commit: b40760bd69c57dae5c57650ee8507e5ac0d54b1c Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Feb 19 18:41:38 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Feb 19 18:44:39 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b40760bd
sci-biology/emboss: Remove old Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/3937 eclass/emboss-r1.eclass | 134 --------------------------------- sci-biology/emboss/emboss-6.6.0.ebuild | 67 ----------------- 2 files changed, 201 deletions(-) diff --git a/eclass/emboss-r1.eclass b/eclass/emboss-r1.eclass deleted file mode 100644 index 2b58de68a2..0000000000 --- a/eclass/emboss-r1.eclass +++ /dev/null @@ -1,134 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -# @ECLASS: emboss-r1.eclass -# @MAINTAINER: -# [email protected] -# [email protected] -# [email protected] -# @AUTHOR: -# Original author: Author Olivier Fisette <[email protected]> -# Next gen author: Justin Lecher <[email protected]> -# Next gen author: Ted Tanberry <[email protected]> -# @BLURB: Use this to easy install EMBOSS and EMBASSY programs (EMBOSS add-ons). -# @DESCRIPTION: -# The inheriting ebuild must set at least EAPI=5 and provide EBO_DESCRIPTION before the inherit line. -# KEYWORDS should be set. Additionally "(R|P)DEPEND"encies and other standard -# ebuild variables can be extended (FOO+=" bar"). -# -# Example: -# -# EAPI="5" -# -# EBO_DESCRIPTION="applications from the CBS group" -# -# inherit emboss-r1 - -# @ECLASS-VARIABLE: EBO_DESCRIPTION -# @DEFAULT_UNSET -# @DESCRIPTION: -# Should be set. Completes the generic description of the embassy module as follows: -# -# EMBOSS integrated version of ${EBO_DESCRIPTION}, e.g. -# -# "EMBOSS integrated version of applications from the CBS group" -# -# Defaults to the upstream name of the module. - -# @ECLASS-VARIABLE: EBO_EXTRA_ECONF -# @DEFAULT_UNSET -# @DESCRIPTION: -# Extra config options passed to econf. - -case ${EAPI:-0} in - 5) ;; - *) die "this eclass doesn't support < EAPI 5" ;; -esac - -inherit autotools-utils eutils flag-o-matic - -HOMEPAGE="http://emboss.sourceforge.net/"; -LICENSE="LGPL-2 GPL-2" - -SLOT="0" -IUSE="mysql pdf png postgres static-libs X" - -DEPEND=" - dev-libs/expat - dev-libs/libpcre:3 - sci-libs/plplot - sys-libs/zlib - mysql? ( virtual/mysql ) - pdf? ( media-libs/libharu ) - png? ( media-libs/gd[png] ) - postgres? ( dev-db/postgresql:= ) - X? ( x11-libs/libXt )" -RDEPEND="${DEPEND}" - -if [[ ${PN} == embassy-* ]]; then - EMBASSY_PACKAGE=yes - # The EMBASSY package name, retrieved from the inheriting ebuild's name - EN=${PN:8} - # The full name and version of the EMBASSY package (excluding the Gentoo - # revision number) - EF=$(echo ${EN} | tr "[:lower:]" "[:upper:]")-${PV} - : ${EBO_DESCRIPTION:=${EN}} - DESCRIPTION="EMBOSS integrated version of ${EBO_DESCRIPTION}" - SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/${EF}.tar.gz -> embassy-${EN}-${PVR}.tar.gz" - DEPEND+=" >=sci-biology/emboss-6.6.0[mysql=,pdf=,png=,postgres=,static-libs=,X=]" - - S="${WORKDIR}"/${EF} -fi - -# @FUNCTION: emboss-r1_src_prepare -# @DESCRIPTION: -# Does the following things -# -# 1. Renames configure.in to configure.ac, if possible -# 2. Applies ${PATCHES[@]} and runs autotools via autotools-utils.eclass -# - -emboss-r1_src_prepare() { - if [[ -e configure.in ]]; then - mv configure.{in,ac} || die - fi - - autotools-utils_src_prepare -} - -# @FUNCTION: emboss-r1_src_configure -# @DESCRIPTION: -# runs econf with following options. -# -# $(use_with X x) -# $(use_with png pngdriver) -# $(use_with pdf hpdf) -# $(use_with mysql mysql) -# $(use_with postgres postgresql) -# $(use_enable static-libs static) -# --enable-large -# --without-java -# --enable-systemlibs -# ${EBO_EXTRA_ECONF} - -emboss-r1_src_configure() { - local myeconfargs=( - $(use_with X x) - $(use_with png pngdriver "${EPREFIX}/usr") - $(use_with pdf hpdf "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config") - $(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config") - --enable-large - --without-java - --enable-systemlibs - ${EBO_EXTRA_ECONF} - ) - - [[ ${EMBASSY_PACKAGE} == yes ]] && \ - append-cppflags "-I${EPREFIX}/usr/include/emboss" - - autotools-utils_src_configure -} - -EXPORT_FUNCTIONS src_prepare src_configure diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild deleted file mode 100644 index 8b1d211efd..0000000000 --- a/sci-biology/emboss/emboss-6.6.0.ebuild +++ /dev/null @@ -1,67 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -AUTOTOOLS_AUTORECONF=1 - -inherit autotools-utils emboss-r1 eutils readme.gentoo-r1 - -DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"; - -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos" -IUSE+=" minimal" -LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0" - -RDEPEND+="!games-action/xbomber - !sys-devel/cons" -PDEPEND+=" - !minimal? ( - sci-biology/aaindex - sci-biology/cutg - sci-biology/primer3 - sci-biology/prints - sci-biology/prosite - sci-biology/rebase - )" - -S="${WORKDIR}"/EMBOSS-${PV} - -DOCS=( ChangeLog AUTHORS NEWS THANKS FAQ ) - -PATCHES=( - "${FILESDIR}"/${P}_fix-build-system.patch - "${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch - "${FILESDIR}"/${P}_plplot-declarations.patch - "${FILESDIR}"/${P}_qa-implicit-declarations.patch -) - -src_install() { - # Use autotools-utils_* to remove useless *.la files - autotools-utils_src_install - - readme.gentoo_create_doc - - # Install env file for setting libplplot and acd files path. - cat > 22emboss <<- EOF - # ACD files location - EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" - EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data" - EOF - doenvd 22emboss - - # Remove useless dummy files - find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files." - - # Move the provided codon files to a different directory. This will avoid - # user confusion and file collisions on case-insensitive file systems (see - # bug #115446). This change is documented in "README.gentoo". - mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ - die "Failed to move CODON directory." -} - -pkg_postinst() { - readme.gentoo_print_elog -}
