Bug 122437 - [maintainer] update biology/emboss and biology/embassy to v5.0.0
Summary: [maintainer] update biology/emboss and biology/embassy to v5.0.0
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: Normal Affects Only Me
Assignee: Rong-En Fan
URL:
Keywords:
Depends on:
Blocks:
 
Reported: 2008-04-04 06:00 UTC by Fernan Aguero
Modified: 2008-04-13 08:30 UTC (History)
0 users

See Also:

Attachments
file.diff (42.13 KB, patch)
2008-04-04 06:00 UTC, Fernan Aguero 		no flags Details | Diff
emboss2.diff (75.20 KB, patch)
2008-04-05 14:43 UTC, Fernan Aguero 		no flags Details | Diff
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Description Fernan Aguero 2008-04-04 06:00:12 UTC 
update to latest release.

Fix: diff -ruN --exclude=CVS /usr/ports/biology/emboss/Makefile emboss/Makefile
--- /usr/ports/biology/emboss/Makefile	Mon Jun 18 20:28:09 2007
+++ emboss/Makefile	Fri Aug 17 12:05:27 2007
@@ -6,26 +6,20 @@
 #
 
 PORTNAME=	emboss
-PORTVERSION=	3.0.0
-PORTREVISION=	1
+PORTVERSION=	5.0.0
+RELEASE=	${PORTNAME:U}-${PORTVERSION}
 CATEGORIES=	biology
 MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/ \
-		ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
-		ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
 		ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
-DISTNAME=	${PORTNAME:U}-${PORTVERSION}
-DISTFILES=	${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
+DISTNAME=	${RELEASE}
+DISTFILES=	${RELEASE}${EXTRACT_SUFX}
 DIST_SUBDIR=	${PORTNAME}
 
-PATCH_WRKSRC=	${WRKDIR}
-
 MAINTAINER=	fernan@iib.unsam.edu.ar
 COMMENT=	A collection of open source tools for genetic sequence analysis
 
 BUILD_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw \
 		primer3:${PORTSDIR}/biology/primer3
-LIB_DEPENDS=	gd.4:${PORTSDIR}/graphics/gd \
-		png.5:${PORTSDIR}/graphics/png
 
 CONFLICTS=	qmail-ldap-[0-9]* digest-[0-9]*
 
@@ -41,20 +35,21 @@
 SUB_FILES=	pkg-message
 SUB_LIST=	PREFIX=${PREFIX} DATADIR=${DATADIR}
 
-DOCSDIR=	${PREFIX}/share/doc/${PORTNAME:U}
+DOCSDIR=	${PREFIX}/share/${PORTNAME:U}/doc
 DATADIR=	${PREFIX}/share/${PORTNAME:U}
 
-DOC_DIRS=	doc/manuals doc/tutorials doc/programs/text doc/programs/html
-CONFIG_FILE=	${WRKSRC}/emboss/emboss.default.template
+CONFIGURE_ARGS+= --with-docroot=${DOCSDIR}
 
-post-patch:
-.if !defined(NOPORTDOCS)
-.for DIR in ${DOC_DIRS}
-	@ ${REINPLACE_CMD} -e \
-	  's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \
-	  ${WRKSRC}/${DIR}/Makefile.in
-.endfor
+.if defined(WITHOUT_X11)
+USE_XLIB=	yes
+USE_MOTIF=	yes
+LIB_DEPENDS=	gd.4:${PORTSDIR}/graphics/gd \
+		png.5:${PORTSDIR}/graphics/png
+CONFIGURE_ARGS+= --without-x
 .endif
+
+DOC_DIRS=	doc/manuals doc/tutorials doc/programs/text doc/programs/html
+CONFIG_FILE=	${WRKSRC}/emboss/emboss.default.template
 
 pre-install:
 	@ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${DATADIR}#' ${CONFIG_FILE}
diff -ruN --exclude=CVS /usr/ports/biology/emboss/distinfo emboss/distinfo
--- /usr/ports/biology/emboss/distinfo	Fri Mar 31 06:43:20 2006
+++ emboss/distinfo	Fri Jul 20 23:38:22 2007
@@ -1,3 +1,3 @@
-MD5 (emboss/EMBOSS-3.0.0.tar.gz) = fa72feded9ab9272e3e731c09f545dcc
-SHA256 (emboss/EMBOSS-3.0.0.tar.gz) = 47a51ba7aeb9f6e7f4cd23c28cffad7c6d28432e92f37d6f08121791ef894dea
-SIZE (emboss/EMBOSS-3.0.0.tar.gz) = 16257908
+MD5 (emboss/EMBOSS-5.0.0.tar.gz) = be4c895220ad34afd65d450ba7d8e34b
+SHA256 (emboss/EMBOSS-5.0.0.tar.gz) = 64e6f09b82a719ff26de7f21fdf7d2bd605d2c664384c1c7b48f9d245d5f40ae
+SIZE (emboss/EMBOSS-5.0.0.tar.gz) = 20666560
diff -ruN --exclude=CVS /usr/ports/biology/emboss/pkg-descr emboss/pkg-descr
--- /usr/ports/biology/emboss/pkg-descr	Fri Aug  3 08:32:41 2001
+++ emboss/pkg-descr	Wed Feb  7 11:49:31 2007
@@ -12,12 +12,8 @@
 
 EMBASSY packages are third party applications which have been integrated with
 the EMBOSS suite, but which are not included in the base EMBOSS distribution
-for licensing or other reasons.  This port includes the currently available
-EMBASSY applications.  During an interactive install the user will be asked
-to choose which of these will be installed (default: all).  Note that the
-EMBASSY versions of PHYLIP and HMMER should not clash with the standalone
-versions (also in ports/biology) due to the fact that their binaries have been
-renamed.
+for licensing or other reasons. The EMBASSY packages live in the
+biology/embassy port. 
 
 WWW: http://www.emboss.org/
 
diff -ruN --exclude=CVS /usr/ports/biology/emboss/pkg-plist emboss/pkg-plist
--- /usr/ports/biology/emboss/pkg-plist	Fri Mar 31 06:43:20 2006
+++ emboss/pkg-plist	Fri Aug 17 11:07:25 2007
@@ -6,6 +6,7 @@
 bin/acdtrace
 bin/acdvalid
 bin/antigenic
+bin/backtranambig
 bin/backtranseq
 bin/banana
 bin/biosed
@@ -43,6 +44,7 @@
 bin/dotpath
 bin/dottup
 bin/dreg
+bin/edialign
 bin/einverted
 bin/embossdata
 bin/embossversion
@@ -54,6 +56,7 @@
 bin/equicktandem
 bin/est2genome
 bin/etandem
+bin/extractalign
 bin/extractfeat
 bin/extractseq
 bin/findkm
@@ -73,6 +76,8 @@
 bin/jembossctl
 bin/lindna
 bin/listor
+bin/makenucseq
+bin/makeprotseq
 bin/marscan
 bin/maskfeat
 bin/maskseq
@@ -138,11 +143,11 @@
 bin/sirna
 bin/sixpack
 bin/skipseq
-bin/syco
 bin/splitter
 bin/stretcher
 bin/stssearch
 bin/supermatcher
+bin/syco
 bin/tcode
 bin/textsearch
 bin/tfextract
@@ -160,22 +165,29 @@
 bin/whichdb
 bin/wobble
 bin/wordcount
+bin/wordfinder
 bin/wordmatch
 bin/wossname
 bin/yank
 bin/runJemboss.csh
-include/drivers.h
-include/pdf.h
-include/plcore.h
-include/plevent.h
-include/plplotP.h
-include/plxwd.h
-include/metadefs.h
-include/plConfig.h
-include/pldebug.h
-include/plplot.h
-include/plstrm.h
-include/plDevs.h
+include/eplplot/drivers.h
+include/eplplot/pdf.h
+include/eplplot/plcore.h
+include/eplplot/plevent.h
+include/eplplot/plplotP.h
+include/eplplot/plxwd.h
+include/eplplot/metadefs.h
+include/eplplot/plConfig.h
+include/eplplot/pldebug.h
+include/eplplot/plplot.h
+include/eplplot/plstrm.h
+include/eplplot/plDevs.h
+include/eplplot/disptab.h
+include/eplplot/pldll.h
+include/eplplot/plhershey-unicode.h
+include/eplplot/ps.h
+include/eplplot/plunicode-type1.h
+include/eplplot/plfci-type1.h
 include/ajax.h
 include/ajarch.h
 include/ajdefine.h
@@ -188,6 +200,7 @@
 include/ajcod.h
 include/ajdan.h
 include/ajdmx.h
+include/ajdom.h
 include/ajdomain.h
 include/ajexcept.h
 include/ajfeat.h
@@ -207,6 +220,7 @@
 include/ajmess.h
 include/ajnam.h
 include/ajnexus.h
+include/ajpat.h
 include/ajpdb.h
 include/ajpdbio.h
 include/ajphylo.h
@@ -255,716 +269,29 @@
 include/embmol.h
 include/embnmer.h
 include/embpat.h
+include/embpatlist.h
 include/embprop.h
 include/embpdb.h
 include/embread.h
 include/embsig.h
 include/embshow.h
 include/embword.h
-lib/libplplot.so.5
-lib/libplplot.so
-lib/libplplot.la
-lib/libplplot.a
-lib/libajax.so.3
+lib/libeplplot.so.5
+lib/libeplplot.so
+lib/libeplplot.la
+lib/libeplplot.a
+lib/libajax.so.5
 lib/libajax.so
 lib/libajax.la
 lib/libajax.a
-lib/libajaxg.so.3
+lib/libajaxg.so.5
 lib/libajaxg.so
 lib/libajaxg.la
 lib/libajaxg.a
-lib/libnucleus.so.3
+lib/libnucleus.so.5
 lib/libnucleus.so
 lib/libnucleus.la
 lib/libnucleus.a
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.sty
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.tex
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.aux
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.dvi
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.log
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.pdf
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.ps
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.toc
-%%PORTDOCS%%%%DOCSDIR%%/manuals/adminguide.tar.gz
-%%PORTDOCS%%%%DOCSDIR%%/manuals/domainatrix.doc
-%%PORTDOCS%%%%DOCSDIR%%/manuals/program.ps.gz
-%%PORTDOCS%%%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.pdf
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.ps
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss.sty
-%%PORTDOCS%%%%DOCSDIR%%/manuals/fdl.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/listor.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/marscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskfeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/matcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/matgen3d.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/megamerger.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/meme.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/menus_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/merger.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/msbar.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwcontam.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwfilter.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/myseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalignrunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/needle.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/needlerunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgreport.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgseek.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/noreturn.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/notseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nthseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_2d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_composition_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_cpg_islands_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_gene_finding_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_motifs_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_mutation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_primers_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_profiles_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_repeats_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_restriction_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_transcription_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_translation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/oddcomp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/palindrome.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pasteseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatdb.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatmotifs.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbparse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbplus.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbtosp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepcoil.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepstats.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_consensus_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_continuous_characters_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_discrete_characters_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_distance_matrix_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_gene_frequencies_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_molecular_sequence_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_tree_drawing_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/preg.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/primersearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/printsextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/profit.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophecy.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophet.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prosextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_2d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_3d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_composition_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_motifs_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_mutation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_profiles_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_sequence_alignment_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/psiphi.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rebaseextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/recoder.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/redata.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/remap.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restover.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restrict.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/revseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocon.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocplot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scope.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scopparse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorecmapdir.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorer.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorerrunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seealso.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqfraggle.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqmatchall.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqnr.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqret.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqretsplit.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsort.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqwords.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showdb.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showfeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showorf.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/shuffleseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigcleave.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggen.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggenlig.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscanlig.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/silent.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sirna.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sites.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sixpack.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/skipseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/splitter.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ssematch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/stretcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/stssearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/substitute.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/substituterunner.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/supermatcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tcode.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/template.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/test_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/textsearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfm.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tranalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/transeq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimest.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/twofeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/union.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_creation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_indexing_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_misc_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/vectorstrip.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/water.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/whichdb.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordcount.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordmatch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wossname.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/yank.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.jpg
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/abiview.1.abiview.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/chaos.1.chaos.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cirdna.1.cirdna.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgplot.1.cpgplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dan.2.dan.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotmatcher.1.dotmatcher.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotpath.1.dotpath.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dottup.1.dottup.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/findkm.1.findkm.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/isochore.1.isochore.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.1.lindna.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.1.octanol.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.1.pepinfo.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.1.pepnet.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.1.pepwheel.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.1.pepwindow.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.1.pepwindowall.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.1.plotcon.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.1.plotorf.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.2.plotorf.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.1.polydot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.1.prettyplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.2.prettyplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.1.syco.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.1.tmap.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.gif
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+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/phylogeny_tree_drawing_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/plotcon.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/plotorf.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/polydot.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/preg.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/prettyplot.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/prettyseq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/primersearch.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/printsextract.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/profit.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/prophecy.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/prophet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/prosextract.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/protein_2d_structure_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/protein_3d_structure_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/protein_composition_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/protein_motifs_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/protein_mutation_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/protein_profiles_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/protein_sequence_alignment_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pscan.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/psiphi.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/rebaseextract.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/recoder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/redata.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/remap.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/restover.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/restrict.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/revseq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/seealso.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/seqmatchall.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/seqret.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/seqretsplit.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/showalign.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/showdb.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/showfeat.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/showorf.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/showseq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/shuffleseq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/sigcleave.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/silent.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/sirna.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/sixpack.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/skipseq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/splitter.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/stretcher.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/stssearch.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/supermatcher.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/syco.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tcode.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tfm.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tcode.2.tcode.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/template.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/test_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/textsearch.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tfextract.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tfscan.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tmap.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tranalign.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/transeq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/trimest.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/trimseq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/twofeat.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/union.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/utils_database_creation_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/utils_database_indexing_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/utils_misc_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/vectorstrip.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/water.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/whichdb.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/wobble.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/wordcount.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/wordfinder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/wordmatch.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/wossname.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/yank.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/emboss_icon.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/abiview.1.abiview.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/banana.1.banana.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/chaos.1.chaos.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cirdna.1.cirdna.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cpgplot.1.cpgplot.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dan.2.dan.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dotmatcher.1.dotmatcher.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dotpath.1.dotpath.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dottup.1.dottup.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/emboss_icon.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/findkm.1.findkm.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/isochore.1.isochore.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/lindna.1.lindna.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/octanol.1.octanol.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepinfo.1.pepinfo.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepnet.1.pepnet.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepwheel.1.pepwheel.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepwindow.1.pepwindow.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/pepwindowall.1.pepwindowall.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/plotcon.1.plotcon.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/plotorf.1.plotorf.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/plotorf.2.plotorf.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/polydot.1.polydot.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/prettyplot.1.prettyplot.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/prettyplot.2.prettyplot.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/syco.1.syco.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/tmap.1.tmap.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/wobble.1.wobble.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/aaindexextract.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/abiview.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/acd_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/acdc.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/acdlog.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/acdpretty.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/acdtable.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/acdtrace.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/acdvalid.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/ajtest.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/alignment_consensus_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/alignment_differences_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/alignment_dot_plots_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/alignment_global_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/alignment_local_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/alignment_multiple_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/antigenic.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/banana.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/backtranambig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/backtranseq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/biosed.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/btwisted.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cai.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/chaos.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/charge.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/checktrans.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/chips.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cirdna.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/codcmp.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/codcopy.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/coderet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/compseq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cons.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cpgplot.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cpgreport.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cusp.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cutgextract.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/cutseq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dan.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dbiblast.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dbifasta.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dbiflat.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dbigcg.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dbxfasta.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dbxflat.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dbxgcg.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/degapseq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/descseq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/diffseq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/digest.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/display_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/distmat.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dotmatcher.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dotpath.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dottup.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/dreg.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/edialign.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/einverted.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/embossdata.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/embossversion.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/emma.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/emowse.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/entret.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/enzyme_kinetics_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/epestfind.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/eprimer3.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/equicktandem.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/est2genome.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/etandem.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/extractfeat.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/extractseq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/feature_tables_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/findkm.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/freak.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/fuzznuc.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/fuzzpro.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/fuzztran.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/garnier.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/geecee.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/getorf.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/groups.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/helixturnhelix.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/iep.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/hmm_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/hmoment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/index.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/infoalign.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/information_group.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/infoseq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/isochore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/emboss/apps/jembossctl.html
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/jembossctl.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/lindna.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/listor.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/makenucseq.txt
+%%POR
Comment 1 Rong-En Fan freebsd_committer freebsd_triage 2008-04-05 08:11:59 UTC 
Responsible Changed
From-To: freebsd-ports-bugs->rafan

I'll take it.
Comment 2 Rong-En Fan freebsd_committer freebsd_triage 2008-04-05 09:13:29 UTC 
State Changed
From-To: open->feedback

There are patches failed during make patch. Please look at it and  
submit a new diff. Thanks!
Comment 3 Fernan Aguero 2008-04-05 14:43:14 UTC 
> There are patches failed during make patch. Please look at it and
> submit a new diff. Thanks!

Let me know if it's fixed now. Thanks!

--
fernan
Comment 4 Rong-En Fan freebsd_committer freebsd_triage 2008-04-05 15:49:14 UTC 
On Sat, Apr 05, 2008 at 10:43:14AM -0300, Fernan Aguero wrote:
> > There are patches failed during make patch. Please look at it and
> > submit a new diff. Thanks!
> 
> Let me know if it's fixed now. Thanks!


$ make patch
===>  Extracting for emboss-5.0.0
=> MD5 Checksum OK for emboss/EMBOSS-5.0.0.tar.gz.
=> SHA256 Checksum OK for emboss/EMBOSS-5.0.0.tar.gz.
===>  Patching for emboss-5.0.0
===>  Applying FreeBSD patches for emboss-5.0.0
Ignoring previously applied (or reversed) patch.
32 out of 32 hunks ignored--saving rejects to ajax/ajindex.c.rej
=> Patch patch-ajindex.c failed to apply cleanly.
*** Error code 1

Stop in /home/rafan/work/FreeBSD/ports/biology/emboss.
*** Error code 1

Stop in /home/rafan/work/FreeBSD/ports/biology/emboss.


In addition, this part looks strange to me:

.if defined(WITHOUT_X11)
USE_XLIB=       yes
USE_MOTIF=      yes
LIB_DEPENDS=    gd.4:${PORTSDIR}/graphics/gd \
                png.5:${PORTSDIR}/graphics/png
CONFIGURE_ARGS+= --without-x
.endif

USE_XLIB when WITHOUT_X11 is defined? 

Regards,
Rong-En Fan

> 
> --
> fernan
Comment 5 dfilter service freebsd_committer freebsd_triage 2008-04-13 08:21:24 UTC 
rafan       2008-04-13 07:21:16 UTC

  FreeBSD ports repository

  Modified files:
    biology/emboss       pkg-plist 
  Log:
  - Sort pkg-plist before updating to 5.0.0
  
  PR:             ports/122437
  Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
  
  Revision  Changes    Path
  1.24      +940 -940  ports/biology/emboss/pkg-plist
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Comment 6 dfilter service freebsd_committer freebsd_triage 2008-04-13 08:22:26 UTC 
rafan       2008-04-13 07:22:21 UTC

  FreeBSD ports repository

  Modified files:
    biology/emboss       Makefile distinfo pkg-descr pkg-plist 
  Removed files:
    biology/emboss/files patch-ajindex.c patch-ajindex.h 
                         patch-ajpdb.c patch-ajseqdb.c 
                         patch-dbxfasta.c patch-dbxflat.c 
                         patch-dbxgcg.c patch-embindex.c 
                         patch-embindex.h patch-marscan.c 
  Log:
  - Update to 5.0.0
  
  PR:             ports/122437
  Submitted by:   Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
  
  Revision  Changes    Path
  1.50      +17 -19    ports/biology/emboss/Makefile
  1.27      +3 -3      ports/biology/emboss/distinfo
  1.2       +0 -5134   ports/biology/emboss/files/patch-ajindex.c (dead)
  1.2       +0 -170    ports/biology/emboss/files/patch-ajindex.h (dead)
  1.2       +0 -67     ports/biology/emboss/files/patch-ajpdb.c (dead)
  1.2       +0 -195    ports/biology/emboss/files/patch-ajseqdb.c (dead)
  1.2       +0 -89     ports/biology/emboss/files/patch-dbxfasta.c (dead)
  1.2       +0 -146    ports/biology/emboss/files/patch-dbxflat.c (dead)
  1.2       +0 -96     ports/biology/emboss/files/patch-dbxgcg.c (dead)
  1.2       +0 -115    ports/biology/emboss/files/patch-embindex.c (dead)
  1.2       +0 -96     ports/biology/emboss/files/patch-embindex.h (dead)
  1.2       +0 -72     ports/biology/emboss/files/patch-marscan.c (dead)
  1.6       +2 -6      ports/biology/emboss/pkg-descr
  1.25      +341 -562  ports/biology/emboss/pkg-plist
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Comment 7 dfilter service freebsd_committer freebsd_triage 2008-04-13 08:22:50 UTC 
rafan       2008-04-13 07:22:42 UTC

  FreeBSD ports repository

  Modified files:
    biology/embassy      Makefile distinfo pkg-plist 
  Log:
  - Update to 5.0.0
  
  PR:             ports/122437
  Submitted by:   Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
  
  Revision  Changes    Path
  1.10      +12 -10    ports/biology/embassy/Makefile
  1.5       +42 -39    ports/biology/embassy/distinfo
  1.4       +290 -32   ports/biology/embassy/pkg-plist
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Comment 8 Rong-En Fan freebsd_committer freebsd_triage 2008-04-13 08:22:56 UTC 
State Changed
From-To: feedback->closed

Committed with minor changes. Thanks!