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 <[email protected]> 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 <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/hisat2.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
