Your message dated Sat, 28 Mar 2026 21:04:33 +0000
with message-id <[email protected]>
and subject line Bug#1132058: fixed in abyss 2.3.10-2
has caused the Debian Bug report #1132058,
regarding abyss: ftbfs with GCC-16
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1132058: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1132058
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:abyss
Version: 2.3.10-1
Severity: important
Tags: sid forky ftbfs
User: [email protected]
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
--- End Message ---
--- Begin Message ---
Source: abyss
Source-Version: 2.3.10-2
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
abyss, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated abyss package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sat, 28 Mar 2026 21:29:14 +0100
Source: abyss
Architecture: source
Version: 2.3.10-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1132058
Changes:
abyss (2.3.10-2) unstable; urgency=medium
.
[ Michael R. Crusoe ]
* 'btllib' is no longer included in the upstream sources, so the
sources don't need to be repacked.
.
[ Andreas Tille ]
* Replace pkg-config with pkgconf in Build-Depends
.
[ Étienne Mollier ]
* gcc-16.patch: new: fix ftbfs with Gcc 16. (Closes: #1132058)
* d/watch: convert to Github uscan template v5.
* d/control: drop redundant Priority: optional.
* d/control: drop redundant Rules-Requires-Root: no.
* d/control: declare compliance to standards version 4.7.3.
* abyss-pe.patch: fix a typo caught by lintian in description.
* d/copyright: remove the old fsf mail address.
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Files:
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