guix-bioinformatics/plink-ng-Makefile-zlib.patch

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