diff --git a/Makefile.std b/Makefile.std index e204486..ca65bd3 100644 --- a/Makefile.std +++ b/Makefile.std @@ -1,64 +1,23 @@ # 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 = +# 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_perm.c plink_rserve.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c Rconnection.cc hfile.c bgzf.c -# 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 -ldl -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 "$(GCC_GTEQ_43)" "1" - CFLAGS=-Wall -O2 -flax-vector-conversions - endif - BLASFLAGS=-framework Accelerate - LINKFLAGS=-ldl - ZLIB=zlib-1.2.8/libz.1.2.8.dylib -endif - -ifeq ($(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 +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_perm.o plink_rserve.o plink_set.o plink_stats.o SFMT.o dcdflib.o pigz.o yarn.o Rconnection.o hfile.o bgzf.o -ifdef NO_LAPACK - BLASFLAGS= -endif -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_perm.c plink_rserve.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c Rconnection.cc hfile.c bgzf.c +# 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". -# In the event that you are still concurrently using PLINK 1.07, we suggest -# renaming that binary to "plink107" and "plink1". (Previously, -# "plink1"/"plink2" was suggested here; that also works for now, but it may -# lead to minor problems when PLINK 2.0 is released.) +# plink: $(SRC) +# g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) plink: $(SRC) - g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) - -plinkw: $(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 diff --git a/pigz.c b/pigz.c index 46b0525..3ce9a6b 100644 --- a/pigz.c +++ b/pigz.c @@ -297,7 +297,7 @@ #include #include #include -#include "zlib-1.2.8/zlib.h" +#include "zlib.h" #include "pigz.h" @@ -513,7 +513,7 @@ int32_t flex_pzwrite_close_null(Pigz_state* ps_ptr, char* writep) { # include #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 84eb929..e0b5cca 100644 --- a/plink_common.h +++ b/plink_common.h @@ -177,7 +177,7 @@ #define VEC_BITS (VEC_BYTES * 8) #define VEC_BITS_M1 (VEC_BITS - 1) -#include "zlib-1.2.8/zlib.h" +#include "zlib.h" #include "SFMT.h" // 64MB of non-workspace memory guaranteed for now.