From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id AD15359CAF for ; Fri, 8 Apr 2016 12:55:27 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 2788321C007; Fri, 8 Apr 2016 12:55:25 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id B9BD821C007 for ; Fri, 8 Apr 2016 12:55:23 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 9844A340C57 for ; Fri, 8 Apr 2016 12:55:22 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 86B7E7F for ; Fri, 8 Apr 2016 12:55:20 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1460119947.fba69b3c82862f7b4673420bbfc4f1e57b6a2971.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/sailfish/files/, sci-biology/sailfish/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/sailfish/files/sailfish-0.9.1-no-boost-static.patch sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch sci-biology/sailfish/sailfish-0.9.1.ebuild sci-biology/sailfish/sailfish-0.9.2.ebuild X-VCS-Directories: sci-biology/sailfish/files/ sci-biology/sailfish/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: fba69b3c82862f7b4673420bbfc4f1e57b6a2971 X-VCS-Branch: master Date: Fri, 8 Apr 2016 12:55:20 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 8b61ce9f-ce9e-45d5-bd68-066c400d8f3d X-Archives-Hash: dd2855a44f5e149ff0000a9e9902443c commit: fba69b3c82862f7b4673420bbfc4f1e57b6a2971 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Fri Apr 8 12:52:27 2016 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Fri Apr 8 12:52:27 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=fba69b3c sci-biology/sailfish: version bump; noted bundled 3rd-party code Package-Manager: portage-2.2.28 ...t-static.patch => sailfish-0.9.2-no-boost-static.patch} | 0 .../{sailfish-0.9.1.ebuild => sailfish-0.9.2.ebuild} | 14 ++++++++++++-- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/sci-biology/sailfish/files/sailfish-0.9.1-no-boost-static.patch b/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch similarity index 100% rename from sci-biology/sailfish/files/sailfish-0.9.1-no-boost-static.patch rename to sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch diff --git a/sci-biology/sailfish/sailfish-0.9.1.ebuild b/sci-biology/sailfish/sailfish-0.9.2.ebuild similarity index 60% rename from sci-biology/sailfish/sailfish-0.9.1.ebuild rename to sci-biology/sailfish/sailfish-0.9.2.ebuild index 8a1b1c0..6350ef6 100644 --- a/sci-biology/sailfish/sailfish-0.9.1.ebuild +++ b/sci-biology/sailfish/sailfish-0.9.2.ebuild @@ -10,17 +10,27 @@ DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads" HOMEPAGE="http://www.cs.cmu.edu/~ckingsf/software/sailfish/" SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" -LICENSE="GPL-3" +LICENSE="GPL-3+" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" -PATCHES=( "${FILESDIR}"/${PN}-0.9.1-no-boost-static.patch ) +PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch ) DEPEND="dev-libs/boost:0 dev-libs/jemalloc dev-cpp/tbb" RDEPEND="${DEPEND}" +# a C++-11 compliant compiler is needs, aka >=gcc-4.7 + +# TODO: disable +# [ 7%] Performing download step (verify and extract) for 'libdivsufsort' +#i +# contains bundled RapMap +# contains bundled libdivsufsort-master +# contains bundled libgff +# contains bundled jellyfish-2.2.3 +# contains bundled sparsehash-sparsehash-2.0.2 src_install() { cmake-utils_src_install