From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id A358D138334 for ; Sun, 24 Jun 2018 14:01:34 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id AE650E0898; Sun, 24 Jun 2018 14:01:33 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 70097E0898 for ; Sun, 24 Jun 2018 14:01:32 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 6CE6B335C89 for ; Sun, 24 Jun 2018 14:01:31 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 20E6E2E2 for ; Sun, 24 Jun 2018 14:01:30 +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: <1529848872.a1d0487c37ba900c1f239f5d73f7d429f018359d.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/salmon/salmon-0.10.2.ebuild sci-biology/salmon/salmon-0.3.2.ebuild sci-biology/salmon/salmon-0.4.2.ebuild sci-biology/salmon/salmon-0.5.0.ebuild sci-biology/salmon/salmon-9999.ebuild X-VCS-Directories: sci-biology/salmon/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: a1d0487c37ba900c1f239f5d73f7d429f018359d X-VCS-Branch: master Date: Sun, 24 Jun 2018 14:01:30 +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: 6a5e6d35-8968-44d5-b679-7be274209f51 X-Archives-Hash: 765bc9900921ae51767092c91a2434c5 commit: a1d0487c37ba900c1f239f5d73f7d429f018359d Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Sun Jun 24 14:01:12 2018 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Jun 24 14:01:12 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a1d0487c sci-biology/salmon: version bump, attempts to get boost picked up cmake does not detect boost for me although the errors speak of pthread and not boost. Older version could probably be dropped soon. Package-Manager: Portage-2.3.40, Repoman-2.3.9 .../salmon/{salmon-0.3.2.ebuild => salmon-0.10.2.ebuild} | 4 +--- sci-biology/salmon/salmon-0.3.2.ebuild | 2 +- sci-biology/salmon/salmon-0.4.2.ebuild | 2 +- sci-biology/salmon/salmon-0.5.0.ebuild | 2 +- sci-biology/salmon/salmon-9999.ebuild | 10 +++++----- 5 files changed, 9 insertions(+), 11 deletions(-) diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild similarity index 85% copy from sci-biology/salmon/salmon-0.3.2.ebuild copy to sci-biology/salmon/salmon-0.10.2.ebuild index 6f5be90fb..34a425403 100644 --- a/sci-biology/salmon/salmon-0.3.2.ebuild +++ b/sci-biology/salmon/salmon-0.10.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2018 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -14,8 +14,6 @@ SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" -PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch ) - DEPEND="dev-libs/boost:0 dev-libs/jemalloc dev-cpp/tbb" diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.3.2.ebuild index 6f5be90fb..b9a50ebd1 100644 --- a/sci-biology/salmon/salmon-0.3.2.ebuild +++ b/sci-biology/salmon/salmon-0.3.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2018 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 diff --git a/sci-biology/salmon/salmon-0.4.2.ebuild b/sci-biology/salmon/salmon-0.4.2.ebuild index f88310f95..42ccf1e6c 100644 --- a/sci-biology/salmon/salmon-0.4.2.ebuild +++ b/sci-biology/salmon/salmon-0.4.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2018 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 diff --git a/sci-biology/salmon/salmon-0.5.0.ebuild b/sci-biology/salmon/salmon-0.5.0.ebuild index f88310f95..42ccf1e6c 100644 --- a/sci-biology/salmon/salmon-0.5.0.ebuild +++ b/sci-biology/salmon/salmon-0.5.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2018 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild index 4f48644c6..d370710b6 100644 --- a/sci-biology/salmon/salmon-9999.ebuild +++ b/sci-biology/salmon/salmon-9999.ebuild @@ -3,11 +3,10 @@ EAPI=6 -inherit cmake-utils git-r3 +inherit multilib cmake-utils git-r3 DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" HOMEPAGE="https://github.com/COMBINE-lab/salmon" -SRC_URI="" EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git" LICENSE="GPL-3" @@ -24,7 +23,7 @@ RDEPEND="${DEPEND}" # https://github.com/gabime/spdlog # https://github.com/efficient/libcuckoo # https://github.com/greg7mdp/sparsepp -# https://github.com/COMBINE-lab/RapMap +# https://github.com/COMBINE-lab/RapMap , actually runs curl to fetch it # https://github.com/Kingsford-Group/libgff # sci-libs/io_lib # @@ -35,11 +34,12 @@ RDEPEND="${DEPEND}" src_configure(){ local mycmakeargs=( - "-DBOOST_ROOT=${EPREFIX}/usr" + "-DBOOST_INCLUDEDIR=${EPREFIX}/usr/include/" + "-DBOOST_LIBRARYDIR=${EPREFIX}/usr/$(get_libdir)/" "-DTBB_INSTALL_DIR=${EPREFIX}/usr" "-DCMAKE_INSTALL_PREFIX=${EPREFIX}/usr" ) - # BUG: the configure step run automatically curl download of 3rd-party stuff + # BUG: the configure step runs automatically curl download of 3rd-party stuff # https://github.com/COMBINE-lab/salmon/issues/19 cmake-utils_src_configure }