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Code Issues Releases Activity

- Updated from 0.07 to 0.12

Browse Source 
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
This commit is contained in:
Aaron Dalton 2006-05-19 23:18:32 +00:00
parent 0d2dd214ae
commit e25d96e450
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=162834
3 changed files with 25 additions and 12 deletions
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19
biology/p5-Bio-Phylo/Makefile
View File

@ -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

6
biology/p5-Bio-Phylo/distinfo
View File

@ -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

12
biology/p5-Bio-Phylo/pkg-plist
View File

@ -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