[med-svn] [bowtie2] 01/01: make build reproducible

[Sascha Steinbiss]

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

satta pushed a commit to branch master
in repository bowtie2.

commit 7a8fee9466dcab583b3b8f339f788e14063eca37
Author: Sascha Steinbiss <satta at debian.org>
Date:   Thu Aug 25 15:33:51 2016 +0000

    make build reproducible
---
 debian/changelog               |   8 +++
 debian/patches/hardening.patch | 140 +++++++++++++++++++++++++++++++++++++++--
 2 files changed, 142 insertions(+), 6 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 1c6ece2..d75a488 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+bowtie2 (2.2.9-4) unstable; urgency=medium
+
+  * Team upload.
+  * Make build reproducible by adding compiler flags
+    setting -fdebug-prefix-map.
+
+ -- Sascha Steinbiss <satta at debian.org>  Thu, 25 Aug 2016 12:47:33 +0000
+
 bowtie2 (2.2.9-3) unstable; urgency=medium
 
   * Team upload.
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index 63cac4c..8f05d40 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -1,16 +1,144 @@
-Description: Patch injects hardening CPPFLAGS
+Description: Patch injects hardening C(PP,XX) FLAGS and LDFLAGS
 Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
+        Sascha Steinbiss <satta at debian.org>
 Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Last-Update: Mon, 30 Jul 2012 13:51:31 +0200
---- bowtie2.orig/Makefile
-+++ bowtie2/Makefile
-@@ -254,7 +254,8 @@
+Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
+--- a/Makefile
++++ b/Makefile
+@@ -254,7 +254,9 @@
       $(FILE_FLAGS) \
       $(PREF_DEF) \
       $(MM_DEF) \
 -     $(SHMEM_DEF)
 +     $(SHMEM_DEF)\
-+     $(CPPFLAGS)
++     $(CPPFLAGS) \
++     $(CFLAGS)
  
  #
  # bowtie2-build targets
+@@ -266,7 +268,7 @@
+ 		$(INC) \
+ 		-o $@ $< \
+ 		$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
+-		$(LIBS) $(BUILD_LIBS)
++		$(LIBS) $(BUILD_LIBS) $(LDFLAGS)
+ 
+ bowtie2-build-l: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
+ 	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
+@@ -274,7 +276,7 @@
+ 		$(INC) \
+ 		-o $@ $< \
+ 		$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
+-		$(LIBS) $(BUILD_LIBS)
++		$(LIBS) $(BUILD_LIBS) $(LDFLAGS)
+ 
+ bowtie2-build-s-debug: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
+ 	$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
+@@ -282,7 +284,7 @@
+ 		$(INC) \
+ 		-o $@ $< \
+ 		$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
+-		$(LIBS) $(BUILD_LIBS)
++		$(LIBS) $(BUILD_LIBS) $(LDFLAGS)
+ 
+ bowtie2-build-l-debug: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
+ 	$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
+@@ -290,7 +292,7 @@
+ 		$(INC) \
+ 		-o $@ $< \
+ 		$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
+-		$(LIBS) $(BUILD_LIBS)
++		$(LIBS) $(BUILD_LIBS) $(LDFLAGS)
+ 
+ #
+ # bowtie2-align targets
+@@ -302,7 +304,7 @@
+ 		$(INC) \
+ 		-o $@ $< \
+ 		$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
+-		$(LIBS) $(SEARCH_LIBS)
++		$(LIBS) $(SEARCH_LIBS) $(LDFLAGS)
+ 
+ bowtie2-align-l: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
+ 	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
+@@ -310,7 +312,7 @@
+ 		$(INC) \
+ 		-o $@ $< \
+ 		$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
+-		$(LIBS) $(SEARCH_LIBS)
++		$(LIBS) $(SEARCH_LIBS) $(LDFLAGS)
+ 
+ bowtie2-align-s-debug: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
+ 	$(CXX) $(DEBUG_FLAGS) \
+@@ -319,7 +321,7 @@
+ 		$(INC) \
+ 		-o $@ $< \
+ 		$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
+-		$(LIBS) $(SEARCH_LIBS)
++		$(LIBS) $(SEARCH_LIBS) $(LDFLAGS)
+ 
+ bowtie2-align-l-debug: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
+ 	$(CXX) $(DEBUG_FLAGS) \
+@@ -328,7 +330,7 @@
+ 		$(INC) \
+ 		-o $@ $< \
+ 		$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
+-		$(LIBS) $(SEARCH_LIBS)
++		$(LIBS) $(SEARCH_LIBS) $(LDFLAGS)
+ 
+ #
+ # bowtie2-inspect targets
+@@ -341,7 +343,7 @@
+ 		$(INC) -I . \
+ 		-o $@ $< \
+ 		$(SHARED_CPPS) \
+-		$(LIBS) $(INSPECT_LIBS)
++		$(LIBS) $(INSPECT_LIBS) $(LDFLAGS)
+ 
+ bowtie2-inspect-l: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
+ 	$(CXX) $(RELEASE_FLAGS) \
+@@ -350,7 +352,7 @@
+ 		$(INC) -I . \
+ 		-o $@ $< \
+ 		$(SHARED_CPPS) \
+-		$(LIBS) $(INSPECT_LIBS)
++		$(LIBS) $(INSPECT_LIBS) $(LDFLAGS)
+ 
+ bowtie2-inspect-s-debug: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS) 
+ 	$(CXX) $(DEBUG_FLAGS) \
+@@ -359,7 +361,7 @@
+ 		$(INC) -I . \
+ 		-o $@ $< \
+ 		$(SHARED_CPPS) \
+-		$(LIBS) $(INSPECT_LIBS)
++		$(LIBS) $(INSPECT_LIBS) $(LDFLAGS)
+ 
+ bowtie2-inspect-l-debug: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
+ 	$(CXX) $(DEBUG_FLAGS) \
+@@ -368,7 +370,7 @@
+ 		$(INC) -I . \
+ 		-o $@ $< \
+ 		$(SHARED_CPPS) \
+-		$(LIBS) $(INSPECT_LIBS)
++		$(LIBS) $(INSPECT_LIBS) $(LDFLAGS)
+ 
+ #
+ # bowtie2-dp targets
+@@ -381,7 +383,7 @@
+ 		$(INC) -I . \
+ 		-o $@ $< \
+ 		$(DP_CPPS) $(SHARED_CPPS) \
+-		$(LIBS) $(SEARCH_LIBS)
++		$(LIBS) $(SEARCH_LIBS) $(LDFLAGS)
+ 
+ bowtie2-dp-debug: bt2_dp.cpp $(HEADERS) $(SHARED_CPPS) $(DP_CPPS)
+ 	$(CXX) $(DEBUG_FLAGS) \
+@@ -390,7 +392,7 @@
+ 		$(INC) -I . \
+ 		-o $@ $< \
+ 		$(DP_CPPS) $(SHARED_CPPS) \
+-		$(LIBS) $(SEARCH_LIBS)
++		$(LIBS) $(SEARCH_LIBS) $(LDFLAGS)
+ 
+ bowtie2.bat:
+ 	echo "@echo off" > bowtie2.bat

-- 
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