From aad647a9c78179904cd8ac55187d85d2900bea27 Mon Sep 17 00:00:00 2001
From: wen <wen@FreeBSD.org>
Date: Tue, 9 Mar 2010 07:34:48 +0000
Subject: - Update to 0.21

---
 biology/p5-Bio-Phylo/Makefile  | 37 +++++++++++++---------------------
 biology/p5-Bio-Phylo/distinfo  |  6 +++---
 biology/p5-Bio-Phylo/pkg-plist | 45 ++++++++++++++++++++++--------------------
 3 files changed, 41 insertions(+), 47 deletions(-)

(limited to 'biology')

diff --git a/biology/p5-Bio-Phylo/Makefile b/biology/p5-Bio-Phylo/Makefile
index 7f0baeccf96..343ca431689 100644
--- a/biology/p5-Bio-Phylo/Makefile
+++ b/biology/p5-Bio-Phylo/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	Bio-Phylo
-PORTVERSION=	0.18
+PORTVERSION=	0.21
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
@@ -22,8 +22,6 @@ BUILD_DEPENDS=	p5-Exception-Class>1.22:${PORTSDIR}/devel/p5-Exception-Class \
 RUN_DEPENDS=	${BUILD_DEPENDS}
 
 MAN3=	Bio::Phylo.3 \
-	Bio::Phylo::Annotation.3 \
-	Bio::Phylo::Dictionary.3 \
 	Bio::Phylo::Factory.3 \
 	Bio::Phylo::Forest::DrawNode.3 \
 	Bio::Phylo::Forest::DrawTree.3 \
@@ -47,23 +45,23 @@ MAN3=	Bio::Phylo.3 \
 	Bio::Phylo::Matrices::Datatype::Continuous.3 \
 	Bio::Phylo::Matrices::Datatype::Standard.3 \
 	Bio::Phylo::Matrices::Datatype::Mixed.3 \
-	Bio::Phylo::Meta.3 \
-	Bio::Phylo::Meta::XMLLiteral.3 \
-	Bio::Phylo::Mediators::NodeMediator.3 \
 	Bio::Phylo::Mediators::TaxaMediator.3 \
+	Bio::Phylo::NeXML::DOM::Element::Twig.3 \
+	Bio::Phylo::NeXML::DOM::Document::Twig.3 \
+	Bio::Phylo::NeXML::DOM::Document::Libxml.3 \
+	Bio::Phylo::NeXML::DOM.3 \
+	Bio::Phylo::NeXML::Meta.3 \
+	Bio::Phylo::NeXML::Writable.3 \
+	Bio::Phylo::NeXML::DOM::Document.3 \
+	Bio::Phylo::NeXML::DOM::Element::Libxml.3 \
+	Bio::Phylo::NeXML::DOM::Element.3 \
+	Bio::Phylo::NeXML::Meta::XMLLiteral.3 \
 	Bio::Phylo::Parsers::Newick.3 \
 	Bio::Phylo::Parsers::Nexml.3 \
 	Bio::Phylo::Parsers::Nexus.3 \
 	Bio::Phylo::Parsers::Table.3 \
 	Bio::Phylo::Parsers::Taxlist.3 \
 	Bio::Phylo::Parsers::Tolweb.3 \
-	Bio::Phylo::PhyloWS::Client.3 \
-	Bio::Phylo::PhyloWS::Service::Tolweb.3 \
-	Bio::Phylo::PhyloWS::Service.3 \
-	Bio::Phylo::PhyloWS::Resource::Description.3 \
-	Bio::Phylo::PhyloWS.3 \
-	Bio::Phylo::PhyloWS::Resource.3 \
-	Bio::Phylo::PhyloWS::Service::Timetree.3 \
 	Bio::Phylo::Project.3 \
 	Bio::Phylo::Set.3 \
 	Bio::Phylo::Taxa.3 \
@@ -78,17 +76,10 @@ MAN3=	Bio::Phylo.3 \
 	Bio::Phylo::Unparsers::Nexus.3 \
 	Bio::Phylo::Unparsers::Pagel.3 \
 	Bio::Phylo::Util::CONSTANT.3 \
-	Bio::Phylo::Util::DOM.3 \
-	Bio::Phylo::Util::DOM::Document::libxml.3 \
-	Bio::Phylo::Util::DOM::Document::twig.3 \
-	Bio::Phylo::Util::DOM::DocumentI.3 \
-	Bio::Phylo::Util::DOM::Element::libxml.3 \
-	Bio::Phylo::Util::DOM::Element::twig.3 \
-	Bio::Phylo::Util::DOM::ElementI.3 \
-	Bio::Phylo::Util::Exceptions.3 \
-	Bio::Phylo::Util::IDPool.3 \
 	Bio::Phylo::Util::Logger.3 \
-	Bio::Phylo::Util::XMLWritable.3
+	Bio::Phylo::Util::IDPool.3 \
+	Bio::Phylo::Util::Exceptions.3 \
+	Bio::Phylo::Util::StackTrace.3
 
 PERL_CONFIGURE=	yes
 
diff --git a/biology/p5-Bio-Phylo/distinfo b/biology/p5-Bio-Phylo/distinfo
index 9bb660c574f..9b4ad69e628 100644
--- a/biology/p5-Bio-Phylo/distinfo
+++ b/biology/p5-Bio-Phylo/distinfo
@@ -1,3 +1,3 @@
-MD5 (Bio-Phylo-0.18.tar.gz) = ae753f02d3c2fb46368c387ed50eb6ae
-SHA256 (Bio-Phylo-0.18.tar.gz) = d1da14b81fe498098fa385f51b0fe779cd64422535f91d93631cc604425d228d
-SIZE (Bio-Phylo-0.18.tar.gz) = 223011
+MD5 (Bio-Phylo-0.21.tar.gz) = 7376e008835c25711a1beb7d36d9c937
+SHA256 (Bio-Phylo-0.21.tar.gz) = 806302334e804fdc0040949f2ec889e7a8d9ad3193cfad9fab5bdff7df53f54b
+SIZE (Bio-Phylo-0.21.tar.gz) = 219585
diff --git a/biology/p5-Bio-Phylo/pkg-plist b/biology/p5-Bio-Phylo/pkg-plist
index 9a3cf20d096..6c2f48982ef 100644
--- a/biology/p5-Bio-Phylo/pkg-plist
+++ b/biology/p5-Bio-Phylo/pkg-plist
@@ -1,7 +1,4 @@
-%%SITE_PERL%%/Bio/._Phylo.pm
 %%SITE_PERL%%/Bio/Phylo.pm
-%%SITE_PERL%%/Bio/Phylo/Annotation.pm
-%%SITE_PERL%%/Bio/Phylo/Dictionary.pm
 %%SITE_PERL%%/Bio/Phylo/Forest.pm
 %%SITE_PERL%%/Bio/Phylo/Forest/DrawNode.pm
 %%SITE_PERL%%/Bio/Phylo/Forest/DrawTree.pm
@@ -25,23 +22,30 @@
 %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Mixed.pm
 %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Continuous.pm
 %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Rna.pm
-%%SITE_PERL%%/Bio/Phylo/Mediators/NodeMediator.pm
 %%SITE_PERL%%/Bio/Phylo/Mediators/TaxaMediator.pm
-%%SITE_PERL%%/Bio/Phylo/Meta.pm
-%%SITE_PERL%%/Bio/Phylo/Meta/XMLLiteral.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document/Libxml.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document/Twig.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document/._Libxml.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document/._Twig.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element/._Twig.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element/Twig.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element/._Libxml.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element/Libxml.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/Meta/._XMLLiteral.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/Meta/XMLLiteral.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/._DOM.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/._Meta.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/Meta.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/Writable.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Newick.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Nexml.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Nexus.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Table.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Taxlist.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Tolweb.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource/Description.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/Tolweb.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/Timetree.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Client.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource.pm
 %%SITE_PERL%%/Bio/Phylo/Project.pm
 %%SITE_PERL%%/Bio/Phylo/Set.pm
 %%SITE_PERL%%/Bio/Phylo/Taxa.pm
@@ -55,18 +59,12 @@
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Nexml.pm
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Nexus.pm
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Pagel.pm
-%%SITE_PERL%%/Bio/Phylo/Util/DOM/Document/libxml.pm
-%%SITE_PERL%%/Bio/Phylo/Util/DOM/Document/twig.pm
-%%SITE_PERL%%/Bio/Phylo/Util/DOM/Element/twig.pm
-%%SITE_PERL%%/Bio/Phylo/Util/DOM/Element/libxml.pm
-%%SITE_PERL%%/Bio/Phylo/Util/DOM/ElementI.pm
-%%SITE_PERL%%/Bio/Phylo/Util/DOM/DocumentI.pm
 %%SITE_PERL%%/Bio/Phylo/Util/Logger.pm
-%%SITE_PERL%%/Bio/Phylo/Util/DOM.pm
 %%SITE_PERL%%/Bio/Phylo/Util/CONSTANT.pm
 %%SITE_PERL%%/Bio/Phylo/Util/Exceptions.pm
 %%SITE_PERL%%/Bio/Phylo/Util/IDPool.pm
-%%SITE_PERL%%/Bio/Phylo/Util/XMLWritable.pm
+%%SITE_PERL%%/Bio/Phylo/Util/StackTrace.pm
+%%SITE_PERL%%/Bio/Phylo/Util/._StackTrace.pm
 %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio-Phylo/.packlist
 @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio-Phylo
 @dirrm %%SITE_PERL%%/Bio/Phylo/Util/DOM/Document
@@ -80,6 +78,11 @@
 @dirrm %%SITE_PERL%%/Bio/Phylo/PhyloWS/Service
 @dirrm %%SITE_PERL%%/Bio/Phylo/PhyloWS
 @dirrm %%SITE_PERL%%/Bio/Phylo/Parsers
+@dirrm %%SITE_PERL%%/Bio/Phylo/NeXML/Meta
+@dirrm %%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element
+@dirrm %%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document
+@dirrm %%SITE_PERL%%/Bio/Phylo/NeXML/DOM
+@dirrm %%SITE_PERL%%/Bio/Phylo/NeXML
 @dirrm %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype
 @dirrm %%SITE_PERL%%/Bio/Phylo/Matrices
 @dirrm %%SITE_PERL%%/Bio/Phylo/Mediators
-- 
cgit