Date: Sun, 10 Feb 2013 18:17:53 +0800 (CST) From: Gea-Suan Lin <gslin@gslin.org> To: FreeBSD-gnats-submit@freebsd.org Cc: perl@FreeBSD.org, gslin@gslin.org Subject: ports/176003: [PATCH] biology/p5-Bio-Phylo: update to 0.52 Message-ID: <20130210101753.AD0AA7E827@colo-p.gslin.org> Resent-Message-ID: <201302101020.r1AAK0DN098685@freefall.freebsd.org>
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>Number: 176003
>Category: ports
>Synopsis: [PATCH] biology/p5-Bio-Phylo: update to 0.52
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: update
>Submitter-Id: current-users
>Arrival-Date: Sun Feb 10 10:20:00 UTC 2013
>Closed-Date:
>Last-Modified:
>Originator: Gea-Suan Lin
>Release: FreeBSD 9.1-RELEASE i386
>Organization:
>Environment:
System: FreeBSD colo-p.gslin.org 9.1-RELEASE FreeBSD 9.1-RELEASE #0 r243826: Tue Dec 4 06:55:39
>Description:
- Update to 0.52
Port maintainer (perl@FreeBSD.org) is cc'd.
Generated with FreeBSD Port Tools 0.99_6 (mode: update, diff: ports)
>How-To-Repeat:
>Fix:
--- p5-Bio-Phylo-0.52.patch begins here ---
diff -ruN --exclude=CVS /usr/ports/biology/p5-Bio-Phylo/Makefile ./Makefile
--- /usr/ports/biology/p5-Bio-Phylo/Makefile 2012-11-17 13:54:52.000000000 +0800
+++ ./Makefile 2013-02-10 08:23:56.000000000 +0800
@@ -1,12 +1,7 @@
-# New ports collection makefile for: Bio-Phylo
-# Date created: 12 Mar 2006
-# Whom: Aaron Dalton <aaron@FreeBSD.org>
-#
# $FreeBSD: ports/biology/p5-Bio-Phylo/Makefile,v 1.36 2012/11/17 05:54:52 svnexp Exp $
-#
PORTNAME= Bio-Phylo
-PORTVERSION= 0.50
+PORTVERSION= 0.52
CATEGORIES= biology perl5
MASTER_SITES= CPAN
PKGNAMEPREFIX= p5-
@@ -40,11 +35,14 @@
Bio::Phylo::Forest::DrawNode.3 \
Bio::Phylo::Forest::DrawTree.3 \
Bio::Phylo::Forest::Node.3 \
+ Bio::Phylo::Forest::NodeRole.3 \
Bio::Phylo::Forest::Tree.3 \
+ Bio::Phylo::Forest::TreeRole.3 \
Bio::Phylo::Generator.3 \
Bio::Phylo::IO.3 \
Bio::Phylo::Identifiable.3 \
Bio::Phylo::Listable.3 \
+ Bio::Phylo::ListableRole.3 \
Bio::Phylo::Manual.3 \
Bio::Phylo::Matrices.3 \
Bio::Phylo::Matrices::Character.3 \
@@ -59,7 +57,9 @@
Bio::Phylo::Matrices::Datatype::Rna.3 \
Bio::Phylo::Matrices::Datatype::Standard.3 \
Bio::Phylo::Matrices::Datum.3 \
+ Bio::Phylo::Matrices::DatumRole.3 \
Bio::Phylo::Matrices::Matrix.3 \
+ Bio::Phylo::Matrices::MatrixRole.3 \
Bio::Phylo::Matrices::TypeSafeData.3 \
Bio::Phylo::Mediators::TaxaMediator.3 \
Bio::Phylo::NeXML::DOM.3 \
@@ -76,6 +76,7 @@
Bio::Phylo::Parsers::Abstract.3 \
Bio::Phylo::Parsers::Adjacency.3 \
Bio::Phylo::Parsers::Fasta.3 \
+ Bio::Phylo::Parsers::Figtree.3 \
Bio::Phylo::Parsers::Json.3 \
Bio::Phylo::Parsers::Newick.3 \
Bio::Phylo::Parsers::Nexml.3 \
@@ -136,7 +137,8 @@
Bio::Phylo::Util::IDPool.3 \
Bio::Phylo::Util::Logger.3 \
Bio::Phylo::Util::OptionalInterface.3 \
- Bio::Phylo::Util::StackTrace.3
+ Bio::Phylo::Util::StackTrace.3 \
+ Bio::PhyloRole.3
post-patch:
@${REINPLACE_CMD} -e '/NAME/ s|Bio-Phylo|Bio::Phylo|' ${WRKSRC}/Makefile.PL
diff -ruN --exclude=CVS /usr/ports/biology/p5-Bio-Phylo/distinfo ./distinfo
--- /usr/ports/biology/p5-Bio-Phylo/distinfo 2012-06-13 02:55:28.000000000 +0800
+++ ./distinfo 2013-02-10 08:22:28.000000000 +0800
@@ -1,2 +1,2 @@
-SHA256 (Bio-Phylo-0.50.tar.gz) = 89e24ac1d68096226194f89b5088910ece4239372e63666011b5fae2a6e0fe3c
-SIZE (Bio-Phylo-0.50.tar.gz) = 378189
+SHA256 (Bio-Phylo-0.52.tar.gz) = 5c023acc76fb643581bc3612a80e9081ad1a795270bbc02a15f4460637c526c3
+SIZE (Bio-Phylo-0.52.tar.gz) = 398024
diff -ruN --exclude=CVS /usr/ports/biology/p5-Bio-Phylo/pkg-plist ./pkg-plist
--- /usr/ports/biology/p5-Bio-Phylo/pkg-plist 2012-06-13 02:55:28.000000000 +0800
+++ ./pkg-plist 2013-02-10 08:25:10.000000000 +0800
@@ -1,3 +1,4 @@
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Phylo/.packlist
%%SITE_PERL%%/Bio/Phylo.pm
%%SITE_PERL%%/Bio/Phylo/EvolutionaryModels.pm
%%SITE_PERL%%/Bio/Phylo/Factory.pm
@@ -5,11 +6,14 @@
%%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/NodeRole.pm
%%SITE_PERL%%/Bio/Phylo/Forest/Tree.pm
+%%SITE_PERL%%/Bio/Phylo/Forest/TreeRole.pm
%%SITE_PERL%%/Bio/Phylo/Generator.pm
%%SITE_PERL%%/Bio/Phylo/IO.pm
%%SITE_PERL%%/Bio/Phylo/Identifiable.pm
%%SITE_PERL%%/Bio/Phylo/Listable.pm
+%%SITE_PERL%%/Bio/Phylo/ListableRole.pm
%%SITE_PERL%%/Bio/Phylo/Manual.pod
%%SITE_PERL%%/Bio/Phylo/Matrices.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Character.pm
@@ -24,7 +28,9 @@
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Rna.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Standard.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datum.pm
+%%SITE_PERL%%/Bio/Phylo/Matrices/DatumRole.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Matrix.pm
+%%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/Dna.pm
@@ -47,6 +53,7 @@
%%SITE_PERL%%/Bio/Phylo/Parsers/Abstract.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Adjacency.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Fasta.pm
+%%SITE_PERL%%/Bio/Phylo/Parsers/Figtree.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Json.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Newick.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Nexml.pm
@@ -102,34 +109,37 @@
%%SITE_PERL%%/Bio/Phylo/Unparsers/Rss1.pm
%%SITE_PERL%%/Bio/Phylo/Unparsers/Taxlist.pm
%%SITE_PERL%%/Bio/Phylo/Util/CONSTANT.pm
+%%SITE_PERL%%/Bio/Phylo/Util/CONSTANT/Int.pm
%%SITE_PERL%%/Bio/Phylo/Util/Dependency.pm
%%SITE_PERL%%/Bio/Phylo/Util/Exceptions.pm
%%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/OptionalInterface.pm
%%SITE_PERL%%/Bio/Phylo/Util/StackTrace.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Phylo/.packlist
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Phylo
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
-@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/Service
-@dirrm %%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource
-@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/Models/Substitution/Dna
-@dirrm %%SITE_PERL%%/Bio/Phylo/Models/Substitution
-@dirrm %%SITE_PERL%%/Bio/Phylo/Models
-@dirrm %%SITE_PERL%%/Bio/Phylo/Mediators
-@dirrm %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype
-@dirrm %%SITE_PERL%%/Bio/Phylo/Matrices
-@dirrm %%SITE_PERL%%/Bio/Phylo/Forest
-@dirrm %%SITE_PERL%%/Bio/Phylo
+%%SITE_PERL%%/Bio/PhyloRole.pm
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/Util/CONSTANT
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/Util
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/Unparsers
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/Treedrawer
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/Taxa
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/PhyloWS/Service
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/PhyloWS
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/Parsers
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/NeXML/Meta
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/NeXML/DOM
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/NeXML
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/Models/Substitution
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/Models
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/Mediators
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/Matrices
+@dirrmtry %%SITE_PERL%%/Bio/Phylo/Forest
+@dirrmtry %%SITE_PERL%%/Bio/Phylo
@dirrmtry %%SITE_PERL%%/Bio
+@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Phylo
+@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
--- p5-Bio-Phylo-0.52.patch ends here ---
>Release-Note:
>Audit-Trail:
>Unformatted:
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