Version Bump; drop old

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 82 insertions, 86 deletions

diff --git a/sci-biology/t-coffee/ChangeLog b/sci-biology/t-coffee/ChangeLog
index cb65b7b1e108..2a02b731b129 100644
--- a/sci-biology/t-coffee/ChangeLog
+++ b/sci-biology/t-coffee/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/t-coffee
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.53 2015/02/09 12:50:38 blueness Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.54 2015/03/29 13:10:18 jlec Exp $
+
+*t-coffee-11.00 (29 Mar 2015)
+
+  29 Mar 2015; Justin Lecher <jlec@gentoo.org> +t-coffee-11.00.ebuild,
+  -t-coffee-8.93.ebuild:
+  Version Bump; drop old
 
   09 Feb 2015; Anthony G. Basile <blueness@gentoo.org> t-coffee-8.69.ebuild,
   t-coffee-8.93.ebuild, t-coffee-9.03.1318-r1.ebuild:
diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest
index c79e7c51add5..a640fd27d931 100644
--- a/sci-biology/t-coffee/Manifest
+++ b/sci-biology/t-coffee/Manifest
@@ -1,31 +1,33 @@
 -----BEGIN PGP SIGNED MESSAGE-----
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+Hash: SHA512
 
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-DIST T-COFFEE_distribution_Version_8.93.tar.gz 4129848 SHA256 a2567d01d683f3e7faad72cc0d4e1749fec97cb64092db50f3d6696f523d8f80 SHA512 b80803df6fdd739fd646ea2a779381f6493d6941030bcc8c2a73e7ef9fc65c4c66a83687d79a01ff0e598c94015b563daf6f7d77d75cf0f5351f483e14767999 WHIRLPOOL 2c5855e745e4397365942a101478328acb4e6c2a52a95bf1d82543c1e0240e9d26a4a807fdbd4a6084434f72d16c84944a60b3191065c5f8398f37c3202112a6
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diff --git a/sci-biology/t-coffee/t-coffee-11.00.ebuild b/sci-biology/t-coffee/t-coffee-11.00.ebuild
new file mode 100644
index 000000000000..a6b447d81942
--- /dev/null
+++ b/sci-biology/t-coffee/t-coffee-11.00.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-11.00.ebuild,v 1.1 2015/03/29 13:10:18 jlec Exp $
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+MY_HASH="8cbe486"
+MY_PV="${PV}.${MY_HASH}"
+MY_P="T-COFFEE_distribution_Version_${MY_PV}"
+
+DESCRIPTION="A multiple sequence alignment package"
+HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
+SRC_URI="http://www.tcoffee.org/Packages/Stable/Version_${MY_PV}/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+	sci-biology/clustalw
+	sci-chemistry/tm-align"
+DEPEND=""
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	sed \
+		-e '/@/s:.*;:\t:g' \
+		-e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \
+		-i t_coffee_source/makefile || die
+}
+
+src_compile() {
+	[[ $(gcc-version) == "3.4" ]] || \
+		[[ $(gcc-version) == "4.1" ]] && \
+		append-flags -fno-unit-at-a-time
+	emake \
+		V=1 \
+		CC="$(tc-getCXX)" \
+		CFLAGS="${CXXFLAGS} -Wno-write-strings -Wno-unused-result" \
+		-C t_coffee_source t_coffee
+}
+
+src_install() {
+	dobin t_coffee_source/t_coffee
+
+	if use examples; then
+		insinto /usr/share/${PN}
+		doins -r example
+	fi
+}
diff --git a/sci-biology/t-coffee/t-coffee-8.93.ebuild b/sci-biology/t-coffee/t-coffee-8.93.ebuild
deleted file mode 100644
index 2092ec91c026..000000000000
--- a/sci-biology/t-coffee/t-coffee-8.93.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-8.93.ebuild,v 1.3 2015/02/09 12:50:38 blueness Exp $
-
-EAPI="2"
-
-inherit eutils flag-o-matic toolchain-funcs
-
-DESCRIPTION="A multiple sequence alignment package"
-HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
-SRC_URI="http://www.tcoffee.org/Packages/T-COFFEE_distribution_Version_${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="examples test"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="sci-biology/clustalw"
-DEPEND="${DEPEND}
-	test? ( dev-lang/perl )"
-
-S="${WORKDIR}/T-COFFEE_distribution_Version_${PV}"
-
-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_prepare() {
-	epatch "${FILESDIR}"/8.69-flags.patch
-	epatch "${FILESDIR}"/8.69-test.patch
-}
-
-src_compile() {
-	[[ $(gcc-version) == "3.4" ]] && append-flags -fno-unit-at-a-time
-	[[ $(gcc-version) == "4.1" ]] && append-flags -fno-unit-at-a-time
-	emake \
-		CC="$(tc-getCC)" CFLAGS="${CFLAGS}" \
-		-C t_coffee_source || die_compile
-}
-
-src_test() {
-	cd "${TCDIR}"
-	perl bin/test.pl || die
-}
-
-src_install() {
-	dobin t_coffee_source/t_coffee || die "Failed to install program."
-
-#	insinto /usr/share/${PN}/lib/html
-#	doins html/* || die "Failed to install Web interface files."
-
-	dodoc doc/*.txt || die "Failed to install text documentation."
-	dohtml doc/*.htm || die "Failed to install HTML documentation."
-
-	insinto /usr/share/doc/${PF}
-	doins doc/*.doc || die "Failed to install DOC documentation."
-
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r example || die "Failed to install example files."
-	fi
-}