[med-svn] [Git][med-team/plink2][master] Update patch

[Dylan Aïssi]

Dylan Aïssi pushed to branch master at Debian Med / plink2


Commits:
698d55b0 by Dylan Aïssi at 2019-12-06T06:55:38Z
Update patch

- - - - -


4 changed files:

- debian/control
- − debian/patches/Disable_opt.patch
- debian/patches/Fix_Makefile.patch
- debian/patches/series


Changes:

=====================================
debian/control
=====================================
@@ -7,6 +7,7 @@ Build-Depends: debhelper-compat (= 12),
                help2man,
                libatlas-base-dev,
                liblapack-dev,
+               libzstd-dev,
                zlib1g-dev
 Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/plink2


=====================================
debian/patches/Disable_opt.patch deleted
=====================================
@@ -1,16 +0,0 @@
-Author: Dylan Aïssi <bob.dybian at gmail.com>
-Description: Not acceptable for a debian package.
-Last-Update: 2017-07-17
-Forwarded: not-needed
-
---- a/build_dynamic/Makefile
-+++ b/build_dynamic/Makefile
-@@ -11,7 +11,7 @@
- #     LD_LIBRARY_PATH to include the appropriate directories)
- #   32-bit binary (also sets STATIC_ZLIB, ZSTD_O2, and NO_SSE42): FORCE_32BIT
- #     (warning: you may need to add a zconf.h symlink to make that work)
--NO_SSE42 =
-+NO_SSE42 = 1
- NO_LAPACK =
- PREFER_CBLAS_F77 =
- ZSTD_O2 = 1


=====================================
debian/patches/Fix_Makefile.patch
=====================================
@@ -1,14 +1,29 @@
-Author: Dylan Aïssi <bob.dybian at gmail.com>
-Description: Take into account the user-provided compiler flags.
-Last-Update: 2017-07-17
-Forwarded: TODO
+Author: Dylan Aïssi daissi at debian.org>
+Description: Fix makefile for Debian packaging.
+Last-Update: 2019-12-06
 
 --- a/build_dynamic/Makefile
 +++ b/build_dynamic/Makefile
-@@ -36,11 +36,11 @@
-   ARCH32 = -m32 -march=i686
-   CXXFLAGS = -std=c++0x
- else
+@@ -17,13 +17,13 @@
+ #     work)
+ #   Debug symbols: set DEBUG to -g
+ NO_AVX2 = 1
+-NO_SSE42 =
++NO_SSE42 = 1
+ CPU_CHECK = 1
+ NO_LAPACK =
+ PREFER_CBLAS_F77 =
+ ZSTD_O2 = 1
+ STATIC_ZLIB =
+-STATIC_ZSTD = 1
++STATIC_ZSTD =
+ 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 @@
+       CPUCHECK_FLAGS = -O2 -DCPU_CHECK_AVX2 ${CXXWARN2}
+     endif
+   endif
 -  CXXFLAGS = -std=c++11
 +  CXXFLAGS += -std=c++11
  endif
@@ -19,22 +34,22 @@ Forwarded: TODO
  # zstd appears to be seriously targeted at -O3; see 26 Jul 2016 entry at
  # cbloom.com/rants.html
  ifdef ZSTD_O2
-@@ -113,13 +113,13 @@
+@@ -144,14 +144,14 @@
  all: plink2 pgen_compress
  
- plink2: $(CSRC) $(ZCSRC) $(CPPSRC)
--	gcc $(CFLAGS) $(CSRC) -c
--	gcc $(ZCFLAGS) $(ZCSRC) -c
--	g++ $(CXXFLAGS) $(CPPSRC) -c
--	g++ $(OBJ) $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS)
-+	gcc $(CPPFLAGS) $(CFLAGS) $(CSRC) -c
-+	gcc $(CPPFLAGS) $(ZCFLAGS) $(ZCSRC) -c
-+	g++ $(CPPFLAGS) $(CXXFLAGS) $(CPPSRC) -c
-+	g++ $(OBJ) $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS) $(LDFLAGS)
+ plink2: $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc
+-	gcc $(CFLAGS) $(CSRC2) -c
++	gcc $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c
+ 	$(SKIP_STATIC_ZSTD) gcc $(ZCFLAGS) $(ZCSRC2) -c
+-	g++ $(CXXFLAGS) $(CCSRC2) -c
++	g++ $(CPPFLAGS) $(CXXFLAGS) $(CCSRC2) -c
+ 	g++ $(CPUCHECK_FLAGS) ../plink2_cpu.cc -c
+-	g++ $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS)
++	g++ $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS) $(LDFLAGS)
  
- pgen_compress: ../pgenlib_internal.cpp ../pgen_compress.cpp
--	g++ $(CXXFLAGS) ../pgenlib_internal.cpp ../pgen_compress.cpp -o pgen_compress
-+	g++ $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) ../pgenlib_internal.cpp ../pgen_compress.cpp -o pgen_compress
+ pgen_compress: $(PGCSRC2)
+-	g++ $(CXXFLAGS) $(PGCSRC2) -o pgen_compress
++	g++ $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress
  
  .PHONY: clean
  clean:


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+Fix_Makefile.patch



View it on GitLab: https://salsa.debian.org/med-team/plink2/commit/698d55b08efd3d65093ced5d82337201e8a3a2a7

-- 
View it on GitLab: https://salsa.debian.org/med-team/plink2/commit/698d55b08efd3d65093ced5d82337201e8a3a2a7
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