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>jo...@maaskola.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>
