Updated and fixed plink-nggn-stable

1 files changed, 0 insertions, 129 deletions

diff --git a/plink-ng-Makefile-zlib-git.patch b/plink-ng-Makefile-zlib-git.patch
deleted file mode 100644
index 79986b8..0000000
--- a/plink-ng-Makefile-zlib-git.patch
+++ /dev/null
@@ -1,129 +0,0 @@
-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 <sys/sysctl.h>
-diff --git a/pigz.c b/pigz.c
-index 46b0525..3ce9a6b 100644
---- a/pigz.c
-+++ b/pigz.c
-@@ -297,7 +297,7 @@
- #include <stdio.h>
- #include <stdlib.h>
- #include <windows.h>
--#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 <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 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.