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-rw-r--r--biology/p5-Bio-Phylo/Makefile11
-rw-r--r--biology/p5-Bio-Phylo/distinfo4
-rw-r--r--biology/p5-Bio-Phylo/pkg-plist44
3 files changed, 37 insertions, 22 deletions
diff --git a/biology/p5-Bio-Phylo/Makefile b/biology/p5-Bio-Phylo/Makefile
index 2e1eab6aa479..9d2409de7bb6 100644
--- a/biology/p5-Bio-Phylo/Makefile
+++ b/biology/p5-Bio-Phylo/Makefile
@@ -6,7 +6,7 @@
#
PORTNAME= Bio-Phylo
-PORTVERSION= 0.49
+PORTVERSION= 0.50
CATEGORIES= biology perl5
MASTER_SITES= CPAN
PKGNAMEPREFIX= p5-
@@ -29,6 +29,7 @@ BUILD_DEPENDS= p5-GD>=0:${PORTSDIR}/graphics/p5-GD \
p5-bioperl>=0:${PORTSDIR}/biology/p5-bioperl \
p5-libxml>=0:${PORTSDIR}/textproc/p5-libxml
RUN_DEPENDS:= ${BUILD_DEPENDS}
+TEST_DEPENDS= p5-JSON>=0:${PORTSDIR}/converters/p5-JSON
PERL_CONFIGURE= yes
@@ -73,6 +74,7 @@ MAN3= Bio::Phylo.3 \
Bio::Phylo::NeXML::Meta::XMLLiteral.3 \
Bio::Phylo::NeXML::Writable.3 \
Bio::Phylo::Parsers::Abstract.3 \
+ Bio::Phylo::Parsers::Adjacency.3 \
Bio::Phylo::Parsers::Fasta.3 \
Bio::Phylo::Parsers::Json.3 \
Bio::Phylo::Parsers::Newick.3 \
@@ -82,6 +84,7 @@ MAN3= Bio::Phylo.3 \
Bio::Phylo::Parsers::Phyloxml.3 \
Bio::Phylo::Parsers::Table.3 \
Bio::Phylo::Parsers::Taxlist.3 \
+ Bio::Phylo::Parsers::Tnrs.3 \
Bio::Phylo::Parsers::Tolweb.3 \
Bio::Phylo::Parsers::Ubiocbmeta.3 \
Bio::Phylo::Parsers::Ubiometa.3 \
@@ -112,9 +115,11 @@ MAN3= Bio::Phylo.3 \
Bio::Phylo::Treedrawer::Svg.3 \
Bio::Phylo::Treedrawer::Swf.3 \
Bio::Phylo::Unparsers::Abstract.3 \
+ Bio::Phylo::Unparsers::Adjacency.3 \
Bio::Phylo::Unparsers::Cdao.3 \
Bio::Phylo::Unparsers::Fasta.3 \
Bio::Phylo::Unparsers::Hennig86.3 \
+ Bio::Phylo::Unparsers::Html.3 \
Bio::Phylo::Unparsers::Json.3 \
Bio::Phylo::Unparsers::Mrp.3 \
Bio::Phylo::Unparsers::Newick.3 \
@@ -124,6 +129,7 @@ MAN3= Bio::Phylo.3 \
Bio::Phylo::Unparsers::Phylip.3 \
Bio::Phylo::Unparsers::Phyloxml.3 \
Bio::Phylo::Unparsers::Rss1.3 \
+ Bio::Phylo::Unparsers::Taxlist.3 \
Bio::Phylo::Util::CONSTANT.3 \
Bio::Phylo::Util::Dependency.3 \
Bio::Phylo::Util::Exceptions.3 \
@@ -132,4 +138,7 @@ MAN3= Bio::Phylo.3 \
Bio::Phylo::Util::OptionalInterface.3 \
Bio::Phylo::Util::StackTrace.3
+post-patch:
+ @${REINPLACE_CMD} -e '/NAME/ s|Bio-Phylo|Bio::Phylo|' ${WRKSRC}/Makefile.PL
+
.include <bsd.port.mk>
diff --git a/biology/p5-Bio-Phylo/distinfo b/biology/p5-Bio-Phylo/distinfo
index ee49135d5e5d..3b1c0a2e5ba6 100644
--- a/biology/p5-Bio-Phylo/distinfo
+++ b/biology/p5-Bio-Phylo/distinfo
@@ -1,2 +1,2 @@
-SHA256 (Bio-Phylo-0.49.tar.gz) = 190133a0c3ca29797c61a9feb359d62f02fac5dee9c5e2f37bb1c5ef96704439
-SIZE (Bio-Phylo-0.49.tar.gz) = 372211
+SHA256 (Bio-Phylo-0.50.tar.gz) = 89e24ac1d68096226194f89b5088910ece4239372e63666011b5fae2a6e0fe3c
+SIZE (Bio-Phylo-0.50.tar.gz) = 378189
diff --git a/biology/p5-Bio-Phylo/pkg-plist b/biology/p5-Bio-Phylo/pkg-plist
index 3b5f2f8f433b..f98aeab859f2 100644
--- a/biology/p5-Bio-Phylo/pkg-plist
+++ b/biology/p5-Bio-Phylo/pkg-plist
@@ -27,12 +27,12 @@
%%SITE_PERL%%/Bio/Phylo/Matrices/Matrix.pm
%%SITE_PERL%%/Bio/Phylo/Matrices/TypeSafeData.pm
%%SITE_PERL%%/Bio/Phylo/Mediators/TaxaMediator.pm
-%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna/K80.pm
+%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna.pm
+%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna/F81.pm
%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna/GTR.pm
%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna/HKY85.pm
-%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna/F81.pm
%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna/JC69.pm
-%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna.pm
+%%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna/K80.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/DOM.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document/Libxml.pm
@@ -40,10 +40,12 @@
%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element/Libxml.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element/Twig.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/Entities.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/Meta.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/Meta/XMLLiteral.pm
%%SITE_PERL%%/Bio/Phylo/NeXML/Writable.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Abstract.pm
+%%SITE_PERL%%/Bio/Phylo/Parsers/Adjacency.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Fasta.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Json.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Newick.pm
@@ -53,7 +55,20 @@
%%SITE_PERL%%/Bio/Phylo/Parsers/Phyloxml.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Table.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Taxlist.pm
+%%SITE_PERL%%/Bio/Phylo/Parsers/Tnrs.pm
%%SITE_PERL%%/Bio/Phylo/Parsers/Tolweb.pm
+%%SITE_PERL%%/Bio/Phylo/Parsers/Ubiocbmeta.pm
+%%SITE_PERL%%/Bio/Phylo/Parsers/Ubiometa.pm
+%%SITE_PERL%%/Bio/Phylo/Parsers/Ubiosearch.pm
+%%SITE_PERL%%/Bio/Phylo/PhyloWS.pm
+%%SITE_PERL%%/Bio/Phylo/PhyloWS/Client.pm
+%%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource.pm
+%%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource/Description.pm
+%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service.pm
+%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/Timetree.pm
+%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/Tolweb.pm
+%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/UbioClassificationBank.pm
+%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/UbioNameBank.pm
%%SITE_PERL%%/Bio/Phylo/Project.pm
%%SITE_PERL%%/Bio/Phylo/Set.pm
%%SITE_PERL%%/Bio/Phylo/Taxa.pm
@@ -71,9 +86,11 @@
%%SITE_PERL%%/Bio/Phylo/Treedrawer/Svg.pm
%%SITE_PERL%%/Bio/Phylo/Treedrawer/Swf.pm
%%SITE_PERL%%/Bio/Phylo/Unparsers/Abstract.pm
+%%SITE_PERL%%/Bio/Phylo/Unparsers/Adjacency.pm
%%SITE_PERL%%/Bio/Phylo/Unparsers/Cdao.pm
%%SITE_PERL%%/Bio/Phylo/Unparsers/Fasta.pm
%%SITE_PERL%%/Bio/Phylo/Unparsers/Hennig86.pm
+%%SITE_PERL%%/Bio/Phylo/Unparsers/Html.pm
%%SITE_PERL%%/Bio/Phylo/Unparsers/Json.pm
%%SITE_PERL%%/Bio/Phylo/Unparsers/Mrp.pm
%%SITE_PERL%%/Bio/Phylo/Unparsers/Newick.pm
@@ -82,6 +99,8 @@
%%SITE_PERL%%/Bio/Phylo/Unparsers/Pagel.pm
%%SITE_PERL%%/Bio/Phylo/Unparsers/Phylip.pm
%%SITE_PERL%%/Bio/Phylo/Unparsers/Phyloxml.pm
+%%SITE_PERL%%/Bio/Phylo/Unparsers/Rss1.pm
+%%SITE_PERL%%/Bio/Phylo/Unparsers/Taxlist.pm
%%SITE_PERL%%/Bio/Phylo/Util/CONSTANT.pm
%%SITE_PERL%%/Bio/Phylo/Util/Dependency.pm
%%SITE_PERL%%/Bio/Phylo/Util/Exceptions.pm
@@ -89,22 +108,9 @@
%%SITE_PERL%%/Bio/Phylo/Util/Logger.pm
%%SITE_PERL%%/Bio/Phylo/Util/OptionalInterface.pm
%%SITE_PERL%%/Bio/Phylo/Util/StackTrace.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio-Phylo/.packlist
-%%SITE_PERL%%/Bio/Phylo/PhyloWS.pm
-%%SITE_PERL%%/Bio/Phylo/NeXML/Entities.pm
-%%SITE_PERL%%/Bio/Phylo/Unparsers/Rss1.pm
-%%SITE_PERL%%/Bio/Phylo/Parsers/Ubiocbmeta.pm
-%%SITE_PERL%%/Bio/Phylo/Parsers/Ubiosearch.pm
-%%SITE_PERL%%/Bio/Phylo/Parsers/Ubiometa.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Client.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/Timetree.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/UbioClassificationBank.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/UbioNameBank.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/Tolweb.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource/Description.pm
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio-Phylo
+%%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
generated by cgit (git 2.34.1) at 2025-01-16 04:20:37 +0800