Date: Mon, 27 Nov 2000 18:10:06 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/23130: Port update: biology/emboss (MAINTAINER) Message-ID: <E140Qr0-000Q0J-00@fling.sanbi.ac.za>
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>Number: 23130 >Category: ports >Synopsis: Port update: biology/emboss (MAINTAINER) >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Mon Nov 27 08:20:00 PST 2000 >Closed-Date: >Last-Modified: >Originator: Johann Visagie >Release: FreeBSD 5.0-CURRENT i386 >Organization: Electric Genetics >Environment: >Description: - Update port biology/emboss from 1.7.0 to 1.8.0 - Removed the :U hack since this modifier has now been MFC'd to RELENG_3 and RELENG_4. - I'm aware of the fact that there's still a building problem with one of the EMBASSY applications (MSE) on pre-4 versions of FreeBSD. I'm still unable to solve this. Workaround: Choose not to install MSE. >How-To-Repeat: >Fix: diff -ruN emboss.bak/Makefile emboss/Makefile --- emboss.bak/Makefile Mon Nov 27 18:00:45 2000 +++ emboss/Makefile Mon Nov 27 18:01:34 2000 @@ -6,14 +6,13 @@ # PORTNAME= emboss -PORTVERSION= 1.7.0 -PORTREVISION= 1 +PORTVERSION= 1.8.0 CATEGORIES= biology MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ ftp://ftp.no.embnet.org/pub/EMBOSS/ -DISTFILES= ${PORTNAME_U}-${PORTVERSION}${EXTRACT_SUFX} +DISTFILES= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX} DIST_SUBDIR= ${PORTNAME} -EXTRACT_ONLY= ${PORTNAME_U}-${PORTVERSION}${EXTRACT_SUFX} +EXTRACT_ONLY= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX} MAINTAINER= johann@egenetics.com @@ -24,9 +23,7 @@ USE_LIBTOOL= yes USE_XLIB= yes PLIST= ${WRKDIR}/pkg-plist - -# Make doesn't know about :U -PORTNAME_U= EMBOSS +PKGMESSAGE= ${WRKDIR}/pkg-message .if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc) .include "${WRKDIRPREFIX}${.CURDIR}/Makefile.inc" @@ -39,7 +36,7 @@ MKDIR="${MKDIR}" \ RM="${RM}" -WRKSRC= ${WRKDIR}/${PORTNAME_U}-${PORTVERSION} +WRKSRC= ${WRKDIR}/${PORTNAME:U}-${PORTVERSION} EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY PHYLIP_VERSION= 3.573c MSE_VERSION= 0.0.4 @@ -109,6 +106,8 @@ @ ${INSTALL_DATA} ${WRKSRC}/emboss/acd/emboss.default \ ${PREFIX}/etc/emboss.default.sample .if !defined(BATCH) + @ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \ + pkg-message > ${PKGMESSAGE} @ ${CAT} ${PKGMESSAGE} .endif diff -ruN emboss.bak/distinfo emboss/distinfo --- emboss.bak/distinfo Mon Nov 27 18:00:45 2000 +++ emboss/distinfo Mon Nov 27 16:06:08 2000 @@ -1,4 +1,4 @@ -MD5 (emboss/EMBOSS-1.7.0.tar.gz) = 61758add8d2d6bdb9e043fe93c37f341 -MD5 (emboss/PHYLIP-3.573c.tar.gz) = e41b0552196e9b7b46ca0e9563e9384a -MD5 (emboss/MSE-0.0.4.tar.gz) = 6ba124ff85465be3541d2e250248cd3d -MD5 (emboss/TOPO-0.1.tar.gz) = 687c6ca8ba945520b11058ba28ee880d +MD5 (emboss/EMBOSS-1.8.0.tar.gz) = 4cbc80557dbbe41fbedb477e00e47aba +MD5 (emboss/MSE-0.0.4.tar.gz) = 800216297fa6c3de76f6d1d7ea194a22 +MD5 (emboss/PHYLIP-3.573c.tar.gz) = bd2ded015838da4236c3d4ac25ae8ede +MD5 (emboss/TOPO-0.1.tar.gz) = 42f4f6e57e4c99b4684b0a4810f2c0a0 diff -ruN emboss.bak/pkg-message emboss/pkg-message --- emboss.bak/pkg-message Mon Nov 27 18:00:45 2000 +++ emboss/pkg-message Mon Nov 27 17:53:30 2000 @@ -3,13 +3,12 @@ The EMBOSS suite has been successfully installed. In order to use the EMBOSS programs, you will need to set some environment -variables in your shell startup file. If EMBOSS was installed to the -default prefix, then: +variables in your shell startup file. -- set PLPLOT_LIB to: "/usr/local/share/EMBOSS" -- set EMBOSS_ACDROOT to: "/usr/local/share/EMBOSS/acd" +- set PLPLOT_LIB to: "%%PREFIX%%/share/EMBOSS" +- set EMBOSS_ACDROOT to: "%%PREFIX%%/share/EMBOSS/acd" -NB: A sample configuration file has been installed to /usr/local/etc as +NB: A sample configuration file has been installed to %%PREFIX%%/etc as emboss.default.sample. This must be renamed to emboss.default and edited to suit your site and its requirements. diff -ruN emboss.bak/pkg-plist emboss/pkg-plist --- emboss.bak/pkg-plist Mon Nov 27 18:00:45 2000 +++ emboss/pkg-plist Mon Nov 27 16:33:07 2000 @@ -8,6 +8,7 @@ bin/chips bin/cirdna bin/codcmp +bin/coderet bin/complex bin/compseq bin/cons @@ -151,10 +152,12 @@ share/EMBOSS/acd/cirdna.acd share/EMBOSS/acd/cluster.acd share/EMBOSS/acd/codcmp.acd +share/EMBOSS/acd/coderet.acd share/EMBOSS/acd/codes.english share/EMBOSS/acd/complex.acd share/EMBOSS/acd/compseq.acd share/EMBOSS/acd/cons.acd +share/EMBOSS/acd/corbatest.acd share/EMBOSS/acd/cpgplot.acd share/EMBOSS/acd/cpgreport.acd share/EMBOSS/acd/cusp.acd @@ -248,6 +251,7 @@ share/EMBOSS/acd/remap.acd share/EMBOSS/acd/restrict.acd share/EMBOSS/acd/revseq.acd +share/EMBOSS/acd/scope.acd share/EMBOSS/acd/seealso.acd share/EMBOSS/acd/seqinfo.acd share/EMBOSS/acd/seqmatchall.acd @@ -532,16 +536,20 @@ share/EMBOSS/data/Ebases.iub share/EMBOSS/data/Edayhoff.freq share/EMBOSS/data/Edna.melt +share/EMBOSS/data/Eembl.ior share/EMBOSS/data/Eenergy.dat share/EMBOSS/data/Efeatures.embl share/EMBOSS/data/Efeatures.gff share/EMBOSS/data/Efreqs.dat share/EMBOSS/data/Ehth.dat share/EMBOSS/data/Ehth87.dat +share/EMBOSS/data/Ememe.dat share/EMBOSS/data/Enakai.dat share/EMBOSS/data/Epepcoil.dat share/EMBOSS/data/Epk.dat share/EMBOSS/data/Epprofile +share/EMBOSS/data/Eprior1.plib +share/EMBOSS/data/Eprior30.plib share/EMBOSS/data/Erna.melt share/EMBOSS/data/Esig.euk share/EMBOSS/data/Esig.pro @@ -666,12 +674,17 @@ share/doc/EMBOSS/programs/html/checktrans.html share/doc/EMBOSS/programs/html/chips.html share/doc/EMBOSS/programs/html/cirdna.html +share/doc/EMBOSS/programs/html/clique.html share/doc/EMBOSS/programs/html/codcmp.html +share/doc/EMBOSS/programs/html/coderet.html share/doc/EMBOSS/programs/html/coding_regions_group.html share/doc/EMBOSS/programs/html/comparison_group.html share/doc/EMBOSS/programs/html/complex.html share/doc/EMBOSS/programs/html/compseq.html share/doc/EMBOSS/programs/html/cons.html +share/doc/EMBOSS/programs/html/consense.html +share/doc/EMBOSS/programs/html/contml.html +share/doc/EMBOSS/programs/html/contrast.html share/doc/EMBOSS/programs/html/cpg_islands_group.html share/doc/EMBOSS/programs/html/cpgplot.html share/doc/EMBOSS/programs/html/cpgplot0.gif @@ -693,31 +706,67 @@ share/doc/EMBOSS/programs/html/dna_sequence_composition_group.html share/doc/EMBOSS/programs/html/dna_sequence_features_group.html share/doc/EMBOSS/programs/html/dna_sequence_properties_group.html +share/doc/EMBOSS/programs/html/dnacomp.html +share/doc/EMBOSS/programs/html/dnadist.html +share/doc/EMBOSS/programs/html/dnainvar.html +share/doc/EMBOSS/programs/html/dnaml.html +share/doc/EMBOSS/programs/html/dnamlk.html +share/doc/EMBOSS/programs/html/dnapars.html +share/doc/EMBOSS/programs/html/dnapenny.html +share/doc/EMBOSS/programs/html/dollop.html +share/doc/EMBOSS/programs/html/dolpenny.html share/doc/EMBOSS/programs/html/dotmatcher.html share/doc/EMBOSS/programs/html/dotmatcher0.gif share/doc/EMBOSS/programs/html/dotpath.html share/doc/EMBOSS/programs/html/dottup.html share/doc/EMBOSS/programs/html/dottup0.gif share/doc/EMBOSS/programs/html/dreg.html +share/doc/EMBOSS/programs/html/eclique.html +share/doc/EMBOSS/programs/html/econsense.html +share/doc/EMBOSS/programs/html/econtml.html +share/doc/EMBOSS/programs/html/econtrast.html +share/doc/EMBOSS/programs/html/ednacomp.html +share/doc/EMBOSS/programs/html/ednadist.html +share/doc/EMBOSS/programs/html/ednainvar.html +share/doc/EMBOSS/programs/html/ednaml.html +share/doc/EMBOSS/programs/html/ednamlk.html +share/doc/EMBOSS/programs/html/ednapars.html +share/doc/EMBOSS/programs/html/ednapenny.html +share/doc/EMBOSS/programs/html/edollop.html +share/doc/EMBOSS/programs/html/edolpenny.html +share/doc/EMBOSS/programs/html/efactor.html +share/doc/EMBOSS/programs/html/efitch.html +share/doc/EMBOSS/programs/html/egendist.html share/doc/EMBOSS/programs/html/einverted.html +share/doc/EMBOSS/programs/html/ekitsch.html share/doc/EMBOSS/programs/html/emboss_icon.gif share/doc/EMBOSS/programs/html/embossdata.html +share/doc/EMBOSS/programs/html/emix.html share/doc/EMBOSS/programs/html/emma.html share/doc/EMBOSS/programs/html/emowse.html +share/doc/EMBOSS/programs/html/eneighbor.html share/doc/EMBOSS/programs/html/entret.html share/doc/EMBOSS/programs/html/enzyme_kinetics_group.html +share/doc/EMBOSS/programs/html/epenny.html +share/doc/EMBOSS/programs/html/eprotdist.html +share/doc/EMBOSS/programs/html/eprotpars.html share/doc/EMBOSS/programs/html/equicktandem.html +share/doc/EMBOSS/programs/html/erestml.html +share/doc/EMBOSS/programs/html/eseqboot.html share/doc/EMBOSS/programs/html/est2genome.html share/doc/EMBOSS/programs/html/etandem.html share/doc/EMBOSS/programs/html/extractseq.html +share/doc/EMBOSS/programs/html/factor.html share/doc/EMBOSS/programs/html/findkm.html share/doc/EMBOSS/programs/html/findkm0.gif +share/doc/EMBOSS/programs/html/fitch.html share/doc/EMBOSS/programs/html/freak.html share/doc/EMBOSS/programs/html/fuzznuc.html share/doc/EMBOSS/programs/html/fuzzpro.html share/doc/EMBOSS/programs/html/fuzztran.html share/doc/EMBOSS/programs/html/garnier.html share/doc/EMBOSS/programs/html/geecee.html +share/doc/EMBOSS/programs/html/gendist.html share/doc/EMBOSS/programs/html/gene_finding_group.html share/doc/EMBOSS/programs/html/getorf.html share/doc/EMBOSS/programs/html/groups.html @@ -728,16 +777,20 @@ share/doc/EMBOSS/programs/html/infoseq.html share/doc/EMBOSS/programs/html/isochore.html share/doc/EMBOSS/programs/html/isochore0.gif +share/doc/EMBOSS/programs/html/kitsch.html share/doc/EMBOSS/programs/html/lindna.html share/doc/EMBOSS/programs/html/maskfeat.html share/doc/EMBOSS/programs/html/maskseq.html share/doc/EMBOSS/programs/html/matcher.html share/doc/EMBOSS/programs/html/megamerger.html share/doc/EMBOSS/programs/html/merger.html +share/doc/EMBOSS/programs/html/mix.html share/doc/EMBOSS/programs/html/motifs_group.html share/doc/EMBOSS/programs/html/msbar.html +share/doc/EMBOSS/programs/html/mse.html share/doc/EMBOSS/programs/html/mutation_group.html share/doc/EMBOSS/programs/html/needle.html +share/doc/EMBOSS/programs/html/neighbor.html share/doc/EMBOSS/programs/html/new_group_group.html share/doc/EMBOSS/programs/html/newcpgreport.html share/doc/EMBOSS/programs/html/newcpgseek.html @@ -752,6 +805,7 @@ share/doc/EMBOSS/programs/html/patmatdb.html share/doc/EMBOSS/programs/html/patmatmotifs.html share/doc/EMBOSS/programs/html/pattern_matching_group.html +share/doc/EMBOSS/programs/html/penny.html share/doc/EMBOSS/programs/html/pepcoil.html share/doc/EMBOSS/programs/html/pepinfo.html share/doc/EMBOSS/programs/html/pepinfo1.gif @@ -784,6 +838,7 @@ share/doc/EMBOSS/programs/html/prophecy.html share/doc/EMBOSS/programs/html/prophet.html share/doc/EMBOSS/programs/html/prosextract.html +share/doc/EMBOSS/programs/html/protdist.html share/doc/EMBOSS/programs/html/protein_sequence_composition_group.html share/doc/EMBOSS/programs/html/protein_sequence_features_group.html share/doc/EMBOSS/programs/html/protein_sequence_properties_group.html @@ -793,11 +848,13 @@ share/doc/EMBOSS/programs/html/reformatting_group.html share/doc/EMBOSS/programs/html/remap.html share/doc/EMBOSS/programs/html/repeats_group.html +share/doc/EMBOSS/programs/html/restml.html share/doc/EMBOSS/programs/html/restrict.html share/doc/EMBOSS/programs/html/restriction_enzymes_group.html share/doc/EMBOSS/programs/html/revseq.html share/doc/EMBOSS/programs/html/secondary_structure_group.html share/doc/EMBOSS/programs/html/seealso.html +share/doc/EMBOSS/programs/html/seqboot.html share/doc/EMBOSS/programs/html/seqmatchall.html share/doc/EMBOSS/programs/html/seqret.html share/doc/EMBOSS/programs/html/seqretall.html @@ -830,6 +887,8 @@ share/doc/EMBOSS/programs/html/tfscan.html share/doc/EMBOSS/programs/html/tmap.html share/doc/EMBOSS/programs/html/tmap0.gif +share/doc/EMBOSS/programs/html/topo.gif +share/doc/EMBOSS/programs/html/topo.html share/doc/EMBOSS/programs/html/transcription_group.html share/doc/EMBOSS/programs/html/transeq.html share/doc/EMBOSS/programs/html/translation_group.html @@ -853,10 +912,15 @@ share/doc/EMBOSS/programs/text/checktrans.txt share/doc/EMBOSS/programs/text/chips.txt share/doc/EMBOSS/programs/text/cirdna.txt +share/doc/EMBOSS/programs/text/clique.txt share/doc/EMBOSS/programs/text/codcmp.txt +share/doc/EMBOSS/programs/text/coderet.txt share/doc/EMBOSS/programs/text/complex.txt share/doc/EMBOSS/programs/text/compseq.txt share/doc/EMBOSS/programs/text/cons.txt +share/doc/EMBOSS/programs/text/consense.txt +share/doc/EMBOSS/programs/text/contml.txt +share/doc/EMBOSS/programs/text/contrast.txt share/doc/EMBOSS/programs/text/cpgplot.txt share/doc/EMBOSS/programs/text/cpgreport.txt share/doc/EMBOSS/programs/text/cusp.txt @@ -869,39 +933,79 @@ share/doc/EMBOSS/programs/text/descseq.txt share/doc/EMBOSS/programs/text/diffseq.txt share/doc/EMBOSS/programs/text/digest.txt +share/doc/EMBOSS/programs/text/dnacomp.txt +share/doc/EMBOSS/programs/text/dnadist.txt +share/doc/EMBOSS/programs/text/dnainvar.txt +share/doc/EMBOSS/programs/text/dnaml.txt +share/doc/EMBOSS/programs/text/dnamlk.txt +share/doc/EMBOSS/programs/text/dnapars.txt +share/doc/EMBOSS/programs/text/dnapenny.txt +share/doc/EMBOSS/programs/text/dollop.txt +share/doc/EMBOSS/programs/text/dolpenny.txt share/doc/EMBOSS/programs/text/dotmatcher.txt share/doc/EMBOSS/programs/text/dotpath.txt share/doc/EMBOSS/programs/text/dottup.txt share/doc/EMBOSS/programs/text/dreg.txt +share/doc/EMBOSS/programs/text/eclique.txt +share/doc/EMBOSS/programs/text/econsense.txt +share/doc/EMBOSS/programs/text/econtml.txt +share/doc/EMBOSS/programs/text/econtrast.txt +share/doc/EMBOSS/programs/text/ednacomp.txt +share/doc/EMBOSS/programs/text/ednadist.txt +share/doc/EMBOSS/programs/text/ednainvar.txt +share/doc/EMBOSS/programs/text/ednaml.txt +share/doc/EMBOSS/programs/text/ednamlk.txt +share/doc/EMBOSS/programs/text/ednapars.txt +share/doc/EMBOSS/programs/text/ednapenny.txt +share/doc/EMBOSS/programs/text/edollop.txt +share/doc/EMBOSS/programs/text/edolpenny.txt +share/doc/EMBOSS/programs/text/efactor.txt +share/doc/EMBOSS/programs/text/efitch.txt +share/doc/EMBOSS/programs/text/egendist.txt share/doc/EMBOSS/programs/text/einverted.txt +share/doc/EMBOSS/programs/text/ekitsch.txt share/doc/EMBOSS/programs/text/embossdata.txt +share/doc/EMBOSS/programs/text/emix.txt share/doc/EMBOSS/programs/text/emma.txt share/doc/EMBOSS/programs/text/emowse.txt +share/doc/EMBOSS/programs/text/eneighbor.txt share/doc/EMBOSS/programs/text/entret.txt +share/doc/EMBOSS/programs/text/epenny.txt +share/doc/EMBOSS/programs/text/eprotdist.txt +share/doc/EMBOSS/programs/text/eprotpars.txt share/doc/EMBOSS/programs/text/equicktandem.txt +share/doc/EMBOSS/programs/text/erestml.txt +share/doc/EMBOSS/programs/text/eseqboot.txt share/doc/EMBOSS/programs/text/est2genome.txt share/doc/EMBOSS/programs/text/etandem.txt share/doc/EMBOSS/programs/text/extractseq.txt +share/doc/EMBOSS/programs/text/factor.txt share/doc/EMBOSS/programs/text/findkm.txt +share/doc/EMBOSS/programs/text/fitch.txt share/doc/EMBOSS/programs/text/freak.txt share/doc/EMBOSS/programs/text/fuzznuc.txt share/doc/EMBOSS/programs/text/fuzzpro.txt share/doc/EMBOSS/programs/text/fuzztran.txt share/doc/EMBOSS/programs/text/garnier.txt share/doc/EMBOSS/programs/text/geecee.txt +share/doc/EMBOSS/programs/text/gendist.txt share/doc/EMBOSS/programs/text/getorf.txt share/doc/EMBOSS/programs/text/helixturnhelix.txt share/doc/EMBOSS/programs/text/iep.txt share/doc/EMBOSS/programs/text/infoseq.txt share/doc/EMBOSS/programs/text/isochore.txt +share/doc/EMBOSS/programs/text/kitsch.txt share/doc/EMBOSS/programs/text/lindna.txt share/doc/EMBOSS/programs/text/maskfeat.txt share/doc/EMBOSS/programs/text/maskseq.txt share/doc/EMBOSS/programs/text/matcher.txt share/doc/EMBOSS/programs/text/megamerger.txt share/doc/EMBOSS/programs/text/merger.txt +share/doc/EMBOSS/programs/text/mix.txt share/doc/EMBOSS/programs/text/msbar.txt +share/doc/EMBOSS/programs/text/mse.txt share/doc/EMBOSS/programs/text/needle.txt +share/doc/EMBOSS/programs/text/neighbor.txt share/doc/EMBOSS/programs/text/newcpgreport.txt share/doc/EMBOSS/programs/text/newcpgseek.txt share/doc/EMBOSS/programs/text/newseq.txt @@ -913,6 +1017,7 @@ share/doc/EMBOSS/programs/text/pasteseq.txt share/doc/EMBOSS/programs/text/patmatdb.txt share/doc/EMBOSS/programs/text/patmatmotifs.txt +share/doc/EMBOSS/programs/text/penny.txt share/doc/EMBOSS/programs/text/pepcoil.txt share/doc/EMBOSS/programs/text/pepinfo.txt share/doc/EMBOSS/programs/text/pepnet.txt @@ -933,13 +1038,16 @@ share/doc/EMBOSS/programs/text/prophecy.txt share/doc/EMBOSS/programs/text/prophet.txt share/doc/EMBOSS/programs/text/prosextract.txt +share/doc/EMBOSS/programs/text/protdist.txt share/doc/EMBOSS/programs/text/pscan.txt share/doc/EMBOSS/programs/text/rebaseextract.txt share/doc/EMBOSS/programs/text/redata.txt share/doc/EMBOSS/programs/text/remap.txt +share/doc/EMBOSS/programs/text/restml.txt share/doc/EMBOSS/programs/text/restrict.txt share/doc/EMBOSS/programs/text/revseq.txt share/doc/EMBOSS/programs/text/seealso.txt +share/doc/EMBOSS/programs/text/seqboot.txt share/doc/EMBOSS/programs/text/seqmatchall.txt share/doc/EMBOSS/programs/text/seqret.txt share/doc/EMBOSS/programs/text/seqretall.txt @@ -962,6 +1070,7 @@ share/doc/EMBOSS/programs/text/tfm.txt share/doc/EMBOSS/programs/text/tfscan.txt share/doc/EMBOSS/programs/text/tmap.txt +share/doc/EMBOSS/programs/text/topo.txt share/doc/EMBOSS/programs/text/transeq.txt share/doc/EMBOSS/programs/text/trimseq.txt share/doc/EMBOSS/programs/text/vectorstrip.txt >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail 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