From owner-freebsd-ports-bugs@FreeBSD.ORG Mon Jul 16 22:50:05 2012 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 71C411065670 for ; Mon, 16 Jul 2012 22:50:05 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id 432788FC12 for ; Mon, 16 Jul 2012 22:50:05 +0000 (UTC) Received: from freefall.freebsd.org (localhost [127.0.0.1]) by freefall.freebsd.org (8.14.5/8.14.5) with ESMTP id q6GMo5Ie096603 for ; Mon, 16 Jul 2012 22:50:05 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.5/8.14.5/Submit) id q6GMo58e096602; Mon, 16 Jul 2012 22:50:05 GMT (envelope-from gnats) Resent-Date: Mon, 16 Jul 2012 22:50:05 GMT Resent-Message-Id: <201207162250.q6GMo58e096602@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 [69.147.83.52]) by hub.freebsd.org (Postfix) with ESMTP id 7AE7B106564A for ; Mon, 16 Jul 2012 22:40:58 +0000 (UTC) (envelope-from reed@herschel.biodesign.asu.edu) Received: from herschel.biodesign.asu.edu (herschel.biodesign.asu.edu [129.219.237.213]) by mx1.freebsd.org (Postfix) with ESMTP id 5E7DE8FC15 for ; Mon, 16 Jul 2012 22:40:58 +0000 (UTC) Received: from herschel.biodesign.asu.edu (localhost [127.0.0.1]) by herschel.biodesign.asu.edu (8.14.5/8.14.5) with ESMTP id q6GMMnFL035580 for ; Mon, 16 Jul 2012 15:22:49 -0700 (MST) (envelope-from reed@herschel.biodesign.asu.edu) Received: (from reed@localhost) by herschel.biodesign.asu.edu (8.14.5/8.14.5/Submit) id q6GMMlaC035579; Mon, 16 Jul 2012 15:22:47 -0700 (MST) (envelope-from reed) Message-Id: <201207162222.q6GMMlaC035579@herschel.biodesign.asu.edu> Date: Mon, 16 Jul 2012 15:22:47 -0700 (MST) From: "Reed A. Cartwright" To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Cc: Subject: ports/169920: Update biology/mafft to latest version X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list Reply-To: "Reed A. Cartwright" List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 16 Jul 2012 22:50:05 -0000 >Number: 169920 >Category: ports >Synopsis: Update biology/mafft to latest version >Confidential: no >Severity: non-critical >Priority: medium >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Mon Jul 16 22:50:04 UTC 2012 >Closed-Date: >Last-Modified: >Originator: Reed A. Cartwright >Release: FreeBSD 9.0-RELEASE-p3 amd64 >Organization: Arizona State University >Environment: System: FreeBSD herschel.biodesign.asu.edu 9.0-RELEASE-p3 FreeBSD 9.0-RELEASE-p3 #0: Tue Jun 12 02:52:29 UTC 2012 root@amd64-builder.daemonology.net:/usr/obj/usr/src/sys/GENERIC amd64 >Description: The port biology/mafft is out of date and does not run successfully on recent version of FreeBSD. >How-To-Repeat: >Fix: A Patch is attached to upgrade the port to version 6.903. If desired, I am willing to take over ownership of the port. --- biolog.mafft.patch begins here --- diff /usr/ports/biology/mafft.orig/Makefile /usr/ports/biology/mafft/Makefile 10c10 < PORTVERSION= 5.743 --- > PORTVERSION= 6.903 12,13c12,13 < MASTER_SITES= http://align.bmr.kyushu-u.ac.jp/mafft/software/ < DISTNAME= ${PORTNAME}-${PORTVERSION}-src --- > MASTER_SITES= http://mafft.cbrc.jp/alignment/software/ > DISTNAME= ${PORTNAME}-${PORTVERSION}-without-extensions-src 17c17,19 < COMMENT= Multiple sequence alignments based on fast Fourier transform --- > COMMENT= Multiple alignment program for amino acid or nucleotide sequences > > LICENSE= BSD 21,22c23,38 < WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} < BUILD_WRKSRC= ${WRKSRC}/src --- > WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}-without-extensions > BUILD_WRKSRC= ${WRKSRC}/core > > USE_GMAKE= yes > > MAN1= mafft.1 mafft-homologs.1 > > LIBEXEC_FILES= dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \ > pair2hat3s multi2hat3s rnatest pairash addsingle splittbfast \ > disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap \ > countlen seq2regtable regtable2seq score getlag dndpre dndpre2 \ > setcore replaceu restoreu setdirection makedirectionlist version > SCRIPT_FILES= mafft mafft-homologs.rb > LN_FILES= einsi fftns fftnsi ginsi linsi mafft-einsi mafft-fftns \ > mafft-fftnsi mafft-ginsi mafft-linsi mafft-nwns mafft-nwnsi \ > mafft-qinsi mafft-xinsi nwns nwnsi 24c40 < MAKE_ENV+= CFLAG="${CFLAGS}" --- > .include 27,28c43,48 < @${REINPLACE_CMD} -E 's,^(CC|PREFIX) =,\1 ?=,' \ < ${WRKSRC}/src/Makefile --- > @${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}|' \ > -e 's|^MANDIR = .*$$|MANDIR = $$(MANPREFIX)/man/man1|' \ > -e 's|^PREFIX = .*$$||' \ > -e 's|^CC = .*$$||' \ > -e 's|^CFLAGS = .*$$||' \ > ${BUILD_WRKSRC}/Makefile 31,33c51,66 < ${INSTALL_SCRIPT} ${WRKSRC}/scripts/mafft ${PREFIX}/bin < ${INSTALL_PROGRAM} ${WRKSRC}/binaries/* ${PREFIX}/bin < @ ${MKDIR} ${EXAMPLESDIR} --- > @${MKDIR} ${PREFIX}/libexec/${PORTNAME} > .for exec in ${LIBEXEC_FILES} > ${INSTALL_PROGRAM} ${WRKSRC}/binaries/${exec} ${PREFIX}/libexec/${PORTNAME} > .endfor > .for exec in ${SCRIPT_FILES} > ${INSTALL_SCRIPT} ${WRKSRC}/scripts/${exec} ${PREFIX}/bin > .endfor > .for exec in ${LN_FILES} > ${LN} -fs ${PREFIX}/bin/mafft ${PREFIX}/bin/${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} ${MAN1PREFIX}/man/man1 > .endfor > @${MKDIR} ${EXAMPLESDIR} 36c69 < @ ${MKDIR} ${DOCSDIR} --- > @${MKDIR} ${DOCSDIR} 37a71 > ${INSTALL_DATA} ${WRKSRC}/license ${DOCSDIR} 40c74 < .include --- > .include diff /usr/ports/biology/mafft.orig/distinfo /usr/ports/biology/mafft/distinfo 1,2c1,2 < SHA256 (mafft-5.743-src.tgz) = 7bf0d450fea1d44fafee27c29c74b3ae4247ad0075b41729d9dc935e2a88de66 < SIZE (mafft-5.743-src.tgz) = 280226 --- > SHA256 (mafft-6.903-without-extensions-src.tgz) = d96326aecdb1f86b63779312c4a6d8f719f32786396567c1d1829341fc6dbcc8 > SIZE (mafft-6.903-without-extensions-src.tgz) = 359536 diff /usr/ports/biology/mafft.orig/pkg-descr /usr/ports/biology/mafft/pkg-descr 7a8,11 > > K. Katoh and H. Toh 2008 (Briefings in Bioinformatics 9:286-298) > Recent developments in the MAFFT multiple sequence alignment program. > 12c16 < WWW: http://align.bmr.kyushu-u.ac.jp/mafft --- > WWW: http://mafft.cbrc.jp/alignment/software/ diff /usr/ports/biology/mafft.orig/pkg-plist /usr/ports/biology/mafft/pkg-plist 1c1,5 < bin/dummy --- > bin/einsi > bin/fftns > bin/fftnsi > bin/ginsi > bin/linsi 3,10c7,15 < bin/disttbfast < bin/dndblast < bin/dndfast7 < bin/dndpre < bin/dndpre2 < bin/dvtditr < bin/f2cl < bin/getlag --- > bin/mafft-distance > bin/mafft-einsi > bin/mafft-fftns > bin/mafft-fftnsi > bin/mafft-ginsi > bin/mafft-homologs.rb > bin/mafft-linsi > bin/mafft-nwns > bin/mafft-nwnsi 12,21c17,52 < bin/multi2hat3s < bin/pair2hat3s < bin/pairalign < bin/pairlocalalign < bin/score < bin/setcore < bin/sextet5 < bin/splitseq < bin/tbfast < bin/tbfast2 --- > bin/mafft-qinsi > bin/mafft-xinsi > bin/nwns > bin/nwnsi > libexec/mafft/addsingle > libexec/mafft/contrafoldwrap > libexec/mafft/countlen > libexec/mafft/disttbfast > 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/makedirectionlist > libexec/mafft/mccaskillwrap > libexec/mafft/multi2hat3s > libexec/mafft/pair2hat3s > libexec/mafft/pairash > libexec/mafft/pairlocalalign > libexec/mafft/regtable2seq > libexec/mafft/replaceu > libexec/mafft/restoreu > libexec/mafft/rnatest > libexec/mafft/score > libexec/mafft/seq2regtable > libexec/mafft/setcore > libexec/mafft/setdirection > libexec/mafft/sextet5 > libexec/mafft/splittbfast > libexec/mafft/tbfast > libexec/mafft/version > %%PORTDOCS%%%%DOCSDIR%%/license 23,29c54,66 < %%EXAMPLESDIR%%/sample < %%EXAMPLESDIR%%/sample.fftns2 < %%EXAMPLESDIR%%/sample.fftnsi < %%EXAMPLESDIR%%/sample.gins1 < %%EXAMPLESDIR%%/sample.ginsi < %%EXAMPLESDIR%%/sample.lins1 < %%EXAMPLESDIR%%/sample.linsi --- > %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample > %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.dpparttree > %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftns2 > %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftnsi > %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.gins1 > %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.ginsi > %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.lins1 > %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.linsi > %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.parttree > %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna > %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.qinsi > %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.xinsi > %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%% 31c68 < @dirrm %%EXAMPLESDIR%% --- > @dirrm libexec/mafft --- biolog.mafft.patch ends here --- >Release-Note: >Audit-Trail: >Unformatted: