Loading debian/control +1 −0 Original line number Diff line number Diff line Loading @@ -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 Loading debian/patches/Disable_opt.patchdeleted 100644 → 0 +0 −16 Original line number Diff line number Diff line Author: Dylan Aïssi <bob.dybian@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 +36 −21 Original line number Diff line number Diff line Author: Dylan Aïssi <bob.dybian@gmail.com> Description: Take into account the user-provided compiler flags. Last-Update: 2017-07-17 Forwarded: TODO Author: Dylan Aïssi daissi@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 Loading @@ -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 +1 −0 Original line number Diff line number Diff line Fix_Makefile.patch Loading
debian/control +1 −0 Original line number Diff line number Diff line Loading @@ -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 Loading
debian/patches/Disable_opt.patchdeleted 100644 → 0 +0 −16 Original line number Diff line number Diff line Author: Dylan Aïssi <bob.dybian@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 +36 −21 Original line number Diff line number Diff line Author: Dylan Aïssi <bob.dybian@gmail.com> Description: Take into account the user-provided compiler flags. Last-Update: 2017-07-17 Forwarded: TODO Author: Dylan Aïssi daissi@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 Loading @@ -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:
