Date: Mon, 7 May 2001 12:46:07 +0200 (SAST) From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/27179: Port update: biology/emboss (MAINTAINER) Message-ID: <200105071046.f47Ak7x03217@shuffle.egenetics.com>
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>Number: 27179 >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 May 07 03:50:01 PDT 2001 >Closed-Date: >Last-Modified: >Originator: Johann Visagie >Release: FreeBSD 5.0-CURRENT i386 >Organization: Electric Genetics >Environment: >Description: - Update the EMBOSS suite (biology/emboss) to version 1.12.0 (somewhat belatedly) >How-To-Repeat: >Fix: diff -ruN emboss.bak/Makefile emboss/Makefile --- emboss.bak/Makefile Mon May 7 12:36:56 2001 +++ emboss/Makefile Wed Apr 18 11:07:07 2001 @@ -6,7 +6,7 @@ # PORTNAME= emboss -PORTVERSION= 1.11.0 +PORTVERSION= 1.12.0 CATEGORIES= biology MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ ftp://ftp.no.embnet.org/pub/EMBOSS/ \ diff -ruN emboss.bak/distinfo emboss/distinfo --- emboss.bak/distinfo Mon May 7 12:36:56 2001 +++ emboss/distinfo Fri May 4 13:14:42 2001 @@ -1,5 +1,5 @@ -MD5 (emboss/EMBOSS-1.11.0.tar.gz) = b7376e98ea7d86eb4b5411013bd98dd3 +MD5 (emboss/EMBOSS-1.12.0.tar.gz) = 7d2d770dcc037624e5ee52c143c8923b MD5 (emboss/EMNU-1.0.4.tar.gz) = 6ebdf128e1b531911ff97d2b8d6a59d8 -MD5 (emboss/MSE-0.0.4.tar.gz) = 96f87f4f321e6c6d65793391971504a1 -MD5 (emboss/PHYLIP-3.573c.tar.gz) = d6062201d6492676c82f2b7b8e9d8c95 -MD5 (emboss/TOPO-0.1.tar.gz) = ab3ff940e689d044476528b47e983184 +MD5 (emboss/MSE-0.0.4.tar.gz) = f490638c4f0b789d0c1117513406d76a +MD5 (emboss/PHYLIP-3.573c.tar.gz) = 4a4fff45f4a51a430731a46f3f37f37f +MD5 (emboss/TOPO-0.1.tar.gz) = fa1a85bfde1054136af5aa9587c2433f diff -ruN emboss.bak/pkg-plist emboss/pkg-plist --- emboss.bak/pkg-plist Mon May 7 12:36:56 2001 +++ emboss/pkg-plist Mon May 7 11:15:51 2001 @@ -62,6 +62,7 @@ bin/backtranseq bin/banana bin/btwisted +bin/cai bin/chaos bin/charge bin/checktrans @@ -84,6 +85,7 @@ bin/descseq bin/diffseq bin/digest +bin/distmat bin/domainer bin/dotmatcher bin/dotpath @@ -161,6 +163,7 @@ bin/restover bin/restrict bin/revseq +bin/scopalign bin/scope bin/seealso bin/seqmatchall @@ -215,6 +218,7 @@ share/EMBOSS/acd/backtranseq.acd share/EMBOSS/acd/banana.acd share/EMBOSS/acd/btwisted.acd +share/EMBOSS/acd/cai.acd share/EMBOSS/acd/chaos.acd share/EMBOSS/acd/charge.acd share/EMBOSS/acd/checktrans.acd @@ -738,134 +742,27 @@ share/EMBOSS/test/wormpep/division.lkp share/EMBOSS/test/wormpep/entrynam.idx share/EMBOSS/test/wormpep/wormpep +share/doc/EMBOSS/manuals/EMBOSS-FreeBSD-HOWTO.txt +share/doc/EMBOSS/manuals/admin.aux +share/doc/EMBOSS/manuals/admin.dvi +share/doc/EMBOSS/manuals/admin.log +share/doc/EMBOSS/manuals/admin.pdf +share/doc/EMBOSS/manuals/admin.ps share/doc/EMBOSS/manuals/admin.sty share/doc/EMBOSS/manuals/admin.tex +share/doc/EMBOSS/manuals/admin.toc +share/doc/EMBOSS/manuals/adminguide.tar.gz +share/doc/EMBOSS/manuals/emboss_qg.pdf +share/doc/EMBOSS/manuals/emboss_qg.ps share/doc/EMBOSS/manuals/program.ps.gz -share/doc/EMBOSS/programs/html/SITE-DIRECTED.html -share/doc/EMBOSS/programs/html/abi_trace_files_group.html -share/doc/EMBOSS/programs/html/abiview.html share/doc/EMBOSS/programs/html/abiview0.gif -share/doc/EMBOSS/programs/html/alignment_global_group.html -share/doc/EMBOSS/programs/html/alignment_group.html -share/doc/EMBOSS/programs/html/alignment_local_group.html -share/doc/EMBOSS/programs/html/alignment_multiple_group.html -share/doc/EMBOSS/programs/html/antigenic.html -share/doc/EMBOSS/programs/html/assorted_group.html -share/doc/EMBOSS/programs/html/backtranseq.html -share/doc/EMBOSS/programs/html/banana.html share/doc/EMBOSS/programs/html/banana0.gif -share/doc/EMBOSS/programs/html/btwisted.html -share/doc/EMBOSS/programs/html/chaos.html share/doc/EMBOSS/programs/html/chaos0.gif -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 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-share/doc/EMBOSS/programs/html/dbifasta.html -share/doc/EMBOSS/programs/html/dbiflat.html -share/doc/EMBOSS/programs/html/dbigcg.html -share/doc/EMBOSS/programs/html/degapseq.html -share/doc/EMBOSS/programs/html/descseq.html -share/doc/EMBOSS/programs/html/diffseq.html -share/doc/EMBOSS/programs/html/digest.html -share/doc/EMBOSS/programs/html/display_alignment_multiple_group.html -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/domainer.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/emnu.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 -share/doc/EMBOSS/programs/html/helixturnhelix.html -share/doc/EMBOSS/programs/html/hydropathy_group.html -share/doc/EMBOSS/programs/html/iep.html -share/doc/EMBOSS/programs/html/index.html -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/marscan.html share/doc/EMBOSS/programs/html/maskfeat.html @@ -890,7 +787,6 @@ share/doc/EMBOSS/programs/html/nrscope.html share/doc/EMBOSS/programs/html/nthseq.html share/doc/EMBOSS/programs/html/octanol.html -share/doc/EMBOSS/programs/html/octanol0.gif share/doc/EMBOSS/programs/html/oddcomp.html share/doc/EMBOSS/programs/html/palindrome.html share/doc/EMBOSS/programs/html/pasteseq.html @@ -900,26 +796,17 @@ 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 -share/doc/EMBOSS/programs/html/pepinfo2.gif share/doc/EMBOSS/programs/html/pepnet.html -share/doc/EMBOSS/programs/html/pepnet0.gif share/doc/EMBOSS/programs/html/pepstats.html share/doc/EMBOSS/programs/html/pepwheel.html -share/doc/EMBOSS/programs/html/pepwheel0.gif share/doc/EMBOSS/programs/html/pepwindow.html -share/doc/EMBOSS/programs/html/pepwindow0.gif share/doc/EMBOSS/programs/html/pepwindowall.html -share/doc/EMBOSS/programs/html/pepwindowall0.gif +share/doc/EMBOSS/programs/html/phylogeny_group.html share/doc/EMBOSS/programs/html/plotcon.html share/doc/EMBOSS/programs/html/plotorf.html -share/doc/EMBOSS/programs/html/plotorf0.gif share/doc/EMBOSS/programs/html/polydot.html -share/doc/EMBOSS/programs/html/polydot0.gif share/doc/EMBOSS/programs/html/preg.html share/doc/EMBOSS/programs/html/prettyplot.html -share/doc/EMBOSS/programs/html/prettyplot3.gif -share/doc/EMBOSS/programs/html/prettyplot4.gif share/doc/EMBOSS/programs/html/prettyseq.html share/doc/EMBOSS/programs/html/prima.html share/doc/EMBOSS/programs/html/primers_group.html @@ -976,16 +863,12 @@ share/doc/EMBOSS/programs/html/stssearch.html share/doc/EMBOSS/programs/html/supermatcher.html share/doc/EMBOSS/programs/html/syco.html -share/doc/EMBOSS/programs/html/syco0.gif -share/doc/EMBOSS/programs/html/syco1.gif share/doc/EMBOSS/programs/html/text_search_group.html share/doc/EMBOSS/programs/html/textsearch.html share/doc/EMBOSS/programs/html/tfextract.html share/doc/EMBOSS/programs/html/tfm.html 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 @@ -997,7 +880,6 @@ share/doc/EMBOSS/programs/html/vectorstrip.html share/doc/EMBOSS/programs/html/water.html share/doc/EMBOSS/programs/html/wobble.html -share/doc/EMBOSS/programs/html/wobble0.gif share/doc/EMBOSS/programs/html/wordcount.html share/doc/EMBOSS/programs/html/wordmatch.html share/doc/EMBOSS/programs/html/wossname.html @@ -1007,7 +889,9 @@ share/doc/EMBOSS/programs/text/backtranseq.txt share/doc/EMBOSS/programs/text/banana.txt share/doc/EMBOSS/programs/text/btwisted.txt +share/doc/EMBOSS/programs/text/cai.txt share/doc/EMBOSS/programs/text/chaos.txt +share/doc/EMBOSS/programs/text/charge.txt share/doc/EMBOSS/programs/text/checktrans.txt share/doc/EMBOSS/programs/text/chips.txt share/doc/EMBOSS/programs/text/cirdna.txt @@ -1033,6 +917,7 @@ 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/distmat.txt share/doc/EMBOSS/programs/text/dnacomp.txt share/doc/EMBOSS/programs/text/dnadist.txt share/doc/EMBOSS/programs/text/dnainvar.txt @@ -1093,6 +978,7 @@ 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/hmoment.txt share/doc/EMBOSS/programs/text/iep.txt share/doc/EMBOSS/programs/text/infoseq.txt share/doc/EMBOSS/programs/text/isochore.txt @@ -1189,6 +1075,7 @@ share/doc/EMBOSS/programs/text/wossname.txt share/doc/EMBOSS/tutorials/biblio.bib share/doc/EMBOSS/tutorials/dottup.ps.gz +share/doc/EMBOSS/tutorials/emboss-talk.ppt share/doc/EMBOSS/tutorials/emboss_tutorial.tex share/doc/EMBOSS/tutorials/pepinfo1.ps.gz share/doc/EMBOSS/tutorials/pepinfo2.ps.gz >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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