[med-svn] [Git][med-team/bowtie2][master] remove -m64 flag

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / bowtie2


Commits:
caecb8ac by Michael R. Crusoe at 2019-12-18T22:40:38Z
remove -m64 flag

- - - - -


3 changed files:

- debian/changelog
- debian/patches/correct_64bit_test
- debian/patches/no_sanity


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+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 at 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
=====================================
@@ -2,13 +2,13 @@ Author: Michael R. Crusoe <michael.crusoe at 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
-+	M64_FLAG :=
- endif
+-endif
++M64_FLAG :=
  
 -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
=====================================
@@ -2,7 +2,7 @@ Author: Michael R. Crusoe <michael.crusoe at 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:



View it on GitLab: https://salsa.debian.org/med-team/bowtie2/commit/caecb8acd4165361dc313746c720330c098d055e

-- 
View it on GitLab: https://salsa.debian.org/med-team/bowtie2/commit/caecb8acd4165361dc313746c720330c098d055e
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