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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: [PATCH] biology/p5-Bio-Phylo: update to 0.52
X-Send-Pr-Version: 3.113
X-GNATS-Notify:

>Number:         176003
>Category:       ports
>Synopsis:       [PATCH] biology/p5-Bio-Phylo: update to 0.52
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    culot
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Sun Feb 10 10:20:00 UTC 2013
>Closed-Date:    Sat Feb 16 14:59:10 UTC 2013
>Last-Modified:  Sat Feb 16 15:00:00 UTC 2013
>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:
Responsible-Changed-From-To: freebsd-ports-bugs->perl 
Responsible-Changed-By: edwin 
Responsible-Changed-When: Sun Feb 10 10:20:08 UTC 2013 
Responsible-Changed-Why:  
Over to maintainer (via the GNATS Auto Assign Tool) 

http://www.freebsd.org/cgi/query-pr.cgi?pr=176003 
Responsible-Changed-From-To: perl->culot 
Responsible-Changed-By: culot 
Responsible-Changed-When: Sun Feb 10 10:26:06 UTC 2013 
Responsible-Changed-Why:  
I'll take it. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=176003 
State-Changed-From-To: open->closed 
State-Changed-By: culot 
State-Changed-When: Sat Feb 16 14:59:09 UTC 2013 
State-Changed-Why:  
Committed, with minor changes. Thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=176003 

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/176003: commit references a PR
Date: Sat, 16 Feb 2013 14:59:00 +0000 (UTC)

 Author: culot
 Date: Sat Feb 16 14:58:51 2013
 New Revision: 312356
 URL: http://svnweb.freebsd.org/changeset/ports/312356
 
 Log:
   - Update to 0.52 [1]
   - Capitalize names (Perl) in COMMENT
   
   PR:		ports/176003 [1]
   Submitted by:	Gea-Suan Lin <gslin@gslin.org>
 
 Modified:
   head/biology/p5-Bio-Phylo/Makefile   (contents, props changed)
   head/biology/p5-Bio-Phylo/distinfo   (contents, props changed)
   head/biology/p5-Bio-Phylo/pkg-plist   (contents, props changed)
 
 Modified: head/biology/p5-Bio-Phylo/Makefile
 ==============================================================================
 --- head/biology/p5-Bio-Phylo/Makefile	Sat Feb 16 14:41:44 2013	(r312355)
 +++ head/biology/p5-Bio-Phylo/Makefile	Sat Feb 16 14:58:51 2013	(r312356)
 @@ -1,18 +1,14 @@
 -# New ports collection makefile for:	Bio-Phylo
 -# Date created:				12 Mar 2006
 -# Whom:					Aaron Dalton <aaron@FreeBSD.org>
 -#
 +# Created by: Aaron Dalton <aaron@FreeBSD.org>
  # $FreeBSD$
 -#
  
  PORTNAME=	Bio-Phylo
 -PORTVERSION=	0.50
 +PORTVERSION=	0.52
  CATEGORIES=	biology perl5
  MASTER_SITES=	CPAN
  PKGNAMEPREFIX=	p5-
  
  MAINTAINER=	perl@FreeBSD.org
 -COMMENT=	Phylogenetic analysis using perl
 +COMMENT=	Phylogenetic analysis using Perl
  
  LICENSE=	ART10 GPLv1
  LICENSE_COMB=	dual
 @@ -40,11 +36,14 @@ MAN3=		Bio::Phylo.3 \
  		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 +58,9 @@ MAN3=		Bio::Phylo.3 \
  		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 +77,7 @@ MAN3=		Bio::Phylo.3 \
  		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 +138,8 @@ MAN3=		Bio::Phylo.3 \
  		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
 
 Modified: head/biology/p5-Bio-Phylo/distinfo
 ==============================================================================
 --- head/biology/p5-Bio-Phylo/distinfo	Sat Feb 16 14:41:44 2013	(r312355)
 +++ head/biology/p5-Bio-Phylo/distinfo	Sat Feb 16 14:58:51 2013	(r312356)
 @@ -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
 
 Modified: head/biology/p5-Bio-Phylo/pkg-plist
 ==============================================================================
 --- head/biology/p5-Bio-Phylo/pkg-plist	Sat Feb 16 14:41:44 2013	(r312355)
 +++ head/biology/p5-Bio-Phylo/pkg-plist	Sat Feb 16 14:58:51 2013	(r312356)
 @@ -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
 @@ -102,15 +109,16 @@
  %%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
 +%%SITE_PERL%%/Bio/PhyloRole.pm
 +@dirrm %%SITE_PERL%%/Bio/Phylo/Util/CONSTANT
  @dirrm %%SITE_PERL%%/Bio/Phylo/Util
  @dirrm %%SITE_PERL%%/Bio/Phylo/Unparsers
  @dirrm %%SITE_PERL%%/Bio/Phylo/Treedrawer
 @@ -133,3 +141,5 @@
  @dirrm %%SITE_PERL%%/Bio/Phylo/Forest
  @dirrm %%SITE_PERL%%/Bio/Phylo
  @dirrmtry %%SITE_PERL%%/Bio
 +@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Phylo
 +@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
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>Unformatted:
