[med-svn] [SCM] abyss branch, master, updated. upstream/1.3.4-16-gaf90083

[Dmitrijs Ledkovs]

The following commit has been merged in the master branch:
commit f3a97e5c9078e26b9612da6ee09d6bab14f7f9f7
Author: Dmitrijs Ledkovs <dmitrij.ledkov at ubuntu.com>
Date:   Mon Jul 1 21:44:13 2013 +0100

    * Fix FTBFS with gcc-4.8, -Werror=unused-local-typedefs.
    * Enable parallel build.

diff --git a/debian/changelog b/debian/changelog
index fcdeec2..26042fe 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+abyss (1.3.4-4) saucy; urgency=low
+
+  * Team upload.
+  * Fix FTBFS with gcc-4.8, -Werror=unused-local-typedefs.
+  * Enable parallel build.
+
+ -- Dmitrijs Ledkovs <dmitrij.ledkov at ubuntu.com>  Mon, 01 Jul 2013 21:06:59 +0100
+
 abyss (1.3.4-3) unstable; urgency=low
 
   * Disable POPCNT
diff --git a/debian/patches/gcc4.8.patch b/debian/patches/gcc4.8.patch
new file mode 100644
index 0000000..1f0efa6
--- /dev/null
+++ b/debian/patches/gcc4.8.patch
@@ -0,0 +1,137 @@
+Description: -Werror=unused-local-typedefs
+Author: Dmitrijs Ledkovs <xnox at debian.org>
+
+--- a/Graph/ContigGraphAlgorithms.h
++++ b/Graph/ContigGraphAlgorithms.h
+@@ -199,7 +199,6 @@
+ template<typename Graph, typename OutIt, typename Predicate>
+ 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<std::logical_and<bool>,
+--- a/Graph/SAMIO.h
++++ b/Graph/SAMIO.h
+@@ -23,8 +23,6 @@
+ 		vertex_property_type;
+ 	typedef typename graph_traits<Graph>::edge_iterator
+ 		edge_iterator;
+-	typedef typename edge_property<Graph>::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<Graph>::vertex_descriptor u,
+ 		const EdgeProp*)
+ {
+-	typedef typename graph_traits<Graph>::vertex_descriptor
+-		vertex_descriptor;
+ 	typedef typename graph_traits<Graph>::out_edge_iterator
+ 		out_edge_iterator;
+ 	typedef typename edge_property<Graph>::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<Graph>::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<string>& ids, vector<bool>& isAmb)
+ {
+-	typedef graph_traits<Graph>::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<Graph> 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<Graph>::adjacency_iterator Ait;
+ 	typedef graph_traits<Graph>::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<Graph>::edge_iterator Eit;
+ 	typedef graph_traits<Graph>::vertex_descriptor V;
+ 	typedef graph_traits<Graph>::vertex_iterator Vit;
+-	typedef edge_bundle_type<Graph>::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<Graph> 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<Graph>::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<Graph> GTraits;
+ 	typedef GTraits::vertex_descriptor V;
+-	typedef GTraits::out_edge_iterator OEit;
+-	typedef GTraits::in_edge_iterator IEit;
+ 
+ 	vector<vertex_descriptor> out;
+ 	out.reserve(sc.size());
diff --git a/debian/patches/series b/debian/patches/series
index f09fd48..321fafb 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 abyss-pe
+gcc4.8.patch
diff --git a/debian/rules b/debian/rules
index 047ef9c..d79163d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -8,5 +8,8 @@ export DH_OPTIONS
 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

-- 
Packaging of abyss in Debian