Verified Commit caecb8ac authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

remove -m64 flag

parent 6f00504f

debian/changelog

+8 −0
Original line number Diff line number Diff line 
bowtie2 (2.3.5.1-6) unstable; urgency=medium



  * Team upload.

  * Remove the -m64 flag; not needed and not as universal as I thought

  * This means we build on arm64. (Closes: #925499)



 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 18 Dec 2019 13:36:56 +0100



bowtie2 (2.3.5.1-5) unstable; urgency=medium



  * Team upload.

debian/patches/correct_64bit_test

+7 −8
Original line number Diff line number Diff line
@@ -2,13 +2,13 @@ Author: Michael R. Crusoe <michael.crusoe@gmail.com> 
Description: Handle -m64 and -msse2 flags better

--- bowtie2.orig/Makefile

+++ bowtie2/Makefile

@@ -198,30 +198,17 @@

@@ -197,31 +197,13 @@

 SEARCH_FRAGMENTS := $(wildcard search_*_phase*.c)

 VERSION := $(shell cat VERSION)

 

 BITS := 32

-BITS := 32

-ifeq (x86_64,$(shell uname -m))

+ifeq (64,$(shell dpkg-architecture -q DEB_TARGET_ARCH_BITS))

 	BITS := 64

-	BITS := 64

-endif

-ifeq (amd64,$(shell uname -m))

-	BITS := 64
@@ -24,16 +24,15 @@ Description: Handle -m64 and -msse2 flags better 
-endif

-ifeq (32,$(BITS))

-  $(error bowtie2 compilation requires a 64-bit platform )

+	M64_FLAG := -m64

+else

-endif

+M64_FLAG :=

 endif

 

-SSE_FLAG := -msse2

-M64_FLAG := -m64

-ifeq (aarch64,$(shell uname -m))

+ifeq (amd64,$(dpkg-architecture -q DEB_TARGET_ARCH))

+	SSE_FLAG := -msse2

+	M64_FLAG := -m64

+else

 	SSE_FLAG =

-	M64_FLAG =

debian/patches/no_sanity

+10 −10
Original line number Diff line number Diff line
@@ -2,7 +2,7 @@ Author: Michael R. Crusoe <michael.crusoe@gmail.com> 
Description: save resources by not making/testing the -fsantize variants

--- bowtie2.orig/Makefile

+++ bowtie2/Makefile

@@ -218,20 +218,6 @@

@@ -213,20 +213,6 @@

 DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(filter-out -fdebug-prefix-map=%,$(DEBUG_FLAGS) $(CXXFLAGS))\""

 RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(filter-out -fdebug-prefix-map=%,$(RELEASE_FLAGS) $(CXXFLAGS))\""
@@ -23,7 +23,7 @@ Description: save resources by not making/testing the -fsantize variants 
 BOWTIE2_BIN_LIST :=     bowtie2-build-s \

                         bowtie2-build-l \

                         bowtie2-align-s \

@@ -244,12 +230,6 @@

@@ -239,12 +225,6 @@

                         bowtie2-align-l-debug \

                         bowtie2-inspect-s-debug \

                         bowtie2-inspect-l-debug
@@ -36,7 +36,7 @@ Description: save resources by not making/testing the -fsantize variants 
 

 GENERAL_LIST := $(wildcard scripts/*.sh) \

                 $(wildcard scripts/*.pl) \

@@ -306,10 +286,9 @@

@@ -301,10 +281,9 @@

 .PHONY: all allall both both-debug

 

 all: $(BOWTIE2_BIN_LIST) ;
@@ -48,7 +48,7 @@ Description: save resources by not making/testing the -fsantize variants 
 

 DEFS := -fno-strict-aliasing \

         -DBOWTIE2_VERSION="\"`cat VERSION`\"" \

@@ -323,14 +302,12 @@

@@ -318,14 +297,12 @@

         $(CPPFLAGS) \

         $(CFLAGS)
@@ -64,7 +64,7 @@ Description: save resources by not making/testing the -fsantize variants 
 	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \

 		$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \

 		$(CPPFLAGS) \

@@ -338,7 +315,7 @@

@@ -333,7 +310,7 @@

 		$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \

 		$(LDFLAGS) $(LDLIBS)
@@ -73,7 +73,7 @@ Description: save resources by not making/testing the -fsantize variants 
 	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \

 		$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \

 		$(CPPFLAGS) \

@@ -366,7 +343,7 @@

@@ -361,7 +338,7 @@

 # bowtie2-align targets

 #
@@ -82,7 +82,7 @@ Description: save resources by not making/testing the -fsantize variants 
 	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \

 		$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \

 		$(CPPFLAGS) \

@@ -374,7 +351,7 @@

@@ -369,7 +346,7 @@

 		$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \

 		$(LDFLAGS) $(LDLIBS)
@@ -91,7 +91,7 @@ Description: save resources by not making/testing the -fsantize variants 
 	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \

 		$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \

 		$(CPPFLAGS) \

@@ -404,7 +381,7 @@

@@ -399,7 +376,7 @@

 # bowtie2-inspect targets

 #
@@ -100,7 +100,7 @@ Description: save resources by not making/testing the -fsantize variants 
 	$(CXX) $(RELEASE_FLAGS) \

 		$(RELEASE_DEFS) $(CXXFLAGS) \

 		$(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \

@@ -413,7 +390,7 @@

@@ -408,7 +385,7 @@

 		$(SHARED_CPPS) \

 		$(LDFLAGS) $(LDLIBS)
@@ -109,7 +109,7 @@ Description: save resources by not making/testing the -fsantize variants 
 	$(CXX) $(RELEASE_FLAGS) \

 		$(RELEASE_DEFS) $(CXXFLAGS) \

 		$(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN  -DBOWTIE_64BIT_INDEX -Wall \

@@ -614,7 +591,7 @@

@@ -609,7 +586,7 @@

 

 .PHONY: clean

 clean: