Bug#702440: New upstream release available
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::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 > 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
Bug#702440: New upstream release available
Hi Andreas, 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. 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. https://github.com/bcgsc/abyss/issues/26 Cheers, Shaun — http://about.me/sjackman On Wed, Aug 14, 2013 at 4:58 PM, Andreas Tille 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
Bug#702440: New upstream release available
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 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#702440: New upstream release available
Package: abyss Priority: wishlist ABySS 1.3.5 is available. Cheers, Shaun
