Your message dated Mon, 19 Aug 2019 00:34:56 +0000
with message-id <[email protected]>
and subject line Bug#925740: fixed in libedlib 1.2.4-2
has caused the Debian Bug report #925740,
regarding libedlib: ftbfs with GCC-9
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]
immediately.)
--
925740: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=925740
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:libedlib
Version: 1.2.4-1
Severity: normal
Tags: sid bullseye
User: [email protected]
Usertags: ftbfs-gcc-9
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-9/g++-9, but succeeds to build with gcc-8/g++-8. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc9-20190321/libedlib_1.2.4-1_unstable_gcc9.log
The last lines of the build log are at the end of this report.
To build with GCC 9, either set CC=gcc-9 CXX=g++-9 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-9/porting_to.html
GCC 9 also passes the linker option --as-needed by default; typical
build issues are passing libraries before object files to the linker,
or underlinking of convenience libraries built from the same source.
[...]
creating edlib.egg-info
writing edlib.egg-info/PKG-INFO
writing dependency_links to edlib.egg-info/dependency_links.txt
writing top-level names to edlib.egg-info/top_level.txt
writing manifest file 'edlib.egg-info/SOURCES.txt'
reading manifest file 'edlib.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'edlib.egg-info/SOURCES.txt'
Copying edlib.egg-info to
/<<PKGBUILDDIR>>/debian/python3-edlib/usr/lib/python3.7/dist-packages/edlib-1.2.3.post1.egg-info
Skipping SOURCES.txt
running install_scripts
/usr/lib/python3/dist-packages/setuptools/dist.py:475: UserWarning: Normalizing
'1.2.3-1' to '1.2.3.post1'
normalized_version,
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
file-rename 's/_static\.a/.a/' `find debian -name libedlib_static.a`
d-shlibmove --commit \
--multiarch \
--devunversioned \
--exclude-la \
--movedev debian/tmp/usr/include/* usr/include \
debian/tmp/usr/lib/*.so
Library package automatic movement utility
set -e
install -d -m 755 debian/libedlib-dev/usr/lib/x86_64-linux-gnu
install -d -m 755 debian/libedlib0/usr/lib/x86_64-linux-gnu
mv debian/tmp/usr/lib/libedlib.a debian/libedlib-dev/usr/lib/x86_64-linux-gnu
mv debian/tmp/usr/lib/libedlib.so debian/libedlib-dev/usr/lib/x86_64-linux-gnu
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/libedlib.so.0
debian/libedlib0/usr/lib/x86_64-linux-gnu
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/libedlib.so.1.2.3
debian/libedlib0/usr/lib/x86_64-linux-gnu
PKGDEV=libedlib-dev
PKGSHL=libedlib0
install -d -m 755 debian/libedlib-dev/usr/include
mv debian/tmp/usr/include/edlib.h debian/libedlib-dev/usr/include
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_python3 -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
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/libedlib0/DEBIAN/symbols doesn't match
completely debian/libedlib0.symbols
--- debian/libedlib0.symbols (libedlib0_1.2.4-1_amd64)
+++ dpkg-gensymbolsR_He6e 2019-03-26 16:47:24.379121607 +0000
@@ -1,7 +1,9 @@
libedlib.so.0 libedlib0 #MINVER#
_ZN18EqualityDefinitionC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPK17EdlibEqualityPairi@Base
1.2.3
_ZN18EqualityDefinitionC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPK17EdlibEqualityPairi@Base
1.2.3
- _ZNSt6vectorIcSaIcEE12emplace_backIJcEEEvDpOT_@Base 1.2.3
+#MISSING: 1.2.4-1# _ZNSt6vectorIcSaIcEE12emplace_backIJcEEEvDpOT_@Base 1.2.3
+
_ZNSt6vectorIcSaIcEE17_M_realloc_insertIJRKcEEEvN9__gnu_cxx17__normal_iteratorIPcS1_EEDpOT_@Base
1.2.4-1
+
_ZNSt6vectorIcSaIcEE17_M_realloc_insertIJcEEEvN9__gnu_cxx17__normal_iteratorIPcS1_EEDpOT_@Base
1.2.4-1
_ZNSt6vectorIiSaIiEE17_M_realloc_insertIJiEEEvN9__gnu_cxx17__normal_iteratorIPiS1_EEDpOT_@Base
1.2.3
edlibAlign@Base 1.2.3
edlibAlignmentToCigar@Base 1.2.3
dh_makeshlibs: failing due to earlier errors
make: *** [debian/rules:12: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned
exit status 2
--- End Message ---
--- Begin Message ---
Source: libedlib
Source-Version: 1.2.4-2
We believe that the bug you reported is fixed in the latest version of
libedlib, 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 libedlib 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: SHA256
Format: 1.8
Date: Sun, 18 Aug 2019 15:49:41 +0200
Source: libedlib
Binary: libedlib0 libedlib-dev edlib-aligner python3-edlib
Architecture: source
Version: 1.2.4-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
edlib-aligner - edlib sequence alignment tool using edit distance
libedlib-dev - library for sequence alignment using edit distance (devel)
libedlib0 - library for sequence alignment using edit distance
python3-edlib - library for sequence alignment using edit distance (Python3
modul
Closes: 925740
Changes:
libedlib (1.2.4-2) unstable; urgency=medium
.
* debhelper-compat 12
* Standards-Version: 4.4.0
* Set upstream metadata fields: Name.
* Adapt symbols file to gcc9
Closes: #925740
Checksums-Sha1:
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e60eed5224be2dffb127b070c7ccf02882a02c02 5872 libedlib_1.2.4-2.debian.tar.xz
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Files:
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84ca76bd20d37a8e0fe6a62deb39ff86 5872 science optional
libedlib_1.2.4-2.debian.tar.xz
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