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wip clean-up: remove emboss packages
Module Name: pkgsrc-wip
Committed By: pin <voidpin%protonmail.com@localhost>
Pushed By: pin
Date: Sat Jul 2 15:51:58 2022 +0200
Changeset: 8444c980add39af82a176852c486b85fadeb020b
Modified Files:
Makefile
Removed Files:
emboss-base/DESCR
emboss-base/MESSAGE
emboss-base/Makefile
emboss-base/Makefile.common
emboss-base/PLIST
emboss-base/TODO
emboss-base/buildlink3.mk
emboss-base/distinfo
emboss-base/files/digestchange
emboss-base/patches/patch-aa
emboss-base/patches/patch-ab
emboss-base/patches/patch-ac
emboss-base/patches/patch-ad
emboss-base/patches/patch-ae
emboss-base/patches/patch-af
emboss-base/patches/patch-ag
emboss-base/patches/patch-ah
emboss-base/patches/patch-ai
emboss-base/patches/patch-aj
emboss-base/patches/patch-ak
emboss-base/patches/patch-al
emboss-domainatrix/DESCR
emboss-domainatrix/Makefile
emboss-domainatrix/PLIST
emboss-domainatrix/distinfo
emboss-domainatrix/patches/patch-aa
emboss-domainatrix/patches/patch-ab
emboss-emnu/DESCR
emboss-emnu/Makefile
emboss-emnu/PLIST
emboss-emnu/distinfo
emboss-emnu/patches/patch-aa
emboss-emnu/patches/patch-ab
emboss-emnu/patches/patch-ac
emboss-hmmer/DESCR
emboss-hmmer/Makefile
emboss-hmmer/PLIST
emboss-hmmer/distinfo
emboss-hmmer/patches/patch-aa
emboss-hmmer/patches/patch-ab
emboss-hmmer/patches/patch-ac
emboss-java/DESCR
emboss-java/MESSAGE
emboss-java/Makefile
emboss-java/PLIST
emboss-java/distinfo
emboss-meme/DESCR
emboss-meme/Makefile
emboss-meme/PLIST
emboss-meme/distinfo
emboss-meme/patches/patch-aa
emboss-meme/patches/patch-ab
emboss-meme/patches/patch-ac
emboss-mse/DESCR
emboss-mse/Makefile
emboss-mse/PLIST
emboss-mse/distinfo
emboss-mse/patches/patch-aa
emboss-mse/patches/patch-ab
emboss-mse/patches/patch-ac
emboss-mse/patches/patch-ad
emboss-mse/patches/patch-ae
emboss-phylip/DESCR
emboss-phylip/Makefile
emboss-phylip/PLIST
emboss-phylip/distinfo
emboss-phylip/patches/patch-aa
emboss-phylip/patches/patch-ab
emboss-topo/DESCR
emboss-topo/Makefile
emboss-topo/PLIST
emboss-topo/distinfo
emboss-topo/patches/patch-aa
emboss-topo/patches/patch-ab
emboss/DESCR
emboss/Makefile
emboss/Makefile.common
emboss/NOTES
emboss/PLIST
emboss/distinfo
Log Message:
wip clean-up: remove emboss packages
Dead upstream, latest release 2013.
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=8444c980add39af82a176852c486b85fadeb020b
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 10 -
emboss-base/DESCR | 10 -
emboss-base/MESSAGE | 14 -
emboss-base/Makefile | 37 -
emboss-base/Makefile.common | 37 -
emboss-base/PLIST | 1446 -----------------------------------
emboss-base/TODO | 1 -
emboss-base/buildlink3.mk | 12 -
emboss-base/distinfo | 17 -
emboss-base/files/digestchange | 126 ---
emboss-base/patches/patch-aa | 22 -
emboss-base/patches/patch-ab | 57 --
emboss-base/patches/patch-ac | 12 -
emboss-base/patches/patch-ad | 99 ---
emboss-base/patches/patch-ae | 22 -
emboss-base/patches/patch-af | 13 -
emboss-base/patches/patch-ag | 13 -
emboss-base/patches/patch-ah | 10 -
emboss-base/patches/patch-ai | 13 -
emboss-base/patches/patch-aj | 19 -
emboss-base/patches/patch-ak | 22 -
emboss-base/patches/patch-al | 88 ---
emboss-domainatrix/DESCR | 1 -
emboss-domainatrix/Makefile | 28 -
emboss-domainatrix/PLIST | 53 --
emboss-domainatrix/distinfo | 7 -
emboss-domainatrix/patches/patch-aa | 13 -
emboss-domainatrix/patches/patch-ab | 42 -
emboss-emnu/DESCR | 1 -
emboss-emnu/Makefile | 34 -
emboss-emnu/PLIST | 3 -
emboss-emnu/distinfo | 8 -
emboss-emnu/patches/patch-aa | 13 -
emboss-emnu/patches/patch-ab | 22 -
emboss-emnu/patches/patch-ac | 53 --
emboss-hmmer/DESCR | 2 -
emboss-hmmer/Makefile | 23 -
emboss-hmmer/PLIST | 22 -
emboss-hmmer/distinfo | 8 -
emboss-hmmer/patches/patch-aa | 13 -
emboss-hmmer/patches/patch-ab | 34 -
emboss-hmmer/patches/patch-ac | 302 --------
emboss-java/DESCR | 3 -
emboss-java/MESSAGE | 7 -
emboss-java/Makefile | 54 --
emboss-java/PLIST | 2 -
emboss-java/distinfo | 5 -
emboss-meme/DESCR | 1 -
emboss-meme/Makefile | 23 -
emboss-meme/PLIST | 4 -
emboss-meme/distinfo | 8 -
emboss-meme/patches/patch-aa | 22 -
emboss-meme/patches/patch-ab | 13 -
emboss-meme/patches/patch-ac | 55 --
emboss-mse/DESCR | 2 -
emboss-mse/Makefile | 34 -
emboss-mse/PLIST | 4 -
emboss-mse/distinfo | 10 -
emboss-mse/patches/patch-aa | 22 -
emboss-mse/patches/patch-ab | 22 -
emboss-mse/patches/patch-ac | 22 -
emboss-mse/patches/patch-ad | 13 -
emboss-mse/patches/patch-ae | 59 --
emboss-phylip/DESCR | 2 -
emboss-phylip/Makefile | 25 -
emboss-phylip/PLIST | 49 --
emboss-phylip/distinfo | 7 -
emboss-phylip/patches/patch-aa | 30 -
emboss-phylip/patches/patch-ab | 33 -
emboss-topo/DESCR | 2 -
emboss-topo/Makefile | 23 -
emboss-topo/PLIST | 3 -
emboss-topo/distinfo | 7 -
emboss-topo/patches/patch-aa | 22 -
emboss-topo/patches/patch-ab | 72 --
emboss/DESCR | 10 -
emboss/Makefile | 31 -
emboss/Makefile.common | 13 -
emboss/NOTES | 1 -
emboss/PLIST | 1 -
emboss/distinfo | 1 -
81 files changed, 3499 deletions(-)
diffs:
diff --git a/Makefile b/Makefile
index 3ca31f1cdf..0cf75e37d4 100644
--- a/Makefile
+++ b/Makefile
@@ -769,16 +769,6 @@ SUBDIR+= emacs-pr-el
SUBDIR+= emacs-session
SUBDIR+= emacs-snapshot
SUBDIR+= emacs-w3m-cvs
-SUBDIR+= emboss
-SUBDIR+= emboss-base
-SUBDIR+= emboss-domainatrix
-SUBDIR+= emboss-emnu
-SUBDIR+= emboss-hmmer
-SUBDIR+= emboss-java
-SUBDIR+= emboss-meme
-SUBDIR+= emboss-mse
-SUBDIR+= emboss-phylip
-SUBDIR+= emboss-topo
SUBDIR+= emerald
SUBDIR+= emerald-themes
SUBDIR+= emirror
diff --git a/emboss-base/DESCR b/emboss-base/DESCR
deleted file mode 100644
index ea029c82f0..0000000000
--- a/emboss-base/DESCR
+++ /dev/null
@@ -1,10 +0,0 @@
-EMBOSS stands for "The European Molecular Biology Open Software Suite"
-and is a new, free Open Source software analysis package specially
-developed for the needs of the molecular biology (e.g. EMBnet) user
-community. The software automatically copes with data in a variety of
-formats and even allows transparent retrieval of sequence data from
-the web. Also, as extensive libraries are provided with the package,
-it is a platform to allow other scientists to develop and release
-software in true open source spirit. EMBOSS also integrates a
-range of currently available packages and tools for sequence analysis
-into a seamless whole.
diff --git a/emboss-base/MESSAGE b/emboss-base/MESSAGE
deleted file mode 100644
index a64d8b1ccf..0000000000
--- a/emboss-base/MESSAGE
+++ /dev/null
@@ -1,14 +0,0 @@
-===========================================================================
-$NetBSD: MESSAGE,v 1.2 2004/12/10 22:02:12 daprice Exp $
-
- You may want to add the following in your .cshrc and .profile to run this
- package correctly:
-
- (.cshrc)
- setenv EMBOSS_DATA ${PREFIX}/share/EMBOSS/data
- setenv EMBOSS_ACDROOT ${PREFIX}/share/EMBOSS/acd
-
- (.profile)
- EMBOSS_DATA=${PREFIX}/share/EMBOSS/data export EMBOSS_DATA;
- EMBOSS_ACDROOT=${PREFIX}/share/EMBOSS/acd export EMBOSS_ACDROOT;
-===========================================================================
diff --git a/emboss-base/Makefile b/emboss-base/Makefile
deleted file mode 100644
index ad0b6d81d6..0000000000
--- a/emboss-base/Makefile
+++ /dev/null
@@ -1,37 +0,0 @@
-# $NetBSD: Makefile,v 1.7 2011/10/26 13:48:59 noud4 Exp $
-
-.include "Makefile.common"
-DISTNAME= EMBOSS-2.9.0
-PKGNAME= emboss-base-2.9.0
-PKGREVISION= 2
-
-COMMENT= European Molecular Biology Open Software Suite
-LICENSE= gnu-gpl-v2
-
-DIST_SUBDIR= emboss/emboss-2.9.0
-
-post-extract:
- ${CP} ${FILESDIR}/digestchange ${WRKSRC}/digestchange
-post-patch:
- ${SH} ${WRKSRC}/digestchange ${WRKSRC}
- ${MV} ${WRKSRC}/doc/programs/text/digest.txt ${WRKSRC}/doc/programs/text/edigest.txt
- ${MV} ${WRKSRC}/doc/programs/html/digest.html ${WRKSRC}/doc/programs/html/edigest.html
- ${MV} ${WRKSRC}/emboss/digest.c ${WRKSRC}/emboss/edigest.c
- ${MV} ${WRKSRC}/emboss/acd/digest.acd ${WRKSRC}/emboss/acd/edigest.acd
- ${RM} -rf ${WRKSRC}/jemboss
-
-post-install:
- ${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/include/emboss
- ${INSTALL_DATA} ${WRKSRC}/ajax/*.h ${DESTDIR}${PREFIX}/include/emboss
- ${INSTALL_DATA} ${WRKSRC}/nucleus/*.h ${DESTDIR}${PREFIX}/include/emboss
- ${INSTALL_DATA} ${WRKSRC}/plplot/*.h ${DESTDIR}${PREFIX}/include/emboss
- ${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/EMBOSS/scripts
- ${INSTALL_DATA} ${WRKSRC}/plplot/lib/plstnd5.fnt ${DESTDIR}${PREFIX}/share/EMBOSS
- ${INSTALL_DATA} ${WRKSRC}/plplot/lib/plxtnd5.fnt ${DESTDIR}${PREFIX}/share/EMBOSS
- ${INSTALL_DATA} ${WRKSRC}/config.guess ${DESTDIR}${PREFIX}/share/EMBOSS/scripts
- ${INSTALL_DATA} ${WRKSRC}/config.sub ${DESTDIR}${PREFIX}/share/EMBOSS/scripts
- ${INSTALL_DATA} ${WRKSRC}/depcomp ${DESTDIR}${PREFIX}/share/EMBOSS/scripts
- ${INSTALL_DATA} ${WRKSRC}/install-sh ${DESTDIR}${PREFIX}/share/EMBOSS/scripts
- ${INSTALL_DATA} ${WRKSRC}/mkinstalldirs ${DESTDIR}${PREFIX}/share/EMBOSS/scripts
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/emboss-base/Makefile.common b/emboss-base/Makefile.common
deleted file mode 100644
index 375d563f3d..0000000000
--- a/emboss-base/Makefile.common
+++ /dev/null
@@ -1,37 +0,0 @@
-# $NetBSD: Makefile.common,v 1.13 2012/11/23 22:33:30 othyro Exp $
-# used by wip/emboss-domainatrix/Makefile
-# used by wip/emboss-emnu/Makefile
-# used by wip/emboss-hmmer/Makefile
-# used by wip/emboss-meme/Makefile
-# used by wip/emboss-mse/Makefile
-# used by wip/emboss-phylip/Makefile
-# used by wip/emboss-topo/Makefile
-
-CATEGORIES= biology
-MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/old/2.9.0/
-
-MAINTAINER= dprice%cs.nmsu.edu@localhost
-HOMEPAGE= http://emboss.sourceforge.net/
-
-USE_PKGLOCALEDIR= yes
-USE_LIBTOOL= yes
-GNU_CONFIGURE= yes
-
-CONFIGURE_ARGS+= --bindir=${PREFIX}/bin
-CONFIGURE_ARGS+= --libdir=${PREFIX}/lib
-CONFIGURE_ARGS+= --includedir=${PREFIX}/include/emboss
-
-CONFIGURE_ARGS+= --x-libraries=${X11BASE}/lib
-CONFIGURE_ARGS+= --datadir=${PREFIX}/share
-CONFIGURE_ARGS+= --infodir=${PREFIX}/doc
-
-CONFIGURE_ARGS+= --with-pngdriver=${BUILDLINK_PREFIX.png}/lib
-
-PKG_DISTFILES_DIR= emboss
-AUTO_MKDIRS= yes
-
-.include "../../graphics/gd/buildlink3.mk"
-.include "../../graphics/png/buildlink3.mk"
-.include "../../mk/jpeg.buildlink3.mk"
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../x11/libX11/buildlink3.mk"
diff --git a/emboss-base/PLIST b/emboss-base/PLIST
deleted file mode 100644
index 18b4d10893..0000000000
--- a/emboss-base/PLIST
+++ /dev/null
@@ -1,1446 +0,0 @@
-@comment $NetBSD: PLIST,v 1.4 2009/10/11 10:44:34 thomasklausner Exp $
-bin/aaindexextract
-bin/abiview
-bin/acdc
-bin/acdpretty
-bin/acdtable
-bin/acdtrace
-bin/acdvalid
-bin/antigenic
-bin/backtranseq
-bin/banana
-bin/biosed
-bin/btwisted
-bin/cai
-bin/chaos
-bin/charge
-bin/checktrans
-bin/chips
-bin/cirdna
-bin/codcmp
-bin/coderet
-bin/compseq
-bin/cons
-bin/cpgplot
-bin/cpgreport
-bin/cusp
-bin/cutgextract
-bin/cutseq
-bin/dan
-bin/dbiblast
-bin/dbifasta
-bin/dbiflat
-bin/dbigcg
-bin/degapseq
-bin/descseq
-bin/diffseq
-bin/distmat
-bin/dotmatcher
-bin/dotpath
-bin/dottup
-bin/dreg
-bin/edigest
-bin/einverted
-bin/embossdata
-bin/embossversion
-bin/emma
-bin/emowse
-bin/entret
-bin/epestfind
-bin/eprimer3
-bin/equicktandem
-bin/est2genome
-bin/etandem
-bin/extractfeat
-bin/extractseq
-bin/findkm
-bin/freak
-bin/fuzznuc
-bin/fuzzpro
-bin/fuzztran
-bin/garnier
-bin/geecee
-bin/getorf
-bin/helixturnhelix
-bin/hmoment
-bin/iep
-bin/infoalign
-bin/infoseq
-bin/isochore
-bin/jembossctl
-bin/lindna
-bin/listor
-bin/marscan
-bin/maskfeat
-bin/maskseq
-bin/matcher
-bin/megamerger
-bin/merger
-bin/msbar
-bin/mwcontam
-bin/mwfilter
-bin/needle
-bin/newcpgreport
-bin/newcpgseek
-bin/newseq
-bin/noreturn
-bin/notseq
-bin/nthseq
-bin/octanol
-bin/oddcomp
-bin/palindrome
-bin/pasteseq
-bin/patmatdb
-bin/patmatmotifs
-bin/pepcoil
-bin/pepinfo
-bin/pepnet
-bin/pepstats
-bin/pepwheel
-bin/pepwindow
-bin/pepwindowall
-bin/plotcon
-bin/plotorf
-bin/polydot
-bin/preg
-bin/prettyplot
-bin/prettyseq
-bin/primersearch
-bin/printsextract
-bin/profit
-bin/prophecy
-bin/prophet
-bin/prosextract
-bin/pscan
-bin/psiphi
-bin/rebaseextract
-bin/recoder
-bin/redata
-bin/remap
-bin/restover
-bin/restrict
-bin/revseq
-bin/seealso
-bin/seqmatchall
-bin/seqret
-bin/seqretsplit
-bin/showalign
-bin/showdb
-bin/showfeat
-bin/showorf
-bin/showseq
-bin/shuffleseq
-bin/sigcleave
-bin/silent
-bin/sirna
-bin/sixpack
-bin/skipseq
-bin/splitter
-bin/stretcher
-bin/stssearch
-bin/supermatcher
-bin/syco
-bin/tcode
-bin/textsearch
-bin/tfextract
-bin/tfm
-bin/tfscan
-bin/tmap
-bin/tranalign
-bin/transeq
-bin/trimest
-bin/trimseq
-bin/twofeat
-bin/union
-bin/vectorstrip
-bin/water
-bin/whichdb
-bin/wobble
-bin/wordcount
-bin/wordmatch
-bin/wossname
-bin/yank
-include/emboss/ajacd.h
-include/emboss/ajalign.h
-include/emboss/ajarch.h
-include/emboss/ajarr.h
-include/emboss/ajassert.h
-include/emboss/ajax.h
-include/emboss/ajbase.h
-include/emboss/ajcall.h
-include/emboss/ajcod.h
-include/emboss/ajdan.h
-include/emboss/ajdefine.h
-include/emboss/ajdmx.h
-include/emboss/ajdomain.h
-include/emboss/ajexcept.h
-include/emboss/ajfeat.h
-include/emboss/ajfeatdata.h
-include/emboss/ajfile.h
-include/emboss/ajfmt.h
-include/emboss/ajgraph.h
-include/emboss/ajgraphstruct.h
-include/emboss/ajgraphxml.h
-include/emboss/ajhist.h
-include/emboss/ajjava.h
-include/emboss/ajlist.h
-include/emboss/ajmath.h
-include/emboss/ajmatrices.h
-include/emboss/ajmem.h
-include/emboss/ajmess.h
-include/emboss/ajnam.h
-include/emboss/ajnexus.h
-include/emboss/ajpdb.h
-include/emboss/ajpdbio.h
-include/emboss/ajphylo.h
-include/emboss/ajrange.h
-include/emboss/ajreg.h
-include/emboss/ajreport.h
-include/emboss/ajseq.h
-include/emboss/ajseqabi.h
-include/emboss/ajseqdata.h
-include/emboss/ajseqdb.h
-include/emboss/ajseqread.h
-include/emboss/ajseqtype.h
-include/emboss/ajseqwrite.h
-include/emboss/ajsort.h
-include/emboss/ajstr.h
-include/emboss/ajsys.h
-include/emboss/ajtable.h
-include/emboss/ajtime.h
-include/emboss/ajtranslate.h
-include/emboss/ajtree.h
-include/emboss/ajutil.h
-include/emboss/ajvector.h
-include/emboss/drivers.h
-include/emboss/embaln.h
-include/emboss/embcom.h
-include/emboss/embcons.h
-include/emboss/embdata.h
-include/emboss/embdbi.h
-include/emboss/embdmx.h
-include/emboss/embdomain.h
-include/emboss/embest.h
-include/emboss/embexit.h
-include/emboss/embgotoh.h
-include/emboss/embgroup.h
-include/emboss/embiep.h
-include/emboss/embindex.h
-include/emboss/embinit.h
-include/emboss/embmat.h
-include/emboss/embmisc.h
-include/emboss/embmol.h
-include/emboss/embnmer.h
-include/emboss/emboss.h
-include/emboss/embpat.h
-include/emboss/embpdb.h
-include/emboss/embprop.h
-include/emboss/embread.h
-include/emboss/embshow.h
-include/emboss/embsig.h
-include/emboss/embword.h
-include/emboss/metadefs.h
-include/emboss/pcre.h
-include/emboss/pcre_chartables.c
-include/emboss/pcre_config.h
-include/emboss/pcre_get.c
-include/emboss/pcre_internal.h
-include/emboss/pcre_printint.c
-include/emboss/pcreposix.h
-include/emboss/pdf.h
-include/emboss/plConfig.h
-include/emboss/plDevs.h
-include/emboss/plcore.h
-include/emboss/pldebug.h
-include/emboss/plevent.h
-include/emboss/plplot.h
-include/emboss/plplotP.h
-include/emboss/plstrm.h
-include/emboss/plxwd.h
-lib/libajax.la
-lib/libajaxg.la
-lib/libnucleus.la
-lib/libplplot.la
-share/EMBOSS/acd/aaindexextract.acd
-share/EMBOSS/acd/abiview.acd
-share/EMBOSS/acd/ajbad.acd
-share/EMBOSS/acd/ajfeatest.acd
-share/EMBOSS/acd/ajtest.acd
-share/EMBOSS/acd/antigenic.acd
-share/EMBOSS/acd/backtranseq.acd
-share/EMBOSS/acd/banana.acd
-share/EMBOSS/acd/biosed.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
-share/EMBOSS/acd/chips.acd
-share/EMBOSS/acd/cirdna.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
-share/EMBOSS/acd/cutgextract.acd
-share/EMBOSS/acd/cutseq.acd
-share/EMBOSS/acd/dan.acd
-share/EMBOSS/acd/dbiblast.acd
-share/EMBOSS/acd/dbifasta.acd
-share/EMBOSS/acd/dbiflat.acd
-share/EMBOSS/acd/dbigcg.acd
-share/EMBOSS/acd/degapseq.acd
-share/EMBOSS/acd/demoalign.acd
-share/EMBOSS/acd/demofeatures.acd
-share/EMBOSS/acd/demolist.acd
-share/EMBOSS/acd/demoreport.acd
-share/EMBOSS/acd/demosequence.acd
-share/EMBOSS/acd/demostring.acd
-share/EMBOSS/acd/demotable.acd
-share/EMBOSS/acd/descseq.acd
-share/EMBOSS/acd/diffseq.acd
-share/EMBOSS/acd/distmat.acd
-share/EMBOSS/acd/dotmatcher.acd
-share/EMBOSS/acd/dotpath.acd
-share/EMBOSS/acd/dottup.acd
-share/EMBOSS/acd/dreg.acd
-share/EMBOSS/acd/edigest.acd
-share/EMBOSS/acd/einverted.acd
-share/EMBOSS/acd/embossdata.acd
-share/EMBOSS/acd/embossversion.acd
-share/EMBOSS/acd/emma.acd
-share/EMBOSS/acd/emowse.acd
-share/EMBOSS/acd/entrails.acd
-share/EMBOSS/acd/entret.acd
-share/EMBOSS/acd/epestfind.acd
-share/EMBOSS/acd/eprimer3.acd
-share/EMBOSS/acd/equicktandem.acd
-share/EMBOSS/acd/est2genome.acd
-share/EMBOSS/acd/etandem.acd
-share/EMBOSS/acd/extractfeat.acd
-share/EMBOSS/acd/extractseq.acd
-share/EMBOSS/acd/findkm.acd
-share/EMBOSS/acd/freak.acd
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-share/EMBOSS/doc/programs/text/pepcoil.txt
-share/EMBOSS/doc/programs/text/pepinfo.txt
-share/EMBOSS/doc/programs/text/pepnet.txt
-share/EMBOSS/doc/programs/text/pepstats.txt
-share/EMBOSS/doc/programs/text/pepwheel.txt
-share/EMBOSS/doc/programs/text/pepwindow.txt
-share/EMBOSS/doc/programs/text/pepwindowall.txt
-share/EMBOSS/doc/programs/text/pestfind.txt
-share/EMBOSS/doc/programs/text/plotcon.txt
-share/EMBOSS/doc/programs/text/plotorf.txt
-share/EMBOSS/doc/programs/text/polydot.txt
-share/EMBOSS/doc/programs/text/preg.txt
-share/EMBOSS/doc/programs/text/prettyplot.txt
-share/EMBOSS/doc/programs/text/prettyseq.txt
-share/EMBOSS/doc/programs/text/primersearch.txt
-share/EMBOSS/doc/programs/text/printsextract.txt
-share/EMBOSS/doc/programs/text/profit.txt
-share/EMBOSS/doc/programs/text/prophecy.txt
-share/EMBOSS/doc/programs/text/prophet.txt
-share/EMBOSS/doc/programs/text/prosextract.txt
-share/EMBOSS/doc/programs/text/protdist.txt
-share/EMBOSS/doc/programs/text/pscan.txt
-share/EMBOSS/doc/programs/text/rebaseextract.txt
-share/EMBOSS/doc/programs/text/recoder.txt
-share/EMBOSS/doc/programs/text/redata.txt
-share/EMBOSS/doc/programs/text/remap.txt
-share/EMBOSS/doc/programs/text/restml.txt
-share/EMBOSS/doc/programs/text/restover.txt
-share/EMBOSS/doc/programs/text/restrict.txt
-share/EMBOSS/doc/programs/text/revseq.txt
-share/EMBOSS/doc/programs/text/scope.txt
-share/EMBOSS/doc/programs/text/seealso.txt
-share/EMBOSS/doc/programs/text/seqboot.txt
-share/EMBOSS/doc/programs/text/seqmatchall.txt
-share/EMBOSS/doc/programs/text/seqret.txt
-share/EMBOSS/doc/programs/text/seqretsplit.txt
-share/EMBOSS/doc/programs/text/showalign.txt
-share/EMBOSS/doc/programs/text/showdb.txt
-share/EMBOSS/doc/programs/text/showfeat.txt
-share/EMBOSS/doc/programs/text/showorf.txt
-share/EMBOSS/doc/programs/text/showseq.txt
-share/EMBOSS/doc/programs/text/shuffleseq.txt
-share/EMBOSS/doc/programs/text/sigcleave.txt
-share/EMBOSS/doc/programs/text/silent.txt
-share/EMBOSS/doc/programs/text/sirna.txt
-share/EMBOSS/doc/programs/text/sixpack.txt
-share/EMBOSS/doc/programs/text/skipseq.txt
-share/EMBOSS/doc/programs/text/splitter.txt
-share/EMBOSS/doc/programs/text/stretcher.txt
-share/EMBOSS/doc/programs/text/stssearch.txt
-share/EMBOSS/doc/programs/text/supermatcher.txt
-share/EMBOSS/doc/programs/text/syco.txt
-share/EMBOSS/doc/programs/text/tcode.txt
-share/EMBOSS/doc/programs/text/textsearch.txt
-share/EMBOSS/doc/programs/text/tfextract.txt
-share/EMBOSS/doc/programs/text/tfm.txt
-share/EMBOSS/doc/programs/text/tfscan.txt
-share/EMBOSS/doc/programs/text/tmap.txt
-share/EMBOSS/doc/programs/text/topo.txt
-share/EMBOSS/doc/programs/text/tranalign.txt
-share/EMBOSS/doc/programs/text/transeq.txt
-share/EMBOSS/doc/programs/text/trimest.txt
-share/EMBOSS/doc/programs/text/trimseq.txt
-share/EMBOSS/doc/programs/text/twofeat.txt
-share/EMBOSS/doc/programs/text/union.txt
-share/EMBOSS/doc/programs/text/vectorstrip.txt
-share/EMBOSS/doc/programs/text/water.txt
-share/EMBOSS/doc/programs/text/whichdb.txt
-share/EMBOSS/doc/programs/text/wobble.txt
-share/EMBOSS/doc/programs/text/wordcount.txt
-share/EMBOSS/doc/programs/text/wordmatch.txt
-share/EMBOSS/doc/programs/text/wossname.txt
-share/EMBOSS/doc/programs/text/yank.txt
-share/EMBOSS/doc/tutorials/emboss-gcg.ppt
-share/EMBOSS/doc/tutorials/emboss-interfaces.ppt
-share/EMBOSS/doc/tutorials/emboss-talk.ppt
-share/EMBOSS/doc/tutorials/emboss_tut.tar.gz
-share/EMBOSS/emboss.default.template
-share/EMBOSS/plstnd5.fnt
-share/EMBOSS/plxtnd5.fnt
-share/EMBOSS/scripts/config.guess
-share/EMBOSS/scripts/config.sub
-share/EMBOSS/scripts/depcomp
-share/EMBOSS/scripts/install-sh
-share/EMBOSS/scripts/mkinstalldirs
-share/EMBOSS/test/data/aaindex1.test
-share/EMBOSS/test/data/aligna.dna
-share/EMBOSS/test/data/aligna.prot
-share/EMBOSS/test/data/alignapart.dna
-share/EMBOSS/test/data/alignapart.prot
-share/EMBOSS/test/data/alignb.dna
-share/EMBOSS/test/data/alignb.prot
-share/EMBOSS/test/data/cutg.codon
-share/EMBOSS/test/data/dna.acedb
-share/EMBOSS/test/data/dna.aln
-share/EMBOSS/test/data/dna.asn1
-share/EMBOSS/test/data/dna.codata
-share/EMBOSS/test/data/dna.embl
-share/EMBOSS/test/data/dna.fasta
-share/EMBOSS/test/data/dna.fitch
-share/EMBOSS/test/data/dna.gcg
-share/EMBOSS/test/data/dna.gcg8
-share/EMBOSS/test/data/dna.genbank
-share/EMBOSS/test/data/dna.ig
-share/EMBOSS/test/data/dna.m-acedb
-share/EMBOSS/test/data/dna.m-codata
-share/EMBOSS/test/data/dna.m-embl
-share/EMBOSS/test/data/dna.m-fasta
-share/EMBOSS/test/data/dna.m-fasta-long
-share/EMBOSS/test/data/dna.m-ncbi
-share/EMBOSS/test/data/dna.m-strider
-share/EMBOSS/test/data/dna.msf
-share/EMBOSS/test/data/dna.msf8
-share/EMBOSS/test/data/dna.ncbi
-share/EMBOSS/test/data/dna.phylip
-share/EMBOSS/test/data/dna.phylip3
-share/EMBOSS/test/data/dna.staden
-share/EMBOSS/test/data/dna.strider
-share/EMBOSS/test/data/dna.text
-share/EMBOSS/test/data/feat.emft
-share/EMBOSS/test/data/feat.fasta
-share/EMBOSS/test/data/feat.pir
-share/EMBOSS/test/data/mw1.dat
-share/EMBOSS/test/data/mw2.dat
-share/EMBOSS/test/data/mw3.dat
-share/EMBOSS/test/data/paamir.pep
-share/EMBOSS/test/data/pax6_cdna.fasta
-share/EMBOSS/test/data/prints.test
-share/EMBOSS/test/data/prosite.dat
-share/EMBOSS/test/data/prosite.doc
-share/EMBOSS/test/data/prot.acedb
-share/EMBOSS/test/data/prot.codata
-share/EMBOSS/test/data/prot.fasta
-share/EMBOSS/test/data/prot.gcg
-share/EMBOSS/test/data/prot.gcg8
-share/EMBOSS/test/data/prot.ig
-share/EMBOSS/test/data/prot.m-acedb
-share/EMBOSS/test/data/prot.m-codata
-share/EMBOSS/test/data/prot.m-fasta
-share/EMBOSS/test/data/prot.m-nbrf
-share/EMBOSS/test/data/prot.m-ncbi
-share/EMBOSS/test/data/prot.m-swiss
-share/EMBOSS/test/data/prot.nbrf
-share/EMBOSS/test/data/prot.ncbi
-share/EMBOSS/test/data/prot.swiss
-share/EMBOSS/test/data/prot.text
-share/EMBOSS/test/data/site.dat
-share/EMBOSS/test/data/tranalign.pep
-share/EMBOSS/test/data/tranalign.seq
-share/EMBOSS/test/data/withrefm
-share/EMBOSS/test/data/z83307.seq
-share/EMBOSS/test/embl/acnum.hit
-share/EMBOSS/test/embl/acnum.trg
-share/EMBOSS/test/embl/des.hit
-share/EMBOSS/test/embl/des.trg
-share/EMBOSS/test/embl/division.lkp
-share/EMBOSS/test/embl/entrynam.idx
-share/EMBOSS/test/embl/est.dat
-share/EMBOSS/test/embl/fun.dat
-share/EMBOSS/test/embl/hum1.dat
-share/EMBOSS/test/embl/inv.dat
-share/EMBOSS/test/embl/keyword.hit
-share/EMBOSS/test/embl/keyword.trg
-share/EMBOSS/test/embl/pln.dat
-share/EMBOSS/test/embl/pro.dat
-share/EMBOSS/test/embl/rod.dat
-share/EMBOSS/test/embl/seqvn.hit
-share/EMBOSS/test/embl/seqvn.trg
-share/EMBOSS/test/embl/sts.dat
-share/EMBOSS/test/embl/taxon.hit
-share/EMBOSS/test/embl/taxon.trg
-share/EMBOSS/test/embl/vrl.dat
-share/EMBOSS/test/embl/vrt.dat
-share/EMBOSS/test/gb/acnum.hit
-share/EMBOSS/test/gb/acnum.trg
-share/EMBOSS/test/gb/ba.ref
-share/EMBOSS/test/gb/ba.seq
-share/EMBOSS/test/gb/des.hit
-share/EMBOSS/test/gb/des.trg
-share/EMBOSS/test/gb/division.lkp
-share/EMBOSS/test/gb/entrynam.idx
-share/EMBOSS/test/gb/htg.ref
-share/EMBOSS/test/gb/htg.seq
-share/EMBOSS/test/gb/keyword.hit
-share/EMBOSS/test/gb/keyword.trg
-share/EMBOSS/test/gb/seqvn.hit
-share/EMBOSS/test/gb/seqvn.trg
-share/EMBOSS/test/gb/taxon.hit
-share/EMBOSS/test/gb/taxon.trg
-share/EMBOSS/test/genbank/acnum.hit
-share/EMBOSS/test/genbank/acnum.trg
-share/EMBOSS/test/genbank/des.hit
-share/EMBOSS/test/genbank/des.trg
-share/EMBOSS/test/genbank/division.lkp
-share/EMBOSS/test/genbank/entrynam.idx
-share/EMBOSS/test/genbank/gbbct1.seq
-share/EMBOSS/test/genbank/gbest1.seq
-share/EMBOSS/test/genbank/gbinv1.seq
-share/EMBOSS/test/genbank/gbpln1.seq
-share/EMBOSS/test/genbank/gbpln2.seq
-share/EMBOSS/test/genbank/gbpri1.seq
-share/EMBOSS/test/genbank/gbrod1.seq
-share/EMBOSS/test/genbank/gbsts1.seq
-share/EMBOSS/test/genbank/gbvrl1.seq
-share/EMBOSS/test/genbank/gbvrt.seq
-share/EMBOSS/test/genbank/keyword.hit
-share/EMBOSS/test/genbank/keyword.trg
-share/EMBOSS/test/genbank/seqvn.hit
-share/EMBOSS/test/genbank/seqvn.trg
-share/EMBOSS/test/genbank/taxon.hit
-share/EMBOSS/test/genbank/taxon.trg
-share/EMBOSS/test/pir/acnum.hit
-share/EMBOSS/test/pir/acnum.trg
-share/EMBOSS/test/pir/des.hit
-share/EMBOSS/test/pir/des.trg
-share/EMBOSS/test/pir/division.lkp
-share/EMBOSS/test/pir/entrynam.idx
-share/EMBOSS/test/pir/keyword.hit
-share/EMBOSS/test/pir/keyword.trg
-share/EMBOSS/test/pir/pir1.header
-share/EMBOSS/test/pir/pir1.names
-share/EMBOSS/test/pir/pir1.numbers
-share/EMBOSS/test/pir/pir1.offset
-share/EMBOSS/test/pir/pir1.ref
-share/EMBOSS/test/pir/pir1.seq
-share/EMBOSS/test/pir/pir2.header
-share/EMBOSS/test/pir/pir2.names
-share/EMBOSS/test/pir/pir2.numbers
-share/EMBOSS/test/pir/pir2.offset
-share/EMBOSS/test/pir/pir2.ref
-share/EMBOSS/test/pir/pir2.seq
-share/EMBOSS/test/pir/pir3.header
-share/EMBOSS/test/pir/pir3.names
-share/EMBOSS/test/pir/pir3.numbers
-share/EMBOSS/test/pir/pir3.offset
-share/EMBOSS/test/pir/pir3.ref
-share/EMBOSS/test/pir/pir3.seq
-share/EMBOSS/test/pir/pir4.header
-share/EMBOSS/test/pir/pir4.names
-share/EMBOSS/test/pir/pir4.numbers
-share/EMBOSS/test/pir/pir4.offset
-share/EMBOSS/test/pir/pir4.ref
-share/EMBOSS/test/pir/pir4.seq
-share/EMBOSS/test/pir/taxon.hit
-share/EMBOSS/test/pir/taxon.trg
-share/EMBOSS/test/swiss/acnum.hit
-share/EMBOSS/test/swiss/acnum.trg
-share/EMBOSS/test/swiss/des.hit
-share/EMBOSS/test/swiss/des.trg
-share/EMBOSS/test/swiss/division.lkp
-share/EMBOSS/test/swiss/entrynam.idx
-share/EMBOSS/test/swiss/keyword.hit
-share/EMBOSS/test/swiss/keyword.trg
-share/EMBOSS/test/swiss/seq.dat
-share/EMBOSS/test/swiss/seqvn.hit
-share/EMBOSS/test/swiss/seqvn.trg
-share/EMBOSS/test/swiss/taxon.hit
-share/EMBOSS/test/swiss/taxon.trg
-share/EMBOSS/test/swnew/acnum.hit
-share/EMBOSS/test/swnew/acnum.trg
-share/EMBOSS/test/swnew/des.hit
-share/EMBOSS/test/swnew/des.trg
-share/EMBOSS/test/swnew/division.lkp
-share/EMBOSS/test/swnew/entrynam.idx
-share/EMBOSS/test/swnew/keyword.hit
-share/EMBOSS/test/swnew/keyword.trg
-share/EMBOSS/test/swnew/new_seq.dat
-share/EMBOSS/test/swnew/seqvn.hit
-share/EMBOSS/test/swnew/seqvn.trg
-share/EMBOSS/test/swnew/taxon.hit
-share/EMBOSS/test/swnew/taxon.trg
-share/EMBOSS/test/swnew/upd_ann.dat
-share/EMBOSS/test/swnew/upd_seq.dat
-share/EMBOSS/test/wormpep/acnum.hit
-share/EMBOSS/test/wormpep/acnum.trg
-share/EMBOSS/test/wormpep/des.hit
-share/EMBOSS/test/wormpep/des.trg
-share/EMBOSS/test/wormpep/division.lkp
-share/EMBOSS/test/wormpep/entrynam.idx
-share/EMBOSS/test/wormpep/wormpep
diff --git a/emboss-base/TODO b/emboss-base/TODO
deleted file mode 100644
index 3502465222..0000000000
--- a/emboss-base/TODO
+++ /dev/null
@@ -1 +0,0 @@
-plplot: there is no configuration option to use a different plplot, using a different one than what it builds when it installs would require some patching, I believe.
diff --git a/emboss-base/buildlink3.mk b/emboss-base/buildlink3.mk
deleted file mode 100644
index b9d48c33f8..0000000000
--- a/emboss-base/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD: buildlink3.mk,v 1.5 2009/05/06 09:35:22 cheusov Exp $
-
-BUILDLINK_TREE+= emboss-base
-
-.if !defined(EMBOSS_BASE_BUILDLINK3_MK)
-EMBOSS_BASE_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.emboss-base+= emboss-base>=2.7.1
-BUILDLINK_PKGSRCDIR.emboss-base?= ../../wip/emboss-base
-.endif # EMBOSS_BASE_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -emboss-base
diff --git a/emboss-base/distinfo b/emboss-base/distinfo
deleted file mode 100644
index 2f96094f7c..0000000000
--- a/emboss-base/distinfo
+++ /dev/null
@@ -1,17 +0,0 @@
-$NetBSD: distinfo,v 1.2 2005/09/28 06:41:12 rillig Exp $
-
-RMD160 (emboss/emboss-2.9.0/EMBOSS-2.9.0.tar.gz) = 2b4d4ec90989a7b56272ff121125c270367b38fe
-SHA512 (emboss/emboss-2.9.0/EMBOSS-2.9.0.tar.gz) = 8cd21d37bbc906e80ce3bd03bbcee8096f22c48979a393bad271f4f2787d2abf6f54b8373a3f2f4127e101ea2d542ef0ac4c955afcd25a22c53fe59a1a56369b
-Size (emboss/emboss-2.9.0/EMBOSS-2.9.0.tar.gz) = 14479274 bytes
-SHA1 (patch-aa) = 21e499e2da7611f8b95e83fb257bd5fa3bc3b0dd
-SHA1 (patch-ab) = 8918930a95270e1391f9cf9f60895c6b6b018304
-SHA1 (patch-ac) = 4dee057b278dc83250abd90fc499e406b7bed6de
-SHA1 (patch-ad) = 7f2586efd65144ab33031f013b49203d7d5ec4a7
-SHA1 (patch-ae) = 8642b0f3ec2ff0a8fef1967894a660e426028ffa
-SHA1 (patch-af) = 9007ab5f025b5e744a4cdb16e6eee446e6c04cd5
-SHA1 (patch-ag) = 466437e78a5d90a502fed0bda77487a80f375ada
-SHA1 (patch-ah) = 2bca4fb7498e33243fed1cc1c38f3fd7a79767d4
-SHA1 (patch-ai) = 95d2fbdc93527759078b9f4946c0d684a168488a
-SHA1 (patch-aj) = d490766aab9679359ccf42ae6ef4007a8f10247a
-SHA1 (patch-ak) = bd6883b8c45f115a208e155bb4f060b9547d3326
-SHA1 (patch-al) = d9d870d9761dc512a28ed7ee8a33b3c62649ac1c
diff --git a/emboss-base/files/digestchange b/emboss-base/files/digestchange
deleted file mode 100644
index e7449073c2..0000000000
--- a/emboss-base/files/digestchange
+++ /dev/null
@@ -1,126 +0,0 @@
-#! /bin/sh
-# David Price
-# 06-29-2004
-# this script reads the working directory, and changes documentation files which
-# reference digest to refer to edigest it is passed the location of the working directory
-# as an argument. this allows the program digest to be placed into the pkg/bin directory
-# without overwriting the pkgtool program digest
-
-pdirs() {
-#function to switch directories based on a passed variable
-
- DIR=$1
- ABSDIR=$2
-
- case $DIR in
-
-
- html) cd ${ABSDIR}/${DIR}
- phtml html
- cd ${ABSDIR}
- ;;
- text) cd ${ABSDIR}/text
- ptext txt
- cd ${ABSDIR}
- ;;
-
- *) echo "ERROR: bad directory given to digestchange script, directory was: $DIR"
- exit 1
- ;;
- esac
-
-
-}
-
-phtml() {
-
-
- for HFILE in *html ; do
-
- sed -e 's|digest\.html|edigest\.html|g' \
- -e 's/>digest/>edigest/g' \
- -e 's/^digest/edigest/g' \
- -e 's|EMBOSS: digest|EMBOSS: edigest|g' \
- -e 's|session with digest|session with edigest|g' \
- -e 's|opsd_human.digest|opsd_human.edigest|g' \
- -e 's|Program: digest|Program: edigest|g' \
- -e 's|% digest|% edigest|g' \
- -e 's|digest[ ]\{10,13\}Protein|edigest Protein|g' \
- ${HFILE} > ${HFILE}.new ;
-
- mv ${HFILE}.new ${HFILE}
- echo "digestchange modified ${HFILE}"
-
- done
-
-
-
- for HMFILE in Makefile* ; do
-
- sed -e 's| digest\.html| edigest\.html|g' ${HMFILE} > ${HMFILE}.new ;
-
- mv ${HMFILE}.new ${HMFILE}
- echo "digestchange modified ${HMFILE}"
-
-
- done
-
-}
-
-ptext() {
-
-
- for TFILE in *txt ; do
-
-
-
- sed -e 's|session with digest|session with edigest|g' \
- -e 's|opsd_human.digest|opsd_human.edigest|g' \
- -e 's/rogram. digest/rogram edigest/g' \
- -e 's|% digest|% edigest|g' \
- -e 's/ \{30,40\}digest/ edigest/g' \
- -e 's/digest \{6,13\}Protein/edigest Protein/g' \
- -e 's/digest( )\{1,3\}Protein/edigest Protein/g' \
- -e 's| digest finds| edigest finds|g' \
- ${TFILE} > ${TFILE}.new ;
-
- mv ${TFILE}.new ${TFILE}
-
- echo "digestchange modified ${TFILE}"
-
- done
-
-
- for TMFILE in Makefile* ; do
-
- sed -e 's| digest\.txt| edigest\.txt|g' ${TMFILE} > ${TMFILE}.new ;
-
- mv ${TMFILE}.new ${TMFILE}
-
- echo "digestchange modified ${TMFILE}"
-
- done
-
-
-}
-
-# Main body of the script
-
-WRKINGDIR=$1
-
-BASEDIR=${WRKINGDIR}/doc/programs
-
-pdirs html $BASEDIR
-pdirs text $BASEDIR
-
-cd $WRKINGDIR
-
-
-
-#emboss/Makefile.in
-#emboss/Makefile.am
-#emboss/acd/Makefile.am
-#emboss/acd/Makefile.in
-#emboss/acd/digest.acd
-#emboss/acd/Makefile
-#emboss/digest.c
diff --git a/emboss-base/patches/patch-aa b/emboss-base/patches/patch-aa
deleted file mode 100644
index a8923bd7bf..0000000000
--- a/emboss-base/patches/patch-aa
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD: patch-aa,v 1.1.1.1 2004/11/11 20:57:22 daprice Exp $
-
---- ajax/Makefile.am.orig Wed Jul 21 15:38:22 2004
-+++ ajax/Makefile.am Wed Jul 21 15:38:53 2004
-@@ -36,7 +36,7 @@
- ajbase.c \
- ajcall.c ajcod.c \
- ajdan.c ajdmx.c ajdomain.c ajexcept.c \
--ajfeat.c ajfile.c ajfmt.c ajgraphxml.c ajjava.c ajlist.c \
-+ajfeat.c ajfile.c ajfmt.c ajgraphxml.c ajlist.c \
- ajmath.c ajmatrices.c ajmem.c ajmess.c ajnam.c ajnexus.c \
- ajpdb.c ajpdbio.c ajphylo.c \
- ajrange.c ajreg.c ajreport.c \
-@@ -52,7 +52,7 @@
- ajbase.h ajcall.h ajcod.h \
- ajdan.h ajdmx.h ajdomain.h ajexcept.h \
- ajfeat.h ajfeatdata.h ajfile.h ajfmt.h \
--ajgraph.h ajgraphxml.h ajgraphstruct.h ajhist.h ajjava.h ajlist.h \
-+ajgraph.h ajgraphxml.h ajgraphstruct.h ajhist.h ajlist.h \
- ajmath.h ajmatrices.h ajmem.h ajmess.h ajnam.h ajnexus.h \
- ajpdb.h ajpdbio.h ajphylo.h \
- ajrange.h ajreg.h ajreport.h \
diff --git a/emboss-base/patches/patch-ab b/emboss-base/patches/patch-ab
deleted file mode 100644
index 056b504188..0000000000
--- a/emboss-base/patches/patch-ab
+++ /dev/null
@@ -1,57 +0,0 @@
-$NetBSD: patch-ab,v 1.1.1.1 2004/11/11 20:57:22 daprice Exp $
-
---- ajax/Makefile.in.orig Wed Jul 21 15:43:52 2004
-+++ ajax/Makefile.in Wed Jul 21 15:45:35 2004
-@@ -56,7 +56,7 @@
- libajax_la_LIBADD =
- am__libajax_la_SOURCES_DIST = ajacd.c ajalign.c ajarr.c ajassert.c \
- ajbase.c ajcall.c ajcod.c ajdan.c ajdmx.c ajdomain.c \
-- ajexcept.c ajfeat.c ajfile.c ajfmt.c ajgraphxml.c ajjava.c \
-+ ajexcept.c ajfeat.c ajfile.c ajfmt.c ajgraphxml.c \
- ajlist.c ajmath.c ajmatrices.c ajmem.c ajmess.c ajnam.c \
- ajnexus.c ajpdb.c ajpdbio.c ajphylo.c ajrange.c ajreg.c \
- ajreport.c ajseq.c ajseqabi.c ajseqdb.c ajseqread.c \
-@@ -65,7 +65,7 @@
- pcre_study.c pcreposix.c ajgraph.c ajhist.c
- am__objects_1 = ajacd.lo ajalign.lo ajarr.lo ajassert.lo ajbase.lo \
- ajcall.lo ajcod.lo ajdan.lo ajdmx.lo ajdomain.lo ajexcept.lo \
-- ajfeat.lo ajfile.lo ajfmt.lo ajgraphxml.lo ajjava.lo ajlist.lo \
-+ ajfeat.lo ajfile.lo ajfmt.lo ajgraphxml.lo ajlist.lo \
- ajmath.lo ajmatrices.lo ajmem.lo ajmess.lo ajnam.lo ajnexus.lo \
- ajpdb.lo ajpdbio.lo ajphylo.lo ajrange.lo ajreg.lo ajreport.lo \
- ajseq.lo ajseqabi.lo ajseqdb.lo ajseqread.lo ajseqtype.lo \
-@@ -92,7 +92,7 @@
- @AMDEP_TRUE@ ./$(DEPDIR)/ajexcept.Plo ./$(DEPDIR)/ajfeat.Plo \
- @AMDEP_TRUE@ ./$(DEPDIR)/ajfile.Plo ./$(DEPDIR)/ajfmt.Plo \
- @AMDEP_TRUE@ ./$(DEPDIR)/ajgraph.Plo ./$(DEPDIR)/ajgraphxml.Plo \
--@AMDEP_TRUE@ ./$(DEPDIR)/ajhist.Plo ./$(DEPDIR)/ajjava.Plo \
-+@AMDEP_TRUE@ ./$(DEPDIR)/ajhist.Plo \
- @AMDEP_TRUE@ ./$(DEPDIR)/ajlist.Plo ./$(DEPDIR)/ajmath.Plo \
- @AMDEP_TRUE@ ./$(DEPDIR)/ajmatrices.Plo ./$(DEPDIR)/ajmem.Plo \
- @AMDEP_TRUE@ ./$(DEPDIR)/ajmess.Plo ./$(DEPDIR)/ajnam.Plo \
-@@ -267,7 +267,7 @@
- ajbase.c \
- ajcall.c ajcod.c \
- ajdan.c ajdmx.c ajdomain.c ajexcept.c \
--ajfeat.c ajfile.c ajfmt.c ajgraphxml.c ajjava.c ajlist.c \
-+ajfeat.c ajfile.c ajfmt.c ajgraphxml.c ajlist.c \
- ajmath.c ajmatrices.c ajmem.c ajmess.c ajnam.c ajnexus.c \
- ajpdb.c ajpdbio.c ajphylo.c \
- ajrange.c ajreg.c ajreport.c \
-@@ -282,7 +282,7 @@
- ajbase.h ajcall.h ajcod.h \
- ajdan.h ajdmx.h ajdomain.h ajexcept.h \
- ajfeat.h ajfeatdata.h ajfile.h ajfmt.h \
--ajgraph.h ajgraphxml.h ajgraphstruct.h ajhist.h ajjava.h ajlist.h \
-+ajgraph.h ajgraphxml.h ajgraphstruct.h ajhist.h ajlist.h \
- ajmath.h ajmatrices.h ajmem.h ajmess.h ajnam.h ajnexus.h \
- ajpdb.h ajpdbio.h ajphylo.h \
- ajrange.h ajreg.h ajreport.h \
-@@ -386,7 +386,6 @@
- @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajgraph.Plo@am__quote@
- @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajgraphxml.Plo@am__quote@
- @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajhist.Plo@am__quote@
--@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajjava.Plo@am__quote@
- @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajlist.Plo@am__quote@
- @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajmath.Plo@am__quote@
- @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajmatrices.Plo@am__quote@
diff --git a/emboss-base/patches/patch-ac b/emboss-base/patches/patch-ac
deleted file mode 100644
index 2eb41b832c..0000000000
--- a/emboss-base/patches/patch-ac
+++ /dev/null
@@ -1,12 +0,0 @@
-$NetBSD: patch-ac,v 1.1.1.1 2004/11/11 20:57:22 daprice Exp $
-
---- ajax/ajax.h.orig Wed Jul 21 13:25:31 2004
-+++ ajax/ajax.h Wed Jul 21 13:25:39 2004
-@@ -68,7 +68,6 @@
- #include "ajdmx.h"
- #include "ajacd.h"
- #include "ajcall.h"
--#include "ajjava.h"
- #include "ajgraphxml.h"
- #include "ajvector.h"
-
diff --git a/emboss-base/patches/patch-ad b/emboss-base/patches/patch-ad
deleted file mode 100644
index d71e19a7a2..0000000000
--- a/emboss-base/patches/patch-ad
+++ /dev/null
@@ -1,99 +0,0 @@
-$NetBSD: patch-ad,v 1.1.1.1 2004/11/11 20:57:22 daprice Exp $
-
---- emboss/Makefile.in.orig Wed Jul 21 13:26:09 2004
-+++ emboss/Makefile.in Wed Jul 21 13:27:14 2004
-@@ -15,7 +15,7 @@
- @SET_MAKE@
-
-
--SOURCES = $(aaindexextract_SOURCES) $(abiview_SOURCES) $(acdc_SOURCES) $(acdlog_SOURCES) $(acdpretty_SOURCES) $(acdtable_SOURCES) $(acdtrace_SOURCES) $(acdvalid_SOURCES) $(ajtest_SOURCES) $(antigenic_SOURCES) $(backtranseq_SOURCES) $(banana_SOURCES) $(biosed_SOURCES) $(btwisted_SOURCES) $(cai_SOURCES) $(chaos_SOURCES) $(charge_SOURCES) $(checktrans_SOURCES) $(chips_SOURCES) $(cirdna_SOURCES) $(codcmp_SOURCES) $(coderet_SOURCES) $(complex_SOURCES) $(compseq_SOURCES) $(cons_SOURCES) $(corbatest_SOURCES) $(cpgplot_SOURCES) $(cpgreport_SOURCES) $(cusp_SOURCES) $(cutgextract_SOURCES) $(cutseq_SOURCES) $(dan_SOURCES) $(dbiblast_SOURCES) $(dbifasta_SOURCES) $(dbiflat_SOURCES) $(dbigcg_SOURCES) $(degapseq_SOURCES) $(demoalign_SOURCES) $(demofeatures_SOURCES) $(demolist_SOURCES) $(demoreport_SOURCES) $(demosequence_SOURCES) $(demostring_SOURCES) $(demotable_SOURCES) $(descseq_SOURCES) $(diffseq_SOURCES) $(digest_SOURCES) $(distmat_SOURCES) $(dotmatcher_SOURCES) $(dotpath_SOURCES) $(
dottup_SOURCES) $(dreg_SOURCES) $(einverted_SOURCES) $(embossdata_SOURCES) $(embossversion_SOURCES) $(emma_SOURCES) $(emowse_SOURCES) $(entrails_SOURCES) $(entret_SOURCES) $(epestfind_SOURCES) $(eprimer3_SOURCES) $(equicktandem_SOURCES) $(est2genome_SOURCES) $(etandem_SOURCES) $(extractfeat_SOURCES) $(extractseq_SOURCES) $(findkm_SOURCES) $(freak_SOURCES) $(fuzznuc_SOURCES) $(fuzzpro_SOURCES) $(fuzztran_SOURCES) $(garnier_SOURCES) $(geecee_SOURCES) $(getorf_SOURCES) giep.c $(helixturnhelix_SOURCES) $(histogramtest_SOURCES) $(hmoment_SOURCES) $(iep_SOURCES) $(infoalign_SOURCES) $(infoseq_SOURCES) $(intconv_SOURCES) $(isochore_SOURCES) $(jembossctl_SOURCES) $(lindna_SOURCES) $(listor_SOURCES) $(marscan_SOURCES) $(maskfeat_SOURCES) $(maskseq_SOURCES) $(matcher_SOURCES) $(megamerger_SOURCES) $(merger_SOURCES) $(msbar_SOURCES) $(mwcontam_SOURCES) $(mwfilter_SOURCES) $(needle_SOURCES) $(newcoils_SOURCES) $(newcpgreport_SOURCES) $(newcpgseek_SOURCES) $(newseq_SOURCES) $(noreturn_SOURCES) $(
notseq_SOURCES) $(nthseq_SOURCES) $(octanol_SOURCES) $(oddcomp_SOURCES) $(palindrome_SOURCES) $(pasteseq_SOURCES) $(patmatdb_SOURCES) $(patmatmotifs_SOURCES) $(patmattest_SOURCES) $(pepcoil_SOURCES) $(pepinfo_SOURCES) $(pepnet_SOURCES) $(pepstats_SOURCES) $(pepwheel_SOURCES) $(pepwindow_SOURCES) $(pepwindowall_SOURCES) $(plotcon_SOURCES) $(plotorf_SOURCES) $(polydot_SOURCES) $(preg_SOURCES) $(prettyplot_SOURCES) $(prettyseq_SOURCES) $(prima_SOURCES) $(primers_SOURCES) $(primersearch_SOURCES) $(printsextract_SOURCES) $(profit_SOURCES) $(prophecy_SOURCES) $(prophet_SOURCES) $(prosextract_SOURCES) $(pscan_SOURCES) $(psiphi_SOURCES) $(rebaseextract_SOURCES) $(recoder_SOURCES) $(redata_SOURCES) $(remap_SOURCES) $(restover_SOURCES) $(restrict_SOURCES) $(revseq_SOURCES) $(seealso_SOURCES) $(seqinfo_SOURCES) $(seqmatchall_SOURCES) $(seqret_SOURCES) $(seqretall_SOURCES) $(seqretallfeat_SOURCES) $(seqretset_SOURCES) $(seqretsingle_SOURCES) $(seqretsplit_SOURCES) $(seqrettype_SOURCES) $(showal
ign_SOURCES) $(showdb_SOURCES) $(showfeat_SOURCES) $(showorf_SOURCES) $(showseq_SOURCES) $(shuffleseq_SOURCES) $(sigcleave_SOURCES) $(silent_SOURCES) $(sirna_SOURCES) $(sixpack_SOURCES) skipseq.c $(splitter_SOURCES) $(stretcher_SOURCES) $(stssearch_SOURCES) $(supermatcher_SOURCES) $(syco_SOURCES) $(tcode_SOURCES) $(testplot_SOURCES) $(textsearch_SOURCES) $(tfextract_SOURCES) $(tfm_SOURCES) $(tfscan_SOURCES) $(tmap_SOURCES) $(tranalign_SOURCES) $(transeq_SOURCES) $(treetypedisplay_SOURCES) $(trimest_SOURCES) $(trimseq_SOURCES) $(twofeat_SOURCES) $(union_SOURCES) $(vectorstrip_SOURCES) $(water_SOURCES) $(whichdb_SOURCES) $(wobble_SOURCES) $(wordcount_SOURCES) $(wordmatch_SOURCES) $(wossname_SOURCES) $(yank_SOURCES)
-+SOURCES = $(aaindexextract_SOURCES) $(abiview_SOURCES) $(acdc_SOURCES) $(acdlog_SOURCES) $(acdpretty_SOURCES) $(acdtable_SOURCES) $(acdtrace_SOURCES) $(acdvalid_SOURCES) $(ajtest_SOURCES) $(antigenic_SOURCES) $(backtranseq_SOURCES) $(banana_SOURCES) $(biosed_SOURCES) $(btwisted_SOURCES) $(cai_SOURCES) $(chaos_SOURCES) $(charge_SOURCES) $(checktrans_SOURCES) $(chips_SOURCES) $(cirdna_SOURCES) $(codcmp_SOURCES) $(coderet_SOURCES) $(complex_SOURCES) $(compseq_SOURCES) $(cons_SOURCES) $(corbatest_SOURCES) $(cpgplot_SOURCES) $(cpgreport_SOURCES) $(cusp_SOURCES) $(cutgextract_SOURCES) $(cutseq_SOURCES) $(dan_SOURCES) $(dbiblast_SOURCES) $(dbifasta_SOURCES) $(dbiflat_SOURCES) $(dbigcg_SOURCES) $(degapseq_SOURCES) $(demoalign_SOURCES) $(demofeatures_SOURCES) $(demolist_SOURCES) $(demoreport_SOURCES) $(demosequence_SOURCES) $(demostring_SOURCES) $(demotable_SOURCES) $(descseq_SOURCES) $(diffseq_SOURCES) $(edigest_SOURCES) $(distmat_SOURCES) $(dotmatcher_SOURCES) $(dotpath_SOURCES) $
(dottup_SOURCES) $(dreg_SOURCES) $(einverted_SOURCES) $(embossdata_SOURCES) $(embossversion_SOURCES) $(emma_SOURCES) $(emowse_SOURCES) $(entrails_SOURCES) $(entret_SOURCES) $(epestfind_SOURCES) $(eprimer3_SOURCES) $(equicktandem_SOURCES) $(est2genome_SOURCES) $(etandem_SOURCES) $(extractfeat_SOURCES) $(extractseq_SOURCES) $(findkm_SOURCES) $(freak_SOURCES) $(fuzznuc_SOURCES) $(fuzzpro_SOURCES) $(fuzztran_SOURCES) $(garnier_SOURCES) $(geecee_SOURCES) $(getorf_SOURCES) giep.c $(helixturnhelix_SOURCES) $(histogramtest_SOURCES) $(hmoment_SOURCES) $(iep_SOURCES) $(infoalign_SOURCES) $(infoseq_SOURCES) $(intconv_SOURCES) $(isochore_SOURCES) $(jembossctl_SOURCES) $(lindna_SOURCES) $(listor_SOURCES) $(marscan_SOURCES) $(maskfeat_SOURCES) $(maskseq_SOURCES) $(matcher_SOURCES) $(megamerger_SOURCES) $(merger_SOURCES) $(msbar_SOURCES) $(mwcontam_SOURCES) $(mwfilter_SOURCES) $(needle_SOURCES) $(newcoils_SOURCES) $(newcpgreport_SOURCES) $(newcpgseek_SOURCES) $(newseq_SOURCES) $(noreturn_SOURCES) $
(notseq_SOURCES) $(nthseq_SOURCES) $(octanol_SOURCES) $(oddcomp_SOURCES) $(palindrome_SOURCES) $(pasteseq_SOURCES) $(patmatdb_SOURCES) $(patmatmotifs_SOURCES) $(patmattest_SOURCES) $(pepcoil_SOURCES) $(pepinfo_SOURCES) $(pepnet_SOURCES) $(pepstats_SOURCES) $(pepwheel_SOURCES) $(pepwindow_SOURCES) $(pepwindowall_SOURCES) $(plotcon_SOURCES) $(plotorf_SOURCES) $(polydot_SOURCES) $(preg_SOURCES) $(prettyplot_SOURCES) $(prettyseq_SOURCES) $(prima_SOURCES) $(primers_SOURCES) $(primersearch_SOURCES) $(printsextract_SOURCES) $(profit_SOURCES) $(prophecy_SOURCES) $(prophet_SOURCES) $(prosextract_SOURCES) $(pscan_SOURCES) $(psiphi_SOURCES) $(rebaseextract_SOURCES) $(recoder_SOURCES) $(redata_SOURCES) $(remap_SOURCES) $(restover_SOURCES) $(restrict_SOURCES) $(revseq_SOURCES) $(seealso_SOURCES) $(seqinfo_SOURCES) $(seqmatchall_SOURCES) $(seqret_SOURCES) $(seqretall_SOURCES) $(seqretallfeat_SOURCES) $(seqretset_SOURCES) $(seqretsingle_SOURCES) $(seqretsplit_SOURCES) $(seqrettype_SOURCES) $(showa
lign_SOURCES) $(showdb_SOURCES) $(showfeat_SOURCES) $(showorf_SOURCES) $(showseq_SOURCES) $(shuffleseq_SOURCES) $(sigcleave_SOURCES) $(silent_SOURCES) $(sirna_SOURCES) $(sixpack_SOURCES) skipseq.c $(splitter_SOURCES) $(stretcher_SOURCES) $(stssearch_SOURCES) $(supermatcher_SOURCES) $(syco_SOURCES) $(tcode_SOURCES) $(testplot_SOURCES) $(textsearch_SOURCES) $(tfextract_SOURCES) $(tfm_SOURCES) $(tfscan_SOURCES) $(tmap_SOURCES) $(tranalign_SOURCES) $(transeq_SOURCES) $(treetypedisplay_SOURCES) $(trimest_SOURCES) $(trimseq_SOURCES) $(twofeat_SOURCES) $(union_SOURCES) $(vectorstrip_SOURCES) $(water_SOURCES) $(whichdb_SOURCES) $(wobble_SOURCES) $(wordcount_SOURCES) $(wordmatch_SOURCES) $(wossname_SOURCES) $(yank_SOURCES)
-
- srcdir = @srcdir@
- top_srcdir = @top_srcdir@
-@@ -58,7 +58,7 @@
- cutgextract$(EXEEXT) cutseq$(EXEEXT) dan$(EXEEXT) \
- dbiblast$(EXEEXT) dbifasta$(EXEEXT) dbiflat$(EXEEXT) \
- dbigcg$(EXEEXT) degapseq$(EXEEXT) descseq$(EXEEXT) \
-- diffseq$(EXEEXT) digest$(EXEEXT) distmat$(EXEEXT) \
-+ diffseq$(EXEEXT) edigest$(EXEEXT) distmat$(EXEEXT) \
- dotmatcher$(EXEEXT) dotpath$(EXEEXT) dottup$(EXEEXT) \
- dreg$(EXEEXT) einverted$(EXEEXT) embossdata$(EXEEXT) \
- embossversion$(EXEEXT) emma$(EXEEXT) emowse$(EXEEXT) \
-@@ -531,13 +531,13 @@
- @ISCYGWIN_TRUE@diffseq_DEPENDENCIES = ../nucleus/libnucleus.la \
- @ISCYGWIN_TRUE@ ../ajax/libajax.la ../plplot/libplplot.la \
- @ISCYGWIN_TRUE@ $(am__DEPENDENCIES_1)
--am_digest_OBJECTS = digest.$(OBJEXT)
--digest_OBJECTS = $(am_digest_OBJECTS)
--digest_LDADD = $(LDADD)
--@ISCYGWIN_FALSE@digest_DEPENDENCIES = ../nucleus/libnucleus.la \
-+am_edigest_OBJECTS = edigest.$(OBJEXT)
-+edigest_OBJECTS = $(am_edigest_OBJECTS)
-+edigest_LDADD = $(LDADD)
-+@ISCYGWIN_FALSE@edigest_DEPENDENCIES = ../nucleus/libnucleus.la \
- @ISCYGWIN_FALSE@ ../ajax/libajaxg.la ../ajax/libajax.la \
- @ISCYGWIN_FALSE@ ../plplot/libplplot.la $(am__DEPENDENCIES_1)
--@ISCYGWIN_TRUE@digest_DEPENDENCIES = ../nucleus/libnucleus.la \
-+@ISCYGWIN_TRUE@edigest_DEPENDENCIES = ../nucleus/libnucleus.la \
- @ISCYGWIN_TRUE@ ../ajax/libajax.la ../plplot/libplplot.la \
- @ISCYGWIN_TRUE@ $(am__DEPENDENCIES_1)
- am_distmat_OBJECTS = distmat.$(OBJEXT)
-@@ -1839,7 +1839,7 @@
- @AMDEP_TRUE@ ./$(DEPDIR)/demosequence.Po \
- @AMDEP_TRUE@ ./$(DEPDIR)/demostring.Po ./$(DEPDIR)/demotable.Po \
- @AMDEP_TRUE@ ./$(DEPDIR)/descseq.Po ./$(DEPDIR)/diffseq.Po \
--@AMDEP_TRUE@ ./$(DEPDIR)/digest.Po ./$(DEPDIR)/distmat.Po \
-+@AMDEP_TRUE@ ./$(DEPDIR)/edigest.Po ./$(DEPDIR)/distmat.Po \
- @AMDEP_TRUE@ ./$(DEPDIR)/dotmatcher.Po ./$(DEPDIR)/dotpath.Po \
- @AMDEP_TRUE@ ./$(DEPDIR)/dottup.Po ./$(DEPDIR)/dreg.Po \
- @AMDEP_TRUE@ ./$(DEPDIR)/einverted.Po ./$(DEPDIR)/embossdata.Po \
-@@ -1942,7 +1942,7 @@
- $(demofeatures_SOURCES) $(demolist_SOURCES) \
- $(demoreport_SOURCES) $(demosequence_SOURCES) \
- $(demostring_SOURCES) $(demotable_SOURCES) $(descseq_SOURCES) \
-- $(diffseq_SOURCES) $(digest_SOURCES) $(distmat_SOURCES) \
-+ $(diffseq_SOURCES) $(edigest_SOURCES) $(distmat_SOURCES) \
- $(dotmatcher_SOURCES) $(dotpath_SOURCES) $(dottup_SOURCES) \
- $(dreg_SOURCES) $(einverted_SOURCES) $(embossdata_SOURCES) \
- $(embossversion_SOURCES) $(emma_SOURCES) $(emowse_SOURCES) \
-@@ -2009,7 +2009,7 @@
- $(demofeatures_SOURCES) $(demolist_SOURCES) \
- $(demoreport_SOURCES) $(demosequence_SOURCES) \
- $(demostring_SOURCES) $(demotable_SOURCES) $(descseq_SOURCES) \
-- $(diffseq_SOURCES) $(digest_SOURCES) $(distmat_SOURCES) \
-+ $(diffseq_SOURCES) $(edigest_SOURCES) $(distmat_SOURCES) \
- $(dotmatcher_SOURCES) $(dotpath_SOURCES) $(dottup_SOURCES) \
- $(dreg_SOURCES) $(einverted_SOURCES) $(embossdata_SOURCES) \
- $(embossversion_SOURCES) $(emma_SOURCES) $(emowse_SOURCES) \
-@@ -2240,7 +2240,7 @@
- degapseq_SOURCES = degapseq.c
- descseq_SOURCES = descseq.c
- diffseq_SOURCES = diffseq.c
--digest_SOURCES = digest.c
-+edigest_SOURCES = edigest.c
- distmat_SOURCES = distmat.c
- dotmatcher_SOURCES = dotmatcher.c
- dotpath_SOURCES = dotpath.c
-@@ -2602,9 +2602,9 @@
- diffseq$(EXEEXT): $(diffseq_OBJECTS) $(diffseq_DEPENDENCIES)
- @rm -f diffseq$(EXEEXT)
- $(LINK) $(diffseq_LDFLAGS) $(diffseq_OBJECTS) $(diffseq_LDADD) $(LIBS)
--digest$(EXEEXT): $(digest_OBJECTS) $(digest_DEPENDENCIES)
-- @rm -f digest$(EXEEXT)
-- $(LINK) $(digest_LDFLAGS) $(digest_OBJECTS) $(digest_LDADD) $(LIBS)
-+edigest$(EXEEXT): $(edigest_OBJECTS) $(edigest_DEPENDENCIES)
-+ @rm -f edigest$(EXEEXT)
-+ $(LINK) $(edigest_LDFLAGS) $(edigest_OBJECTS) $(edigest_LDADD) $(LIBS)
- distmat$(EXEEXT): $(distmat_OBJECTS) $(distmat_DEPENDENCIES)
- @rm -f distmat$(EXEEXT)
- $(LINK) $(distmat_LDFLAGS) $(distmat_OBJECTS) $(distmat_LDADD) $(LIBS)
-@@ -3081,7 +3081,7 @@
- @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/demotable.Po@am__quote@
- @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/descseq.Po@am__quote@
- @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/diffseq.Po@am__quote@
--@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/digest.Po@am__quote@
-+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/edigest.Po@am__quote@
- @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/distmat.Po@am__quote@
- @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/dotmatcher.Po@am__quote@
- @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/dotpath.Po@am__quote@
diff --git a/emboss-base/patches/patch-ae b/emboss-base/patches/patch-ae
deleted file mode 100644
index df437e1c02..0000000000
--- a/emboss-base/patches/patch-ae
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD: patch-ae,v 1.1.1.1 2004/11/11 20:57:21 daprice Exp $
-
---- emboss/Makefile.am.orig Wed Jul 21 15:08:17 2004
-+++ emboss/Makefile.am Wed Jul 21 15:08:42 2004
-@@ -29,7 +29,7 @@
- cai chaos charge checktrans chips cirdna codcmp coderet \
- compseq cons cpgplot cpgreport cusp cutgextract cutseq \
- dan dbiblast dbifasta dbiflat dbigcg \
--degapseq descseq diffseq digest distmat \
-+degapseq descseq diffseq edigest distmat \
- dotmatcher dotpath dottup dreg \
- einverted embossdata embossversion emma emowse entret \
- epestfind eprimer3 equicktandem est2genome etandem extractfeat extractseq \
-@@ -97,7 +97,7 @@
- degapseq_SOURCES = degapseq.c
- descseq_SOURCES = descseq.c
- diffseq_SOURCES = diffseq.c
--digest_SOURCES = digest.c
-+edigest_SOURCES = edigest.c
- distmat_SOURCES = distmat.c
- dotmatcher_SOURCES = dotmatcher.c
- dotpath_SOURCES = dotpath.c
diff --git a/emboss-base/patches/patch-af b/emboss-base/patches/patch-af
deleted file mode 100644
index 4bdebf0f53..0000000000
--- a/emboss-base/patches/patch-af
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-af,v 1.1.1.1 2004/11/11 20:57:22 daprice Exp $
-
---- emboss/acd/Makefile.am.orig Wed Jul 21 13:29:15 2004
-+++ emboss/acd/Makefile.am Wed Jul 21 13:29:34 2004
-@@ -12,7 +12,7 @@
- demoreport.acd demosequence.acd \
- demostring.acd demotable.acd \
- descseq.acd diffseq.acd \
-- digest.acd distmat.acd \
-+ edigest.acd distmat.acd \
- dotmatcher.acd dotpath.acd dottup.acd \
- dreg.acd einverted.acd embossdata.acd embossversion.acd emma.acd \
- emowse.acd entrails.acd entret.acd epestfind.acd eprimer3.acd \
diff --git a/emboss-base/patches/patch-ag b/emboss-base/patches/patch-ag
deleted file mode 100644
index 4fd2a89986..0000000000
--- a/emboss-base/patches/patch-ag
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-ag,v 1.1.1.1 2004/11/11 20:57:21 daprice Exp $
-
---- emboss/acd/Makefile.in.orig Wed Jul 21 13:43:21 2004
-+++ emboss/acd/Makefile.in Wed Jul 21 13:43:39 2004
-@@ -193,7 +193,7 @@
- demoreport.acd demosequence.acd \
- demostring.acd demotable.acd \
- descseq.acd diffseq.acd \
-- digest.acd distmat.acd \
-+ edigest.acd distmat.acd \
- dotmatcher.acd dotpath.acd dottup.acd \
- dreg.acd einverted.acd embossdata.acd embossversion.acd emma.acd \
- emowse.acd entrails.acd entret.acd epestfind.acd eprimer3.acd \
diff --git a/emboss-base/patches/patch-ah b/emboss-base/patches/patch-ah
deleted file mode 100644
index b8c9c0892a..0000000000
--- a/emboss-base/patches/patch-ah
+++ /dev/null
@@ -1,10 +0,0 @@
-$NetBSD: patch-ah,v 1.1.1.1 2004/11/11 20:57:21 daprice Exp $
-
---- emboss/acd/digest.acd.orig Wed Jul 21 13:44:47 2004
-+++ emboss/acd/digest.acd Wed Jul 21 13:45:07 2004
-@@ -1,4 +1,4 @@
--application: digest [
-+application: edigest [
- documentation: "Protein proteolytic enzyme or reagent
- cleavage digest"
- groups: "Protein:Motifs"
diff --git a/emboss-base/patches/patch-ai b/emboss-base/patches/patch-ai
deleted file mode 100644
index 820bef9412..0000000000
--- a/emboss-base/patches/patch-ai
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-ai,v 1.1.1.1 2004/11/11 20:57:21 daprice Exp $
-
---- emboss/acd/Makefile.orig Wed Jul 21 13:45:49 2004
-+++ emboss/acd/Makefile Wed Jul 21 13:46:08 2004
-@@ -193,7 +193,7 @@
- demoreport.acd demosequence.acd \
- demostring.acd demotable.acd \
- descseq.acd diffseq.acd \
-- digest.acd distmat.acd \
-+ edigest.acd distmat.acd \
- dotmatcher.acd dotpath.acd dottup.acd \
- dreg.acd einverted.acd embossdata.acd embossversion.acd emma.acd \
- emowse.acd entrails.acd entret.acd epestfind.acd eprimer3.acd \
diff --git a/emboss-base/patches/patch-aj b/emboss-base/patches/patch-aj
deleted file mode 100644
index 9003f33bca..0000000000
--- a/emboss-base/patches/patch-aj
+++ /dev/null
@@ -1,19 +0,0 @@
-$NetBSD: patch-aj,v 1.1.1.1 2004/11/11 20:57:21 daprice Exp $
-
---- emboss/digest.c.orig Wed Jul 21 13:46:26 2004
-+++ emboss/digest.c Wed Jul 21 13:47:10 2004
-@@ -1,4 +1,4 @@
--/* @source digest application
-+/* @source edigest application
- **
- ** Calculate protein proteolytic (and CNBr) digest fragments
- **
-@@ -68,7 +68,7 @@
- ajint npart;
-
-
-- embInit("digest", argc, argv);
-+ embInit("edigest", argc, argv);
-
- a = ajAcdGetSeq("sequence");
- menu = ajAcdGetList("menu");
diff --git a/emboss-base/patches/patch-ak b/emboss-base/patches/patch-ak
deleted file mode 100644
index a9c03db241..0000000000
--- a/emboss-base/patches/patch-ak
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD: patch-ak,v 1.1.1.1 2004/11/11 20:57:22 daprice Exp $
-
---- Makefile.in.orig Wed Jul 21 13:47:50 2004
-+++ Makefile.in Wed Jul 21 13:49:00 2004
-@@ -200,7 +200,7 @@
- sysconfdir = @sysconfdir@
- target_alias = @target_alias@
- AUTOMAKE_OPTIONS = gnits
--SUBDIRS = plplot ajax nucleus emboss test doc jemboss
-+SUBDIRS = plplot ajax nucleus emboss test doc #jemboss
-
- # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\"
-
-@@ -629,7 +629,7 @@
- tar cBf - emboss/data | ( cd $(distdir); tar xBf - ; cd emboss/data; rm -rf CVS */CVS */*/CVS )
- tar cBf - plplot/lib | ( cd $(distdir); tar xBf - ; find plplot -name CVS -exec rm -rf {} \; )
- tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS -exec rm -rf {} \; )
-- tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS -exec rm -rf {} \;; find jemboss -name Makefile -exec rm -rf {} \; )
-+# tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS -exec rm -rf {} \;; find jemboss -name Makefile -exec rm -rf {} \; )
- # Tell versions [3.59,3.63) of GNU make to not export all variables.
- # Otherwise a system limit (for SysV at least) may be exceeded.
- .NOEXPORT:
diff --git a/emboss-base/patches/patch-al b/emboss-base/patches/patch-al
deleted file mode 100644
index ca2cbf37b7..0000000000
--- a/emboss-base/patches/patch-al
+++ /dev/null
@@ -1,88 +0,0 @@
-$NetBSD: patch-al,v 1.1.1.1 2004/11/11 20:57:21 daprice Exp $
-
---- configure.orig Thu Jul 15 07:54:41 2004
-+++ configure Mon Aug 9 11:31:48 2004
-@@ -24484,7 +24484,7 @@
-
-
-
-- ac_config_files="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile test/embl/Makefile test/genbank/Makefile test/gb/Makefile test/pir/Makefile test/swiss/Makefile test/swnew/Makefile test/wormpep/Makefile emboss/data/Makefile emboss/data/AAINDEX/Makefile emboss/dat
a/CODONS/Makefile emboss/data/REBASE/Makefile emboss/data/PRINTS/Makefile emboss/data/PROSITE/Makefile doc/Makefile doc/manuals/Makefile doc/tutorials/Makefile doc/programs/Makefile doc/programs/html/Makefile doc/programs/text/Makefile jemboss/Makefile jemboss/api/Makefile jemboss/api/org/Makefile jemboss/api/org/emboss/Makefile jemboss/api/org/emboss/jemboss/Makefile jemboss/api/org/emboss/jemboss/gui/Makefile jemboss/api/org/emboss/jemboss/gui/filetree/Makefile jemboss/api/org/emboss/jemboss/gui/form/Makefile jemboss/api/org/emboss/jemboss/gui/sequenceChooser/Makefile jemboss/api/org/emboss/jemboss/gui/startup/Makefile jemboss/api/org/emboss/jemboss/parser/Makefile jemboss/api/org/emboss/jemboss/parser/acd/Makefile jemboss/api/org/emboss/jemboss/programs/Makefile jemboss/api/org/emboss/jemboss/soap/Makefile jemboss/images/Makefile jemboss/lib/Makefile jemboss/lib/axis/Makefile jemboss/org/Makefile jemboss/org/emboss/Makefile jemboss/org/emboss/jemboss/Makefile jemboss/org/emboss/je
mboss/gui/Makefile jemboss/org/emboss/jemboss/gui/filetree/Makefile jemboss/org/emboss/jemboss/gui/form/Makefile jemboss/org/emboss/jemboss/gui/startup/Makefile jemboss/org/emboss/jemboss/gui/sequenceChooser/Makefile jemboss/org/emboss/jemboss/parser/Makefile jemboss/org/emboss/jemboss/parser/acd/Makefile jemboss/org/emboss/jemboss/programs/Makefile jemboss/org/emboss/jemboss/server/Makefile jemboss/org/emboss/jemboss/soap/Makefile jemboss/org/emboss/jemboss/editor/Makefile jemboss/org/emboss/jemboss/draw/Makefile jemboss/resources/Makefile jemboss/utils/Makefile Makefile"
-+ ac_config_files="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile test/embl/Makefile test/genbank/Makefile test/gb/Makefile test/pir/Makefile test/swiss/Makefile test/swnew/Makefile test/wormpep/Makefile emboss/data/Makefile emboss/data/AAINDEX/Makefile emboss/dat
a/CODONS/Makefile emboss/data/REBASE/Makefile emboss/data/PRINTS/Makefile emboss/data/PROSITE/Makefile doc/Makefile doc/manuals/Makefile doc/tutorials/Makefile doc/programs/Makefile doc/programs/html/Makefile doc/programs/text/Makefile Makefile"
- cat >confcache <<\_ACEOF
- # This file is a shell script that caches the results of configure
- # tests run on this system so they can be shared between configure
-@@ -25150,40 +25150,40 @@
- "doc/programs/Makefile" ) CONFIG_FILES="$CONFIG_FILES doc/programs/Makefile" ;;
- "doc/programs/html/Makefile" ) CONFIG_FILES="$CONFIG_FILES doc/programs/html/Makefile" ;;
- "doc/programs/text/Makefile" ) CONFIG_FILES="$CONFIG_FILES doc/programs/text/Makefile" ;;
-- "jemboss/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/Makefile" ;;
-- "jemboss/api/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/Makefile" ;;
-- "jemboss/api/org/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/org/Makefile" ;;
-- "jemboss/api/org/emboss/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/org/emboss/Makefile" ;;
-- "jemboss/api/org/emboss/jemboss/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/org/emboss/jemboss/Makefile" ;;
-- "jemboss/api/org/emboss/jemboss/gui/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/org/emboss/jemboss/gui/Makefile" ;;
-- "jemboss/api/org/emboss/jemboss/gui/filetree/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/org/emboss/jemboss/gui/filetree/Makefile" ;;
-- "jemboss/api/org/emboss/jemboss/gui/form/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/org/emboss/jemboss/gui/form/Makefile" ;;
-- "jemboss/api/org/emboss/jemboss/gui/sequenceChooser/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/org/emboss/jemboss/gui/sequenceChooser/Makefile" ;;
-- "jemboss/api/org/emboss/jemboss/gui/startup/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/org/emboss/jemboss/gui/startup/Makefile" ;;
-- "jemboss/api/org/emboss/jemboss/parser/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/org/emboss/jemboss/parser/Makefile" ;;
-- "jemboss/api/org/emboss/jemboss/parser/acd/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/org/emboss/jemboss/parser/acd/Makefile" ;;
-- "jemboss/api/org/emboss/jemboss/programs/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/org/emboss/jemboss/programs/Makefile" ;;
-- "jemboss/api/org/emboss/jemboss/soap/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/org/emboss/jemboss/soap/Makefile" ;;
-- "jemboss/images/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/images/Makefile" ;;
-- "jemboss/lib/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/lib/Makefile" ;;
-- "jemboss/lib/axis/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/lib/axis/Makefile" ;;
-- "jemboss/org/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/Makefile" ;;
-- "jemboss/org/emboss/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/Makefile" ;;
-- "jemboss/org/emboss/jemboss/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/jemboss/Makefile" ;;
-- "jemboss/org/emboss/jemboss/gui/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/jemboss/gui/Makefile" ;;
-- "jemboss/org/emboss/jemboss/gui/filetree/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/jemboss/gui/filetree/Makefile" ;;
-- "jemboss/org/emboss/jemboss/gui/form/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/jemboss/gui/form/Makefile" ;;
-- "jemboss/org/emboss/jemboss/gui/startup/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/jemboss/gui/startup/Makefile" ;;
-- "jemboss/org/emboss/jemboss/gui/sequenceChooser/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/jemboss/gui/sequenceChooser/Makefile" ;;
-- "jemboss/org/emboss/jemboss/parser/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/jemboss/parser/Makefile" ;;
-- "jemboss/org/emboss/jemboss/parser/acd/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/jemboss/parser/acd/Makefile" ;;
-- "jemboss/org/emboss/jemboss/programs/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/jemboss/programs/Makefile" ;;
-- "jemboss/org/emboss/jemboss/server/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/jemboss/server/Makefile" ;;
-- "jemboss/org/emboss/jemboss/soap/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/jemboss/soap/Makefile" ;;
-- "jemboss/org/emboss/jemboss/editor/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/jemboss/editor/Makefile" ;;
-- "jemboss/org/emboss/jemboss/draw/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/jemboss/draw/Makefile" ;;
-- "jemboss/resources/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/resources/Makefile" ;;
-- "jemboss/utils/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/utils/Makefile" ;;
-+ #"jemboss/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/Makefile" ;;
-+ #"jemboss/api/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/Makefile" ;;
-+ #"jemboss/api/org/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/api/org/Makefile" ;;
-+ #"jemboss/api/org/emboss/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/api/org/emboss/Makefile" ;;
-+# "jemboss/api/org/emboss/jemboss/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/api/org/emboss/jemboss/Makefile" ;;
-+# "jemboss/api/org/emboss/jemboss/gui/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/api/org/emboss/jemboss/gui/Makefile" ;;
-+# "jemboss/api/org/emboss/jemboss/gui/filetree/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/api/org/emboss/jemboss/gui/filetree/Makefile" ;;
-+# "jemboss/api/org/emboss/jemboss/gui/form/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/api/org/emboss/jemboss/gui/form/Makefile" ;;
-+# "jemboss/api/org/emboss/jemboss/gui/sequenceChooser/Makefile" ) #CONFIG_FILES="$CONFIG_FILES jemboss/api/org/emboss/jemboss/gui/sequenceChooser/Makefile" ;;
-+# "jemboss/api/org/emboss/jemboss/gui/startup/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/api/org/emboss/jemboss/gui/startup/Makefile" ;;
-+# "jemboss/api/org/emboss/jemboss/parser/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/api/org/emboss/jemboss/parser/Makefile" ;;
-+# "jemboss/api/org/emboss/jemboss/parser/acd/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/api/org/emboss/jemboss/parser/acd/Makefile" ;;
-+# "jemboss/api/org/emboss/jemboss/programs/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/api/org/emboss/jemboss/programs/Makefile" ;;
-+# "jemboss/api/org/emboss/jemboss/soap/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/api/org/emboss/jemboss/soap/Makefile" ;;
-+# "jemboss/images/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/images/Makefile" ;;
-+# "jemboss/lib/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/lib/Makefile" ;;
-+# "jemboss/lib/axis/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/lib/axis/Makefile" ;;
-+# "jemboss/org/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/Makefile" ;;
-+# "jemboss/org/emboss/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/org/emboss/Makefile" #;;
-+# "jemboss/org/emboss/jemboss/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/org/emboss/jemboss/Makefile" ;;
-+# "jemboss/org/emboss/jemboss/gui/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/org/emboss/jemboss/gui/Makefile" ;;
-+# "jemboss/org/emboss/jemboss/gui/filetree/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/org/emboss/jemboss/gui/filetree/Makefile" ;;
-+# "jemboss/org/emboss/jemboss/gui/form/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/org/emboss/jemboss/gui/form/Makefile" ;;
-+# "jemboss/org/emboss/jemboss/gui/startup/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/org/emboss/jemboss/gui/startup/Makefile" ;;
-+# "jemboss/org/emboss/jemboss/gui/sequenceChooser/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/org/emboss/jemboss/gui/sequenceChooser/Makefile" ;;
-+# "jemboss/org/emboss/jemboss/parser/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/org/emboss/jemboss/parser/Makefile" ;;
-+# "jemboss/org/emboss/jemboss/parser/acd/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/org/emboss/jemboss/parser/acd/Makefile" ;;
-+# "jemboss/org/emboss/jemboss/programs/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/org/emboss/jemboss/programs/Makefile" ;;
-+# "jemboss/org/emboss/jemboss/server/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/org/emboss/jemboss/server/Makefile" ;;
-+# "jemboss/org/emboss/jemboss/soap/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/org/emboss/jemboss/soap/Makefile" ;;
-+# "jemboss/org/emboss/jemboss/editor/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/org/emboss/jemboss/editor/Makefile" ;;
-+# "jemboss/org/emboss/jemboss/draw/Makefile" ) CONFIG_FILES="$CONFIG_FILES #jemboss/org/emboss/jemboss/draw/Makefile" ;;
-+# "jemboss/resources/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/resources/Makefile" ;;
-+# "jemboss/utils/Makefile" ) CONFIG_FILES="$CONFIG_FILES jemboss/utils/Makefile" ;;
- "Makefile" ) CONFIG_FILES="$CONFIG_FILES Makefile" ;;
- "depfiles" ) CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
- *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
diff --git a/emboss-domainatrix/DESCR b/emboss-domainatrix/DESCR
deleted file mode 100644
index 5b9da9955e..0000000000
--- a/emboss-domainatrix/DESCR
+++ /dev/null
@@ -1 +0,0 @@
-DOMAINATRIX is a supplimentary package for EMBOSS.
diff --git a/emboss-domainatrix/Makefile b/emboss-domainatrix/Makefile
deleted file mode 100644
index d479ba3464..0000000000
--- a/emboss-domainatrix/Makefile
+++ /dev/null
@@ -1,28 +0,0 @@
-# $NetBSD: Makefile,v 1.3 2012/09/02 11:14:10 noud4 Exp $
-#
-
-.include "../emboss-base/Makefile.common"
-.include "../emboss/Makefile.common"
-
-DISTNAME= DOMAINATRIX-1.0.0
-PKGNAME= emboss-domainatrix-1.0.0
-PKGREVISION= 1
-
-COMMENT= Collection of bioinformatic programs for EMBOSS
-LICENSE= gnu-gpl-v2
-
-BUILD_TARGET= #empty
-DIST_SUBDIR= emboss/domainatrix-1.0.0-20040715
-
-pre-configure:
- ${SED} -e 's|../../../plplot/libplplot.la|${PREFIX}/lib/libplplot.la|' \
- -e 's|../../../ajax/libajaxg.la|${PREFIX}/lib/libajaxg.la|' \
- -e 's|../../../ajax/libajax.la|${PREFIX}/lib/libajax.la|' \
- -e 's|../../../nucleus/libnucleus.la|${PREFIX}/lib/libnucleus.la|' \
- -e 's|/../../depcomp|/depcomp|' \
- -e 's|@INCLUDE@|${PREFIX}/include/emboss|' \
- -e 's|@X116@|-Wl,-R${X11BASE}/lib|' \
- ${WRKSRC}/src/Makefile.in > ${WRKSRC}/src/Makefile.in.bak
- ${MV} ${WRKSRC}/src/Makefile.in.bak ${WRKSRC}/src/Makefile.in
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/emboss-domainatrix/PLIST b/emboss-domainatrix/PLIST
deleted file mode 100644
index 5333c3740f..0000000000
--- a/emboss-domainatrix/PLIST
+++ /dev/null
@@ -1,53 +0,0 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2004/11/15 19:45:00 daprice Exp $
-bin/contacts
-bin/domainer
-bin/fraggle
-bin/hetparse
-bin/hmmgen
-bin/interface
-bin/libscan
-bin/pdbparse
-bin/pdbplus
-bin/pdbtosp
-bin/profgen
-bin/rocplot
-bin/scopalign
-bin/scopnr
-bin/scopparse
-bin/scoprep
-bin/scopreso
-bin/scopseqs
-bin/seqalign
-bin/seqnr
-bin/seqsearch
-bin/seqsort
-bin/seqwords
-bin/siggen
-bin/sigplot
-bin/sigscan
-share/EMBOSS/acd/contacts.acd
-share/EMBOSS/acd/domainer.acd
-share/EMBOSS/acd/fraggle.acd
-share/EMBOSS/acd/hetparse.acd
-share/EMBOSS/acd/hmmgen.acd
-share/EMBOSS/acd/interface.acd
-share/EMBOSS/acd/libscan.acd
-share/EMBOSS/acd/pdbparse.acd
-share/EMBOSS/acd/pdbplus.acd
-share/EMBOSS/acd/pdbtosp.acd
-share/EMBOSS/acd/profgen.acd
-share/EMBOSS/acd/rocplot.acd
-share/EMBOSS/acd/scopalign.acd
-share/EMBOSS/acd/scopnr.acd
-share/EMBOSS/acd/scopparse.acd
-share/EMBOSS/acd/scoprep.acd
-share/EMBOSS/acd/scopreso.acd
-share/EMBOSS/acd/scopseqs.acd
-share/EMBOSS/acd/seqalign.acd
-share/EMBOSS/acd/seqnr.acd
-share/EMBOSS/acd/seqsearch.acd
-share/EMBOSS/acd/seqsort.acd
-share/EMBOSS/acd/seqwords.acd
-share/EMBOSS/acd/siggen.acd
-share/EMBOSS/acd/sigplot.acd
-share/EMBOSS/acd/sigscan.acd
diff --git a/emboss-domainatrix/distinfo b/emboss-domainatrix/distinfo
deleted file mode 100644
index 42594ed36e..0000000000
--- a/emboss-domainatrix/distinfo
+++ /dev/null
@@ -1,7 +0,0 @@
-$NetBSD: distinfo,v 1.2 2006/08/26 15:41:20 kristerw Exp $
-
-RMD160 (emboss/domainatrix-1.0.0-20040715/DOMAINATRIX-1.0.0.tar.gz) = 12b798ea19a74659df134bc44c170fb52e0879a9
-SHA512 (emboss/domainatrix-1.0.0-20040715/DOMAINATRIX-1.0.0.tar.gz) = 2bdd2b0da4e5818cc24450c7f5b2900794211c93e58bf50a1230c934d0dc97118c70c53e6b5b12ebd8a899b46e5177c8481391207624fa6b476f170e2f9f9396
-Size (emboss/domainatrix-1.0.0-20040715/DOMAINATRIX-1.0.0.tar.gz) = 551090 bytes
-SHA1 (patch-aa) = cabe38402d2da8b447c53b820059c2eaed4db7bd
-SHA1 (patch-ab) = e72d544c796489d4b441a21147af9a125c4f370f
diff --git a/emboss-domainatrix/patches/patch-aa b/emboss-domainatrix/patches/patch-aa
deleted file mode 100644
index 4b2d62df0c..0000000000
--- a/emboss-domainatrix/patches/patch-aa
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-aa,v 1.1.1.1 2004/11/15 19:45:00 daprice Exp $
-
---- emboss_acd/Makefile.in.orig Tue Jul 27 13:37:11 2004
-+++ emboss_acd/Makefile.in Tue Jul 27 13:37:11 2004
-@@ -43,7 +43,7 @@
- $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- SOURCES =
- DIST_SOURCES =
diff --git a/emboss-domainatrix/patches/patch-ab b/emboss-domainatrix/patches/patch-ab
deleted file mode 100644
index dd83bea11a..0000000000
--- a/emboss-domainatrix/patches/patch-ab
+++ /dev/null
@@ -1,42 +0,0 @@
-$NetBSD: patch-ab,v 1.1.1.1 2004/11/15 19:45:00 daprice Exp $
-
---- src/Makefile.in.orig Thu Jul 15 09:42:02 2004
-+++ src/Makefile.in Tue Jul 27 14:25:14 2004
-@@ -55,7 +55,7 @@
- $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- am__installdirs = "$(DESTDIR)$(bindir)"
- binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
-@@ -503,7 +503,7 @@
- @ISCYGWIN_TRUE@@LOCALLINK_TRUE@ ../../../ajax/libajax.la \
- @ISCYGWIN_TRUE@@LOCALLINK_TRUE@ ../../../plplot/libplplot.la \
- @ISCYGWIN_TRUE@@LOCALLINK_TRUE@ $(am__DEPENDENCIES_1)
--DEFAULT_INCLUDES = -I. -I$(srcdir)
-+DEFAULT_INCLUDES = -I.
- depcomp = $(SHELL) $(top_srcdir)/depcomp
- am__depfiles_maybe = depfiles
- @AMDEP_TRUE@DEP_FILES = ./$(DEPDIR)/contacts.Po \
-@@ -638,7 +638,7 @@
- SHELL = @SHELL@
- STRIP = @STRIP@
- VERSION = @VERSION@
--XLIB = @XLIB@
-+XLIB = @X116@ @XLIB@
- X_CFLAGS = @X_CFLAGS@
- X_EXTRA_LIBS = @X_EXTRA_LIBS@
- X_LIBS = @X_LIBS@
-@@ -687,8 +687,8 @@
- sysconfdir = @sysconfdir@
- target_alias = @target_alias@
- SUBDIRS =
--@LOCALLINK_FALSE@INCLUDES = -I${embprefix}/include
--@LOCALLINK_TRUE@INCLUDES = -I../../../plplot -I../../../ajax -I../../../nucleus
-+@LOCALLINK_FALSE@INCLUDES = -I@INCLUDE@
-+@LOCALLINK_TRUE@INCLUDES = -I@INCLUDE@
- @ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS =
- @ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_FALSE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lajax -lnucleus
- @ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_TRUE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L../../../plplot/.libs -L../../../ajax/.libs -L../../../nucleus/.libs -lajax -lnucleus
diff --git a/emboss-emnu/DESCR b/emboss-emnu/DESCR
deleted file mode 100644
index d721a1f31a..0000000000
--- a/emboss-emnu/DESCR
+++ /dev/null
@@ -1 +0,0 @@
-EMNU provides a simple menu for EMBOSS applications.
diff --git a/emboss-emnu/Makefile b/emboss-emnu/Makefile
deleted file mode 100644
index 456a757f50..0000000000
--- a/emboss-emnu/Makefile
+++ /dev/null
@@ -1,34 +0,0 @@
-# $NetBSD: Makefile,v 1.5 2012/09/02 11:14:10 noud4 Exp $
-#
-
-.include "../emboss-base/Makefile.common"
-.include "../emboss/Makefile.common"
-
-DISTNAME= EMNU-1.05
-PKGNAME= emboss-emnu-1.05
-PKGREVISION= 1
-
-COMMENT= Simple menu for EMBOSS applications
-LICENSE= gnu-gpl-v2
-
-BUILD_TARGET= #empty
-DIST_SUBDIR= emboss/emnu-1.05-20041107
-GNU_CONFIGURE= yes
-#ncurses required for the redrawwin function
-USE_NCURSES= yes
-
-pre-configure:
- ${SED} -e 's|../../../plplot/libplplot.la|${PREFIX}/lib/libplplot.la|' \
- -e 's|../../../ajax/libajax.la|${PREFIX}/lib/libajax.la|' \
- -e 's|../../../nucleus/libnucleus.la|${PREFIX}/lib/libnucleus.la|' \
- -e 's|@NCURSES@|-L${PREFIX}/lib -lncurses|' \
- -e 's|@X116@|-Wl,-R${X11BASE}/lib|' \
- -e 's|@INCLUDE@|-I${PREFIX}/include/emboss|' \
- ${WRKSRC}/source/Makefile.in > ${WRKSRC}/source/Makefile.in.bak
- ${MV} ${WRKSRC}/source/Makefile.in.bak ${WRKSRC}/source/Makefile.in
- ${SED} -e 's|@X116@|-Wl,-R${X11BASE}/lib|' \
- ${WRKSRC}/Makefile.in > ${WRKSRC}/Makefile.in.bak
- ${MV} ${WRKSRC}/Makefile.in.bak ${WRKSRC}/Makefile.in
-
-.include "../../devel/ncurses/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/emboss-emnu/PLIST b/emboss-emnu/PLIST
deleted file mode 100644
index 70c4a0e824..0000000000
--- a/emboss-emnu/PLIST
+++ /dev/null
@@ -1,3 +0,0 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2004/11/15 20:09:38 daprice Exp $
-bin/emnu
-share/EMBOSS/acd/emnu.acd
diff --git a/emboss-emnu/distinfo b/emboss-emnu/distinfo
deleted file mode 100644
index b1f395c28b..0000000000
--- a/emboss-emnu/distinfo
+++ /dev/null
@@ -1,8 +0,0 @@
-$NetBSD: distinfo,v 1.3 2006/08/26 15:41:20 kristerw Exp $
-
-RMD160 (emboss/emnu-1.05-20041107/EMNU-1.05.tar.gz) = 9919870d6d2a823eb7dfe69d0ceb1cb853b78b96
-SHA512 (emboss/emnu-1.05-20041107/EMNU-1.05.tar.gz) = e38f92e1751e00a445faf121371c12ea39ccbe7315365148ca3c2a4b2bf109b040ddc80e063b2a6cd2a8b474be891d30dc08a1822603565b7e56f1d88fe684ec
-Size (emboss/emnu-1.05-20041107/EMNU-1.05.tar.gz) = 341879 bytes
-SHA1 (patch-aa) = 7651e9aa9e8dc8fc8a0444f70eda5121fc467f1c
-SHA1 (patch-ab) = ef4e491662f95246f5070375514b6959de050b57
-SHA1 (patch-ac) = c306a01fe4bfba54a136ef3d57db79387481fcfe
diff --git a/emboss-emnu/patches/patch-aa b/emboss-emnu/patches/patch-aa
deleted file mode 100644
index 5cc21d5e2a..0000000000
--- a/emboss-emnu/patches/patch-aa
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-aa,v 1.1.1.1 2004/11/15 20:09:38 daprice Exp $
-
---- Makefile.in.orig Tue Jul 27 13:47:16 2004
-+++ Makefile.in Tue Jul 27 13:47:39 2004
-@@ -156,7 +156,7 @@
- SHELL = @SHELL@
- STRIP = @STRIP@
- VERSION = @VERSION@
--XLIB = @XLIB@
-+XLIB = @XLIB@ @X116@
- X_CFLAGS = @X_CFLAGS@
- X_EXTRA_LIBS = @X_EXTRA_LIBS@
- X_LIBS = @X_LIBS@
diff --git a/emboss-emnu/patches/patch-ab b/emboss-emnu/patches/patch-ab
deleted file mode 100644
index bf07641909..0000000000
--- a/emboss-emnu/patches/patch-ab
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD: patch-ab,v 1.1.1.1 2004/11/15 20:09:38 daprice Exp $
-
---- emboss_acd/Makefile.in.orig Tue Jul 27 13:50:02 2004
-+++ emboss_acd/Makefile.in Tue Jul 27 13:50:48 2004
-@@ -43,7 +43,7 @@
- $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- SOURCES =
- DIST_SOURCES =
-@@ -182,7 +182,7 @@
- sharedstatedir = @sharedstatedir@
- sysconfdir = @sysconfdir@
- target_alias = @target_alias@
--pkgdata_DATA = *.acd
-+pkgdata_DATA = emnu.acd
- all: all-am
-
- .SUFFIXES:
diff --git a/emboss-emnu/patches/patch-ac b/emboss-emnu/patches/patch-ac
deleted file mode 100644
index d988e5742a..0000000000
--- a/emboss-emnu/patches/patch-ac
+++ /dev/null
@@ -1,53 +0,0 @@
-$NetBSD: patch-ac,v 1.1.1.1 2004/11/15 20:09:38 daprice Exp $
-
---- source/Makefile.in.orig Thu Jul 15 09:45:32 2004
-+++ source/Makefile.in Tue Jul 27 14:30:13 2004
-@@ -47,7 +47,7 @@
- $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- am__installdirs = "$(DESTDIR)$(bindir)"
- binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
-@@ -61,8 +61,8 @@
- @LOCALLINK_TRUE@ ../../../ajax/libajax.la \
- @LOCALLINK_TRUE@ ../../../plplot/libplplot.la \
- @LOCALLINK_TRUE@ $(am__DEPENDENCIES_1)
--DEFAULT_INCLUDES = -I. -I$(srcdir)
--depcomp = $(SHELL) $(top_srcdir)/depcomp
-+DEFAULT_INCLUDES = -I.
-+depcomp = $(SHELL) ../depcomp
- am__depfiles_maybe = depfiles
- @AMDEP_TRUE@DEP_FILES = ./$(DEPDIR)/emnu.Po
- COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-@@ -128,7 +128,7 @@
- JAVA_OK = @JAVA_OK@
- LDFLAGS = @LDFLAGS@
- LIBOBJS = @LIBOBJS@
--LIBS = @LIBS@
-+LIBS = @NCURSES@ @LIBS@
- LIBTOOL = @LIBTOOL@
- LN_S = @LN_S@
- LOCALLINK_FALSE = @LOCALLINK_FALSE@
-@@ -160,7 +160,7 @@
- SHELL = @SHELL@
- STRIP = @STRIP@
- VERSION = @VERSION@
--XLIB = @XLIB@
-+XLIB = @X116@ @XLIB@
- X_CFLAGS = @X_CFLAGS@
- X_EXTRA_LIBS = @X_EXTRA_LIBS@
- X_LIBS = @X_LIBS@
-@@ -208,8 +208,8 @@
- sharedstatedir = @sharedstatedir@
- sysconfdir = @sysconfdir@
- target_alias = @target_alias@
--@LOCALLINK_FALSE@INCLUDES = -I${embprefix}/include
--@LOCALLINK_TRUE@INCLUDES = -I../../../plplot -I../../../nucleus -I../../../ajax
-+@LOCALLINK_FALSE@INCLUDES = @INCLUDE@
-+@LOCALLINK_TRUE@INCLUDES = @INCLUDE@
- @ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS =
- @ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_FALSE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lajax
- @ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_TRUE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L../../../ajax/.libs -lajax
diff --git a/emboss-hmmer/DESCR b/emboss-hmmer/DESCR
deleted file mode 100644
index 15430e4e12..0000000000
--- a/emboss-hmmer/DESCR
+++ /dev/null
@@ -1,2 +0,0 @@
-HMMER is a collection of bioinformatic programs that is supplimentary
-to EMBOSS package.
diff --git a/emboss-hmmer/Makefile b/emboss-hmmer/Makefile
deleted file mode 100644
index e850030a4c..0000000000
--- a/emboss-hmmer/Makefile
+++ /dev/null
@@ -1,23 +0,0 @@
-# $NetBSD: Makefile,v 1.6 2012/11/13 22:25:30 othyro Exp $
-#
-
-.include "../emboss-base/Makefile.common"
-.include "../emboss/Makefile.common"
-
-DISTNAME= HMMER-2.1.1
-PKGNAME= emboss-hmmer-2.1.1
-PKGREVISION= 2
-
-COMMENT= Collection of bioinformatic programs supplimenting the EMBOSS package
-LICENSE= gnu-gpl-v2
-
-DIST_SUBDIR= emboss/hmmer-2.1.1-20041107
-BUILD_TARGET= #EMPTY
-
-pre-configure:
- ${SED} -e 's|../../../ajax/libajax.la|${PREFIX}/lib/libajax.la|' \
- -e 's|@INCLUDE@|${PREFIX}/include/emboss|' \
- ${WRKSRC}/src/Makefile.in > ${WRKSRC}/src/Makefile.in.bak
- ${MV} ${WRKSRC}/src/Makefile.in.bak ${WRKSRC}/src/Makefile.in
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/emboss-hmmer/PLIST b/emboss-hmmer/PLIST
deleted file mode 100644
index 8f324506bd..0000000000
--- a/emboss-hmmer/PLIST
+++ /dev/null
@@ -1,22 +0,0 @@
-@comment $NetBSD: PLIST,v 1.2 2004/12/14 19:10:58 daprice Exp $
-bin/ealistat
-bin/ehmmalign
-bin/ehmmbuild
-bin/ehmmcalibrate
-bin/ehmmconvert
-bin/ehmmemit
-bin/ehmmfetch
-bin/ehmmindex
-bin/ehmmpfam
-bin/ehmmsearch
-lib/libhmmer.la
-share/EMBOSS/acd/ealistat.acd
-share/EMBOSS/acd/ehmmalign.acd
-share/EMBOSS/acd/ehmmbuild.acd
-share/EMBOSS/acd/ehmmcalibrate.acd
-share/EMBOSS/acd/ehmmconvert.acd
-share/EMBOSS/acd/ehmmemit.acd
-share/EMBOSS/acd/ehmmfetch.acd
-share/EMBOSS/acd/ehmmindex.acd
-share/EMBOSS/acd/ehmmpfam.acd
-share/EMBOSS/acd/ehmmsearch.acd
diff --git a/emboss-hmmer/distinfo b/emboss-hmmer/distinfo
deleted file mode 100644
index 7ff0c7c22a..0000000000
--- a/emboss-hmmer/distinfo
+++ /dev/null
@@ -1,8 +0,0 @@
-$NetBSD: distinfo,v 1.4 2012/09/02 11:14:10 noud4 Exp $
-
-RMD160 (emboss/hmmer-2.1.1-20041107/HMMER-2.1.1.tar.gz) = 994d284b5fca77a6264643c8711a696cc0752051
-SHA512 (emboss/hmmer-2.1.1-20041107/HMMER-2.1.1.tar.gz) = bc6e65ff0b72d5205f97ae4e945851ab75b521571ac719f07523b28a72403e8e4ccf0ab1e7db4f29aa22179c89f57c63e4b562f989a3c86c67a7bca0cde74c76
-Size (emboss/hmmer-2.1.1-20041107/HMMER-2.1.1.tar.gz) = 555504 bytes
-SHA1 (patch-aa) = 19ece4e7116ecaec51cd9abef3460c5093241263
-SHA1 (patch-ab) = 2dc7c3085966d064005b8419f5724702e473d3d3
-SHA1 (patch-ac) = 91e569cda3fefdf152bc8d2727ce1d86e5259e5f
diff --git a/emboss-hmmer/patches/patch-aa b/emboss-hmmer/patches/patch-aa
deleted file mode 100644
index 5ec59f4c58..0000000000
--- a/emboss-hmmer/patches/patch-aa
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-aa,v 1.1.1.1 2004/11/15 20:21:19 daprice Exp $
-
---- emboss_acd/Makefile.in.orig Tue Jul 27 14:11:54 2004
-+++ emboss_acd/Makefile.in Tue Jul 27 14:11:54 2004
-@@ -43,7 +43,7 @@
- $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- SOURCES =
- DIST_SOURCES =
diff --git a/emboss-hmmer/patches/patch-ab b/emboss-hmmer/patches/patch-ab
deleted file mode 100644
index c93920d6e1..0000000000
--- a/emboss-hmmer/patches/patch-ab
+++ /dev/null
@@ -1,34 +0,0 @@
-$NetBSD: patch-ab,v 1.1.1.1 2004/11/15 20:21:19 daprice Exp $
-
---- src/Makefile.in.orig Tue Jul 27 14:15:13 2004
-+++ src/Makefile.in Tue Jul 27 14:17:37 2004
-@@ -53,7 +53,7 @@
- $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)"
- libLTLIBRARIES_INSTALL = $(INSTALL)
-@@ -172,8 +172,8 @@
- @LOCALLINK_TRUE@ ../../../ajax/libajax.la \
- @LOCALLINK_TRUE@ ../../../plplot/libplplot.la \
- @LOCALLINK_TRUE@ $(am__DEPENDENCIES_1)
--DEFAULT_INCLUDES = -I. -I$(srcdir)
--depcomp = $(SHELL) $(top_srcdir)/depcomp
-+DEFAULT_INCLUDES = -I.
-+depcomp = $(SHELL) ../depcomp
- am__depfiles_maybe = depfiles
- @AMDEP_TRUE@DEP_FILES = ./$(DEPDIR)/aligneval.Plo \
- @AMDEP_TRUE@ ./$(DEPDIR)/alignio.Plo ./$(DEPDIR)/alphabet.Plo \
-@@ -356,7 +356,7 @@
- target_alias = @target_alias@
- lib_LTLIBRARIES = libhmmer.la
--@LOCALLINK_FALSE@INCLUDES = -IINCLUDE -I${embprefix}/include
--@LOCALLINK_TRUE@INCLUDES = -IINCLUDE -I../../../ajax
-+@LOCALLINK_FALSE@INCLUDES = -IINCLUDE -I@INCLUDE@
-+@LOCALLINK_TRUE@INCLUDES = -IINCLUDE -I@INCLUDE@
- @ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS =
- @ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_FALSE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lajax
- @ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_TRUE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L../../../ajax/.libs -lajax
diff --git a/emboss-hmmer/patches/patch-ac b/emboss-hmmer/patches/patch-ac
deleted file mode 100644
index cc79666f37..0000000000
--- a/emboss-hmmer/patches/patch-ac
+++ /dev/null
@@ -1,302 +0,0 @@
-$NetBSD: patch-ac,v 1.2 2011/10/26 14:52:36 noud4 Exp $
-
---- src/sqio.c.orig 2011-10-26 13:18:53.000000000 +0000
-+++ src/sqio.c 2011-10-26 13:18:55.000000000 +0000
-@@ -219,7 +219,7 @@
- }
- }
-
--/* Function: getline()
-+/* Function: mygetline()
- * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis]
- *
- * Purpose: read a line from a sequence file into V->sbuffer.
-@@ -235,7 +235,7 @@
- * Returns: (void)
- */
- static void
--getline(struct ReadSeqVars *V)
-+mygetline(struct ReadSeqVars *V)
- {
- char *cp;
-
-@@ -305,7 +305,7 @@
- V->seqlen = 0;
- if (addfirst) addseq(V->sbuffer, V);
- do {
-- getline(V);
-+ mygetline(V);
- /* feof() alone is a bug; files not necessarily \n terminated */
- if (*(V->sbuffer) == '\0' && feof(V->f))
- done = TRUE;
-@@ -333,7 +333,7 @@
- char *sptr;
- /* load first line of entry */
- while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
-- getline(V);
-+ mygetline(V);
- if (feof(V->f)) return;
-
- if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
-@@ -342,7 +342,7 @@
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
- }
- do {
-- getline(V);
-+ mygetline(V);
- if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
- SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
- else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
-@@ -351,7 +351,7 @@
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
- }
- } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
-- getline(V); /* skip next line, coords */
-+ mygetline(V); /* skip next line, coords */
-
- readLoop(0, endPIR, V);
-
-@@ -365,7 +365,7 @@
- /* get next line
- */
- while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
-- getline(V);
-+ mygetline(V);
- }
-
-
-@@ -383,7 +383,7 @@
- char *nm;
- /* position past ';' comments */
- do {
-- getline(V);
-+ mygetline(V);
- } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
-
- if (!feof(V->f))
-@@ -395,7 +395,7 @@
- }
-
- while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
-- getline(V);
-+ mygetline(V);
- }
-
- static int
-@@ -417,7 +417,7 @@
- if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
- SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
- }
-- getline(V);
-+ mygetline(V);
- }
-
- if (! feof(V->f))
-@@ -426,7 +426,7 @@
- /* load next line
- */
- while ((!feof(V->f)) && (*V->sbuffer != ';'))
-- getline(V);
-+ mygetline(V);
- }
-
-
-@@ -444,7 +444,7 @@
- int in_definition;
-
- while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
-- getline(V);
-+ mygetline(V);
-
- if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
- {
-@@ -455,7 +455,7 @@
- in_definition = FALSE;
- while (! feof(V->f))
- {
-- getline(V);
-+ mygetline(V);
- if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
- {
- if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
-@@ -488,11 +488,11 @@
-
-
- while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
-- getline(V);
-+ mygetline(V);
- /* SRE: V->s now holds "//", so sequential
- reads are wedged: fixed Tue Jul 13 1993 */
- while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
-- getline(V);
-+ mygetline(V);
- }
-
- static int
-@@ -521,7 +521,7 @@
- Die("bogus GCGdata format? %s", V->sbuffer);
-
- /* second line contains free text description */
-- getline(V);
-+ mygetline(V);
- SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
-
- if (binary) {
-@@ -541,7 +541,7 @@
- else readLoop(0, endGCGdata, V);
-
- while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
-- getline(V);
-+ mygetline(V);
- }
-
- static int
-@@ -561,12 +561,12 @@
- if ((sptr = strtok(NULL, "\n")) != NULL)
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
- /* workaround for long NCBI NR lines */
-- while (V->longline && ! feof(V->f)) getline(V);
-+ while (V->longline && ! feof(V->f)) mygetline(V);
-
- readLoop(0, endPearson, V);
-
- while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
-- getline(V);
-+ mygetline(V);
- }
-
-
-@@ -593,7 +593,7 @@
-
- /* make sure we have first line */
- while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
-- getline(V);
-+ mygetline(V);
-
- if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
- {
-@@ -602,7 +602,7 @@
- }
-
- do {
-- getline(V);
-+ mygetline(V);
- if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
- {
- if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
-@@ -626,7 +626,7 @@
-
- /* load next record's ID line */
- while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
-- getline(V);
-+ mygetline(V);
- }
-
-
-@@ -642,7 +642,7 @@
- {
- char *sptr;
-
-- getline(V); /*s == "seqLen seqid string..."*/
-+ mygetline(V); /*s == "seqLen seqid string..."*/
-
- if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
-@@ -653,7 +653,7 @@
- readLoop(0, endZuker, V);
-
- while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
-- getline(V);
-+ mygetline(V);
- }
-
- static void
-@@ -675,7 +675,7 @@
-
- do {
- done = feof(V->f);
-- getline(V);
-+ mygetline(V);
- if (! done) addseq(V->sbuffer, V);
- } while (!done);
- }
-@@ -687,7 +687,7 @@
- char *sptr;
- int dostruc = FALSE;
-
-- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
-+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) mygetline(V);
-
- if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
-@@ -695,7 +695,7 @@
- /*CONSTCOND*/
- while (1)
- {
-- getline(V);
-+ mygetline(V);
- if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
-
- if (strncmp(V->sbuffer, "SRC ", 4) == 0)
-@@ -727,14 +727,14 @@
- while (1)
- {
- /* sequence line */
-- getline(V);
-+ mygetline(V);
- if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
- break;
- addseq(V->sbuffer, V);
- /* structure line */
- if (dostruc)
- {
-- getline(V);
-+ mygetline(V);
- if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
- addstruc(V->sbuffer, V);
- }
-@@ -742,7 +742,7 @@
-
-
- while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
-- getline(V);
-+ mygetline(V);
- }
-
-
-@@ -822,7 +822,7 @@
-
- /* Load the first line.
- */
-- getline(dbfp);
-+ mygetline(dbfp);
-
- return dbfp;
- }
-@@ -839,7 +839,7 @@
- Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
-
- fseek(sqfp->f, offset, SEEK_SET);
-- getline(sqfp);
-+ mygetline(sqfp);
- }
-
-
-@@ -859,7 +859,7 @@
- if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
- else {
- rewind(sqfp->f);
-- getline(sqfp);
-+ mygetline(sqfp);
- }
- }
-
-@@ -954,7 +954,7 @@
- do { /* skip leading comments on GCG file */
- gotuw = (strstr(V->sbuffer,"..") != NULL);
- if (gotuw) readUWGCG(V);
-- getline(V);
-+ mygetline(V);
- } while (! feof(V->f));
- break;
-
diff --git a/emboss-java/DESCR b/emboss-java/DESCR
deleted file mode 100644
index 49671f9f38..0000000000
--- a/emboss-java/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-This package installs a C library which provides and interface between jemboss,
-the java emboss interface and the emboss C libraries and programs.
-Jemboss requires it to run.
diff --git a/emboss-java/MESSAGE b/emboss-java/MESSAGE
deleted file mode 100644
index 4c3a36484d..0000000000
--- a/emboss-java/MESSAGE
+++ /dev/null
@@ -1,7 +0,0 @@
-===========================================================================
-$NetBSD: MESSAGE,v 1.2 2006/10/29 11:23:07 shattered Exp $
-
-This package creates an i386-linux version of the emboss libraries,
-so that jemboss (the java gui for emboss) can work correctly.
-
-===========================================================================
diff --git a/emboss-java/Makefile b/emboss-java/Makefile
deleted file mode 100644
index e24d36032f..0000000000
--- a/emboss-java/Makefile
+++ /dev/null
@@ -1,54 +0,0 @@
-# $NetBSD: Makefile,v 1.8 2012/09/02 11:14:10 noud4 Exp $
-
-DISTNAME= EMBOSS-2.9.0
-PKGNAME= emboss-java-0.0.3
-PKGREVISION= 2
-CATEGORIES= biology
-#MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/
-
-MAINTAINER= dprice%cs.nmsu.edu@localhost
-HOMEPAGE= http://emboss.sourceforge.net/
-COMMENT= Interface between emboss and jemboss
-LICENSE= gnu-lgpl-v2.1
-
-DEPENDS+= emboss-base>=2.9.0:../../wip/emboss-base
-
-WRKSRC= ${WRKDIR}/${DISTNAME}
-USE_JAVA= yes
-USE_PKGLOCALEDIR= yes
-USE_LIBTOOL= yes
-LIBTOOL_OVERRIDE= ${WRKSRC}/libtool
-HAS_CONFIGURE= yes
-CHECK_SHLIBS= no
-USE_LANGUAGES+= c c++
-DIST_SUBDIR= emboss/emboss-2.9.0
-
-CONFIGUE_ARGS+= --with-java=${PKG_JAVA_HOME}/include
-CONFIGUE_ARGS+= --with-javaos=${PKG_JAVA_HOME}/include/netbsd
-CONFIGUE_ARGS+= --build=i386-netbsd
-CONFIGUE_ARGS+= --prefix=${PREFIX}
-
-INSTALLATION_DIRS= lib
-
-post-patch:
- ${SED} -e 's:@CROSSPKG@:${PREFIX}/lib:' \
- ${WRKSRC}/ajax/Makefile.in > \
- ${WRKSRC}/ajax/Makefile.in.bak
- ${MV} ${WRKSRC}/ajax/Makefile.in.bak \
- ${WRKSRC}/ajax/Makefile.in
-
-do-build:
- cd ${WRKSRC}/ajax && ${SETENV} ${MAKE_ENV} ${MAKE_PROGRAM}
-
-do-install:
- ${CP} ${WRKSRC}/ajax/.libs/libajax.so.0.1.0 ${WRKSRC}/ajax/.libs/libajaxj.so
- ${CP} ${WRKSRC}/ajax/.libs/libajaxj.so ${DESTDIR}${PREFIX}/lib/libajaxj.so
- ${CP} ${WRKSRC}/ajax/.libs/libajax.a ${WRKSRC}/ajax/.libs/libajaxj.a
- ${CP} ${WRKSRC}/ajax/.libs/libajaxj.a ${DESTDIR}${PREFIX}/lib/libajaxj.a
- ${CP} ${WRKSRC}/ajax/.libs/libajax.la ${WRKSRC}/ajax/.libs/libajaxj.la
- ${CP} ${WRKSRC}/ajax/.libs/libajaxj.la ${DESTDIR}${PREFIX}/lib/libajaxj.la
-
-.include "../../wip/emboss-base/buildlink3.mk"
-.include "../../mk/java-vm.mk"
-.include "../../x11/libX11/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/emboss-java/PLIST b/emboss-java/PLIST
deleted file mode 100644
index 5425a9467e..0000000000
--- a/emboss-java/PLIST
+++ /dev/null
@@ -1,2 +0,0 @@
-@comment $NetBSD: PLIST,v 1.2 2006/10/29 11:23:07 shattered Exp $
-lib/libajaxj.la
diff --git a/emboss-java/distinfo b/emboss-java/distinfo
deleted file mode 100644
index 252de02cdf..0000000000
--- a/emboss-java/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD: distinfo,v 1.2 2005/09/28 06:41:12 rillig Exp $
-
-RMD160 (emboss/emboss-2.9.0/EMBOSS-2.9.0.tar.gz) = 2b4d4ec90989a7b56272ff121125c270367b38fe
-SHA512 (emboss/emboss-2.9.0/EMBOSS-2.9.0.tar.gz) = 8cd21d37bbc906e80ce3bd03bbcee8096f22c48979a393bad271f4f2787d2abf6f54b8373a3f2f4127e101ea2d542ef0ac4c955afcd25a22c53fe59a1a56369b
-Size (emboss/emboss-2.9.0/EMBOSS-2.9.0.tar.gz) = 14479274 bytes
diff --git a/emboss-meme/DESCR b/emboss-meme/DESCR
deleted file mode 100644
index 41f394f7be..0000000000
--- a/emboss-meme/DESCR
+++ /dev/null
@@ -1 +0,0 @@
-MEME is a motif detection tool for EMBOSS package.
diff --git a/emboss-meme/Makefile b/emboss-meme/Makefile
deleted file mode 100644
index 8f3ce9e3c0..0000000000
--- a/emboss-meme/Makefile
+++ /dev/null
@@ -1,23 +0,0 @@
-# $NetBSD: Makefile,v 1.3 2012/09/02 11:14:10 noud4 Exp $
-#
-
-.include "../emboss-base/Makefile.common"
-.include "../emboss/Makefile.common"
-
-DISTNAME= MEME-2.3.1
-PKGNAME= emboss-meme-2.3.1
-PKGREVISION= 1
-
-COMMENT= Motif detection tool for EMBOSS
-LICENSE= gnu-gpl-v2
-
-DIST_SUBDIR= emboss/meme-2.3.1-20041107
-BUILD_TARGET= #empty
-
-pre-configure:
- ${SED} -e 's|@EMBOSSLIB@|${PREFIX}/lib|' \
- -e 's|@INCLUDE@|${PREFIX}/include/emboss|' \
- ${WRKSRC}/src/Makefile.in > ${WRKSRC}/src/Makefile.in.bak
- ${MV} ${WRKSRC}/src/Makefile.in.bak ${WRKSRC}/src/Makefile.in
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/emboss-meme/PLIST b/emboss-meme/PLIST
deleted file mode 100644
index 4b6d484751..0000000000
--- a/emboss-meme/PLIST
+++ /dev/null
@@ -1,4 +0,0 @@
-@comment $NetBSD: PLIST,v 1.2 2004/12/14 18:38:10 daprice Exp $
-bin/meme
-lib/libmeme.la
-share/EMBOSS/acd/meme.acd
diff --git a/emboss-meme/distinfo b/emboss-meme/distinfo
deleted file mode 100644
index b1ab9e954e..0000000000
--- a/emboss-meme/distinfo
+++ /dev/null
@@ -1,8 +0,0 @@
-$NetBSD: distinfo,v 1.2 2006/08/26 15:41:20 kristerw Exp $
-
-RMD160 (emboss/meme-2.3.1-20041107/MEME-2.3.1.tar.gz) = b7e6a60c49d758bb79f4b97f82d8675a839782ee
-SHA512 (emboss/meme-2.3.1-20041107/MEME-2.3.1.tar.gz) = f0b86c2860f229d90ac4f9ccdd6ef2324dc7925b3a7c23590bc8c60c6e6e130b6ccfa1ac8891df2cfc248e356dcb2cb8b0b9c17eb281570477f32c3c9392cdce
-Size (emboss/meme-2.3.1-20041107/MEME-2.3.1.tar.gz) = 417514 bytes
-SHA1 (patch-aa) = d7b7d55c81df79f4c437fb6b2378322a69bbd204
-SHA1 (patch-ab) = 125cd943e6fe3e4133f1ab947caa1d01d84b76fb
-SHA1 (patch-ac) = 2e4931f73c58e9fba786ffae9b9b593fa89079ae
diff --git a/emboss-meme/patches/patch-aa b/emboss-meme/patches/patch-aa
deleted file mode 100644
index 2cc73ca2bc..0000000000
--- a/emboss-meme/patches/patch-aa
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD: patch-aa,v 1.1.1.1 2004/11/15 20:23:10 daprice Exp $
-
---- emboss_acd/Makefile.in.orig Tue Jul 27 14:52:27 2004
-+++ emboss_acd/Makefile.in Tue Jul 27 14:53:16 2004
-@@ -43,7 +43,7 @@
- $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- SOURCES =
- DIST_SOURCES =
-@@ -182,7 +182,7 @@
- sharedstatedir = @sharedstatedir@
- sysconfdir = @sysconfdir@
- target_alias = @target_alias@
--pkgdata_DATA = *.acd
-+pkgdata_DATA = meme.acd
- all: all-am
-
- .SUFFIXES:
diff --git a/emboss-meme/patches/patch-ab b/emboss-meme/patches/patch-ab
deleted file mode 100644
index 23bae672a4..0000000000
--- a/emboss-meme/patches/patch-ab
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-ab,v 1.1.1.1 2004/11/15 20:23:10 daprice Exp $
-
---- src/INCLUDE/Makefile.in.orig Tue Jul 27 15:04:08 2004
-+++ src/INCLUDE/Makefile.in Tue Jul 27 15:04:25 2004
-@@ -43,7 +43,7 @@
- $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../../mkinstalldirs
- CONFIG_CLEAN_FILES =
- SOURCES =
- DIST_SOURCES =
diff --git a/emboss-meme/patches/patch-ac b/emboss-meme/patches/patch-ac
deleted file mode 100644
index b02e56d668..0000000000
--- a/emboss-meme/patches/patch-ac
+++ /dev/null
@@ -1,55 +0,0 @@
-$NetBSD: patch-ac,v 1.1.1.1 2004/11/15 20:23:10 daprice Exp $
-
---- src/Makefile.in.orig Tue Jul 27 14:54:57 2004
-+++ src/Makefile.in Tue Jul 27 15:03:11 2004
-@@ -48,7 +48,7 @@
- $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)"
- libLTLIBRARIES_INSTALL = $(INSTALL)
-@@ -70,12 +70,12 @@
- am__DEPENDENCIES_1 =
- @LOCALLINK_FALSE@meme_DEPENDENCIES = libmeme.la $(am__DEPENDENCIES_1)
- @LOCALLINK_TRUE@meme_DEPENDENCIES = libmeme.la \
--@LOCALLINK_TRUE@ ../../../nucleus/libnucleus.la \
--@LOCALLINK_TRUE@ ../../../ajax/libajax.la \
--@LOCALLINK_TRUE@ ../../../plplot/libplplot.la \
-+@LOCALLINK_TRUE@ @EMBOSSLIB@/libnucleus.la \
-+@LOCALLINK_TRUE@ @EMBOSSLIB@/libajax.la \
-+@LOCALLINK_TRUE@ @EMBOSSLIB@/libplplot.la \
- @LOCALLINK_TRUE@ $(am__DEPENDENCIES_1)
- DEFAULT_INCLUDES = -I. -I$(srcdir)
--depcomp = $(SHELL) $(top_srcdir)/depcomp
-+depcomp = $(SHELL) ../depcomp
- am__depfiles_maybe = depfiles
- @AMDEP_TRUE@DEP_FILES = ./$(DEPDIR)/align.Plo ./$(DEPDIR)/banner.Plo \
- @AMDEP_TRUE@ ./$(DEPDIR)/chi.Plo ./$(DEPDIR)/clock.Plo \
-@@ -246,11 +246,11 @@
- target_alias = @target_alias@
- SUBDIRS = INCLUDE
- lib_LTLIBRARIES = libmeme.la
--@LOCALLINK_FALSE@INCLUDES = -IINCLUDE -I${embprefix}/include
--@LOCALLINK_TRUE@INCLUDES = -IINCLUDE -I../../../ajax
-+@LOCALLINK_FALSE@INCLUDES = -IINCLUDE -I@INCLUDE@
-+@LOCALLINK_TRUE@INCLUDES = -IINCLUDE -I@INCLUDE@
- @ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS =
--@ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_FALSE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L../../../ajax/.libs -lajax
--@ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_TRUE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L../../../ajax/.libs -lajax
-+@ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_FALSE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L@EMBOSSLIB@ -lajax
-+@ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_TRUE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L@EMBOSSLIB@ -lajax
- MEMESRC = clock.c display.c em.c init.c meme_util.c seq2theta.c \
- shorten.c starts.c prior.c split.c align.c justlike.c \
- oops.c tcm.c zoops.c banner.c logs.c palindrome.c gamma.c \
-@@ -262,7 +262,7 @@
- libmeme_la_LDFLAGS = -version-info 2:3:1
- meme_SOURCES = meme.c
- @LOCALLINK_FALSE@LDADD = libmeme.la -L${embprefix}/lib -lnucleus -lajax -lplplot $(XLIB)
--@LOCALLINK_TRUE@LDADD = libmeme.la ../../../nucleus/libnucleus.la ../../../ajax/libajax.la ../../../plplot/libplplot.la $(XLIB)
-+@LOCALLINK_TRUE@LDADD = libmeme.la @EMBOSSLIB@/libnucleus.la @EMBOSSLIB@/libajax.la @EMBOSSLIB@/libplplot.la $(XLIB)
- all: all-recursive
-
- .SUFFIXES:
diff --git a/emboss-mse/DESCR b/emboss-mse/DESCR
deleted file mode 100644
index 1493ee2af8..0000000000
--- a/emboss-mse/DESCR
+++ /dev/null
@@ -1,2 +0,0 @@
-MSE is a sequence alignment tool, and is in a form of a supplimentary package
-for EMBOSS.
diff --git a/emboss-mse/Makefile b/emboss-mse/Makefile
deleted file mode 100644
index 1dde5d5109..0000000000
--- a/emboss-mse/Makefile
+++ /dev/null
@@ -1,34 +0,0 @@
-# $NetBSD: Makefile,v 1.4 2006/10/29 11:23:07 shattered Exp $
-#
-
-.include "../../wip/emboss-base/Makefile.common"
-.include "../../wip/emboss/Makefile.common"
-
-DISTNAME= MSE-1.0.0
-PKGNAME= emboss-mse-1.0.0
-
-COMMENT= Multiple Sequence Editor for EMBOSS
-LICENSE= gnu-gpl-v2
-
-#ncurses required because:
-#mse.c: In function `Initscr':
-#mse.c:148: dereferencing pointer to incomplete type
-#mse.c:149: dereferencing pointer to incomplete type
-#mse.c 148 __Cols=Display->_maxx;
-#mse.c 149 __Rows=Display->_maxy;
-USE_NCURSES= yes
-DIST_SUBDIR= emboss/mse-1.0.0-20041107
-BUILD_TARGET= #empty
-
-pre-configure:
- ${SED} -e 's|@EMBOSSLIB@|${PREFIX}/lib|' \
- -e 's|@NCURSES@|-L${PREFIX}/lib -lncurses|' \
- -e 's|@INCLUDE@|${PREFIX}/include -I${PREFIX}/include/emboss|' \
- ${WRKSRC}/source/Makefile.in > ${WRKSRC}/source/Makefile.in.bak
- ${MV} ${WRKSRC}/source/Makefile.in.bak ${WRKSRC}/source/Makefile.in
- ${SED} -e 's|@NCURSES@|-L${PREFIX}/lib -lncurses|' \
- ${WRKSRC}/h/Makefile.in > ${WRKSRC}/h/Makefile.in.bak
- ${MV} ${WRKSRC}/h/Makefile.in.bak ${WRKSRC}/h/Makefile.in
-
-.include "../../devel/ncurses/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/emboss-mse/PLIST b/emboss-mse/PLIST
deleted file mode 100644
index c1590f6ecc..0000000000
--- a/emboss-mse/PLIST
+++ /dev/null
@@ -1,4 +0,0 @@
-@comment $NetBSD: PLIST,v 1.2 2005/03/18 22:30:55 daprice Exp $
-bin/mse
-lib/libckit.la
-share/EMBOSS/acd/mse.acd
diff --git a/emboss-mse/distinfo b/emboss-mse/distinfo
deleted file mode 100644
index 0a11374238..0000000000
--- a/emboss-mse/distinfo
+++ /dev/null
@@ -1,10 +0,0 @@
-$NetBSD: distinfo,v 1.4 2007/01/07 01:58:19 shattered Exp $
-
-RMD160 (emboss/mse-1.0.0-20041107/MSE-1.0.0.tar.gz) = a22ef98dcc5ee0ab818293915076559de35eb1b4
-SHA512 (emboss/mse-1.0.0-20041107/MSE-1.0.0.tar.gz) = a6908cf223307e0e3b7cdc5e91fee8241bbbd463444557d137367e3e34d2be784c9dddd46102a008bc05758fea458437f5659616077e33b7b4b83c9a7fe4afc8
-Size (emboss/mse-1.0.0-20041107/MSE-1.0.0.tar.gz) = 407726 bytes
-SHA1 (patch-aa) = 0408aadfa10c505cbdf93d8022da1550d9073b52
-SHA1 (patch-ab) = 0ed3942c71f223f31008244b4bb9a76af2607be8
-SHA1 (patch-ac) = 800b48a7b6015d91523576deea292c4535d5b0d7
-SHA1 (patch-ad) = 5181c41a40a223c9e4ce79a36d65a8336513cbfa
-SHA1 (patch-ae) = be239a7312a8f2bfbf4f1c91629bc98db469f09b
diff --git a/emboss-mse/patches/patch-aa b/emboss-mse/patches/patch-aa
deleted file mode 100644
index 10e103afb5..0000000000
--- a/emboss-mse/patches/patch-aa
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD: patch-aa,v 1.1.1.1 2004/11/15 20:26:18 daprice Exp $
-
---- ckit/Makefile.in.orig Tue Aug 24 11:33:35 2004
-+++ ckit/Makefile.in Tue Aug 24 11:34:50 2004
-@@ -46,7 +46,7 @@
- $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- am__installdirs = "$(DESTDIR)$(libdir)"
- libLTLIBRARIES_INSTALL = $(INSTALL)
-@@ -58,7 +58,7 @@
- am_libckit_la_OBJECTS = $(am__objects_1)
- libckit_la_OBJECTS = $(am_libckit_la_OBJECTS)
- DEFAULT_INCLUDES = -I. -I$(srcdir)
--depcomp = $(SHELL) $(top_srcdir)/depcomp
-+depcomp = $(SHELL) ../depcomp
- am__depfiles_maybe = depfiles
- @AMDEP_TRUE@DEP_FILES = ./$(DEPDIR)/datafiles.Plo ./$(DEPDIR)/gcg.Plo \
- @AMDEP_TRUE@ ./$(DEPDIR)/next.Plo ./$(DEPDIR)/nextseqentry.Plo \
diff --git a/emboss-mse/patches/patch-ab b/emboss-mse/patches/patch-ab
deleted file mode 100644
index 21e5bb55a7..0000000000
--- a/emboss-mse/patches/patch-ab
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD: patch-ab,v 1.1.1.1 2004/11/15 20:26:18 daprice Exp $
-
---- emboss_acd/Makefile.in.orig Thu Jul 15 09:57:21 2004
-+++ emboss_acd/Makefile.in Tue Aug 24 12:18:37 2004
-@@ -43,7 +43,7 @@
- $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- SOURCES =
- DIST_SOURCES =
-@@ -182,7 +182,7 @@
- sharedstatedir = @sharedstatedir@
- sysconfdir = @sysconfdir@
- target_alias = @target_alias@
--pkgdata_DATA = *.acd
-+pkgdata_DATA = mse.acd
- all: all-am
-
- .SUFFIXES:
diff --git a/emboss-mse/patches/patch-ac b/emboss-mse/patches/patch-ac
deleted file mode 100644
index fa632286d2..0000000000
--- a/emboss-mse/patches/patch-ac
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD: patch-ac,v 1.1.1.1 2004/11/15 20:26:18 daprice Exp $
-
---- h/Makefile.in.orig Tue Aug 24 11:44:20 2004
-+++ h/Makefile.in Tue Aug 24 11:45:38 2004
-@@ -45,7 +45,7 @@
- $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- SOURCES =
- DIST_SOURCES =
-@@ -103,7 +103,7 @@
- JAVA_OK = @JAVA_OK@
- LDFLAGS = @LDFLAGS@
- LIBOBJS = @LIBOBJS@
--LIBS = @LIBS@
-+LIBS = @NCURSES@ @LIBS@
- LIBTOOL = @LIBTOOL@
- LN_S = @LN_S@
- LOCALLINK_FALSE = @LOCALLINK_FALSE@
diff --git a/emboss-mse/patches/patch-ad b/emboss-mse/patches/patch-ad
deleted file mode 100644
index 216afe9aed..0000000000
--- a/emboss-mse/patches/patch-ad
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-ad,v 1.1.1.1 2004/11/15 20:26:18 daprice Exp $
-
---- h/mse.h.orig Tue Aug 24 11:46:12 2004
-+++ h/mse.h Tue Aug 24 11:46:32 2004
-@@ -12,7 +12,7 @@
- /*#include "smgmacros.h"*/
- #include "macros.h"
- #include "ckit.h"
--#include <curses.h>
-+#include <ncurses.h>
-
- /*---------------------------------------*/
- /* Match "Curses" attributes
diff --git a/emboss-mse/patches/patch-ae b/emboss-mse/patches/patch-ae
deleted file mode 100644
index 9e8cc30655..0000000000
--- a/emboss-mse/patches/patch-ae
+++ /dev/null
@@ -1,59 +0,0 @@
-$NetBSD: patch-ae,v 1.1.1.1 2004/11/15 20:26:18 daprice Exp $
-
---- source/Makefile.in.orig Thu Jul 15 09:57:21 2004
-+++ source/Makefile.in Tue Aug 24 12:19:38 2004
-@@ -47,7 +47,7 @@
- $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- am__installdirs = "$(DESTDIR)$(bindir)"
- binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
-@@ -59,12 +59,12 @@
- @LOCALLINK_FALSE@mse_DEPENDENCIES = ../ckit/libckit.la \
- @LOCALLINK_FALSE@ $(am__DEPENDENCIES_1)
- @LOCALLINK_TRUE@mse_DEPENDENCIES = ../ckit/libckit.la \
--@LOCALLINK_TRUE@ ../../../nucleus/libnucleus.la \
--@LOCALLINK_TRUE@ ../../../ajax/libajax.la \
--@LOCALLINK_TRUE@ ../../../plplot/libplplot.la \
-+@LOCALLINK_TRUE@ @EMBOSSLIB@/nucleus/libnucleus.la \
-+@LOCALLINK_TRUE@ @EMBOSSLIB@/ajax/libajax.la \
-+@LOCALLINK_TRUE@ @EMBOSSLIB@/plplot/libplplot.la \
- @LOCALLINK_TRUE@ $(am__DEPENDENCIES_1)
- DEFAULT_INCLUDES = -I. -I$(srcdir)
--depcomp = $(SHELL) $(top_srcdir)/depcomp
-+depcomp = $(SHELL) ../depcomp
- am__depfiles_maybe = depfiles
- @AMDEP_TRUE@DEP_FILES = ./$(DEPDIR)/mse.Po
- COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-@@ -130,7 +130,7 @@
- JAVA_OK = @JAVA_OK@
- LDFLAGS = @LDFLAGS@
- LIBOBJS = @LIBOBJS@
--LIBS = @LIBS@
-+LIBS = @NCURSES@ @LIBS@
- LIBTOOL = @LIBTOOL@
- LN_S = @LN_S@
- LOCALLINK_FALSE = @LOCALLINK_FALSE@
-@@ -210,14 +210,14 @@
- sharedstatedir = @sharedstatedir@
- sysconfdir = @sysconfdir@
- target_alias = @target_alias@
--@LOCALLINK_FALSE@INCLUDES = -I../h -I${embprefix}/include
--@LOCALLINK_TRUE@INCLUDES = -I../h -I../../../ajax
-+@LOCALLINK_FALSE@INCLUDES = -I../h -I@INCLUDE@
-+@LOCALLINK_TRUE@INCLUDES = -I../h -I@INCLUDE@
- @ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS =
- @ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_FALSE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lajax
--@ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_TRUE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L../../../ajax/.libs -lajax
-+@ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_TRUE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L@EMBOSSLIB@ -lajax
- mse_SOURCES = mse.c
--@LOCALLINK_FALSE@LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lajax -lplplot $(XLIB)
--@LOCALLINK_TRUE@LDADD = ../ckit/libckit.la ../../../nucleus/libnucleus.la ../../../ajax/libajax.la ../../../plplot/libplplot.la $(XLIB)
-+@LOCALLINK_FALSE@LDADD = ../ckit/libckit.la -L@EMBOSSLIB@/lib -lnucleus -lajax -lplplot $(XLIB)
-+@LOCALLINK_TRUE@LDADD = ../ckit/libckit.la @EMBOSSLIB@/nucleus/libnucleus.la @EMBOSSLIB@/ajax/libajax.la @EMBOSSLIB@/plplot/libplplot.la $(XLIB)
- all: all-am
-
- .SUFFIXES:
diff --git a/emboss-phylip/DESCR b/emboss-phylip/DESCR
deleted file mode 100644
index c3543427fa..0000000000
--- a/emboss-phylip/DESCR
+++ /dev/null
@@ -1,2 +0,0 @@
-PHYLIP is a package of programs for inferring phylogenies. This
-package is specifically modified for EMBOSS distribution.
diff --git a/emboss-phylip/Makefile b/emboss-phylip/Makefile
deleted file mode 100644
index 07b8ecad68..0000000000
--- a/emboss-phylip/Makefile
+++ /dev/null
@@ -1,25 +0,0 @@
-# $NetBSD: Makefile,v 1.4 2012/11/13 22:25:30 othyro Exp $
-#
-
-.include "../emboss-base/Makefile.common"
-.include "../emboss/Makefile.common"
-
-DISTNAME= PHYLIP-3.57c
-PKGNAME= emboss-phylip-3.57c
-PKGREVISION= 1
-
-COMMENT= Package of programs for inferring phylogenies
-LICENSE= gnu-gpl-v2
-
-DIST_SUBDIR= emboss/phylip-3.57c-20041107
-BUILD_TARGET= #empty
-
-pre-configure:
- ${SED} -e 's|../../../ajax/libajax.la|${PREFIX}/lib/libajax.la|' \
- -e 's|@INCLUDE@|${PREFIX}/include/emboss|' \
- ${WRKSRC}/src/Makefile.in > \
- ${WRKSRC}/src/Makefile.in.bak
- ${MV} ${WRKSRC}/src/Makefile.in.bak \
- ${WRKSRC}/src/Makefile.in
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/emboss-phylip/PLIST b/emboss-phylip/PLIST
deleted file mode 100644
index ab6403d47e..0000000000
--- a/emboss-phylip/PLIST
+++ /dev/null
@@ -1,49 +0,0 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2004/11/15 20:27:50 daprice Exp $
-bin/eclique
-bin/econsense
-bin/econtml
-bin/econtrast
-bin/ednacomp
-bin/ednadist
-bin/ednainvar
-bin/ednaml
-bin/ednamlk
-bin/ednapars
-bin/ednapenny
-bin/edollop
-bin/edolpenny
-bin/efactor
-bin/efitch
-bin/egendist
-bin/ekitsch
-bin/emix
-bin/eneighbor
-bin/epenny
-bin/eprotdist
-bin/eprotpars
-bin/erestml
-bin/eseqboot
-share/EMBOSS/acd/eclique.acd
-share/EMBOSS/acd/econsense.acd
-share/EMBOSS/acd/econtml.acd
-share/EMBOSS/acd/econtrast.acd
-share/EMBOSS/acd/ednacomp.acd
-share/EMBOSS/acd/ednadist.acd
-share/EMBOSS/acd/ednainvar.acd
-share/EMBOSS/acd/ednaml.acd
-share/EMBOSS/acd/ednamlk.acd
-share/EMBOSS/acd/ednapars.acd
-share/EMBOSS/acd/ednapenny.acd
-share/EMBOSS/acd/edollop.acd
-share/EMBOSS/acd/edolpenny.acd
-share/EMBOSS/acd/efactor.acd
-share/EMBOSS/acd/efitch.acd
-share/EMBOSS/acd/egendist.acd
-share/EMBOSS/acd/ekitsch.acd
-share/EMBOSS/acd/emix.acd
-share/EMBOSS/acd/eneighbor.acd
-share/EMBOSS/acd/epenny.acd
-share/EMBOSS/acd/eprotdist.acd
-share/EMBOSS/acd/eprotpars.acd
-share/EMBOSS/acd/erestml.acd
-share/EMBOSS/acd/eseqboot.acd
diff --git a/emboss-phylip/distinfo b/emboss-phylip/distinfo
deleted file mode 100644
index 570834832a..0000000000
--- a/emboss-phylip/distinfo
+++ /dev/null
@@ -1,7 +0,0 @@
-$NetBSD: distinfo,v 1.2 2006/08/26 15:41:20 kristerw Exp $
-
-RMD160 (emboss/phylip-3.57c-20041107/PHYLIP-3.57c.tar.gz) = 5ea09fd74cc384808d73c9ed6169a53ac0d25dbf
-SHA512 (emboss/phylip-3.57c-20041107/PHYLIP-3.57c.tar.gz) = 4925c8dba3d5ff900a30051888fab0f254b02c9e96faf2c598103d424fd9ce2c86aeb72ec116996720b4fb63c25303003fff25d93447be29368eb1a44067f326
-Size (emboss/phylip-3.57c-20041107/PHYLIP-3.57c.tar.gz) = 856814 bytes
-SHA1 (patch-aa) = 2bdc12ddba3e42d3de93d4ae3647a0334f4d5431
-SHA1 (patch-ab) = b221e8a888a81c85899b8d207cc3be07b7370617
diff --git a/emboss-phylip/patches/patch-aa b/emboss-phylip/patches/patch-aa
deleted file mode 100644
index 6845beae0c..0000000000
--- a/emboss-phylip/patches/patch-aa
+++ /dev/null
@@ -1,30 +0,0 @@
-$NetBSD: patch-aa,v 1.1.1.1 2004/11/15 20:27:50 daprice Exp $
-
---- emboss_acd/Makefile.in.orig 2004-11-09 15:09:42.000000000 -0700
-+++ emboss_acd/Makefile.in 2004-11-09 15:11:51.000000000 -0700
-@@ -44,7 +44,7 @@
- $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(install_sh) -d
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- SOURCES =
- DIST_SOURCES =
-@@ -191,7 +191,15 @@
- sharedstatedir = @sharedstatedir@
- sysconfdir = @sysconfdir@
- target_alias = @target_alias@
--pkgdata_DATA = *.acd
-+pkgdata_DATA = econtrast.acd edollop.acd epenny.acd \
-+ednacomp.acd edolpenny.acd eprotdist.acd \
-+ednadist.acd efactor.acd eprotpars.acd \
-+ednainvar.acd efitch.acd erestml.acd \
-+ednaml.acd egendist.acd eseqboot.acd \
-+eclique.acd ednamlk.acd ekitsch.acd \
-+econsense.acd ednapars.acd emix.acd \
-+econtml.acd ednapenny.acd eneighbor.acd
-+
- all: all-am
-
- .SUFFIXES:
diff --git a/emboss-phylip/patches/patch-ab b/emboss-phylip/patches/patch-ab
deleted file mode 100644
index af7b6574d1..0000000000
--- a/emboss-phylip/patches/patch-ab
+++ /dev/null
@@ -1,33 +0,0 @@
-$NetBSD: patch-ab,v 1.1.1.1 2004/11/15 20:27:50 daprice Exp $
-
---- src/Makefile.in.orig 2004-10-01 01:13:52.000000000 -0600
-+++ src/Makefile.in 2004-11-09 15:04:45.000000000 -0700
-@@ -55,7 +55,7 @@
- $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(install_sh) -d
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- am__installdirs = "$(DESTDIR)$(bindir)"
- binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
-@@ -267,7 +267,7 @@
- @LOCALLINK_TRUE@ ../../../plplot/libplplot.la \
- @LOCALLINK_TRUE@ $(am__DEPENDENCIES_1)
- DEFAULT_INCLUDES = -I. -I$(srcdir)
--depcomp = $(SHELL) $(top_srcdir)/depcomp
-+depcomp = $(SHELL) ../depcomp
- am__depfiles_maybe = depfiles
- COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-@@ -429,8 +429,8 @@
- sharedstatedir = @sharedstatedir@
- sysconfdir = @sysconfdir@
- target_alias = @target_alias@
--@LOCALLINK_FALSE@INCLUDES = -I../include -I${embprefix}/include
--@LOCALLINK_TRUE@INCLUDES = -I../include -I../../../ajax
-+@LOCALLINK_FALSE@INCLUDES = -I../include -I@INCLUDE@
-+@LOCALLINK_TRUE@INCLUDES = -I../include -I@INCLUDE@
- @ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS =
- @ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_FALSE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lajax
- @ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_TRUE@AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L../../../ajax/.libs -lajax
diff --git a/emboss-topo/DESCR b/emboss-topo/DESCR
deleted file mode 100644
index ed7f0140ac..0000000000
--- a/emboss-topo/DESCR
+++ /dev/null
@@ -1,2 +0,0 @@
-Topo draws an image of a transmembrane protein. It is a supplimentary
-program for EMBOSS package.
diff --git a/emboss-topo/Makefile b/emboss-topo/Makefile
deleted file mode 100644
index 9587a357fd..0000000000
--- a/emboss-topo/Makefile
+++ /dev/null
@@ -1,23 +0,0 @@
-# $NetBSD: Makefile,v 1.3 2012/09/02 11:14:10 noud4 Exp $
-#
-
-.include "../emboss-base/Makefile.common"
-.include "../emboss/Makefile.common"
-
-DISTNAME= TOPO-1.0.0
-PKGNAME= emboss-topo-1.0.0
-PKGREVISION= 1
-
-COMMENT= Draws an image of a transmembrane protein
-LICENSE= gnu-gpl-v2
-
-DIST_SUBDIR= ${PKG_DISTFILES_DIR}/topo-1.0.0-20041107
-BUILD_TARGET= #empty
-
-pre-configure:
- ${SED} -e 's|@X116@|-Wl,-R${X11BASE}/lib|' \
- -e 's|@INCLUDE@|${PREFIX}/include/emboss|' \
- ${WRKSRC}/source/Makefile.in > ${WRKSRC}/source/Makefile.in.bak
- ${MV} ${WRKSRC}/source/Makefile.in.bak ${WRKSRC}/source/Makefile.in
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/emboss-topo/PLIST b/emboss-topo/PLIST
deleted file mode 100644
index 1c489a4ef3..0000000000
--- a/emboss-topo/PLIST
+++ /dev/null
@@ -1,3 +0,0 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2004/11/15 20:30:04 daprice Exp $
-bin/topo
-share/EMBOSS/acd/topo.acd
diff --git a/emboss-topo/distinfo b/emboss-topo/distinfo
deleted file mode 100644
index ac76cb1f44..0000000000
--- a/emboss-topo/distinfo
+++ /dev/null
@@ -1,7 +0,0 @@
-$NetBSD: distinfo,v 1.2 2006/08/26 15:41:20 kristerw Exp $
-
-RMD160 (emboss/topo-1.0.0-20041107/TOPO-1.0.0.tar.gz) = 2172cef2a870f6b6b8c91a5841cebb84241394eb
-SHA512 (emboss/topo-1.0.0-20041107/TOPO-1.0.0.tar.gz) = f7e68c14d2af1c716b4d7d7b546e6c51a8745aa464597cd0212e73503e8d56d0eceecf560ae940e5514daec5acb9c6d0101814523cec8a76545b468e8a4c9ec8
-Size (emboss/topo-1.0.0-20041107/TOPO-1.0.0.tar.gz) = 345281 bytes
-SHA1 (patch-aa) = acbd68a1b0e9516abcebba93cd6897e2d28d7621
-SHA1 (patch-ab) = c510e8ed9c43990f04456ae312e8b42eea196759
diff --git a/emboss-topo/patches/patch-aa b/emboss-topo/patches/patch-aa
deleted file mode 100644
index 05b9d22ed4..0000000000
--- a/emboss-topo/patches/patch-aa
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD: patch-aa,v 1.1.1.1 2004/11/15 20:30:04 daprice Exp $
-
---- emboss_acd/Makefile.in.orig 2004-07-15 09:34:27.000000000 -0600
-+++ emboss_acd/Makefile.in 2004-07-26 12:57:12.000000000 -0600
-@@ -43,7 +43,7 @@
- $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- SOURCES =
- DIST_SOURCES =
-@@ -182,7 +182,7 @@
- sharedstatedir = @sharedstatedir@
- sysconfdir = @sysconfdir@
- target_alias = @target_alias@
--pkgdata_DATA = *.acd
-+pkgdata_DATA = topo.acd
- all: all-am
-
- .SUFFIXES:
diff --git a/emboss-topo/patches/patch-ab b/emboss-topo/patches/patch-ab
deleted file mode 100644
index 36d9e57f66..0000000000
--- a/emboss-topo/patches/patch-ab
+++ /dev/null
@@ -1,72 +0,0 @@
-$NetBSD: patch-ab,v 1.1.1.1 2004/11/15 20:30:04 daprice Exp $
-
---- source/Makefile.in.orig 2004-07-15 09:34:27.000000000 -0600
-+++ source/Makefile.in 2004-07-26 12:48:29.000000000 -0600
-@@ -49,7 +49,7 @@
- $(top_srcdir)/m4/sgi.m4 $(top_srcdir)/configure.in
- am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
- $(ACLOCAL_M4)
--mkinstalldirs = $(mkdir_p)
-+mkinstalldirs = $(SHELL) ../mkinstalldirs
- CONFIG_CLEAN_FILES =
- am__installdirs = "$(DESTDIR)$(bindir)"
- binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
-@@ -60,20 +60,20 @@
- am__DEPENDENCIES_1 =
- @ISCYGWIN_FALSE@@LOCALLINK_FALSE@topo_DEPENDENCIES = \
- @ISCYGWIN_FALSE@@LOCALLINK_FALSE@ $(am__DEPENDENCIES_1)
--@ISCYGWIN_FALSE@@LOCALLINK_TRUE@topo_DEPENDENCIES = ../../../nucleus/libnucleus.la \
--@ISCYGWIN_FALSE@@LOCALLINK_TRUE@ ../../../ajax/libajaxg.la \
--@ISCYGWIN_FALSE@@LOCALLINK_TRUE@ ../../../ajax/libajax.la \
--@ISCYGWIN_FALSE@@LOCALLINK_TRUE@ ../../../plplot/libplplot.la \
-+@ISCYGWIN_FALSE@@LOCALLINK_TRUE@topo_DEPENDENCIES = $(libdir)/nucleus/libnucleus.la \
-+@ISCYGWIN_FALSE@@LOCALLINK_TRUE@ $(libdir)/ajax/libajaxg.la \
-+@ISCYGWIN_FALSE@@LOCALLINK_TRUE@ $(libdir)/ajax/libajax.la \
-+@ISCYGWIN_FALSE@@LOCALLINK_TRUE@ $(libdir)/plplot/libplplot.la \
- @ISCYGWIN_FALSE@@LOCALLINK_TRUE@ $(am__DEPENDENCIES_1)
- @ISCYGWIN_TRUE@@LOCALLINK_FALSE@topo_DEPENDENCIES = \
- @ISCYGWIN_TRUE@@LOCALLINK_FALSE@ $(am__DEPENDENCIES_1)
- @ISCYGWIN_TRUE@@LOCALLINK_TRUE@topo_DEPENDENCIES = \
--@ISCYGWIN_TRUE@@LOCALLINK_TRUE@ ../../../nucleus/libnucleus.la \
--@ISCYGWIN_TRUE@@LOCALLINK_TRUE@ ../../../ajax/libajax.la \
--@ISCYGWIN_TRUE@@LOCALLINK_TRUE@ ../../../plplot/libplplot.la \
-+@ISCYGWIN_TRUE@@LOCALLINK_TRUE@ $(libdir)/nucleus/libnucleus.la \
-+@ISCYGWIN_TRUE@@LOCALLINK_TRUE@ $(libdir)/ajax/libajax.la \
-+@ISCYGWIN_TRUE@@LOCALLINK_TRUE@ $(libdir)/plplot/libplplot.la \
- @ISCYGWIN_TRUE@@LOCALLINK_TRUE@ $(am__DEPENDENCIES_1)
- DEFAULT_INCLUDES = -I. -I$(srcdir)
--depcomp = $(SHELL) $(top_srcdir)/depcomp
-+depcomp = $(SHELL) ../depcomp
- am__depfiles_maybe = depfiles
- @AMDEP_TRUE@DEP_FILES = ./$(DEPDIR)/topo.Po
- COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
-@@ -104,7 +104,7 @@
- AWK = @AWK@
- CC = @CC@
- CCDEPMODE = @CCDEPMODE@
--CFLAGS = @CFLAGS@
-+CFLAGS = @CFLAGS@ -I@INCLUDE@
- CPP = @CPP@
- CPPFLAGS = @CPPFLAGS@
- CXX = @CXX@
-@@ -172,7 +172,7 @@
- SHELL = @SHELL@
- STRIP = @STRIP@
- VERSION = @VERSION@
--XLIB = @XLIB@
-+XLIB = @X116@ @XLIB@
- X_CFLAGS = @X_CFLAGS@
- X_EXTRA_LIBS = @X_EXTRA_LIBS@
- X_LIBS = @X_LIBS@
-@@ -228,9 +228,9 @@
- topo_SOURCES = topo.c
- noinst_HEADERS = common.h
- @ISCYGWIN_FALSE@@LOCALLINK_FALSE@LDADD = -L${embprefix}/lib -lnucleus -lajaxg -lajax -lplplot $(XLIB)
--@ISCYGWIN_FALSE@@LOCALLINK_TRUE@LDADD = ../../../nucleus/libnucleus.la ../../../ajax/libajaxg.la ../../../ajax/libajax.la ../../../plplot/libplplot.la $(XLIB)
-+@ISCYGWIN_FALSE@@LOCALLINK_TRUE@LDADD = $(libdir)/nucleus/libnucleus.la $(libdir)/ajax/libajaxg.la $(libdir)/ajax/libajax.la $(libdir)/plplot/libplplot.la $(XLIB)
- @ISCYGWIN_TRUE@@LOCALLINK_FALSE@LDADD = -L${embprefix}/lib -lnucleus -lajax -lplplot $(XLIB)
--@ISCYGWIN_TRUE@@LOCALLINK_TRUE@LDADD = ../../../nucleus/libnucleus.la ../../../ajax/libajax.la ../../../plplot/libplplot.la $(XLIB)
-+@ISCYGWIN_TRUE@@LOCALLINK_TRUE@LDADD = $(libdir)/nucleus/libnucleus.la $(libdir)/ajax/libajax.la $(libdir)/plplot/libplplot.la $(XLIB)
- all: all-am
-
- .SUFFIXES:
diff --git a/emboss/DESCR b/emboss/DESCR
deleted file mode 100644
index ea029c82f0..0000000000
--- a/emboss/DESCR
+++ /dev/null
@@ -1,10 +0,0 @@
-EMBOSS stands for "The European Molecular Biology Open Software Suite"
-and is a new, free Open Source software analysis package specially
-developed for the needs of the molecular biology (e.g. EMBnet) user
-community. The software automatically copes with data in a variety of
-formats and even allows transparent retrieval of sequence data from
-the web. Also, as extensive libraries are provided with the package,
-it is a platform to allow other scientists to develop and release
-software in true open source spirit. EMBOSS also integrates a
-range of currently available packages and tools for sequence analysis
-into a seamless whole.
diff --git a/emboss/Makefile b/emboss/Makefile
deleted file mode 100644
index 5927ac5797..0000000000
--- a/emboss/Makefile
+++ /dev/null
@@ -1,31 +0,0 @@
-# $NetBSD: Makefile,v 1.6 2012/09/02 11:14:09 noud4 Exp $
-#
-
-DISTNAME= EMBOSS-2.9.0
-PKGNAME= emboss-2.9.0
-PKGREVISION= 1
-CATEGORIES= biology
-MASTER_SITES= #empty
-DISTFILES= #empty
-LICENSE= gnu-gpl-v2
-
-MAINTAINER= dprice%cs.nmsu.edu@localhost
-HOMEPAGE= http://emboss.sourceforge.net/
-COMMENT= European Molecular Biology Open Software Suite
-
-DEPENDS+= emboss-base>=2.9.0:../../wip/emboss-base
-DEPENDS+= emboss-domainatrix>=1.0.0:../../wip/emboss-domainatrix
-DEPENDS+= emboss-emnu>=1.05:../../wip/emboss-emnu
-DEPENDS+= emboss-hmmer>=2.1.1:../../wip/emboss-hmmer
-DEPENDS+= emboss-meme>=2.3.1:../../wip/emboss-meme
-#DEPENDS+= emboss-mse>=1.0.0:../../wip/emboss-mse
-DEPENDS+= emboss-phylip>=3.57c:../../wip/emboss-phylip
-DEPENDS+= emboss-topo>=1.0.0:../../wip/emboss-topo
-
-NO_CONFIGURE= yes
-NO_BUILD= yes
-
-do-install:
- #empty
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/emboss/Makefile.common b/emboss/Makefile.common
deleted file mode 100644
index 7705f90988..0000000000
--- a/emboss/Makefile.common
+++ /dev/null
@@ -1,13 +0,0 @@
-# $NetBSD: Makefile.common,v 1.4 2008/05/24 15:34:09 tnn2 Exp $
-# used by wip/emboss-domainatrix/Makefile
-# used by wip/emboss-emnu/Makefile
-# used by wip/emboss-hmmer/Makefile
-# used by wip/emboss-meme/Makefile
-# used by wip/emboss-mse/Makefile
-# used by wip/emboss-phylip/Makefile
-# used by wip/emboss-topo/Makefile
-
-post-extract:
- ${CP} ${PREFIX}/share/EMBOSS/scripts/* ${WRKSRC}
-
-.include "../../wip/emboss-base/buildlink3.mk"
diff --git a/emboss/NOTES b/emboss/NOTES
deleted file mode 100644
index 717b77e833..0000000000
--- a/emboss/NOTES
+++ /dev/null
@@ -1 +0,0 @@
-This is a wrapper package for the emboss suite.
diff --git a/emboss/PLIST b/emboss/PLIST
deleted file mode 100644
index e22915605b..0000000000
--- a/emboss/PLIST
+++ /dev/null
@@ -1 +0,0 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2004/11/16 20:23:37 daprice Exp $
diff --git a/emboss/distinfo b/emboss/distinfo
deleted file mode 100644
index bd207e8e66..0000000000
--- a/emboss/distinfo
+++ /dev/null
@@ -1 +0,0 @@
-$NetBSD: distinfo,v 1.3 2006/10/29 11:23:07 shattered Exp $
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