Your message dated Wed, 02 Dec 2020 17:18:46 +0000
with message-id <e1kkvma-000cgm...@fasolo.debian.org>
and subject line Bug#976254: fixed in rnahybrid 2.1.2-6
has caused the Debian Bug report #976254,
regarding rnahybrid: Does not build from source "multiple definition of"
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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--
976254: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=976254
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: rnahybrid
Severity: serious
Tags: ftbfs
Justification: FTBFS
Hi,
I tried to rebuild the package but the build ends in:
...
gcc -g -O2 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong
-Wformat -Werror=format-security -g -O2
-fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o
RNAeffective rnaeffective.o hybrid_core.o numerical.o energy.o input.o fasta.o
random.o mt19937-1.o plot.o -lg2 -lm
/usr/bin/ld: /usr/bin/ld: /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:13:
multiple definition of `x'; rnahybrid.o:./src/hybrid_core.h:13: first defined
here
hybrid_core.o:./src/hybrid_core.h:/usr/bin/ld: hybrid_core.o13: multiple
definition of `x'; :./src/hybrid_core.h:15: multiple definition of `y';
rnahybrid.o:./src/hybrid_core.h:15: first defined herehybrid_core.o
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:28: multiple definition of `r1';
rnahybrid.o:./src/hybrid_core.h:28: first defined here
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:28: multiple definition of `r2';
rnahybrid.o:./src/hybrid_core.h:28: first defined here
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:28: multiple definition of `r3';
rnahybrid.o:./src/hybrid_core.h:28: first defined here
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:13:./src/hybrid_core.h:28:
multiple definition of `r4'; rnahybrid.o:./src/hybrid_core.h:28: first defined
here
/usr/bin/ld: hybrid_core.o: multiple definition of `x';
:./src/hybrid_core.h:30: multiple definition of `a1';
rnahybrid.o:./src/hybrid_core.h:30: first defined here
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:30: multiple definition of `a2';
rnahybrid.o:./src/hybrid_core.h:30: first defined
herernaeffective.o:./src/hybrid_core.h:13: first defined here
/usr/bin/ld: hybrid_core.o
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:30: multiple definition of `a3';
rnahybrid.o:./src/hybrid_core.h:30: first defined here
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:30: multiple definition of `a4';
rnahybrid.o:./src/hybrid_core.h:30: first defined here
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:30: multiple definition of `a5';
rnahybrid.o:./src/hybrid_core.h:30: first defined here
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:30: multiple definition of `a6';
rnahybrid.o:./src/hybrid_core.h:30: first defined here
/usr/bin/ld:./src/hybrid_core.h:15: multiple definition of `y';
rnaeffective.o:./src/hybrid_core.h:15: first defined here
/usr/bin/ld: hybrid_core.o: hybrid_core.o:./src/hybrid_core.h:23: multiple
definition of `helix_start'; rnahybrid.o:./src/hybrid_core.h:23: first defined
here
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:23: multiple definition of
`helix_end'; rnahybrid.o:./src/hybrid_core.h:23: first defined here
/usr/bin/ld: hybrid_core.o:./src/energy.h:50: multiple definition of `canPair';
rnahybrid.o:./src/energy.h:50: first defined here
/usr/bin/ld:./src/hybrid_core.h:28: multiple definition of `r1';
rnaeffective.o:./src/hybrid_core.h:28: first defined here
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:28: multiple definition of `r2';
rnaeffective.o:./src/hybrid_core.h:28: first defined here
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:28: multiple definition of `r3';
rnaeffective.o:./src/hybrid_core.h:28: first defined here
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:28: multiple definition of `r4';
rnaeffective.o:./src/hybrid_core.h:28: first defined here
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:30: multiple definition of `a1';
rnaeffective.o:./src/hybrid_core.h:30: first defined here
/usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:30: multiple definition of `a2';
rnaeffective.o:./src/hybrid_core.h:30: first defined here
/usr/bin/ld:
rnacalibrate.ohybrid_core.o::./src/hybrid_core.h:./src/hybrid_core.h:3013:
multiple definition of `: first defined herea3'
...
Kind regards
Andreas.
-- System Information:
Debian Release: bullseye/sid
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'testing'), (50, 'buildd-unstable'), (1,
'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 5.9.0-3-amd64 (SMP w/4 CPU threads)
Kernel taint flags: TAINT_WARN
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
--- End Message ---
--- Begin Message ---
Source: rnahybrid
Source-Version: 2.1.2-6
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
rnahybrid, 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 976...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated rnahybrid 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 02 Dec 2020 17:55:42 +0100
Source: rnahybrid
Architecture: source
Version: 2.1.2-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 976254
Changes:
rnahybrid (2.1.2-6) unstable; urgency=medium
.
[ Andreas Tille ]
* Standards-Version: 4.5.1 (routine-update)
* debhelper-compat 13 (routine-update)
* autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Refer to specific version of license GPL-2+.
* Remove obsolete field Name from debian/upstream/metadata (already present
in
machine-readable debian/copyright).
.
[ Hamid Nassiby ]
* Resolve FTBFS with GCC 10 by building with -fcommon
Closes: #976254
Checksums-Sha1:
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b4e978df7b3bdf1c557b6824fe71993f0f3463c3 6832 rnahybrid_2.1.2-6.debian.tar.xz
95ddd6a998a3ac11d3d7c4372971fb78b9c9715f 6640 rnahybrid_2.1.2-6_amd64.buildinfo
Checksums-Sha256:
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rnahybrid_2.1.2-6.dsc
4834e332435b4ee0230b4efd4b54817ef3491de01d9a1bd86d1b05a775c7acbe 6832
rnahybrid_2.1.2-6.debian.tar.xz
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rnahybrid_2.1.2-6_amd64.buildinfo
Files:
0fb742524c865a56451924bf327d68d0 2283 science optional rnahybrid_2.1.2-6.dsc
753c39b812fabd1982bdda32749ea247 6832 science optional
rnahybrid_2.1.2-6.debian.tar.xz
b51e4de70283b03c6c3cb88e441d99fd 6640 science optional
rnahybrid_2.1.2-6_amd64.buildinfo
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