svn commit: r457333 - head/biology/p5-Bio-Phylo
Sunpoet Po-Chuan Hsieh
sunpoet at FreeBSD.org
Tue Dec 26 23:20:32 UTC 2017
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
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