From owner-svn-ports-all@freebsd.org Sat Feb 15 23:09:20 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 B0A9824BDEB; Sat, 15 Feb 2020 23:09:20 +0000 (UTC) (envelope-from jwb@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 48KmCh49R4z4JDH; Sat, 15 Feb 2020 23:09:20 +0000 (UTC) (envelope-from jwb@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 8A7BA1C556; Sat, 15 Feb 2020 23:09:20 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 01FN9KNb025022; Sat, 15 Feb 2020 23:09:20 GMT (envelope-from jwb@FreeBSD.org) Received: (from jwb@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 01FN9Kmk025021; Sat, 15 Feb 2020 23:09:20 GMT (envelope-from jwb@FreeBSD.org) Message-Id: <202002152309.01FN9Kmk025021@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jwb set sender to jwb@FreeBSD.org using -f From: "Jason W. Bacon" Date: Sat, 15 Feb 2020 23:09:20 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r526244 - head/biology/kallisto X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: head/biology/kallisto X-SVN-Commit-Revision: 526244 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, 15 Feb 2020 23:09:20 -0000 Author: jwb Date: Sat Feb 15 23:09:19 2020 New Revision: 526244 URL: https://svnweb.freebsd.org/changeset/ports/526244 Log: biology/kallisto: Upgrade to 0.46.2 Kallisto no longer builds in hdf5 by default, but it is still required for some downstream tools like Sleuth. Forcing it ON for now, but will disable it in a future upgrade. Reported by: portscout Modified: head/biology/kallisto/Makefile head/biology/kallisto/distinfo Modified: head/biology/kallisto/Makefile ============================================================================== --- head/biology/kallisto/Makefile Sat Feb 15 22:34:02 2020 (r526243) +++ head/biology/kallisto/Makefile Sat Feb 15 23:09:19 2020 (r526244) @@ -2,7 +2,7 @@ PORTNAME= kallisto DISTVERSIONPREFIX= v -DISTVERSION= 0.46.1 +DISTVERSION= 0.46.2 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -15,7 +15,7 @@ LIB_DEPENDS= libhdf5.so:science/hdf5 \ libsz.so:science/szip \ libhts.so:biology/htslib -USES= cmake:noninja compiler:c++11-lang +USES= cmake:noninja compiler:c++11-lang localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= pachterlab @@ -25,8 +25,12 @@ PORTEXAMPLES= * PLIST_FILES= bin/kallisto EXAMPLES_PLIST_FILES= bin/kallisto-test +# hdf5 is being phased out and is no longer build in by default, but is still +# required for Sleuth and other downstream tools. Remove this after Sleuth +# et all catch up. +CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON + OPTIONS_DEFINE= EXAMPLES -LDFLAGS+= -L${LOCALBASE}/lib post-install-EXAMPLES-on: ${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin Modified: head/biology/kallisto/distinfo ============================================================================== --- head/biology/kallisto/distinfo Sat Feb 15 22:34:02 2020 (r526243) +++ head/biology/kallisto/distinfo Sat Feb 15 23:09:19 2020 (r526244) @@ -1,3 +1,3 @@ -TIMESTAMP = 1572972210 -SHA256 (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 492ef081395e8858fcd9832aceb8b61c79358f00afb45e6709146c0fb51dd231 -SIZE (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 2254560 +TIMESTAMP = 1581611719 +SHA256 (pachterlab-kallisto-v0.46.2_GH0.tar.gz) = 10bab0c2929d8c345750e02735b305bbbfa89e8a48f42c4b9af44f3d44ff4c82 +SIZE (pachterlab-kallisto-v0.46.2_GH0.tar.gz) = 2693857