[med-svn] [hisat2] 03/05: Adapt patches
Andreas Tille
tille at debian.org
Mon Sep 4 13:09:22 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to tag debian/2.1.0-1
in repository hisat2.
commit f259adecc8389a0f4157e213fb9aefef64f4d731
Author: Andreas Tille <tille at debian.org>
Date: Mon Sep 4 14:48:58 2017 +0200
Adapt patches
---
debian/patches/hardening | 34 +++++++++++++++++-----------------
debian/patches/reproducibile | 14 +++++++++-----
2 files changed, 26 insertions(+), 22 deletions(-)
diff --git a/debian/patches/hardening b/debian/patches/hardening
index f8a91e9..cf386a8 100644
--- a/debian/patches/hardening
+++ b/debian/patches/hardening
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: Enable the passing of extra compilation flags, for hardening
---- hisat2.orig/Makefile
-+++ hisat2/Makefile
-@@ -157,7 +157,7 @@
+--- a/Makefile
++++ b/Makefile
+@@ -157,7 +157,7 @@ SSE_FLAG=-msse2
DEBUG_FLAGS = -O0 -g3 $(BIToS_FLAG) $(SSE_FLAG)
DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
@@ -11,7 +11,7 @@ Description: Enable the passing of extra compilation flags, for hardening
RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
NOASSERT_FLAGS = -DNDEBUG
FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
-@@ -253,7 +253,7 @@
+@@ -255,7 +255,7 @@ hisat-bp-bin: hisat_bp.cpp $(SEARCH_CPPS
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
@@ -20,7 +20,7 @@ Description: Enable the passing of extra compilation flags, for hardening
hisat-bp-bin-debug: hisat_bp.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -262,7 +262,7 @@
+@@ -264,7 +264,7 @@ hisat-bp-bin-debug: hisat_bp.cpp $(SEARC
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
@@ -29,7 +29,7 @@ Description: Enable the passing of extra compilation flags, for hardening
#
-@@ -275,7 +275,7 @@
+@@ -277,7 +277,7 @@ hisat2-build-s: hisat2_build.cpp $(SHARE
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
@@ -38,7 +38,7 @@ Description: Enable the passing of extra compilation flags, for hardening
hisat2-build-l: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
-@@ -283,7 +283,7 @@
+@@ -285,7 +285,7 @@ hisat2-build-l: hisat2_build.cpp $(SHARE
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
@@ -47,7 +47,7 @@ Description: Enable the passing of extra compilation flags, for hardening
hisat2-build-s-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
-@@ -291,7 +291,7 @@
+@@ -293,7 +293,7 @@ hisat2-build-s-debug: hisat2_build.cpp $
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
@@ -56,7 +56,7 @@ Description: Enable the passing of extra compilation flags, for hardening
hisat2-build-l-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
-@@ -299,7 +299,7 @@
+@@ -301,7 +301,7 @@ hisat2-build-l-debug: hisat2_build.cpp $
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
@@ -65,7 +65,7 @@ Description: Enable the passing of extra compilation flags, for hardening
#
# hisat2 targets
-@@ -311,7 +311,7 @@
+@@ -313,7 +313,7 @@ hisat2-align-s: hisat2.cpp $(SEARCH_CPPS
$(INC) $(SEARCH_INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
@@ -74,7 +74,7 @@ Description: Enable the passing of extra compilation flags, for hardening
hisat2-align-l: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
-@@ -319,7 +319,7 @@
+@@ -321,7 +321,7 @@ hisat2-align-l: hisat2.cpp $(SEARCH_CPPS
$(INC) $(SEARCH_INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
@@ -83,7 +83,7 @@ Description: Enable the passing of extra compilation flags, for hardening
hisat2-align-s-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -328,7 +328,7 @@
+@@ -330,7 +330,7 @@ hisat2-align-s-debug: hisat2.cpp $(SEARC
$(INC) $(SEARCH_INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
@@ -92,7 +92,7 @@ Description: Enable the passing of extra compilation flags, for hardening
hisat2-align-l-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -337,7 +337,7 @@
+@@ -339,7 +339,7 @@ hisat2-align-l-debug: hisat2.cpp $(SEARC
$(INC) $(SEARCH_INC) \
-o $@ $< \
$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
@@ -101,7 +101,7 @@ Description: Enable the passing of extra compilation flags, for hardening
#
# hisat2-inspect targets
-@@ -350,7 +350,7 @@
+@@ -352,7 +352,7 @@ hisat2-inspect-s: hisat2_inspect.cpp $(H
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
@@ -110,7 +110,7 @@ Description: Enable the passing of extra compilation flags, for hardening
hisat2-inspect-l: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(RELEASE_FLAGS) \
-@@ -359,7 +359,7 @@
+@@ -361,7 +361,7 @@ hisat2-inspect-l: hisat2_inspect.cpp $(H
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
@@ -119,7 +119,7 @@ Description: Enable the passing of extra compilation flags, for hardening
hisat2-inspect-s-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -368,7 +368,7 @@
+@@ -370,7 +370,7 @@ hisat2-inspect-s-debug: hisat2_inspect.c
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
@@ -128,7 +128,7 @@ Description: Enable the passing of extra compilation flags, for hardening
hisat2-inspect-l-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -377,7 +377,7 @@
+@@ -379,7 +379,7 @@ hisat2-inspect-l-debug: hisat2_inspect.c
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
diff --git a/debian/patches/reproducibile b/debian/patches/reproducibile
index a4d5afd..c48eb6d 100644
--- a/debian/patches/reproducibile
+++ b/debian/patches/reproducibile
@@ -2,7 +2,7 @@ Author: Michael R. Crusoe
Description: Make build reproducible
--- a/Makefile
+++ b/Makefile
-@@ -26,7 +26,7 @@
+@@ -26,7 +26,7 @@ GCC_SUFFIX =
CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
CXX = $(CPP)
@@ -11,7 +11,7 @@ Description: Make build reproducible
BOWTIE_MM = 1
BOWTIE_SHARED_MEM = 0
-@@ -130,7 +130,7 @@
+@@ -130,7 +130,7 @@ BUILD_CPPS = diff_sample.cpp
HISAT2_CPPS_MAIN = $(SEARCH_CPPS) hisat2_main.cpp
HISAT2_BUILD_CPPS_MAIN = $(BUILD_CPPS) hisat2_build_main.cpp
@@ -20,16 +20,20 @@ Description: Make build reproducible
VERSION = $(shell cat VERSION)
# Convert BITS=?? to a -m flag
-@@ -183,14 +183,14 @@
+@@ -183,16 +183,16 @@ HISAT2_BIN_LIST_AUX = hisat2-build-s-deb
hisat2-inspect-s-debug \
hisat2-inspect-l-debug
-GENERAL_LIST = $(wildcard scripts/*.sh) \
- $(wildcard scripts/*.pl) \
- $(wildcard *.py) \
+- $(wildcard hisatgenotype_modules/*.py) \
+- $(wildcard hisatgenotype_scripts/*.py) \
+GENERAL_LIST = $(sort $(wildcard scripts/*.sh)) \
+ $(sort $(wildcard scripts/*.pl)) \
+ $(sort $(wildcard *.py)) \
++ $(sort $(wildcard hisatgenotype_modules/*.py)) \
++ $(sort $(wildcard hisatgenotype_scripts/*.py)) \
doc/manual.inc.html \
doc/README \
doc/style.css \
@@ -40,7 +44,7 @@ Description: Make build reproducible
example/reference/22_20-21M.fa \
example/reference/22_20-21M.snp \
$(PTHREAD_PKG) \
-@@ -213,10 +213,10 @@
+@@ -215,10 +215,10 @@ endif
# the Windows FIND tool instead.
FIND=$(shell which find)
@@ -55,7 +59,7 @@ Description: Make build reproducible
doc/strip_markdown.pl \
Makefile \
$(GENERAL_LIST)
-@@ -233,15 +233,20 @@
+@@ -235,15 +235,20 @@ both: hisat2-align-s hisat2-align-l hisa
both-debug: hisat2-align-s-debug hisat2-align-l-debug hisat2-build-s-debug hisat2-build-l-debug
--
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