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- diff --git a/Makefile.std b/Makefile.std
- index 95b0940..30206be 100644
- --- a/Makefile.std
- +++ b/Makefile.std
- @@ -1,62 +1,22 @@
- # General-purpose Makefile for PLINK 1.90
- #
- -# Compilation options:
- -# Do not link to LAPACK NO_LAPACK
-
- -# Leave blank after "=" to disable; put "= 1" to enable
- -# (when enabled, "#define NOLAPACK" must be uncommented in plink_common.h)
- -NO_LAPACK =
- -
- -
- -# should autodetect system
- -SYS = UNIX
- -ifdef SystemRoot
- - SYS = WIN
- -else
- - UNAME := $(shell uname)
- - ifeq ($(UNAME), Darwin)
- - SYS = MAC
- - endif
- -endif
- -
- -CFLAGS=-Wall -O2
- -BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas
- -LINKFLAGS=-lm -lpthread
- -ZLIB=zlib-1.2.8/libz.so.1.2.8
- -
- -ifeq ($(SYS), MAC)
- - GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40300)
- - ifeq "$(GCC_GTEQ_43)" "1"
- - CFLAGS=-Wall -O2 -flax-vector-conversions
- - endif
- - BLASFLAGS=-framework Accelerate
- - LINKFLAGS=
- - ZLIB=zlib-1.2.8/libz.1.2.8.dylib
- -endif
- -
- -ifeq ($(SYS), WIN)
- -# Note that, unlike the Linux and Mac build processes, this STATICALLY links
- -# LAPACK, since we have not gotten around to trying dynamically-linked LAPACK
- -# on Windows.
- -# If you don't already have LAPACK built, you'll probably want to turn on
- -# NO_LAPACK.
- - BLASFLAGS=-L. lapack/liblapack.a -L. lapack/librefblas.a
- - LINKFLAGS=-lm -static-libgcc
- - ZLIB=zlib-1.2.8/libz.a
- -endif
- -
- -ifdef NO_LAPACK
- - BLASFLAGS=
- -endif
- +# CFLAGS=-Wall -O2
- +# BLASFLAGS=-lblas -llapack -latlas
- +LINKFLAGS=-lm -lpthread -lopenblas -llapack -latlas -lstdc++
- +ZLIB=-lz
-
- SRC = plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_dosage.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c
-
- +OBJ = plink.o plink_assoc.o plink_calc.o plink_cluster.o plink_cnv.o plink_common.o plink_data.o plink_dosage.o plink_family.o plink_filter.o plink_glm.o plink_help.o plink_homozyg.o plink_lasso.o plink_ld.o plink_matrix.o plink_misc.o plink_set.o plink_stats.o SFMT.o dcdflib.o pigz.o yarn.o
- +
- # In the likely event that you are concurrently using PLINK 1.07, we suggest
- # either renaming that binary to "plink1" or this one to "plink2".
-
- -plink: $(SRC)
- - g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
- +# plink: $(SRC)
- +# g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
-
- -plinkw: $(SRC)
- +plink: $(SRC)
- g++ $(CFLAGS) $(SRC) -c
- - gfortran -O2 $(OBJ) -o plink -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
- + gfortran $(OBJ) -o plink2 $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
- + # gfortran $^ -o plink2 -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
- diff --git a/dose2plink.c b/dose2plink.c
- index dc1f33a..ca2d31c 100644
- --- a/dose2plink.c
- +++ b/dose2plink.c
- @@ -96,7 +96,7 @@
- #endif
- #endif
-
- -#include "zlib-1.2.8/zlib.h"
- +#include "zlib.h"
-
- #ifdef __APPLE__
- #include <sys/sysctl.h>
- diff --git a/pigz.c b/pigz.c
- index 6605925..3f4ca54 100644
- --- a/pigz.c
- +++ b/pigz.c
- @@ -303,7 +303,7 @@
- #include <stdio.h>
- #include <stdlib.h>
- #include <windows.h>
- -#include "zlib-1.2.8/zlib.h"
- +#include "zlib.h"
-
- void pigz_init(uint32_t setprocs) {
- return;
- @@ -383,7 +383,7 @@ void parallel_compress(char* out_fname, uint32_t do_append, uint32_t(* emitn)(ui
- # include <sys/pstat.h>
- #endif
-
- -#include "zlib-1.2.8/zlib.h" /* deflateInit2(), deflateReset(), deflate(), */
- +#include "zlib.h" /* deflateInit2(), deflateReset(), deflate(), */
- /* deflateEnd(), deflateSetDictionary(), crc32(),
- inflateBackInit(), inflateBack(), inflateBackEnd(),
- Z_DEFAULT_COMPRESSION, Z_DEFAULT_STRATEGY,
- diff --git a/plink_common.h b/plink_common.h
- index 5dd77e8..4da9371 100644
- --- a/plink_common.h
- +++ b/plink_common.h
- @@ -139,7 +139,7 @@
-
- #endif // __LP64__
-
- -#include "zlib-1.2.8/zlib.h"
- +#include "zlib.h"
- #include "SFMT.h"
-
- // 64MB of non-workspace memory guaranteed for now
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