o
> -MF CMakeFiles/raptor_search.dir/raptor_search.cpp.o.d -o CMakeFiles/raptor_search.dir/raptor_search.cpp.o -c /<<PKGBUILDDIR>>/src/search/raptor_search.cpp
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/upgrade && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/upgrade/CMakeFiles/raptor_upgrade.dir/raptor_upgrade.cpp.o
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> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/argument_parsing && /usr/bin/c++ -DRAPTOR_DATE=\"Unavailable\" -DRAPTOR_VERSION="\"3.0.0 (commit unavailable)\"" -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/build_parsing.cpp.o -MF CMakeFiles/raptor_argument_parsing.dir/build_parsing.cpp.o.d -o CMakeFiles/raptor_argument_parsing.dir/build_parsing.cpp.o -c /<<PKGBUILDDIR>>/src/argument_parsing/build_parsing.cpp
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/argument_parsing && /usr/bin/c++ -DRAPTOR_DATE=\"Unavailable\" -DRAPTOR_VERSION="\"3.0.0 (commit unavailable)\"" -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/__/build/hibf/parse_chopper_pack_line.cpp.o -MF CMakeFiles/raptor_argument_parsing.dir/__/build/hibf/parse_chopper_pack_line.cpp.o.d -o CMakeFiles/raptor_argument_parsing.dir/__/build/hibf/parse_chopper_pack_line.cpp.o -c /<<PKGBUILDDIR>>/src/build/hibf/parse_chopper_pack_line.cpp
> make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 15%] Building CXX object src/threshold/CMakeFiles/raptor_threshold.dir/multiple_error_model.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/threshold && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/threshold/CMakeFiles/raptor_threshold.dir/multiple_error_model.cpp.o
> -MF CMakeFiles/raptor_threshold.dir/multiple_error_model.cpp.o.d -o CMakeFiles/raptor_threshold.dir/multiple_error_model.cpp.o -c /<<PKGBUILDDIR>>/src/threshold/multiple_error_model.cpp
> [ 17%] Building CXX object src/threshold/CMakeFiles/raptor_threshold.dir/one_error_model.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/threshold && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/threshold/CMakeFiles/raptor_threshold.dir/one_error_model.cpp.o
> -MF CMakeFiles/raptor_threshold.dir/one_error_model.cpp.o.d -o CMakeFiles/raptor_threshold.dir/one_error_model.cpp.o -c /<<PKGBUILDDIR>>/src/threshold/one_error_model.cpp
> [ 19%] Building CXX object src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/compute_bin_size.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/argument_parsing && /usr/bin/c++ -DRAPTOR_DATE=\"Unavailable\" -DRAPTOR_VERSION="\"3.0.0 (commit unavailable)\"" -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/compute_bin_size.cpp.o -MF CMakeFiles/raptor_argument_parsing.dir/compute_bin_size.cpp.o.d -o CMakeFiles/raptor_argument_parsing.dir/compute_bin_size.cpp.o -c /<<PKGBUILDDIR>>/src/argument_parsing/compute_bin_size.cpp
> [ 21%] Building CXX object src/threshold/CMakeFiles/raptor_threshold.dir/one_indirect_error_model.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/threshold && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/threshold/CMakeFiles/raptor_threshold.dir/one_indirect_error_model.cpp.o
> -MF CMakeFiles/raptor_threshold.dir/one_indirect_error_model.cpp.o.d -o CMakeFiles/raptor_threshold.dir/one_indirect_error_model.cpp.o -c /<<PKGBUILDDIR>>/src/threshold/one_indirect_error_model.cpp
> [ 23%] Building CXX object src/search/CMakeFiles/raptor_search.dir/search_ibf.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/search && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/search/CMakeFiles/raptor_search.dir/search_ibf.cpp.o
> -MF CMakeFiles/raptor_search.dir/search_ibf.cpp.o.d -o CMakeFiles/raptor_search.dir/search_ibf.cpp.o -c /<<PKGBUILDDIR>>/src/search/search_ibf.cpp
> [ 25%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/chopper_build.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/hibf/CMakeFiles/raptor_build_hibf.dir/chopper_build.cpp.o
> -MF CMakeFiles/raptor_build_hibf.dir/chopper_build.cpp.o.d -o CMakeFiles/raptor_build_hibf.dir/chopper_build.cpp.o -c /<<PKGBUILDDIR>>/src/build/hibf/chopper_build.cpp
> [ 27%] Building CXX object src/threshold/CMakeFiles/raptor_threshold.dir/pascal_row.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/threshold && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/threshold/CMakeFiles/raptor_threshold.dir/pascal_row.cpp.o
> -MF CMakeFiles/raptor_threshold.dir/pascal_row.cpp.o.d -o CMakeFiles/raptor_threshold.dir/pascal_row.cpp.o -c /<<PKGBUILDDIR>>/src/threshold/pascal_row.cpp
> In file included from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:28,
> from /<<PKGBUILDDIR>>/src/build/hibf/chopper_build.cpp:13:
> /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
> 20 | : public T, public std::iterator<std::input_iterator_tag, T> {
> | ^~~~~~~~
> In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
> from /usr/include/c++/13/vector:62,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/core.h:45,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:26:
> /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
> 127 | struct _GLIBCXX17_DEPRECATED iterator
> | ^~~~~~~~
> [ 29%] Building CXX object src/threshold/CMakeFiles/raptor_threshold.dir/precompute_correction.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/threshold && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/threshold/CMakeFiles/raptor_threshold.dir/precompute_correction.cpp.o
> -MF CMakeFiles/raptor_threshold.dir/precompute_correction.cpp.o.d -o CMakeFiles/raptor_threshold.dir/precompute_correction.cpp.o -c /<<PKGBUILDDIR>>/src/threshold/precompute_correction.cpp
> [ 31%] Building CXX object src/threshold/CMakeFiles/raptor_threshold.dir/precompute_threshold.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/threshold && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/threshold/CMakeFiles/raptor_threshold.dir/precompute_threshold.cpp.o
> -MF CMakeFiles/raptor_threshold.dir/precompute_threshold.cpp.o.d -o CMakeFiles/raptor_threshold.dir/precompute_threshold.cpp.o -c /<<PKGBUILDDIR>>/src/threshold/precompute_threshold.cpp
> In file included from /<<PKGBUILDDIR>>/include/raptor/build/hibf/create_ibfs_from_chopper_pack.hpp:16,
> from /<<PKGBUILDDIR>>/src/build/hibf/chopper_build.cpp:16:
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size]
> 27 | alignas(std::hardware_destructive_interference_size) std::atomic<size_t> ibf_number{};
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: the default value for the current CPU tuning is 64 bytes
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:28:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size]
> 28 | alignas(std::hardware_destructive_interference_size) std::atomic<size_t> user_bin_number{};
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> [ 33%] Linking CXX static library ../../lib/libraptor_threshold.a
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/threshold && /usr/bin/cmake -P CMakeFiles/raptor_threshold.dir/cmake_clean_target.cmake
> [ 35%] Linking CXX static library ../../lib/libraptor_upgrade.a
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/upgrade && /usr/bin/cmake -P CMakeFiles/raptor_upgrade.dir/cmake_clean_target.cmake
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/threshold && /usr/bin/cmake -E cmake_link_script CMakeFiles/raptor_threshold.dir/link.txt --verbose=1
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/upgrade && /usr/bin/cmake -E cmake_link_script CMakeFiles/raptor_upgrade.dir/link.txt --verbose=1
> /usr/bin/ar qc ../../lib/libraptor_threshold.a CMakeFiles/raptor_threshold.dir/multiple_error_model.cpp.o CMakeFiles/raptor_threshold.dir/one_error_model.cpp.o CMakeFiles/raptor_threshold.dir/one_indirect_error_model.cpp.o CMakeFiles/raptor_threshold.dir/pascal_row.cpp.o CMakeFiles/raptor_threshold.dir/precompute_correction.cpp.o CMakeFiles/raptor_threshold.dir/precompute_threshold.cpp.o
> /usr/bin/ar qc ../../lib/libraptor_upgrade.a CMakeFiles/raptor_upgrade.dir/raptor_upgrade.cpp.o
> /usr/bin/ranlib ../../lib/libraptor_threshold.a
> /usr/bin/ranlib ../../lib/libraptor_upgrade.a
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 35%] Built target raptor_threshold
> [ 35%] Built target raptor_upgrade
> [ 37%] Building CXX object src/search/CMakeFiles/raptor_search.dir/search_partitioned_ibf.cpp.o
> [ 39%] Building CXX object src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/init_shared_meta.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/search && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/search/CMakeFiles/raptor_search.dir/search_partitioned_ibf.cpp.o
> -MF CMakeFiles/raptor_search.dir/search_partitioned_ibf.cpp.o.d -o CMakeFiles/raptor_search.dir/search_partitioned_ibf.cpp.o -c /<<PKGBUILDDIR>>/src/search/search_partitioned_ibf.cpp
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/argument_parsing && /usr/bin/c++ -DRAPTOR_DATE=\"Unavailable\" -DRAPTOR_VERSION="\"3.0.0 (commit unavailable)\"" -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/init_shared_meta.cpp.o -MF CMakeFiles/raptor_argument_parsing.dir/init_shared_meta.cpp.o.d -o CMakeFiles/raptor_argument_parsing.dir/init_shared_meta.cpp.o -c /<<PKGBUILDDIR>>/src/argument_parsing/init_shared_meta.cpp
> [ 41%] Linking CXX static library ../../lib/libraptor_prepare.a
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/prepare && /usr/bin/cmake -P CMakeFiles/raptor_prepare.dir/cmake_clean_target.cmake
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/prepare && /usr/bin/cmake -E cmake_link_script CMakeFiles/raptor_prepare.dir/link.txt --verbose=1
> /usr/bin/ar qc ../../lib/libraptor_prepare.a CMakeFiles/raptor_prepare.dir/compute_minimiser.cpp.o
> /usr/bin/ranlib ../../lib/libraptor_prepare.a
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 41%] Built target raptor_prepare
> make -f _deps/raptor_chopper_project-build/src/CMakeFiles/chopper_layout_lib.dir/build.make _deps/raptor_chopper_project-build/src/CMakeFiles/chopper_layout_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>>/lib/chopper/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build/src/CMakeFiles/chopper_layout_lib.dir/DependInfo.cmake "--color="
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> make -f _deps/raptor_chopper_project-build/src/CMakeFiles/chopper_layout_lib.dir/build.make _deps/raptor_chopper_project-build/src/CMakeFiles/chopper_layout_lib.dir/build
> make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 43%] Building CXX object _deps/raptor_chopper_project-build/src/CMakeFiles/chopper_layout_lib.dir/chopper_layout.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build/src && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -DSHARG_HAS_BZIP2=1 -DSHARG_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/lib/chopper/src/../include -I/<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -I/<<PKGBUILDDIR>>/lib/simde/simde -I/<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/sharg-parser/include/ -I/<<PKGBUILDDIR>>/lib/submodules/lemon/include/ -fopenmp -fopenmp-simd -DSIMDE_ENABLE_OPENMP
> -Wno-psabi -pedantic -Wall -Wextra -std=c++20 -MD -MT _deps/raptor_chopper_project-build/src/CMakeFiles/chopper_layout_lib.dir/chopper_layout.cpp.o -MF CMakeFiles/chopper_layout_lib.dir/chopper_layout.cpp.o.d -o CMakeFiles/chopper_layout_lib.dir/chopper_layout.cpp.o -c /<<PKGBUILDDIR>>/lib/chopper/src/chopper_layout.cpp
> [ 45%] Building CXX object src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/parse_bin_path.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/argument_parsing && /usr/bin/c++ -DRAPTOR_DATE=\"Unavailable\" -DRAPTOR_VERSION="\"3.0.0 (commit unavailable)\"" -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/parse_bin_path.cpp.o -MF CMakeFiles/raptor_argument_parsing.dir/parse_bin_path.cpp.o.d -o CMakeFiles/raptor_argument_parsing.dir/parse_bin_path.cpp.o -c /<<PKGBUILDDIR>>/src/argument_parsing/parse_bin_path.cpp
> [ 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="\"3.0.0 (commit unavailable)\"" -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -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
> [ 49%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/compute_kmers.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/hibf/CMakeFiles/raptor_build_hibf.dir/compute_kmers.cpp.o
> -MF CMakeFiles/raptor_build_hibf.dir/compute_kmers.cpp.o.d -o CMakeFiles/raptor_build_hibf.dir/compute_kmers.cpp.o -c /<<PKGBUILDDIR>>/src/build/hibf/compute_kmers.cpp
> [ 50%] 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="\"3.0.0 (commit unavailable)\"" -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -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
> [ 52%] Building CXX object src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/upgrade_parsing.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/argument_parsing && /usr/bin/c++ -DRAPTOR_DATE=\"Unavailable\" -DRAPTOR_VERSION="\"3.0.0 (commit unavailable)\"" -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/upgrade_parsing.cpp.o -MF CMakeFiles/raptor_argument_parsing.dir/upgrade_parsing.cpp.o.d -o CMakeFiles/raptor_argument_parsing.dir/upgrade_parsing.cpp.o -c /<<PKGBUILDDIR>>/src/argument_parsing/upgrade_parsing.cpp
> [ 54%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/construct_ibf.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/hibf/CMakeFiles/raptor_build_hibf.dir/construct_ibf.cpp.o
> -MF CMakeFiles/raptor_build_hibf.dir/construct_ibf.cpp.o.d -o CMakeFiles/raptor_build_hibf.dir/construct_ibf.cpp.o -c /<<PKGBUILDDIR>>/src/build/hibf/construct_ibf.cpp
> [ 56%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/create_ibfs_from_chopper_pack.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/hibf/CMakeFiles/raptor_build_hibf.dir/create_ibfs_from_chopper_pack.cpp.o
> -MF CMakeFiles/raptor_build_hibf.dir/create_ibfs_from_chopper_pack.cpp.o.d -o CMakeFiles/raptor_build_hibf.dir/create_ibfs_from_chopper_pack.cpp.o -c /<<PKGBUILDDIR>>/src/build/hibf/create_ibfs_from_chopper_pack.cpp
> In file included from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:28,
> from /<<PKGBUILDDIR>>/src/build/hibf/construct_ibf.cpp:13:
> /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
> 20 | : public T, public std::iterator<std::input_iterator_tag, T> {
> | ^~~~~~~~
> In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
> from /usr/include/c++/13/vector:62,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/core.h:45,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:26:
> /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
> 127 | struct _GLIBCXX17_DEPRECATED iterator
> | ^~~~~~~~
> [ 58%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/hierarchical_build.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/hibf/CMakeFiles/raptor_build_hibf.dir/hierarchical_build.cpp.o
> -MF CMakeFiles/raptor_build_hibf.dir/hierarchical_build.cpp.o.d -o CMakeFiles/raptor_build_hibf.dir/hierarchical_build.cpp.o -c /<<PKGBUILDDIR>>/src/build/hibf/hierarchical_build.cpp
> [ 60%] Linking CXX static library ../../../lib/libchopper_layout_lib.a
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build/src && /usr/bin/cmake -P CMakeFiles/chopper_layout_lib.dir/cmake_clean_target.cmake
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/chopper_layout_lib.dir/link.txt --verbose=1
> /usr/bin/ar qc ../../../lib/libchopper_layout_lib.a CMakeFiles/chopper_layout_lib.dir/chopper_layout.cpp.o
> In file included from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:28,
> from /<<PKGBUILDDIR>>/src/build/hibf/create_ibfs_from_chopper_pack.cpp:13:
> /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
> 20 | : public T, public std::iterator<std::input_iterator_tag, T> {
> | ^~~~~~~~
> In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
> from /usr/include/c++/13/vector:62,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/core.h:45,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:26:
> /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
> 127 | struct _GLIBCXX17_DEPRECATED iterator
> | ^~~~~~~~
> /usr/bin/ranlib ../../../lib/libchopper_layout_lib.a
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 60%] Built target chopper_layout_lib
> make -f src/build/CMakeFiles/raptor_build.dir/build.make src/build/CMakeFiles/raptor_build.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/build /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/CMakeFiles/raptor_build.dir/DependInfo.cmake "--color="
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> make -f src/build/CMakeFiles/raptor_build.dir/build.make src/build/CMakeFiles/raptor_build.dir/build
> make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 62%] Building CXX object src/build/CMakeFiles/raptor_build.dir/build_ibf.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/CMakeFiles/raptor_build.dir/build_ibf.cpp.o
> -MF CMakeFiles/raptor_build.dir/build_ibf.cpp.o.d -o CMakeFiles/raptor_build.dir/build_ibf.cpp.o -c /<<PKGBUILDDIR>>/src/build/build_ibf.cpp
> In file included from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:28,
> from /<<PKGBUILDDIR>>/src/build/hibf/hierarchical_build.cpp:13:
> /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
> 20 | : public T, public std::iterator<std::input_iterator_tag, T> {
> | ^~~~~~~~
> In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
> from /usr/include/c++/13/vector:62,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/core.h:45,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:26:
> /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
> 127 | struct _GLIBCXX17_DEPRECATED iterator
> | ^~~~~~~~
> [ 64%] Building CXX object src/build/CMakeFiles/raptor_build.dir/max_count_per_partition.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/CMakeFiles/raptor_build.dir/max_count_per_partition.cpp.o
> -MF CMakeFiles/raptor_build.dir/max_count_per_partition.cpp.o.d -o CMakeFiles/raptor_build.dir/max_count_per_partition.cpp.o -c /<<PKGBUILDDIR>>/src/build/max_count_per_partition.cpp
> In file included from /<<PKGBUILDDIR>>/include/raptor/build/hibf/create_ibfs_from_chopper_pack.hpp:16,
> from /<<PKGBUILDDIR>>/src/build/hibf/create_ibfs_from_chopper_pack.cpp:15:
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size]
> 27 | alignas(std::hardware_destructive_interference_size) std::atomic<size_t> ibf_number{};
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: the default value for the current CPU tuning is 64 bytes
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:28:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size]
> 28 | alignas(std::hardware_destructive_interference_size) std::atomic<size_t> user_bin_number{};
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> In file included from /<<PKGBUILDDIR>>/include/raptor/build/hibf/construct_ibf.hpp:18,
> from /<<PKGBUILDDIR>>/src/build/hibf/construct_ibf.cpp:16:
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size]
> 27 | alignas(std::hardware_destructive_interference_size) std::atomic<size_t> ibf_number{};
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: the default value for the current CPU tuning is 64 bytes
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:28:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size]
> 28 | alignas(std::hardware_destructive_interference_size) std::atomic<size_t> user_bin_number{};
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> [ 66%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/insert_into_ibf.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/hibf/CMakeFiles/raptor_build_hibf.dir/insert_into_ibf.cpp.o
> -MF CMakeFiles/raptor_build_hibf.dir/insert_into_ibf.cpp.o.d -o CMakeFiles/raptor_build_hibf.dir/insert_into_ibf.cpp.o -c /<<PKGBUILDDIR>>/src/build/hibf/insert_into_ibf.cpp
> In file included from /<<PKGBUILDDIR>>/include/raptor/build/hibf/construct_ibf.hpp:18,
> from /<<PKGBUILDDIR>>/src/build/hibf/hierarchical_build.cpp:16:
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size]
> 27 | alignas(std::hardware_destructive_interference_size) std::atomic<size_t> ibf_number{};
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: the default value for the current CPU tuning is 64 bytes
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:28:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size]
> 28 | alignas(std::hardware_destructive_interference_size) std::atomic<size_t> user_bin_number{};
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> [ 68%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/loop_over_children.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/hibf/CMakeFiles/raptor_build_hibf.dir/loop_over_children.cpp.o
> -MF CMakeFiles/raptor_build_hibf.dir/loop_over_children.cpp.o.d -o CMakeFiles/raptor_build_hibf.dir/loop_over_children.cpp.o -c /<<PKGBUILDDIR>>/src/build/hibf/loop_over_children.cpp
> [ 70%] Linking CXX static library ../../lib/libraptor_search.a
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/search && /usr/bin/cmake -P CMakeFiles/raptor_search.dir/cmake_clean_target.cmake
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/search && /usr/bin/cmake -E cmake_link_script CMakeFiles/raptor_search.dir/link.txt --verbose=1
> /usr/bin/ar qc ../../lib/libraptor_search.a CMakeFiles/raptor_search.dir/raptor_search.cpp.o CMakeFiles/raptor_search.dir/search_hibf.cpp.o CMakeFiles/raptor_search.dir/search_ibf.cpp.o CMakeFiles/raptor_search.dir/search_partitioned_ibf.cpp.o
> /usr/bin/ranlib ../../lib/libraptor_search.a
> In file included from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:28,
> from /<<PKGBUILDDIR>>/src/build/hibf/loop_over_children.cpp:13:
> /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
> 20 | : public T, public std::iterator<std::input_iterator_tag, T> {
> | ^~~~~~~~
> In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
> from /usr/include/c++/13/vector:62,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/core.h:45,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:26:
> /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
> 127 | struct _GLIBCXX17_DEPRECATED iterator
> | ^~~~~~~~
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 70%] Built target raptor_search
> [ 72%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/parse_chopper_pack_header.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/hibf/CMakeFiles/raptor_build_hibf.dir/parse_chopper_pack_header.cpp.o
> -MF CMakeFiles/raptor_build_hibf.dir/parse_chopper_pack_header.cpp.o.d -o CMakeFiles/raptor_build_hibf.dir/parse_chopper_pack_header.cpp.o -c /<<PKGBUILDDIR>>/src/build/hibf/parse_chopper_pack_header.cpp
> In file included from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:28,
> from /<<PKGBUILDDIR>>/src/build/hibf/parse_chopper_pack_header.cpp:17:
> /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
> 20 | : public T, public std::iterator<std::input_iterator_tag, T> {
> | ^~~~~~~~
> In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
> from /usr/include/c++/13/algorithm:60,
> from /<<PKGBUILDDIR>>/src/build/hibf/parse_chopper_pack_header.cpp:13:
> /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
> 127 | struct _GLIBCXX17_DEPRECATED iterator
> | ^~~~~~~~
> [ 74%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/parse_chopper_pack_line.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/hibf/CMakeFiles/raptor_build_hibf.dir/parse_chopper_pack_line.cpp.o
> -MF CMakeFiles/raptor_build_hibf.dir/parse_chopper_pack_line.cpp.o.d -o CMakeFiles/raptor_build_hibf.dir/parse_chopper_pack_line.cpp.o -c /<<PKGBUILDDIR>>/src/build/hibf/parse_chopper_pack_line.cpp
> [ 76%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/read_chopper_pack_file.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/hibf/CMakeFiles/raptor_build_hibf.dir/read_chopper_pack_file.cpp.o
> -MF CMakeFiles/raptor_build_hibf.dir/read_chopper_pack_file.cpp.o.d -o CMakeFiles/raptor_build_hibf.dir/read_chopper_pack_file.cpp.o -c /<<PKGBUILDDIR>>/src/build/hibf/read_chopper_pack_file.cpp
> [ 78%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/update_parent_kmers.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/hibf/CMakeFiles/raptor_build_hibf.dir/update_parent_kmers.cpp.o
> -MF CMakeFiles/raptor_build_hibf.dir/update_parent_kmers.cpp.o.d -o CMakeFiles/raptor_build_hibf.dir/update_parent_kmers.cpp.o -c /<<PKGBUILDDIR>>/src/build/hibf/update_parent_kmers.cpp
> [ 80%] Building CXX object src/build/hibf/CMakeFiles/raptor_build_hibf.dir/update_user_bins.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/hibf/CMakeFiles/raptor_build_hibf.dir/update_user_bins.cpp.o
> -MF CMakeFiles/raptor_build_hibf.dir/update_user_bins.cpp.o.d -o CMakeFiles/raptor_build_hibf.dir/update_user_bins.cpp.o -c /<<PKGBUILDDIR>>/src/build/hibf/update_user_bins.cpp
> In file included from /<<PKGBUILDDIR>>/include/raptor/build/hibf/hierarchical_build.hpp:18,
> from /<<PKGBUILDDIR>>/src/build/hibf/loop_over_children.cpp:17:
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size]
> 27 | alignas(std::hardware_destructive_interference_size) std::atomic<size_t> ibf_number{};
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: the default value for the current CPU tuning is 64 bytes
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:28:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size]
> 28 | alignas(std::hardware_destructive_interference_size) std::atomic<size_t> user_bin_number{};
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> In file included from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:28,
> from /<<PKGBUILDDIR>>/src/build/hibf/read_chopper_pack_file.cpp:13:
> /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
> 20 | : public T, public std::iterator<std::input_iterator_tag, T> {
> | ^~~~~~~~
> In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
> from /usr/include/c++/13/vector:62,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/core.h:45,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:26:
> /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
> 127 | struct _GLIBCXX17_DEPRECATED iterator
> | ^~~~~~~~
> In file included from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/graph_extender.h:30,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:28,
> from /<<PKGBUILDDIR>>/src/build/hibf/update_user_bins.cpp:13:
> /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
> 20 | : public T, public std::iterator<std::input_iterator_tag, T> {
> | ^~~~~~~~
> In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
> from /usr/include/c++/13/vector:62,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/core.h:45,
> from /<<PKGBUILDDIR>>/lib/submodules/lemon/include/lemon/list_graph.h:26:
> /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
> 127 | struct _GLIBCXX17_DEPRECATED iterator
> | ^~~~~~~~
> [ 82%] Building CXX object src/build/CMakeFiles/raptor_build.dir/raptor_build.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/build/CMakeFiles/raptor_build.dir/raptor_build.cpp.o
> -MF CMakeFiles/raptor_build.dir/raptor_build.cpp.o.d -o CMakeFiles/raptor_build.dir/raptor_build.cpp.o -c /<<PKGBUILDDIR>>/src/build/raptor_build.cpp
> make -f src/layout/CMakeFiles/raptor_layout.dir/build.make src/layout/CMakeFiles/raptor_layout.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/layout /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/layout /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/layout/CMakeFiles/raptor_layout.dir/DependInfo.cmake "--color="
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> make -f src/layout/CMakeFiles/raptor_layout.dir/build.make src/layout/CMakeFiles/raptor_layout.dir/build
> make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 84%] Building CXX object src/layout/CMakeFiles/raptor_layout.dir/raptor_layout.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/layout && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -DSHARG_HAS_BZIP2=1 -DSHARG_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/lib/chopper/src/../include -I/<<PKGBUILDDIR>>/lib/simde/simde -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -isystem /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/layout/CMakeFiles/raptor_layout.dir/raptor_layout.cpp.o -MF CMakeFiles/raptor_layout.dir/raptor_layout.cpp.o.d -o CMakeFiles/raptor_layout.dir/raptor_layout.cpp.o -c /<<PKGBUILDDIR>>/src/layout/raptor_layout.cpp
> [ 86%] Linking CXX static library ../../lib/libraptor_argument_parsing.a
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/argument_parsing && /usr/bin/cmake -P CMakeFiles/raptor_argument_parsing.dir/cmake_clean_target.cmake
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/argument_parsing && /usr/bin/cmake -E cmake_link_script CMakeFiles/raptor_argument_parsing.dir/link.txt --verbose=1
> /usr/bin/ar qc ../../lib/libraptor_argument_parsing.a CMakeFiles/raptor_argument_parsing.dir/__/build/hibf/parse_chopper_pack_line.cpp.o CMakeFiles/raptor_argument_parsing.dir/build_parsing.cpp.o CMakeFiles/raptor_argument_parsing.dir/compute_bin_size.cpp.o CMakeFiles/raptor_argument_parsing.dir/init_shared_meta.cpp.o CMakeFiles/raptor_argument_parsing.dir/parse_bin_path.cpp.o CMakeFiles/raptor_argument_parsing.dir/prepare_parsing.cpp.o CMakeFiles/raptor_argument_parsing.dir/search_parsing.cpp.o CMakeFiles/raptor_argument_parsing.dir/upgrade_parsing.cpp.o
> /usr/bin/ranlib ../../lib/libraptor_argument_parsing.a
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 86%] Built target raptor_argument_parsing
> make -f _deps/raptor_chopper_project-build/src/CMakeFiles/chopper.dir/build.make _deps/raptor_chopper_project-build/src/CMakeFiles/chopper.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>>/lib/chopper/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build/src/CMakeFiles/chopper.dir/DependInfo.cmake "--color="
> In file included from /<<PKGBUILDDIR>>/include/raptor/build/hibf/read_chopper_pack_file.hpp:17,
> from /<<PKGBUILDDIR>>/src/build/hibf/read_chopper_pack_file.cpp:17:
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size]
> 27 | alignas(std::hardware_destructive_interference_size) std::atomic<size_t> ibf_number{};
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: the default value for the current CPU tuning is 64 bytes
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:28:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size]
> 28 | alignas(std::hardware_destructive_interference_size) std::atomic<size_t> user_bin_number{};
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> make -f _deps/raptor_chopper_project-build/src/CMakeFiles/chopper.dir/build.make _deps/raptor_chopper_project-build/src/CMakeFiles/chopper.dir/build
> make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 88%] Building CXX object _deps/raptor_chopper_project-build/src/CMakeFiles/chopper.dir/chopper.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build/src && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -DSHARG_HAS_BZIP2=1 -DSHARG_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/lib/chopper/src/../include -I/<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -I/<<PKGBUILDDIR>>/lib/simde/simde -I/<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/sharg-parser/include/ -I/<<PKGBUILDDIR>>/lib/submodules/lemon/include/ -fopenmp -fopenmp-simd -DSIMDE_ENABLE_OPENMP
> -Wno-psabi -pedantic -Wall -Wextra -std=c++20 -MD -MT _deps/raptor_chopper_project-build/src/CMakeFiles/chopper.dir/chopper.cpp.o -MF CMakeFiles/chopper.dir/chopper.cpp.o.d -o CMakeFiles/chopper.dir/chopper.cpp.o -c /<<PKGBUILDDIR>>/lib/chopper/src/chopper.cpp
> In file included from /<<PKGBUILDDIR>>/include/raptor/build/hibf/update_user_bins.hpp:15,
> from /<<PKGBUILDDIR>>/src/build/hibf/update_user_bins.cpp:15:
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size]
> 27 | alignas(std::hardware_destructive_interference_size) std::atomic<size_t> ibf_number{};
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: its value can vary between compiler versions or with different ‘-mtune’ or ‘-mcpu’ flags
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: the default value for the current CPU tuning is 64 bytes
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:27:18: note: you can stabilize this value with ‘--param hardware_destructive_interference_size=64’, or disable this warning with ‘-Wno-interference-size’
> /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:28:18: warning: use of ‘std::hardware_destructive_interference_size’ [-Winterference-size]
> 28 | alignas(std::hardware_destructive_interference_size) std::atomic<size_t> user_bin_number{};
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> [ 90%] Linking CXX static library ../../lib/libraptor_build.a
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build && /usr/bin/cmake -P CMakeFiles/raptor_build.dir/cmake_clean_target.cmake
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build && /usr/bin/cmake -E cmake_link_script CMakeFiles/raptor_build.dir/link.txt --verbose=1
> /usr/bin/ar qc ../../lib/libraptor_build.a CMakeFiles/raptor_build.dir/build_ibf.cpp.o CMakeFiles/raptor_build.dir/max_count_per_partition.cpp.o CMakeFiles/raptor_build.dir/raptor_build.cpp.o
> /usr/bin/ranlib ../../lib/libraptor_build.a
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 90%] Built target raptor_build
> [ 92%] Linking CXX static library ../../../lib/libraptor_build_hibf.a
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf && /usr/bin/cmake -P CMakeFiles/raptor_build_hibf.dir/cmake_clean_target.cmake
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf && /usr/bin/cmake -E cmake_link_script CMakeFiles/raptor_build_hibf.dir/link.txt --verbose=1
> /usr/bin/ar qc ../../../lib/libraptor_build_hibf.a CMakeFiles/raptor_build_hibf.dir/bin_size_in_bits.cpp.o CMakeFiles/raptor_build_hibf.dir/chopper_build.cpp.o CMakeFiles/raptor_build_hibf.dir/compute_kmers.cpp.o CMakeFiles/raptor_build_hibf.dir/construct_ibf.cpp.o CMakeFiles/raptor_build_hibf.dir/create_ibfs_from_chopper_pack.cpp.o CMakeFiles/raptor_build_hibf.dir/hierarchical_build.cpp.o CMakeFiles/raptor_build_hibf.dir/insert_into_ibf.cpp.o CMakeFiles/raptor_build_hibf.dir/loop_over_children.cpp.o CMakeFiles/raptor_build_hibf.dir/parse_chopper_pack_header.cpp.o CMakeFiles/raptor_build_hibf.dir/parse_chopper_pack_line.cpp.o CMakeFiles/raptor_build_hibf.dir/read_chopper_pack_file.cpp.o CMakeFiles/raptor_build_hibf.dir/update_parent_kmers.cpp.o CMakeFiles/raptor_build_hibf.dir/update_user_bins.cpp.o
> /usr/bin/ranlib ../../../lib/libraptor_build_hibf.a
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 92%] Built target raptor_build_hibf
> [ 94%] Linking CXX static library ../../lib/libraptor_layout.a
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/layout && /usr/bin/cmake -P CMakeFiles/raptor_layout.dir/cmake_clean_target.cmake
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/layout && /usr/bin/cmake -E cmake_link_script CMakeFiles/raptor_layout.dir/link.txt --verbose=1
> /usr/bin/ar qc ../../lib/libraptor_layout.a CMakeFiles/raptor_layout.dir/raptor_layout.cpp.o
> /usr/bin/ranlib ../../lib/libraptor_layout.a
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 94%] Built target raptor_layout
> make -f src/CMakeFiles/raptor.dir/build.make src/CMakeFiles/raptor.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/raptor.dir/DependInfo.cmake "--color="
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> make -f src/CMakeFiles/raptor.dir/build.make src/CMakeFiles/raptor.dir/build
> make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 96%] Building CXX object src/CMakeFiles/raptor.dir/raptor.cpp.o
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DRAPTOR_DATE=\"Unavailable\" -DRAPTOR_VERSION="\"3.0.0 (commit unavailable)\"" -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -DSHARG_HAS_BZIP2=1 -DSHARG_HAS_ZLIB=1 -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/lib/chopper/src/../include -I/<<PKGBUILDDIR>>/lib/simde/simde -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/test/include -isystem /<<PKGBUILDDIR>>/lib/sharg-parser/include -isystem /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include -isystem /<<PKGBUILDDIR>>/lib/chopper/include -isystem /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/
> -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/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 -s -MD -MT src/CMakeFiles/raptor.dir/raptor.cpp.o -MF CMakeFiles/raptor.dir/raptor.cpp.o.d -o CMakeFiles/raptor.dir/raptor.cpp.o -c /<<PKGBUILDDIR>>/src/raptor.cpp
> [ 98%] Linking CXX executable ../bin/raptor
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/raptor.dir/link.txt --verbose=1
> /usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/sharg-parser/include/ -I/<<PKGBUILDDIR>>/lib/submodules/lemon/include/ -Wl,-z,relro -Wl,-z,now -std=c++20 -fopenmp -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -mpopcnt -flto=auto -s CMakeFiles/raptor.dir/raptor.cpp.o -o ../bin/raptor ../lib/libraptor_argument_parsing.a ../lib/libraptor_build.a ../lib/libraptor_build_hibf.a ../lib/libraptor_prepare.a ../lib/libraptor_search.a ../lib/libraptor_threshold.a ../lib/libraptor_upgrade.a ../lib/libraptor_layout.a ../lib/libchopper_layout_lib.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libbz2.so
> -lrt /usr/lib/x86_64-linux-gnu/libxxhash.a /usr/lib/x86_64-linux-gnu/libxxhash.so
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [ 98%] Built target raptor
> [100%] Linking CXX executable ../../../bin/chopper
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/_deps/raptor_chopper_project-build/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/chopper.dir/link.txt --verbose=1
> /usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/seqan3/submodules/sdsl-lite/include/ -I/usr/include/simde -I/<<PKGBUILDDIR>>/lib/submodules/sharg-parser/include/ -I/<<PKGBUILDDIR>>/lib/submodules/lemon/include/ -fopenmp -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -Wl,-z,relro -Wl,-z,now CMakeFiles/chopper.dir/chopper.cpp.o -o ../../../bin/chopper ../../../lib/libchopper_layout_lib.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libbz2.so -lrt /usr/lib/x86_64-linux-gnu/libxxhash.a
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> [100%] Built target chopper
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> /usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles 0
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> obj-*/bin/raptor --export-help man > debian/raptor.1
> obj-*/bin/raptor build --export-help man > debian/raptor-build.1
> obj-*/bin/raptor search --export-help man > debian/raptor-search.1
> obj-*/bin/raptor layout --export-help man > debian/raptor-layout.1
> obj-*/bin/raptor prepare --export-help man > debian/raptor-prepare.1
> obj-*/bin/raptor upgrade --export-help man > debian/raptor-upgrade.1
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> debian/rules override_dh_auto_build-indep
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> mkdir doc_build && cd doc_build && cmake ../test/documentation && /usr/bin/make && ctest . --output-on-failure && cd latex && /usr/bin/make
> mkdir: cannot create directory ‘doc_build’: File exists
> make[1]: *** [debian/rules:27: override_dh_auto_build-indep] Error 1
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> make: *** [debian/rules:11: binary] Error 2
> dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
>
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b' failed to run.
The full build log is available from:
http://qa-logs.debian.net/2023/08/16/seqan-raptor_3.0.0+ds-2_unstable.log
If you reassign this bug to another package, please mark 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.
More information about the Debian-med-packaging
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