Date: Sat, 3 Nov 2018 23:24:29 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r483954 - in head/biology/bowtie: . files Message-ID: <201811032324.wA3NOT7C079048@repo.freebsd.org>
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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@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; }
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