From owner-freebsd-ports-bugs@FreeBSD.ORG Tue May 13 02:40:00 2014 Return-Path: Delivered-To: freebsd-ports-bugs@smarthost.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id B9750D37 for ; Tue, 13 May 2014 02:40:00 +0000 (UTC) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:1900:2254:206c::16:87]) (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 917512FD4 for ; Tue, 13 May 2014 02:40:00 +0000 (UTC) Received: from freefall.freebsd.org (localhost [127.0.0.1]) by freefall.freebsd.org (8.14.8/8.14.8) with ESMTP id s4D2e0on051735 for ; Tue, 13 May 2014 02:40:00 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.8/8.14.8/Submit) id s4D2e0XP051734; Tue, 13 May 2014 02:40:00 GMT (envelope-from gnats) Resent-Date: Tue, 13 May 2014 02:40:00 GMT Resent-Message-Id: <201405130240.s4D2e0XP051734@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, "Reed A. Cartwright" Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 235C1D17 for ; Tue, 13 May 2014 02:36:30 +0000 (UTC) Received: from herschel.biodesign.asu.edu (herschel.biodesign.asu.edu [129.219.237.213]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "herschel.biodesign.asu.edu", Issuer "herschel.biodesign.asu.edu" (not verified)) by mx1.freebsd.org (Postfix) with ESMTPS id 039402FC4 for ; Tue, 13 May 2014 02:36:29 +0000 (UTC) Received: from herschel.biodesign.asu.edu (localhost [127.0.0.1]) by herschel.biodesign.asu.edu (8.14.7/8.14.7) with ESMTP id s4D2E2jj094302 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-GCM-SHA384 bits=256 verify=NO) for ; Mon, 12 May 2014 19:14:02 -0700 (MST) (envelope-from reed@herschel.biodesign.asu.edu) Received: (from reed@localhost) by herschel.biodesign.asu.edu (8.14.7/8.14.7/Submit) id s4D2E2vS094301; Mon, 12 May 2014 19:14:02 -0700 (MST) (envelope-from reed) Message-Id: <201405130214.s4D2E2vS094301@herschel.biodesign.asu.edu> Date: Mon, 12 May 2014 19:14:02 -0700 (MST) From: "Reed A. Cartwright" Reply-To: "Reed A. Cartwright" To: FreeBSD-gnats-submit@freebsd.org X-Send-Pr-Version: 3.114 Subject: ports/189746: [maintainer update] Update biology/mafft X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 13 May 2014 02:40:00 -0000 >Number: 189746 >Category: ports >Synopsis: [maintainer update] Update biology/mafft >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Tue May 13 02:40:00 UTC 2014 >Closed-Date: >Last-Modified: >Originator: Reed A. Cartwright >Release: FreeBSD 10.0-RELEASE-p2 amd64 >Organization: ASU >Environment: System: FreeBSD herschel.biodesign.asu.edu 10.0-RELEASE-p2 FreeBSD 10.0-RELEASE-p2 #0: Tue Apr 29 17:06:01 UTC 2014 root@amd64-builder.daemonology.net:/usr/obj/usr/src/sys/GENERIC amd64 >Description: Update biology/mafft to 7.149 and support staging >How-To-Repeat: >Fix: Patch is attached --- mafft.diff begins here --- Index: Makefile =================================================================== --- Makefile (revision 353911) +++ Makefile (working copy) @@ -1,8 +1,8 @@ -# Created by: Fernan Aguero +# Created by: Reed A. Cartwright # $FreeBSD$ PORTNAME= mafft -PORTVERSION= 6.903 +PORTVERSION= 7.149 CATEGORIES= biology MASTER_SITES= http://mafft.cbrc.jp/alignment/software/ DISTNAME= ${PORTNAME}-${PORTVERSION}-without-extensions-src @@ -11,28 +11,27 @@ MAINTAINER= cartwright@asu.edu COMMENT= Multiple alignment program for amino acid or nucleotide sequences -LICENSE= BSD +LICENSE= BSD2CLAUSE -RUN_DEPENDS= lav2ps:${PORTSDIR}/biology/fasta3 - WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}-without-extensions BUILD_WRKSRC= ${WRKSRC}/core -USES= gmake +USES= gmake shebangfix -MAN1= mafft.1 mafft-homologs.1 +SHEBANG_FILES= core/mafftash_premafft.tmpl LIBEXEC_FILES= dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \ - pair2hat3s multi2hat3s rnatest pairash addsingle splittbfast \ + pair2hat3s multi2hat3s pairash addsingle splittbfast \ disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap \ - countlen seq2regtable regtable2seq score getlag dndpre dndpre2 \ + countlen seq2regtable regtable2seq score getlag dndpre \ setcore replaceu restoreu setdirection makedirectionlist version +PERL_LIBEXEC_FILES= mafftash_premafft.pl SCRIPT_FILES= mafft mafft-homologs.rb LN_FILES= einsi fftns fftnsi ginsi linsi mafft-einsi mafft-fftns \ mafft-fftnsi mafft-ginsi mafft-linsi mafft-nwns mafft-nwnsi \ mafft-qinsi mafft-xinsi nwns nwnsi +MAN1_FILES= mafft.1 mafft-homologs.1 -NO_STAGE= yes .include .if ${ARCH} == "sparc64" @@ -48,27 +47,28 @@ ${BUILD_WRKSRC}/Makefile do-install: - @${MKDIR} ${PREFIX}/libexec/${PORTNAME} + @${MKDIR} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} .for exec in ${LIBEXEC_FILES} - ${INSTALL_PROGRAM} ${WRKSRC}/binaries/${exec} ${PREFIX}/libexec/${PORTNAME} + ${INSTALL_PROGRAM} ${WRKSRC}/binaries/${exec} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} .endfor +.for exec in ${PERL_LIBEXEC_FILES} + ${INSTALL_SCRIPT} ${WRKSRC}/binaries/${exec} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} +.endfor .for exec in ${SCRIPT_FILES} - ${INSTALL_SCRIPT} ${WRKSRC}/scripts/${exec} ${PREFIX}/bin + ${INSTALL_SCRIPT} ${WRKSRC}/scripts/${exec} ${STAGEDIR}${PREFIX}/bin .endfor .for exec in ${LN_FILES} - ${LN} -fs ${PREFIX}/bin/mafft ${PREFIX}/bin/${exec} + ${LN} -sf mafft ${STAGEDIR}${PREFIX}/bin/${exec} .endfor - ${LN} -fs ${PREFIX}/libexec/${PORTNAME}/mafft-distance ${PREFIX}/bin/mafft-distance - ${LN} -fs ${PREFIX}/libexec/${PORTNAME}/mafft-profile ${PREFIX}/bin/mafft-profile -.for man in ${MAN1} - ${INSTALL_MAN} ${WRKSRC}/binaries/${man} ${MAN1PREFIX}/man/man1 + ${LN} -sf ../libexec/${PORTNAME}/mafft-distance ${STAGEDIR}${PREFIX}/bin/mafft-distance + ${LN} -sf ../libexec/${PORTNAME}/mafft-profile ${STAGEDIR}${PREFIX}/bin/mafft-profile +.for man in ${MAN1_FILES} + ${INSTALL_MAN} ${WRKSRC}/binaries/${man} ${STAGEDIR}${MAN1PREFIX}/man/man1 .endfor - @${MKDIR} ${EXAMPLESDIR} - ${INSTALL_DATA} ${WRKSRC}/test/* ${EXAMPLESDIR} -.if ${PORT_OPTIONS:MDOCS} - @${MKDIR} ${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/readme ${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/license ${DOCSDIR} -.endif + @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} + ${INSTALL_DATA} ${WRKSRC}/test/* ${STAGEDIR}${EXAMPLESDIR} + @${MKDIR} ${STAGEDIR}${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/readme ${STAGEDIR}${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/license ${STAGEDIR}${DOCSDIR} .include Index: distinfo =================================================================== --- distinfo (revision 353911) +++ distinfo (working copy) @@ -1,2 +1,2 @@ -SHA256 (mafft-6.903-without-extensions-src.tgz) = d96326aecdb1f86b63779312c4a6d8f719f32786396567c1d1829341fc6dbcc8 -SIZE (mafft-6.903-without-extensions-src.tgz) = 359536 +SHA256 (mafft-7.149-without-extensions-src.tgz) = cfd909ee28afcc191f99c7ca37a507ddbefe9fbc416ef5692528c68a60c7b29a +SIZE (mafft-7.149-without-extensions-src.tgz) = 373846 Index: pkg-plist =================================================================== --- pkg-plist (revision 353911) +++ pkg-plist (working copy) @@ -25,12 +25,12 @@ libexec/mafft/dndblast libexec/mafft/dndfast7 libexec/mafft/dndpre -libexec/mafft/dndpre2 libexec/mafft/dvtditr libexec/mafft/f2cl libexec/mafft/getlag libexec/mafft/mafft-distance libexec/mafft/mafft-profile +libexec/mafft/mafftash_premafft.pl libexec/mafft/makedirectionlist libexec/mafft/mccaskillwrap libexec/mafft/multi2hat3s @@ -40,7 +40,6 @@ libexec/mafft/regtable2seq libexec/mafft/replaceu libexec/mafft/restoreu -libexec/mafft/rnatest libexec/mafft/score libexec/mafft/seq2regtable libexec/mafft/setcore @@ -49,14 +48,18 @@ libexec/mafft/splittbfast libexec/mafft/tbfast libexec/mafft/version +man/man1/mafft-homologs.1.gz +man/man1/mafft.1.gz %%PORTDOCS%%%%DOCSDIR%%/license %%PORTDOCS%%%%DOCSDIR%%/readme %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.allowshift %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.dpparttree %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftns2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftnsi %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.gins1 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.ginsi +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.ginsi.allowshift %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.lins1 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.linsi %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.parttree @@ -63,6 +66,6 @@ %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.qinsi %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.xinsi -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%% -%%PORTDOCS%%@dirrm %%DOCSDIR%% -@dirrm libexec/mafft +@dirrmtry libexec/mafft +%%PORTDOCS%%@dirrmtry %%DOCSDIR%% +%%PORTEXAMPLES%%@dirrmtry %%EXAMPLESDIR%% --- mafft.diff ends here --- >Release-Note: >Audit-Trail: >Unformatted: