[med-svn] [cufflinks] 07/12: use debian packaged liblemon

[Andreas Tille]

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tille pushed a commit to branch master
in repository cufflinks.

commit e99e0f4fa7eb41b50058982b24cb5a09f21bdd77
Author: Andreas Tille <tille at debian.org>
Date:   Fri Aug 5 21:32:39 2016 +0200

    use debian packaged liblemon
---
 debian/patches/series                             |  1 +
 debian/patches/use_debian_packaged_liblemon.patch | 56 +++++++++++++++++++++++
 2 files changed, 57 insertions(+)

diff --git a/debian/patches/series b/debian/patches/series
index 7f0e077..8a05716 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,3 +5,4 @@ gffread_show_usage.patch
 0003-fix_includes_path.patch
 format-security.patch
 lib_eigen.patch
+use_debian_packaged_liblemon.patch
diff --git a/debian/patches/use_debian_packaged_liblemon.patch b/debian/patches/use_debian_packaged_liblemon.patch
new file mode 100644
index 0000000..7e0fac0
--- /dev/null
+++ b/debian/patches/use_debian_packaged_liblemon.patch
@@ -0,0 +1,56 @@
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -54,44 +54,6 @@ noinst_HEADERS = \
+     graph_optimize.h \
+     jensen_shannon.h \
+     sampling.h \
+-	lemon/maps.h \
+-	lemon/bin_heap.h \
+-	lemon/fib_heap.h \
+-	lemon/bipartite_matching.h \
+-	lemon/topology.h \
+-	lemon/bucket_heap.h \
+-	lemon/smart_graph.h \
+-	lemon/list_graph.h \
+-	lemon/error.h \
+-	lemon/graph_utils.h \
+-	lemon/bfs.h \
+-	lemon/dfs.h \
+-	lemon/math.h \
+-	lemon/tolerance.h \
+-	lemon/graph_adaptor.h \
+-	lemon/concept_check.h \
+-	lemon/bits/default_map.h \
+-	lemon/bits/array_map.h \
+-	lemon/bits/vector_map.h \
+-	lemon/bits/debug_map.h \
+-	lemon/bits/map_extender.h \
+-	lemon/bits/base_extender.h \
+-	lemon/bits/graph_adaptor_extender.h \
+-	lemon/bits/graph_extender.h \
+-	lemon/bits/invalid.h \
+-	lemon/bits/path_dump.h \
+-	lemon/bits/traits.h \
+-	lemon/bits/utility.h \
+-	lemon/bits/alteration_notifier.h \
+-	lemon/bits/variant.h \
+-	lemon/concepts/graph.h \
+-	lemon/concepts/bpugraph.h \
+-	lemon/concepts/graph_components.h \
+-	lemon/concepts/ugraph.h \
+-	lemon/concepts/heap.h \
+-	lemon/concepts/maps.h \
+-	lemon/concepts/path.h \
+-	lemon/concepts/matrix_maps.h \
+     locfit/design.h	\
+     locfit/lfcons.h	\
+     locfit/lfstruc.h \
+@@ -206,7 +168,7 @@ CLEANFILES = $(bin_SCRIPTS)
+ #	(echo '#!$(PYTHON)'; sed '/^#!/d' $<) > $@
+ 
+ cufflinks_SOURCES = cufflinks.cpp  
+-cufflinks_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB)  $(BOOST_SERIALIZATION_LIB)  $(BAM_LIB) 
++cufflinks_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB)  $(BOOST_SERIALIZATION_LIB)  $(BAM_LIB) -llemon
+ cufflinks_LDFLAGS =  $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) 
+ 
+ cuffcompare_SOURCES = cuffcompare.cpp

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