[med-svn] [pbdagcon] 04/08: Update patches
Afif Elghraoui
afif at moszumanska.debian.org
Mon Oct 24 04:08:29 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository pbdagcon.
commit 31669ba676efd7cf3c446bac87b18fc7dfa8890f
Author: Afif Elghraoui <afif at debian.org>
Date: Sun Oct 23 19:37:27 2016 -0700
Update patches
---
debian/patches/compiler-flags.patch | 30 +++++------
debian/patches/disable-dazcon-tests.patch | 16 ------
debian/patches/external-libs.patch | 29 ----------
debian/patches/gtest-directory.patch | 90 -------------------------------
debian/patches/series | 3 --
5 files changed, 12 insertions(+), 156 deletions(-)
diff --git a/debian/patches/compiler-flags.patch b/debian/patches/compiler-flags.patch
index 012ece9..ded5083 100644
--- a/debian/patches/compiler-flags.patch
+++ b/debian/patches/compiler-flags.patch
@@ -1,23 +1,17 @@
Description: Prevent override of dpkg-buildflags
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: not-needed
-Last-Update: 2015-12-11
---- pbdagcon.orig/src/cpp/Makefile
-+++ pbdagcon/src/cpp/Makefile
-@@ -5,13 +5,13 @@
- PBDAGCON_OBJECTS := BlasrM5AlnProvider.o main.o SimpleAligner.o
- DAZCON_OBJECTS := DB.o align.o DazAlnProvider.o dazcon.o
-
--CXXFLAGS = -O3 -std=c++11 -Wall -Wuninitialized -pedantic -I third-party \
-+CXXFLAGS += -O3 -std=c++11 -Wall -Wuninitialized -pedantic -I third-party \
- -I $(BOOST_HEADERS)
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: no
+Last-Update: 2016-10-23
+--- pbdagcon.orig/src/cpp/makefile
++++ pbdagcon/src/cpp/makefile
+@@ -8,8 +8,8 @@
+ DAZCON_OBJECTS := DB.o QV.o align.o DazAlnProvider.o dazcon.o
+ CPPFLAGS += -MMD -MP
+-CXXFLAGS = -O3 -std=c++11 -Wall -Wuninitialized -pedantic
-CFLAGS = -O3 -Wall -Wextra -fno-strict-aliasing
++CXXFLAGS += -O3 -std=c++11 -Wall -Wuninitialized -pedantic
+CFLAGS += -O3 -Wall -Wextra -fno-strict-aliasing
- INCDIRS := -I$(PBDATA) -I$(BLASR) $(EXTRA_INCDIRS)
--LDFLAGS := -L$(PBDATA) -L$(BLASR) $(EXTRA_LDFLAGS)
-+LDFLAGS += -L$(PBDATA) -L$(BLASR) $(EXTRA_LDFLAGS)
-
- all: pbdagcon
-
+ INCDIRS := \
+ ${DAZZ_DB_INCLUDE} \
diff --git a/debian/patches/disable-dazcon-tests.patch b/debian/patches/disable-dazcon-tests.patch
deleted file mode 100644
index 9648bb0..0000000
--- a/debian/patches/disable-dazcon-tests.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Description: Don't run tests requiring dazcon
- We don't have Dazzler headers yet, so these will probably fail.
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: not-needed
-Last-Update: 2015-12-10
---- pbdagcon.orig/test/cpp/Makefile
-+++ pbdagcon/test/cpp/Makefile
-@@ -28,7 +28,7 @@
-
- all: check
-
--check: test_target_hit test_alngraph test_alignment test_simple_aligner
-+check: test_alngraph test_alignment test_simple_aligner
-
- # XXX: need to mock out db_ in order to run test_target
-
diff --git a/debian/patches/external-libs.patch b/debian/patches/external-libs.patch
deleted file mode 100644
index 12ed885..0000000
--- a/debian/patches/external-libs.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-Description: Allow library paths to be overridden externally
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: no
-Last-Update: 2015-11-27
---- pbdagcon.orig/Makefile
-+++ pbdagcon/Makefile
-@@ -1,6 +1,9 @@
- .PHONY: all clean test init-submodule cpp-github cpp cpp-check cpp-clean
- SHELL = /bin/bash -e
-
-+export BLASR ?= $(PWD)/blasr_libcpp/alignment
-+export PBDATA ?= $(PWD)/blasr_libcpp/pbdata
-+
- all: cpp-github
-
- clean: cpp-clean
-@@ -27,10 +30,10 @@
-
- # C++ project build directives
- cpp-github:
-- $(MAKE) -C src/cpp BLASR=$(PWD)/blasr_libcpp/alignment PBDATA=$(PWD)/blasr_libcpp/pbdata
-+ $(MAKE) -C src/cpp
-
- cpp-github-check:
-- $(MAKE) -C test/cpp BLASR=$(PWD)/blasr_libcpp/alignment PBDATA=$(PWD)/blasr_libcpp/pbdata
-+ $(MAKE) -C test/cpp
-
- cpp:
- $(MAKE) -C src/cpp
diff --git a/debian/patches/gtest-directory.patch b/debian/patches/gtest-directory.patch
deleted file mode 100644
index e18aa93..0000000
--- a/debian/patches/gtest-directory.patch
+++ /dev/null
@@ -1,90 +0,0 @@
-Description: Set gtest source directory to system-wide directory
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: not-needed
-Last-Update: 2015-12-10
-
---- pbdagcon.orig/test/cpp/Makefile
-+++ pbdagcon/test/cpp/Makefile
-@@ -6,22 +6,23 @@
- include $(SRCDIR)/boost.mk
- include gtest.mk
-
--GTEST_CPPFLAGS += -isystem $(GTEST_DIR)/include
- GTEST_CXXFLAGS += -g -Wall -Wextra -pthread
-
--INCDIRS := -I$(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)
- LDLIBS := -lpbdata -lblasr -lpthread ${EXTRA_LDLIBS}
-
--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 \
-- $(SRCDIR)/SimpleAligner.o
--vpath %.cc $(gtest_version)/src
-+ $(SRCDIR)/SimpleAligner.o
-+
-+GTEST_SRCDIR = $(GTEST_DIR)/src
-+vpath %.cc $(GTEST_SRCDIR)
-
- BUILDMSG = "=== Building $@ ==="
-
-@@ -31,35 +33,38 @@
-
- # XXX: need to mock out db_ in order to run test_target
-
--test_target_hit: $(GTEST_OBJECTS) $(DAZCON_OBJECTS) TargetHitTest.o
-+test_target_hit: gtest_main.a $(DAZCON_OBJECTS) TargetHitTest.o
- @echo $(BUILDMSG)
- $(CXX) $^ -o $@ -lpthread
- ./$@
-
--test_target: $(GTEST_OBJECTS) $(DAZCON_OBJECTS) TargetTest.o
-+test_target: gtest_main.a $(DAZCON_OBJECTS) TargetTest.o
- @echo $(BUILDMSG)
- $(CXX) $^ -o $@ -lpthread
- ./$@
-
--test_alngraph: $(GTEST_OBJECTS) $(PBDAGCON_OBJECTS) AlnGraphBoostTest.o
-+test_alngraph: gtest_main.a $(PBDAGCON_OBJECTS) AlnGraphBoostTest.o
- @echo $(BUILDMSG)
-- $(CXX) $^ -static -o $@ $(LDFLAGS) $(LDLIBS)
-+ $(CXX) $^ -o $@ $(LDFLAGS) $(LDLIBS)
- ./$@
-
--test_alignment: $(GTEST_OBJECTS) $(PBDAGCON_OBJECTS) AlignmentTest.o
-+test_alignment: gtest_main.a $(PBDAGCON_OBJECTS) AlignmentTest.o
- @echo $(BUILDMSG)
-- $(CXX) $^ -static -o $@ $(LDFLAGS) $(LDLIBS)
-+ $(CXX) $^ -o $@ $(LDFLAGS) $(LDLIBS)
- ./$@
-
--test_simple_aligner: $(GTEST_OBJECTS) $(PBDAGCON_OBJECTS) SimpleAlignerTest.o
-+test_simple_aligner: gtest_main.a $(PBDAGCON_OBJECTS) SimpleAlignerTest.o
- @echo $(BUILDMSG)
-- $(CXX) $^ -static -o $@ $(LDFLAGS) $(LDLIBS)
-+ $(CXX) $^ -o $@ $(LDFLAGS) $(LDLIBS)
- ./$@
-
- $(SRCDIR)/AlnGraphBoost.o: $(BOOST_HEADERS)
-
-+gtest_main.a: $(GTEST_OBJECTS)
-+ $(AR) $(ARFLAGS) $@ $^
-+
- $(GTEST_OBJECTS): $(GTEST_DIR)
-- $(CXX) $(GTEST_CPPFLAGS) -I$(GTEST_DIR) $(GTEST_CXXFLAGS) -c $</src/$(@:.o=.cc)
-+ $(CXX) $(GTEST_CPPFLAGS) -I$(GTEST_DIR) $(GTEST_CXXFLAGS) -c $(GTEST_SRCDIR)/$(@:.o=.cc)
-
- $(BOOST_HEADERS):
- @echo Fetching boost headers from $(URI)
-@@ -75,3 +80,4 @@
- $(RM) $(SRCDIR)/*.o
- $(RM) *.o
- $(RM) test_*
-+ $(RM) gtest_main.a
diff --git a/debian/patches/series b/debian/patches/series
index 93876f6..a4675fc 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1 @@
-external-libs.patch
compiler-flags.patch
-gtest-directory.patch
-disable-dazcon-tests.patch
--
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