Date: Sat, 7 Sep 2013 02:50:41 +0900 From: KATO Tsuguru <tkato432@yahoo.com> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/181883: biology/fasta3: Update to version 36.3.6c Message-ID: <20130907025041.96465d47c8df0c050b7e1a2d@yahoo.com> Resent-Message-ID: <201309061810.r86IA3iw054539@freefall.freebsd.org>
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>Number: 181883 >Category: ports >Synopsis: biology/fasta3: Update to version 36.3.6c >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Fri Sep 06 18:10:03 UTC 2013 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 8.4-RELEASE-p3 i386 >Organization: >Environment: >Description: - Update to version 36.3.6c >How-To-Repeat: >Fix: diff -urN /usr/ports/biology/fasta3/Makefile biology/fasta3/Makefile --- /usr/ports/biology/fasta3/Makefile 2013-09-05 01:47:14.000000000 +0900 +++ biology/fasta3/Makefile 2013-09-07 00:00:00.000000000 +0900 @@ -2,7 +2,7 @@ # $FreeBSD: head/biology/fasta3/Makefile 323293 2013-07-19 14:08:02Z wen $ PORTNAME= fasta3 -PORTVERSION= 36.3.6 +PORTVERSION= 36.3.6c CATEGORIES= biology MASTER_SITES= http://faculty.virginia.edu/wrpearson/fasta/fasta36/ DISTNAME= fasta-${PORTVERSION} @@ -10,18 +10,31 @@ 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= ${BUILD_WRKSRC} -SUB_FILES= pkg-message + MAKEFILE= Makefile.freebsd +MAKE_ENV= THR_LIBS="-pthread" XDIR="${PREFIX}/bin" \ + FASTA_HOST="$$(${UNAME} -n)" -XDIR= ${PREFIX}/bin -FASTA_HOST!= /usr/bin/uname -n +SUB_FILES= pkg-message + +PLIST_SUB= VER="${PORTVERSION:R:R}" -MAKE_ENV+= THR_LIBS=${PTHREAD_LIBS} XDIR=${XDIR} \ - FASTA_HOST='"${FASTA_HOST}"' +MLINKS= fasta36.1 tfasta35.1 fasta36.1 fastx35.1 \ + fasta36.1 tfastx35.1 fasta36.1 fasty35.1 \ + fasta36.1 tfasty35.1 fasta36.1 ssearch35.1 \ + fasta36.1 fastf35.1 fasta36.1 fasts35.1 \ + fasta36.1 tfasts35.1 fasta36.1 fastm35.1 \ + fasta36.1 tfastf35.1 fasta36.1 ggsearch35.1 \ + fasta36.1 lalign35.1 fasta36.1 prss35.1 \ + fasta36.1 prfx35.1 +MAN1= fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1 FASTA3_DOCS= README.versions \ fasta_func.doc readme.* fasta.defaults \ @@ -29,39 +42,36 @@ DATA= data/*.mat EXAMPLES= seq/*.aa seq/*.lc seq/*.seq seq/*.lib -MAN1= fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1 -MLINKS= fasta36.1 tfasta35.1 fasta36.1 fastx35.1 fasta36.1 tfastx35.1 \ - fasta36.1 fasty35.1 fasta36.1 tfasty35.1 fasta36.1 ssearch35.1 \ - fasta36.1 fastf35.1 fasta36.1 fasts35.1 fasta36.1 tfasts35.1 \ - fasta36.1 fastm35.1 fasta36.1 tfastf35.1 fasta36.1 ggsearch35.1 \ - fasta36.1 lalign35.1 fasta36.1 prss35.1 fasta36.1 prfx35.1 -PLIST_SUB= VER=${PORTVERSION:R:R} +.include <bsd.port.options.mk> 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} * ${PREFIX}/bin) + (cd ${WRKSRC}/conf && ${INSTALL_DATA} fastlibs ${PREFIX}/etc/fastlibs.sample) + @${MKDIR} ${DATADIR} .for data in ${DATA} - ${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR} -.endfor - @ ${MKDIR} ${EXAMPLESDIR} -.for ex in ${EXAMPLES} - ${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR} + (cd ${WRKSRC} && ${INSTALL_DATA} ${data} ${DATADIR}) .endfor .for manpage in ${MAN1} - ${INSTALL_MAN} ${WRKSRC}/doc/${manpage} ${MAN1PREFIX}/man/man1/ + (cd ${WRKSRC}/doc && ${INSTALL_MAN} ${manpage} ${MAN1PREFIX}/man/man1) +.endfor +.if ${PORT_OPTIONS:MDOCS} + @${MKDIR} ${DOCSDIR} +.for i in COPYRIGHT FASTA_LIST README + (cd ${WRKSRC} && ${INSTALL_DATA} ${i} ${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} + (cd ${WRKSRC}/doc && ${INSTALL_DATA} ${docfile} ${DOCSDIR}) +.endfor +.endif +.if ${PORT_OPTIONS:MEXAMPLES} + @${MKDIR} ${EXAMPLESDIR} +.for ex in ${EXAMPLES} + (cd ${WRKSRC} && ${INSTALL_DATA} ${ex} ${EXAMPLESDIR}) .endfor .endif - @ ${CAT} ${PKGMESSAGE} + @${CAT} ${PKGMESSAGE} .include <bsd.port.mk> diff -urN /usr/ports/biology/fasta3/distinfo biology/fasta3/distinfo --- /usr/ports/biology/fasta3/distinfo 2013-09-05 01:47:14.000000000 +0900 +++ biology/fasta3/distinfo 2013-09-07 00:00:00.000000000 +0900 @@ -1,2 +1,2 @@ -SHA256 (fasta-36.3.6.tar.gz) = d6c526c307941fe8c98a16406cb01df6bb5712d3c2b7f4a90e126ceba682db6f -SIZE (fasta-36.3.6.tar.gz) = 995298 +SHA256 (fasta-36.3.6c.tar.gz) = a6abe630a061ddf9d52064aedf5466896b410fccf7adc8802bce8363e7c9e8dd +SIZE (fasta-36.3.6c.tar.gz) = 996137 diff -urN /usr/ports/biology/fasta3/pkg-plist biology/fasta3/pkg-plist --- /usr/ports/biology/fasta3/pkg-plist 2013-09-05 01:47:14.000000000 +0900 +++ biology/fasta3/pkg-plist 2013-09-07 00:00:00.000000000 +0900 @@ -17,11 +17,17 @@ bin/tfastx%%VER%% bin/tfasty%%VER%% etc/fastlibs.sample -%%PORTDOCS%%%%DOCSDIR%%/README %%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 +39,51 @@ %%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 +97,6 @@ %%DATADIR%%/pam250.mat %%DATADIR%%/rna.mat %%DATADIR%%/vtml160.mat -%%PORTDOCS%%@dirrm %%DOCSDIR%% -@dirrm %%EXAMPLESDIR%% @dirrm %%DATADIR%% +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%% +%%PORTDOCS%%@dirrm %%DOCSDIR%% >Release-Note: >Audit-Trail: >Unformatted:
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