3 files changed, 46 insertions, 40 deletions

diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile
index 650a028aa69c..256e1b4acc5a 100644
--- a/biology/p5-bioperl/Makefile
+++ b/biology/p5-bioperl/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	bioperl
 PORTVERSION=	0.7.1
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	ftp://bioperl.org/pub/DIST/ \
 		http://bioperl.org/Core/Latest/ \
@@ -17,6 +18,8 @@ DISTFILES=	${DISTNAME}${EXTRACT_SUFX}
 
 MAINTAINER=	wjv@FreeBSD.org
 
+# These are all run-time dependencies, but listing them in ${BUILD_DEPENDS}
+# prevents a flood of build-time warnings.
 BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
 		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser \
 		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp \
@@ -27,6 +30,7 @@ BUILD_DEPENDS=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:
 		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Node.pm:${PORTSDIR}/textproc/p5-XML-Node \
 		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Parser/PerlSAX.pm:${PORTSDIR}/textproc/p5-libxml \
 		${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer
+RUN_DEPENDS=	${BUILD_DEPENDS}
 
 PERL_CONFIGURE=	YES
 
@@ -44,9 +48,11 @@ EXT_WRKSRC=	${WRKDIR}/bioperl-ext-06/Bio/Ext/Align
 
 .if defined(WITH_CORBA_CLIENT)
 BUILD_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
+RUN_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
 .endif
 .if defined(WITH_CORBA_SERVER)
 BUILD_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
+RUN_DEPENDS+=	${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
 .endif
 .if defined(WITH_GUI)
 RUN_DEPENDS+=	ptksh:${PORTSDIR}/x11-toolkits/p5-Tk
diff --git a/biology/p5-bioperl/pkg-descr b/biology/p5-bioperl/pkg-descr
index bcf40d4ea703..da0a26873122 100644
--- a/biology/p5-bioperl/pkg-descr
+++ b/biology/p5-bioperl/pkg-descr
@@ -6,8 +6,8 @@ Bioperl Project.  It forms the basis of a large number of bioinformatics and
 genomics applications.
 
 (For an interesting aside on "How Perl saved the Human Genome Project", see
-http://bio.perl.org/GetStarted/tpj_ls_bio.html)
+http://bioperl.org/GetStarted/tpj_ls_bio.html)
 
-WWW: http://bio.perl.org/
+WWW: http://bioperl.org/
 
--- Johann Visagie <johann@egenetics.com>
+-- Johann Visagie <wjv@FreeBSD.org>
diff --git a/biology/p5-bioperl/pkg-plist b/biology/p5-bioperl/pkg-plist
index 3c0b78e2315d..ad038a26dacf 100644
--- a/biology/p5-bioperl/pkg-plist
+++ b/biology/p5-bioperl/pkg-plist
@@ -1,36 +1,36 @@
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/Base.pm
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/Client.pm
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/ORB.pm
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/PrimarySeq.pm
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/Seq.pm
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/CorbaClient/SeqFeature.pm
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/DB/Biocorba.pm
-%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/5.6.0/Bio/SeqIO/biocorba.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/AnonymousSeq.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/Base.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/BioEnv.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeq.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeqDB.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeqIterator.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/PrimarySeqVector.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/Seq.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqDB.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqFeature.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqFeatureIterator.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/SeqFeatureVector.pm
-%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/5.6.0/Bio/CorbaServer/Server.pm
-%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/AnnotMap.pm
-%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/BioTkPerl8_1.pm
-%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/GO_Browser.pm
-%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/HitDisplay.pm
-%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/README
-%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/SeqCanvas.pm
-%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/Tkpsh.pl
-%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_Map.pm
-%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_SeqSubs.pm
-%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_Sequence.pm
-%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/Bio/Tk/bioTk_Utilities.pm
-%%PLIST_GUI%%lib/perl5/site_perl/5.6.0/mach/auto/Bio/Tk/.packlist
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/Base.pm
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/Client.pm
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/ORB.pm
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/PrimarySeq.pm
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/Seq.pm
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient/SeqFeature.pm
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/Biocorba.pm
+%%PLIST_CORBA_CLIENT%%lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/biocorba.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/AnonymousSeq.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/Base.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/BioEnv.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/PrimarySeq.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/PrimarySeqDB.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/PrimarySeqIterator.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/PrimarySeqVector.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/Seq.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/SeqDB.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/SeqFeature.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/SeqFeatureIterator.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/SeqFeatureVector.pm
+%%PLIST_CORBA_SERVER%%lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer/Server.pm
+%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/AnnotMap.pm
+%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/BioTkPerl8_1.pm
+%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/GO_Browser.pm
+%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/HitDisplay.pm
+%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/README
+%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/SeqCanvas.pm
+%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/Tkpsh.pl
+%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/bioTk_Map.pm
+%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/bioTk_SeqSubs.pm
+%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/bioTk_Sequence.pm
+%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk/bioTk_Utilities.pm
+%%PLIST_GUI%%lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Tk/.packlist
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext/Align.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/.packlist
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/.packlist
@@ -213,10 +213,10 @@ lib/perl5/site_perl/%%PERL_VER%%/biodesign.pod
 lib/perl5/site_perl/%%PERL_VER%%/bioperl.pod
 lib/perl5/site_perl/%%PERL_VER%%/biostart.pod
 lib/perl5/site_perl/%%PERL_VER%%/bptutorial.pl
-%%PLIST_GUI%%@dirrm lib/perl5/site_perl/5.6.0/mach/auto/Bio/Tk
-%%PLIST_GUI%%@dirrm lib/perl5/site_perl/5.6.0/Bio/Tk
-%%PLIST_CORBA_SERVER%%@dirrm lib/perl5/site_perl/5.6.0/Bio/CorbaServer
-%%PLIST_CORBA_CLIENT%%@dirrm lib/perl5/site_perl/5.6.0/Bio/CorbaClient
+%%PLIST_GUI%%@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Tk
+%%PLIST_GUI%%@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tk
+%%PLIST_CORBA_SERVER%%@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaServer
+%%PLIST_CORBA_CLIENT%%@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/CorbaClient
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation/IO
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Variation
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4