[med-svn] [pbdagcon] 01/02: Adjust packaging for differences in pbseqlib organization

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository pbdagcon.

commit 12c8de50afb6533b8ac044ab45f2214d77a6edce
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Fri Jan 22 07:47:03 2016 -0800

    Adjust packaging for differences in pbseqlib organization
    
    These changes correspond to what was also necessary for blasr.
    pbseqlib's libraries can't be on the default LD Library path
    because they don't have versioned sonames (and are only used internally).
    We resort to using rpath to deal with this.
---
 debian/lintian-overrides             |  5 +++++
 debian/patches/gtest-directory.patch | 11 ++++++++---
 debian/rules                         |  8 ++++++++
 3 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/debian/lintian-overrides b/debian/lintian-overrides
new file mode 100644
index 0000000..beb4687
--- /dev/null
+++ b/debian/lintian-overrides
@@ -0,0 +1,5 @@
+# libblasr/libpbdata/libpbihdf (pbseqlib) are internal libraries
+# used only by blasr and pbdagcon
+binary-or-shlib-defines-rpath usr/bin/* /usr/lib/*/blasr
+binary-or-shlib-defines-rpath usr/bin/* /usr/lib/*/pbdata
+binary-or-shlib-defines-rpath usr/bin/* /usr/lib/*/pbihdf
diff --git a/debian/patches/gtest-directory.patch b/debian/patches/gtest-directory.patch
index be34822..d061086 100644
--- a/debian/patches/gtest-directory.patch
+++ b/debian/patches/gtest-directory.patch
@@ -5,7 +5,7 @@ Last-Update: 2015-12-10
 
 --- pbdagcon.orig/test/cpp/Makefile
 +++ pbdagcon/test/cpp/Makefile
-@@ -6,10 +6,10 @@
+@@ -6,22 +6,24 @@
  include $(SRCDIR)/boost.mk
  include gtest.mk
  
@@ -14,11 +14,16 @@ Last-Update: 2015-12-10
  GTEST_CXXFLAGS += -g -Wall -Wextra -pthread
  
 -INCDIRS := -I$(PBDATA) -I$(BLASR) -I$(BOOST_HEADERS) -I$(GTEST_DIR)/include -I$(GTEST_DIR) $(EXTRA_INCDIRS)
+-LDFLAGS := -L$(PBDATA) -L$(BLASR) $(EXTRA_LDFLAGS)
 +INCDIRS := -I$(PBDATA) -I$(BLASR) -I$(BOOST_HEADERS) -I$(GTEST_DIR) $(EXTRA_INCDIRS)
- LDFLAGS := -L$(PBDATA) -L$(BLASR) $(EXTRA_LDFLAGS)
++LDFLAGS += -L$(PBDATA) -L$(BLASR) $(EXTRA_LDFLAGS)
  LDLIBS := -lpbdata -lblasr -lpthread ${EXTRA_LDLIBS}
  
-@@ -20,8 +20,10 @@
+-CXXFLAGS := -O3 -std=c++11 $(INCDIRS) -I$(SRCDIR)
++CXXFLAGS += -O3 -std=c++11 $(INCDIRS) -I$(SRCDIR)
+ 
+ GTEST_OBJECTS := gtest-all.o gtest_main.o
+ DAZCON_OBJECTS := $(SRCDIR)/DB.o $(SRCDIR)/align.o $(SRCDIR)/Alignment.o \
  			      $(SRCDIR)/DazAlnProvider.o
  
  PBDAGCON_OBJECTS := $(SRCDIR)/AlnGraphBoost.o $(SRCDIR)/Alignment.o \
diff --git a/debian/rules b/debian/rules
index 40deaec..ce402a3 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,11 +1,19 @@
 #!/usr/bin/make -f
 
 #DH_VERBOSE = 1
+include /usr/share/dpkg/default.mk
 
 export boost := /usr/include/boost
 export BLASR := /usr/include/blasr
 export PBDATA := /usr/include/pbdata
 export gtest := /usr/src/gtest
 
+LIBBLASR = /usr/lib/$(DEB_HOST_MULTIARCH)/blasr
+LIBPBDATA = /usr/lib/$(DEB_HOST_MULTIARCH)/pbdata
+LIBPBIHDF = /usr/lib/$(DEB_HOST_MULTIARCH)/pbihdf
+
+export DEB_LDFLAGS_MAINT_APPEND = -L$(LIBBLASR) -L$(LIBPBDATA)
+export LD_RUN_PATH=$(LIBBLASR):$(LIBPBDATA):$(LIBPBIHDF)
+
 %:
 	dh $@ --parallel

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