Date: Tue, 29 Oct 2013 18:10:04 GMT From: KATO Tsuguru <tkato432@yahoo.com> To: freebsd-ports-bugs@FreeBSD.org Subject: Re: ports/181883: biology/fasta3: Update to version 36.3.6c Message-ID: <201310291810.r9TIA4bR021659@freefall.freebsd.org>
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The following reply was made to PR ports/181883; it has been noted by GNATS. From: KATO Tsuguru <tkato432@yahoo.com> To: bug-followup@FreeBSD.org Cc: Subject: Re: ports/181883: biology/fasta3: Update to version 36.3.6c Date: Wed, 30 Oct 2013 02:50:31 +0900 This is a multi-part message in MIME format. --Multipart=_Wed__30_Oct_2013_02_50_31_+0900_Dt.rccrvI5XLIxQ7 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Version 36.3.6d has been released. --Multipart=_Wed__30_Oct_2013_02_50_31_+0900_Dt.rccrvI5XLIxQ7 Content-Type: text/x-diff; name="biology_fasta3.diff" Content-Disposition: attachment; filename="biology_fasta3.diff" Content-Transfer-Encoding: 7bit diff -urN /usr/ports/biology/fasta3/Makefile biology/fasta3/Makefile --- /usr/ports/biology/fasta3/Makefile 2013-09-22 01:13:54.000000000 +0900 +++ biology/fasta3/Makefile 2013-10-30 00:00:00.000000000 +0900 @@ -2,7 +2,7 @@ # $FreeBSD: head/biology/fasta3/Makefile 327709 2013-09-20 15:55:44Z bapt $ 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 +10,62 @@ 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} +.include <bsd.port.options.mk> -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 <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 2013-10-30 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-36.3.6d.tar.gz) = 6392741abecc8b25daeee53389584f48cee8a8ea7340c7f8cc97e149720a5730 +SIZE (fasta-36.3.6d.tar.gz) = 997714 diff -urN /usr/ports/biology/fasta3/files/patch-Makefile.freebsd biology/fasta3/files/patch-Makefile.freebsd --- /usr/ports/biology/fasta3/files/patch-Makefile.freebsd 2013-09-05 01:47:14.000000000 +0900 +++ biology/fasta3/files/patch-Makefile.freebsd 2013-10-30 00:00:00.000000000 +0900 @@ -13,7 +13,7 @@ BIN = ../bin -XDIR = /usr/local/bin -+XDIR = ${LOCALBASE}/bin ++XDIR?= ${LOCALBASE}/bin LIB_M+= -lm 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 2013-10-30 00:00:00.000000000 +0900 @@ -17,11 +17,38 @@ 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 @@ %%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 @@ %%DATADIR%%/pam250.mat %%DATADIR%%/rna.mat %%DATADIR%%/vtml160.mat -%%PORTDOCS%%@dirrm %%DOCSDIR%% -@dirrm %%EXAMPLESDIR%% @dirrm %%DATADIR%% +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%% +%%PORTDOCS%%@dirrm %%DOCSDIR%% --Multipart=_Wed__30_Oct_2013_02_50_31_+0900_Dt.rccrvI5XLIxQ7--
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