[med-svn] [mugsy] 01/01: Update from outdated libboost

[Andreas Tille]

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tille pushed a commit to branch master
in repository mugsy.

commit 8e2b76dfd80f13e4149712b810d0985c3a10042c
Author: Andreas Tille <tille at debian.org>
Date:   Wed Apr 15 09:17:23 2015 +0200

    Update from outdated libboost
---
 debian/patches/adapt_to_latest_boost_version.patch | 31 ++++++++++++++++++++++
 debian/patches/libboost_linking.patch              | 20 ++++++++++++++
 debian/patches/series                              |  2 ++
 3 files changed, 53 insertions(+)

diff --git a/debian/patches/adapt_to_latest_boost_version.patch b/debian/patches/adapt_to_latest_boost_version.patch
new file mode 100644
index 0000000..d9fadb4
--- /dev/null
+++ b/debian/patches/adapt_to_latest_boost_version.patch
@@ -0,0 +1,31 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Updated: Mon, 13 Apr 2015 15:21:26 +0200
+Description: Adapt from outdated to current libboost
+
+--- a/chaining/synchain-mugsy.cpp
++++ b/chaining/synchain-mugsy.cpp
+@@ -101,11 +101,11 @@
+ #include <boost/graph/dijkstra_shortest_paths.hpp>
+ #include <boost/graph/graph_traits.hpp>
+ #include <boost/graph/properties.hpp>
+-#include <boost/property_map.hpp>
++#include <boost/property_map/property_map.hpp>
+ #include <boost/graph/breadth_first_search.hpp>
+ 
+ #include <boost/graph/edmonds_karp_max_flow.hpp>
+-#include <boost/graph/kolmogorov_max_flow.hpp>
++#include <boost/graph/boykov_kolmogorov_max_flow.hpp>
+ #include <boost/graph/push_relabel_max_flow.hpp>
+ 
+ #include <boost/graph/adjacency_list.hpp>
+--- a/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
++++ b/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
+@@ -68,7 +68,7 @@ time_t lasttime;
+ #include <boost/graph/properties.hpp>
+ 
+ #include <boost/graph/edmonds_karp_max_flow.hpp>
+-#include <boost/graph/kolmogorov_max_flow.hpp>
++#include <boost/graph/boykov_kolmogorov_max_flow.hpp>
+ #include <boost/graph/push_relabel_max_flow.hpp>
+ 
+ #include <boost/graph/adjacency_list.hpp>
diff --git a/debian/patches/libboost_linking.patch b/debian/patches/libboost_linking.patch
new file mode 100644
index 0000000..7a33b42
--- /dev/null
+++ b/debian/patches/libboost_linking.patch
@@ -0,0 +1,20 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Updated: Mon, 13 Apr 2015 15:21:26 +0200
+Description: Fix broken local path to libboost
+
+--- a/chaining/Makefile
++++ b/chaining/Makefile
+@@ -15,10 +15,10 @@ endif
+ ifndef AUX_BIN_DIR
+ AUX_BIN_DIR := $(CURDIR)
+ endif
+-OBJ_RULE = $(CXX) $(CPPFLAGS) $< -static -I /usr/local/projects/angiuoli/boost/include/boost-1_38 -c -o $@
+-BIN_RULE = $(CXX) $(CPPFLAGS) $^ -static -L /usr/local/projects/angiuoli/boost/lib/ -lbgl-viz -lboost_graph-gcc41-mt -o $(BIN_DIR)/$@; \
++OBJ_RULE = $(CXX) $(CPPFLAGS) $< -c -o $@
++BIN_RULE = $(CXX) $(CPPFLAGS) $(LDFLAGS) $^ -o $(BIN_DIR)/$@; \
+            chmod 755 $(BIN_DIR)/$@
+-AUX_BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
++AUX_BIN_RULE = $(CXX) $(CPPFLAGS) $(LDFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
+            chmod 755 $(AUX_BIN_DIR)/$@
+ VPATH := $(AUX_BIN_DIR):$(BIN_DIR)
+ 
diff --git a/debian/patches/series b/debian/patches/series
index cca2a8b..ea50bd4 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,3 @@
 use_debian_packaged_mummer.patch
+adapt_to_latest_boost_version.patch
+libboost_linking.patch

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