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 <andr...@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-packag...@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org