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 28F7A138334 for ; Tue, 19 Feb 2019 11:24:32 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 1E054E0864; Tue, 19 Feb 2019 11:24:31 +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 D0381E0864 for ; Tue, 19 Feb 2019 11:24:30 +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 B056F335CF2 for ; Tue, 19 Feb 2019 11:24:28 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 2A36C4FF for ; Tue, 19 Feb 2019 11:24:27 +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: <1550575458.51f9e3636c1422b40200dcc11c4122f356cfe4de.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/bowtie/bowtie-9999.ebuild X-VCS-Directories: sci-biology/bowtie/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 51f9e3636c1422b40200dcc11c4122f356cfe4de X-VCS-Branch: master Date: Tue, 19 Feb 2019 11:24:27 +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-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 71278e4c-3e1a-4e3d-945b-1861c273f669 X-Archives-Hash: 3fc04f2e45edb3a4304feb1b7f7e01bc commit: 51f9e3636c1422b40200dcc11c4122f356cfe4de Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Tue Feb 19 11:24:18 2019 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Feb 19 11:24:18 2019 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=51f9e363 sci-biology/bowtie: removing -9999 ebuild Package-Manager: Portage-2.3.61, Repoman-2.3.12 Signed-off-by: Martin Mokrejs fold.natur.cuni.cz> sci-biology/bowtie/bowtie-9999.ebuild | 81 ----------------------------------- 1 file changed, 81 deletions(-) diff --git a/sci-biology/bowtie/bowtie-9999.ebuild b/sci-biology/bowtie/bowtie-9999.ebuild deleted file mode 100644 index d54d0a544..000000000 --- a/sci-biology/bowtie/bowtie-9999.ebuild +++ /dev/null @@ -1,81 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit flag-o-matic toolchain-funcs git-r3 - -DESCRIPTION="Popular short read aligner for Next-generation sequencing data" -HOMEPAGE="http://bowtie-bio.sourceforge.net/" -EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git" -EGIT_BRANCH="bug_fixes" - -LICENSE="Artistic" -SLOT="1" -KEYWORDS="" - -IUSE="examples +tbb" - -RDEPEND="tbb? ( dev-cpp/tbb )" -DEPEND="${RDEPEND} - sci-biology/seqan:1.4 - app-arch/unzip" - -DOCS=( AUTHORS NEWS TUTORIAL doc/README ) -HTML_DOCS=( doc/{manual.html,style.css} ) - -PATCHES=( "${FILESDIR}/bowtie-9999-fix-isa-return-type.patch" ) -# not needed -# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b -#PATCHES=( -# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch" -# "${FILESDIR}/${P}-fix-Intel-compilation.patch" -# "${FILESDIR}/${P}-unbundle-seqan.patch" -#) -# other patches to be still considered -# "${FILESDIR}/${P}-fix-setBegin-call.patch" -# "${FILESDIR}/${P}-seqan-popcount.patch" -# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch" -# "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch" -# "${FILESDIR}/${P}-spelling.patch" -# "${FILESDIR}/${P}-tbb-tinythread-missing.patch" -#) - -src_prepare() { - default - - # remove bundled libraries, use system seqan 1.4 - # rm -rf SeqAn-1.1/ third_party/ || die - - # innocuous non-security flags, prevent log pollution - append-cxxflags \ - -Wno-unused-local-typedefs \ - -Wno-unused-but-set-variable \ - -Wno-unused-variable -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CFLAGS="" \ - CXXFLAGS="" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="${CXXFLAGS}" \ - WITH_TBB="$(usex tbb 1 0)" -} - -src_install() { - dobin ${PN} ${PN}-* - - exeinto /usr/libexec/${PN} - doexe scripts/* - - newman MANUAL ${PN}.1 - einstalldocs - - if use examples; then - insinto /usr/share/${PN} - doins -r genomes indexes - fi -}