Date: Fri, 8 Sep 2006 08:57:19 +0800 (CST) From: Jin-Shan Tseng <tjs@cdpa.nsysu.edu.tw> To: FreeBSD-gnats-submit@FreeBSD.org Cc: aaron@FreeBSD.org Subject: ports/103008: [PATCH] biology/p5-Bio-Phylo: update to 0.14 Message-ID: <200609080057.k880vJm4022835@Pluto.CDPA.nsysu.edu.tw> Resent-Message-ID: <200609080100.k8810diC092756@freefall.freebsd.org>
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>Number: 103008 >Category: ports >Synopsis: [PATCH] biology/p5-Bio-Phylo: update to 0.14 >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: Fri Sep 08 01:00:38 GMT 2006 >Closed-Date: >Last-Modified: >Originator: Jin-Shan Tseng >Release: FreeBSD 6.1-STABLE i386 >Organization: FreeBSD @ Taiwan >Environment: System: FreeBSD Pluto.CDPA.nsysu.edu.tw 6.1-STABLE FreeBSD 6.1-STABLE #0: Wed Aug 30 13:11:16 CST 2006 >Description: - Update to 0.14 Port maintainer (aaron@FreeBSD.org) is cc'd. Generated with FreeBSD Port Tools 0.77 >How-To-Repeat: >Fix: --- p5-Bio-Phylo-0.14.patch begins here --- diff -ruN --exclude=CVS /usr/ports/biology/p5-Bio-Phylo/Makefile /root/p5-Bio-Phylo/Makefile --- /usr/ports/biology/p5-Bio-Phylo/Makefile Sat May 20 07:18:32 2006 +++ /root/p5-Bio-Phylo/Makefile Fri Sep 8 08:50:04 2006 @@ -6,7 +6,7 @@ # PORTNAME= Bio-Phylo -PORTVERSION= 0.12 +PORTVERSION= 0.14 CATEGORIES= biology perl5 MASTER_SITES= ${MASTER_SITE_PERL_CPAN} MASTER_SITE_SUBDIR= Bio @@ -15,15 +15,15 @@ MAINTAINER= aaron@FreeBSD.org COMMENT= Phylogenetic analysis using perl -BUILD_DEPENDS= ${SITE_PERL}/${PERL_ARCH}/Math/Random.pm:${PORTSDIR}/math/p5-Math-Random \ - ${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \ - ${SITE_PERL}/Exception/Class.pm:${PORTSDIR}/devel/p5-Exception-Class \ - ${SITE_PERL}/${PERL_ARCH}/Scalar/Util.pm:${PORTSDIR}/lang/p5-Scalar-List-Utils \ - ${SITE_PERL}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \ - ${SITE_PERL}/XML/Simple.pm:${PORTSDIR}/textproc/p5-XML-Simple -RUN_DEPENDS= ${BUILD_DEPENDS} +RUN_DEPENDS= p5-Exception-Class>=1.23:${PORTSDIR}/devel/p5-Exception-Class \ + p5-Math-Random>=0.67:${PORTSDIR}/math/p5-Math-Random \ + p5-IO-String>=1.05:${PORTSDIR}/devel/p5-IO-String \ + p5-SVG>=1.07:${PORTSDIR}/textproc/p5-SVG + +MAN1= dndtag.pl.1 MAN3= Bio::Phylo.3 \ + Bio::Phylo::ConfigData.3 \ Bio::Phylo::Forest.3 \ Bio::Phylo::Forest::Node.3 \ Bio::Phylo::Forest::Tree.3 \ @@ -32,12 +32,8 @@ Bio::Phylo::Listable.3 \ Bio::Phylo::Manual.3 \ Bio::Phylo::Matrices.3 \ - Bio::Phylo::Matrices::Alignment.3 \ Bio::Phylo::Matrices::Datum.3 \ Bio::Phylo::Matrices::Matrix.3 \ - Bio::Phylo::Matrices::Sequence.3 \ - Bio::Phylo::Parsers::Fastnewick.3 \ - Bio::Phylo::Parsers::Fastnexus.3 \ Bio::Phylo::Parsers::Newick.3 \ Bio::Phylo::Parsers::Nexus.3 \ Bio::Phylo::Parsers::Table.3 \ @@ -54,12 +50,12 @@ Bio::Phylo::Util::Exceptions.3 \ Bio::Phylo::Util::IDPool.3 -PERL_CONFIGURE= yes +PERL_MODBUILD= yes .include <bsd.port.pre.mk> -.if ${PERL_LEVEL} < 500800 -IGNORE= requires at least Perl 5.8 due to dependencies. Please install lang/perl5.8 and try again +.if ${PERL_LEVEL} < 500702 +IGNORE= requires at least Perl 5.7.2 due to dependencies. Please install lang/perl5.8 and try again .endif .include <bsd.port.post.mk> diff -ruN --exclude=CVS /usr/ports/biology/p5-Bio-Phylo/distinfo /root/p5-Bio-Phylo/distinfo --- /usr/ports/biology/p5-Bio-Phylo/distinfo Sat May 20 07:18:32 2006 +++ /root/p5-Bio-Phylo/distinfo Fri Sep 8 08:11:37 2006 @@ -1,3 +1,3 @@ -MD5 (Bio-Phylo-0.12.tar.gz) = 82a8bbe68d7f2f2e67369c5c19ea1d72 -SHA256 (Bio-Phylo-0.12.tar.gz) = 7560554ba4e27296fa2411bf4c5beab26aef6dcaf729aa21a910509e894c455d -SIZE (Bio-Phylo-0.12.tar.gz) = 105975 +MD5 (Bio-Phylo-0.14.tar.gz) = a3e8b1af9c5d15128b4a6a9320d89a7f +SHA256 (Bio-Phylo-0.14.tar.gz) = d35f125ea23a70ceedffef567b6f7838bea8ab62704d09f0704c14138855c99f +SIZE (Bio-Phylo-0.14.tar.gz) = 106299 diff -ruN --exclude=CVS /usr/ports/biology/p5-Bio-Phylo/pkg-descr /root/p5-Bio-Phylo/pkg-descr --- /usr/ports/biology/p5-Bio-Phylo/pkg-descr Sun May 14 00:48:15 2006 +++ /root/p5-Bio-Phylo/pkg-descr Fri Sep 8 08:36:35 2006 @@ -2,5 +2,5 @@ inherit from it, the methods defined here are applicable to all. Consult the manual for usage examples: Bio::Phylo::Manual. -WWW: http://search.cpan.org/dist/Bio-Phylo +WWW: http://search.cpan.org/dist/Bio-Phylo/ Author: Rutger Vos <rvosa@sfu.ca> diff -ruN --exclude=CVS /usr/ports/biology/p5-Bio-Phylo/pkg-plist /root/p5-Bio-Phylo/pkg-plist --- /usr/ports/biology/p5-Bio-Phylo/pkg-plist Sat May 20 07:18:32 2006 +++ /root/p5-Bio-Phylo/pkg-plist Fri Sep 8 08:45:16 2006 @@ -1,42 +1,38 @@ -bin/LRmb.pl -bin/age2bl.pl -bin/bremer.pl -bin/dnd2svg.pl -bin/droptip.pl +@comment $FreeBSD$ bin/postmb.pl -%%SITE_PERL%%/Bio/Phylo.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/Matrices.pm -%%SITE_PERL%%/Bio/Phylo/Matrices/Alignment.pm -%%SITE_PERL%%/Bio/Phylo/Matrices/Datum.pm -%%SITE_PERL%%/Bio/Phylo/Matrices/Matrix.pm -%%SITE_PERL%%/Bio/Phylo/Matrices/Sequence.pm -%%SITE_PERL%%/Bio/Phylo/Parsers/Fastnewick.pm -%%SITE_PERL%%/Bio/Phylo/Parsers/Fastnexus.pm -%%SITE_PERL%%/Bio/Phylo/Parsers/Newick.pm -%%SITE_PERL%%/Bio/Phylo/Parsers/Nexus.pm -%%SITE_PERL%%/Bio/Phylo/Parsers/Table.pm -%%SITE_PERL%%/Bio/Phylo/Parsers/Taxlist.pm -%%SITE_PERL%%/Bio/Phylo/Taxa.pm -%%SITE_PERL%%/Bio/Phylo/Taxa/Taxon.pm -%%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/Newick.pm -%%SITE_PERL%%/Bio/Phylo/Unparsers/Nexus.pm -%%SITE_PERL%%/Bio/Phylo/Unparsers/Pagel.pm -%%SITE_PERL%%/Bio/Phylo/Util/CONSTANT.pm -%%SITE_PERL%%/Bio/Phylo/Util/Exceptions.pm +bin/droptip.pl +bin/dndtag.pl +bin/dnd2svg.pl +bin/bremer.pl +bin/age2bl.pl +bin/LRmb.pl %%SITE_PERL%%/Bio/Phylo/Util/IDPool.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/Phylo/Util/Exceptions.pm +%%SITE_PERL%%/Bio/Phylo/Util/CONSTANT.pm +%%SITE_PERL%%/Bio/Phylo/Unparsers/Pagel.pm +%%SITE_PERL%%/Bio/Phylo/Unparsers/Nexus.pm +%%SITE_PERL%%/Bio/Phylo/Unparsers/Newick.pm +%%SITE_PERL%%/Bio/Phylo/Unparsers/Mrp.pm +%%SITE_PERL%%/Bio/Phylo/Treedrawer/Svg.pm +%%SITE_PERL%%/Bio/Phylo/Treedrawer.pm +%%SITE_PERL%%/Bio/Phylo/Taxa/Taxon.pm +%%SITE_PERL%%/Bio/Phylo/Taxa.pm +%%SITE_PERL%%/Bio/Phylo/Parsers/Taxlist.pm +%%SITE_PERL%%/Bio/Phylo/Parsers/Table.pm +%%SITE_PERL%%/Bio/Phylo/Parsers/Nexus.pm +%%SITE_PERL%%/Bio/Phylo/Parsers/Newick.pm +%%SITE_PERL%%/Bio/Phylo/Matrices/Matrix.pm +%%SITE_PERL%%/Bio/Phylo/Matrices/Datum.pm +%%SITE_PERL%%/Bio/Phylo/Matrices.pm +%%SITE_PERL%%/Bio/Phylo/Manual.pod +%%SITE_PERL%%/Bio/Phylo/Listable.pm +%%SITE_PERL%%/Bio/Phylo/IO.pm +%%SITE_PERL%%/Bio/Phylo/Generator.pm +%%SITE_PERL%%/Bio/Phylo/Forest/Tree.pm +%%SITE_PERL%%/Bio/Phylo/Forest/Node.pm +%%SITE_PERL%%/Bio/Phylo/Forest.pm +%%SITE_PERL%%/Bio/Phylo/ConfigData.pm +%%SITE_PERL%%/Bio/Phylo.pm @dirrm %%SITE_PERL%%/Bio/Phylo/Util @dirrm %%SITE_PERL%%/Bio/Phylo/Unparsers @dirrm %%SITE_PERL%%/Bio/Phylo/Treedrawer --- p5-Bio-Phylo-0.14.patch ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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