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Date:      Sun, 6 Apr 2008 19:46:25 -0000
From:      "wenheping@gmail.com" <wenheping@gmail.com>
To:        "FreeBSD gnats submit" <FreeBSD-gnats-submit@FreeBSD.org>
Subject:   ports/122490: [Update] biology/emboss: update to 5.0.0
Message-ID:  <1207511185.30413@fb7.wenjing.com>
Resent-Message-ID: <200804061420.m36EK0GU026845@freefall.freebsd.org>

---

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>Number:         122490
>Category:       ports
>Synopsis:       [Update] biology/emboss: update to 5.0.0
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Sun Apr 06 14:20:00 UTC 2008
>Closed-Date:
>Last-Modified:
>Originator:     wenheping@gmail.com
>Release:        FreeBSD 7.0-RELEASE i386
>Organization:
ChangAn Middle School 
>Environment:


System: FreeBSD 7.0-RELEASE #0: Sun Feb 24 19:59:52 UTC 2008
    root@logan.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC



>Description:


update emboss to 5.0.0 to 3.0.0


>How-To-Repeat:





>Fix:


--- emboss.diff.txt begins here ---
--- Makefile.orig	2008-04-02 16:29:38.000000000 +0000
+++ Makefile	2008-04-06 19:09:34.000000000 +0000
@@ -6,13 +6,10 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	3.0.0
+PORTVERSION=	5.0.0
 PORTREVISION=	2
 CATEGORIES=	biology
-MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/ \
-		ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
-		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
-		ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
+MASTER_SITES=	SF
 DISTNAME=	${PORTNAME:U}-${PORTVERSION}
 DISTFILES=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
 DIST_SUBDIR=	${PORTNAME}
@@ -33,7 +30,7 @@
 USE_GMAKE=	yes
 GNU_CONFIGURE=	yes
 USE_AUTOTOOLS=	libtool:15
-INSTALLS_SHLIB=	yes
+USE_LDCONFIG=	yes
 USE_MOTIF=	yes
 SUB_FILES=	pkg-message
 SUB_LIST=	PREFIX=${PREFIX} DATADIR=${DATADIR}
--- distinfo.orig	2006-03-31 09:43:20.000000000 +0000
+++ distinfo	2008-04-06 14:05:43.000000000 +0000
@@ -1,3 +1,3 @@
-MD5 (emboss/EMBOSS-3.0.0.tar.gz) = fa72feded9ab9272e3e731c09f545dcc
-SHA256 (emboss/EMBOSS-3.0.0.tar.gz) = 47a51ba7aeb9f6e7f4cd23c28cffad7c6d28432e92f37d6f08121791ef894dea
-SIZE (emboss/EMBOSS-3.0.0.tar.gz) = 16257908
+MD5 (emboss/EMBOSS-5.0.0.tar.gz) = be4c895220ad34afd65d450ba7d8e34b
+SHA256 (emboss/EMBOSS-5.0.0.tar.gz) = 64e6f09b82a719ff26de7f21fdf7d2bd605d2c664384c1c7b48f9d245d5f40ae
+SIZE (emboss/EMBOSS-5.0.0.tar.gz) = 20666560
--- pkg-plist.orig	2006-03-31 09:43:20.000000000 +0000
+++ pkg-plist	2008-04-06 19:07:06.000000000 +0000
@@ -6,6 +6,7 @@
 bin/acdtrace
 bin/acdvalid
 bin/antigenic
+bin/backtranambig
 bin/backtranseq
 bin/banana
 bin/biosed
@@ -25,8 +26,8 @@
 bin/cpgreport
 bin/cusp
 bin/cutgextract
-bin/dan
 bin/cutseq
+bin/dan
 bin/dbiblast
 bin/dbifasta
 bin/dbiflat
@@ -43,6 +44,7 @@
 bin/dotpath
 bin/dottup
 bin/dreg
+bin/edialign
 bin/einverted
 bin/embossdata
 bin/embossversion
@@ -54,6 +56,7 @@
 bin/equicktandem
 bin/est2genome
 bin/etandem
+bin/extractalign
 bin/extractfeat
 bin/extractseq
 bin/findkm
@@ -73,6 +76,8 @@
 bin/jembossctl
 bin/lindna
 bin/listor
+bin/makenucseq
+bin/makeprotseq
 bin/marscan
 bin/maskfeat
 bin/maskseq
@@ -123,6 +128,7 @@
 bin/restover
 bin/restrict
 bin/revseq
+bin/runJemboss.csh
 bin/seealso
 bin/seqmatchall
 bin/seqret
@@ -138,11 +144,11 @@
 bin/sirna
 bin/sixpack
 bin/skipseq
-bin/syco
 bin/splitter
 bin/stretcher
 bin/stssearch
 bin/supermatcher
+bin/syco
 bin/tcode
 bin/textsearch
 bin/tfextract
@@ -160,34 +166,23 @@
 bin/whichdb
 bin/wobble
 bin/wordcount
+bin/wordfinder
 bin/wordmatch
 bin/wossname
 bin/yank
-bin/runJemboss.csh
-include/drivers.h
-include/pdf.h
-include/plcore.h
-include/plevent.h
-include/plplotP.h
-include/plxwd.h
-include/metadefs.h
-include/plConfig.h
-include/pldebug.h
-include/plplot.h
-include/plstrm.h
-include/plDevs.h
-include/ajax.h
-include/ajarch.h
-include/ajdefine.h
 include/ajacd.h
 include/ajalign.h
+include/ajarch.h
 include/ajarr.h
 include/ajassert.h
+include/ajax.h
 include/ajbase.h
 include/ajcall.h
 include/ajcod.h
 include/ajdan.h
+include/ajdefine.h
 include/ajdmx.h
+include/ajdom.h
 include/ajdomain.h
 include/ajexcept.h
 include/ajfeat.h
@@ -195,8 +190,8 @@
 include/ajfile.h
 include/ajfmt.h
 include/ajgraph.h
-include/ajgraphxml.h
 include/ajgraphstruct.h
+include/ajgraphxml.h
 include/ajhist.h
 include/ajindex.h
 include/ajjava.h
@@ -207,6 +202,7 @@
 include/ajmess.h
 include/ajnam.h
 include/ajnexus.h
+include/ajpat.h
 include/ajpdb.h
 include/ajpdbio.h
 include/ajphylo.h
@@ -229,14 +225,6 @@
 include/ajtree.h
 include/ajutil.h
 include/ajvector.h
-include/pcre.h
-include/pcre_chartables.c
-include/pcre_config.h
-include/pcre_get.c
-include/pcre_printint.c
-include/pcre_internal.h
-include/pcreposix.h
-include/emboss.h
 include/embaln.h
 include/embcom.h
 include/embcons.h
@@ -254,1818 +242,1604 @@
 include/embmisc.h
 include/embmol.h
 include/embnmer.h
+include/emboss.h
 include/embpat.h
-include/embprop.h
+include/embpatlist.h
 include/embpdb.h
+include/embprop.h
 include/embread.h
-include/embsig.h
 include/embshow.h
+include/embsig.h
 include/embword.h
-lib/libplplot.so.5
-lib/libplplot.so
-lib/libplplot.la
-lib/libplplot.a
-lib/libajax.so.3
-lib/libajax.so
-lib/libajax.la
+include/eplplot/disptab.h
+include/eplplot/drivers.h
+include/eplplot/metadefs.h
+include/eplplot/pdf.h
+include/eplplot/plConfig.h
+include/eplplot/plDevs.h
+include/eplplot/plcore.h
+include/eplplot/pldebug.h
+include/eplplot/pldll.h
+include/eplplot/plevent.h
+include/eplplot/plfci-type1.h
+include/eplplot/plhershey-unicode.h
+include/eplplot/plplot.h
+include/eplplot/plplotP.h
+include/eplplot/plstrm.h
+include/eplplot/plunicode-type1.h
+include/eplplot/plxwd.h
+include/eplplot/ps.h
+include/pcre.h
+include/pcre_chartables.c
+include/pcre_config.h
+include/pcre_get.c
+include/pcre_internal.h
+include/pcre_printint.c
+include/pcreposix.h
 lib/libajax.a
-lib/libajaxg.so.3
-lib/libajaxg.so
-lib/libajaxg.la
+lib/libajax.la
+lib/libajax.so
+lib/libajax.so.5
 lib/libajaxg.a
-lib/libnucleus.so.3
-lib/libnucleus.so
-lib/libnucleus.la
+lib/libajaxg.la
+lib/libajaxg.so
+lib/libajaxg.so.5
+lib/libeplplot.a
+lib/libeplplot.la
+lib/libeplplot.so
+lib/libeplplot.so.5
 lib/libnucleus.a
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.sty
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.tex
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.aux
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.dvi
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.log
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.pdf
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.ps
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.toc
-%%PORTDOCS%%%%DOCSDIR%%/manuals/adminguide.tar.gz
-%%PORTDOCS%%%%DOCSDIR%%/manuals/domainatrix.doc
-%%PORTDOCS%%%%DOCSDIR%%/manuals/program.ps.gz
-%%PORTDOCS%%%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.pdf
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.ps
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss.sty
-%%PORTDOCS%%%%DOCSDIR%%/manuals/fdl.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/listor.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/marscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskfeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/matcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/matgen3d.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/megamerger.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/meme.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/menus_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/merger.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/msbar.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwcontam.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwfilter.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/myseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalignrunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/needle.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/needlerunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgreport.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgseek.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/noreturn.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/notseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nthseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_2d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_composition_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_cpg_islands_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_gene_finding_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_motifs_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_mutation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_primers_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_profiles_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_repeats_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_restriction_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_transcription_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_translation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/oddcomp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/palindrome.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pasteseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatdb.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatmotifs.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbparse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbplus.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbtosp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepcoil.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepstats.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_consensus_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_continuous_characters_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_discrete_characters_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_distance_matrix_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_gene_frequencies_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_molecular_sequence_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_tree_drawing_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/preg.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/primersearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/printsextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/profit.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophecy.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophet.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prosextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_2d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_3d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_composition_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_motifs_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_mutation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_profiles_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_sequence_alignment_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/psiphi.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rebaseextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/recoder.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/redata.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/remap.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restover.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restrict.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/revseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocon.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocplot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scope.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scopparse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorecmapdir.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorer.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorerrunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seealso.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqfraggle.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqmatchall.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqnr.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqret.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqretsplit.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsort.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqwords.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showdb.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showfeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showorf.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/shuffleseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigcleave.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggen.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggenlig.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscanlig.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/silent.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sirna.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sites.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sixpack.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/skipseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/splitter.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ssematch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/stretcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/stssearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/substitute.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/substituterunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/supermatcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tcode.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/template.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/test_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/textsearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfm.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tranalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/transeq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimest.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/twofeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/union.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_creation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_indexing_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_misc_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/vectorstrip.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/water.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/whichdb.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordcount.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordmatch.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/chaos.1.chaos.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cirdna.1.cirdna.gif
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdc.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdlog.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/acdpretty.html
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+@dirrm share/EMBOSS/test/pir
+@dirrm share/EMBOSS/test/genbank
+@dirrm share/EMBOSS/test/embl
+@dirrm share/EMBOSS/test/data
+@dirrm share/EMBOSS/test
+@dirrm share/EMBOSS/jemboss/utils
+@dirrm share/EMBOSS/jemboss/resources
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/soap
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/server
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/programs
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/parser
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/startup
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/sequenceChooser
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/form
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/graphics
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/editor
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/draw
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss
+@dirrm share/EMBOSS/jemboss/org/emboss
+@dirrm share/EMBOSS/jemboss/org
+@dirrm share/EMBOSS/jemboss/lib/axis
+@dirrm share/EMBOSS/jemboss/lib
+@dirrm share/EMBOSS/jemboss/images
+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/soap
+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/programs
+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/acd
+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser
+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/startup
+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/sequenceChooser
+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form
+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/filetree
+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui
+@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss
+@dirrm share/EMBOSS/jemboss/api/org/emboss
+@dirrm share/EMBOSS/jemboss/api/org
+@dirrm share/EMBOSS/jemboss/api
+@dirrm share/EMBOSS/jemboss
+@dirrm share/EMBOSS/data/REBASE
+@dirrm share/EMBOSS/data/PROSITE
+@dirrm share/EMBOSS/data/PRINTS
+@dirrm share/EMBOSS/data/CODONS
+@dirrm share/EMBOSS/data/AAINDEX
+@dirrm share/EMBOSS/data
+@dirrm share/EMBOSS/acd
+@dirrm share/EMBOSS
+@dirrm include/eplplot
Only in files.orig: patch-ajindex.c
Only in files.orig: patch-ajindex.h
Only in files.orig: patch-ajpdb.c
Only in files.orig: patch-ajseqdb.c
Only in files.orig: patch-dbxfasta.c
Only in files.orig: patch-dbxflat.c
Only in files.orig: patch-dbxgcg.c
Only in files.orig: patch-embindex.c
Only in files.orig: patch-embindex.h
Only in files.orig: patch-emboss.default.template
Only in files.orig: patch-marscan.c
Only in files.orig: pre-install.in
--- emboss.diff.txt ends here ---



>Release-Note:
>Audit-Trail:
>Unformatted:

---

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