[gentoo-commits] proj/sci:master commit in: sci-biology/discrover/

[Horea Christian]

commit:     0a98a3bfa820bf8ffd6d9258daa3a3469f15427a
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 04:31:16 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 04:31:16 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0a98a3bf

sci-biology/discrover: removed deprecated package

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/discrover/discrover-1.6.0.ebuild | 78 ---------------------------
 sci-biology/discrover/discrover-9999.ebuild  | 79 ----------------------------
 sci-biology/discrover/metadata.xml           | 28 ----------
 3 files changed, 185 deletions(-)

diff --git a/sci-biology/discrover/discrover-1.6.0.ebuild b/sci-biology/discrover/discrover-1.6.0.ebuild
deleted file mode 100644
index 5840283fd..000000000
--- a/sci-biology/discrover/discrover-1.6.0.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit cmake-utils
-
-DESCRIPTION="A sequence motif discovery tool that uses discriminative learning"
-HOMEPAGE="https://github.com/maaskola/discrover"
-SRC_URI="https://github.com/maaskola/discrover/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+cairo dreme doc +lto misc_scripts +rmathlib tcmalloc"
-
-RDEPEND="
-	dev-libs/boost
-	cairo? ( x11-libs/cairo )
-	dreme? ( sci-biology/meme )
-	rmathlib? ( dev-lang/R )
-	tcmalloc? ( dev-util/google-perftools )
-"
-DEPEND="${RDEPEND}
-	doc? (
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		dev-texlive/texlive-latexrecommended
-		media-gfx/imagemagick
-	)
-	lto? ( >=sys-devel/gcc-4.8:* )
-"
-pkg_pretend() {
-	if use lto; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 8 ]] ) ; then
-			eerror "Compilation with link-time optimization and GCC older than 4.8 is not supported."
-			eerror "Please either disable the USE flag 'lto' or use >=sys-devel/gcc-4.8."
-			die "Compiling with USE flag 'lto' is not supported with <sys-devel/gcc-4.8."
-		fi
-	fi
-}
-src_configure() {
-	local mycmakeargs=(
-		$(cmake-utils_use_with cairo CAIRO)
-		$(cmake-utils_use_with dreme DREME)
-		$(cmake-utils_use_with doc DOC)
-		$(cmake-utils_use_with lto LTO)
-		$(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
-		$(cmake-utils_use_with rmathlib RMATHLIB)
-		$(cmake-utils_use_with tcmalloc TCMALLOC)
-		-DDOC_DIR="${EPREFIX}${PREFIX}/share/doc/${PF}"
-	)
-
-	unset R_HOME
-
-	if use rmathlib ; then
-		echo
-		elog "Using statistical routines from standalone Rmathlib."
-		echo
-	fi
-	if use dreme ; then
-		echo
-		elog "Linking to DREME from the MEME suite."
-		echo
-	else
-		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."
-		echo
-	fi
-
-	if use doc ; then
-		echo
-		elog "User manual available at /usr/share/doc/discrover/discrover-manual.pdf"
-		echo
-	fi
-
-	cmake-utils_src_configure
-}

diff --git a/sci-biology/discrover/discrover-9999.ebuild b/sci-biology/discrover/discrover-9999.ebuild
deleted file mode 100644
index 627f32059..000000000
--- a/sci-biology/discrover/discrover-9999.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-inherit cmake-utils git-r3
-
-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/${PN}"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="+cairo dreme doc +lto misc_scripts +rmathlib tcmalloc"
-
-RDEPEND="
-	dev-libs/boost
-	cairo? ( x11-libs/cairo )
-	dreme? ( sci-biology/meme )
-	rmathlib? ( dev-lang/R )
-	tcmalloc? ( dev-util/google-perftools )
-"
-DEPEND="${RDEPEND}
-	doc? (
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		dev-texlive/texlive-latexrecommended
-		media-gfx/imagemagick
-	)
-	lto? ( >=sys-devel/gcc-4.8:* )
-"
-pkg_pretend() {
-	if use lto; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 8 ]] ) ; then
-			eerror "Compilation with link-time optimization and GCC older than 4.8 is not supported."
-			eerror "Please either disable the USE flag 'lto' or use >=sys-devel/gcc-4.8."
-			die "Compiling with USE flag 'lto' is not supported with <sys-devel/gcc-4.8."
-		fi
-	fi
-}
-src_configure() {
-	local mycmakeargs=(
-		$(cmake-utils_use_with cairo CAIRO)
-		$(cmake-utils_use_with dreme DREME)
-		$(cmake-utils_use_with doc DOC)
-		$(cmake-utils_use_with lto LTO)
-		$(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
-		$(cmake-utils_use_with rmathlib RMATHLIB)
-		$(cmake-utils_use_with tcmalloc TCMALLOC)
-		-DDOC_DIR="${EPREFIX}${PREFIX}/share/doc/${PF}"
-	)
-
-	unset R_HOME
-
-	if use rmathlib ; then
-		echo
-		elog "Using statistical routines from standalone Rmathlib."
-		echo
-	fi
-	if use dreme ; then
-		echo
-		elog "Linking to DREME from the MEME suite."
-		echo
-	else
-		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."
-		echo
-	fi
-
-	if use doc ; then
-		echo
-		elog "User manual available at /usr/share/doc/discrover/discrover-manual.pdf"
-		echo
-	fi
-
-	cmake-utils_src_configure
-}

diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml
deleted file mode 100644
index 6f5916ea8..000000000
--- a/sci-biology/discrover/metadata.xml
+++ /dev/null
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jonas@××××××××.de</email>
-		<name>Jonas Maaskola</name>
-	</maintainer>
-	<use>
-		<flag name="cairo">
-Use Cairo for sequence logo plotting capabilities
-</flag>
-		<flag name="dreme">
-Enable usage of DREME from the MEME package for seeding
-</flag>
-		<flag name="lto">
-Compile with link-time optimization (LTO)
-</flag>
-		<flag name="misc_scripts">
-Install miscellaneous scripts
-</flag>
-		<flag name="rmathlib">
-Link to the standalone Rmathlib for statistical routines
-</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">maaskola/discrover</remote-id>
-	</upstream>
-</pkgmetadata>