From owner-svn-ports-all@freebsd.org Mon Jan 13 04:06:15 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 0B4801F5BB6; Mon, 13 Jan 2020 04:06:15 +0000 (UTC) (envelope-from yuri@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 47x0Py6Wlmz3xv4; Mon, 13 Jan 2020 04:06:14 +0000 (UTC) (envelope-from yuri@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 DAFA8269F4; Mon, 13 Jan 2020 04:06:14 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 00D46EAh086165; Mon, 13 Jan 2020 04:06:14 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 00D46ELm086163; Mon, 13 Jan 2020 04:06:14 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <202001130406.00D46ELm086163@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Mon, 13 Jan 2020 04:06:14 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r522851 - head/biology/abyss X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: head/biology/abyss X-SVN-Commit-Revision: 522851 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: Mon, 13 Jan 2020 04:06:15 -0000 Author: yuri Date: Mon Jan 13 04:06:14 2020 New Revision: 522851 URL: https://svnweb.freebsd.org/changeset/ports/522851 Log: biology/abyss: Update 2.1.5 -> 2.2.3 Reported by: portscout Modified: head/biology/abyss/Makefile head/biology/abyss/distinfo head/biology/abyss/pkg-plist Modified: head/biology/abyss/Makefile ============================================================================== --- head/biology/abyss/Makefile Mon Jan 13 03:32:40 2020 (r522850) +++ head/biology/abyss/Makefile Mon Jan 13 04:06:14 2020 (r522851) @@ -1,14 +1,9 @@ # $FreeBSD$ PORTNAME= abyss -DISTVERSION= 2.1.5 -PORTREVISION= 6 +DISTVERSION= 2.2.3 CATEGORIES= biology -MASTER_SITES= http://www.bcgsc.ca/platform/bioinfo/software/${PORTNAME}/releases/${DISTVERSION}/ -PATCH_SITES= https://github.com/bcgsc/${PORTNAME}/commit/ -PATCHFILES= 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch:-p1 - MAINTAINER= yuri@FreeBSD.org COMMENT= Assembly By Short Sequences: parallel, paired-end sequence assembler @@ -24,11 +19,13 @@ LIB_DEPENDS= libffi.so:devel/libffi \ RUN_DEPENDS= bash:shells/bash \ gmake:devel/gmake -USES= compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite -SHEBANG_FILES= bin/${PORTNAME}-* +USES= autoreconf compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite +SHEBANG_FILES= bin/${PORTNAME}-* DataBase/abyss-db-txt SHEBANG_LANG= make make_OLD_CMD= /usr/bin/make make_CMD= ${PREFIX}/bin/gmake +USE_GITHUB= yes +GH_ACCOUNT= bcgsc GNU_CONFIGURE= yes CONFIGURE_ARGS= --without-sparsehash # configure fails to find std::hash, reported to the ML: https://groups.google.com/forum/#!topic/trans-abyss/SZDBKR5bKxs Modified: head/biology/abyss/distinfo ============================================================================== --- head/biology/abyss/distinfo Mon Jan 13 03:32:40 2020 (r522850) +++ head/biology/abyss/distinfo Mon Jan 13 04:06:14 2020 (r522851) @@ -1,5 +1,3 @@ -TIMESTAMP = 1561103807 -SHA256 (abyss-2.1.5.tar.gz) = 65bfc8241e6ff5adf7601ae4ae93a75e3db86d6bff5d593c75aaff7f0ef41757 -SIZE (abyss-2.1.5.tar.gz) = 1201318 -SHA256 (25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch) = 93ad66c42610c4fba8cfbe256a2ab689bf4a76974c3b97a9e1094863614ad934 -SIZE (25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch) = 1701 +TIMESTAMP = 1578886491 +SHA256 (bcgsc-abyss-2.2.3_GH0.tar.gz) = c7b93290b2ccffcf2f3ca42262621c636108f6dbc21f5684ebeeb4f682200675 +SIZE (bcgsc-abyss-2.2.3_GH0.tar.gz) = 1203318 Modified: head/biology/abyss/pkg-plist ============================================================================== --- head/biology/abyss/pkg-plist Mon Jan 13 03:32:40 2020 (r522850) +++ head/biology/abyss/pkg-plist Mon Jan 13 04:06:14 2020 (r522851) @@ -45,7 +45,6 @@ bin/abyss-overlap bin/abyss-paired-dbg bin/abyss-pe bin/abyss-samtoafg -bin/abyss-samtobreak bin/abyss-scaffold bin/abyss-sealer bin/abyss-stack-size