[Debian-med-packaging] Bug#1132058: abyss: ftbfs with GCC-16

[Emanuele Rocca]

Package: src:abyss
Version: 2.3.10-1
Severity: important
Tags: sid forky ftbfs
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-16

Hi,

abyss fails to build in a test rebuild on at least amd64 and arm64 with
gcc-16/g++-16, but builds properly with gcc-15/g++-15. The severity of this
report will be raised before the forky release.

The full build log can be found at:
https://people.debian.org/~ema/gcc-16-rebuilds/output-1/abyss_arm64.build.xz

The last lines of the build log are at the end of this report.

To build with GCC 16, either set CC=gcc-16 CXX=g++-16 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures include unused (but set) variables, array subscripts
partly outside array bounds, and new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-16/porting_to.html

Please only close this issue after double-checking that the package can be
built correctly.

Please do not reassign this bug to another package. If a fix in another package
is required, then file a bug for the other package (or clone), and mark this
bug as blocked by the bug in the other package.

[...]


ranlib libdialign.a
gcc  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o dialign museq.o libdialign.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/dialign'
Making all in Align
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Align'
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc
rm -f libalign.a
ar cr libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o 
ranlib libalign.a
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Align'
Making all in ABYSS
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/ABYSS'
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm  ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/ABYSS'
Making all in Parallel
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Parallel'
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -lmpi  -ldl -lm 
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -lmpi  -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Parallel'
Making all in Bloom
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Bloom'
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../vendor -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Bloom'
Making all in BloomDBG
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/BloomDBG'
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I../vendor -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/BloomDBG'
Making all in Konnector
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Konnector'
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm 
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Konnector'
Making all in Consensus
make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Consensus'
g++ -std=gnu++11 -std=c++11 -std=gnu++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp
Consensus.cpp: In function ‘void consensus(const std::string&, const std::string&)’:
Consensus.cpp:379:18: error: variable ‘numIgnored’ set but not used [-Werror=unused-but-set-variable=]
  379 |         unsigned numIgnored = 0;
      |                  ^~~~~~~~~~
cc1plus: all warnings being treated as errors
make[4]: *** [Makefile:415: Consensus-Consensus.o] Error 1
make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Consensus'
make[3]: *** [Makefile:493: all-recursive] Error 1
make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10'
make[2]: *** [Makefile:413: all] Error 2
make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.10'
dh_auto_build: error: make -j128 returned exit code 2
make[1]: *** [debian/rules:18: override_dh_auto_build] Error 25
make[1]: Leaving directory '/build/reproducible-path/abyss-2.3.10'
make: *** [debian/rules:11: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2