plink2: Upgrade to latest commit

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun May 20 07:50:24 2018 -0500
Changeset:	2ff7c37f055d416c7c91bd99a8941b9bf3d0376f

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

Log Message:
plink2: Upgrade to latest commit

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=2ff7c37f055d416c7c91bd99a8941b9bf3d0376f

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

diffstat:
 plink2/Makefile               |  4 ++--
 plink2/distinfo               | 10 +++++-----
 plink2/patches/patch-Makefile | 29 +++++++++++++++++++++++------
 3 files changed, 30 insertions(+), 13 deletions(-)

diffs:
diff --git a/plink2/Makefile b/plink2/Makefile
index 22ff834e95..67f4aca6c6 100644
--- a/plink2/Makefile
+++ b/plink2/Makefile
@@ -9,7 +9,7 @@ DISTNAME=	plink-ng-${PORTVERSION}
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=chrchang/}
 GITHUB_PROJECT=	plink-ng
-GITHUB_TAG=	aabd8ab97667e47373ce0411a3799d9310c92a83
+GITHUB_TAG=	f758bbd77e04eb0cb46fbc633be60b22b8b3cc2d
 
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	http://pngu.mgh.harvard.edu/~purcell/plink/
@@ -31,7 +31,7 @@ MAKE_FLAGS+=	ZLIB=-lz BLASFLAGS64="-L${PREFIX}/lib -llapack -lcblas -lblas"
 # Keep debug info until at least next beta
 # INSTALL_TARGET=	install-strip
 
-PORTVERSION=	0.0.0.20180511
+PORTVERSION=	0.0.0.20180518
 USE_BUILTIN.zlib=	no
 
 .include "options.mk"
diff --git a/plink2/distinfo b/plink2/distinfo
index 8ababcbaf1..cf3c71a929 100644
--- a/plink2/distinfo
+++ b/plink2/distinfo
@@ -1,8 +1,8 @@
 $NetBSD$
 
-SHA1 (plink-ng-0.0.0.20180511-aabd8ab97667e47373ce0411a3799d9310c92a83.tar.gz) = 312f656aadf2db13e2ceb5d075b62d98a7ab1ba6
-RMD160 (plink-ng-0.0.0.20180511-aabd8ab97667e47373ce0411a3799d9310c92a83.tar.gz) = 04967fd66db20e6ad602420e9e0fca50fcfe78ba
-SHA512 (plink-ng-0.0.0.20180511-aabd8ab97667e47373ce0411a3799d9310c92a83.tar.gz) = 13ac75941d2b0a0f65ebc28d2df64b98896ab691dff17715dfdfd241f6dbb07c0d2d645d0318c75b613d2b72c79ea422f2824cc0c18489e4f5f80d73d24331f3
-Size (plink-ng-0.0.0.20180511-aabd8ab97667e47373ce0411a3799d9310c92a83.tar.gz) = 2375640 bytes
-SHA1 (patch-Makefile) = 8fc5a80af3d576b5272f303b7e37bd849c31ca8c
+SHA1 (plink-ng-0.0.0.20180518-f758bbd77e04eb0cb46fbc633be60b22b8b3cc2d.tar.gz) = 54d0a0dedbb9dfdd5e9be1570df9463f54f2fc3b
+RMD160 (plink-ng-0.0.0.20180518-f758bbd77e04eb0cb46fbc633be60b22b8b3cc2d.tar.gz) = 7be21109553e1a984f96e19887b5179bd6e94937
+SHA512 (plink-ng-0.0.0.20180518-f758bbd77e04eb0cb46fbc633be60b22b8b3cc2d.tar.gz) = 412f3b27b509fd731f816739a8155c77d407af6761749ce9b3eaabfa0e701426134c1bf4862101c379bbf63f97b425726b49283aa0dd96d74976c56e03a15426
+Size (plink-ng-0.0.0.20180518-f758bbd77e04eb0cb46fbc633be60b22b8b3cc2d.tar.gz) = 2392148 bytes
+SHA1 (patch-Makefile) = 7c87e9c912ba4ae175663942768c6ba811bef177
 SHA1 (patch-plink2__base.h) = 08cc1710f2824985dc132149ca102f82e0488bf1
diff --git a/plink2/patches/patch-Makefile b/plink2/patches/patch-Makefile
index 9e23304054..982622d1c7 100644
--- a/plink2/patches/patch-Makefile
+++ b/plink2/patches/patch-Makefile
@@ -1,14 +1,31 @@
 $NetBSD$
 
-# Remove non-portable ABI options
---- Makefile.orig	2018-05-13 15:49:21.061390795 +0000
+# Remove non-portable CPU features
+
+--- Makefile.orig	2018-05-20 12:46:52.707854971 +0000
 +++ Makefile
-@@ -6,7 +6,7 @@
+@@ -1,12 +1,13 @@
+ 
+ ###########################################################################
+ # Note: This Makefile is intended for development.  For production
+-# builds, use build_dynamic/Makefile.
++# builds, use build_dynamic/Makefile or edit out assumptions such as
++# -mavx2.
+ ###########################################################################
  
  # Does not currently support -DCPU_CHECK_...
  
--BASEFLAGS=-mavx2 -mbmi -mbmi2 -mlzcnt -DNDEBUG -DZSTD_MULTITHREAD
+-BASEFLAGS=-g -mavx2 -mbmi -mbmi2 -mlzcnt -DZSTD_MULTITHREAD
 +BASEFLAGS=-DNDEBUG -DZSTD_MULTITHREAD
- # BASEFLAGS=-mavx2 -mbmi -mbmi2 -mlzcnt -DZSTD_MULTITHREAD
- # BASEFLAGS=-msse4.2 -DZSTD_MULTITHREAD
+ # BASEFLAGS=-g -mavx2 -mbmi -mbmi2 -mlzcnt -DZSTD_MULTITHREAD
+ # BASEFLAGS=-g -msse4.2 -DZSTD_MULTITHREAD
+ 
+@@ -23,7 +24,7 @@ BLASFLAGS64	?= -llapack -lf77blas -latla
+ ARCH32		?=
+ 
+ # Mandatory flags added to defaults or env settings
+-CFLAGS		+= -std=gnu99 $(BASEFLAGS) $(CWARN) $(CINCLUDE) $(ZSTD_INCLUDE)
++CFLAGS		+= -std=gnu99 $(BASEFLAGS) $(CWARN2) $(CINCLUDE) $(ZSTD_INCLUDE)
+ CXXFLAGS	+= -std=c++14 $(BASEFLAGS) $(CXXWARN)
+ LDFLAGS		+= -lm -lpthread -L. $(ZLIB)