[med-svn] [Git][med-team/plink2][master] 3 commits: Refresh patch
Dylan Aïssi
gitlab at salsa.debian.org
Thu Nov 12 10:47:25 GMT 2020
Dylan Aïssi pushed to branch master at Debian Med / plink2
Commits:
f288d354 by Dylan Aïssi at 2020-11-11T10:57:48+01:00
Refresh patch
- - - - -
37076545 by Dylan Aïssi at 2020-11-12T11:13:58+01:00
Remove d/p/simde, upstream applied
- - - - -
bce6865f by Dylan Aïssi at 2020-11-12T11:16:33+01:00
Refresh patch
- - - - -
4 changed files:
- debian/patches/Fix_Makefile.patch
- debian/patches/series
- − debian/patches/simde
- debian/patches/use_packaged_libdeflate → debian/patches/use_packaged_libdeflate.patch
Changes:
=====================================
debian/patches/Fix_Makefile.patch
=====================================
@@ -34,22 +34,22 @@ Last-Update: 2019-12-06
# zstd appears to be seriously targeted at -O3; see 26 Jul 2016 entry at
# cbloom.com/rants.html
ifdef ZSTD_O2
-@@ -148,14 +148,14 @@
- all: plink2 pgen_compress
+@@ -150,14 +150,14 @@
+ all: plink2$(SFX) pgen_compress$(SFX)
- plink2: $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc
+ plink2$(SFX): $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc
- $(CC) $(CFLAGS) $(CSRC2) -c
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c
- $(SKIP_STATIC_ZSTD) gcc $(ZCFLAGS) $(ZCSRC2) -c
+ $(SKIP_STATIC_ZSTD) $(CC) $(ZCFLAGS) $(ZCSRC2) -c
- $(CXX) $(CXXFLAGS) $(CCSRC2) -c
- $(CXX) $(CPUCHECK_FLAGS) ../plink2_cpu.cc -c
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CCSRC2) -c
-+ $(CXX) $(CPUCHECK_FLAGS) $(CXXFLAGS) $(CPPFLAGS) ../plink2_cpu.cc -c
- $(CXX) $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS)
++ $(CXX) $(CPUCHECK_FLAGS) $(CPPFLAGS) ../plink2_cpu.cc -c
+ $(CXX) $(OBJ2) plink2_cpu.o $(ARCH32) -o $@ $(BLASFLAGS) $(LINKFLAGS)
- pgen_compress: $(PGCSRC2)
-- $(CXX) $(CXXFLAGS) $(PGCSRC2) -o pgen_compress
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress
+ pgen_compress$(SFX): $(PGCSRC2)
+- $(CXX) $(CXXFLAGS) $(PGCSRC2) -o $@
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(PGCSRC2) -o $@
.PHONY: clean
clean:
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,2 @@
Fix_Makefile.patch
-simde
-use_packaged_libdeflate
+use_packaged_libdeflate.patch
=====================================
debian/patches/simde deleted
=====================================
@@ -1,95 +0,0 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-Description: Enable buidling on non-AMD64
-Forwarded: https://github.com/chrchang/plink-ng/pull/146
---- a/include/plink2_base.h
-+++ b/include/plink2_base.h
-@@ -134,14 +134,8 @@
- #endif
-
- #ifdef __LP64__
--# ifndef __SSE2__
--// possible todo: remove this requirement, the 32-bit VecW-using code does most
--// of what we need. But little point in doing this before we have e.g. an
--// ARM-based machine to test with that scientists would plausibly want to run
--// plink2 on.
--# error "64-bit builds currently require SSE2. Try producing a 32-bit build instead."
--# endif
--# include <emmintrin.h>
-+# define SIMDE_ENABLE_NATIVE_ALIASES
-+# include <simde/x86/sse2.h>
- # ifdef __SSE4_2__
- # define USE_SSE42
- # include <smmintrin.h>
---- a/Makefile
-+++ b/Makefile
-@@ -6,7 +6,7 @@
-
- # Does not currently support -DCPU_CHECK_...
-
--BASEFLAGS=-g -mavx2 -mbmi -mbmi2 -mlzcnt -DZSTD_MULTITHREAD
-+BASEFLAGS=-g -DZSTD_MULTITHREAD
- # BASEFLAGS=-g -msse4.2 -DZSTD_MULTITHREAD
- # BASEFLAGS=-g -DZSTD_MULTITHREAD
-
---- a/include/SFMT.h
-+++ b/include/SFMT.h
-@@ -129,7 +129,8 @@
- 128-bit SIMD like data type for standard C
- ------------------------------------------*/
- #ifdef __LP64__
-- #include <emmintrin.h>
-+ #define SIMDE_ENABLE_NATIVE_ALIASES
-+ #include <simde/x86/sse2.h>
-
- /** 128-bit data structure */
- union W128_T {
---- a/plink2.cc
-+++ b/plink2.cc
-@@ -3113,7 +3113,7 @@
- #ifdef __APPLE__
- fesetenv(FE_DFL_DISABLE_SSE_DENORMS_ENV);
- #else
--# ifdef __LP64__
-+# if defined __LP64__ && defined __x86_64__
- _MM_SET_FLUSH_ZERO_MODE(_MM_FLUSH_ZERO_ON);
- # endif
- #endif
---- a/build_dynamic/Makefile
-+++ b/build_dynamic/Makefile
-@@ -145,17 +145,19 @@
- CXXFLAGS += -Wno-sign-compare
- endif
-
--all: plink2 pgen_compress
-+SFX ?= ""
-
--plink2: $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc
-+all: plink2$(SFX) pgen_compress$(SFX)
-+
-+plink2$(SFX): $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc
- $(CC) $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c
- $(SKIP_STATIC_ZSTD) gcc $(ZCFLAGS) $(ZCSRC2) -c
- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CCSRC2) -c
- $(CXX) $(CPUCHECK_FLAGS) $(CXXFLAGS) $(CPPFLAGS) ../plink2_cpu.cc -c
-- $(CXX) $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS)
-+ $(CXX) $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2$(SFX) $(BLASFLAGS) $(LINKFLAGS) $(LDFLAGS)
-
--pgen_compress: $(PGCSRC2)
-- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress
-+pgen_compress$(SFX): $(PGCSRC2)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress$(SFX)
-
- .PHONY: clean
- clean:
---- a/plink2_glm.cc
-+++ b/plink2_glm.cc
-@@ -19,6 +19,9 @@
- #include "plink2_glm.h"
- #include "plink2_matrix.h"
-
-+#define SIMDE_ENABLE_NATIVE_ALIASES
-+#include <simde/x86/sse2.h>
-+
- #ifdef __cplusplus
- namespace plink2 {
- #endif
=====================================
debian/patches/use_packaged_libdeflate → debian/patches/use_packaged_libdeflate.patch
=====================================
@@ -6,7 +6,7 @@ Description: Use the Debian packaged version of libdeflate
CWARN2 = -Wall -Wextra -Wshadow -Wformat-security
CXXWARN2 = ${CWARN2} -Wold-style-cast
--CSRC = include/SFMT.c libdeflate/lib/adler32.c libdeflate/lib/aligned_malloc.c libdeflate/lib/crc32.c libdeflate/lib/deflate_compress.c libdeflate/lib/deflate_decompress.c libdeflate/lib/gzip_compress.c libdeflate/lib/gzip_decompress.c libdeflate/lib/zlib_compress.c libdeflate/lib/zlib_decompress.c libdeflate/lib/x86/cpu_features.c
+-CSRC = include/SFMT.c libdeflate/lib/adler32.c libdeflate/lib/crc32.c libdeflate/lib/deflate_compress.c libdeflate/lib/deflate_decompress.c libdeflate/lib/gzip_compress.c libdeflate/lib/gzip_decompress.c libdeflate/lib/utils.c libdeflate/lib/zlib_compress.c libdeflate/lib/zlib_decompress.c libdeflate/lib/arm/arm_cpu_features.c libdeflate/lib/x86/x86_cpu_features.c
+CSRC = include/SFMT.c
ZCSRC = zstd/lib/common/debug.c zstd/lib/common/entropy_common.c zstd/lib/common/zstd_common.c zstd/lib/common/error_private.c zstd/lib/common/xxhash.c zstd/lib/common/fse_decompress.c zstd/lib/common/pool.c zstd/lib/common/threading.c zstd/lib/compress/fse_compress.c zstd/lib/compress/hist.c zstd/lib/compress/huf_compress.c zstd/lib/compress/zstd_double_fast.c zstd/lib/compress/zstd_fast.c zstd/lib/compress/zstd_lazy.c zstd/lib/compress/zstd_ldm.c zstd/lib/compress/zstd_opt.c zstd/lib/compress/zstd_compress.c zstd/lib/compress/zstd_compress_literals.c zstd/lib/compress/zstd_compress_sequences.c zstd/lib/compress/zstd_compress_superblock.c zstd/lib/compress/zstdmt_compress.c zstd/lib/decompress/huf_decompress.c zstd/lib/decompress/zstd_decompress.c zstd/lib/decompress/zstd_ddict.c zstd/lib/decompress/zstd_decompress_block.c
@@ -15,18 +15,18 @@ Description: Use the Debian packaged version of libdeflate
OBJ3 = $(CSRC2:.c=.o) $(ZCSRC2:.c=.o) $(CCSRC2:.cc=.o)
--CINCLUDE = -Ilibdeflate -Ilibdeflate/common
--CINCLUDE2 = -I../libdeflate -I../libdeflate/common
-+#CINCLUDE = -Ilibdeflate -Ilibdeflate/common
-+#CINCLUDE2 = -I../libdeflate -I../libdeflate/common
+-CINCLUDE = -Ilibdeflate -Ilibdeflate/common -Isimde
+-CINCLUDE2 = -I../libdeflate -I../libdeflate/common -I../simde
++#CINCLUDE = -Ilibdeflate -Ilibdeflate/common -Isimde
++#CINCLUDE2 = -I../libdeflate -I../libdeflate/common -I../simde
+ CXXINCLUDE = -Isimde
+ CXXINCLUDE2 = -I../simde
ZSTD_INCLUDE = -Izstd/lib -Izstd/lib/common
- ZSTD_INCLUDE2 = -I../zstd/lib -I../zstd/lib/common
-
-@@ -30,5 +30,5 @@
- PGCOBJ = $(PGCSRC:.c=.o)
+@@ -32,5 +32,5 @@
+ PGCOBJ = $(PGCSRC:.cc=.o)
PGCSRC2 = $(foreach fname,$(PGCSRC),../$(fname))
--CLEAN = *.o include/*.o libdeflate/lib/*.o libdeflate/lib/x86/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o bin/plink2 bin/pgen_compress
+-CLEAN = *.o include/*.o libdeflate/lib/*.o libdeflate/lib/arm/*.o libdeflate/lib/x86/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o bin/plink2 bin/pgen_compress
+CLEAN = *.o include/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o bin/plink2 bin/pgen_compress
CLEAN3 = $(foreach expr,$(CLEAN),../$(expr))
--- a/include/plink2_bgzf.h
View it on GitLab: https://salsa.debian.org/med-team/plink2/-/compare/fee4d5fc88ccc5267185c977396a359d5f52b602...bce6865ff8b3375f07b2fc4cf233eea182ea43eb
--
View it on GitLab: https://salsa.debian.org/med-team/plink2/-/compare/fee4d5fc88ccc5267185c977396a359d5f52b602...bce6865ff8b3375f07b2fc4cf233eea182ea43eb
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