Index: head/biology/freebayes/Makefile
===================================================================
--- head/biology/freebayes/Makefile	(revision 549475)
+++ head/biology/freebayes/Makefile	(revision 549476)
@@ -1,55 +1,55 @@
 # $FreeBSD$
 
 PORTNAME=		freebayes
 DISTVERSIONPREFIX=	v
 DISTVERSION=		1.2.0
-PORTREVISION=	2
+PORTREVISION=		3
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Bayesian haplotype-based polymorphism discovery and genotyping
 
 LICENSE=	MIT
 
 BROKEN_aarch64=		fails to compile: invalid conversion between vector type and integer type
 BROKEN_armv6=		fails to compile: invalid conversion between vector type and integer type
 BROKEN_armv7=		fails to compile: invalid conversion between vector type and integer type
 
 # Submodules use older versions than the ports, so we cannot safely unbundle
 # No shared libs are built by the submodules so there will be no conflicts
 USES=		compiler:c++11-lang gmake tar:xz
 USE_GITHUB=	yes
 GH_ACCOUNT=	ekg
 GH_TUPLE=	walaj:SeqLib:5941c68:SeqLib/SeqLib-temp \
 		jwalabroad:bwa:c02766e:bwa/SeqLib/bwa \
 		jwalabroad:fermi-lite:5bc90f8:fermi/SeqLib/fermi-lite \
 		samtools:htslib:49fdfbd:htslib/SeqLib/htslib \
 		ekg:bamtools:e77a43f:bamtools/bamtools \
 		ekg:intervaltree:dbb4c51:interval1/intervaltree \
 		vcflib:vcflib:5e3ce04:vcflib/vcflib-temp \
 		ekg:fastahack:c68cebb:fastahack/vcflib/fastahack \
 		ekg:filevercmp:1a9b779:filevercmp/vcflib/filevercmp \
 		ekg:fsom:a6ef318:fsom/vcflib/fsom \
 		google:googletest:d225acc:google/vcflib/googletest \
 		ekg:intervaltree:b704f19:interval2/vcflib/intervaltree \
 		ekg:multichoose:73d35da:multichoose/vcflib/multichoose \
 		ekg:smithwaterman:84c08d7:smithwaterman/vcflib/smithwaterman \
 		ekg:tabixpp:80012f8:tabixpp/vcflib/tabixpp \
 		samtools:htslib:0f298ce:hts2/vcflib/tabixpp/htslib
 
 # GCC disables sse2 by default on i386, but it's required for vcflib
 CXXFLAGS+=		--std=c++11
 CFLAGS_i386=		-msse2
 MAKE_JOBS_UNSAFE=	yes
 PLIST_FILES=		bin/bamleftalign bin/freebayes
 
 # GH_TUPLEs cannot seem to share a top-level subdirectory, so we work around
 # by dumping the parent in a temp directory and then moving the contents
 post-extract:
 	${MV} -n ${WRKSRC}/SeqLib-temp/* ${WRKSRC}/SeqLib
 	${MV} -n ${WRKSRC}/vcflib-temp/* ${WRKSRC}/vcflib
 
 do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin
 
 .include <bsd.port.mk>
Index: head/biology/freebayes/files/patch-SeqLib_bwa_rle.h
===================================================================
--- head/biology/freebayes/files/patch-SeqLib_bwa_rle.h	(nonexistent)
+++ head/biology/freebayes/files/patch-SeqLib_bwa_rle.h	(revision 549476)
@@ -0,0 +1,11 @@
+--- SeqLib/bwa/rle.h.orig	2016-10-13 18:10:17 UTC
++++ SeqLib/bwa/rle.h
+@@ -30,7 +30,7 @@ extern "C" {
+  *** 43+3 codec ***
+  ******************/
+ 
+-const uint8_t rle_auxtab[8];
++extern const uint8_t rle_auxtab[8];
+ 
+ #define RLE_MIN_SPACE 18
+ #define rle_nptr(block) ((uint16_t*)(block))

Property changes on: head/biology/freebayes/files/patch-SeqLib_bwa_rle.h
___________________________________________________________________
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
Index: head/biology/freebayes/files/patch-SeqLib_fermi-lite_rle.h
===================================================================
--- head/biology/freebayes/files/patch-SeqLib_fermi-lite_rle.h	(nonexistent)
+++ head/biology/freebayes/files/patch-SeqLib_fermi-lite_rle.h	(revision 549476)
@@ -0,0 +1,11 @@
+--- SeqLib/fermi-lite/rle.h.orig	2016-09-01 20:47:53 UTC
++++ SeqLib/fermi-lite/rle.h
+@@ -30,7 +30,7 @@ extern "C" {
+  *** 43+3 codec ***
+  ******************/
+ 
+-const uint8_t rle_auxtab[8];
++extern const uint8_t rle_auxtab[8];
+ 
+ #define RLE_MIN_SPACE 18
+ #define rle_nptr(block) ((uint16_t*)(block))

Property changes on: head/biology/freebayes/files/patch-SeqLib_fermi-lite_rle.h
___________________________________________________________________
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