Attachment 70629 Details for Bug 103008 – p5-Bio-Phylo-0.14.patch

[patch] p5-Bio-Phylo-0.14.patch

p5-Bio-Phylo-0.14.patch (text/plain), 6.17 KB, created by tjs on 2006-09-08 02:00:38 UTC

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Creator: tjs

Created: 2006-09-08 02:00:38 UTC

Size: 6.17 KB

patch

obsolete

>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

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Attachments on bug 103008: 70629