Your message dated Fri, 03 Jul 2015 19:04:27 +0000
with message-id <e1zb6gb-00049k...@franck.debian.org>
and subject line Bug#777922: fixed in jellyfish 2.2.3-1
has caused the Debian Bug report #777922,
regarding jellyfish: ftbfs with GCC-5
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.)
--
777922: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=777922
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:jellyfish
Version: 2.1.4-1
Severity: normal
Tags: sid stretch
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-5
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-5/g++-5, but succeeds to build with gcc-4.9/g++-4.9. The
severity of this report may be raised before the stretch release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc5-20150205/jellyfish_2.1.4-1_unstable_gcc5.log
The last lines of the build log are at the end of this report.
To build with GCC 5, either set CC=gcc-5 CXX=g++-5 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t experimental install g++
Common build failures are C11 as the default C mode, 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-5/porting_to.html
[...]
jellyfish/merge_files.cc:50:14: warning: 'template<class> class std::auto_ptr'
is deprecated [-Wdeprecated-declarations]
typedef std::auto_ptr<RectangularBinaryMatrix> matrix_ptr;
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from ./include/jellyfish/err.hpp:21,
from ./jellyfish/merge_files.hpp:21,
from jellyfish/merge_files.cc:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
CXXLD bin/jellyfish
make[3]: Leaving directory '/«PKGBUILDDIR»'
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_auto_test -a
make[1]: Entering directory '/«PKGBUILDDIR»'
make check-am
make[2]: Entering directory '/«PKGBUILDDIR»'
make libgtest.la libgtest_main.la bin/generate_sequence bin/test_all
make[3]: Entering directory '/«PKGBUILDDIR»'
CXX unit_tests/gtest/src/libgtest_la-gtest-all.lo
CXXLD libgtest.la
CXX unit_tests/gtest/src/libgtest_main_la-gtest_main.lo
CXXLD libgtest_main.la
CXX jellyfish/generate_sequence.o
CXX jellyfish/mersenne.o
CXX jellyfish/backtrace.o
CXX jellyfish/dbg.o
CXXLD bin/generate_sequence
CXX unit_tests/bin_test_all-test_main.o
In file included from ./unit_tests/gtest/gtest.h:308:0,
from unit_tests/test_main.cc:20:
/usr/include/c++/5/sstream:335:7: error: 'struct std::basic_stringbuf<_CharT,
_Traits, _Alloc>::__xfer_bufptrs' redeclared with different access
struct __xfer_bufptrs
^
make[3]: *** [unit_tests/bin_test_all-test_main.o] Error 1
Makefile:1285: recipe for target 'unit_tests/bin_test_all-test_main.o' failed
make[3]: Leaving directory '/«PKGBUILDDIR»'
make[2]: *** [check-am] Error 2
Makefile:2163: recipe for target 'check-am' failed
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: *** [check] Error 2
Makefile:2166: recipe for target 'check' failed
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_auto_test: make -j1 check returned exit code 2
make: *** [build-arch] Error 2
debian/rules:8: recipe for target 'build-arch' failed
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--- End Message ---
--- Begin Message ---
Source: jellyfish
Source-Version: 2.2.3-1
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 777...@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: SHA256
Format: 1.8
Date: Fri, 03 Jul 2015 20:06:28 +0200
Source: jellyfish
Binary: jellyfish libjellyfish-2.0-2 libjellyfish-2.0-dev jellyfish-examples
Architecture: source amd64
Version: 2.2.3-1
Distribution: unstable
Urgency: medium
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
jellyfish-examples - count k-mers in DNA sequences (examples for testing)
libjellyfish-2.0-2 - count k-mers in DNA sequences (dynamic library of
jellyfish)
libjellyfish-2.0-dev - count k-mers in DNA sequences (development files of
jellyfish)
Closes: 777922
Changes:
jellyfish (2.2.3-1) unstable; urgency=medium
.
[ Andreas Tille ]
* Replace unneeded dependency by @builddeps@ in debian/tests/control
* New version needs valgrind as Build-Depends to pass all tests
* New version closes: #777922
.
[ Charles Plessy ]
* New upstream release.
* Removed yaggo and clang patches, obsoleted upstream.
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jellyfish-examples_2.2.3-1_amd64.deb
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Files:
72da3d03b6f032681cfb2907678df200 2299 science optional jellyfish_2.2.3-1.dsc
a63398ce1cbde0eddcb3493f5b84a9b7 658367 science optional
jellyfish_2.2.3.orig.tar.gz
c78a36153866ff73c6564542cf33ab2a 6976 science optional
jellyfish_2.2.3-1.debian.tar.xz
f989efe45cd19b658a74282ed282de1a 469270 science optional
jellyfish-examples_2.2.3-1_amd64.deb
fe73d676cdfc8a47f54cf370e52b1894 349040 science optional
jellyfish_2.2.3-1_amd64.deb
667f5f70bff36ac49ffa4a4af36a04a8 64078 libs optional
libjellyfish-2.0-2_2.2.3-1_amd64.deb
5c27e8f547bb39fcb94f2849519f77ac 117700 libdevel optional
libjellyfish-2.0-dev_2.2.3-1_amd64.deb
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