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biology/bowtie: Patch for gcc8 and clean up

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PR:             232929
Reported by:    gerald
Approved by:    jrm (mentor, implicit)
This commit is contained in:
Jason W. Bacon 2018-11-03 23:24:29 +00:00
parent 8503d5208f
commit aa9337b9b9
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=483954
2 changed files with 17 additions and 6 deletions
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12
biology/bowtie/Makefile
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@ -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@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

11
biology/bowtie/files/patch-ebwt.h Normal file
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@ -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; }