From owner-svn-ports-head@FreeBSD.ORG Sun Oct 12 03:16:11 2014 Return-Path: Delivered-To: svn-ports-head@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id A933D52E; Sun, 12 Oct 2014 03:16:11 +0000 (UTC) Received: from svn.freebsd.org (svn.freebsd.org [IPv6:2001:1900:2254:2068::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 951F4BC2; Sun, 12 Oct 2014 03:16:11 +0000 (UTC) Received: from svn.freebsd.org ([127.0.1.70]) by svn.freebsd.org (8.14.9/8.14.9) with ESMTP id s9C3GB6G064619; Sun, 12 Oct 2014 03:16:11 GMT (envelope-from wen@FreeBSD.org) Received: (from wen@localhost) by svn.freebsd.org (8.14.9/8.14.9/Submit) id s9C3GAHi064616; Sun, 12 Oct 2014 03:16:10 GMT (envelope-from wen@FreeBSD.org) Message-Id: <201410120316.s9C3GAHi064616@svn.freebsd.org> X-Authentication-Warning: svn.freebsd.org: wen set sender to wen@FreeBSD.org using -f From: Wen Heping Date: Sun, 12 Oct 2014 03:16:10 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r370680 - in head/biology/plinkseq: . files X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.18-1 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 12 Oct 2014 03:16:11 -0000 Author: wen Date: Sun Oct 12 03:16:10 2014 New Revision: 370680 URL: https://svnweb.freebsd.org/changeset/ports/370680 QAT: https://qat.redports.org/buildarchive/r370680/ Log: - Update to 0.10 PR: 194309 Submitted by: jwbacon@tds.net(maintainer) Deleted: head/biology/plinkseq/files/ Modified: head/biology/plinkseq/Makefile head/biology/plinkseq/distinfo head/biology/plinkseq/pkg-plist Modified: head/biology/plinkseq/Makefile ============================================================================== --- head/biology/plinkseq/Makefile Sun Oct 12 01:51:39 2014 (r370679) +++ head/biology/plinkseq/Makefile Sun Oct 12 03:16:10 2014 (r370680) @@ -2,29 +2,39 @@ # $FreeBSD$ PORTNAME= plinkseq -PORTVERSION= 0.08 -PORTREVISION= 3 +PORTVERSION= 0.10 CATEGORIES= biology science -MASTER_SITES= http://atgu.mgh.harvard.edu/${PORTNAME}/dist/version-${PORTVERSION}/ +MASTER_SITES= http://psychgen.u.hpc.mssm.edu/plinkseq_downloads/ +# Default DISTNAME is correct, so leave it alone. +DISTFILES= ${PORTNAME}-src-${PORTVERSION}.tgz MAINTAINER= jwbacon@tds.net COMMENT= Toolset for working with human genetic variation data LICENSE= GPLv2 -LIB_DEPENDS= libprotobuf.so:${PORTSDIR}/devel/protobuf - -USES= dos2unix libtool shebangfix -SHEBANG_FILES= ${WRKSRC}/browser/pbrowse.in ${WRKSRC}/index/index.in -USE_LDCONFIG= yes -GNU_CONFIGURE= yes -CONFIGURE_ARGS+=--with-protobuf=${LOCALBASE} +USES= libtool gmake post-patch: - ${REINPLACE_CMD} -e 's|PF_INET|AF_INET|g' ${WRKSRC}/browser/mongoose.c - ${REINPLACE_CMD} -e 's|-ldl||g' \ - ${WRKSRC}/browser/Makefile.in \ - ${WRKSRC}/client/Makefile.in \ - ${WRKSRC}/index/Makefile.in + ${REINPLACE_CMD} \ + -e 's|PF_INET|AF_INET|g' \ + ${WRKSRC}/sources/mongoose/sources/lib/mongoose.c + ${REINPLACE_CMD} \ + -e 's|g++|${CXX}|g' \ + -e 's|gcc|${CC}|g' \ + -e 's|CXXFLAGS = -O3|CXXFLAGS = ${CXXFLAGS}|g' \ + -e 's|ALL_CFLAGS =-O3|ALL_CFLAGS = ${CFLAGS}|g' \ + ${WRKSRC}/config_defs.Makefile + ${REINPLACE_CMD} \ + -e 's| -ldl||g' \ + -e 's| $$(STATIC_FLAG)||g' \ + ${WRKSRC}/Makefile + +do-install: +.for f in behead browser gcol mm mongoose pdas pseq smp tab2vcf + ${INSTALL_PROGRAM} ${WRKSRC}/build/execs/${f} ${STAGEDIR}${PREFIX}/bin +.endfor + ${INSTALL_DATA} ${WRKSRC}/sources/plinkseq/build/lib/libplinkseq.a \ + ${STAGEDIR}${PREFIX}/lib .include Modified: head/biology/plinkseq/distinfo ============================================================================== --- head/biology/plinkseq/distinfo Sun Oct 12 01:51:39 2014 (r370679) +++ head/biology/plinkseq/distinfo Sun Oct 12 03:16:10 2014 (r370680) @@ -1,2 +1,2 @@ -SHA256 (plinkseq-0.08.tar.gz) = 6bde88925a82a79c6fa2401a197865cf6d659163fd5f11c5fb426701b54bb24f -SIZE (plinkseq-0.08.tar.gz) = 2991871 +SHA256 (plinkseq-src-0.10.tgz) = e9d4705acf8b22eddba0c48cf502e3bd4236f3b60b010f39f94deecf37e94b58 +SIZE (plinkseq-src-0.10.tgz) = 6090698 Modified: head/biology/plinkseq/pkg-plist ============================================================================== --- head/biology/plinkseq/pkg-plist Sun Oct 12 01:51:39 2014 (r370679) +++ head/biology/plinkseq/pkg-plist Sun Oct 12 03:16:10 2014 (r370680) @@ -1,12 +1,10 @@ bin/behead +bin/browser bin/gcol -bin/index -bin/index.cgi +bin/mm bin/mongoose -bin/pbrowse -bin/pbrowse.cgi +bin/pdas bin/pseq +bin/smp bin/tab2vcf -lib/libplinkseq.so -lib/libplinkseq.so.0 -lib/libplinkseq.so.0.0.0 +lib/libplinkseq.a