[med-svn] [spades] 04/04: do not use bundled headers

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository spades.

commit 56f008aa2b1cfb006ae799bfbc639f5d428d15ff
Author: Sascha Steinbiss <satta at debian.org>
Date:   Tue Jul 19 20:58:19 2016 +0000

    do not use bundled headers
---
 debian/changelog                                   |  4 +--
 debian/patches/0114_use_debian_provided_libs.patch | 33 ++++++++++++++++++++++
 2 files changed, 35 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 91a4603..7dc517b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,8 @@
-spades (3.8.2+dfsg2-1) UNRELEASED; urgency=medium
+spades (3.8.2+dfsg2-1) unstable; urgency=medium
 
   * Make sure bundled headers are not used by cleaning orig tarball.
 
- -- Sascha Steinbiss <satta at debian.org>  Tue, 19 Jul 2016 16:54:29 +0000
+ -- Sascha Steinbiss <satta at debian.org>  Tue, 19 Jul 2016 20:57:51 +0000
 
 spades (3.8.2+dfsg-1) unstable; urgency=medium
 
diff --git a/debian/patches/0114_use_debian_provided_libs.patch b/debian/patches/0114_use_debian_provided_libs.patch
index 14f6460..812a66b 100644
--- a/debian/patches/0114_use_debian_provided_libs.patch
+++ b/debian/patches/0114_use_debian_provided_libs.patch
@@ -92,3 +92,36 @@ Author: Sascha Steinbiss <satta at debian.org>
              components/connected_component.cpp paths/bidirectional_path.cpp graph_support/scaff_supplementary.cpp)
 -target_link_libraries(graph_support hattrie)
 +target_link_libraries(graph_support hat-trie)
+--- a/src/modules/assembly_graph/graph_alignment/kmer_map.hpp
++++ b/src/modules/assembly_graph/graph_alignment/kmer_map.hpp
+@@ -9,7 +9,7 @@
+ 
+ #include "data_structures/sequence/runtime_k.hpp"
+ 
+-#include <htrie/hat-trie.h>
++#include <hat-trie/hat-trie.h>
+ #include <boost/iterator/iterator_facade.hpp>
+ 
+ namespace debruijn_graph {
+--- a/src/modules/math/kmer_coverage_model.cpp
++++ b/src/modules/math/kmer_coverage_model.cpp
+@@ -18,7 +18,7 @@
+ #include <boost/math/distributions/geometric.hpp>
+ #include <boost/math/distributions/pareto.hpp>
+ 
+-#include <nlopt/nlopt.hpp>
++#include <nlopt.hpp>
+ 
+ #include <vector>
+ 
+--- a/src/modules/algorithms/path_extend/overlap_analysis.hpp
++++ b/src/modules/algorithms/path_extend/overlap_analysis.hpp
+@@ -2,7 +2,7 @@
+ 
+ #include "dev_support/logger/logger.hpp"
+ #include "dev_support/range.hpp"
+-#include "ssw/ssw_cpp.h"
++#include "ssw_cpp.h"
+ 
+ namespace debruijn_graph {
+ using omnigraph::Range;

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