From owner-svn-ports-all@freebsd.org Sat Mar 28 12:27:22 2020 Return-Path: Delivered-To: svn-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 77AF027AC2F; Sat, 28 Mar 2020 12:27:22 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 48qHzZ0mcwz4888; Sat, 28 Mar 2020 12:27:21 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 29BB6C884; Sat, 28 Mar 2020 12:27:12 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 02SCRBCt076514; Sat, 28 Mar 2020 12:27:11 GMT (envelope-from jrm@FreeBSD.org) Received: (from jrm@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 02SCRBhg076512; Sat, 28 Mar 2020 12:27:11 GMT (envelope-from jrm@FreeBSD.org) Message-Id: <202003281227.02SCRBhg076512@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jrm set sender to jrm@FreeBSD.org using -f From: Joseph Mingrone Date: Sat, 28 Mar 2020 12:27:11 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r529331 - head/biology/hyphy X-SVN-Group: ports-head X-SVN-Commit-Author: jrm X-SVN-Commit-Paths: head/biology/hyphy X-SVN-Commit-Revision: 529331 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 28 Mar 2020 12:27:22 -0000 Author: jrm Date: Sat Mar 28 12:27:11 2020 New Revision: 529331 URL: https://svnweb.freebsd.org/changeset/ports/529331 Log: biology/hyphy: Update to version 2.5.8 Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.8 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 Mar 28 12:22:18 2020 (r529330) +++ head/biology/hyphy/Makefile Sat Mar 28 12:27:11 2020 (r529331) @@ -1,7 +1,7 @@ # $FreeBSD$ PORTNAME= hyphy -DISTVERSION= 2.5.7 +DISTVERSION= 2.5.8 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org Modified: head/biology/hyphy/distinfo ============================================================================== --- head/biology/hyphy/distinfo Sat Mar 28 12:22:18 2020 (r529330) +++ head/biology/hyphy/distinfo Sat Mar 28 12:27:11 2020 (r529331) @@ -1,3 +1,3 @@ -TIMESTAMP = 1584664580 -SHA256 (veg-hyphy-2.5.7_GH0.tar.gz) = fdcbad1f2f2c7fc83f5f7cec464aedf1114d68b84a34a65b59caeb462b631caf -SIZE (veg-hyphy-2.5.7_GH0.tar.gz) = 6081964 +TIMESTAMP = 1585349961 +SHA256 (veg-hyphy-2.5.8_GH0.tar.gz) = df528ba5cd86071017a005ae9a7cd76f8d35b7270e62840ae5fc4231092ac9b8 +SIZE (veg-hyphy-2.5.8_GH0.tar.gz) = 6093096 Modified: head/biology/hyphy/pkg-plist ============================================================================== --- head/biology/hyphy/pkg-plist Sat Mar 28 12:22:18 2020 (r529330) +++ head/biology/hyphy/pkg-plist Sat Mar 28 12:27:11 2020 (r529331) @@ -1,5 +1,4 @@ bin/hyphy -lib/hyphy/TemplateBatchFiles/simpleBootstrap.bf lib/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod lib/hyphy/GeneticCodes/Ascidian_mtDNA.cod lib/hyphy/GeneticCodes/Blepharisma_Nuclear.cod @@ -181,6 +180,7 @@ lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL-con lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FEL.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/MEME.bf +lib/hyphy/TemplateBatchFiles/SelectionAnalyses/PRIME.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX-SRV.bf lib/hyphy/TemplateBatchFiles/SelectionAnalyses/RELAX.bf @@ -385,6 +385,7 @@ lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf lib/hyphy/TemplateBatchFiles/libv3/models/codon/BS_REL.bf lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_MH.bf +lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV_TRIP.bf lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf @@ -427,6 +428,7 @@ lib/hyphy/TemplateBatchFiles/relative_nucleotide_rates lib/hyphy/TemplateBatchFiles/relrateBootstrap.bf lib/hyphy/TemplateBatchFiles/relratioBootstrap.bf lib/hyphy/TemplateBatchFiles/selectModelParameters.bf +lib/hyphy/TemplateBatchFiles/simpleBootstrap.bf lib/hyphy/data/brown.nuc lib/hyphy/data/integrase_BDA.nex lib/hyphy/data/p51.aa