Your message dated Sun, 13 Aug 2023 19:13:36 +0000
with message-id <[email protected]>
and subject line Bug#1037742: fixed in libssw 1.1-14
has caused the Debian Bug report #1037742,
regarding libssw: ftbfs with GCC-13
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.
(NB: If you are a system administrator and have no idea what this
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misconfiguration somewhere. Please contact [email protected]
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--
1037742: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037742
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:libssw
Version: 1.1-13
Severity: normal
Tags: sid trixie
User: [email protected]
Usertags: ftbfs-gcc-13
[This bug is targeted to the upcoming trixie release]
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-13/g++-13, but succeeds to build with gcc-12/g++-12. The
severity of this report will be raised before the trixie release.
The full build log can be found at:
http://qa-logs.debian.net/2023/05/22/logs/libssw_1.1-13_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 13, either set CC=gcc-13 CXX=g++-13 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-13/porting_to.html
[...]
Query: 907
CCCCTTTCTGCAT-TAT--TTAATGATTTTCTCA-TAT----GTCA-CTCTTAAATGTAC 957
Target: 9707 TGTTGATTGTTTC-CTTT 9723
|**|*||| |||| ||||
Query: 958 TTCTAATT-TTTCACTTT 974
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
sed 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' debian/libssw0.install.in >
debian/libssw0.install
sed 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' debian/libssw-dev.install.in >
debian/libssw-dev.install
sed -e 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' \
-e 's/@DEB_JAVA_PKG_VERSION@/1.1/g' debian/libssw-dev.links.in >
debian/libssw-dev.links
sed 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' debian/libssw-java.install.in >
debian/libssw-java.install
sed -e 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' \
-e 's/@DEB_JAVA_PKG_VERSION@/1.1/g' debian/libssw-java.links.in >
debian/libssw-java.links
mv src/ssw.jar src/ssw-1.1.jar
dh_auto_install
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install
jh_installjavadoc
dh_installdocs
dh_installchangelogs
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
LD_LIBRARY_PATH=`pwd`/src help2man --version-string=' ' --help-option=' ' \
-I debian/extra-man-info.txt \
-N -n 'fast Smith-Waterman aligner' \
--no-discard-stderr src/ssw-align \
| fgrep -v ERROR > debian/ssw-align.1
dh_installman
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl
dh_link
jh_installlibs
jh_classpath
jh_manifest
jh_exec
jh_depends
mh_installpoms
mh_linkjars --skip-clean-poms
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols
file: see diff output below
dpkg-gensymbols: warning: debian/libssw0/DEBIAN/symbols doesn't match
completely debian/libssw0.symbols
--- debian/libssw0.symbols (libssw0_1.1-13_amd64)
+++ dpkg-gensymbolsRLn4HN 2023-05-22 02:10:01.559468309 +0000
@@ -22,9 +22,9 @@
_ZNK20StripedSmithWaterman7Aligner5AlignEPKcRKNS_6FilterEPNS_9AlignmentE@Base
1.1
_ZNK20StripedSmithWaterman7Aligner5AlignEPKcS2_RKiRKNS_6FilterEPNS_9AlignmentE@Base
1.1
(optional)_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_@Base
1.1
- _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev@Base 1.1
- _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev@Base 1.1
- _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev@Base 1.1
+#MISSING: 1.1-13#
_ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev@Base 1.1
+#MISSING: 1.1-13#
_ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev@Base 1.1
+#MISSING: 1.1-13#
_ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev@Base 1.1
align_destroy@Base 1.1
init_destroy@Base 1.1
mark_mismatch@Base 1.1
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:20: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: libssw
Source-Version: 1.1-14
Done: Michael R. Crusoe <[email protected]>
We believe that the bug you reported is fixed in the latest version of
libssw, 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.
Michael R. Crusoe <[email protected]> (supplier of updated libssw 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: Sun, 13 Aug 2023 20:51:28 +0200
Source: libssw
Architecture: source
Version: 1.1-14
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Closes: 1037742 1042114
Changes:
libssw (1.1-14) unstable; urgency=medium
.
* d/libssw0.symbols: update for gcc-13.
Closes: #1037742, #1042114
* Standards-Version: 4.6.2 (routine-update)
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--- End Message ---
