svn commit: r483910 - in head/biology/bowtie: . files
Jason W. Bacon
jwb at FreeBSD.org
Sat Nov 3 21:10:08 UTC 2018
Author: jwb
Date: Sat Nov 3 21:10:06 2018
New Revision: 483910
URL: https://svnweb.freebsd.org/changeset/ports/483910
Log:
biology/bowtie: Patch
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 20:29:12 2018 (r483909)
+++ head/biology/bowtie/Makefile Sat Nov 3 21:10:06 2018 (r483910)
@@ -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
@@ -13,13 +13,14 @@ LICENSE= ART10
# May also work on other 64-bit platforms, but untested
ONLY_FOR_ARCHS= amd64
+
+USES= gmake perl5 python:run shebangfix
# 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_PERL5= run
-SHEBANG_FILES= scripts/*.pl bowtie bowtie-build \
- bowtie-inspect
+
+SHEBANG_FILES= scripts/*.pl bowtie bowtie-build bowtie-inspect
USE_GITHUB= yes
GH_ACCOUNT= BenLangmead
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 21:10:06 2018 (r483910)
@@ -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; }
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