From owner-svn-ports-all@freebsd.org Tue Dec 26 23:20:32 2017 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 1B5F7E89E6E; Tue, 26 Dec 2017 23:20:32 +0000 (UTC) (envelope-from sunpoet@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 967B56C3B6; Tue, 26 Dec 2017 23:20:30 +0000 (UTC) (envelope-from sunpoet@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id vBQNKTr2053013; Tue, 26 Dec 2017 23:20:29 GMT (envelope-from sunpoet@FreeBSD.org) Received: (from sunpoet@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id vBQNKSd0053010; Tue, 26 Dec 2017 23:20:28 GMT (envelope-from sunpoet@FreeBSD.org) Message-Id: <201712262320.vBQNKSd0053010@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: sunpoet set sender to sunpoet@FreeBSD.org using -f From: Sunpoet Po-Chuan Hsieh Date: Tue, 26 Dec 2017 23:20:28 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r457333 - head/biology/p5-Bio-Phylo X-SVN-Group: ports-head X-SVN-Commit-Author: sunpoet X-SVN-Commit-Paths: head/biology/p5-Bio-Phylo X-SVN-Commit-Revision: 457333 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.25 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 26 Dec 2017 23:20:32 -0000 Author: sunpoet Date: Tue Dec 26 23:20:28 2017 New Revision: 457333 URL: https://svnweb.freebsd.org/changeset/ports/457333 Log: Update to 2.0.1 Changes: https://github.com/rvosa/bio-phylo/releases Modified: head/biology/p5-Bio-Phylo/Makefile head/biology/p5-Bio-Phylo/distinfo head/biology/p5-Bio-Phylo/pkg-plist Modified: head/biology/p5-Bio-Phylo/Makefile ============================================================================== --- head/biology/p5-Bio-Phylo/Makefile Tue Dec 26 23:20:23 2017 (r457332) +++ head/biology/p5-Bio-Phylo/Makefile Tue Dec 26 23:20:28 2017 (r457333) @@ -2,8 +2,8 @@ # $FreeBSD$ PORTNAME= Bio-Phylo -PORTVERSION= 0.58 -PORTREVISION= 1 +PORTVERSION= 2.0.1 +DISTVERSIONPREFIX= v CATEGORIES= biology perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- @@ -15,11 +15,14 @@ LICENSE= ART10 GPLv1+ LICENSE_COMB= dual LICENSE_FILE_ART10= ${WRKSRC}/COPYING -BUILD_DEPENDS= p5-BioPerl>=0:biology/p5-BioPerl \ +BUILD_DEPENDS= p5-Archive-Zip>=0:archivers/p5-Archive-Zip \ + p5-BioPerl>=0:biology/p5-BioPerl \ p5-GD>=0:graphics/p5-GD \ p5-Math-CDF>=0:math/p5-Math-CDF \ p5-Math-Random>=0:math/p5-Math-Random \ p5-PDF-API2>=0:textproc/p5-PDF-API2 \ + p5-RDF-Query>=0:textproc/p5-RDF-Query \ + p5-RDF-Trine>=0:textproc/p5-RDF-Trine \ p5-SVG>=0:textproc/p5-SVG \ p5-SWF-Builder>=0:graphics/p5-SWF-Builder \ p5-XML-LibXML>=0:textproc/p5-XML-LibXML \ Modified: head/biology/p5-Bio-Phylo/distinfo ============================================================================== --- head/biology/p5-Bio-Phylo/distinfo Tue Dec 26 23:20:23 2017 (r457332) +++ head/biology/p5-Bio-Phylo/distinfo Tue Dec 26 23:20:28 2017 (r457333) @@ -1,2 +1,3 @@ -SHA256 (Bio-Phylo-0.58.tar.gz) = b8bbd3ea0d2029abac7c8119ef84d607d9c5a226477e8955bc38bac99d44167c -SIZE (Bio-Phylo-0.58.tar.gz) = 459056 +TIMESTAMP = 1514221175 +SHA256 (Bio-Phylo-v2.0.1.tar.gz) = 30bf253800a12ac501222ea42d17612f0557af6329daf05465b538569a894f4d +SIZE (Bio-Phylo-v2.0.1.tar.gz) = 541665 Modified: head/biology/p5-Bio-Phylo/pkg-plist ============================================================================== --- head/biology/p5-Bio-Phylo/pkg-plist Tue Dec 26 23:20:23 2017 (r457332) +++ head/biology/p5-Bio-Phylo/pkg-plist Tue Dec 26 23:20:28 2017 (r457333) @@ -35,6 +35,7 @@ %%SITE_PERL%%/Bio/Phylo/Matrices/MatrixRole.pm %%SITE_PERL%%/Bio/Phylo/Matrices/TypeSafeData.pm %%SITE_PERL%%/Bio/Phylo/Mediators/TaxaMediator.pm +%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Binary.pm %%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna.pm %%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna/F81.pm %%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna/GTR.pm @@ -52,8 +53,11 @@ %%SITE_PERL%%/Bio/Phylo/NeXML/Meta.pm %%SITE_PERL%%/Bio/Phylo/NeXML/Meta/XMLLiteral.pm %%SITE_PERL%%/Bio/Phylo/NeXML/Writable.pm +%%SITE_PERL%%/Bio/Phylo/NeXML/XML2JSON.pm %%SITE_PERL%%/Bio/Phylo/Parsers/Abstract.pm %%SITE_PERL%%/Bio/Phylo/Parsers/Adjacency.pm +%%SITE_PERL%%/Bio/Phylo/Parsers/Cdao.pm +%%SITE_PERL%%/Bio/Phylo/Parsers/Dwca.pm %%SITE_PERL%%/Bio/Phylo/Parsers/Fasta.pm %%SITE_PERL%%/Bio/Phylo/Parsers/Fastq.pm %%SITE_PERL%%/Bio/Phylo/Parsers/Figtree.pm @@ -61,6 +65,7 @@ %%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/Nhx.pm %%SITE_PERL%%/Bio/Phylo/Parsers/Phylip.pm %%SITE_PERL%%/Bio/Phylo/Parsers/Phyloxml.pm %%SITE_PERL%%/Bio/Phylo/Parsers/Table.pm @@ -99,6 +104,7 @@ %%SITE_PERL%%/Bio/Phylo/Unparsers/Adjacency.pm %%SITE_PERL%%/Bio/Phylo/Unparsers/Cdao.pm %%SITE_PERL%%/Bio/Phylo/Unparsers/Fasta.pm +%%SITE_PERL%%/Bio/Phylo/Unparsers/Figtree.pm %%SITE_PERL%%/Bio/Phylo/Unparsers/Hennig86.pm %%SITE_PERL%%/Bio/Phylo/Unparsers/Html.pm %%SITE_PERL%%/Bio/Phylo/Unparsers/Json.pm @@ -106,6 +112,7 @@ %%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/Nhx.pm %%SITE_PERL%%/Bio/Phylo/Unparsers/Nwmsrdf.pm %%SITE_PERL%%/Bio/Phylo/Unparsers/Pagel.pm %%SITE_PERL%%/Bio/Phylo/Unparsers/Phylip.pm @@ -119,6 +126,7 @@ %%SITE_PERL%%/Bio/Phylo/Util/IDPool.pm %%SITE_PERL%%/Bio/Phylo/Util/Logger.pm %%SITE_PERL%%/Bio/Phylo/Util/MOP.pm +%%SITE_PERL%%/Bio/Phylo/Util/Math.pm %%SITE_PERL%%/Bio/Phylo/Util/OptionalInterface.pm %%SITE_PERL%%/Bio/Phylo/Util/StackTrace.pm %%SITE_PERL%%/Bio/PhyloRole.pm @@ -159,6 +167,13 @@ %%PERL5_MAN3%%/Bio::Phylo::Matrices::MatrixRole.3.gz %%PERL5_MAN3%%/Bio::Phylo::Matrices::TypeSafeData.3.gz %%PERL5_MAN3%%/Bio::Phylo::Mediators::TaxaMediator.3.gz +%%PERL5_MAN3%%/Bio::Phylo::Models::Substitution::Binary.3.gz +%%PERL5_MAN3%%/Bio::Phylo::Models::Substitution::Dna.3.gz +%%PERL5_MAN3%%/Bio::Phylo::Models::Substitution::Dna::F81.3.gz +%%PERL5_MAN3%%/Bio::Phylo::Models::Substitution::Dna::GTR.3.gz +%%PERL5_MAN3%%/Bio::Phylo::Models::Substitution::Dna::HKY85.3.gz +%%PERL5_MAN3%%/Bio::Phylo::Models::Substitution::Dna::JC69.3.gz +%%PERL5_MAN3%%/Bio::Phylo::Models::Substitution::Dna::K80.3.gz %%PERL5_MAN3%%/Bio::Phylo::NeXML::DOM.3.gz %%PERL5_MAN3%%/Bio::Phylo::NeXML::DOM::Document.3.gz %%PERL5_MAN3%%/Bio::Phylo::NeXML::DOM::Document::Libxml.3.gz @@ -170,8 +185,11 @@ %%PERL5_MAN3%%/Bio::Phylo::NeXML::Meta.3.gz %%PERL5_MAN3%%/Bio::Phylo::NeXML::Meta::XMLLiteral.3.gz %%PERL5_MAN3%%/Bio::Phylo::NeXML::Writable.3.gz +%%PERL5_MAN3%%/Bio::Phylo::NeXML::XML2JSON.3.gz %%PERL5_MAN3%%/Bio::Phylo::Parsers::Abstract.3.gz %%PERL5_MAN3%%/Bio::Phylo::Parsers::Adjacency.3.gz +%%PERL5_MAN3%%/Bio::Phylo::Parsers::Cdao.3.gz +%%PERL5_MAN3%%/Bio::Phylo::Parsers::Dwca.3.gz %%PERL5_MAN3%%/Bio::Phylo::Parsers::Fasta.3.gz %%PERL5_MAN3%%/Bio::Phylo::Parsers::Fastq.3.gz %%PERL5_MAN3%%/Bio::Phylo::Parsers::Figtree.3.gz @@ -179,6 +197,7 @@ %%PERL5_MAN3%%/Bio::Phylo::Parsers::Newick.3.gz %%PERL5_MAN3%%/Bio::Phylo::Parsers::Nexml.3.gz %%PERL5_MAN3%%/Bio::Phylo::Parsers::Nexus.3.gz +%%PERL5_MAN3%%/Bio::Phylo::Parsers::Nhx.3.gz %%PERL5_MAN3%%/Bio::Phylo::Parsers::Phylip.3.gz %%PERL5_MAN3%%/Bio::Phylo::Parsers::Phyloxml.3.gz %%PERL5_MAN3%%/Bio::Phylo::Parsers::Table.3.gz @@ -217,6 +236,7 @@ %%PERL5_MAN3%%/Bio::Phylo::Unparsers::Adjacency.3.gz %%PERL5_MAN3%%/Bio::Phylo::Unparsers::Cdao.3.gz %%PERL5_MAN3%%/Bio::Phylo::Unparsers::Fasta.3.gz +%%PERL5_MAN3%%/Bio::Phylo::Unparsers::Figtree.3.gz %%PERL5_MAN3%%/Bio::Phylo::Unparsers::Hennig86.3.gz %%PERL5_MAN3%%/Bio::Phylo::Unparsers::Html.3.gz %%PERL5_MAN3%%/Bio::Phylo::Unparsers::Json.3.gz @@ -224,6 +244,7 @@ %%PERL5_MAN3%%/Bio::Phylo::Unparsers::Newick.3.gz %%PERL5_MAN3%%/Bio::Phylo::Unparsers::Nexml.3.gz %%PERL5_MAN3%%/Bio::Phylo::Unparsers::Nexus.3.gz +%%PERL5_MAN3%%/Bio::Phylo::Unparsers::Nhx.3.gz %%PERL5_MAN3%%/Bio::Phylo::Unparsers::Nwmsrdf.3.gz %%PERL5_MAN3%%/Bio::Phylo::Unparsers::Pagel.3.gz %%PERL5_MAN3%%/Bio::Phylo::Unparsers::Phylip.3.gz @@ -237,6 +258,7 @@ %%PERL5_MAN3%%/Bio::Phylo::Util::IDPool.3.gz %%PERL5_MAN3%%/Bio::Phylo::Util::Logger.3.gz %%PERL5_MAN3%%/Bio::Phylo::Util::MOP.3.gz +%%PERL5_MAN3%%/Bio::Phylo::Util::Math.3.gz %%PERL5_MAN3%%/Bio::Phylo::Util::OptionalInterface.3.gz %%PERL5_MAN3%%/Bio::Phylo::Util::StackTrace.3.gz %%PERL5_MAN3%%/Bio::PhyloRole.3.gz