From owner-svn-ports-head@FreeBSD.ORG Tue Oct 29 19:32:17 2013 Return-Path: Delivered-To: svn-ports-head@freebsd.org 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 ESMTP id 28C963AB; Tue, 29 Oct 2013 19:32:17 +0000 (UTC) (envelope-from pawel@FreeBSD.org) 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)) (No client certificate requested) by mx1.freebsd.org (Postfix) with ESMTPS id 05F702FAC; Tue, 29 Oct 2013 19:32:17 +0000 (UTC) Received: from svn.freebsd.org ([127.0.1.70]) by svn.freebsd.org (8.14.7/8.14.7) with ESMTP id r9TJWGGx003193; Tue, 29 Oct 2013 19:32:16 GMT (envelope-from pawel@svn.freebsd.org) Received: (from pawel@localhost) by svn.freebsd.org (8.14.7/8.14.5/Submit) id r9TJWGj6003188; Tue, 29 Oct 2013 19:32:16 GMT (envelope-from pawel@svn.freebsd.org) Message-Id: <201310291932.r9TJWGj6003188@svn.freebsd.org> From: Pawel Pekala Date: Tue, 29 Oct 2013 19:32:16 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r331982 - in head/biology/fasta3: . 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: 2.1.14 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: Tue, 29 Oct 2013 19:32:17 -0000 Author: pawel Date: Tue Oct 29 19:32:15 2013 New Revision: 331982 URL: http://svnweb.freebsd.org/changeset/ports/331982 Log: Update to version 36.3.6d PR: ports/181883 Submitted by: KATO Tsuguru Modified: head/biology/fasta3/Makefile head/biology/fasta3/distinfo (contents, props changed) head/biology/fasta3/files/patch-Makefile.freebsd (contents, props changed) head/biology/fasta3/pkg-descr head/biology/fasta3/pkg-plist (contents, props changed) Modified: head/biology/fasta3/Makefile ============================================================================== --- head/biology/fasta3/Makefile Tue Oct 29 19:11:18 2013 (r331981) +++ head/biology/fasta3/Makefile Tue Oct 29 19:32:15 2013 (r331982) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= fasta3 -PORTVERSION= 36.3.6 +PORTVERSION= 36.3.6d CATEGORIES= biology MASTER_SITES= http://faculty.virginia.edu/wrpearson/fasta/fasta36/ DISTNAME= fasta-${PORTVERSION} @@ -10,59 +10,60 @@ DISTNAME= fasta-${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Collection of programs for searching DNA and protein databases +OPTIONS_DEFINE= DOCS EXAMPLES + NO_CDROM= May not be sold or incorporated into a commercial product + WRKSRC= ${WRKDIR}/${DISTNAME} BUILD_WRKSRC= ${WRKSRC}/src INSTALL_WRKSRC= ${BUILD_WRKSRC} -SUB_FILES= pkg-message + MAKEFILE= Makefile.freebsd +MAKE_ENV= THR_LIBS="-pthread" XDIR="${STAGEDIR}${PREFIX}/bin" \ + FASTA_HOST="$$(${UNAME} -n)" -XDIR= ${PREFIX}/bin -FASTA_HOST!= /usr/bin/uname -n +SUB_FILES= pkg-message -MAKE_ENV+= THR_LIBS=${PTHREAD_LIBS} XDIR=${XDIR} \ - FASTA_HOST='"${FASTA_HOST}"' +PLIST_SUB= VER="${PORTVERSION:R:R}" -FASTA3_DOCS= README.versions \ +MAN1_LINKS= fastf35.1 fasts35.1 fastm35.1 fastx35.1 fasty35.1 \ + ggsearch35.1 lalign35.1 ssearch35.1 tfasta35.1 tfastf35.1 \ + tfasts35.1 tfastx35.1 tfasty35.1 prfx35.1 prss35.1 +MAN1_FILES= fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1 +DOC_FILES= README.versions \ fasta_func.doc readme.* fasta.defaults \ fasta.options fasta_versions.html changes*.html DATA= data/*.mat EXAMPLES= seq/*.aa seq/*.lc seq/*.seq seq/*.lib -MAN1= fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1 -MLINKS= fasta36.1 tfasta35.1 fasta36.1 fastx35.1 fasta36.1 tfastx35.1 \ - fasta36.1 fasty35.1 fasta36.1 tfasty35.1 fasta36.1 ssearch35.1 \ - fasta36.1 fastf35.1 fasta36.1 fasts35.1 fasta36.1 tfasts35.1 \ - fasta36.1 fastm35.1 fasta36.1 tfastf35.1 fasta36.1 ggsearch35.1 \ - fasta36.1 lalign35.1 fasta36.1 prss35.1 fasta36.1 prfx35.1 -PLIST_SUB= VER=${PORTVERSION:R:R} - -NO_STAGE= yes post-patch: - @ ${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}/ + @${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC} + post-install: - ${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin/ - ${INSTALL_DATA} ${WRKSRC}/conf/fastlibs ${PREFIX}/etc/fastlibs.sample - @ ${MKDIR} ${DATADIR} + (cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} * ${STAGEDIR}${PREFIX}/bin) + (cd ${WRKSRC}/conf && ${INSTALL_DATA} fastlibs \ + ${STAGEDIR}${PREFIX}/etc/fastlibs.sample) + @${MKDIR} ${STAGEDIR}${DATADIR} .for data in ${DATA} - ${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR} + (cd ${WRKSRC} && ${INSTALL_DATA} ${data} ${STAGEDIR}${DATADIR}) .endfor - @ ${MKDIR} ${EXAMPLESDIR} -.for ex in ${EXAMPLES} - ${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR} +.for manpage in ${MAN1_FILES} + (cd ${WRKSRC}/doc && ${INSTALL_MAN} ${manpage} \ + ${STAGEDIR}${MAN1PREFIX}/man/man1) +.endfor +.for links in ${MAN1_LINKS} + (${LN} -sf fasta36.1 ${STAGEDIR}${MAN1PREFIX}/man/man1/${links}) .endfor -.for manpage in ${MAN1} - ${INSTALL_MAN} ${WRKSRC}/doc/${manpage} ${MAN1PREFIX}/man/man1/ + @${MKDIR} ${STAGEDIR}${DOCSDIR} +.for i in COPYRIGHT FASTA_LIST README + (cd ${WRKSRC} && ${INSTALL_DATA} ${i} ${STAGEDIR}${DOCSDIR}) .endfor -.if !defined(NOPORTDOCS) - @ ${MKDIR} ${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/COPYRIGHT ${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/FASTA_LIST ${DOCSDIR} -.for docfile in ${FASTA3_DOCS} - @ ${INSTALL_DATA} ${WRKSRC}/doc/${docfile} ${DOCSDIR} +.for docfile in ${DOC_FILES} + (cd ${WRKSRC}/doc && ${INSTALL_DATA} ${docfile} ${STAGEDIR}${DOCSDIR}) +.endfor + @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} +.for ex in ${EXAMPLES} + (cd ${WRKSRC} && ${INSTALL_DATA} ${ex} ${STAGEDIR}${EXAMPLESDIR}) .endfor -.endif - @ ${CAT} ${PKGMESSAGE} .include Modified: head/biology/fasta3/distinfo ============================================================================== --- head/biology/fasta3/distinfo Tue Oct 29 19:11:18 2013 (r331981) +++ head/biology/fasta3/distinfo Tue Oct 29 19:32:15 2013 (r331982) @@ -1,2 +1,2 @@ -SHA256 (fasta-36.3.6.tar.gz) = d6c526c307941fe8c98a16406cb01df6bb5712d3c2b7f4a90e126ceba682db6f -SIZE (fasta-36.3.6.tar.gz) = 995298 +SHA256 (fasta-36.3.6d.tar.gz) = 6392741abecc8b25daeee53389584f48cee8a8ea7340c7f8cc97e149720a5730 +SIZE (fasta-36.3.6d.tar.gz) = 997714 Modified: head/biology/fasta3/files/patch-Makefile.freebsd ============================================================================== --- head/biology/fasta3/files/patch-Makefile.freebsd Tue Oct 29 19:11:18 2013 (r331981) +++ head/biology/fasta3/files/patch-Makefile.freebsd Tue Oct 29 19:32:15 2013 (r331982) @@ -13,7 +13,7 @@ BIN = ../bin -XDIR = /usr/local/bin -+XDIR = ${LOCALBASE}/bin ++XDIR?= ${LOCALBASE}/bin LIB_M+= -lm Modified: head/biology/fasta3/pkg-descr ============================================================================== --- head/biology/fasta3/pkg-descr Tue Oct 29 19:11:18 2013 (r331981) +++ head/biology/fasta3/pkg-descr Tue Oct 29 19:32:15 2013 (r331982) @@ -14,5 +14,4 @@ Molecular Biology 132:185-219. The FASTA3 suite is distributed freely subject to the condition that it may not be sold or incorporated into a commercial product. -Author: William R Pearson WWW: http://fasta.bioch.virginia.edu/ Modified: head/biology/fasta3/pkg-plist ============================================================================== --- head/biology/fasta3/pkg-plist Tue Oct 29 19:11:18 2013 (r331981) +++ head/biology/fasta3/pkg-plist Tue Oct 29 19:32:15 2013 (r331982) @@ -17,11 +17,38 @@ bin/tfasts%%VER%% bin/tfastx%%VER%% bin/tfasty%%VER%% etc/fastlibs.sample -%%PORTDOCS%%%%DOCSDIR%%/README +man/man1/fasta36.1.gz +man/man1/fastf3.1.gz +man/man1/fastf35.1.gz +man/man1/fastm35.1.gz +man/man1/fasts3.1.gz +man/man1/fasts35.1.gz +man/man1/fastx35.1.gz +man/man1/fasty35.1.gz +man/man1/ggsearch35.1.gz +man/man1/lalign35.1.gz +man/man1/map_db.1.gz +man/man1/prfx35.1.gz +man/man1/prss3.1.gz +man/man1/prss35.1.gz +man/man1/ps_lav.1.gz +man/man1/ssearch35.1.gz +man/man1/tfasta35.1.gz +man/man1/tfastf35.1.gz +man/man1/tfasts35.1.gz +man/man1/tfastx35.1.gz +man/man1/tfasty35.1.gz %%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT %%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST +%%PORTDOCS%%%%DOCSDIR%%/README %%PORTDOCS%%%%DOCSDIR%%/README.versions +%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html +%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html +%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html +%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults +%%PORTDOCS%%%%DOCSDIR%%/fasta.options %%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc +%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html %%PORTDOCS%%%%DOCSDIR%%/readme.v30 %%PORTDOCS%%%%DOCSDIR%%/readme.v30t6 %%PORTDOCS%%%%DOCSDIR%%/readme.v30t7 @@ -33,57 +60,51 @@ etc/fastlibs.sample %%PORTDOCS%%%%DOCSDIR%%/readme.v35 %%PORTDOCS%%%%DOCSDIR%%/readme.v36 %%PORTDOCS%%%%DOCSDIR%%/readme.w32 -%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults -%%PORTDOCS%%%%DOCSDIR%%/fasta.options -%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html -%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html -%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html -%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html -%%EXAMPLESDIR%%/dyr_human.aa -%%EXAMPLESDIR%%/egmsmg.aa -%%EXAMPLESDIR%%/gstt1_drome.aa -%%EXAMPLESDIR%%/gtm1_human.aa -%%EXAMPLESDIR%%/gtt1_drome.aa -%%EXAMPLESDIR%%/h10_human.aa -%%EXAMPLESDIR%%/hahu.aa -%%EXAMPLESDIR%%/lcbo.aa -%%EXAMPLESDIR%%/m1r.aa -%%EXAMPLESDIR%%/m2.aa -%%EXAMPLESDIR%%/mchu.aa -%%EXAMPLESDIR%%/mgstm1.aa -%%EXAMPLESDIR%%/ms1.aa -%%EXAMPLESDIR%%/musplfm.aa -%%EXAMPLESDIR%%/mwkw.aa -%%EXAMPLESDIR%%/mwrtc1.aa -%%EXAMPLESDIR%%/myosin_bp.aa -%%EXAMPLESDIR%%/n0.aa -%%EXAMPLESDIR%%/n1.aa -%%EXAMPLESDIR%%/n2.aa -%%EXAMPLESDIR%%/n2s.aa -%%EXAMPLESDIR%%/n2t.aa -%%EXAMPLESDIR%%/ngt.aa -%%EXAMPLESDIR%%/ngts.aa -%%EXAMPLESDIR%%/oohu.aa -%%EXAMPLESDIR%%/prio_atepa.aa -%%EXAMPLESDIR%%/qrhuld.aa -%%EXAMPLESDIR%%/titin_hum.aa -%%EXAMPLESDIR%%/xurt8c.aa -%%EXAMPLESDIR%%/xurtg.aa -%%EXAMPLESDIR%%/mgstm1.lc -%%EXAMPLESDIR%%/xurt8c.lc -%%EXAMPLESDIR%%/bovgh.seq -%%EXAMPLESDIR%%/bovprl.seq -%%EXAMPLESDIR%%/gst.seq -%%EXAMPLESDIR%%/hsgstm1b.seq -%%EXAMPLESDIR%%/humgstd.seq -%%EXAMPLESDIR%%/mgstm1.seq -%%EXAMPLESDIR%%/mgstm1_genclone.seq -%%EXAMPLESDIR%%/mgtt2_x.seq -%%EXAMPLESDIR%%/titin_hum.seq -%%EXAMPLESDIR%%/mu.lib -%%EXAMPLESDIR%%/n2_fs.lib -%%EXAMPLESDIR%%/n_fs.lib -%%EXAMPLESDIR%%/prot_test.lib +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovgh.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovprl.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dyr_human.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/egmsmg.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gst.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gstt1_drome.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtm1_human.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtt1_drome.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h10_human.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hahu.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hsgstm1b.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/humgstd.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lcbo.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/m1r.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/m2.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mchu.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.lc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1_genclone.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgtt2_x.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ms1.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mu.lib +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/musplfm.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwkw.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwrtc1.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myosin_bp.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n0.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n1.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2_fs.lib +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2s.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2t.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n_fs.lib +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngt.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngts.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/oohu.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prio_atepa.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prot_test.lib +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/qrhuld.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.aa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.lc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurtg.aa %%DATADIR%%/blosum45.mat %%DATADIR%%/blosum50.mat %%DATADIR%%/blosum62.mat @@ -97,6 +118,6 @@ etc/fastlibs.sample %%DATADIR%%/pam250.mat %%DATADIR%%/rna.mat %%DATADIR%%/vtml160.mat -%%PORTDOCS%%@dirrm %%DOCSDIR%% -@dirrm %%EXAMPLESDIR%% @dirrm %%DATADIR%% +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%% +%%PORTDOCS%%@dirrm %%DOCSDIR%%