3 files changed, 58 insertions, 44 deletions

diff --git a/biology/p5-Bio-NEXUS/Makefile b/biology/p5-Bio-NEXUS/Makefile
index 7e1106d67802..d1f940540c85 100644
--- a/biology/p5-Bio-NEXUS/Makefile
+++ b/biology/p5-Bio-NEXUS/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	Bio-NEXUS
-PORTVERSION=	0.77
+PORTVERSION=	0.78
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
@@ -16,28 +16,43 @@ COMMENT=	An object-oriented Perl API for the NEXUS file format
 
 BUILD_DEPENDS=	p5-Clone-PP>=1.02:${PORTSDIR}/devel/p5-Clone-PP
 RUN_DEPENDS:=	${BUILD_DEPENDS}
-TEST_DEPENDS=	p5-Test-Pod>=0:${PORTSDIR}/devel/p5-Test-Pod \
-		p5-Test-Pod-Coverage>=0:${PORTSDIR}/devel/p5-Test-Pod-Coverage \
-		p5-Test-Deep>=0.106:${PORTSDIR}/devel/p5-Test-Deep
+
+TEST_DEPENDS=	p5-Test-Deep>=0.106:${PORTSDIR}/devel/p5-Test-Deep \
+		p5-Test-Pod>=0:${PORTSDIR}/devel/p5-Test-Pod \
+		p5-Test-Pod-Coverage>=0:${PORTSDIR}/devel/p5-Test-Pod-Coverage
 
 PERL_CONFIGURE=	yes
 
-MAN1=		nextool.pl.1 nex2text_tree.pl.1 nexplot.pl.1
-MAN3=		Bio::NEXUS::DataBlock.3 Bio::NEXUS::CodonsBlock.3 \
-		Bio::NEXUS::NotesBlock.3 Bio::NEXUS::NHXCmd.3 \
-		Bio::NEXUS::HistoryBlock.3 Bio::NEXUS::TaxUnit.3 \
-		Bio::NEXUS::CharactersBlock.3 Bio::NEXUS::SpanBlock.3 \
-		Bio::NEXUS::UnalignedBlock.3 Bio::NEXUS::TaxUnitSet.3 \
-		Bio::NEXUS::DistancesBlock.3 Bio::NEXUS::UnknownBlock.3 \
-		Bio::NEXUS::Node.3 Bio::NEXUS::Matrix.3 \
-		Bio::NEXUS::Tree.3 Bio::NEXUS::WeightSet.3 \
-		Bio::NEXUS::TreesBlock.3 Bio::NEXUS::Util::Exceptions.3 \
-		Bio::NEXUS::SetsBlock.3 Bio::NEXUS::TaxaBlock.3 \
-		Bio::NEXUS::Util::Logger.3 Bio::NEXUS::AssumptionsBlock.3 \
-		Bio::NEXUS::Block.3 Bio::NEXUS::Functions.3 \
+MAN1=		nex2text_tree.pl.1 \
+		nexplot.pl.1 \
+		nextool.pl.1
+MAN3=		Bio::NEXUS.3 \
+		Bio::NEXUS::AssumptionsBlock.3 \
+		Bio::NEXUS::Block.3 \
+		Bio::NEXUS::CharactersBlock.3 \
+		Bio::NEXUS::CodonsBlock.3 \
+		Bio::NEXUS::DataBlock.3 \
+		Bio::NEXUS::DistancesBlock.3 \
+		Bio::NEXUS::Functions.3 \
+		Bio::NEXUS::HistoryBlock.3 \
+		Bio::NEXUS::Matrix.3 \
+		Bio::NEXUS::NHXCmd.3 \
+		Bio::NEXUS::Node.3 \
+		Bio::NEXUS::NotesBlock.3 \
+		Bio::NEXUS::SetsBlock.3 \
+		Bio::NEXUS::SpanBlock.3 \
+		Bio::NEXUS::TaxUnit.3 \
+		Bio::NEXUS::TaxUnitSet.3 \
+		Bio::NEXUS::TaxaBlock.3 \
 		Bio::NEXUS::Tools::GraphicsParams.3 \
 		Bio::NEXUS::Tools::NexModifier.3 \
 		Bio::NEXUS::Tools::NexPlotter.3 \
-		Bio::NEXUS.3
+		Bio::NEXUS::Tree.3 \
+		Bio::NEXUS::TreesBlock.3 \
+		Bio::NEXUS::UnalignedBlock.3 \
+		Bio::NEXUS::UnknownBlock.3 \
+		Bio::NEXUS::Util::Exceptions.3 \
+		Bio::NEXUS::Util::Logger.3 \
+		Bio::NEXUS::WeightSet.3
 
 .include <bsd.port.mk>
diff --git a/biology/p5-Bio-NEXUS/distinfo b/biology/p5-Bio-NEXUS/distinfo
index 682880e68921..1cf41375bc44 100644
--- a/biology/p5-Bio-NEXUS/distinfo
+++ b/biology/p5-Bio-NEXUS/distinfo
@@ -1,2 +1,2 @@
-SHA256 (Bio-NEXUS-0.77.tar.gz) = 4b8273b0f6ab39c4e4192dc0ff307703902342e5af3d6dea72de4ce44f02c750
-SIZE (Bio-NEXUS-0.77.tar.gz) = 1037607
+SHA256 (Bio-NEXUS-0.78.tar.gz) = a99cda4e97fd40ee0bee05089a034e84280be9532b0300cd98ed16c303bc85dc
+SIZE (Bio-NEXUS-0.78.tar.gz) = 1033563
diff --git a/biology/p5-Bio-NEXUS/pkg-plist b/biology/p5-Bio-NEXUS/pkg-plist
index fe620d9770d2..0a4a467e3f4f 100644
--- a/biology/p5-Bio-NEXUS/pkg-plist
+++ b/biology/p5-Bio-NEXUS/pkg-plist
@@ -2,38 +2,37 @@ bin/nex2text_tree.pl
 bin/nexplot.pl
 bin/nextool.pl
 %%SITE_PERL%%/Bio/NEXUS.pm
-%%SITE_PERL%%/Bio/NEXUS/._UnalignedBlock.pm
-%%SITE_PERL%%/Bio/NEXUS/DataBlock.pm
-%%SITE_PERL%%/Bio/NEXUS/CodonsBlock.pm
-%%SITE_PERL%%/Bio/NEXUS/NotesBlock.pm
-%%SITE_PERL%%/Bio/NEXUS/NHXCmd.pm
-%%SITE_PERL%%/Bio/NEXUS/HistoryBlock.pm
-%%SITE_PERL%%/Bio/NEXUS/TaxUnit.pm
+%%SITE_PERL%%/Bio/NEXUS/AssumptionsBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/Block.pm
 %%SITE_PERL%%/Bio/NEXUS/CharactersBlock.pm
-%%SITE_PERL%%/Bio/NEXUS/SpanBlock.pm
-%%SITE_PERL%%/Bio/NEXUS/UnalignedBlock.pm
-%%SITE_PERL%%/Bio/NEXUS/TaxUnitSet.pm
+%%SITE_PERL%%/Bio/NEXUS/CodonsBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/DataBlock.pm
 %%SITE_PERL%%/Bio/NEXUS/DistancesBlock.pm
-%%SITE_PERL%%/Bio/NEXUS/UnknownBlock.pm
-%%SITE_PERL%%/Bio/NEXUS/Node.pm
+%%SITE_PERL%%/Bio/NEXUS/Functions.pm
+%%SITE_PERL%%/Bio/NEXUS/HistoryBlock.pm
 %%SITE_PERL%%/Bio/NEXUS/Matrix.pm
-%%SITE_PERL%%/Bio/NEXUS/Tree.pm
-%%SITE_PERL%%/Bio/NEXUS/WeightSet.pm
+%%SITE_PERL%%/Bio/NEXUS/NHXCmd.pm
+%%SITE_PERL%%/Bio/NEXUS/Node.pm
+%%SITE_PERL%%/Bio/NEXUS/NotesBlock.pm
 %%SITE_PERL%%/Bio/NEXUS/SetsBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/SpanBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/TaxUnit.pm
+%%SITE_PERL%%/Bio/NEXUS/TaxUnitSet.pm
 %%SITE_PERL%%/Bio/NEXUS/TaxaBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/Tools/GraphicsParams.pm
+%%SITE_PERL%%/Bio/NEXUS/Tools/NexModifier.pm
+%%SITE_PERL%%/Bio/NEXUS/Tools/NexPlotter.pm
+%%SITE_PERL%%/Bio/NEXUS/Tree.pm
 %%SITE_PERL%%/Bio/NEXUS/TreesBlock.pm
-%%SITE_PERL%%/Bio/NEXUS/AssumptionsBlock.pm
-%%SITE_PERL%%/Bio/NEXUS/Block.pm
-%%SITE_PERL%%/Bio/NEXUS/Functions.pm
+%%SITE_PERL%%/Bio/NEXUS/UnalignedBlock.pm
+%%SITE_PERL%%/Bio/NEXUS/UnknownBlock.pm
 %%SITE_PERL%%/Bio/NEXUS/Util/Exceptions.pm
 %%SITE_PERL%%/Bio/NEXUS/Util/Logger.pm
-%%SITE_PERL%%/Bio/NEXUS/Tools/NexModifier.pm
-%%SITE_PERL%%/Bio/NEXUS/Tools/NexPlotter.pm
-%%SITE_PERL%%/Bio/NEXUS/Tools/GraphicsParams.pm
+%%SITE_PERL%%/Bio/NEXUS/WeightSet.pm
 %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/NEXUS/.packlist
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/NEXUS
+@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/NEXUS
 @dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
-@dirrmtry %%SITE_PERL%%/Bio/NEXUS/Tools
-@dirrmtry %%SITE_PERL%%/Bio/NEXUS/Util
-@dirrmtry %%SITE_PERL%%/Bio/NEXUS
+@dirrm %%SITE_PERL%%/Bio/NEXUS/Util
+@dirrm %%SITE_PERL%%/Bio/NEXUS/Tools
+@dirrm %%SITE_PERL%%/Bio/NEXUS
 @dirrmtry %%SITE_PERL%%/Bio