[Debian-med-packaging] Bug#1143671: libmaus2: FTBFS: /usr/include/c++/16/atomic:215:21: error: static assertion failed: std::atomic requires a trivially copyable type
Santiago Vila
sanvila at debian.org
Wed Aug 5 12:24:19 BST 2026
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 ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2057:52: warning: variable ‘bpos’ set but not used [-Wunused-but-set-variable=]
2057 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2089:52: warning: variable ‘bpos’ set but not used [-Wunused-but-set-variable=]
2089 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2136:42: warning: variable ‘apos’ set but not used [-Wunused-but-set-variable=]
2136 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2169:42: warning: variable ‘apos’ 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 ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2057:52: warning: variable ‘bpos’ set but not used [-Wunused-but-set-variable=]
2057 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2089:52: warning: variable ‘bpos’ set but not used [-Wunused-but-set-variable=]
2089 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2136:42: warning: variable ‘apos’ set but not used [-Wunused-but-set-variable=]
2136 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2169:42: warning: variable ‘apos’ 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 ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2057:52: warning: variable ‘bpos’ set but not used [-Wunused-but-set-variable=]
2057 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2089:52: warning: variable ‘bpos’ set but not used [-Wunused-but-set-variable=]
2089 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2136:42: warning: variable ‘apos’ set but not used [-Wunused-but-set-variable=]
2136 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2169:42: warning: variable ‘apos’ 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 ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2057:52: warning: variable ‘bpos’ set but not used [-Wunused-but-set-variable=]
2057 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2089:52: warning: variable ‘bpos’ set but not used [-Wunused-but-set-variable=]
2089 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2136:42: warning: variable ‘apos’ set but not used [-Wunused-but-set-variable=]
2136 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2169:42: warning: variable ‘apos’ 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 ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2057:52: warning: variable ‘bpos’ set but not used [-Wunused-but-set-variable=]
2057 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2089:52: warning: variable ‘bpos’ set but not used [-Wunused-but-set-variable=]
2089 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2136:42: warning: variable ‘apos’ set but not used [-Wunused-but-set-variable=]
2136 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2169:42: warning: variable ‘apos’ 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 ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2057:52: warning: variable ‘bpos’ set but not used [-Wunused-but-set-variable=]
2057 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2089:52: warning: variable ‘bpos’ set but not used [-Wunused-but-set-variable=]
2089 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2136:42: warning: variable ‘apos’ set but not used [-Wunused-but-set-variable=]
2136 | uint64_t apos = 0, bpos = 0;
| ^~~~
./libmaus2/lcs/AlignmentTraceContainer.hpp: In static member function ‘static 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)’:
./libmaus2/lcs/AlignmentTraceContainer.hpp:2169:42: warning: variable ‘apos’ 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 ‘struct std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::ThreadWorkPackageData> >’:
./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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
• ‘false’ evaluates to false
/usr/include/c++/16/atomic: In instantiation of ‘struct std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::ThreadPoolDispatchable> >’:
./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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
• ‘false’ evaluates to false
/usr/include/c++/16/atomic: In instantiation of ‘struct std::atomic<std::shared_ptr<char []> >’:
./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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
• ‘false’ evaluates to false
/usr/include/c++/16/atomic: In instantiation of ‘struct std::atomic<std::shared_ptr<std::atomic<long unsigned int> []> >’:
./libmaus2/avl/AtomicAVLPtrValueMap.hpp:418:67: required from ‘struct libmaus2::avl::AtomicAVLPtrValueMap<std::type_index, libmaus2::parallel::AtomicPtrStack<libmaus2::parallel::threadpool::ThreadWorkPackageData> >’
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
• ‘false’ evaluates to false
/usr/include/c++/16/atomic: In instantiation of ‘struct std::atomic<std::shared_ptr<std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::ThreadWorkPackage> > []> >’:
./libmaus2/parallel/AtomicPtrStack.hpp:35:6: required from ‘struct libmaus2::parallel::AtomicPtrStack<libmaus2::parallel::threadpool::ThreadWorkPackage>’
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
• ‘false’ evaluates to false
/usr/include/c++/16/atomic: In instantiation of ‘struct std::atomic<std::shared_ptr<std::atomic<std::shared_ptr<libmaus2::exception::LibMausException> > []> >’:
./libmaus2/parallel/AtomicPtrStack.hpp:35:6: required from ‘struct libmaus2::parallel::AtomicPtrStack<libmaus2::exception::LibMausException>’
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
• ‘false’ evaluates to false
/usr/include/c++/16/atomic: In instantiation of ‘struct std::atomic<std::shared_ptr<std::atomic<std::shared_ptr<std::thread> > []> >’:
./libmaus2/parallel/AtomicPtrStack.hpp:35:6: required from ‘struct libmaus2::parallel::AtomicPtrStack<std::thread>’
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
• ‘false’ evaluates to false
/usr/include/c++/16/atomic: In instantiation of ‘struct std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::ThreadPoolDispatcher> >’:
/usr/include/c++/16/bits/stl_pair.h:312:11: required from ‘struct std::pair<const std::atomic<std::type_index>, const std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::ThreadPoolDispatcher> > >’
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
• ‘false’ evaluates to false
/usr/include/c++/16/atomic: In instantiation of ‘struct std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::ThreadWorkPackage> >’:
./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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
• ‘false’ evaluates to false
/usr/include/c++/16/atomic: In instantiation of ‘struct std::atomic<std::shared_ptr<std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::ThreadWorkPackageData> > []> >’:
./libmaus2/parallel/AtomicPtrStack.hpp:35:6: required from ‘struct libmaus2::parallel::AtomicPtrStack<libmaus2::parallel::threadpool::ThreadWorkPackageData>’
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
• ‘false’ evaluates to false
/usr/include/c++/16/atomic: In instantiation of ‘struct std::atomic<std::shared_ptr<libmaus2::parallel::AtomicPtrStack<libmaus2::parallel::threadpool::ThreadWorkPackageData> > >’:
/usr/include/c++/16/bits/stl_pair.h:312:11: required from ‘struct std::pair<const std::atomic<std::type_index>, const std::atomic<std::shared_ptr<libmaus2::parallel::AtomicPtrStack<libmaus2::parallel::threadpool::ThreadWorkPackageData> > > >’
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
• ‘false’ evaluates to false
/usr/include/c++/16/atomic: In instantiation of ‘struct std::atomic<std::shared_ptr<std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::input::ThreadPoolInputBlock> > []> >’:
./libmaus2/parallel/AtomicPtrStack.hpp:35:6: required from ‘struct libmaus2::parallel::AtomicPtrStack<libmaus2::parallel::threadpool::input::ThreadPoolInputBlock>’
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
• ‘false’ evaluates to false
/usr/include/c++/16/atomic: In instantiation of ‘struct std::atomic<std::shared_ptr<libmaus2::parallel::threadpool::input::ThreadPoolInputBlock> >’:
./libmaus2/parallel/AtomicPtrQueue.hpp:89:23: required from ‘bool 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>]’
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
• ‘false’ 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
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