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 676F1138A1A for ; Wed, 18 Feb 2015 16:41:34 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 4E03DE0973; Wed, 18 Feb 2015 16:41:27 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 38547E0973 for ; Wed, 18 Feb 2015 16:41:26 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id F077E3408AE for ; Wed, 18 Feb 2015 16:41:24 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id A2D6A12094 for ; Wed, 18 Feb 2015 16:41:23 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1424265685.f2888f2e2f6610f9876bb14d112f8fdcb696248a.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/discrover/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/discrover/ChangeLog sci-biology/discrover/discrover-1.5.2.ebuild sci-biology/discrover/discrover-9999.ebuild sci-biology/discrover/metadata.xml X-VCS-Directories: sci-biology/discrover/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: f2888f2e2f6610f9876bb14d112f8fdcb696248a X-VCS-Branch: master Date: Wed, 18 Feb 2015 16:41:23 +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: afcb5d6a-b4ae-4123-9726-6a31dd85d73b X-Archives-Hash: f10d66f384b1572ad8df1cd424bb2071 commit: f2888f2e2f6610f9876bb14d112f8fdcb696248a Author: Justin Lecher gentoo org> AuthorDate: Wed Feb 18 13:21:25 2015 +0000 Commit: Justin Lecher gentoo org> CommitDate: Wed Feb 18 13:21:25 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f2888f2e sci-biology/discrover: fix SLOT operators; correct ruby deps Package-Manager: portage-2.2.17 --- sci-biology/discrover/ChangeLog | 4 ++++ sci-biology/discrover/discrover-1.5.2.ebuild | 28 +++++++++++++++------------ sci-biology/discrover/discrover-9999.ebuild | 29 ++++++++++++++++------------ sci-biology/discrover/metadata.xml | 24 +++++++++++------------ 4 files changed, 49 insertions(+), 36 deletions(-) diff --git a/sci-biology/discrover/ChangeLog b/sci-biology/discrover/ChangeLog index fd6eb45..aba75b4 100644 --- a/sci-biology/discrover/ChangeLog +++ b/sci-biology/discrover/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 18 Feb 2015; Justin Lecher discrover-1.5.2.ebuild, + discrover-9999.ebuild, metadata.xml: + sci-biology/discrover: fix SLOT operators; correct ruby deps + *discrover-1.5.2 (27 Jan 2015) 27 Jan 2015; Jonas Maaskola +discrover-1.5.2.ebuild, diff --git a/sci-biology/discrover/discrover-1.5.2.ebuild b/sci-biology/discrover/discrover-1.5.2.ebuild index b17687e..f0992e2 100644 --- a/sci-biology/discrover/discrover-1.5.2.ebuild +++ b/sci-biology/discrover/discrover-1.5.2.ebuild @@ -3,7 +3,11 @@ # $Header: $ EAPI=5 -inherit cmake-utils + +USE_RUBY="ruby19" +RUBY_OPTIONAL=yes + +inherit cmake-utils ruby-fakegem DESCRIPTION="A sequence motif discovery tool that uses discriminative learning" HOMEPAGE="https://github.com/maaskola/discrover" @@ -19,14 +23,14 @@ RDEPEND=" cairo? ( x11-libs/cairo ) dreme? ( sci-biology/meme ) tikzlogo? ( - dev-lang/ruby + $(ruby_implementations_depend) dev-texlive/texlive-latex dev-texlive/texlive-latexextra dev-tex/pgf dev-tex/xcolor media-gfx/imagemagick ) - misc_scripts? ( dev-lang/ruby ) + misc_scripts? ( $(ruby_implementations_depend) ) rmathlib? ( dev-lang/R ) tcmalloc? ( dev-util/google-perftools ) " @@ -37,7 +41,7 @@ DEPEND="${RDEPEND} dev-texlive/texlive-latexrecommended media-gfx/imagemagick ) - lto? ( >=sys-devel/gcc-4.8 ) + lto? ( >=sys-devel/gcc-4.8:* ) " pkg_pretend() { if use lto; then @@ -64,25 +68,25 @@ src_configure() { unset R_HOME if use rmathlib ; then - elog + echo elog "Using statistical routines from standalone Rmathlib." - elog + echo fi if use dreme ; then - elog + echo elog "Linking to DREME from the MEME suite." - elog + echo else - elog + echo elog "Not linking to DREME from the MEME suite (sci-biology/meme)." elog "You will not be able to use DREME to find seeds." - elog + echo fi if use doc ; then - elog + echo elog "User manual available at /usr/share/doc/discrover/discrover-manual.pdf" - elog + echo fi cmake-utils_src_configure diff --git a/sci-biology/discrover/discrover-9999.ebuild b/sci-biology/discrover/discrover-9999.ebuild index 34ce8c0..8131e9b 100644 --- a/sci-biology/discrover/discrover-9999.ebuild +++ b/sci-biology/discrover/discrover-9999.ebuild @@ -3,10 +3,15 @@ # $Header: $ EAPI=5 -inherit cmake-utils git-r3 + +USE_RUBY="ruby19" +RUBY_OPTIONAL=yes + +inherit cmake-utils git-r3 ruby-fakegem DESCRIPTION="A sequence motif discovery tool that uses discriminative learning" HOMEPAGE="https://github.com/maaskola/discrover" +SRC_URI="" EGIT_REPO_URI="https://github.com/maaskola/${PN}" LICENSE="GPL-3+" @@ -19,14 +24,14 @@ RDEPEND=" cairo? ( x11-libs/cairo ) dreme? ( sci-biology/meme ) tikzlogo? ( - dev-lang/ruby + $(ruby_implementations_depend) dev-texlive/texlive-latex dev-texlive/texlive-latexextra dev-tex/pgf dev-tex/xcolor media-gfx/imagemagick ) - misc_scripts? ( dev-lang/ruby ) + misc_scripts? ( $(ruby_implementations_depend) ) rmathlib? ( dev-lang/R ) tcmalloc? ( dev-util/google-perftools ) " @@ -37,7 +42,7 @@ DEPEND="${RDEPEND} dev-texlive/texlive-latexrecommended media-gfx/imagemagick ) - lto? ( >=sys-devel/gcc-4.8 ) + lto? ( >=sys-devel/gcc-4.8:* ) " pkg_pretend() { if use lto; then @@ -64,25 +69,25 @@ src_configure() { unset R_HOME if use rmathlib ; then - elog + echo elog "Using statistical routines from standalone Rmathlib." - elog + echo fi if use dreme ; then - elog + echo elog "Linking to DREME from the MEME suite." - elog + echo else - elog + echo elog "Not linking to DREME from the MEME suite (sci-biology/meme)." elog "You will not be able to use DREME to find seeds." - elog + echo fi if use doc ; then - elog + echo elog "User manual available at /usr/share/doc/discrover/discrover-manual.pdf" - elog + echo fi cmake-utils_src_configure diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml index 0862889..6bfaf6c 100644 --- a/sci-biology/discrover/metadata.xml +++ b/sci-biology/discrover/metadata.xml @@ -1,28 +1,28 @@ - - jonas@maaskola.de - Jonas Maaskola - - - + + jonas@maaskola.de + Jonas Maaskola + + + Use Cairo for sequence logo plotting capabilities - + Enable usage of DREME from the MEME package for seeding - + Compile with link-time optimization (LTO) - + Enable LaTeX/TikZ based ruby script for sequence logo drawing - + Install miscellaneous scripts, e.g. for sequence length statistics - + Link to the standalone Rmathlib for statistical routines - +