svn commit: r483954 - in head/biology/bowtie: . files

[Jason W. Bacon]

Author: jwb
Date: Sat Nov  3 23:24:29 2018
New Revision: 483954
URL: https://svnweb.freebsd.org/changeset/ports/483954

Log:
  biology/bowtie: Patch for gcc8 and clean up
  
  PR:             232929
  Reported by:    gerald
  Approved by:    jrm (mentor, implicit)

Added:
  head/biology/bowtie/files/patch-ebwt.h   (contents, props changed)
Modified:
  head/biology/bowtie/Makefile

Modified: head/biology/bowtie/Makefile
==============================================================================
--- head/biology/bowtie/Makefile	Sat Nov  3 23:16:49 2018	(r483953)
+++ head/biology/bowtie/Makefile	Sat Nov  3 23:24:29 2018	(r483954)
@@ -1,9 +1,9 @@
 # $FreeBSD$
 
 PORTNAME=		bowtie
-PORTVERSION=		1.1.2
-PORTREVISION=	6
 DISTVERSIONPREFIX=	v
+DISTVERSION=		1.1.2
+PORTREVISION=		7
 CATEGORIES=		biology
 
 MAINTAINER=	jwb at FreeBSD.org
@@ -13,15 +13,15 @@ LICENSE=	ART10
 
 # May also work on other 64-bit platforms, but untested
 ONLY_FOR_ARCHS=	amd64
+
 # FIXME: bowtie-align intermittently dumps core when compiled with clang
 # GCC 4.2 does not provide good performance
-USE_GCC=	yes
 USES=		gmake perl5 python:run shebangfix
+USE_GCC=	yes
 USE_PERL5=	run
-SHEBANG_FILES=	scripts/*.pl bowtie bowtie-build \
-		bowtie-inspect
-
 USE_GITHUB=	yes
+
+SHEBANG_FILES=	scripts/*.pl bowtie bowtie-build bowtie-inspect
 GH_ACCOUNT=	BenLangmead
 
 OPTIONS_DEFINE=	DOCS

Added: head/biology/bowtie/files/patch-ebwt.h
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/bowtie/files/patch-ebwt.h	Sat Nov  3 23:24:29 2018	(r483954)
@@ -0,0 +1,11 @@
+--- ebwt.h.orig	2018-11-03 20:51:56 UTC
++++ ebwt.h
+@@ -860,7 +860,7 @@ public:
+ 	TIndexOffU*   ftab() const         { return _ftab; }
+ 	TIndexOffU*   eftab() const        { return _eftab; }
+ 	TIndexOffU*   offs() const         { return _offs; }
+-	uint32_t*   isa() const          { return _isa; } /* check */
++	uint32_t*   isa() const          { return (uint32_t)_isa; } /* check */
+ 	TIndexOffU*   plen() const         { return _plen; }
+ 	TIndexOffU*   rstarts() const      { return _rstarts; }
+ 	uint8_t*    ebwt() const         { return _ebwt; }