plink2: Makefile patches accepted upstream

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu May 3 19:14:00 2018 -0500
Changeset:	4bb346d16dafdd5c1b2b1e4c2ada225bfb778aae

Modified Files:
	plink2/Makefile
	plink2/distinfo
Removed Files:
	plink2/patches/patch-Makefile

Log Message:
plink2: Makefile patches accepted upstream

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=4bb346d16dafdd5c1b2b1e4c2ada225bfb778aae

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 plink2/Makefile               | 12 +++---
 plink2/distinfo               | 11 +++--
 plink2/patches/patch-Makefile | 93 -------------------------------------------
 3 files changed, 11 insertions(+), 105 deletions(-)

diffs:
diff --git a/plink2/Makefile b/plink2/Makefile
index e0f37654d4..cc9167c681 100644
--- a/plink2/Makefile
+++ b/plink2/Makefile
@@ -6,10 +6,10 @@
 ###########################################################
 
 DISTNAME=	plink-ng-${PORTVERSION}
-CATEGORIES=	wip biology
+CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=chrchang/}
 GITHUB_PROJECT=	plink-ng
-GITHUB_TAG=	d046d8dfbbba50065644bbe9647edbe94a29b1a2
+GITHUB_TAG=	e81056a32d67cd73a69579e2dbb374d16196f305
 
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	http://pngu.mgh.harvard.edu/~purcell/plink/
@@ -26,14 +26,14 @@ USE_TOOLS+=	gmake
 
 WRKSRC=		${WRKDIR}/${GITHUB_PROJECT}-${GITHUB_TAG}/2.0
 
-CFLAGS+=	-DDYNAMIC_ZLIB -I${PREFIX}/include
-CXXFLAGS+=	-DDYNAMIC_ZLIB -I${PREFIX}/include
+CFLAGS+=	-DDYNAMIC_ZLIB -I${PREFIX}/include -g
+CXXFLAGS+=	-DDYNAMIC_ZLIB -I${PREFIX}/include -g
 
 # Check this
 MAKE_FLAGS+=	ZLIB=-lz BLASFLAGS64="-L${PREFIX}/lib -lopenblas_pthread"
-INSTALL_TARGET=	install-strip
+# INSTALL_TARGET=	install-strip
 
-PORTVERSION=	g20180428
+PORTVERSION=	0.0.0.20180503
 
 .include "../../wip/openblas_pthread/buildlink3.mk"
 .include "../../wip/cblas/buildlink3.mk"
diff --git a/plink2/distinfo b/plink2/distinfo
index 3f588c4ccb..349e9e7e7c 100644
--- a/plink2/distinfo
+++ b/plink2/distinfo
@@ -1,8 +1,7 @@
 $NetBSD$
 
-SHA1 (plink-ng-g20180428-d046d8dfbbba50065644bbe9647edbe94a29b1a2.tar.gz) = e8195a41e11df02d85dde78815addc292a99ccf2
-RMD160 (plink-ng-g20180428-d046d8dfbbba50065644bbe9647edbe94a29b1a2.tar.gz) = 26bd7f222afe85ff880e6bbe3e30220439c235ff
-SHA512 (plink-ng-g20180428-d046d8dfbbba50065644bbe9647edbe94a29b1a2.tar.gz) = 75faf6427c12535b180694efe89b94764f2807254f458821ef5f438762f8ded5d4b432a0534e66851ef4c4e1e5dc965bae870d1bb143ffe5c7c235854a501448
-Size (plink-ng-g20180428-d046d8dfbbba50065644bbe9647edbe94a29b1a2.tar.gz) = 2359459 bytes
-SHA1 (patch-Makefile) = 3110bb122f7992fc70723cef23e278adf19836e3
-SHA1 (patch-plink2__base.h) = edeb6ef6ca2cf4b11c7ee008ef8bbec6c979d739
+SHA1 (plink-ng-0.0.0.20180503-e81056a32d67cd73a69579e2dbb374d16196f305.tar.gz) = 1616e95b928da07cdbe237e7558ff6085ae7a0fa
+RMD160 (plink-ng-0.0.0.20180503-e81056a32d67cd73a69579e2dbb374d16196f305.tar.gz) = 3a064362785e5193070df2a7027f714912a671c2
+SHA512 (plink-ng-0.0.0.20180503-e81056a32d67cd73a69579e2dbb374d16196f305.tar.gz) = c6dc6d187f1664e3489817dbe6ba0a19c548a9b9e42b7033cb751f2254b6a66ebd0b562663924bcca351db0d4bcabb2683a79cfd1339777fea7ac8d3f2965650
+Size (plink-ng-0.0.0.20180503-e81056a32d67cd73a69579e2dbb374d16196f305.tar.gz) = 2363822 bytes
+SHA1 (patch-plink2__base.h) = 54489e47f233e3dfe0d7df693da97a3913c69752
diff --git a/plink2/patches/patch-Makefile b/plink2/patches/patch-Makefile
deleted file mode 100644
index b0e3d1084b..0000000000
--- a/plink2/patches/patch-Makefile
+++ /dev/null
@@ -1,93 +0,0 @@
-$NetBSD$
-
-# Respect env, add install target
-
---- Makefile.orig	2018-04-28 18:49:38 UTC
-+++ Makefile
-@@ -1,43 +1,68 @@
-+
- BASEFLAGS=-Wall -Wextra -Wshadow -Wformat-security -mavx2 -mbmi -mbmi2 -mlzcnt -DNDEBUG -DZSTD_MULTITHREAD
- # BASEFLAGS=-Wall -Wextra -Wshadow -Wformat-security -mavx2 -mbmi -mbmi2 -mlzcnt -DZSTD_MULTITHREAD
- # BASEFLAGS=-Wall -Wextra -Wshadow -Wformat-security -msse4.2 -DNDEBUG -DZSTD_MULTITHREAD
--CFLAGS=-O3 -std=gnu99
--# this actually needs to be named "CXXFLAGS"
--CXXFLAGS=-O2 -std=c++14 -Wold-style-cast
- 
--CFLAGS += ${BASEFLAGS}
--CXXFLAGS += ${BASEFLAGS}
-+include Makefile.src
- 
--ZLIB=../zlib-1.2.11/libz-64.a
--BLASFLAGS64=-llapack -lf77blas -latlas
--LINKFLAGS=-lm -lpthread -L. ${ZLIB}
--ARCH32=
-+# Respect the environment:
-+# Use defaults below only if not set in env or make arguments
-+CC		?= gcc
-+CXX		?= g++
-+CFLAGS		?= -O3
-+CXXFLAGS	?= -O2
-+ZLIB		?= ../zlib-1.2.11/libz-64.a
-+BLASFLAGS64	?= -llapack -lf77blas -latlas
-+ARCH32		?=
-+
-+# Mandatory flags added to defaults or env settings
-+CFLAGS		+= -std=gnu99 $(BASEFLAGS) $(CINCLUDE) $(ZSTD_INCLUDE)
-+CXXFLAGS	+= -std=c++14 -Wold-style-cast $(BASEFLAGS)
-+LDFLAGS		+= -lm -lpthread -L. $(ZLIB)
-+
-+# Installation defaults
-+MKDIR		?= mkdir
-+INSTALL		?= install
-+STRIP_CMD	?= strip
-+PREFIX		?= /usr/local
-+DESTDIR		?= .
- 
- UNAME := $(shell uname)
- ifeq ($(UNAME), Darwin)
-   BLASFLAGS=-framework Accelerate
-   BLASFLAGS64=-framework Accelerate
--  LINKFLAGS=-ldl -lpthread -lz
-+  LDFLAGS=-ldl -lpthread -lz
- endif
- 
--include Makefile.src
--CFLAGS += ${CINCLUDE} ${ZSTD_INCLUDE}
--
- %.o: %.c
--	gcc -c $(CFLAGS) $(ARCH32) -o $@ $<
-+	$(CC) -c $(CFLAGS) $(ARCH32) -o $@ $<
-+
- %.o: %.cc
--	g++ -c $(CXXFLAGS) $(ARCH32) -o $@ $<
-+	$(CXX) -c $(CXXFLAGS) $(ARCH32) -o $@ $<
- 
- all: plink2 pgen_compress
- 
- # for clean build, "make clean" first
-+# Run mkdir for both plink2 and pgen_compress as we don't know which
-+# target will run first
- plink2: $(OBJ)
--	g++ $(ARCH32) $(OBJ) -o bin/plink2 $(BLASFLAGS64) $(LINKFLAGS)
-+	$(MKDIR) -p bin
-+	$(CXX) $(ARCH32) $(OBJ) -o bin/plink2 $(BLASFLAGS64) $(LDFLAGS)
- 
- # basic pgenlib_internal.h usage example; also needed for tests
- pgen_compress: plink2_base.o pgenlib_internal.o pgen_compress.o
--	g++ plink2_base.o pgenlib_internal.o pgen_compress.o -o bin/pgen_compress
-+	$(MKDIR) -p bin
-+	$(CXX) plink2_base.o pgenlib_internal.o pgen_compress.o \
-+		-o bin/pgen_compress
-+
-+.PHONY: install-strip install clean
-+
-+install-strip: install
-+	$(STRIP_CMD) $(DESTDIR)$(PREFIX)/bin/*
-+
-+install: all
-+	$(MKDIR) -p $(DESTDIR)$(PREFIX)/bin
-+	$(INSTALL) -c bin/* $(DESTDIR)$(PREFIX)/bin
- 
--.PHONY: clean
- clean:
- 	rm -f $(CLEAN)