The following commit has been merged in the master branch:
commit f3a97e5c9078e26b9612da6ee09d6bab14f7f9f7
Author: Dmitrijs Ledkovs <[email protected]>
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 <[email protected]> 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 <[email protected]>
+
+--- 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
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