From e25d96e450941e3ba43eaffb0182be94c9949163 Mon Sep 17 00:00:00 2001 From: Aaron Dalton Date: Fri, 19 May 2006 23:18:32 +0000 Subject: [PATCH] - Updated from 0.07 to 0.12 Approved by: tobez (implicit) 0.08 20/Feb/2006 15:14 Improved referential integrity between nodes, taxa, and data. Implemented Fastnexus parser Node object silently implements Bio::Tree::NodeI interface if BioPerl is installed Tree object silently implements Bio::Tree::TreeI interface if BioPerl is installed Added convertor methods for XML and CIPRES Implemented more Matrix methods Implemented symbol tables in Bio::Phylo::Util::CONSTANT Implemented visit method for listable objects Implemented caching infrastructure for calculations Changed object-model to inside-out arrays Added Biodiversity measures code by Aki Mimoto Moved constants and exceptions to Bio::Phylo::Util::* Fixed memory leak due to circular references --- biology/p5-Bio-Phylo/Makefile | 19 +++++++++++++------ biology/p5-Bio-Phylo/distinfo | 6 +++--- biology/p5-Bio-Phylo/pkg-plist | 12 +++++++++--- 3 files changed, 25 insertions(+), 12 deletions(-) diff --git a/biology/p5-Bio-Phylo/Makefile b/biology/p5-Bio-Phylo/Makefile index edd4ea96ac55..32e882e5d35e 100644 --- a/biology/p5-Bio-Phylo/Makefile +++ b/biology/p5-Bio-Phylo/Makefile @@ -6,7 +6,7 @@ # PORTNAME= Bio-Phylo -PORTVERSION= 0.07 +PORTVERSION= 0.12 CATEGORIES= biology perl5 MASTER_SITES= ${MASTER_SITE_PERL_CPAN} MASTER_SITE_SUBDIR= Bio @@ -18,12 +18,12 @@ 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 + ${SITE_PERL}/${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} MAN3= Bio::Phylo.3 \ - Bio::Phylo::CONSTANT.3 \ - Bio::Phylo::Exceptions.3 \ Bio::Phylo::Forest.3 \ Bio::Phylo::Forest::Node.3 \ Bio::Phylo::Forest::Tree.3 \ @@ -36,6 +36,8 @@ MAN3= Bio::Phylo.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 \ @@ -43,9 +45,14 @@ MAN3= Bio::Phylo.3 \ Bio::Phylo::Taxa.3 \ Bio::Phylo::Taxa::Taxon.3 \ Bio::Phylo::Treedrawer.3 \ - Bio::Phylo::Treedrawer::SVG.3 \ + Bio::Phylo::Treedrawer::Svg.3 \ + Bio::Phylo::Unparsers::Mrp.3 \ Bio::Phylo::Unparsers::Newick.3 \ - Bio::Phylo::Unparsers::Pagel.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 PERL_CONFIGURE= yes diff --git a/biology/p5-Bio-Phylo/distinfo b/biology/p5-Bio-Phylo/distinfo index 3c4ba97880e8..3102dcf208cc 100644 --- a/biology/p5-Bio-Phylo/distinfo +++ b/biology/p5-Bio-Phylo/distinfo @@ -1,3 +1,3 @@ -MD5 (Bio-Phylo-0.07.tar.gz) = 12b6ca632bc25e5c3fd647990cb5c959 -SHA256 (Bio-Phylo-0.07.tar.gz) = c98ab09053b9b0e9b30c72f7b09448e908ddde71c5db2489b6924c710f654923 -SIZE (Bio-Phylo-0.07.tar.gz) = 69580 +MD5 (Bio-Phylo-0.12.tar.gz) = 82a8bbe68d7f2f2e67369c5c19ea1d72 +SHA256 (Bio-Phylo-0.12.tar.gz) = 7560554ba4e27296fa2411bf4c5beab26aef6dcaf729aa21a910509e894c455d +SIZE (Bio-Phylo-0.12.tar.gz) = 105975 diff --git a/biology/p5-Bio-Phylo/pkg-plist b/biology/p5-Bio-Phylo/pkg-plist index 19f9db94060e..d12ffba57be8 100644 --- a/biology/p5-Bio-Phylo/pkg-plist +++ b/biology/p5-Bio-Phylo/pkg-plist @@ -5,8 +5,6 @@ bin/dnd2svg.pl bin/droptip.pl bin/postmb.pl %%SITE_PERL%%/Bio/Phylo.pm -%%SITE_PERL%%/Bio/Phylo/CONSTANT.pm -%%SITE_PERL%%/Bio/Phylo/Exceptions.pm %%SITE_PERL%%/Bio/Phylo/Forest.pm %%SITE_PERL%%/Bio/Phylo/Forest/Node.pm %%SITE_PERL%%/Bio/Phylo/Forest/Tree.pm @@ -19,6 +17,8 @@ bin/postmb.pl %%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 @@ -26,12 +26,18 @@ bin/postmb.pl %%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/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 +%%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 +@dirrm %%SITE_PERL%%/Bio/Phylo/Util @dirrm %%SITE_PERL%%/Bio/Phylo/Unparsers @dirrm %%SITE_PERL%%/Bio/Phylo/Treedrawer @dirrm %%SITE_PERL%%/Bio/Phylo/Taxa