Index: head/biology/abyss/Makefile
===================================================================
--- head/biology/abyss/Makefile	(revision 504787)
+++ head/biology/abyss/Makefile	(revision 504788)
@@ -1,36 +1,39 @@
 # $FreeBSD$
 
 PORTNAME=	abyss
 DISTVERSION=	2.1.5
 PORTREVISION=	2
 CATEGORIES=	biology
 MASTER_SITES=	http://www.bcgsc.ca/platform/bioinfo/software/${PORTNAME}/releases/${DISTVERSION}/
 
+PATCH_SITES=	https://github.com/bcgsc/${PORTNAME}/commit/
+PATCHFILES=	25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch:-p1
+
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Assembly By Short Sequences: parallel, paired-end sequence assembler
 
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	${LOCALBASE}/include/boost/version.hpp:devel/boost-libs \
 		ghc:lang/ghc \
 		pandoc:textproc/hs-pandoc # pandoc is required just for one man page: abyss-sealer
 LIB_DEPENDS=	libffi.so:devel/libffi \
 		libgmp.so:math/gmp \
 		libomp.so:devel/openmp
 RUN_DEPENDS=	bash:shells/bash \
 		gmake:devel/gmake
 
-USES=		gmake iconv:wchar_t localbase:ldflags shebangfix sqlite
+USES=		compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite
 SHEBANG_FILES=	bin/${PORTNAME}-*
 SHEBANG_LANG=	make
 make_OLD_CMD=	/usr/bin/make
 make_CMD=	${PREFIX}/bin/gmake
 GNU_CONFIGURE=	yes
 CONFIGURE_ARGS=	--without-sparsehash # configure fails to find std::hash, reported to the ML: https://groups.google.com/forum/#!topic/trans-abyss/SZDBKR5bKxs
 
 OPTIONS_DEFINE=	DOCS
 
 PORTDOCS=	*
 
 .include <bsd.port.mk>
Index: head/biology/abyss/distinfo
===================================================================
--- head/biology/abyss/distinfo	(revision 504787)
+++ head/biology/abyss/distinfo	(revision 504788)
@@ -1,3 +1,5 @@
-TIMESTAMP = 1551061546
+TIMESTAMP = 1561103807
 SHA256 (abyss-2.1.5.tar.gz) = 65bfc8241e6ff5adf7601ae4ae93a75e3db86d6bff5d593c75aaff7f0ef41757
 SIZE (abyss-2.1.5.tar.gz) = 1201318
+SHA256 (25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch) = 93ad66c42610c4fba8cfbe256a2ab689bf4a76974c3b97a9e1094863614ad934
+SIZE (25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch) = 1701
Index: head/biology/abyss/files/patch-Common_city.cc
===================================================================
--- head/biology/abyss/files/patch-Common_city.cc	(nonexistent)
+++ head/biology/abyss/files/patch-Common_city.cc	(revision 504788)
@@ -0,0 +1,13 @@
+--- Common/city.cc.orig	2018-09-21 23:44:14 UTC
++++ Common/city.cc
+@@ -65,6 +65,10 @@ static uint32 UNALIGNED_LOAD32(const char *p) {
+ #define bswap_32(x) OSSwapInt32(x)
+ #define bswap_64(x) OSSwapInt64(x)
+ 
++#elif defined(__FreeBSD__)
++#include <sys/endian.h>
++#define bswap_32(x) bswap32(x)
++#define bswap_64(x) bswap64(x)
+ #else
+ #include <byteswap.h>
+ #endif

Property changes on: head/biology/abyss/files/patch-Common_city.cc
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property