- Update to 0.18

- Adopt

Feature safe:	yes

3 files changed, 72 insertions, 35 deletions

diff --git a/biology/p5-Bio-Phylo/Makefile b/biology/p5-Bio-Phylo/Makefile
index 263a1a415eba..7f0baeccf969 100644
--- a/biology/p5-Bio-Phylo/Makefile
+++ b/biology/p5-Bio-Phylo/Makefile
@@ -6,13 +6,12 @@
 #
 
 PORTNAME=	Bio-Phylo
-PORTVERSION=	0.16
-PORTREVISION=	2
+PORTVERSION=	0.18
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
 
-MAINTAINER=	ports@FreeBSD.org
+MAINTAINER=	wen@FreeBSD.org
 COMMENT=	Phylogenetic analysis using perl
 
 BUILD_DEPENDS=	p5-Exception-Class>1.22:${PORTSDIR}/devel/p5-Exception-Class \
@@ -22,25 +21,18 @@ BUILD_DEPENDS=	p5-Exception-Class>1.22:${PORTSDIR}/devel/p5-Exception-Class \
 		p5-SVG>=1.07:${PORTSDIR}/textproc/p5-SVG
 RUN_DEPENDS=	${BUILD_DEPENDS}
 
-MAN1=	dndtag.pl.1 \
-	droptip.pl.1 \
-	bremer.pl.1 \
-	age2bl.pl.1 \
-	dnd2svg.pl.1
 MAN3=	Bio::Phylo.3 \
-	Bio::ObjectCompat.3 \
-	Bio::Phylo::Adaptor.3 \
-	Bio::Phylo::ConfigData.3 \
+	Bio::Phylo::Annotation.3 \
+	Bio::Phylo::Dictionary.3 \
+	Bio::Phylo::Factory.3 \
+	Bio::Phylo::Forest::DrawNode.3 \
+	Bio::Phylo::Forest::DrawTree.3 \
 	Bio::Phylo::Forest.3 \
 	Bio::Phylo::Forest::Node.3 \
 	Bio::Phylo::Forest::Tree.3 \
 	Bio::Phylo::Generator.3 \
 	Bio::Phylo::IO.3 \
 	Bio::Phylo::Listable.3 \
-	Bio::Phylo::Adaptor::Bioperl::Datum.3 \
-	Bio::Phylo::Adaptor::Bioperl::Matrix.3 \
-	Bio::Phylo::Adaptor::Bioperl::Node.3 \
-	Bio::Phylo::Adaptor::Bioperl::Tree.3 \
 	Bio::Phylo::Manual.3 \
 	Bio::Phylo::Matrices.3 \
 	Bio::Phylo::Matrices::Datum.3 \
@@ -55,11 +47,25 @@ 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::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 \
 	Bio::Phylo::Taxa::TaxaLinker.3 \
 	Bio::Phylo::Taxa::Taxon.3 \
@@ -68,13 +74,22 @@ MAN3=	Bio::Phylo.3 \
 	Bio::Phylo::Treedrawer::Svg.3 \
 	Bio::Phylo::Unparsers::Mrp.3 \
 	Bio::Phylo::Unparsers::Newick.3 \
+	Bio::Phylo::Unparsers::Nexml.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
 
-PERL_MODBUILD=	5.7.2+
+PERL_CONFIGURE=	yes
 
 .include <bsd.port.mk>
diff --git a/biology/p5-Bio-Phylo/distinfo b/biology/p5-Bio-Phylo/distinfo
index 068eea7902e3..9bb660c574f0 100644
--- a/biology/p5-Bio-Phylo/distinfo
+++ b/biology/p5-Bio-Phylo/distinfo
@@ -1,3 +1,3 @@
-MD5 (Bio-Phylo-0.16.tar.gz) = 78c6d2ceced9b013898e7aa7b61010c0
-SHA256 (Bio-Phylo-0.16.tar.gz) = 17317e23c7423b197e08984aead6e52c454e47badbdfa8447fa499175e2789cd
-SIZE (Bio-Phylo-0.16.tar.gz) = 129830
+MD5 (Bio-Phylo-0.18.tar.gz) = ae753f02d3c2fb46368c387ed50eb6ae
+SHA256 (Bio-Phylo-0.18.tar.gz) = d1da14b81fe498098fa385f51b0fe779cd64422535f91d93631cc604425d228d
+SIZE (Bio-Phylo-0.18.tar.gz) = 223011
diff --git a/biology/p5-Bio-Phylo/pkg-plist b/biology/p5-Bio-Phylo/pkg-plist
index 945716b52c14..9a3cf20d0969 100644
--- a/biology/p5-Bio-Phylo/pkg-plist
+++ b/biology/p5-Bio-Phylo/pkg-plist
@@ -1,25 +1,17 @@
-bin/LRmb.pl
-bin/age2bl.pl
-bin/bremer.pl
-bin/dnd2svg.pl
-bin/dndtag.pl
-bin/droptip.pl
-bin/postmb.pl
+%%SITE_PERL%%/Bio/._Phylo.pm
 %%SITE_PERL%%/Bio/Phylo.pm
-%%SITE_PERL%%/Bio/ObjectCompat.pod
-%%SITE_PERL%%/Bio/Phylo/Adaptor.pm
-%%SITE_PERL%%/Bio/Phylo/ConfigData.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
 %%SITE_PERL%%/Bio/Phylo/Forest/Node.pm
 %%SITE_PERL%%/Bio/Phylo/Forest/Tree.pm
 %%SITE_PERL%%/Bio/Phylo/Generator.pm
 %%SITE_PERL%%/Bio/Phylo/IO.pm
+%%SITE_PERL%%/Bio/Phylo/Factory.pm
 %%SITE_PERL%%/Bio/Phylo/Listable.pm
 %%SITE_PERL%%/Bio/Phylo/Manual.pod
-%%SITE_PERL%%/Bio/Phylo/Adaptor/Bioperl/Node.pm
-%%SITE_PERL%%/Bio/Phylo/Adaptor/Bioperl/Datum.pm
-%%SITE_PERL%%/Bio/Phylo/Adaptor/Bioperl/Tree.pm
-%%SITE_PERL%%/Bio/Phylo/Adaptor/Bioperl/Matrix.pm
 %%SITE_PERL%%/Bio/Phylo/Matrices.pm
 %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype.pm
 %%SITE_PERL%%/Bio/Phylo/Matrices/Datum.pm
@@ -33,11 +25,25 @@ bin/postmb.pl
 %%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/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
 %%SITE_PERL%%/Bio/Phylo/Taxa/Taxon.pm
 %%SITE_PERL%%/Bio/Phylo/Taxa/TaxaLinker.pm
@@ -46,22 +52,38 @@ bin/postmb.pl
 %%SITE_PERL%%/Bio/Phylo/Treedrawer/Svg.pm
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Mrp.pm
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Newick.pm
+%%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
-@dirrm %%SITE_PERL%%/Bio/Phylo/Adaptor/Bioperl
-@dirrm %%SITE_PERL%%/Bio/Phylo/Adaptor
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio-Phylo/.packlist
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio-Phylo
+@dirrm %%SITE_PERL%%/Bio/Phylo/Util/DOM/Document
+@dirrm %%SITE_PERL%%/Bio/Phylo/Util/DOM/Element
+@dirrm %%SITE_PERL%%/Bio/Phylo/Util/DOM
 @dirrm %%SITE_PERL%%/Bio/Phylo/Util
 @dirrm %%SITE_PERL%%/Bio/Phylo/Unparsers
 @dirrm %%SITE_PERL%%/Bio/Phylo/Treedrawer
 @dirrm %%SITE_PERL%%/Bio/Phylo/Taxa
+@dirrm %%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource
+@dirrm %%SITE_PERL%%/Bio/Phylo/PhyloWS/Service
+@dirrm %%SITE_PERL%%/Bio/Phylo/PhyloWS
 @dirrm %%SITE_PERL%%/Bio/Phylo/Parsers
 @dirrm %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype
 @dirrm %%SITE_PERL%%/Bio/Phylo/Matrices
 @dirrm %%SITE_PERL%%/Bio/Phylo/Mediators
+@dirrm %%SITE_PERL%%/Bio/Phylo/Meta
 @dirrm %%SITE_PERL%%/Bio/Phylo/Forest
 @dirrm %%SITE_PERL%%/Bio/Phylo
 @dirrmtry %%SITE_PERL%%/Bio