Date: Sun, 29 Mar 2009 11:00:14 GMT From: Wen Heping <wenheping@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: misc/133179: [Update]biology/p5-Bio-Phylo:update to 0.17RC9 Message-ID: <200903291100.n2TB0EZJ019905@www.freebsd.org> Resent-Message-ID: <200903291110.n2TBA0HD074147@freefall.freebsd.org>
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>Number: 133179
>Category: misc
>Synopsis: [Update]biology/p5-Bio-Phylo:update to 0.17RC9
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: sw-bug
>Submitter-Id: current-users
>Arrival-Date: Sun Mar 29 11:10:00 UTC 2009
>Closed-Date:
>Last-Modified:
>Originator: Wen Heping
>Release: FreeBSD 8.0-CURRENT
>Organization:
ChangAn Middle School
>Environment:
FreeBSD fb8.wenjing.com 8.0-CURRENT FreeBSD 8.0-CURRENT #0: Sun Mar 22 22:12:06 CST 2009 root@fb8.wenjing.com:/usr/obj/usr/src/sys/GENERIC i386
>Description:
update to 0.17RC9 from 0.16 and take over the maintainership
>How-To-Repeat:
>Fix:
Patch attached with submission follows:
--- Makefile.orig 2009-03-19 23:21:12.000000000 +0800
+++ Makefile 2009-03-29 18:08:44.000000000 +0800
@@ -6,12 +6,13 @@
#
PORTNAME= Bio-Phylo
-PORTVERSION= 0.16
+PORTVERSION= 0.17r9
CATEGORIES= biology perl5
MASTER_SITES= CPAN
PKGNAMEPREFIX= p5-
+DISTNAME= ${PORTNAME}-0.17_RC9
-MAINTAINER= ports@FreeBSD.org
+MAINTAINER= wenheping@gmail.com
COMMENT= Phylogenetic analysis using perl
BUILD_DEPENDS= p5-Exception-Class>1.22:${PORTSDIR}/devel/p5-Exception-Class \
@@ -21,25 +22,18 @@
p5-SVG>=1.07:${PORTSDIR}/textproc/p5-SVG
RUN_DEPENDS= ${BUILD_DEPENDS}
-MAN1= dndtag.pl.1 \
- droptip.pl.1 \
- bremer.pl.1 \
- age2bl.pl.1 \
- dnd2svg.pl.1
MAN3= Bio::Phylo.3 \
- Bio::ObjectCompat.3 \
- Bio::Phylo::Adaptor.3 \
- Bio::Phylo::ConfigData.3 \
+ Bio::Phylo::Annotation.3 \
+ Bio::Phylo::Dictionary.3 \
+ Bio::Phylo::Factory.3 \
Bio::Phylo::Forest.3 \
Bio::Phylo::Forest::Node.3 \
Bio::Phylo::Forest::Tree.3 \
+ Bio::Phylo::Forest::DrawNode.3 \
+ Bio::Phylo::Forest::DrawTree.3 \
Bio::Phylo::Generator.3 \
Bio::Phylo::IO.3 \
Bio::Phylo::Listable.3 \
- Bio::Phylo::Adaptor::Bioperl::Datum.3 \
- Bio::Phylo::Adaptor::Bioperl::Matrix.3 \
- Bio::Phylo::Adaptor::Bioperl::Node.3 \
- Bio::Phylo::Adaptor::Bioperl::Tree.3 \
Bio::Phylo::Manual.3 \
Bio::Phylo::Matrices.3 \
Bio::Phylo::Matrices::Datum.3 \
@@ -54,11 +48,16 @@
Bio::Phylo::Matrices::Datatype::Continuous.3 \
Bio::Phylo::Matrices::Datatype::Standard.3 \
Bio::Phylo::Matrices::Datatype::Mixed.3 \
+ Bio::Phylo::Mediators::NodeMediator.3 \
Bio::Phylo::Mediators::TaxaMediator.3 \
+ Bio::Phylo::Parsers::Nexml.3 \
Bio::Phylo::Parsers::Newick.3 \
Bio::Phylo::Parsers::Nexus.3 \
Bio::Phylo::Parsers::Table.3 \
Bio::Phylo::Parsers::Taxlist.3 \
+ Bio::Phylo::Parsers::Tolweb.3 \
+ Bio::Phylo::Project.3 \
+ Bio::Phylo::Set.3 \
Bio::Phylo::Taxa.3 \
Bio::Phylo::Taxa::TaxaLinker.3 \
Bio::Phylo::Taxa::Taxon.3 \
@@ -66,14 +65,16 @@
Bio::Phylo::Treedrawer.3 \
Bio::Phylo::Treedrawer::Svg.3 \
Bio::Phylo::Unparsers::Mrp.3 \
+ Bio::Phylo::Unparsers::Nexml.3 \
Bio::Phylo::Unparsers::Newick.3 \
Bio::Phylo::Unparsers::Nexus.3 \
Bio::Phylo::Unparsers::Pagel.3 \
Bio::Phylo::Util::CONSTANT.3 \
Bio::Phylo::Util::Exceptions.3 \
Bio::Phylo::Util::IDPool.3 \
+ Bio::Phylo::Util::Logger.3 \
Bio::Phylo::Util::XMLWritable.3
-PERL_MODBUILD= 5.7.2+
+PERL_CONFIGURE= yes
.include <bsd.port.mk>
--- distinfo.orig 2007-06-20 04:15:58.000000000 +0800
+++ distinfo 2009-03-29 11:02:26.000000000 +0800
@@ -1,3 +1,3 @@
-MD5 (Bio-Phylo-0.16.tar.gz) = 78c6d2ceced9b013898e7aa7b61010c0
-SHA256 (Bio-Phylo-0.16.tar.gz) = 17317e23c7423b197e08984aead6e52c454e47badbdfa8447fa499175e2789cd
-SIZE (Bio-Phylo-0.16.tar.gz) = 129830
+MD5 (Bio-Phylo-0.17_RC9.tar.gz) = 382d911edde6ed7b6229bfb26128b2b7
+SHA256 (Bio-Phylo-0.17_RC9.tar.gz) = ba0929b685fb420eb31c4041bc9aacd42caadca26aded3312649437e4d8f4057
+SIZE (Bio-Phylo-0.17_RC9.tar.gz) = 268067
--- pkg-plist.orig 2009-03-19 23:21:14.000000000 +0800
+++ pkg-plist 2009-03-29 13:26:36.000000000 +0800
@@ -1,25 +1,19 @@
-bin/LRmb.pl
-bin/age2bl.pl
-bin/bremer.pl
-bin/dnd2svg.pl
-bin/dndtag.pl
-bin/droptip.pl
-bin/postmb.pl
%%SITE_PERL%%/Bio/Phylo.pm
-%%SITE_PERL%%/Bio/ObjectCompat.pod
-%%SITE_PERL%%/Bio/Phylo/Adaptor.pm
-%%SITE_PERL%%/Bio/Phylo/ConfigData.pm
-%%SITE_PERL%%/Bio/Phylo/Forest.pm
-%%SITE_PERL%%/Bio/Phylo/Forest/Node.pm
-%%SITE_PERL%%/Bio/Phylo/Forest/Tree.pm
%%SITE_PERL%%/Bio/Phylo/Generator.pm
%%SITE_PERL%%/Bio/Phylo/IO.pm
%%SITE_PERL%%/Bio/Phylo/Listable.pm
%%SITE_PERL%%/Bio/Phylo/Manual.pod
-%%SITE_PERL%%/Bio/Phylo/Adaptor/Bioperl/Node.pm
-%%SITE_PERL%%/Bio/Phylo/Adaptor/Bioperl/Datum.pm
-%%SITE_PERL%%/Bio/Phylo/Adaptor/Bioperl/Tree.pm
-%%SITE_PERL%%/Bio/Phylo/Adaptor/Bioperl/Matrix.pm
+%%SITE_PERL%%/Bio/Phylo/Forest.pm
+%%SITE_PERL%%/Bio/Phylo/Annotation.pm
+%%SITE_PERL%%/Bio/Phylo/Project.pm
+%%SITE_PERL%%/Bio/Phylo/Set.pm
+%%SITE_PERL%%/Bio/Phylo/Dictionary.pm
+%%SITE_PERL%%/Bio/Phylo/Factory.pm
+%%SITE_PERL%%/Bio/Phylo/Forest/Node.pm
+%%SITE_PERL%%/Bio/Phylo/Forest/DrawNode.pm
+%%SITE_PERL%%/Bio/Phylo/Forest/Tree.pm
+%%SITE_PERL%%/Bio/Phylo/Forest/DrawTree.pm
+%%SITE_PERL%%/Bio/Phylo/Mediators/NodeMediator.pm
%%SITE_PERL%%/Bio/Phylo/Matrices.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/Datum.pm
@@ -36,6 +30,8 @@
%%SITE_PERL%%/Bio/Phylo/Mediators/TaxaMediator.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Newick.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Nexus.pm
+%%SITE_PERL%%/Bio/Phylo/Parsers/Nexml.pm
+%%SITE_PERL%%/Bio/Phylo/Parsers/Tolweb.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Table.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Taxlist.pm
%%SITE_PERL%%/Bio/Phylo/Taxa.pm
@@ -45,6 +41,7 @@
%%SITE_PERL%%/Bio/Phylo/Treedrawer.pm
%%SITE_PERL%%/Bio/Phylo/Treedrawer/Svg.pm
%%SITE_PERL%%/Bio/Phylo/Unparsers/Mrp.pm
+%%SITE_PERL%%/Bio/Phylo/Unparsers/Nexml.pm
%%SITE_PERL%%/Bio/Phylo/Unparsers/Newick.pm
%%SITE_PERL%%/Bio/Phylo/Unparsers/Nexus.pm
%%SITE_PERL%%/Bio/Phylo/Unparsers/Pagel.pm
@@ -52,8 +49,9 @@
%%SITE_PERL%%/Bio/Phylo/Util/Exceptions.pm
%%SITE_PERL%%/Bio/Phylo/Util/IDPool.pm
%%SITE_PERL%%/Bio/Phylo/Util/XMLWritable.pm
-@dirrm %%SITE_PERL%%/Bio/Phylo/Adaptor/Bioperl
-@dirrm %%SITE_PERL%%/Bio/Phylo/Adaptor
+%%SITE_PERL%%/Bio/Phylo/Util/Logger.pm
+%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio-Phylo/.packlist
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio-Phylo
@dirrm %%SITE_PERL%%/Bio/Phylo/Util
@dirrm %%SITE_PERL%%/Bio/Phylo/Unparsers
@dirrm %%SITE_PERL%%/Bio/Phylo/Treedrawer
>Release-Note:
>Audit-Trail:
>Unformatted:
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