diff -Nru abyss-1.3.4/debian/changelog abyss-1.3.4/debian/changelog --- abyss-1.3.4/debian/changelog 2013-01-04 10:09:04.000000000 +0000 +++ abyss-1.3.4/debian/changelog 2013-07-01 20:44:32.000000000 +0000 @@ -1,3 +1,11 @@ +abyss (1.3.4-4) unstable; urgency=low + + * Team upload. + * Fix FTBFS with gcc-4.8, -Werror=unused-local-typedefs. + * Enable parallel build. + + -- Dmitrijs Ledkovs Mon, 01 Jul 2013 21:06:59 +0100 + abyss (1.3.4-3) unstable; urgency=low * Disable POPCNT diff -Nru abyss-1.3.4/debian/patches/gcc4.8.patch abyss-1.3.4/debian/patches/gcc4.8.patch --- abyss-1.3.4/debian/patches/gcc4.8.patch 1970-01-01 00:00:00.000000000 +0000 +++ abyss-1.3.4/debian/patches/gcc4.8.patch 2013-07-01 20:43:19.000000000 +0000 @@ -0,0 +1,137 @@ +Description: -Werror=unused-local-typedefs +Author: Dmitrijs Ledkovs + +--- a/Graph/ContigGraphAlgorithms.h ++++ b/Graph/ContigGraphAlgorithms.h +@@ -199,7 +199,6 @@ + template + OutIt assemble_if(Graph& g, OutIt out, Predicate pred0) + { +- typedef typename Graph::vertex_descriptor vertex_descriptor; + typedef typename Graph::vertex_iterator vertex_iterator; + // pred(e) = !isPalindrome(e) && pred0(e) + binary_compose, +--- a/Graph/SAMIO.h ++++ b/Graph/SAMIO.h +@@ -23,8 +23,6 @@ + vertex_property_type; + typedef typename graph_traits::edge_iterator + edge_iterator; +- typedef typename edge_property::type +- edge_property_type; + + out << "@HD\tVN:1.0\n" + "@PG\tID:" << program << "\tVN:" VERSION "\t" +--- a/Graph/DotIO.h ++++ b/Graph/DotIO.h +@@ -33,8 +33,6 @@ + typename graph_traits::vertex_descriptor u, + const EdgeProp*) + { +- typedef typename graph_traits::vertex_descriptor +- vertex_descriptor; + typedef typename graph_traits::out_edge_iterator + out_edge_iterator; + typedef typename edge_property::type edge_property_type; +--- a/Map/overlap.cc ++++ b/Map/overlap.cc +@@ -272,7 +272,6 @@ + /** Read contigs and add vertices to the graph. */ + static void addVertices(const string& path, Graph& g) + { +- typedef vertex_property::type VP; + if (opt::verbose > 0) + cerr << "Reading `" << path << "'...\n"; + ifstream in(path.c_str()); +--- a/MergePaths/PathConsensus.cpp ++++ b/MergePaths/PathConsensus.cpp +@@ -184,8 +184,6 @@ + static ContigPaths readPaths(const string& inPath, + vector& ids, vector& isAmb) + { +- typedef graph_traits::vertex_descriptor V; +- + assert(ids.empty()); + assert(isAmb.empty()); + assert(g_ambpath_contig.empty()); +--- a/Graph/PopBubbles.h ++++ b/Graph/PopBubbles.h +@@ -161,7 +161,6 @@ + void scaffoldBubble(Graph& g, const Bubble& bubble) + { + typedef graph_traits GTraits; +- typedef typename GTraits::adjacency_iterator Ait; + typedef typename GTraits::vertex_descriptor V; + assert(bubble.size() > 2); + +--- a/PopBubbles/PopBubbles.cpp ++++ b/PopBubbles/PopBubbles.cpp +@@ -464,7 +464,6 @@ + */ + static void scaffoldBubble(Graph& g, const Bubble& bubble) + { +- typedef graph_traits::adjacency_iterator Ait; + typedef graph_traits::vertex_descriptor V; + assert(opt::scaffold); + assert(bubble.size() > 2); +--- a/Common/cholesky.hpp ++++ b/Common/cholesky.hpp +@@ -53,8 +53,6 @@ + { + using namespace ublas; + +- typedef typename MATRIX::value_type T; +- + assert( A.size1() == A.size2() ); + assert( A.size1() == L.size1() ); + assert( A.size2() == L.size2() ); +@@ -95,8 +93,6 @@ + { + using namespace ublas; + +- typedef typename MATRIX::value_type T; +- + const MATRIX& A_c(A); + + const size_t n = A.size1(); +--- a/Scaffold/drawgraph.cc ++++ b/Scaffold/drawgraph.cc +@@ -164,7 +164,6 @@ + typedef graph_traits::edge_iterator Eit; + typedef graph_traits::vertex_descriptor V; + typedef graph_traits::vertex_iterator Vit; +- typedef edge_bundle_type::type EP; + + Graph g; + if (optind < argc) { +--- a/Scaffold/scaffold.cc ++++ b/Scaffold/scaffold.cc +@@ -121,8 +121,6 @@ + static void filterGraph(Graph& g, unsigned minContigLength) + { + typedef graph_traits GTraits; +- typedef GTraits::edge_descriptor E; +- typedef GTraits::edge_iterator Eit; + typedef GTraits::vertex_descriptor V; + typedef GTraits::vertex_iterator Vit; + +@@ -237,8 +235,6 @@ + */ + static void pruneTips(Graph& g) + { +- typedef graph_traits::vertex_descriptor V; +- + /** Identify the tips. */ + size_t n = 0; + pruneTips(g, CountingOutputIterator(n)); +--- a/FilterGraph/FilterGraph.cpp ++++ b/FilterGraph/FilterGraph.cpp +@@ -279,8 +279,6 @@ + { + typedef graph_traits GTraits; + typedef GTraits::vertex_descriptor V; +- typedef GTraits::out_edge_iterator OEit; +- typedef GTraits::in_edge_iterator IEit; + + vector out; + out.reserve(sc.size()); diff -Nru abyss-1.3.4/debian/patches/series abyss-1.3.4/debian/patches/series --- abyss-1.3.4/debian/patches/series 2013-01-04 10:09:04.000000000 +0000 +++ abyss-1.3.4/debian/patches/series 2013-07-01 20:43:19.000000000 +0000 @@ -1 +1,2 @@ abyss-pe +gcc4.8.patch diff -Nru abyss-1.3.4/debian/rules abyss-1.3.4/debian/rules --- abyss-1.3.4/debian/rules 2013-01-04 10:09:04.000000000 +0000 +++ abyss-1.3.4/debian/rules 2013-07-01 20:43:13.000000000 +0000 @@ -8,5 +8,8 @@ override_dh_auto_configure: dh_auto_configure -- --with-mpi=/usr/lib/openmpi --disable-popcnt +override_dh_auto_build: + dh_auto_build --parallel + override_dh_auto_install: dh_auto_install --destdir=debian/tmp