1 files changed, 0 insertions, 126 deletions
diff --git a/gn/packages/patches/plink-ng-Makefile-zlib.patch b/gn/packages/patches/plink-ng-Makefile-zlib.patch
deleted file mode 100644
index f3bb269..0000000
--- a/gn/packages/patches/plink-ng-Makefile-zlib.patch
+++ /dev/null
@@ -1,126 +0,0 @@
-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