[med-svn] [libvcflib] 01/02: Sort out some linking issues

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository libvcflib.

commit 94585384d187a459564b398ec90b36c3a7850fb7
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jun 23 17:16:50 2016 +0200

    Sort out some linking issues
---
 debian/patches/use_debian_packaged_smithwaterman.patch | 10 ++++++----
 debian/patches/use_debian_packaged_tabixpp.patch       | 11 +++++++++++
 2 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/debian/patches/use_debian_packaged_smithwaterman.patch b/debian/patches/use_debian_packaged_smithwaterman.patch
index 3dfa590..e714993 100644
--- a/debian/patches/use_debian_packaged_smithwaterman.patch
+++ b/debian/patches/use_debian_packaged_smithwaterman.patch
@@ -1,14 +1,16 @@
 --- a/Makefile
 +++ b/Makefile
-@@ -124,7 +124,7 @@ LEFTALIGN = smithwaterman/LeftAlign.o
+@@ -124,8 +124,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
  FSOM = fsom/fsom.o
  FILEVERCMP = filevercmp/filevercmp.o
  
--INCLUDES = -Itabixpp/htslib -I$(INC_DIR) -L. -Ltabixpp/htslib
-+INCLUDES = `pkg-config --cflags libsmithwaterman` -Itabixpp/htslib -I$(INC_DIR) -L. -Ltabixpp/htslib
- LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp
+-INCLUDES = -I$(INC_DIR)
+-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp
++INCLUDES = `pkg-config --cflags libsmithwaterman` -I$(INC_DIR)
++LDFLAGS += -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman`
  
  
+ all: $(OBJECTS) $(BINS)
 @@ -156,17 +156,20 @@ $(OBJECTS): $(SOURCES) $(HEADERS) multic
  	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
  
diff --git a/debian/patches/use_debian_packaged_tabixpp.patch b/debian/patches/use_debian_packaged_tabixpp.patch
index 1bc601a..0a77adb 100644
--- a/debian/patches/use_debian_packaged_tabixpp.patch
+++ b/debian/patches/use_debian_packaged_tabixpp.patch
@@ -9,6 +9,17 @@
  FASTAHACK = fastahack/Fasta.o
  SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
  REPEATS = smithwaterman/Repeats.o
+@@ -124,8 +124,8 @@ LEFTALIGN = smithwaterman/LeftAlign.o
+ FSOM = fsom/fsom.o
+ FILEVERCMP = filevercmp/filevercmp.o
+ 
+-INCLUDES = -Itabixpp/htslib -I$(INC_DIR) -L. -Ltabixpp/htslib
+-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp
++INCLUDES = -I$(INC_DIR)
++LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp
+ 
+ 
+ all: $(OBJECTS) $(BINS)
 @@ -152,7 +152,7 @@ profiling:
  gprof:
  	$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all

-- 
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