sci-biology/mafft: Drop old; Bump version

(Portage version: 2.2.0_alpha186/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)

10 files changed, 10 insertions, 412 deletions

diff --git a/sci-biology/mafft/ChangeLog b/sci-biology/mafft/ChangeLog
index cabb62ab804a..c4cbac384ba2 100644
--- a/sci-biology/mafft/ChangeLog
+++ b/sci-biology/mafft/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/mafft
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.18 2013/06/24 09:53:38 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.19 2013/07/03 07:17:58 jlec Exp $
+
+*mafft-7.050 (03 Jul 2013)
+
+  03 Jul 2013; Justin Lecher <jlec@gentoo.org> -mafft-6.240-r1.ebuild,
+  -mafft-6.707.ebuild, -mafft-6.811.ebuild, -mafft-7.037.ebuild,
+  -mafft-7.040.ebuild, -mafft-7.043.ebuild, -mafft-7.045.ebuild,
+  -mafft-7.046.ebuild, -mafft-7.047.ebuild, +mafft-7.050.ebuild:
+  Drop old; Bump version
 
 *mafft-7.047 (24 Jun 2013)
 
diff --git a/sci-biology/mafft/mafft-6.240-r1.ebuild b/sci-biology/mafft/mafft-6.240-r1.ebuild
deleted file mode 100644
index 781407badf3b..000000000000
--- a/sci-biology/mafft/mafft-6.240-r1.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-6.240-r1.ebuild,v 1.4 2010/06/24 19:30:59 jlec Exp $
-
-inherit toolchain-funcs multilib eutils
-
-DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="http://align.bmr.kyushu-u.ac.jp/mafft/software/"
-SRC_URI="http://align.bmr.kyushu-u.ac.jp/mafft/software/${P}-src.tgz"
-LICENSE="free-noncomm"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${P}-mktemp.patch
-	sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
-}
-
-src_compile() {
-	cd src
-	emake \
-		PREFIX="/usr/$(get_libdir)/${PN}" \
-		CC="$(tc-getCC)" \
-		CFLAG="${CFLAGS}" \
-		|| die "make failed"
-}
-
-src_install() {
-	pushd src
-	emake PREFIX="${D}usr/$(get_libdir)/${PN}" install || die "install failed"
-	popd
-	dodoc readme || die
-}
diff --git a/sci-biology/mafft/mafft-6.707.ebuild b/sci-biology/mafft/mafft-6.707.ebuild
deleted file mode 100644
index eb4dcb75ad2a..000000000000
--- a/sci-biology/mafft/mafft-6.707.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-6.707.ebuild,v 1.2 2010/06/24 19:30:59 jlec Exp $
-
-inherit toolchain-funcs multilib eutils
-
-EXTENSIONS="-without-extensions"
-
-DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="http://align.bmr.kyushu-u.ac.jp/mafft/software/"
-SRC_URI="http://align.bmr.kyushu-u.ac.jp/mafft/software/${P}${EXTENSIONS}-src.tgz"
-LICENSE="free-noncomm"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-RDEPEND=""
-DEPEND="${RDEPEND}"
-S=${WORKDIR}/${P}${EXTENSIONS}
-
-src_unpack() {
-	unpack ${A}
-	sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
-}
-
-src_compile() {
-	pushd core
-	emake \
-		PREFIX=/usr \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS}" \
-		|| die "make failed"
-	popd
-}
-
-src_install() {
-	pushd core
-	emake PREFIX="${D}usr" install || die "install failed"
-	popd
-	dodoc readme || die
-}
diff --git a/sci-biology/mafft/mafft-6.811.ebuild b/sci-biology/mafft/mafft-6.811.ebuild
deleted file mode 100644
index 21d8a4f299e3..000000000000
--- a/sci-biology/mafft/mafft-6.811.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-6.811.ebuild,v 1.3 2011/11/21 15:30:19 jlec Exp $
-
-EAPI="3"
-
-inherit eutils flag-o-matic multilib toolchain-funcs
-
-EXTENSIONS="-without-extensions"
-
-DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
-
-LICENSE="free-noncomm"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos ~x86-macos"
-IUSE="threads"
-
-S="${WORKDIR}"/${P}${EXTENSIONS}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-respect.patch
-	use threads && append-flags -Denablemultithread
-	sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile
-	sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
-}
-
-src_compile() {
-	pushd core
-	emake \
-		PREFIX="${EPREFIX}"/usr \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS}" \
-		|| die "make failed"
-	popd
-}
-
-src_install() {
-	pushd core
-	emake PREFIX="${ED}usr" install || die "install failed"
-	popd
-	dodoc readme || die
-}
diff --git a/sci-biology/mafft/mafft-7.037.ebuild b/sci-biology/mafft/mafft-7.037.ebuild
deleted file mode 100644
index b8547f6c6f66..000000000000
--- a/sci-biology/mafft/mafft-7.037.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-7.037.ebuild,v 1.3 2013/05/21 18:04:05 jlec Exp $
-
-EAPI=5
-
-inherit eutils flag-o-matic multilib toolchain-funcs
-
-EXTENSIONS="-without-extensions"
-
-DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos ~x86-macos"
-IUSE="threads"
-
-S="${WORKDIR}"/${P}${EXTENSIONS}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-respect.patch
-	use threads && append-flags -Denablemultithread
-	sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die
-	sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
-}
-
-src_compile() {
-	pushd core
-	emake \
-		$(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
-		PREFIX="${EPREFIX}"/usr \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS}"
-	popd
-}
-
-src_install() {
-	pushd core
-	emake PREFIX="${ED}usr" install
-	popd
-	dodoc readme
-}
diff --git a/sci-biology/mafft/mafft-7.040.ebuild b/sci-biology/mafft/mafft-7.040.ebuild
deleted file mode 100644
index c4fb15ccb35f..000000000000
--- a/sci-biology/mafft/mafft-7.040.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-7.040.ebuild,v 1.2 2013/05/26 08:42:20 jlec Exp $
-
-EAPI=5
-
-inherit eutils flag-o-matic multilib toolchain-funcs
-
-EXTENSIONS="-without-extensions"
-
-DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos ~x86-macos"
-IUSE="threads"
-
-S="${WORKDIR}"/${P}${EXTENSIONS}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-7.037-respect.patch
-	use threads && append-flags -Denablemultithread
-	sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die
-	sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
-}
-
-src_compile() {
-	pushd core
-	emake \
-		$(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
-		PREFIX="${EPREFIX}"/usr \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS}"
-	popd
-}
-
-src_test() {
-	export MAFFT_BINARIES="${S}"/core
-	cd test || die
-	bash ../core/mafft sample > test.fftns2 || die
-	bash ../core/mafft --maxiterate 100  sample > test.fftnsi || die
-	bash ../core/mafft --globalpair sample > test.gins1 || die
-	bash ../core/mafft --globalpair --maxiterate 100  sample > test.ginsi || die
-	bash ../core/mafft --localpair sample > test.lins1 || die
-	bash ../core/mafft --localpair --maxiterate 100  sample > test.linsi || die
-
-	diff test.fftns2 sample.fftns2 || die
-	diff test.fftnsi sample.fftnsi || die
-	diff test.gins1 sample.gins1 || die
-	diff test.ginsi sample.ginsi || die
-	diff test.lins1 sample.lins1 || die
-}
-
-src_install() {
-	pushd core
-	emake PREFIX="${ED}usr" install
-	popd
-	dodoc readme
-}
diff --git a/sci-biology/mafft/mafft-7.043.ebuild b/sci-biology/mafft/mafft-7.043.ebuild
deleted file mode 100644
index e431b4805ecd..000000000000
--- a/sci-biology/mafft/mafft-7.043.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-7.043.ebuild,v 1.2 2013/05/26 11:12:15 jlec Exp $
-
-EAPI=5
-
-inherit eutils flag-o-matic multilib toolchain-funcs
-
-EXTENSIONS="-without-extensions"
-
-DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos ~x86-macos"
-IUSE="threads"
-
-S="${WORKDIR}"/${P}${EXTENSIONS}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-7.037-respect.patch
-	use threads && append-cppflags -Denablemultithread
-	sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die
-	sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
-}
-
-src_compile() {
-	pushd core
-	emake \
-		$(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
-		PREFIX="${EPREFIX}"/usr \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS}"
-	popd
-}
-
-src_test() {
-	export MAFFT_BINARIES="${S}"/core
-	cd test || die
-	bash ../core/mafft sample > test.fftns2 || die
-	bash ../core/mafft --maxiterate 100  sample > test.fftnsi || die
-	bash ../core/mafft --globalpair sample > test.gins1 || die
-	bash ../core/mafft --globalpair --maxiterate 100  sample > test.ginsi || die
-	bash ../core/mafft --localpair sample > test.lins1 || die
-	bash ../core/mafft --localpair --maxiterate 100  sample > test.linsi || die
-
-	diff test.fftns2 sample.fftns2 || die
-	diff test.fftnsi sample.fftnsi || die
-	diff test.gins1 sample.gins1 || die
-	diff test.ginsi sample.ginsi || die
-	diff test.lins1 sample.lins1 || die
-}
-
-src_install() {
-	pushd core
-	emake PREFIX="${ED}usr" install
-	popd
-	dodoc readme
-}
diff --git a/sci-biology/mafft/mafft-7.045.ebuild b/sci-biology/mafft/mafft-7.045.ebuild
deleted file mode 100644
index 209ae84cf352..000000000000
--- a/sci-biology/mafft/mafft-7.045.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-7.045.ebuild,v 1.1 2013/06/06 06:20:05 jlec Exp $
-
-EAPI=5
-
-inherit eutils flag-o-matic multilib toolchain-funcs
-
-EXTENSIONS="-without-extensions"
-
-DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos ~x86-macos"
-IUSE="threads"
-
-S="${WORKDIR}"/${P}${EXTENSIONS}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-7.037-respect.patch
-	use threads && append-cppflags -Denablemultithread
-	sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die
-	sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
-}
-
-src_compile() {
-	pushd core > /dev/null || die
-	emake \
-		$(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
-		PREFIX="${EPREFIX}"/usr \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS}"
-	popd > /dev/null || die
-}
-
-src_test() {
-	export MAFFT_BINARIES="${S}"/core
-	cd test || die
-	bash ../core/mafft sample > test.fftns2 || die
-	bash ../core/mafft --maxiterate 100  sample > test.fftnsi || die
-	bash ../core/mafft --globalpair sample > test.gins1 || die
-	bash ../core/mafft --globalpair --maxiterate 100  sample > test.ginsi || die
-	bash ../core/mafft --localpair sample > test.lins1 || die
-	bash ../core/mafft --localpair --maxiterate 100  sample > test.linsi || die
-
-	diff test.fftns2 sample.fftns2 || die
-	diff test.fftnsi sample.fftnsi || die
-	diff test.gins1 sample.gins1 || die
-	diff test.ginsi sample.ginsi || die
-	diff test.lins1 sample.lins1 || die
-}
-
-src_install() {
-	pushd core
-	emake PREFIX="${ED}usr" install
-	popd
-	dodoc readme
-}
diff --git a/sci-biology/mafft/mafft-7.046.ebuild b/sci-biology/mafft/mafft-7.046.ebuild
deleted file mode 100644
index 121e8324c8c5..000000000000
--- a/sci-biology/mafft/mafft-7.046.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-7.046.ebuild,v 1.1 2013/06/12 13:42:20 jlec Exp $
-
-EAPI=5
-
-inherit eutils flag-o-matic multilib toolchain-funcs
-
-EXTENSIONS="-without-extensions"
-
-DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos ~x86-macos"
-IUSE="threads"
-
-S="${WORKDIR}"/${P}${EXTENSIONS}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-7.037-respect.patch
-	use threads && append-cppflags -Denablemultithread
-	sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die
-	sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
-}
-
-src_compile() {
-	pushd core > /dev/null || die
-	emake \
-		$(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \
-		PREFIX="${EPREFIX}"/usr \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS}"
-	popd > /dev/null || die
-}
-
-src_test() {
-	export MAFFT_BINARIES="${S}"/core
-	cd test || die
-	bash ../core/mafft sample > test.fftns2 || die
-	bash ../core/mafft --maxiterate 100  sample > test.fftnsi || die
-	bash ../core/mafft --globalpair sample > test.gins1 || die
-	bash ../core/mafft --globalpair --maxiterate 100  sample > test.ginsi || die
-	bash ../core/mafft --localpair sample > test.lins1 || die
-	bash ../core/mafft --localpair --maxiterate 100  sample > test.linsi || die
-
-	diff test.fftns2 sample.fftns2 || die
-	diff test.fftnsi sample.fftnsi || die
-	diff test.gins1 sample.gins1 || die
-	diff test.ginsi sample.ginsi || die
-	diff test.lins1 sample.lins1 || die
-}
-
-src_install() {
-	pushd core
-	emake PREFIX="${ED}usr" install
-	popd
-	dodoc readme
-}
diff --git a/sci-biology/mafft/mafft-7.047.ebuild b/sci-biology/mafft/mafft-7.050.ebuild
index af05cef5af3b..d33c78cfdbd6 100644
--- a/sci-biology/mafft/mafft-7.047.ebuild
+++ b/sci-biology/mafft/mafft-7.050.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-7.047.ebuild,v 1.1 2013/06/24 09:53:38 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-7.050.ebuild,v 1.1 2013/07/03 07:17:58 jlec Exp $
 
 EAPI=5