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Date:      Sat, 30 May 2020 19:39:11 +0000 (UTC)
From:      Joseph Mingrone <jrm@FreeBSD.org>
To:        ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org
Subject:   svn commit: r537106 - head/biology/hyphy
Message-ID:  <202005301939.04UJdBEF007692@repo.freebsd.org>

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Author: jrm
Date: Sat May 30 19:39:11 2020
New Revision: 537106
URL: https://svnweb.freebsd.org/changeset/ports/537106

Log:
  biology/hyphy: Update to version 2.5.14
  
  Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.14

Modified:
  head/biology/hyphy/Makefile   (contents, props changed)
  head/biology/hyphy/distinfo   (contents, props changed)
  head/biology/hyphy/pkg-plist   (contents, props changed)

Modified: head/biology/hyphy/Makefile
==============================================================================
--- head/biology/hyphy/Makefile	Sat May 30 19:28:56 2020	(r537105)
+++ head/biology/hyphy/Makefile	Sat May 30 19:39:11 2020	(r537106)
@@ -1,7 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	hyphy
-DISTVERSION=	2.5.12
+DISTVERSION=	2.5.14
 CATEGORIES=	biology
 
 MAINTAINER=	jrm@FreeBSD.org

Modified: head/biology/hyphy/distinfo
==============================================================================
--- head/biology/hyphy/distinfo	Sat May 30 19:28:56 2020	(r537105)
+++ head/biology/hyphy/distinfo	Sat May 30 19:39:11 2020	(r537106)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1588470249
-SHA256 (veg-hyphy-2.5.12_GH0.tar.gz) = ed3659371806efb6542d53ed149758a005884428fc94a27b51f897381368853f
-SIZE (veg-hyphy-2.5.12_GH0.tar.gz) = 6099625
+TIMESTAMP = 1590865541
+SHA256 (veg-hyphy-2.5.14_GH0.tar.gz) = 14d2513ca5c639c160764a02f03cdd8f5e2efe2579817d3b5d9b4fbb5fe64878
+SIZE (veg-hyphy-2.5.14_GH0.tar.gz) = 6206705

Modified: head/biology/hyphy/pkg-plist
==============================================================================
--- head/biology/hyphy/pkg-plist	Sat May 30 19:28:56 2020	(r537105)
+++ head/biology/hyphy/pkg-plist	Sat May 30 19:39:11 2020	(r537106)
@@ -1,435 +1,435 @@
 bin/hyphy
-lib/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod
-lib/hyphy/GeneticCodes/Ascidian_mtDNA.cod
-lib/hyphy/GeneticCodes/Blepharisma_Nuclear.cod
-lib/hyphy/GeneticCodes/Ciliate.cod
-lib/hyphy/GeneticCodes/Echinoderm_mtDNA.cod
-lib/hyphy/GeneticCodes/Euplotid_Nuclear.cod
-lib/hyphy/GeneticCodes/Flatworm_mtDNA.cod
-lib/hyphy/GeneticCodes/Invertebrate_mtDNA.cod
-lib/hyphy/GeneticCodes/Mold_mtDNA.cod
-lib/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod
-lib/hyphy/GeneticCodes/Vertebratemtdna.cod
-lib/hyphy/GeneticCodes/Yeast_mtDNA.cod
-lib/hyphy/SubstitutionClasses/AAEFV/Equal
-lib/hyphy/SubstitutionClasses/AAEFV/Estimated
-lib/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set
-lib/hyphy/SubstitutionClasses/AAEFV/Observed In Partition
-lib/hyphy/SubstitutionClasses/CodonEFV/Equal
-lib/hyphy/SubstitutionClasses/CodonEFV/Observed Codon
-lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params.
-lib/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params.
-lib/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete
-lib/hyphy/SubstitutionClasses/Heterogeneity/Beta
-lib/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma
-lib/hyphy/SubstitutionClasses/Heterogeneity/General Discrete
-lib/hyphy/SubstitutionClasses/Heterogeneity/Half Normal
-lib/hyphy/SubstitutionClasses/Heterogeneity/Lognormal
-lib/hyphy/SubstitutionClasses/NucEFV/Equal
-lib/hyphy/SubstitutionClasses/NucEFV/Estimated
-lib/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set
-lib/hyphy/SubstitutionClasses/NucEFV/Observed In Partition
-lib/hyphy/SubstitutionClasses/aa.bf
-lib/hyphy/SubstitutionClasses/codon.bf
-lib/hyphy/SubstitutionClasses/dinuc.bf
-lib/hyphy/SubstitutionClasses/nuc.bf
-lib/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl
-lib/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl
-lib/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl
-lib/hyphy/SubstitutionModels/Aminoacid/Jones.mdl
-lib/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl
-lib/hyphy/SubstitutionModels/Binary/F81.mdl
-lib/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl
-lib/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl
-lib/hyphy/SubstitutionModels/Codon/MG94.mdl
-lib/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl
-lib/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl
-lib/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl
-lib/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl
-lib/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl
-lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl
-lib/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl
-lib/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl
-lib/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf
-lib/hyphy/SubstitutionModels/Nucleotide/F81.mdl
-lib/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl
-lib/hyphy/SubstitutionModels/Nucleotide/REV.mdl
-lib/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl
-lib/hyphy/SubstitutionModels/Nucleotide/TrN.mdl
-lib/hyphy/SubstitutionModels/User/Nucleotide/JC69
-lib/hyphy/SubstitutionModels/User/Nucleotide/K2P
-lib/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl
-lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl
-lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl
-lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl
-lib/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl
-lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def
-lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def
-lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def
-lib/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def
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-lib/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma1.def
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-lib/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf
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-lib/hyphy/TemplateBatchFiles/ClusterByDistanceRange.bf
-lib/hyphy/TemplateBatchFiles/CodonBivariateRateProcessor.bf
-lib/hyphy/TemplateBatchFiles/CodonModelCompare.bf
-lib/hyphy/TemplateBatchFiles/CodonToProtein.bf
-lib/hyphy/TemplateBatchFiles/ConvertDataFile.bf
-lib/hyphy/TemplateBatchFiles/DistanceMatrix.bf
-lib/hyphy/TemplateBatchFiles/Distances/CodonTools.def
-lib/hyphy/TemplateBatchFiles/Distances/CodonTools2.def
-lib/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def
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-lib/hyphy/TemplateBatchFiles/Distances/K2P
-lib/hyphy/TemplateBatchFiles/Distances/K2P_RV
-lib/hyphy/TemplateBatchFiles/Distances/Modified_Nei_Gojobori
-lib/hyphy/TemplateBatchFiles/Distances/Nei_Gojobori
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-lib/hyphy/TemplateBatchFiles/Distances/PC_MH
-lib/hyphy/TemplateBatchFiles/Distances/PC_RV
-lib/hyphy/TemplateBatchFiles/Distances/T3P
-lib/hyphy/TemplateBatchFiles/Distances/TN84
-lib/hyphy/TemplateBatchFiles/Distances/TN93
-lib/hyphy/TemplateBatchFiles/Distances/TN93_RV
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-lib/hyphy/TemplateBatchFiles/Distances/Unaligned_LZ_FR
-lib/hyphy/TemplateBatchFiles/Distances/p_Distance
-lib/hyphy/TemplateBatchFiles/Distances/p_Distance_aa
-lib/hyphy/TemplateBatchFiles/Distances/p_Distance_binary
-lib/hyphy/TemplateBatchFiles/Distances/p_Distance_codon
-lib/hyphy/TemplateBatchFiles/F_ST.bf
-lib/hyphy/TemplateBatchFiles/FitnessAAModels.bf
-lib/hyphy/TemplateBatchFiles/GARD.bf
-lib/hyphy/TemplateBatchFiles/GA_CHC.ibf
-lib/hyphy/TemplateBatchFiles/GA_CHC_Binary.ibf
-lib/hyphy/TemplateBatchFiles/GUI/crayolaColors.def
-lib/hyphy/TemplateBatchFiles/Gateaux.bf
-lib/hyphy/TemplateBatchFiles/GateauxMR.bf
-lib/hyphy/TemplateBatchFiles/KHTest.bf
-lib/hyphy/TemplateBatchFiles/LEISR.bf
-lib/hyphy/TemplateBatchFiles/LHT.bf
-lib/hyphy/TemplateBatchFiles/LRTRecombTest.bf
-lib/hyphy/TemplateBatchFiles/LZ_Complexity.bf
-lib/hyphy/TemplateBatchFiles/LocalMolClock.bf
-lib/hyphy/TemplateBatchFiles/MGvsGY.bf
-lib/hyphy/TemplateBatchFiles/MergeSequences.bf
-lib/hyphy/TemplateBatchFiles/MergeSites.bf
-lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/BranchAPriori.bf
-lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/CountSubstitutions.bf
-lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/EffectOfTopology.bf
-lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/ErrorEstimates.bf
-lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LRT.bf
-lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/LocalvsGlobal.bf
-lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NeutralExpectation.bf
-lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/NucleotideBiases.bf
-lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/Phylohandbook.bf
-lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/WhatsInTheMean.bf
-lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/dSdN.bf
-lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/Drosophilia_adh.nex
-lib/hyphy/TemplateBatchFiles/Miscellaneous/phylohandbook/datasets/H5N1_HA_5.nex
-lib/hyphy/TemplateBatchFiles/ModelTest.bf
-lib/hyphy/TemplateBatchFiles/MolClockAllRoots.bf
-lib/hyphy/TemplateBatchFiles/MolecularClock.bf
-lib/hyphy/TemplateBatchFiles/NeighborJoining.bf
-lib/hyphy/TemplateBatchFiles/NielsenYang.bf
-lib/hyphy/TemplateBatchFiles/NucModelCompare.bf
-lib/hyphy/TemplateBatchFiles/PARRIS.bf
-lib/hyphy/TemplateBatchFiles/PairwiseRelativeRate.bf
-lib/hyphy/TemplateBatchFiles/PairwiseRelativeRatio.bf
-lib/hyphy/TemplateBatchFiles/PartitionDataFile.bf
-lib/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit.bf
-lib/hyphy/TemplateBatchFiles/ProteinAnalyses/ProteinGTRFit_helper.ibf
-lib/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md
-lib/hyphy/TemplateBatchFiles/ProteinAnalyses/plusF_helper.ibf
-lib/hyphy/TemplateBatchFiles/ProteinAnalyses/relative_prot_rates.bf
-lib/hyphy/TemplateBatchFiles/ReduceDataSetMatrix.bf
-lib/hyphy/TemplateBatchFiles/RelativeRate.bf
-lib/hyphy/TemplateBatchFiles/RelativeRatio.bf
-lib/hyphy/TemplateBatchFiles/SGASimProcessor.bf
-lib/hyphy/TemplateBatchFiles/SGEmulator.bf
-lib/hyphy/TemplateBatchFiles/SGEmulator_MF.bf
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-lib/hyphy/TemplateBatchFiles/Samplers/lhc-ErrorEst.bf
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-lib/hyphy/TemplateBatchFiles/Samplers/lhc_supp.ibf
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-lib/hyphy/TemplateBatchFiles/SeqAlignmentCodon.bf
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-lib/hyphy/TemplateBatchFiles/SeqAlignmentNucShared.ibf
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-lib/hyphy/TemplateBatchFiles/SequentialAddition.ibf
-lib/hyphy/TemplateBatchFiles/SimilarityPlot.bf
-lib/hyphy/TemplateBatchFiles/SimmondsAI.bf
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-lib/hyphy/TemplateBatchFiles/TemplateModels/CF3x4.bf
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-lib/hyphy/TemplateBatchFiles/TemplateModels/Custom_AA_empirical.mdl
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-lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F.mdl
-lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+F3x4.mdl
-lib/hyphy/TemplateBatchFiles/TemplateModels/ECM+MLFREQS.mdl
-lib/hyphy/TemplateBatchFiles/TemplateModels/ECM.mdl
-lib/hyphy/TemplateBatchFiles/TemplateModels/EIAA.mdl
-lib/hyphy/TemplateBatchFiles/TemplateModels/EIAAFreq.mdl
-lib/hyphy/TemplateBatchFiles/TemplateModels/EX.dat
-lib/hyphy/TemplateBatchFiles/TemplateModels/EX.mdl
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-lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/H5N1
-lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVBetween
-lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/HIVWithin
-lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/IAV
-lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/JTT
-lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LCAP
-lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/LG
-lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/MtArt
-lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/VT
-lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/WAG
-lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/cpREV
-lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/modellist.ibf
-lib/hyphy/TemplateBatchFiles/TemplateModels/EmpiricalAA/mtMAM
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-lib/hyphy/TemplateBatchFiles/TemplateModels/F84P.mdl
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-lib/hyphy/TemplateBatchFiles/TemplateModels/GY94.mdl
-lib/hyphy/TemplateBatchFiles/TemplateModels/GY94customF3x4.mdl
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-lib/hyphy/TemplateBatchFiles/TemplateModels/HIVbetween+F.mdl
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