Package: src:libmaus2 Version: 2.0.813+ds-5 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202608/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:libmaus2, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: no obvious need to run autopoint autoreconf: running: aclocal --force -I m4 autoreconf: configure.ac: tracing autoreconf: running: libtoolize --copy --force libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' [... snipped ...] /bin/bash ../libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c -o libmaus2/lcs/simd_align_256_la-SimdX86BandedGlobalAlignmentY256_8.lo `test -f 'libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_8.cpp' || echo './'`libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_8.cpp libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_8.cpp -fPIC -DPIC -o libmaus2/lcs/.libs/simd_align_256_la-SimdX86BandedGlobalAlignmentY256_8.o In file included from ./libmaus2/lcs/SimdX86BandedGlobalAlignmentTemplate.hpp:32, from ./libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_8.hpp:26, from libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_8.cpp:21: ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceA(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2057:52: warning: variable âbposâ set but not used [-Wunused-but-set-variable=] 2057 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceMaxA(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2089:52: warning: variable âbposâ set but not used [-Wunused-but-set-variable=] 2089 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceB(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2136:42: warning: variable âaposâ set but not used [-Wunused-but-set-variable=] 2136 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceMaxB(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2169:42: warning: variable âaposâ set but not used [-Wunused-but-set-variable=] 2169 | uint64_t apos = 0, bpos = 0; | ^~~~ /bin/bash ../libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c -o libmaus2/lcs/simd_align_256_la-SimdX86BandedGlobalAlignmentY256_16.lo `test -f 'libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_16.cpp' || echo './'`libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_16.cpp libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_16.cpp -fPIC -DPIC -o libmaus2/lcs/.libs/simd_align_256_la-SimdX86BandedGlobalAlignmentY256_16.o libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_8.cpp -o libmaus2/lcs/simd_align_256_la-SimdX86BandedGlobalAlignmentY256_8.o >/dev/null 2>&1 In file included from ./libmaus2/lcs/SimdX86BandedGlobalAlignmentTemplate.hpp:32, from ./libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_16.hpp:26, from libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_16.cpp:21: ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceA(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2057:52: warning: variable âbposâ set but not used [-Wunused-but-set-variable=] 2057 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceMaxA(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2089:52: warning: variable âbposâ set but not used [-Wunused-but-set-variable=] 2089 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceB(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2136:42: warning: variable âaposâ set but not used [-Wunused-but-set-variable=] 2136 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceMaxB(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2169:42: warning: variable âaposâ set but not used [-Wunused-but-set-variable=] 2169 | uint64_t apos = 0, bpos = 0; | ^~~~ libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_16.cpp -o libmaus2/lcs/simd_align_256_la-SimdX86BandedGlobalAlignmentY256_16.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c -o libmaus2/lcs/simd_align_256_la-SimdX86BandedGlobalAlignmentScoreY256_16.lo `test -f 'libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreY256_16.cpp' || echo './'`libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreY256_16.cpp libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreY256_16.cpp -fPIC -DPIC -o libmaus2/lcs/.libs/simd_align_256_la-SimdX86BandedGlobalAlignmentScoreY256_16.o In file included from ./libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreTemplate.hpp:32, from ./libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreY256_16.hpp:26, from libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreY256_16.cpp:21: ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceA(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2057:52: warning: variable âbposâ set but not used [-Wunused-but-set-variable=] 2057 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceMaxA(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2089:52: warning: variable âbposâ set but not used [-Wunused-but-set-variable=] 2089 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceB(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2136:42: warning: variable âaposâ set but not used [-Wunused-but-set-variable=] 2136 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceMaxB(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2169:42: warning: variable âaposâ set but not used [-Wunused-but-set-variable=] 2169 | uint64_t apos = 0, bpos = 0; | ^~~~ /bin/bash ../libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c -o libmaus2/lcs/simd_align_256_la-SimdX86GlobalAlignmentY256_8.lo `test -f 'libmaus2/lcs/SimdX86GlobalAlignmentY256_8.cpp' || echo './'`libmaus2/lcs/SimdX86GlobalAlignmentY256_8.cpp libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c libmaus2/lcs/SimdX86GlobalAlignmentY256_8.cpp -fPIC -DPIC -o libmaus2/lcs/.libs/simd_align_256_la-SimdX86GlobalAlignmentY256_8.o libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreY256_16.cpp -o libmaus2/lcs/simd_align_256_la-SimdX86BandedGlobalAlignmentScoreY256_16.o >/dev/null 2>&1 In file included from ./libmaus2/lcs/SimdX86GlobalAlignmentTemplate.hpp:32, from ./libmaus2/lcs/SimdX86GlobalAlignmentY256_8.hpp:26, from libmaus2/lcs/SimdX86GlobalAlignmentY256_8.cpp:21: ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceA(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2057:52: warning: variable âbposâ set but not used [-Wunused-but-set-variable=] 2057 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceMaxA(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2089:52: warning: variable âbposâ set but not used [-Wunused-but-set-variable=] 2089 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceB(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2136:42: warning: variable âaposâ set but not used [-Wunused-but-set-variable=] 2136 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceMaxB(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2169:42: warning: variable âaposâ set but not used [-Wunused-but-set-variable=] 2169 | uint64_t apos = 0, bpos = 0; | ^~~~ libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c libmaus2/lcs/SimdX86GlobalAlignmentY256_8.cpp -o libmaus2/lcs/simd_align_256_la-SimdX86GlobalAlignmentY256_8.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c -o libmaus2/lcs/simd_align_256_la-SimdX86GlobalAlignmentY256_16.lo `test -f 'libmaus2/lcs/SimdX86GlobalAlignmentY256_16.cpp' || echo './'`libmaus2/lcs/SimdX86GlobalAlignmentY256_16.cpp libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c libmaus2/lcs/SimdX86GlobalAlignmentY256_16.cpp -fPIC -DPIC -o libmaus2/lcs/.libs/simd_align_256_la-SimdX86GlobalAlignmentY256_16.o In file included from ./libmaus2/lcs/SimdX86GlobalAlignmentTemplate.hpp:32, from ./libmaus2/lcs/SimdX86GlobalAlignmentY256_16.hpp:26, from libmaus2/lcs/SimdX86GlobalAlignmentY256_16.cpp:21: ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceA(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2057:52: warning: variable âbposâ set but not used [-Wunused-but-set-variable=] 2057 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceMaxA(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2089:52: warning: variable âbposâ set but not used [-Wunused-but-set-variable=] 2089 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceB(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2136:42: warning: variable âaposâ set but not used [-Wunused-but-set-variable=] 2136 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceMaxB(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2169:42: warning: variable âaposâ set but not used [-Wunused-but-set-variable=] 2169 | uint64_t apos = 0, bpos = 0; | ^~~~ /bin/bash ../libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c -o libmaus2/lcs/simd_align_256_la-AlignmentOneAgainstManyAVX2.lo `test -f 'libmaus2/lcs/AlignmentOneAgainstManyAVX2.cpp' || echo './'`libmaus2/lcs/AlignmentOneAgainstManyAVX2.cpp libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c libmaus2/lcs/AlignmentOneAgainstManyAVX2.cpp -fPIC -DPIC -o libmaus2/lcs/.libs/simd_align_256_la-AlignmentOneAgainstManyAVX2.o libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c libmaus2/lcs/SimdX86GlobalAlignmentY256_16.cpp -o libmaus2/lcs/simd_align_256_la-SimdX86GlobalAlignmentY256_16.o >/dev/null 2>&1 In file included from ./libmaus2/lcs/Aligner.hpp:21, from ./libmaus2/lcs/NP.hpp:21, from libmaus2/lcs/AlignmentOneAgainstManyAVX2.cpp:20: ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceA(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2057:52: warning: variable âbposâ set but not used [-Wunused-but-set-variable=] 2057 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceMaxA(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2089:52: warning: variable âbposâ set but not used [-Wunused-but-set-variable=] 2089 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceB(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2136:42: warning: variable âaposâ set but not used [-Wunused-but-set-variable=] 2136 | uint64_t apos = 0, bpos = 0; | ^~~~ ./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function âstatic std::pair<long unsigned int, long unsigned int> libmaus2::lcs::AlignmentTraceContainer::advanceMaxB(const libmaus2::lcs::BaseConstants::step_type*, const libmaus2::lcs::BaseConstants::step_type*, uint64_t)â: ./libmaus2/lcs/AlignmentTraceContainer.hpp:2169:42: warning: variable âaposâ set but not used [-Wunused-but-set-variable=] 2169 | uint64_t apos = 0, bpos = 0; | ^~~~ x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c -o test/testThreadPoolRead-testThreadPoolRead.o `test -f 'test/testThreadPoolRead.cpp' || echo './'`test/testThreadPoolRead.cpp libtool: compile: x86_64-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -msse2 -mssse3 -msse4.1 -mavx2 -std=c++17 -pthread -fopenmp -W -Wall -Wnon-virtual-dtor -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++17 -pthread -fopenmp -c libmaus2/lcs/AlignmentOneAgainstManyAVX2.cpp -o libmaus2/lcs/simd_align_256_la-AlignmentOneAgainstManyAVX2.o >/dev/null 2>&1 In file included from ./libmaus2/parallel/threadpool/ThreadPool.hpp:22, from ./libmaus2/parallel/threadpool/input/InputThreadControl.hpp:21, from ./libmaus2/parallel/threadpool/input/InputThreadTrivialReturnInterface.hpp:21, from test/testThreadPoolRead.cpp:18: /usr/include/c++/16/atomic: In instantiation of âstruct std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::ThreadWorkPackageData> >â: ./libmaus2/parallel/threadpool/ThreadWorkPackage.hpp:40:62: required from here 40 | libmaus2::util::atomic_shared_ptr<ThreadWorkPackageData> data; | ^~~~ /usr/include/c++/16/atomic:215:21: error: static assertion failed: std::atomic requires a trivially copyable type 215 | static_assert(__is_trivially_copyable(_Tp), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ⢠âfalseâ evaluates to false /usr/include/c++/16/atomic: In instantiation of âstruct std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::ThreadPoolDispatchable> >â: ./libmaus2/parallel/threadpool/ThreadPoolDispatcher.hpp:39:84: required from here 39 | libmaus2::util::atomic_shared_ptr<ThreadPoolDispatchable> P; | ^ /usr/include/c++/16/atomic:215:21: error: static assertion failed: std::atomic requires a trivially copyable type 215 | static_assert(__is_trivially_copyable(_Tp), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ⢠âfalseâ evaluates to false /usr/include/c++/16/atomic: In instantiation of âstruct std::atomic<std::shared_ptr<char []> >â: ./libmaus2/avl/AtomicAVLPtrValueMap.hpp:410:48: required from here 410 | libmaus2::util::atomic_shared_ptr< char[] > AC; | ^~ /usr/include/c++/16/atomic:215:21: error: static assertion failed: std::atomic requires a trivially copyable type 215 | static_assert(__is_trivially_copyable(_Tp), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ⢠âfalseâ evaluates to false /usr/include/c++/16/atomic: In instantiation of âstruct std::atomic<std::shared_ptr<std::atomic<long unsigned int> []> >â: ./libmaus2/avl/AtomicAVLPtrValueMap.hpp:418:67: required from âstruct libmaus2::avl::AtomicAVLPtrValueMap<std::type_index, libmaus2::parallel::AtomicPtrStack<libmaus2::parallel::threadpool::ThreadWorkPackageData> >â 418 | libmaus2::util::atomic_shared_ptr< std::atomic<index_type>[] > F; | ^ ./libmaus2/parallel/threadpool/ThreadPool.hpp:52:118: required from here 52 | libmaus2::avl::AtomicAVLPtrValueMap<std::type_index, libmaus2::parallel::AtomicPtrStack<ThreadWorkPackageData> > dataMap; | ^~~~~~~ /usr/include/c++/16/atomic:215:21: error: static assertion failed: std::atomic requires a trivially copyable type 215 | static_assert(__is_trivially_copyable(_Tp), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ⢠âfalseâ evaluates to false /usr/include/c++/16/atomic: In instantiation of âstruct std::atomic<std::shared_ptr<std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::ThreadWorkPackage> > []> >â: ./libmaus2/parallel/AtomicPtrStack.hpp:35:6: required from âstruct libmaus2::parallel::AtomicPtrStack<libmaus2::parallel::threadpool::ThreadWorkPackage>â 35 | > p; | ^ ./libmaus2/parallel/threadpool/ThreadPool.hpp:53:59: required from here 53 | libmaus2::parallel::AtomicPtrStack<ThreadWorkPackage> packageStack; | ^~~~~~~~~~~~ /usr/include/c++/16/atomic:215:21: error: static assertion failed: std::atomic requires a trivially copyable type 215 | static_assert(__is_trivially_copyable(_Tp), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ⢠âfalseâ evaluates to false /usr/include/c++/16/atomic: In instantiation of âstruct std::atomic<std::shared_ptr<std::atomic<std::shared_ptr<libmaus2::exception::LibMausException> > []> >â: ./libmaus2/parallel/AtomicPtrStack.hpp:35:6: required from âstruct libmaus2::parallel::AtomicPtrStack<libmaus2::exception::LibMausException>â 35 | > p; | ^ ./libmaus2/parallel/threadpool/ThreadPool.hpp:65:79: required from here 65 | libmaus2::parallel::AtomicPtrStack<libmaus2::exception::LibMausException> panicStack; | ^~~~~~~~~~ /usr/include/c++/16/atomic:215:21: error: static assertion failed: std::atomic requires a trivially copyable type 215 | static_assert(__is_trivially_copyable(_Tp), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ⢠âfalseâ evaluates to false /usr/include/c++/16/atomic: In instantiation of âstruct std::atomic<std::shared_ptr<std::atomic<std::shared_ptr<std::thread> > []> >â: ./libmaus2/parallel/AtomicPtrStack.hpp:35:6: required from âstruct libmaus2::parallel::AtomicPtrStack<std::thread>â 35 | > p; | ^ ./libmaus2/parallel/threadpool/ThreadPool.hpp:66:55: required from here 66 | libmaus2::parallel::AtomicPtrStack< std::thread > Vthread; | ^~~~~~~ /usr/include/c++/16/atomic:215:21: error: static assertion failed: std::atomic requires a trivially copyable type 215 | static_assert(__is_trivially_copyable(_Tp), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ⢠âfalseâ evaluates to false /usr/include/c++/16/atomic: In instantiation of âstruct std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::ThreadPoolDispatcher> >â: /usr/include/c++/16/bits/stl_pair.h:312:11: required from âstruct std::pair<const std::atomic<std::type_index>, const std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::ThreadPoolDispatcher> > >â 312 | _T2 second; ///< The second member | ^~~~~~ ./libmaus2/parallel/threadpool/ThreadPool.hpp:159:15: required from here 159 | return it->second.load().get(); | ^~ /usr/include/c++/16/atomic:215:21: error: static assertion failed: std::atomic requires a trivially copyable type 215 | static_assert(__is_trivially_copyable(_Tp), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ⢠âfalseâ evaluates to false /usr/include/c++/16/atomic: In instantiation of âstruct std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::ThreadWorkPackage> >â: ./libmaus2/parallel/threadpool/ThreadPool.hpp:283:14: required from here 283 | ptr = it->load(); | ^~ /usr/include/c++/16/atomic:215:21: error: static assertion failed: std::atomic requires a trivially copyable type 215 | static_assert(__is_trivially_copyable(_Tp), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ⢠âfalseâ evaluates to false /usr/include/c++/16/atomic: In instantiation of âstruct std::atomic<std::shared_ptr<std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::ThreadWorkPackageData> > []> >â: ./libmaus2/parallel/AtomicPtrStack.hpp:35:6: required from âstruct libmaus2::parallel::AtomicPtrStack<libmaus2::parallel::threadpool::ThreadWorkPackageData>â 35 | > p; | ^ ./libmaus2/parallel/threadpool/ThreadPool.hpp:318:85: required from here 318 | libmaus2::util::shared_ptr < AtomicPtrStack<ThreadWorkPackageData> > nobj(new AtomicPtrStack<ThreadWorkPackageData>); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/16/atomic:215:21: error: static assertion failed: std::atomic requires a trivially copyable type 215 | static_assert(__is_trivially_copyable(_Tp), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ⢠âfalseâ evaluates to false /usr/include/c++/16/atomic: In instantiation of âstruct std::atomic<std::shared_ptr<libmaus2::parallel::AtomicPtrStack<libmaus2::parallel::threadpool::ThreadWorkPackageData> > >â: /usr/include/c++/16/bits/stl_pair.h:312:11: required from âstruct std::pair<const std::atomic<std::type_index>, const std::atomic<std::shared_ptr<libmaus2::parallel::AtomicPtrStack<libmaus2::parallel::threadpool::ThreadWorkPackageData> > > >â 312 | _T2 second; ///< The second member | ^~~~~~ ./libmaus2/parallel/threadpool/ThreadPool.hpp:325:15: required from here 325 | return it->second.load(); | ^~ /usr/include/c++/16/atomic:215:21: error: static assertion failed: std::atomic requires a trivially copyable type 215 | static_assert(__is_trivially_copyable(_Tp), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ⢠âfalseâ evaluates to false /usr/include/c++/16/atomic: In instantiation of âstruct std::atomic<std::shared_ptr<std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::input::ThreadPoolInputBlock> > []> >â: ./libmaus2/parallel/AtomicPtrStack.hpp:35:6: required from âstruct libmaus2::parallel::AtomicPtrStack<libmaus2::parallel::threadpool::input::ThreadPoolInputBlock>â 35 | > p; | ^ ./libmaus2/parallel/threadpool/input/ThreadPoolInputInfo.hpp:51:63: required from here 51 | libmaus2::parallel::AtomicPtrStack<ThreadPoolInputBlock> freeBlocks; | ^~~~~~~~~~ /usr/include/c++/16/atomic:215:21: error: static assertion failed: std::atomic requires a trivially copyable type 215 | static_assert(__is_trivially_copyable(_Tp), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ⢠âfalseâ evaluates to false /usr/include/c++/16/atomic: In instantiation of âstruct std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::input::ThreadPoolInputBlock> >â: ./libmaus2/parallel/AtomicPtrQueue.hpp:89:23: required from âbool libmaus2::parallel::AtomicPtrQueue<type>::pop(libmaus2::util::shared_ptr<value_type>&) [with type = libmaus2::parallel::threadpool::input::ThreadPoolInputBlock; libmaus2::util::shared_ptr<value_type> = std::shared_ptr<libmaus2::parallel::threadpool::input::ThreadPoolInputBlock>]â 89 | T = p.load().get()[l++ % ln].load(); | ~~~~~~~~~~~~~~^ ./libmaus2/parallel/threadpool/input/ThreadPoolInputInfo.hpp:112:27: required from here 112 | while ( outQueue.pop(block) ) | ~~~~~~~~~~~~^~~~~~~ /usr/include/c++/16/atomic:215:21: error: static assertion failed: std::atomic requires a trivially copyable type 215 | static_assert(__is_trivially_copyable(_Tp), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ⢠âfalseâ evaluates to false make[3]: *** [Makefile:10377: test/testThreadPoolRead-testThreadPoolRead.o] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: Leaving directory '/<<PKGBUILDDIR>>/src' make[2]: *** [Makefile:687: all-recursive] Error 1 make[2]: Leaving directory '/<<PKGBUILDDIR>>' make[1]: *** [Makefile:571: all] Error 2 make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_build: error: make -j2 returned exit code 2 make: *** [debian/rules:16: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 --------------------------------------------------------------------------------
