Source: seqan-raptor Version: 3.0.0+ds-2 Severity: minor Tags: trixie sid ftbfs User: [email protected] Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build User: [email protected] 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 > <[email protected]> > 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⦠> -- â¦adding submodule include: /<<PKGBUILDDIR>>/lib/chopper/include > -- â¦adding submodule include: > /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include > -- â¦adding submodule include: /<<PKGBUILDDIR>>/lib/sharg-parser/include > -- â¦adding submodule include: > /<<PKGBUILDDIR>>/lib/sharg-parser/test/include > -- â¦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⦠> -- â¦adding submodule include: /<<PKGBUILDDIR>>/lib/chopper/include > -- â¦adding submodule include: > /<<PKGBUILDDIR>>/lib/robin-hood-hashing/src/include > -- â¦adding submodule include: /<<PKGBUILDDIR>>/lib/sharg-parser/include > -- â¦adding submodule include: > /<<PKGBUILDDIR>>/lib/sharg-parser/test/include > -- â¦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 > /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/upgrade/CMakeFiles/raptor_upgrade.dir/build.make > src/upgrade/CMakeFiles/raptor_upgrade.dir/depend > make -f > _deps/raptor_chopper_project-build/CMakeFiles/xxhash_project.dir/build.make > _deps/raptor_chopper_project-build/CMakeFiles/xxhash_project.dir/depend > make -f > src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/build.make > src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/depend > make -f src/prepare/CMakeFiles/raptor_prepare.dir/build.make > src/prepare/CMakeFiles/raptor_prepare.dir/depend > make -f src/build/hibf/CMakeFiles/raptor_build_hibf.dir/build.make > src/build/hibf/CMakeFiles/raptor_build_hibf.dir/depend > 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' > cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends > "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/argument_parsing > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/argument_parsing > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/DependInfo.cmake > "--color=" > 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/prepare > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/prepare > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/prepare/CMakeFiles/raptor_prepare.dir/DependInfo.cmake > "--color=" > 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/hibf > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/build/hibf/CMakeFiles/raptor_build_hibf.dir/DependInfo.cmake > "--color=" > 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/search > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/search > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/search/CMakeFiles/raptor_search.dir/DependInfo.cmake > "--color=" > 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/threshold > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/threshold > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/threshold/CMakeFiles/raptor_threshold.dir/DependInfo.cmake > "--color=" > make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make -f > _deps/raptor_chopper_project-build/CMakeFiles/xxhash_project.dir/build.make > _deps/raptor_chopper_project-build/CMakeFiles/xxhash_project.dir/build > make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make -f src/upgrade/CMakeFiles/raptor_upgrade.dir/build.make > src/upgrade/CMakeFiles/raptor_upgrade.dir/build > make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make -f src/search/CMakeFiles/raptor_search.dir/build.make > src/search/CMakeFiles/raptor_search.dir/build > make -f > src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/build.make > src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/build > make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make[4]: Nothing to be done for > '_deps/raptor_chopper_project-build/CMakeFiles/xxhash_project.dir/build'. > make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make -f src/build/hibf/CMakeFiles/raptor_build_hibf.dir/build.make > src/build/hibf/CMakeFiles/raptor_build_hibf.dir/build > make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make -f src/prepare/CMakeFiles/raptor_prepare.dir/build.make > src/prepare/CMakeFiles/raptor_prepare.dir/build > make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > [ 3%] Building CXX object > src/upgrade/CMakeFiles/raptor_upgrade.dir/raptor_upgrade.cpp.o > [ 3%] Building CXX object > src/search/CMakeFiles/raptor_search.dir/raptor_search.cpp.o > [ 5%] Building CXX object > src/build/hibf/CMakeFiles/raptor_build_hibf.dir/bin_size_in_bits.cpp.o > [ 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 > -MF CMakeFiles/raptor_upgrade.dir/raptor_upgrade.cpp.o.d -o > CMakeFiles/raptor_upgrade.dir/raptor_upgrade.cpp.o -c > /<<PKGBUILDDIR>>/src/upgrade/raptor_upgrade.cpp > [ 7%] Building CXX object > src/prepare/CMakeFiles/raptor_prepare.dir/compute_minimiser.cpp.o > cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/prepare && /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/prepare/CMakeFiles/raptor_prepare.dir/compute_minimiser.cpp.o > -MF CMakeFiles/raptor_prepare.dir/compute_minimiser.cpp.o.d -o > CMakeFiles/raptor_prepare.dir/compute_minimiser.cpp.o -c > /<<PKGBUILDDIR>>/src/prepare/compute_minimiser.cpp > 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/bin_size_in_bits.cpp.o > -MF CMakeFiles/raptor_build_hibf.dir/bin_size_in_bits.cpp.o.d -o > CMakeFiles/raptor_build_hibf.dir/bin_size_in_bits.cpp.o -c > /<<PKGBUILDDIR>>/src/build/hibf/bin_size_in_bits.cpp > make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make -f src/threshold/CMakeFiles/raptor_threshold.dir/build.make > src/threshold/CMakeFiles/raptor_threshold.dir/build > [ 9%] Building CXX object > src/search/CMakeFiles/raptor_search.dir/search_hibf.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_hibf.cpp.o > -MF CMakeFiles/raptor_search.dir/search_hibf.cpp.o.d -o > CMakeFiles/raptor_search.dir/search_hibf.cpp.o -c > /<<PKGBUILDDIR>>/src/search/search_hibf.cpp > [ 11%] Building CXX object > src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/__/build/hibf/parse_chopper_pack_line.cpp.o > [ 13%] Building CXX object > src/argument_parsing/CMakeFiles/raptor_argument_parsing.dir/build_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/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: âtemplate<class _Category, class _Tp, class _Distance, class > _Pointer, class _Reference> struct std::iteratorâ 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 âstd::hardware_destructive_interference_sizeâ [-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 â-mtuneâ or > â-mcpuâ 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 â--param > hardware_destructive_interference_size=64â, or disable this warning with > â-Wno-interference-sizeâ > /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:28:18: warning: use > of âstd::hardware_destructive_interference_sizeâ [-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: âtemplate<class _Category, class _Tp, class _Distance, class > _Pointer, class _Reference> struct std::iteratorâ 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: âtemplate<class _Category, class _Tp, class _Distance, class > _Pointer, class _Reference> struct std::iteratorâ 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: âtemplate<class _Category, class _Tp, class _Distance, class > _Pointer, class _Reference> struct std::iteratorâ 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 âstd::hardware_destructive_interference_sizeâ [-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 â-mtuneâ or > â-mcpuâ 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 â--param > hardware_destructive_interference_size=64â, or disable this warning with > â-Wno-interference-sizeâ > /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:28:18: warning: use > of âstd::hardware_destructive_interference_sizeâ [-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 âstd::hardware_destructive_interference_sizeâ [-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 â-mtuneâ or > â-mcpuâ 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 â--param > hardware_destructive_interference_size=64â, or disable this warning with > â-Wno-interference-sizeâ > /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:28:18: warning: use > of âstd::hardware_destructive_interference_sizeâ [-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 âstd::hardware_destructive_interference_sizeâ [-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 â-mtuneâ or > â-mcpuâ 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 â--param > hardware_destructive_interference_size=64â, or disable this warning with > â-Wno-interference-sizeâ > /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:28:18: warning: use > of âstd::hardware_destructive_interference_sizeâ [-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: âtemplate<class _Category, class _Tp, class _Distance, class > _Pointer, class _Reference> struct std::iteratorâ 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: âtemplate<class _Category, class _Tp, class _Distance, class > _Pointer, class _Reference> struct std::iteratorâ 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 âstd::hardware_destructive_interference_sizeâ [-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 â-mtuneâ or > â-mcpuâ 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 â--param > hardware_destructive_interference_size=64â, or disable this warning with > â-Wno-interference-sizeâ > /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:28:18: warning: use > of âstd::hardware_destructive_interference_sizeâ [-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: âtemplate<class _Category, class _Tp, class _Distance, class > _Pointer, class _Reference> struct std::iteratorâ 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: âtemplate<class _Category, class _Tp, class _Distance, class > _Pointer, class _Reference> struct std::iteratorâ 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 âstd::hardware_destructive_interference_sizeâ [-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 â-mtuneâ or > â-mcpuâ 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 â--param > hardware_destructive_interference_size=64â, or disable this warning with > â-Wno-interference-sizeâ > /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:28:18: warning: use > of âstd::hardware_destructive_interference_sizeâ [-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 âstd::hardware_destructive_interference_sizeâ [-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 â-mtuneâ or > â-mcpuâ 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 â--param > hardware_destructive_interference_size=64â, or disable this warning with > â-Wno-interference-sizeâ > /<<PKGBUILDDIR>>/include/raptor/build/hibf/build_data.hpp:28:18: warning: use > of âstd::hardware_destructive_interference_sizeâ [-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 âdoc_buildâ: 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.
