- Welcome X.org 7.2 \o/.

- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

35 files changed, 40 insertions, 20 deletions

diff --git a/biology/L-Breeder/Makefile b/biology/L-Breeder/Makefile
index 39c96044318d..0c6fbc1f92c3 100644
--- a/biology/L-Breeder/Makefile
+++ b/biology/L-Breeder/Makefile
@@ -8,7 +8,7 @@
 
 PORTNAME=	LBreeder
 PORTVERSION=	1.0
-PORTREVISION=	7
+PORTREVISION=	8
 CATEGORIES=	biology
 MASTER_SITES=	http://www.simonyi.ox.ac.uk/dawkins/software/yan/L-Breeder/
 DISTNAME=	${PORTNAME}-source
diff --git a/biology/adun/Makefile b/biology/adun/Makefile
index 70118deea485..7491feeaedac 100644
--- a/biology/adun/Makefile
+++ b/biology/adun/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	adun
 PORTVERSION=	0.6
+PORTREVISION=	1
 CATEGORIES=	biology gnustep
 MASTER_SITES=	http://download.gna.org/adun/
 DISTNAME=	Adun${PORTVERSION}
diff --git a/biology/artemis/Makefile b/biology/artemis/Makefile
index c4998b28dd7c..ee85444fc5ef 100644
--- a/biology/artemis/Makefile
+++ b/biology/artemis/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=	artemis
 PORTVERSION=	7
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	biology java
 MASTER_SITES=	http://www.sanger.ac.uk/Software/Artemis/v${PORTVERSION}/
 DISTNAME=	artemis_compiled_v${PORTVERSION}_${PORTREVISION}
diff --git a/biology/artemis/distinfo b/biology/artemis/distinfo
index 804338297593..3355a8ea32d4 100644
--- a/biology/artemis/distinfo
+++ b/biology/artemis/distinfo
@@ -1,3 +1,3 @@
-MD5 (artemis_compiled_v7_1.tar.gz) = f81f52a99a7c7b40c2a5289e71e0ea03
-SHA256 (artemis_compiled_v7_1.tar.gz) = d770c48464be5903107379775765883f7827833be7339d90d3dc8e1430c0646e
-SIZE (artemis_compiled_v7_1.tar.gz) = 4055125
+MD5 (artemis_compiled_v7_2.tar.gz) = f81f52a99a7c7b40c2a5289e71e0ea03
+SHA256 (artemis_compiled_v7_2.tar.gz) = d770c48464be5903107379775765883f7827833be7339d90d3dc8e1430c0646e
+SIZE (artemis_compiled_v7_2.tar.gz) = 4055125
diff --git a/biology/biococoa/Makefile b/biology/biococoa/Makefile
index 92374d11797d..c49584bbd5cb 100644
--- a/biology/biococoa/Makefile
+++ b/biology/biococoa/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	biococoa
 PORTVERSION=	1.6.0
+PORTREVISION=	1
 CATEGORIES=	biology gnustep
 MASTER_SITES=	${MASTER_SITE_DEBIAN}
 MASTER_SITE_SUBDIR=	pool/main/b/biococoa.app
diff --git a/biology/biojava/Makefile b/biology/biojava/Makefile
index 5b27da842616..9d693b4d5072 100644
--- a/biology/biojava/Makefile
+++ b/biology/biojava/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	biojava
 DISTVERSION=	1.5-beta2
+PORTREVISION=	1
 PORTEPOCH=	1
 CATEGORIES=	biology java
 MASTER_SITES=	http://www.biojava.org/download/bj15b/all/:source	\
diff --git a/biology/boinc-simap/Makefile b/biology/boinc-simap/Makefile
index b765a9f23046..4c9da0ba6961 100644
--- a/biology/boinc-simap/Makefile
+++ b/biology/boinc-simap/Makefile
@@ -6,6 +6,7 @@
 
 PORTNAME=	boinc-simap
 PORTVERSION=	${SIMAP_VERSION}.${HMMER_VERSION}
+PORTREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	http://boinc.bio.wzw.tum.de/boincsimap/download/
 DISTNAME=	${SIMAP_BINARY} ${HMMER_BINARY}
diff --git a/biology/embassy/Makefile b/biology/embassy/Makefile
index bdabee8ee1b0..93d67cee5f74 100644
--- a/biology/embassy/Makefile
+++ b/biology/embassy/Makefile
@@ -8,6 +8,7 @@
 
 PORTNAME=	embassy
 PORTVERSION=	3.0.0
+PORTREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/ \
 		ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index 2fdecddae40f..bc9016cc0d67 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	emboss
 PORTVERSION=	3.0.0
+PORTREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/ \
 		ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
diff --git a/biology/garlic/Makefile b/biology/garlic/Makefile
index 7a6a15a906d3..210279060ebc 100644
--- a/biology/garlic/Makefile
+++ b/biology/garlic/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	garlic
 PORTVERSION=	1.5
+PORTREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	http://garlic.mefos.hr/sources/garlic-${PORTVERSION}/
 DISTFILES=	${DISTNAME}${EXTRACT_SUFX}
diff --git a/biology/genpak/Makefile b/biology/genpak/Makefile
index 7e71a07bd9c8..3ac7d7c088f2 100644
--- a/biology/genpak/Makefile
+++ b/biology/genpak/Makefile
@@ -8,7 +8,7 @@
 
 PORTNAME=	genpak
 PORTVERSION=	0.26
-PORTREVISION=	3
+PORTREVISION=	4
 CATEGORIES=	biology
 MASTER_SITES=	http://www.bioinformatics.org/genpak/download/
 DISTNAME=	gp-${PORTVERSION}
diff --git a/biology/gperiodic/Makefile b/biology/gperiodic/Makefile
index e3d318199230..e49c771662a2 100644
--- a/biology/gperiodic/Makefile
+++ b/biology/gperiodic/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=	gperiodic
 PORTVERSION=	2.0.8
-PORTREVISION=	3
+PORTREVISION=	4
 CATEGORIES=	biology
 MASTER_SITES=	http://koti.welho.com/jfrantz/software/
 
diff --git a/biology/gperiodic/pkg-plist b/biology/gperiodic/pkg-plist
index eaf00bcb6513..db8a172e1e3b 100644
--- a/biology/gperiodic/pkg-plist
+++ b/biology/gperiodic/pkg-plist
@@ -11,5 +11,3 @@ share/locale/pl/LC_MESSAGES/gperiodic.mo
 share/locale/sv/LC_MESSAGES/gperiodic.mo
 share/locale/tr/LC_MESSAGES/gperiodic.mo
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrmtry share/locale/pl/LC_MESSAGES
-@dirrmtry share/locale/pl
diff --git a/biology/jalview/Makefile b/biology/jalview/Makefile
index 9596bb7d00e5..f7f974292de0 100644
--- a/biology/jalview/Makefile
+++ b/biology/jalview/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	jalview
 PORTVERSION=	2.07
+PORTREVISION=	1
 CATEGORIES=	biology java
 MASTER_SITES=	http://www.jalview.org/source/
 DISTNAME=	${PORTNAME}_${PORTVERSION:S/./_/}
diff --git a/biology/kinemage/Makefile b/biology/kinemage/Makefile
index 4cdf21027885..aaee515e2745 100644
--- a/biology/kinemage/Makefile
+++ b/biology/kinemage/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	kinemage
 PORTVERSION=	5.79
+PORTREVISION=	1
 CATEGORIES=	biology
 # There is no distfile to fetch here, just a dir of badly formatted sources
 #MASTER_SITES=	ftp://kinemage.biochem.duke.edu/OPEN_SOURCE/
diff --git a/biology/lsysexp/Makefile b/biology/lsysexp/Makefile
index 383d1e411121..dac8bf722cde 100644
--- a/biology/lsysexp/Makefile
+++ b/biology/lsysexp/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=	lsysexp
 PORTVERSION=	0.67
-PORTREVISION=	5
+PORTREVISION=	6
 CATEGORIES=	biology
 MASTER_SITES=	http://coscorrosa.com/programs/${PORTNAME}/download/ \
 		http://freebsd.unixfreunde.de/sources/
diff --git a/biology/molden/Makefile b/biology/molden/Makefile
index e3f721e4a781..1d8b3661b115 100644
--- a/biology/molden/Makefile
+++ b/biology/molden/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	molden
 PORTVERSION=	4.5
+PORTREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.cmbi.kun.nl/pub/molgraph/molden/
 DISTNAME=	${PORTNAME}${PORTVERSION}
diff --git a/biology/molden/distinfo b/biology/molden/distinfo
index 040963ee046e..7268a4f6579c 100644
--- a/biology/molden/distinfo
+++ b/biology/molden/distinfo
@@ -1,3 +1,3 @@
-MD5 (molden-4.5/molden4.5.tar.Z) = 2706a205de011f2dca042f8c7fe95834
-SHA256 (molden-4.5/molden4.5.tar.Z) = 84b6905ec786bde9af8bfa6439b0c066b65a98028ffaf1ebc543e58b31fe2ca7
-SIZE (molden-4.5/molden4.5.tar.Z) = 3605279
+MD5 (molden-4.5_1/molden4.5.tar.Z) = 2706a205de011f2dca042f8c7fe95834
+SHA256 (molden-4.5_1/molden4.5.tar.Z) = 84b6905ec786bde9af8bfa6439b0c066b65a98028ffaf1ebc543e58b31fe2ca7
+SIZE (molden-4.5_1/molden4.5.tar.Z) = 3605279
diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile
index 643c83de3c40..ba50ca954b8b 100644
--- a/biology/ncbi-toolkit/Makefile
+++ b/biology/ncbi-toolkit/Makefile
@@ -8,6 +8,7 @@
 
 PORTNAME=	ncbi-toolkit
 PORTVERSION=	2006.05.07	# containing BLAST v2.2.14
+PORTREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
 DISTNAME=	ncbi
diff --git a/biology/p5-Bio-Das/Makefile b/biology/p5-Bio-Das/Makefile
index ff7ae0854f05..868337eaa4da 100644
--- a/biology/p5-Bio-Das/Makefile
+++ b/biology/p5-Bio-Das/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	Bio-Das
 PORTVERSION=	1.03
+PORTREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	http://www.biodas.org/download/Bio::Das/ \
 		${MASTER_SITE_PERL_CPAN}
diff --git a/biology/p5-Bio-Phylo/Makefile b/biology/p5-Bio-Phylo/Makefile
index 96d4d20471e8..3cd6454e72a8 100644
--- a/biology/p5-Bio-Phylo/Makefile
+++ b/biology/p5-Bio-Phylo/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	Bio-Phylo
 PORTVERSION=	0.15
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	${MASTER_SITE_PERL_CPAN}
 MASTER_SITE_SUBDIR=	Bio
diff --git a/biology/p5-bioperl-devel/Makefile b/biology/p5-bioperl-devel/Makefile
index a5bedc037594..ec32aeaa90a4 100644
--- a/biology/p5-bioperl-devel/Makefile
+++ b/biology/p5-bioperl-devel/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	bioperl
 PORTVERSION=	1.5.1
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	http://bioperl.org/DIST/
 PKGNAMEPREFIX=	p5-
diff --git a/biology/p5-bioperl-run-devel/Makefile b/biology/p5-bioperl-run-devel/Makefile
index b6738ab318ac..10d10f59033b 100644
--- a/biology/p5-bioperl-run-devel/Makefile
+++ b/biology/p5-bioperl-run-devel/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	bioperl-run
 PORTVERSION=	1.5.1
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	http://bioperl.org/DIST/
 PKGNAMEPREFIX=	p5-
@@ -14,7 +15,7 @@ PKGNAMEPREFIX=	p5-
 MAINTAINER=	mauricio@arareko.net
 COMMENT=	Wrapper modules for common bioinformatics tools (developer release)
 
-BUILD_DEPENDS=	p5-bioperl=1.5.1:${PORTSDIR}/biology/p5-bioperl-devel \
+BUILD_DEPENDS=	p5-bioperl=1.5.1_1:${PORTSDIR}/biology/p5-bioperl-devel \
 		${SITE_PERL}/Algorithm/Diff.pm:${PORTSDIR}/devel/p5-Algorithm-Diff
 RUN_DEPENDS=	${BUILD_DEPENDS}
 
diff --git a/biology/p5-bioperl-run/Makefile b/biology/p5-bioperl-run/Makefile
index 2e81e0d0d882..2decb02726d5 100644
--- a/biology/p5-bioperl-run/Makefile
+++ b/biology/p5-bioperl-run/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	bioperl-run
 PORTVERSION=	1.4
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	http://bioperl.org/DIST/ \
 		${MASTER_SITE_PERL_CPAN}
@@ -15,7 +16,7 @@ PKGNAMEPREFIX=	p5-
 MAINTAINER=	mauricio@arareko.net
 COMMENT=	Wrapper modules for common bioinformatics tools
 
-BUILD_DEPENDS=	p5-bioperl=1.4:${PORTSDIR}/biology/p5-bioperl \
+BUILD_DEPENDS=	p5-bioperl=1.4_1:${PORTSDIR}/biology/p5-bioperl \
 		${SITE_PERL}/Algorithm/Diff.pm:${PORTSDIR}/devel/p5-Algorithm-Diff
 RUN_DEPENDS=	${BUILD_DEPENDS}
 
diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile
index ef6f01a65d10..7b2cbc1d6974 100644
--- a/biology/p5-bioperl/Makefile
+++ b/biology/p5-bioperl/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	bioperl
 PORTVERSION=	1.4
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	http://bioperl.org/DIST/ \
 		${MASTER_SITE_PERL_CPAN}
diff --git a/biology/phylip/Makefile b/biology/phylip/Makefile
index bfd1b0407eb5..9e21481d7033 100644
--- a/biology/phylip/Makefile
+++ b/biology/phylip/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	phylip
 PORTVERSION=	3.66
+PORTREVISION=	1
 PORTEPOCH=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://evolution.genetics.washington.edu/pub/phylip/ \
diff --git a/biology/platon/Makefile b/biology/platon/Makefile
index fe2338f4610c..2fa1e0481200 100644
--- a/biology/platon/Makefile
+++ b/biology/platon/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	platon
 PORTVERSION=	2007.01.09
+PORTREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://xraysoft.chem.uu.nl/pub/unix/
 DISTNAME=	platon
diff --git a/biology/povchem/Makefile b/biology/povchem/Makefile
index 0536e1e852a8..b6e9d4d064fd 100644
--- a/biology/povchem/Makefile
+++ b/biology/povchem/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=	povchem
 PORTVERSION=	1.0
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	biology graphics
 MASTER_SITES=	http://www.chemicalgraphics.com/paul/PC_Dist/v1.00/
 DISTFILES=	povchem.c \
diff --git a/biology/protomol/Makefile b/biology/protomol/Makefile
index 39252c9bd9f7..dd40c86556d6 100644
--- a/biology/protomol/Makefile
+++ b/biology/protomol/Makefile
@@ -6,6 +6,7 @@
 
 PORTNAME=	protomol
 PORTVERSION=	2.0.3
+PORTREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
 MASTER_SITE_SUBDIR=	${PORTNAME}
diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile
index cc0bf319a59d..77cc58f9e6f3 100644
--- a/biology/pymol/Makefile
+++ b/biology/pymol/Makefile
@@ -6,6 +6,7 @@
 
 PORTNAME=	pymol
 PORTVERSION=	0.99rc6
+PORTREVISION=	1
 CATEGORIES=	biology python
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
 MASTER_SITE_SUBDIR=	pymol
diff --git a/biology/rasmol/Makefile b/biology/rasmol/Makefile
index 93283da28967..bea4f4e3a1b6 100644
--- a/biology/rasmol/Makefile
+++ b/biology/rasmol/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	rasmol
 PORTVERSION=	2.7.2.1.1
+PORTREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.bernstein-plus-sons.com/software/
 DISTNAME=	RasMol_${PORTVERSION}
diff --git a/biology/seaview/Makefile b/biology/seaview/Makefile
index e1b630d628b0..6cbc32c036b4 100644
--- a/biology/seaview/Makefile
+++ b/biology/seaview/Makefile
@@ -8,7 +8,7 @@
 
 PORTNAME=	seaview
 PORTVERSION=	2006.02.13
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	biology
 MASTER_SITES=	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/
 DISTNAME=	${PORTNAME}${PORTVERSION:S/.//g}
diff --git a/biology/treeviewx/Makefile b/biology/treeviewx/Makefile
index 5b835cd769a3..44d599a230a8 100644
--- a/biology/treeviewx/Makefile
+++ b/biology/treeviewx/Makefile
@@ -8,7 +8,7 @@
 
 PORTNAME=	treeviewx
 PORTVERSION=	0.5.1
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	biology
 MASTER_SITES=	http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/${PORTVERSION:S/.1//}/
 DISTNAME=	tv-${PORTVERSION}
diff --git a/biology/xdrawchem/Makefile b/biology/xdrawchem/Makefile
index 3fe6f3d62af0..5d37c87ca9a8 100644
--- a/biology/xdrawchem/Makefile
+++ b/biology/xdrawchem/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=	xdrawchem
 PORTVERSION=	1.9.9
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
 MASTER_SITE_SUBDIR=	xdrawchem
diff --git a/biology/xmolwt/Makefile b/biology/xmolwt/Makefile
index 0ce0b99716ff..519a59dcf0c8 100644
--- a/biology/xmolwt/Makefile
+++ b/biology/xmolwt/Makefile
@@ -6,7 +6,7 @@
 
 PORTNAME=	xmolwt
 PORTVERSION=	0.7
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	biology
 MASTER_SITES=	http://www.st.hirosaki-u.ac.jp/~rmiya/xmolwt/