Your message dated Sat, 17 Oct 2026 16:06:47 +0000
with message-id <[email protected]>
and subject line Bug#1150081: fixed in abyss 2.3.10-3
has caused the Debian Bug report #1150081,
regarding abyss: FTBFS: collect2: error: ld returned 1 exit status
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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--
1150081: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1150081
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:abyss
Version: 2.3.10-2
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/202610/
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:abyss, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<<PKGBUILDDIR>>
-isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2
-isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -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
x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<<PKGBUILDDIR>>
-isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2
-isystem/<<PKGBUILDDIR>>/boost_1_56_0 -Wall -Wextra -Werror -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -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
x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations
-L/usr/lib/x86_64-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
/usr/bin/x86_64-linux-gnu-ld.bfd: ABYSS_P-CommLayer.o: undefined reference to
symbol 'ompi_mpi_unsigned_long_long'
/usr/bin/x86_64-linux-gnu-ld.bfd: /usr/lib/x86_64-linux-gnu/libopen_mpi.so.40:
error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[4]: *** [Makefile:431: ABYSS-P] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: Leaving directory '/<<PKGBUILDDIR>>/Parallel'
make[3]: *** [Makefile:502: all-recursive] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: *** [Makefile:422: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j2 returned exit code 2
make[1]: *** [debian/rules:18: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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: 2.3.10-3
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, 17 Oct 2026 17:43:32 +0200
Source: abyss
Architecture: source
Version: 2.3.10-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1150081
Changes:
abyss (2.3.10-3) unstable; urgency=medium
.
* mpi-libs.patch: new: fix a link error against openmpi. (Closes: #1150081)
* d/control: declare compliance to standards version 4.7.4.
* d/control: bump to debhelper 14 in single-binary mode.
Checksums-Sha1:
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2b1ad8a31ee65295640f2b3202c6a371970756df 1499760 abyss_2.3.10-3.debian.tar.xz
Checksums-Sha256:
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abyss_2.3.10-3.dsc
9d90594502ffd6cf0884585deaf1ba24324ee7c231c5725e372c2dbc91430690 1499760
abyss_2.3.10-3.debian.tar.xz
Files:
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1a8417593eab3eb96d353ed7a8cf7a2e 1499760 science optional
abyss_2.3.10-3.debian.tar.xz
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