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