[med-svn] [pbdagcon] 01/02: Adjust packaging for differences in pbseqlib organization
Afif Elghraoui
afif-guest at moszumanska.debian.org
Fri Jan 22 15:48:49 UTC 2016
This is an automated email from the git hooks/post-receive script.
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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