[Debian-med-packaging] Bug#702440: New upstream release available

[Andreas Tille]

Hi Shaun,

On Thu, Aug 15, 2013 at 10:54:56AM -0700, Shaun Jackman wrote:
> 
>     My home machine is running OS X and I use Homebrew to manage packages, and at work I don't have root access on the Linux servers, so I use Linuxbrew to manage packages. To maintain a Debian package, there's a little extra effort required to fire up a VM. I opened the bug report to document that a new version of ABySS is available. If you have time to update the package, that's great, otherwise it'll wait until I find some time to do it.

I admit that I most probably might forget this and could possibly
 
>     Thanks for the bug report. It's an easy one line fix (delete the offending line) and will definitely be included in the next release of ABySS. Here's a link to the upstream bug report.

It seems to be not that easy:

g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I.  -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc
In file included from GraphIO.h:8:0,
                 from gc.cc:6:
DotIO.h: In function 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*)':
DotIO.h:37:3: error: typedef 'vertex_descriptor' locally defined but not used [-Werror=unused-local-typedefs]
   vertex_descriptor;
   ^
In file included from GraphIO.h:10:0,
                 from gc.cc:6:
SAMIO.h: In function 'std::ostream& write_sam(std::ostream&, const Graph&, const string&, const
SAMIO.h:27:3: error: typedef 'edge_property_type' locally defined but not used [-Werror=unused-
   edge_property_type;
   ^
cc1plus: all warnings being treated as errors


It would be really great if you could possibly send a working patch.

Kind regards

      Andreas.

> On Wed, Aug 14, 2013 at 4:58 PM, Andreas Tille <andreas at fam-tille.de>
> wrote:
> 
> > Hi Shaun,
> > I wonder if there is any reason that you did just files a bug report
> > about a new version and did not simply uploaded the package as you
> > formerly did.  Could you please drop the Debian Med team some note if
> > something prevents you from doing so.
> > BTW, I checked the latest version and injected it into the Git
> > repository but I realised that it does not build because of:
> > g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I.  -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libassembly_a-DotWriter.o `test -f 'DotWriter.cpp' || echo './'`DotWriter.cpp
> > In file included from DotWriter.cpp:5:0:
> > ../Graph/ContigGraphAlgorithms.h: In function 'OutIt assemble_if(Graph&, OutIt, Predicate)':
> > ../Graph/ContigGraphAlgorithms.h:202:44: error: typedef 'vertex_descriptor' locally defined but not used [-Werror=unused-local-typedefs]
> >   typedef typename Graph::vertex_descriptor vertex_descriptor;
> >                                             ^
> > cc1plus: all warnings being treated as errors
> > make[3]: *** [libassembly_a-DotWriter.o] Error 1
> > make[3]: Leaving directory `/tmp/buildd/abyss-1.3.6/Assembly'
> > make[2]: *** [all-recursive] Error 1
> > make[2]: Leaving directory `/tmp/buildd/abyss-1.3.6'
> > make[1]: *** [all] Error 2
> > make[1]: Leaving directory `/tmp/buildd/abyss-1.3.6'
> > dh_auto_build: make -j1 returned exit code 2
> > Since you are upstream dealing with things like this would be way
> > simpler if you just fix these things upstream rather than leaving us
> > poor packagers alone with patching.
> > Kind regards
> >        Andras.
> > -- 
> > http://fam-tille.de

> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging


-- 
http://fam-tille.de