Merge branch 'master' into gnome-3.24gnome-3.24

18 files changed, 19 insertions, 30 deletions

diff --git a/biology/bowtie/Makefile b/biology/bowtie/Makefile
index 8d419e80cf16..07561719db5e 100644
--- a/biology/bowtie/Makefile
+++ b/biology/bowtie/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=		bowtie
 PORTVERSION=		1.1.2
-PORTREVISION=	3
+PORTREVISION=	4
 DISTVERSIONPREFIX=	v
 CATEGORIES=		biology
 
diff --git a/biology/cd-hit/Makefile b/biology/cd-hit/Makefile
index 5c348f176127..f71685847cc8 100644
--- a/biology/cd-hit/Makefile
+++ b/biology/cd-hit/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	cd-hit
 PORTVERSION=	4.6.6
-PORTREVISION=	1
+PORTREVISION=	2
 DISTVERSIONPREFIX=	V
 CATEGORIES=	biology
 
diff --git a/biology/crux/Makefile b/biology/crux/Makefile
index 86b1fb5860e8..75f95844dda6 100644
--- a/biology/crux/Makefile
+++ b/biology/crux/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	crux
 PORTVERSION=	1.2.0
-PORTREVISION=	7
+PORTREVISION=	8
 CATEGORIES=	biology python
 MASTER_SITES=	http://www.canonware.com/download/Crux/
 
diff --git a/biology/fasttree/Makefile b/biology/fasttree/Makefile
index 1dcc0db615ba..617ac37291d0 100644
--- a/biology/fasttree/Makefile
+++ b/biology/fasttree/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	FastTree
 PORTVERSION=	2.1.8
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	biology
 MASTER_SITES=	http://www.microbesonline.org/fasttree/
 EXTRACT_SUFX=	.c
diff --git a/biology/jellyfish/Makefile b/biology/jellyfish/Makefile
index 5225aae87fbd..22f1c3506485 100644
--- a/biology/jellyfish/Makefile
+++ b/biology/jellyfish/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	jellyfish
 PORTVERSION=	2.2.6
-PORTREVISION=	1
+PORTREVISION=	2
 DISTVERSIONPREFIX=	v
 CATEGORIES=	biology
 
diff --git a/biology/molden/Makefile b/biology/molden/Makefile
index f24a91257ab9..999d80767849 100644
--- a/biology/molden/Makefile
+++ b/biology/molden/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	molden
 PORTVERSION=	5.7
-PORTREVISION=	10
+PORTREVISION=	11
 PORTEPOCH=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/
diff --git a/biology/mopac/Makefile b/biology/mopac/Makefile
index a160df902f3c..65b3d4a60d5b 100644
--- a/biology/mopac/Makefile
+++ b/biology/mopac/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	mopac
 PORTVERSION=	7.${MOPAC_SUBVERSION}
-PORTREVISION=	2
+PORTREVISION=	3
 PORTEPOCH=	1
 CATEGORIES=	biology
 MASTER_SITES=	http://bioinformatics.org/ghemical/download/%SUBDIR%/
diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile
index d12f3154dc45..fe2cb96360f3 100644
--- a/biology/ncbi-blast+/Makefile
+++ b/biology/ncbi-blast+/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	blast+
 PORTVERSION=	2.5.0
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	biology
 MASTER_SITES=	http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ \
 		http://acadix.biz/Ports/distfiles/
diff --git a/biology/p5-BioPerl/Makefile b/biology/p5-BioPerl/Makefile
index 5ec3da283c7c..82fb358da082 100644
--- a/biology/p5-BioPerl/Makefile
+++ b/biology/p5-BioPerl/Makefile
@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	BioPerl
-PORTVERSION=	1.007001
-PORTREVISION=	2
+PORTVERSION=	1.007002
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
diff --git a/biology/p5-BioPerl/distinfo b/biology/p5-BioPerl/distinfo
index de8de98486f3..28d3fb904493 100644
--- a/biology/p5-BioPerl/distinfo
+++ b/biology/p5-BioPerl/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1479828383
-SHA256 (BioPerl-1.007001.tar.gz) = 9da1dbcd10452f53194c98c6cc2f604a59124507dcc1e6a8440565f44dd07b40
-SIZE (BioPerl-1.007001.tar.gz) = 12486953
+TIMESTAMP = 1505232617
+SHA256 (BioPerl-1.007002.tar.gz) = 17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1
+SIZE (BioPerl-1.007002.tar.gz) = 12362741
diff --git a/biology/p5-BioPerl/pkg-plist b/biology/p5-BioPerl/pkg-plist
index f24234684afb..8027beef64d8 100644
--- a/biology/p5-BioPerl/pkg-plist
+++ b/biology/p5-BioPerl/pkg-plist
@@ -36,7 +36,6 @@ bin/bp_netinstall.pl
 bin/bp_nexus2nh.pl
 bin/bp_nrdb.pl
 bin/bp_oligo_count.pl
-bin/bp_pairwise_kaks.pl
 bin/bp_parse_hmmsearch.pl
 bin/bp_process_gadfly.pl
 bin/bp_process_sgd.pl
@@ -769,10 +768,6 @@ bin/bp_unflatten_seq.pl
 %%SITE_PERL%%/Bio/Tools/Phylo/Gumby.pm
 %%SITE_PERL%%/Bio/Tools/Phylo/Molphy.pm
 %%SITE_PERL%%/Bio/Tools/Phylo/Molphy/Result.pm
-%%SITE_PERL%%/Bio/Tools/Phylo/PAML.pm
-%%SITE_PERL%%/Bio/Tools/Phylo/PAML/Codeml.pm
-%%SITE_PERL%%/Bio/Tools/Phylo/PAML/ModelResult.pm
-%%SITE_PERL%%/Bio/Tools/Phylo/PAML/Result.pm
 %%SITE_PERL%%/Bio/Tools/Phylo/Phylip/ProtDist.pm
 %%SITE_PERL%%/Bio/Tools/Prediction/Exon.pm
 %%SITE_PERL%%/Bio/Tools/Prediction/Gene.pm
@@ -893,7 +888,6 @@ bin/bp_unflatten_seq.pl
 %%PERL5_MAN1%%/bp_nexus2nh.pl.1.gz
 %%PERL5_MAN1%%/bp_nrdb.pl.1.gz
 %%PERL5_MAN1%%/bp_oligo_count.pl.1.gz
-%%PERL5_MAN1%%/bp_pairwise_kaks.pl.1.gz
 %%PERL5_MAN1%%/bp_parse_hmmsearch.pl.1.gz
 %%PERL5_MAN1%%/bp_process_gadfly.pl.1.gz
 %%PERL5_MAN1%%/bp_process_sgd.pl.1.gz
@@ -1623,10 +1617,6 @@ bin/bp_unflatten_seq.pl
 %%PERL5_MAN3%%/Bio::Tools::Phylo::Gumby.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Phylo::Molphy.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Phylo::Molphy::Result.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Phylo::PAML.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Phylo::PAML::Codeml.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Phylo::PAML::ModelResult.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Phylo::PAML::Result.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Phylo::Phylip::ProtDist.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Prediction::Exon.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Prediction::Gene.3.gz
diff --git a/biology/plink/Makefile b/biology/plink/Makefile
index 43c14f1ddf97..98c9dd3e1dd3 100644
--- a/biology/plink/Makefile
+++ b/biology/plink/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	plink
 PORTVERSION=	1.07
-PORTREVISION=	6
+PORTREVISION=	7
 CATEGORIES=	biology science
 MASTER_SITES=	http://pngu.mgh.harvard.edu/~purcell/plink/dist/
 DISTNAME=	${PORTNAME}-${PORTVERSION}-src
diff --git a/biology/psi88/Makefile b/biology/psi88/Makefile
index 89cb93ec4c80..6ce0d9fe629d 100644
--- a/biology/psi88/Makefile
+++ b/biology/psi88/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	psi88
 PORTVERSION=	1.0
-PORTREVISION=	10
+PORTREVISION=	11
 CATEGORIES=	biology
 MASTER_SITES=	http://www.ccl.net/cca/software/SOURCES/FORTRAN/psi88/
 DISTNAME=	${PORTNAME}
diff --git a/biology/seqan-apps/Makefile b/biology/seqan-apps/Makefile
index e18467daa1c5..541910be643d 100644
--- a/biology/seqan-apps/Makefile
+++ b/biology/seqan-apps/Makefile
@@ -4,7 +4,7 @@
 PORTNAME=	seqan-apps
 PORTVERSION=	2.2.0
 DISTVERSIONPREFIX=	seqan-v
-PORTREVISION=	4
+PORTREVISION=	6
 CATEGORIES=	biology
 
 MAINTAINER=	h2+fbsdports@fsfe.org
diff --git a/biology/seqtools/Makefile b/biology/seqtools/Makefile
index a76ddf96aa65..20eb535a15a0 100644
--- a/biology/seqtools/Makefile
+++ b/biology/seqtools/Makefile
@@ -2,7 +2,7 @@
 
 PORTNAME=	seqtools
 PORTVERSION=	4.44.1
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/
 
diff --git a/biology/ssaha/Makefile b/biology/ssaha/Makefile
index c7f6966f8a47..024151cd6d03 100644
--- a/biology/ssaha/Makefile
+++ b/biology/ssaha/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	ssaha
 PORTVERSION=	3.1c
-PORTREVISION=	4
+PORTREVISION=	5
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha/
 DISTNAME=	${PORTNAME}_v${PORTVERSION:S/.//}
diff --git a/biology/t_coffee/Makefile b/biology/t_coffee/Makefile
index d7a37f4b9c6e..ad4b555386d6 100644
--- a/biology/t_coffee/Makefile
+++ b/biology/t_coffee/Makefile
@@ -4,7 +4,7 @@
 PORTNAME=	t_coffee
 PORTVERSION=	9.03
 DISTVERSIONSUFFIX=	.r1318
-PORTREVISION=	5
+PORTREVISION=	6
 CATEGORIES=	biology
 MASTER_SITES=	http://www.tcoffee.org/Packages/Stable/Version_${PORTVERSION}${DISTVERSIONSUFFIX}/
 DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}${DISTVERSIONSUFFIX}
diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile
index a9f98b84e13b..66c499bc4931 100644
--- a/biology/tinker/Makefile
+++ b/biology/tinker/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	tinker
 PORTVERSION=	7.1.3
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	biology
 MASTER_SITES=	http://dasher.wustl.edu/tinker/downloads/