From a8659f2c3a739594f865ddb2381c38d14c4d611e Mon Sep 17 00:00:00 2001 From: gerald Date: Sun, 10 Sep 2017 20:55:38 +0000 Subject: Bump PORTREVISION for ports depending on the canonical version of GCC (via Mk/bsd.default-versions.mk and lang/gcc) which has moved from GCC 5.4 to GCC 6.4 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang, c++14-lang, c++0x, c11, or gcc-c++11-lib. PR: 219275 --- biology/bowtie/Makefile | 2 +- biology/cd-hit/Makefile | 2 +- biology/crux/Makefile | 2 +- biology/fasttree/Makefile | 2 +- biology/jellyfish/Makefile | 2 +- biology/molden/Makefile | 2 +- biology/mopac/Makefile | 2 +- biology/ncbi-blast+/Makefile | 2 +- biology/plink/Makefile | 2 +- biology/psi88/Makefile | 2 +- biology/seqan-apps/Makefile | 2 +- biology/seqtools/Makefile | 2 +- biology/ssaha/Makefile | 2 +- biology/t_coffee/Makefile | 2 +- biology/tinker/Makefile | 2 +- 15 files changed, 15 insertions(+), 15 deletions(-) (limited to 'biology') 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/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/ -- cgit From db001c41f327033ce8ba3912a44ad319a24bae03 Mon Sep 17 00:00:00 2001 From: wen Date: Wed, 13 Sep 2017 01:45:35 +0000 Subject: - Update to 1.007002 Changes: http://search.cpan.org/src/CJFIELDS/BioPerl-1.007002/Changes --- biology/p5-BioPerl/Makefile | 3 +-- biology/p5-BioPerl/distinfo | 6 +++--- biology/p5-BioPerl/pkg-plist | 10 ---------- 3 files changed, 4 insertions(+), 15 deletions(-) (limited to 'biology') 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 -- cgit