Your message dated Fri, 15 Oct 2021 12:48:46 +0000
with message-id <[email protected]>
and subject line Bug#984104: fixed in libfastahack 1.0.0+dfsg-9
has caused the Debian Bug report #984104,
regarding libfastahack: 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.)
--
984104: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984104
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:libfastahack
Version: 1.0.0+dfsg-7
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/libfastahack_1.0.0+dfsg-7_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.
[...]
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libfastahack.so.0
debian/libfastahack0/usr/lib/x86_64-linux-gnu
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libfastahack.so.0.0.0
debian/libfastahack0/usr/lib/x86_64-linux-gnu
PKGDEV=libfastahack-dev
PKGSHL=libfastahack0
install -d -m 755 debian/libfastahack-dev/usr/include
mv debian/tmp/usr/include/fastahack debian/libfastahack-dev/usr/include
install -d -m 755 debian/libfastahack-dev/usr/lib/x86_64-linux-gnu/pkgconfig
mv debian/tmp/usr/lib/*/pkgconfig/*.pc
debian/libfastahack-dev/usr/lib/x86_64-linux-gnu/pkgconfig
find debian -name libfastahack.la -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs
dh_installchangelogs
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
help2man --no-discard-stderr --no-info --version-string=1.0.0+dfsg-7 \
--name="fastahack - indexing and extracting sequences and subsequences
from FASTA files" \
./fastahack > debian/fastahack.1
dh_installman
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
debian/rules override_dh_makeshlibs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
echo "On architecture amd64 symbols file is provided"
On architecture amd64 symbols file is provided
dh_makeshlibs
dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols
file: see diff output below
dpkg-gensymbols: warning: debian/libfastahack0/DEBIAN/symbols doesn't match
completely debian/libfastahack0.symbols
--- debian/libfastahack0.symbols (libfastahack0_1.0.0+dfsg-7_amd64)
+++ dpkg-gensymbolsKCtwDB 2021-03-01 21:09:58.987468905 +0000
@@ -32,9 +32,9 @@
_ZN15FastaIndexEntryD1Ev@Base 0.0+git20160702.bbc645f
_ZN15FastaIndexEntryD2Ev@Base 0.0+git20160702.bbc645f
_ZNKSt5ctypeIcE8do_widenEc@Base 0.0+git20160702.bbc645f
-
(optional)_ZNSt12_Destroy_auxILb0EE9__destroyIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvT_S9_@Base
1.0.0+dfsg
-
(optional)_ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15FastaIndexEntryED1Ev@Base
1.0.0+dfsg
-
(optional)_ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15FastaIndexEntryED2Ev@Base
1.0.0+dfsg
+#MISSING: 1.0.0+dfsg-7#
(optional)_ZNSt12_Destroy_auxILb0EE9__destroyIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvT_S9_@Base
1.0.0+dfsg
+#MISSING: 1.0.0+dfsg-7#
(optional)_ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15FastaIndexEntryED1Ev@Base
1.0.0+dfsg
+#MISSING: 1.0.0+dfsg-7#
(optional)_ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15FastaIndexEntryED2Ev@Base
1.0.0+dfsg
_ZNSt6vectorI15FastaIndexEntrySaIS0_EE17_M_realloc_insertIJRKS0_EEEvN9__gnu_cxx17__normal_iteratorIPS0_S2_EEDpOT_@Base
0.0+git20160702.bbc645f
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base
0.0+git20160702.bbc645f
(optional)_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base
0.0+git20160702.bbc645f
@@ -45,13 +45,13 @@
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15FastaIndexEntryESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE17_M_emplace_uniqueIJS6_IS5_S8_EEEES6_ISt17_Rb_tree_iteratorIS9_EbEDpOT_@Base
0.0+git20160702.bbc645f
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15FastaIndexEntryESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE24_M_get_insert_unique_posERS7_@Base
0.0+git20160702.bbc645f
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15FastaIndexEntryESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS9_ERS7_@Base
0.0+git20160702.bbc645f
-
_ZSt11__push_heapIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEElS2_NS0_5__ops14_Iter_comp_valIPFbS2_S2_EEEEvT_T0_SE_T1_RT2_@Base
0.0+git20160702.bbc645f
+#MISSING: 1.0.0+dfsg-7#
_ZSt11__push_heapIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEElS2_NS0_5__ops14_Iter_comp_valIPFbS2_S2_EEEEvT_T0_SE_T1_RT2_@Base
0.0+git20160702.bbc645f
_ZSt11__remove_ifIPcN9__gnu_cxx5__ops16_Iter_equals_valIKcEEET_S6_S6_T0_@Base
0.0+git20160702.bbc645f
_ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEElS2_NS0_5__ops15_Iter_comp_iterIPFbS2_S2_EEEEvT_T0_SE_T1_T2_@Base
0.0+git20160702.bbc645f
_ZSt13__heap_selectIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEENS0_5__ops15_Iter_comp_iterIPFbS2_S2_EEEEvT_SD_SD_T0_@Base
1.0.0+dfsg
_ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEENS0_5__ops15_Iter_comp_iterIPFbS2_S2_EEEEvT_SD_T0_@Base
0.0+git20160702.bbc645f
_ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEElNS0_5__ops15_Iter_comp_iterIPFbS2_S2_EEEEvT_SD_T0_T1_@Base
0.0+git20160702.bbc645f
-
(optional)_ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEENS0_5__ops15_Iter_comp_iterIPFbS2_S2_EEEEvT_SD_SD_SD_T0_@Base
1.0.0+dfsg
+#MISSING: 1.0.0+dfsg-7#
(optional)_ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEENS0_5__ops15_Iter_comp_iterIPFbS2_S2_EEEEvT_SD_SD_SD_T0_@Base
1.0.0+dfsg
_ZSt25__unguarded_linear_insertIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEENS0_5__ops14_Val_comp_iterIPFbS2_S2_EEEEvT_T0_@Base
0.0+git20160702.bbc645f
_ZlsRSoR10FastaIndex@Base 0.0+git20160702.bbc645f
_ZlsRSoRK15FastaIndexEntry@Base 0.0+git20160702.bbc645f
dh_makeshlibs: error: failing due to earlier errors
make[1]: *** [debian/rules:41: override_dh_makeshlibs] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:9: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: libfastahack
Source-Version: 1.0.0+dfsg-9
Done: Michael R. Crusoe <[email protected]>
We believe that the bug you reported is fixed in the latest version of
libfastahack, 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 libfastahack 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: Fri, 15 Oct 2021 14:19:02 +0200
Source: libfastahack
Architecture: source
Version: 1.0.0+dfsg-9
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Closes: 984104
Changes:
libfastahack (1.0.0+dfsg-9) unstable; urgency=medium
.
* Team upload.
* Mark another symbol as optional for GCC 11. Closes: #984104
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