Version bump and removed old ebuilds (fixes bug #232323). According to the website and docs, t-coffee is now released under the GPL-2, hence changed the license info and uploaded the tarball to our mirrors.

(Portage version: 2.2_rc8/cvs/Linux 2.6.26-SENTINEL-2 i686)

3 files changed, 29 insertions, 87 deletions

diff --git a/sci-biology/t-coffee/ChangeLog b/sci-biology/t-coffee/ChangeLog
index b22c550d65a8..0cdccee89417 100644
--- a/sci-biology/t-coffee/ChangeLog
+++ b/sci-biology/t-coffee/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-biology/t-coffee
 # Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.33 2008/07/14 17:01:42 nixnut Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.34 2008/09/06 11:29:59 markusle Exp $
+
+*t-coffee-6.82 (06 Sep 2008)
+
+  06 Sep 2008; Markus Dittrich <markusle@gentoo.org> -t-coffee-4.96.ebuild,
+  -t-coffee-5.05.ebuild, +t-coffee-6.82.ebuild:
+  Version bump and removed old ebuilds (fixes bug #232323). According 
+  to the website and docs, t-coffee is now released under the GPL-2,
+  hence changed the license info and uploaded the tarball to our
+  mirrors.
 
   14 Jul 2008; nixnut <nixnut@gentoo.org> t-coffee-5.65.ebuild:
   Stable on ppc wrt bug 221165
diff --git a/sci-biology/t-coffee/t-coffee-5.05.ebuild b/sci-biology/t-coffee/t-coffee-5.05.ebuild
deleted file mode 100644
index 8d4fe5cc152a..000000000000
--- a/sci-biology/t-coffee/t-coffee-5.05.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2007 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-5.05.ebuild,v 1.2 2007/07/02 15:24:09 peper Exp $
-
-inherit toolchain-funcs flag-o-matic
-
-DESCRIPTION="A multiple sequence alignment package"
-LICENSE="t-coffee"
-HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
-SRC_URI="http://www.tcoffee.org/Packages/T-COFFEE_distribution_Version_${PV}.tar.gz"
-
-SLOT="0"
-IUSE=""
-KEYWORDS="~ppc ~x86"
-
-RESTRICT="mirror"
-
-DEPEND="sci-biology/clustalw"
-
-TCDIR="${WORKDIR}/T-COFFEE_distribution_Version_${PV}"
-S="${TCDIR}/t_coffee_source"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	sed -e "s/CC	= cc/CC	= $(tc-getCC) ${CFLAGS}/" -i makefile || die \
-		"Failed to patch makefile."
-}
-
-die_compile() {
-	echo
-	eerror "If you experience an internal compiler error (consult the above"
-	eerror "messages), try compiling t-coffee using very modest compiler flags."
-	eerror "See bug #114745 on the Gentoo Bugzilla for more details."
-	die "Compilation failed"
-}
-
-src_compile() {
-	[[ $(gcc-version) == "3.4" ]] && append-flags -fno-unit-at-a-time
-	[[ $(gcc-version) == "4.1" ]] && append-flags -fno-unit-at-a-time
-	make all || die_compile
-}
-
-src_install() {
-	dobin "${TCDIR}"/bin/t_coffee || die "Failed to install program."
-
-	insinto /usr/share/${PN}/lib/html
-	doins "${TCDIR}"/html/* || die "Failed to install Web interface files."
-
-	cd "${TCDIR}"/doc
-	dodoc aln_compare.doc.txt README4T-COFFEE seq_reformat.doc.txt \
-			t_coffee_technical.txt t_coffee_tutorial.txt || die \
-			"Failed to install text documentation."
-	dohtml t_coffee_technical.htm t_coffee_tutorial.htm || die \
-			"Failed to install HTML documentation."
-	insinto /usr/share/doc/${PF}
-	doins t_coffee.pdf t_coffee_technical.doc t_coffee_tutorial.doc || die \
-	"Failed to install DOC and PDF documentation."
-
-	insinto /usr/share/${PN}/example
-	doins "${TCDIR}"/example/* || die "Failed to install example files."
-}
diff --git a/sci-biology/t-coffee/t-coffee-4.96.ebuild b/sci-biology/t-coffee/t-coffee-6.82.ebuild
index 9d64608a95fc..c91b5280abe7 100644
--- a/sci-biology/t-coffee/t-coffee-4.96.ebuild
+++ b/sci-biology/t-coffee/t-coffee-6.82.ebuild
@@ -1,32 +1,23 @@
-# Copyright 1999-2007 Gentoo Foundation
+# Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-4.96.ebuild,v 1.5 2007/07/02 15:24:09 peper Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-6.82.ebuild,v 1.1 2008/09/06 11:29:59 markusle Exp $
 
 inherit toolchain-funcs flag-o-matic
 
 DESCRIPTION="A multiple sequence alignment package"
-LICENSE="t-coffee"
+LICENSE="GPL-2"
 HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
 SRC_URI="http://www.tcoffee.org/Packages/T-COFFEE_distribution_Version_${PV}.tar.gz"
 
 SLOT="0"
 IUSE=""
-KEYWORDS="~ppc x86"
-
-RESTRICT="mirror"
+KEYWORDS="~amd64 ~ppc ~x86"
 
 DEPEND="sci-biology/clustalw"
 
 TCDIR="${WORKDIR}/T-COFFEE_distribution_Version_${PV}"
 S="${TCDIR}/t_coffee_source"
 
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	sed -e "s/CC	= cc/CC	= $(tc-getCC) ${CFLAGS}/" -i makefile || die \
-		"Failed to patch makefile."
-}
-
 die_compile() {
 	echo
 	eerror "If you experience an internal compiler error (consult the above"
@@ -38,25 +29,29 @@ die_compile() {
 src_compile() {
 	[[ $(gcc-version) == "3.4" ]] && append-flags -fno-unit-at-a-time
 	[[ $(gcc-version) == "4.1" ]] && append-flags -fno-unit-at-a-time
-	make all || die_compile
+	CC="$(tc-getCC)" CFLAGS="${CFLAGS}" emake || die_compile
 }
 
 src_install() {
-	dobin "${TCDIR}"/bin/t_coffee || die "Failed to install program."
+	dobin t_coffee || die "Failed to install program."
 
 	insinto /usr/share/${PN}/lib/html
-	doins "${TCDIR}"/html/* || die "Failed to install Web interface files."
+	doins "${TCDIR}"/html/* \
+		|| die "Failed to install Web interface files."
 
 	cd "${TCDIR}"/doc
-	dodoc aln_compare.doc.txt README4T-COFFEE seq_reformat.doc.txt \
-			t_coffee_technical.txt t_coffee_tutorial.txt || die \
-			"Failed to install text documentation."
-	dohtml t_coffee_technical.htm t_coffee_tutorial.htm || die \
-			"Failed to install HTML documentation."
+	dodoc aln_compare.doc.txt seq_reformat.doc.txt \
+			t_coffee_technical.txt t_coffee_tutorial.txt \
+			|| die "Failed to install text documentation."
+
+	dohtml t_coffee_technical.htm t_coffee_tutorial.htm \
+		|| die "Failed to install HTML documentation."
+
 	insinto /usr/share/doc/${PF}
-	doins t_coffee.pdf t_coffee_technical.doc t_coffee_tutorial.doc || die \
-	"Failed to install DOC and PDF documentation."
+	doins t_coffee_technical.doc t_coffee_tutorial.doc \
+		|| die "Failed to install DOC documentation."
 
 	insinto /usr/share/${PN}/example
-	doins "${TCDIR}"/example/* || die "Failed to install example files."
+	doins "${TCDIR}"/example/* \
+		|| die "Failed to install example files."
 }