[med-svn] [Git][med-team/plink2][master] 4 commits: Remove debian/patches/crossbuild, applied upstream

Dylan Aïssi gitlab at salsa.debian.org
Thu Sep 10 09:56:09 BST 2020 


Dylan Aïssi pushed to branch master at Debian Med / plink2


Commits:
f6c79fd8 by Dylan Aïssi at 2020-09-10T10:47:18+02:00
Remove debian/patches/crossbuild, applied upstream

- - - - -
8b6f0d10 by Dylan Aïssi at 2020-09-10T10:51:28+02:00
Refresh debian/patches/Fix_Makefile.patch

- - - - -
4e4588ee by Dylan Aïssi at 2020-09-10T10:55:06+02:00
Refresh debian/patches/simde

- - - - -
4d245ac2 by Dylan Aïssi at 2020-09-10T10:55:54+02:00
Refresh debian/patches/use_packaged_libdeflate

- - - - -


5 changed files:

- debian/patches/Fix_Makefile.patch
- − debian/patches/crossbuild
- debian/patches/series
- debian/patches/simde
- debian/patches/use_packaged_libdeflate


Changes:

=====================================
debian/patches/Fix_Makefile.patch
=====================================
@@ -2,8 +2,8 @@ Author: Dylan Aïssi daissi at debian.org>
 Description: Fix makefile for Debian packaging.
 Last-Update: 2019-12-06
 
---- plink2.orig/build_dynamic/Makefile
-+++ plink2/build_dynamic/Makefile
+--- a/build_dynamic/Makefile
++++ b/build_dynamic/Makefile
 @@ -17,13 +17,13 @@
  #     work)
  #   Debug symbols: set DEBUG to -g
@@ -20,7 +20,7 @@ Last-Update: 2019-12-06
  DYNAMIC_MKL =
  MKLROOT = /home/ubuntu/intel/mkl
  MKL_IOMP5_DIR = /home/ubuntu/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64
-@@ -64,11 +64,11 @@
+@@ -66,11 +66,11 @@
        CPUCHECK_FLAGS = -O2 -DCPU_CHECK_AVX2 ${CXXWARN2}
      endif
    endif
@@ -34,23 +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
-@@ -146,14 +146,14 @@
+@@ -148,14 +148,14 @@
  all: plink2 pgen_compress
  
  plink2: $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc
--	gcc $(CFLAGS) $(CSRC2) -c
-+	gcc $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c
+-	$(CC) $(CFLAGS) $(CSRC2) -c
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c
  	$(SKIP_STATIC_ZSTD) gcc $(ZCFLAGS) $(ZCSRC2) -c
--	g++ $(CXXFLAGS) $(CCSRC2) -c
--	g++ $(CPUCHECK_FLAGS) ../plink2_cpu.cc -c
--	g++ $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS)
-+	g++ $(CPPFLAGS) $(CXXFLAGS) $(CCSRC2) -c
-+	g++ $(CPUCHECK_FLAGS) $(CXXFLAGS) $(CPPFLAGS) ../plink2_cpu.cc -c
-+	g++ $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS) $(LDFLAGS)
+-	$(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)
  
  pgen_compress: $(PGCSRC2)
--	g++ $(CXXFLAGS) $(PGCSRC2) -o pgen_compress
-+	g++ $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress
+-	$(CXX) $(CXXFLAGS) $(PGCSRC2) -o pgen_compress
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress
  
  .PHONY: clean
  clean:


=====================================
debian/patches/crossbuild deleted
=====================================
@@ -1,35 +0,0 @@
-From: Michael R. Crusoe <crusoe at debian.org>
-Subject: enable cross building
-Forwarded: https://github.com/chrchang/plink-ng/pull/145
---- plink2.orig/build_dynamic/Makefile
-+++ plink2/build_dynamic/Makefile
-@@ -29,6 +29,8 @@
- MKL_IOMP5_DIR = /home/ubuntu/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64
- FORCE_32BIT =
- DEBUG =
-+CC ?= gcc
-+CXX ?= g++
- 
- BASEFLAGS=-DZSTD_MULTITHREAD
- # ***** end configuration *****
-@@ -146,14 +148,14 @@
- all: plink2$(SFX) pgen_compress$(SFX)
- 
- plink2$(SFX): $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc
--	gcc $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c
--	$(SKIP_STATIC_ZSTD) gcc $(ZCFLAGS) $(ZCSRC2) -c
--	g++ $(CPPFLAGS) $(CXXFLAGS) $(CCSRC2) -c
--	g++ $(CPUCHECK_FLAGS) $(CXXFLAGS) $(CPPFLAGS) ../plink2_cpu.cc -c
--	g++ $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2$(SFX) $(BLASFLAGS) $(LINKFLAGS) $(LDFLAGS)
-+	$(CC) $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c
-+	$(SKIP_STATIC_ZSTD) $(CC) $(ZCFLAGS) $(ZCSRC2) -c
-+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CCSRC2) -c
-+	$(CXX) $(CPUCHECK_FLAGS) $(CXXFLAGS) $(CPPFLAGS) ../plink2_cpu.cc -c
-+	$(CXX) $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2$(SFX) $(BLASFLAGS) $(LINKFLAGS) $(LDFLAGS)
- 
- pgen_compress$(SFX): $(PGCSRC2)
--	g++ $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress$(SFX)
-+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress$(SFX)
- 
- .PHONY: clean
- clean:


=====================================
debian/patches/series
=====================================
@@ -1,4 +1,3 @@
 Fix_Makefile.patch
 simde
 use_packaged_libdeflate
-crossbuild


=====================================
debian/patches/simde
=====================================
@@ -1,8 +1,8 @@
 Author: Michael R. Crusoe <michael.crusoe at gmail.com>
 Description: Enable buidling on non-AMD64
 Forwarded: https://github.com/chrchang/plink-ng/pull/146
---- plink2.orig/include/plink2_base.h
-+++ plink2/include/plink2_base.h
+--- a/include/plink2_base.h
++++ b/include/plink2_base.h
 @@ -134,14 +134,8 @@
  #endif
  
@@ -20,8 +20,8 @@ Forwarded: https://github.com/chrchang/plink-ng/pull/146
  #  ifdef __SSE4_2__
  #    define USE_SSE42
  #    include <smmintrin.h>
---- plink2.orig/Makefile
-+++ plink2/Makefile
+--- a/Makefile
++++ b/Makefile
 @@ -6,7 +6,7 @@
  
  # Does not currently support -DCPU_CHECK_...
@@ -31,8 +31,8 @@ Forwarded: https://github.com/chrchang/plink-ng/pull/146
  # BASEFLAGS=-g -msse4.2 -DZSTD_MULTITHREAD
  # BASEFLAGS=-g -DZSTD_MULTITHREAD
  
---- plink2.orig/include/SFMT.h
-+++ plink2/include/SFMT.h
+--- a/include/SFMT.h
++++ b/include/SFMT.h
 @@ -129,7 +129,8 @@
    128-bit SIMD like data type for standard C
    ------------------------------------------*/
@@ -43,9 +43,9 @@ Forwarded: https://github.com/chrchang/plink-ng/pull/146
  
  /** 128-bit data structure */
  union W128_T {
---- plink2.orig/plink2.cc
-+++ plink2/plink2.cc
-@@ -3067,7 +3067,7 @@
+--- a/plink2.cc
++++ b/plink2.cc
+@@ -3113,7 +3113,7 @@
  #ifdef __APPLE__
    fesetenv(FE_DFL_DISABLE_SSE_DENORMS_ENV);
  #else
@@ -54,9 +54,9 @@ Forwarded: https://github.com/chrchang/plink-ng/pull/146
    _MM_SET_FLUSH_ZERO_MODE(_MM_FLUSH_ZERO_ON);
  #  endif
  #endif
---- plink2.orig/build_dynamic/Makefile
-+++ plink2/build_dynamic/Makefile
-@@ -143,17 +143,19 @@
+--- a/build_dynamic/Makefile
++++ b/build_dynamic/Makefile
+@@ -145,17 +145,19 @@
    CXXFLAGS += -Wno-sign-compare
  endif
  
@@ -67,22 +67,22 @@ Forwarded: https://github.com/chrchang/plink-ng/pull/146
 +all: plink2$(SFX) pgen_compress$(SFX)
 +
 +plink2$(SFX): $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc
- 	gcc $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c
+ 	$(CC) $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c
  	$(SKIP_STATIC_ZSTD) gcc $(ZCFLAGS) $(ZCSRC2) -c
- 	g++ $(CPPFLAGS) $(CXXFLAGS) $(CCSRC2) -c
- 	g++ $(CPUCHECK_FLAGS) $(CXXFLAGS) $(CPPFLAGS) ../plink2_cpu.cc -c
--	g++ $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS) $(LDFLAGS)
-+	g++ $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2$(SFX) $(BLASFLAGS) $(LINKFLAGS) $(LDFLAGS)
+ 	$(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)
--	g++ $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress
+-	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress
 +pgen_compress$(SFX): $(PGCSRC2)
-+	g++ $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress$(SFX)
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress$(SFX)
  
  .PHONY: clean
  clean:
---- plink2.orig/plink2_glm.cc
-+++ plink2/plink2_glm.cc
+--- a/plink2_glm.cc
++++ b/plink2_glm.cc
 @@ -19,6 +19,9 @@
  #include "plink2_glm.h"
  #include "plink2_matrix.h"


=====================================
debian/patches/use_packaged_libdeflate
=====================================
@@ -1,7 +1,7 @@
 Author: Michael R. Crusoe <michael.crusoe at gmail.com>
 Description: Use the Debian packaged version of libdeflate
---- plink2.orig/Makefile.src
-+++ plink2/Makefile.src
+--- a/Makefile.src
++++ b/Makefile.src
 @@ -5,7 +5,7 @@
  CWARN2 = -Wall -Wextra -Wshadow -Wformat-security
  CXXWARN2 = ${CWARN2} -Wold-style-cast
@@ -9,7 +9,7 @@ Description: Use the Debian packaged version of libdeflate
 -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
  
- 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/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
+ 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
  
 @@ -21,8 +21,8 @@
  
@@ -29,8 +29,8 @@ Description: Use the Debian packaged version of libdeflate
 -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 zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o bin/plink2 bin/pgen_compress
  CLEAN3 = $(foreach expr,$(CLEAN),../$(expr))
---- plink2.orig/include/plink2_bgzf.h
-+++ plink2/include/plink2_bgzf.h
+--- a/include/plink2_bgzf.h
++++ b/include/plink2_bgzf.h
 @@ -35,7 +35,7 @@
  
  #include "plink2_string.h"



View it on GitLab: https://salsa.debian.org/med-team/plink2/-/compare/97abfe719aa0dadda2b4e009abb012eed096ea80...4d245ac2ed1ed8163239503987c404887291ba44

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View it on GitLab: https://salsa.debian.org/med-team/plink2/-/compare/97abfe719aa0dadda2b4e009abb012eed096ea80...4d245ac2ed1ed8163239503987c404887291ba44
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