23 files changed, 125 insertions, 125 deletions

diff --git a/biology/p5-AcePerl/Makefile b/biology/p5-AcePerl/Makefile
index 2b4b08201a56..c2811aba4af0 100644
--- a/biology/p5-AcePerl/Makefile
+++ b/biology/p5-AcePerl/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	AcePerl
 PORTVERSION=	1.92
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	biology databases perl5
 MASTER_SITES=	CPAN
 MASTER_SITE_SUBDIR=	Ace
diff --git a/biology/p5-AcePerl/pkg-plist b/biology/p5-AcePerl/pkg-plist
index 3ac0b3ad9024..8b3ea9e627b5 100644
--- a/biology/p5-AcePerl/pkg-plist
+++ b/biology/p5-AcePerl/pkg-plist
@@ -1,113 +1,112 @@
 bin/ace.pl
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/AceSubs.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/GeneSubs.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/SearchSubs.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/SiteDefs.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/TreeSubs.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Freesubs.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Fk.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/anchored_arrow.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/arrow.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/box.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/crossbox.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/dot.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/ex.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/graded_segments.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/group.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/line.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/primers.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/segments.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/span.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/toomany.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/transcript.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/triangle.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/GlyphFactory.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Panel.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Track.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Iterator.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Local.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Model.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Object.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Object/Wormbase.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/RPC.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Feature.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/FeatureList.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/GappedAlignment.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Gene.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Homol.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Multi.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Transcript.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Ace/SocketServer.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/GFF/Filehandle.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/.packlist
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Freesubs/Freesubs.so
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_asAce.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_asHTML.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_asTable.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_asXML.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_default_makeHTML.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_insert.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_special_dump.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_to_ace_date.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_xmlNumber.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/add_row.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/add_tree.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asAce.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asDNA.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asGif.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asHTML.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asPeptide.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asString.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asTable.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asXML.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/autosplit.ix
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/comment.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/commit.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/date_style.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/debug.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/delete.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/escapeXML.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/isComment.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/kill.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/replace.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/rollback.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/tags.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/timestamp.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/RPC/RPC.so
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature/autosplit.ix
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Sequence/autosplit.ix
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/_register_iterator.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/_restore_iterator.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/_save_iterator.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/_unregister_iterator.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/auto_save.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/autosplit.ix
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/class_count.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/classes.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/date.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/date_style.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/datetime.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/debug.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/fetch_many.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/find.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/freeprotect.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/grep.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/layout.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/new.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/parse.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/parse_file.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/parse_longtext.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/pick.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/ping.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/put.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/split.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/status.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/timestamps.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/title.al
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/version.al
+%%SITE_ARCH%%/Ace.pm
+%%SITE_ARCH%%/Ace/Browser/AceSubs.pm
+%%SITE_ARCH%%/Ace/Browser/GeneSubs.pm
+%%SITE_ARCH%%/Ace/Browser/SearchSubs.pm
+%%SITE_ARCH%%/Ace/Browser/SiteDefs.pm
+%%SITE_ARCH%%/Ace/Browser/TreeSubs.pm
+%%SITE_ARCH%%/Ace/Freesubs.pm
+%%SITE_ARCH%%/Ace/Graphics/Fk.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/anchored_arrow.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/arrow.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/box.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/crossbox.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/dot.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/ex.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/graded_segments.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/group.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/line.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/primers.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/segments.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/span.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/toomany.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/transcript.pm
+%%SITE_ARCH%%/Ace/Graphics/Glyph/triangle.pm
+%%SITE_ARCH%%/Ace/Graphics/GlyphFactory.pm
+%%SITE_ARCH%%/Ace/Graphics/Panel.pm
+%%SITE_ARCH%%/Ace/Graphics/Track.pm
+%%SITE_ARCH%%/Ace/Iterator.pm
+%%SITE_ARCH%%/Ace/Local.pm
+%%SITE_ARCH%%/Ace/Model.pm
+%%SITE_ARCH%%/Ace/Object.pm
+%%SITE_ARCH%%/Ace/Object/Wormbase.pm
+%%SITE_ARCH%%/Ace/RPC.pm
+%%SITE_ARCH%%/Ace/Sequence.pm
+%%SITE_ARCH%%/Ace/Sequence/Feature.pm
+%%SITE_ARCH%%/Ace/Sequence/FeatureList.pm
+%%SITE_ARCH%%/Ace/Sequence/GappedAlignment.pm
+%%SITE_ARCH%%/Ace/Sequence/Gene.pm
+%%SITE_ARCH%%/Ace/Sequence/Homol.pm
+%%SITE_ARCH%%/Ace/Sequence/Multi.pm
+%%SITE_ARCH%%/Ace/Sequence/Transcript.pm
+%%SITE_ARCH%%/Ace/SocketServer.pm
+%%SITE_ARCH%%/GFF/Filehandle.pm
+%%SITE_ARCH%%/auto/Ace/Freesubs/Freesubs.so
+%%SITE_ARCH%%/auto/Ace/Object/_asAce.al
+%%SITE_ARCH%%/auto/Ace/Object/_asHTML.al
+%%SITE_ARCH%%/auto/Ace/Object/_asTable.al
+%%SITE_ARCH%%/auto/Ace/Object/_asXML.al
+%%SITE_ARCH%%/auto/Ace/Object/_default_makeHTML.al
+%%SITE_ARCH%%/auto/Ace/Object/_insert.al
+%%SITE_ARCH%%/auto/Ace/Object/_special_dump.al
+%%SITE_ARCH%%/auto/Ace/Object/_to_ace_date.al
+%%SITE_ARCH%%/auto/Ace/Object/_xmlNumber.al
+%%SITE_ARCH%%/auto/Ace/Object/add_row.al
+%%SITE_ARCH%%/auto/Ace/Object/add_tree.al
+%%SITE_ARCH%%/auto/Ace/Object/asAce.al
+%%SITE_ARCH%%/auto/Ace/Object/asDNA.al
+%%SITE_ARCH%%/auto/Ace/Object/asGif.al
+%%SITE_ARCH%%/auto/Ace/Object/asHTML.al
+%%SITE_ARCH%%/auto/Ace/Object/asPeptide.al
+%%SITE_ARCH%%/auto/Ace/Object/asString.al
+%%SITE_ARCH%%/auto/Ace/Object/asTable.al
+%%SITE_ARCH%%/auto/Ace/Object/asXML.al
+%%SITE_ARCH%%/auto/Ace/Object/autosplit.ix
+%%SITE_ARCH%%/auto/Ace/Object/comment.al
+%%SITE_ARCH%%/auto/Ace/Object/commit.al
+%%SITE_ARCH%%/auto/Ace/Object/date_style.al
+%%SITE_ARCH%%/auto/Ace/Object/debug.al
+%%SITE_ARCH%%/auto/Ace/Object/delete.al
+%%SITE_ARCH%%/auto/Ace/Object/escapeXML.al
+%%SITE_ARCH%%/auto/Ace/Object/isComment.al
+%%SITE_ARCH%%/auto/Ace/Object/kill.al
+%%SITE_ARCH%%/auto/Ace/Object/replace.al
+%%SITE_ARCH%%/auto/Ace/Object/rollback.al
+%%SITE_ARCH%%/auto/Ace/Object/tags.al
+%%SITE_ARCH%%/auto/Ace/Object/timestamp.al
+%%SITE_ARCH%%/auto/Ace/RPC/RPC.so
+%%SITE_ARCH%%/auto/Ace/Sequence/Feature/autosplit.ix
+%%SITE_ARCH%%/auto/Ace/Sequence/autosplit.ix
+%%SITE_ARCH%%/auto/Ace/_register_iterator.al
+%%SITE_ARCH%%/auto/Ace/_restore_iterator.al
+%%SITE_ARCH%%/auto/Ace/_save_iterator.al
+%%SITE_ARCH%%/auto/Ace/_unregister_iterator.al
+%%SITE_ARCH%%/auto/Ace/auto_save.al
+%%SITE_ARCH%%/auto/Ace/autosplit.ix
+%%SITE_ARCH%%/auto/Ace/class_count.al
+%%SITE_ARCH%%/auto/Ace/classes.al
+%%SITE_ARCH%%/auto/Ace/date.al
+%%SITE_ARCH%%/auto/Ace/date_style.al
+%%SITE_ARCH%%/auto/Ace/datetime.al
+%%SITE_ARCH%%/auto/Ace/debug.al
+%%SITE_ARCH%%/auto/Ace/fetch_many.al
+%%SITE_ARCH%%/auto/Ace/find.al
+%%SITE_ARCH%%/auto/Ace/freeprotect.al
+%%SITE_ARCH%%/auto/Ace/grep.al
+%%SITE_ARCH%%/auto/Ace/layout.al
+%%SITE_ARCH%%/auto/Ace/new.al
+%%SITE_ARCH%%/auto/Ace/parse.al
+%%SITE_ARCH%%/auto/Ace/parse_file.al
+%%SITE_ARCH%%/auto/Ace/parse_longtext.al
+%%SITE_ARCH%%/auto/Ace/pick.al
+%%SITE_ARCH%%/auto/Ace/ping.al
+%%SITE_ARCH%%/auto/Ace/put.al
+%%SITE_ARCH%%/auto/Ace/split.al
+%%SITE_ARCH%%/auto/Ace/status.al
+%%SITE_ARCH%%/auto/Ace/timestamps.al
+%%SITE_ARCH%%/auto/Ace/title.al
+%%SITE_ARCH%%/auto/Ace/version.al
 %%PERL5_MAN3%%/Ace.3.gz
 %%PERL5_MAN3%%/Ace::Browser::AceSubs.3.gz
 %%PERL5_MAN3%%/Ace::Browser::SearchSubs.3.gz
diff --git a/biology/p5-Bio-ASN1-EntrezGene/Makefile b/biology/p5-Bio-ASN1-EntrezGene/Makefile
index e9a3ff4706b9..3128b0bf287b 100644
--- a/biology/p5-Bio-ASN1-EntrezGene/Makefile
+++ b/biology/p5-Bio-ASN1-EntrezGene/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	Bio-ASN1-EntrezGene
 PORTVERSION=	1.091
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
diff --git a/biology/p5-Bio-ASN1-EntrezGene/pkg-plist b/biology/p5-Bio-ASN1-EntrezGene/pkg-plist
index 4014f2c6c051..93ec702b33f3 100644
--- a/biology/p5-Bio-ASN1-EntrezGene/pkg-plist
+++ b/biology/p5-Bio-ASN1-EntrezGene/pkg-plist
@@ -2,7 +2,6 @@
 %%SITE_PERL%%/Bio/ASN1/EntrezGene/Indexer.pm
 %%SITE_PERL%%/Bio/ASN1/Sequence.pm
 %%SITE_PERL%%/Bio/ASN1/Sequence/Indexer.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/ASN1/EntrezGene/.packlist
 %%PERL5_MAN3%%/Bio::ASN1::EntrezGene.3.gz
 %%PERL5_MAN3%%/Bio::ASN1::EntrezGene::Indexer.3.gz
 %%PERL5_MAN3%%/Bio::ASN1::Sequence.3.gz
diff --git a/biology/p5-Bio-Das-Lite/Makefile b/biology/p5-Bio-Das-Lite/Makefile
index 2eee0e238e50..73b80589b8f6 100644
--- a/biology/p5-Bio-Das-Lite/Makefile
+++ b/biology/p5-Bio-Das-Lite/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	Bio-Das-Lite
 PORTVERSION=	2.11
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
diff --git a/biology/p5-Bio-Das/Makefile b/biology/p5-Bio-Das/Makefile
index 1d4072d3d466..75777ff55cae 100644
--- a/biology/p5-Bio-Das/Makefile
+++ b/biology/p5-Bio-Das/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	Bio-Das
 PORTVERSION=	1.17
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
diff --git a/biology/p5-Bio-Das/pkg-plist b/biology/p5-Bio-Das/pkg-plist
index a67510c448d1..964ca2c88bff 100644
--- a/biology/p5-Bio-Das/pkg-plist
+++ b/biology/p5-Bio-Das/pkg-plist
@@ -1,4 +1,3 @@
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Das/.packlist
 %%SITE_PERL%%/Bio/Das.pm
 %%SITE_PERL%%/Bio/Das/DSN.pm
 %%SITE_PERL%%/Bio/Das/Request.pm
diff --git a/biology/p5-Bio-GFF3/Makefile b/biology/p5-Bio-GFF3/Makefile
index e601a9aa03f7..42e857150553 100644
--- a/biology/p5-Bio-GFF3/Makefile
+++ b/biology/p5-Bio-GFF3/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	Bio-GFF3
 PORTVERSION=	2.0
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
diff --git a/biology/p5-Bio-GFF3/pkg-plist b/biology/p5-Bio-GFF3/pkg-plist
index b8448e9b489d..5aac13a355e5 100644
--- a/biology/p5-Bio-GFF3/pkg-plist
+++ b/biology/p5-Bio-GFF3/pkg-plist
@@ -4,7 +4,6 @@ bin/gff3_from_fasta
 %%SITE_PERL%%/Bio/GFF3/LowLevel/Parser/1_0_backcompat.pm
 %%SITE_PERL%%/Bio/GFF3/Transform/FromFasta.pm
 %%SITE_PERL%%/Bio/GFF3/Transform/SyncDirectives.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/GFF3/.packlist
 %%PERL5_MAN3%%/Bio::GFF3::LowLevel.3.gz
 %%PERL5_MAN3%%/Bio::GFF3::LowLevel::Parser.3.gz
 %%PERL5_MAN3%%/Bio::GFF3::LowLevel::Parser::1_0_backcompat.3.gz
diff --git a/biology/p5-Bio-Glite/Makefile b/biology/p5-Bio-Glite/Makefile
index 72cc005a3ff8..d8c4e60be310 100644
--- a/biology/p5-Bio-Glite/Makefile
+++ b/biology/p5-Bio-Glite/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	Bio-Glite
 PORTVERSION=	0.10
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
diff --git a/biology/p5-Bio-Glite/pkg-plist b/biology/p5-Bio-Glite/pkg-plist
index e3d6145ee56c..259cb4ffa6f3 100644
--- a/biology/p5-Bio-Glite/pkg-plist
+++ b/biology/p5-Bio-Glite/pkg-plist
@@ -1,3 +1,2 @@
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Glite/.packlist
 %%SITE_PERL%%/Bio/Glite.pm
 %%PERL5_MAN3%%/Bio::Glite.3.gz
diff --git a/biology/p5-Bio-Graphics/Makefile b/biology/p5-Bio-Graphics/Makefile
index 956a14bca537..2a11c4d43576 100644
--- a/biology/p5-Bio-Graphics/Makefile
+++ b/biology/p5-Bio-Graphics/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	Bio-Graphics
 PORTVERSION=	2.38
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
diff --git a/biology/p5-Bio-MAGETAB/Makefile b/biology/p5-Bio-MAGETAB/Makefile
index d71995b281d1..6fc139d50a68 100644
--- a/biology/p5-Bio-MAGETAB/Makefile
+++ b/biology/p5-Bio-MAGETAB/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	Bio-MAGETAB
 PORTVERSION=	1.31
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
diff --git a/biology/p5-Bio-MAGETAB/pkg-plist b/biology/p5-Bio-MAGETAB/pkg-plist
index dc6cee706cc3..14895b84aeb0 100644
--- a/biology/p5-Bio-MAGETAB/pkg-plist
+++ b/biology/p5-Bio-MAGETAB/pkg-plist
@@ -2,7 +2,6 @@ bin/deploy_magetab_db.pl
 bin/fix_ae_magetab.pl
 bin/read_magetab.pl
 bin/unload_magetab_namespace.pl
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/MAGETAB/.packlist
 %%SITE_PERL%%/Bio/MAGETAB/Util/Reader/DataMatrix.pm
 %%SITE_PERL%%/Bio/MAGETAB/Util/Reader/TagValueFile.pm
 %%SITE_PERL%%/Bio/MAGETAB/Util/Reader/Tabfile.pm
diff --git a/biology/p5-Bio-NEXUS/Makefile b/biology/p5-Bio-NEXUS/Makefile
index e0939852cde2..8cc58db52931 100644
--- a/biology/p5-Bio-NEXUS/Makefile
+++ b/biology/p5-Bio-NEXUS/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	Bio-NEXUS
 PORTVERSION=	0.78
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
diff --git a/biology/p5-Bio-NEXUS/pkg-plist b/biology/p5-Bio-NEXUS/pkg-plist
index 76b687a4ebb3..933493e67e5a 100644
--- a/biology/p5-Bio-NEXUS/pkg-plist
+++ b/biology/p5-Bio-NEXUS/pkg-plist
@@ -29,7 +29,6 @@ bin/nextool.pl
 %%SITE_PERL%%/Bio/NEXUS/Util/Exceptions.pm
 %%SITE_PERL%%/Bio/NEXUS/Util/Logger.pm
 %%SITE_PERL%%/Bio/NEXUS/WeightSet.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/NEXUS/.packlist
 %%PERL5_MAN3%%/Bio::NEXUS.3.gz
 %%PERL5_MAN3%%/Bio::NEXUS::AssumptionsBlock.3.gz
 %%PERL5_MAN3%%/Bio::NEXUS::Block.3.gz
diff --git a/biology/p5-Bio-Phylo/Makefile b/biology/p5-Bio-Phylo/Makefile
index 6e07cfade123..81cf4f7f3494 100644
--- a/biology/p5-Bio-Phylo/Makefile
+++ b/biology/p5-Bio-Phylo/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	Bio-Phylo
 PORTVERSION=	0.56
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
diff --git a/biology/p5-Bio-Phylo/pkg-plist b/biology/p5-Bio-Phylo/pkg-plist
index c353f68e831c..671eb4ae3bd5 100644
--- a/biology/p5-Bio-Phylo/pkg-plist
+++ b/biology/p5-Bio-Phylo/pkg-plist
@@ -1,4 +1,3 @@
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Phylo/.packlist
 %%SITE_PERL%%/Bio/Phylo.pm
 %%SITE_PERL%%/Bio/Phylo/EvolutionaryModels.pm
 %%SITE_PERL%%/Bio/Phylo/Factory.pm
diff --git a/biology/p5-Bio-SCF/Makefile b/biology/p5-Bio-SCF/Makefile
index fb055f5a202b..7a6d05896f77 100644
--- a/biology/p5-Bio-SCF/Makefile
+++ b/biology/p5-Bio-SCF/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	Bio-SCF
 PORTVERSION=	1.03
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
diff --git a/biology/p5-Bio-SCF/pkg-plist b/biology/p5-Bio-SCF/pkg-plist
index 34287acfedd0..25370a67bab4 100644
--- a/biology/p5-Bio-SCF/pkg-plist
+++ b/biology/p5-Bio-SCF/pkg-plist
@@ -1,5 +1,4 @@
-%%SITE_PERL%%/%%PERL_ARCH%%/Bio/SCF/Arrays.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/Bio/SCF.pm
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/SCF/SCF.so
-%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/SCF/.packlist
+%%SITE_ARCH%%/Bio/SCF/Arrays.pm
+%%SITE_ARCH%%/Bio/SCF.pm
+%%SITE_ARCH%%/auto/Bio/SCF/SCF.so
 %%PERL5_MAN3%%/Bio::SCF.3.gz
diff --git a/biology/p5-bioperl-run/Makefile b/biology/p5-bioperl-run/Makefile
index f5f14b13fdb4..bfae420c62d1 100644
--- a/biology/p5-bioperl-run/Makefile
+++ b/biology/p5-bioperl-run/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	bioperl-run
 PORTVERSION=	1.6.901
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 PKGNAMEPREFIX=	p5-
 
diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile
index 7f2a9ff819ee..6eda916ff372 100644
--- a/biology/p5-bioperl/Makefile
+++ b/biology/p5-bioperl/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	bioperl
 PORTVERSION=	1.6.924
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
diff --git a/biology/velvet/Makefile b/biology/velvet/Makefile
index 200cf9f0a3cc..f49cdca0428b 100644
--- a/biology/velvet/Makefile
+++ b/biology/velvet/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	velvet
 PORTVERSION=	1.2.10
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	biology
 MASTER_SITES=	http://www.ebi.ac.uk/~zerbino/velvet/
 DISTNAME=	${PORTNAME}_${PORTVERSION}