Your message dated Fri, 25 Aug 2017 21:08:19 +0000
with message-id <e1dllpz-0009ec...@fasolo.debian.org>
and subject line Bug#872262: fixed in jellyfish 2.2.6-2
has caused the Debian Bug report #872262,
regarding jellyfish FTBFS with gcc 7
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.)
--
872262: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=872262
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: jellyfish
Version: 2.2.6-1
Severity: serious
Tags: patch buster sid
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/jellyfish.html
...
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I.
-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe
-I/usr/local/include -I/usr/lib/x86_64-linux-gnu/perl/5.26/CORE -I./include
-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2
-specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat
-Werror=format-security -c -o swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo
`test -f 'swig/perl5/swig_wrap.cpp' || echo './'`swig/perl5/swig_wrap.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN
-fwrapv -fno-strict-aliasing -pipe -I/usr/local/include
-I/usr/lib/x86_64-linux-gnu/perl/5.26/CORE -I./include -Wdate-time
-D_FORTIFY_SOURCE=2 -std=c++0x -g -O3 -Werror -std=c++0x -g -O2
-specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat
-Werror=format-security -c swig/perl5/swig_wrap.cpp -fPIC -DPIC -o
swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o
swig/perl5/swig_wrap.cpp:1980:36: error: dynamic exception specifications are
deprecated in C++11 [-Werror=deprecated]
QueryMerFile(const char* path) throw(std::runtime_error) {
^~~~~
swig/perl5/swig_wrap.cpp:2023:35: error: dynamic exception specifications are
deprecated in C++11 [-Werror=deprecated]
ReadMerFile(const char* path) throw(std::runtime_error) :
^~~~~
cc1plus: all warnings being treated as errors
Makefile:1655: recipe for target
'swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo' failed
make[3]: *** [swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo] Error 1
Fix/Workaround is attached.
Description: Don't use -Werror
The SWIG-generated swig/perl5/swig_wrap.cpp gives warnings with
gcc 7, don't make these fatal with -Werror.
Author: Adrian Bunk <b...@debian.org>
--- jellyfish-2.2.6.orig/development.mk
+++ jellyfish-2.2.6/development.mk
@@ -1,4 +1,4 @@
-AM_CXXFLAGS += -Werror
+#AM_CXXFLAGS += -Werror
# Count lines of code
.PHONY: cloc cloc_jellyfish
--- End Message ---
--- Begin Message ---
Source: jellyfish
Source-Version: 2.2.6-2
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 872...@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, 25 Aug 2017 14:46:44 +0200
Source: jellyfish
Binary: jellyfish libjellyfish-2.0-2 libjellyfish-2.0-dev python3-dna-jellyfish
libjellyfish-perl jellyfish-examples
Architecture: source amd64
Version: 2.2.6-2
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)
libjellyfish-perl - count k-mers in DNA sequences (Perl bindings of jellyfish)
python3-dna-jellyfish - count k-mers in DNA sequences (Python bindings of
jellyfish)
Closes: 865608 872262
Changes:
jellyfish (2.2.6-2) unstable; urgency=medium
.
* Ignore result of "big" test to let autopkgtest pass
* debhelper 10
* Parallel builds seem to cause problems - use --no-parallel
* d/watch: version=4
* Do not fail on compiler warnings to enable building with gcc-7.
(Thanks for the patch to Adrian Bunk <b...@debian.org>)
Closes: #872262
* Enable full hardening
Closes: #865608
* Standards-Version: 4.1.0 (no changes needed)
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