Your message dated Wed, 13 Oct 2021 08:22:10 +0000
with message-id <[email protected]>
and subject line Bug#984207: fixed in libsmithwaterman
0.0+git20160702.2610e25-12
has caused the Debian Bug report #984207,
regarding libsmithwaterman: ftbfs with GCC-11
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
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
984207: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984207
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:libsmithwaterman
Version: 0.0+git20160702.2610e25-11
Severity: normal
Tags: sid bookworm
User: [email protected]
Usertags: ftbfs-gcc-11
[This bug is not targeted to the upcoming bullseye 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-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.
The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/libsmithwaterman_0.0+git20160702.2610e25-11_unstable_gcc11.log
The last lines of the build log are at the end of this report.
To build with GCC 11, either set CC=gcc-11 CXX=g++-11 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-11/porting_to.html
GCC 11 defaults to the GNU++17 standard. If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.
[...]
dh_fixperms -O--no-parallel
dh_missing -O--no-parallel
dh_dwz -a -O--no-parallel
dh_strip -a -O--no-parallel
dh_makeshlibs -a -O--no-parallel
Use of uninitialized value $rest in pattern match (m//) at
/usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 51.
dpkg-gensymbols: warning: failed to parse line in
debian/libsmithwaterman0.symbols: (arch=!ppc64el)
_ZNSt12_Vector_baseIfSaIfEED1Ev@Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at
/usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 52.
dpkg-gensymbols: warning: failed to parse line in
debian/libsmithwaterman0.symbols: (arch=!ppc64el)
_ZNSt12_Vector_baseIfSaIfEED2Ev@Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at
/usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 53.
dpkg-gensymbols: warning: failed to parse line in
debian/libsmithwaterman0.symbols: (arch=!ppc64el)
_ZNSt15_Rb_tree_headerC1EOS_@Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at
/usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 54.
dpkg-gensymbols: warning: failed to parse line in
debian/libsmithwaterman0.symbols: (arch=!ppc64el)
_ZNSt15_Rb_tree_headerC2EOS_@Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at
/usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 64.
dpkg-gensymbols: warning: failed to parse line in
debian/libsmithwaterman0.symbols: (arch=!s390x)
_ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EE17_M_realloc_insertIJRKS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base
0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at
/usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 73.
dpkg-gensymbols: warning: failed to parse line in
debian/libsmithwaterman0.symbols: (arch=!s390x)
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_@Base
0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at
/usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 51.
dpkg-gensymbols: warning: failed to parse line in
debian/libsmithwaterman0.symbols: (arch=!ppc64el)
_ZNSt12_Vector_baseIfSaIfEED1Ev@Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at
/usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 52.
dpkg-gensymbols: warning: failed to parse line in
debian/libsmithwaterman0.symbols: (arch=!ppc64el)
_ZNSt12_Vector_baseIfSaIfEED2Ev@Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at
/usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 53.
dpkg-gensymbols: warning: failed to parse line in
debian/libsmithwaterman0.symbols: (arch=!ppc64el)
_ZNSt15_Rb_tree_headerC1EOS_@Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at
/usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 54.
dpkg-gensymbols: warning: failed to parse line in
debian/libsmithwaterman0.symbols: (arch=!ppc64el)
_ZNSt15_Rb_tree_headerC2EOS_@Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at
/usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 64.
dpkg-gensymbols: warning: failed to parse line in
debian/libsmithwaterman0.symbols: (arch=!s390x)
_ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EE17_M_realloc_insertIJRKS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base
0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at
/usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 73.
dpkg-gensymbols: warning: failed to parse line in
debian/libsmithwaterman0.symbols: (arch=!s390x)
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_@Base
0.0+git20160702.2610e25
dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see
diff output below
dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols
file: see diff output below
dpkg-gensymbols: warning: debian/libsmithwaterman0/DEBIAN/symbols doesn't match
completely debian/libsmithwaterman0.symbols
--- debian/libsmithwaterman0.symbols
(libsmithwaterman0_0.0+git20160702.2610e25-11_amd64)
+++ dpkg-gensymbolsMAYCWR 2021-03-01 21:09:07.449138917 +0000
@@ -48,7 +48,11 @@
_ZN20CBandedSmithWatermanD1Ev@Base 0.0+git20160702.2610e25
_ZN20CBandedSmithWatermanD2Ev@Base 0.0+git20160702.2610e25
(optional)_ZNKSt5ctypeIcE8do_widenEc@Base 0.0+git20160702.2610e25
- (arch=!ppc64el
optional)_ZNSt6vectorI11IndelAlleleSaIS0_EE12emplace_backIJS0_EEEvDpOT_@Base
0.0+git20160702.2610e25
+ _ZNSt12_Vector_baseIfSaIfEED1Ev@Base 0.0+git20160702.2610e25-11
+ _ZNSt12_Vector_baseIfSaIfEED2Ev@Base 0.0+git20160702.2610e25-11
+ _ZNSt15_Rb_tree_headerC1EOS_@Base 0.0+git20160702.2610e25-11
+ _ZNSt15_Rb_tree_headerC2EOS_@Base 0.0+git20160702.2610e25-11
+#MISSING: 0.0+git20160702.2610e25-11# (arch=!ppc64el
optional)_ZNSt6vectorI11IndelAlleleSaIS0_EE12emplace_backIJS0_EEEvDpOT_@Base
0.0+git20160702.2610e25
_ZNSt6vectorI11IndelAlleleSaIS0_EE17_M_realloc_insertIJRKS0_EEEvN9__gnu_cxx17__normal_iteratorIPS0_S2_EEDpOT_@Base
0.0+git20160702.2610e25
(arch=!s390x
optional)_ZNSt6vectorI11IndelAlleleSaIS0_EE17_M_realloc_insertIJS0_EEEvN9__gnu_cxx17__normal_iteratorIPS0_S2_EEDpOT_@Base
0.0+git20160702.2610e25
_ZNSt6vectorI11IndelAlleleSaIS0_EED1Ev@Base 0.0+git20160702.2610e25
@@ -56,14 +60,18 @@
(arch=!s390x
optional)_ZNSt6vectorISt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4lessIS6_ESaISt4pairIKS6_iEEESaISD_EE17_M_realloc_insertIJSD_EEEvN9__gnu_cxx17__normal_iteratorIPSD_SF_EEDpOT_@Base
0.0+git20160702.2610e25
_ZNSt6vectorISt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4lessIS6_ESaISt4pairIKS6_iEEESaISD_EED1Ev@Base
0.0+git20160702.2610e25
_ZNSt6vectorISt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4lessIS6_ESaISt4pairIKS6_iEEESaISD_EED2Ev@Base
0.0+git20160702.2610e25
-
(optional)_ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EE12emplace_backIJS7_EEEvDpOT_@Base
0.0+git20160702.2610e25
+#MISSING: 0.0+git20160702.2610e25-11#
(optional)_ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EE12emplace_backIJS7_EEEvDpOT_@Base
0.0+git20160702.2610e25
+
_ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EE17_M_realloc_insertIJRKS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base
0.0+git20160702.2610e25-11
(arch=!s390x
optional)_ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base
0.0+git20160702.2610e25
_ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EED1Ev@Base
0.0+git20160702.2610e25
_ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EED2Ev@Base
0.0+git20160702.2610e25
(arch=!s390x
optional)_ZNSt6vectorIfSaIfEE17_M_realloc_insertIJfEEEvN9__gnu_cxx17__normal_iteratorIPfS1_EEDpOT_@Base
0.0+git20160702.2610e25
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_@Base
0.0+git20160702.2610e25-11
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_@Base
0.0+git20160702.2610e25-11
_ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev@Base
0.0+git20160702.2610e25
_ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev@Base
0.0+git20160702.2610e25
_ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev@Base
0.0+git20160702.2610e25
+
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_@Base
0.0+git20160702.2610e25-11
(arch=!s390x !ppc64el
optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_@Base
0.0+git20160702.2610e25
_ZeqRK11IndelAlleleS1_@Base 0.0+git20160702.2610e25
_ZlsRSoRK11IndelAllele@Base 0.0+git20160702.2610e25
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: libsmithwaterman
Source-Version: 0.0+git20160702.2610e25-12
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
libsmithwaterman, 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.
Andreas Tille <[email protected]> (supplier of updated libsmithwaterman 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: Wed, 13 Oct 2021 10:01:23 +0200
Source: libsmithwaterman
Architecture: source
Version: 0.0+git20160702.2610e25-12
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 984207
Changes:
libsmithwaterman (0.0+git20160702.2610e25-12) unstable; urgency=medium
.
* Packaging update
* Standards-Version: 4.6.0 (routine-update)
* Apply multi-arch hints.
+ libsmithwaterman-dev, libsmithwaterman0: Add Multi-Arch: same.
* Drop symbols file to reduce maintenance burden
Closes: #984207
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Files:
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--- End Message ---
