From owner-svn-ports-all@freebsd.org Thu Nov 30 02:59:17 2017 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id CA1A2DF3991; Thu, 30 Nov 2017 02:59:17 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id A111C7074A; Thu, 30 Nov 2017 02:59:17 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id vAU2xGT1042697; Thu, 30 Nov 2017 02:59:16 GMT (envelope-from jwb@FreeBSD.org) Received: (from jwb@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id vAU2xGlA042692; Thu, 30 Nov 2017 02:59:16 GMT (envelope-from jwb@FreeBSD.org) Message-Id: <201711300259.vAU2xGlA042692@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jwb set sender to jwb@FreeBSD.org using -f From: "Jason W. Bacon" Date: Thu, 30 Nov 2017 02:59:16 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r455161 - in head/biology/bowtie2: . files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology/bowtie2: . files X-SVN-Commit-Revision: 455161 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.25 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 30 Nov 2017 02:59:17 -0000 Author: jwb Date: Thu Nov 30 02:59:16 2017 New Revision: 455161 URL: https://svnweb.freebsd.org/changeset/ports/455161 Log: biology/bowtie2: Upgrade to 2.3.3.1 Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13300 Deleted: head/biology/bowtie2/files/patch-aligner__result.cpp Modified: head/biology/bowtie2/Makefile head/biology/bowtie2/distinfo head/biology/bowtie2/files/patch-Makefile head/biology/bowtie2/pkg-plist Modified: head/biology/bowtie2/Makefile ============================================================================== --- head/biology/bowtie2/Makefile Thu Nov 30 02:21:29 2017 (r455160) +++ head/biology/bowtie2/Makefile Thu Nov 30 02:59:16 2017 (r455161) @@ -1,25 +1,23 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= bowtie2 -PORTVERSION= 2.3.0 -PORTREVISION= 2 +PORTVERSION= 2.3.3.1 DISTVERSIONPREFIX= v CATEGORIES= biology -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Ultrafast, memory-efficient short read aligner LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/LICENSE -LIB_DEPENDS+= libtbb.so:devel/tbb - # May also work on other 64-bit platforms, but untested ONLY_FOR_ARCHS= amd64 +LIB_DEPENDS= libtbb.so:devel/tbb + USES= gmake perl5 python shebangfix USE_PERL5= run -SHEBANG_FILES= bowtie2-build bowtie2-inspect scripts/*.pl +SHEBANG_FILES= bowtie2-build bowtie2-inspect scripts/*.pl USE_GITHUB= yes GH_ACCOUNT= BenLangmead Modified: head/biology/bowtie2/distinfo ============================================================================== --- head/biology/bowtie2/distinfo Thu Nov 30 02:21:29 2017 (r455160) +++ head/biology/bowtie2/distinfo Thu Nov 30 02:59:16 2017 (r455161) @@ -1,3 +1,3 @@ -TIMESTAMP = 1487550143 -SHA256 (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 9804fddf36233f3f92c11e2250224de3395790cf35c8280c66387075df078221 -SIZE (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 5810016 +TIMESTAMP = 1511991430 +SHA256 (BenLangmead-bowtie2-v2.3.3.1_GH0.tar.gz) = 8b9c0b9c595ebcddcac5feaf6acb44b2294d6deb91de107596ecad242a1a58e9 +SIZE (BenLangmead-bowtie2-v2.3.3.1_GH0.tar.gz) = 5796279 Modified: head/biology/bowtie2/files/patch-Makefile ============================================================================== --- head/biology/bowtie2/files/patch-Makefile Thu Nov 30 02:21:29 2017 (r455160) +++ head/biology/bowtie2/files/patch-Makefile Thu Nov 30 02:59:16 2017 (r455161) @@ -1,6 +1,6 @@ ---- Makefile.orig 2016-12-30 15:40:06 UTC +--- Makefile.orig 2017-10-05 16:45:18 UTC +++ Makefile -@@ -21,8 +21,8 @@ +@@ -21,10 +21,11 @@ # Makefile for bowtie, bowtie2-build, bowtie2-inspect # @@ -9,36 +9,21 @@ +PREFIX ?= /usr/local +bindir = $(PREFIX)/bin - INC = + INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) ++INC += -I${LOCALBASE}/include + LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz GCC_PREFIX = $(shell dirname `which gcc`) -@@ -62,6 +62,8 @@ ifeq (1, $(POPCNT_CAPABILITY)) - INC += -I third_party - endif + GCC_SUFFIX = +@@ -98,7 +99,7 @@ endif -+INC += -I ${LOCALBASE}/include -+ - MM_DEF = - - ifeq (1,$(BOWTIE_MM)) -@@ -75,7 +77,7 @@ ifeq (1,$(BOWTIE_SHARED_MEM)) - endif - - PTHREAD_PKG = --PTHREAD_LIB = -+PTHREAD_LIB = - - #if we're not using TBB, then we can't use queuing locks - ifeq (1,$(NO_TBB)) -@@ -94,7 +96,7 @@ endif - #default is to use Intel TBB ifneq (1,$(NO_TBB)) -- LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy -+ LIBS = $(PTHREAD_LIB) -L${LOCALBASE}/lib -ltbb -ltbbmalloc +- LIBS += $(PTHREAD_LIB) -ltbb -ltbbmalloc$(if $(RELEASE_BUILD),,_proxy) ++ LIBS += $(PTHREAD_LIB) -L${LOCALBASE}/lib -ltbb -ltbbmalloc override EXTRA_FLAGS += -DWITH_TBB else - LIBS = $(PTHREAD_LIB) -@@ -185,7 +187,7 @@ SSE_FLAG=-msse2 + LIBS += $(PTHREAD_LIB) +@@ -189,7 +190,7 @@ SSE_FLAG=-msse2 DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG) DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" Modified: head/biology/bowtie2/pkg-plist ============================================================================== --- head/biology/bowtie2/pkg-plist Thu Nov 30 02:21:29 2017 (r455160) +++ head/biology/bowtie2/pkg-plist Thu Nov 30 02:59:16 2017 (r455161) @@ -34,7 +34,6 @@ bin/bowtie2-inspect-s %%PORTDOCS%%%%DOCSDIR%%/images/university.small.horizontal.white.png %%PORTDOCS%%%%DOCSDIR%%/manual.html %%PORTDOCS%%%%DOCSDIR%%/release.txt -%%PORTDOCS%%%%DOCSDIR%%/strip_markdown.pl %%PORTDOCS%%%%DOCSDIR%%/style.css %%PORTDOCS%%%%DOCSDIR%%/website/faq.shtml %%PORTDOCS%%%%DOCSDIR%%/website/faq.ssi