Your message dated Wed, 05 Jun 2013 13:03:17 +0000
with message-id <e1ukdmz-0002dg...@franck.debian.org>
and subject line Bug#701423: fixed in jellyfish 1.1.10-1
has caused the Debian Bug report #701423,
regarding jellyfish: ftbfs with eglibc-2.17
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 ow...@bugs.debian.org
immediately.)
--
701423: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=701423
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:jellyfish
Version: 1.1.5-1
Severity: important
Tags: sid jessie
User: debian-gl...@lists.debian.org
Usertags: ftbfs-glibc-2.17
The package fails to build in a test rebuild on at least amd64 with
eglibc-2.17, but succeeds to build with eglibc-2.13. The
severity of this report may be raised before the jessie release.
The test rebuild was done together with GCC-4.8, so some issues
might be caused by the updated GCC as well.
./jellyfish/err.hpp:42:46: error: ignoring return value of 'char*
strerror_r(int, char*, size_t)', declared with attribute warn_unused_result
[-Werror=unused-result]
The full build log can be found at:
http://people.debian.org/~doko/logs-20130217/gcc48/jellyfish_1.1.5-1_unstable_gcc48.log
The last lines of the build log are at the end of this report.
To install eglibc from experimental,
apt-get -t experimental install libc6-dev
To build with GCC 4.8, either set CC=gcc-4.8 CXX=g++-4.8 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t experimental install g++ g++-4.7 g++-4.8 libc6-dev
[...]
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
configure: creating ./config.status
config.status: creating Makefile
config.status: creating tests/compat.sh
config.status: creating jellyfish-1.1.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_build -a
make[1]: Entering directory `/«PKGBUILDDIR»'
make all-am
make[2]: Entering directory `/«PKGBUILDDIR»'
CXX jellyfish/libjellyfish_la-square_binary_matrix.lo
/bin/bash ./libtool --silent --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I.
-Wall -Werror -Wnon-virtual-dtor -I. -D_FORTIFY_SOURCE=2 -g -O3 -g -O2
-fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c
-o jellyfish/libjellyfish_la-square_binary_matrix.lo `test -f
'jellyfish/square_binary_matrix.cc' || echo
'./'`jellyfish/square_binary_matrix.cc
CXX jellyfish/libjellyfish_la-err.lo
/bin/bash ./libtool --silent --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I.
-Wall -Werror -Wnon-virtual-dtor -I. -D_FORTIFY_SOURCE=2 -g -O3 -g -O2
-fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c
-o jellyfish/libjellyfish_la-err.lo `test -f 'jellyfish/err.cc' || echo
'./'`jellyfish/err.cc
In file included from jellyfish/err.cc:17:0:
./jellyfish/err.hpp: In static member function 'static void
err::no_t::write(std::ostream&, int)':
./jellyfish/err.hpp:42:46: error: ignoring return value of 'char*
strerror_r(int, char*, size_t)', declared with attribute warn_unused_result
[-Werror=unused-result]
strerror_r(e, err_str, sizeof(err_str));
^
cc1plus: all warnings being treated as errors
make[2]: *** [jellyfish/libjellyfish_la-err.lo] Error 1
make[1]: *** [all] Error 2
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_build: make -j1 returned exit code 2
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--- End Message ---
--- Begin Message ---
Source: jellyfish
Source-Version: 1.1.10-1
We believe that the bug you reported is fixed in the latest version of
jellyfish, 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 701...@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 jellyfish 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: SHA1
Format: 1.8
Date: Wed, 05 Jun 2013 11:58:53 +0200
Source: jellyfish
Binary: jellyfish
Architecture: source amd64
Version: 1.1.10-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
jellyfish - count k-mers in DNA sequences
Closes: 701423
Changes:
jellyfish (1.1.10-1) unstable; urgency=low
.
* New upstream version
Closes: #701423
* debian/{rules,install}: Make sure dynamic library will be installed
* debian/control:
- Removed DM-Upload-Allowed
- Standards-Version: 3.9.4 (no changes needed)
- Build-Depends autotools-dev
- canonical VCS URLs
* debian/lintian-overrides: Upstream decided to use a dynamic library
without really intending to make this a development package
* debian/doc-base: docbase control file
* debian/patches/man: refreshed + DEP3 description
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--- End Message ---