Fix int types and network libs on SunOS

biology/bwa/Makefile

@@ -1,10 +1,11 @@
-# $NetBSD: Makefile,v 1.2 2015/11/07 20:20:54 dholland Exp $
+# $NetBSD: Makefile,v 1.3 2015/12/12 16:56:04 wiedi Exp $
 #
 
 DISTNAME=	bwa-0.7.9a
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=bio-bwa/}
 EXTRACT_SUFX=	.tar.bz2
+PKGREVISION=	1
 
 MAINTAINER=	[email protected]
 HOMEPAGE=	http://bio-bwa.sourceforge.net/
@@ -19,6 +20,9 @@ INSTALLATION_DIRS=	bin ${PKGMANDIR}/man1
 # unconditionally uses <emmintrin.h>
 ONLY_FOR_PLATFORM=	*-*-x86_64 *-*-i386 *-*-ia64
 
+CFLAGS.SunOS+=	-Du_int32_t=uint32_t
+LDFLAGS.SunOS+=	-lsocket -lnsl
+
 do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/bwa ${DESTDIR}${PREFIX}/bin
 	${INSTALL_SCRIPT} ${WRKSRC}/*.pl ${DESTDIR}${PREFIX}/bin

biology/bwa/distinfo

@@ -1,6 +1,7 @@
-$NetBSD: distinfo,v 1.2 2015/11/02 18:42:20 agc Exp $
+$NetBSD: distinfo,v 1.3 2015/12/12 16:56:04 wiedi Exp $
 
 SHA1 (bwa-0.7.9a.tar.bz2) = a77ce327e8acba554b1d27bfdd1c148f79726484
 RMD160 (bwa-0.7.9a.tar.bz2) = a51b7c686a206144eab2aee0a372d5ae46fcfce1
 SHA512 (bwa-0.7.9a.tar.bz2) = 93804b2c0ac0f675e76f762441e1eec039d7f1cf77b033fd88f2e6c39d9cd4b5c21bba9fb44e34a3dab28c630c3855792a707e5b33109d4be0097cec97eaa686
 Size (bwa-0.7.9a.tar.bz2) = 166193 bytes
+SHA1 (patch-Makefile) = 2bb665cb579d20a07ae7c2be8ba0ed874d60d5b0

biology/bwa/patches/patch-Makefile

@@ -0,0 +1,24 @@
+$NetBSD: patch-Makefile,v 1.1 2015/12/12 16:56:04 wiedi Exp $
+
+Don't overwrite pkgsrc CC and CFLAGS
+
+--- Makefile.orig	2014-05-19 13:11:41.000000000 +0000
++++ Makefile
+@@ -1,6 +1,6 @@
+-CC=			gcc
++#CC=			gcc
+ #CC=			clang --analyze
+-CFLAGS=		-g -Wall -Wno-unused-function -O2
++#CFLAGS=		-g -Wall -Wno-unused-function -O2
+ WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
+ AR=			ar
+ DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
+@@ -11,7 +11,7 @@ AOBJS=		QSufSort.o bwt_gen.o bwase.o bwa
+ 			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
+ PROG=		bwa
+ INCLUDES=	
+-LIBS=		-lm -lz -lpthread
++LIBS=		-lm -lz -lpthread $(LDFLAGS)
+ SUBDIRS=	.
+
+ .SUFFIXES:.c .o .cc