Latest version - thanks to Martin Mokrejs on bug #201495

Package-Manager: portage-2.1.4_rc7

4 files changed, 88 insertions, 15 deletions

diff --git a/sci-biology/t-coffee/ChangeLog b/sci-biology/t-coffee/ChangeLog
index 83ed2b9f93ae..2fa04cf550a0 100644
--- a/sci-biology/t-coffee/ChangeLog
+++ b/sci-biology/t-coffee/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/t-coffee
 # Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.23 2007/07/02 15:24:09 peper Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.24 2007/12/07 05:53:05 je_fro Exp $
+
+*t-coffee-5.31 (07 Dec 2007)
+
+  07 Dec 2007; Jeff Gardner <je_fro@gentoo.org> +t-coffee-5.31.ebuild:
+  Latest version - thanks to Martin Mokrejs on bug #201495
 
   02 Jul 2007; Piotr Jaroszyński <peper@gentoo.org> t-coffee-4.96.ebuild,
   t-coffee-5.05.ebuild:
diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest
index a86ad3e6ae21..39d97356c227 100644
--- a/sci-biology/t-coffee/Manifest
+++ b/sci-biology/t-coffee/Manifest
@@ -1,8 +1,6 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 DIST T-COFFEE_distribution_Version_4.96.tar.gz 2863327 RMD160 d6a7722f1fe3b2a8b186fad49e8bc136d812b610 SHA1 b8ae0be131ae470f5aa596369afa9fc9fbc18701 SHA256 49181acd69a5723fd5b11f579b1efe685b5289bf187985b25b40c514b0af0213
 DIST T-COFFEE_distribution_Version_5.05.tar.gz 2869348 RMD160 edc62c922280ac627089d44997ce859b56950955 SHA1 be137ec323630dc3795deddc71663ece907ef0e8 SHA256 494be7bfca83ee9701fb0fc5aba829fff0592c11173b95f239e39390ca3eeae8
+DIST T-COFFEE_distribution_Version_5.31.tar.gz 2857478 RMD160 95cb261c57fe31b3c26bdac85c10a4609692c2eb SHA1 dde68b94c26bb8727a9a667ecec0cd919ee14dc5 SHA256 43a38a6e9d0dc4bd663704b69c94c3aefd15608e5113703fad8d42f8fdc1a615
 EBUILD t-coffee-4.96.ebuild 1999 RMD160 416bc737b1c260d4df3ea530c3d09cf3c496a9c4 SHA1 76bfced9e81d24a244c0edb5551b5c8aff83eefe SHA256 e970a9c90f832902c9a05c128700a0a1ef8004048b10c7fd7ef667b332e2bd24
 MD5 ab3465f9b6c189385de70add8d67bebc t-coffee-4.96.ebuild 1999
 RMD160 416bc737b1c260d4df3ea530c3d09cf3c496a9c4 t-coffee-4.96.ebuild 1999
@@ -11,10 +9,14 @@ EBUILD t-coffee-5.05.ebuild 2000 RMD160 7ffc3c8ecd0a3811cd79f567cf2db6da290a1e02
 MD5 3945227e250df9f23764b9b27e749e50 t-coffee-5.05.ebuild 2000
 RMD160 7ffc3c8ecd0a3811cd79f567cf2db6da290a1e02 t-coffee-5.05.ebuild 2000
 SHA256 388a66b197f2c06e6d3f3e984903251ad8110cbfec619d703648269a4587894a t-coffee-5.05.ebuild 2000
-MISC ChangeLog 3219 RMD160 f486d0ef1941a268ead08a0928a33a2aa3d5c485 SHA1 8bdcb011a90cde965f92448d127580120d0cfa66 SHA256 0eecb573cc8f1ec77b528231183783d9bf80a1578c558fdec3d3498d39e0a8da
-MD5 8416569554142613ff616ddf59a43415 ChangeLog 3219
-RMD160 f486d0ef1941a268ead08a0928a33a2aa3d5c485 ChangeLog 3219
-SHA256 0eecb573cc8f1ec77b528231183783d9bf80a1578c558fdec3d3498d39e0a8da ChangeLog 3219
+EBUILD t-coffee-5.31.ebuild 1994 RMD160 b2d1acb4c78f0527f2b3ca2298d7d1d87b9f92c2 SHA1 78f0b57920eb2c4d6cf11cda1a2d9fbfcda3cbf9 SHA256 0e04016b28a703787d9abbf6cbb8cac0727fd9731ed588157f3363975c7619b9
+MD5 2a0e496660563f7be39f0be7ab919a70 t-coffee-5.31.ebuild 1994
+RMD160 b2d1acb4c78f0527f2b3ca2298d7d1d87b9f92c2 t-coffee-5.31.ebuild 1994
+SHA256 0e04016b28a703787d9abbf6cbb8cac0727fd9731ed588157f3363975c7619b9 t-coffee-5.31.ebuild 1994
+MISC ChangeLog 3381 RMD160 7055e89dc4bdcf7636637fc00d36d0793644b4d0 SHA1 c28f9137bdbe2fab4390a691a0b51533acb79296 SHA256 ac8eea7eec15e9e640dc4e85028e4c53798a91dca6b1fc7e8c13a37021bbd071
+MD5 c78ca5108a698031c64132d4a557ed2d ChangeLog 3381
+RMD160 7055e89dc4bdcf7636637fc00d36d0793644b4d0 ChangeLog 3381
+SHA256 ac8eea7eec15e9e640dc4e85028e4c53798a91dca6b1fc7e8c13a37021bbd071 ChangeLog 3381
 MISC metadata.xml 763 RMD160 1163b25c489923e806ccf77dd3b4b5a486da0c28 SHA1 9a6b86bfa165e9b7c0a9b8631990bbfb727fe410 SHA256 8ff6c199eb54e1a49903130ed1aebbe32a0c0b1698aaec2044530c27533270a2
 MD5 d5530b7c0b5defb31d0e1ad80fad02d6 metadata.xml 763
 RMD160 1163b25c489923e806ccf77dd3b4b5a486da0c28 metadata.xml 763
@@ -25,10 +27,6 @@ SHA256 2a6ffaf1bef9217315fb872171f49b5810002e900edb2ecc136d9a9f24503d7c files/di
 MD5 56d859aa293b43ac7c981e8e10b5dbc0 files/digest-t-coffee-5.05 307
 RMD160 b35e86ce914c46e0f661a07dcd54896e1a92027c files/digest-t-coffee-5.05 307
 SHA256 6caf3d7baff8202f79d5201ee4ab95ccba5cac470e67827c28aa8c7e32c5f9b5 files/digest-t-coffee-5.05 307
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.4 (GNU/Linux)
-
-iD8DBQFGiRieppoStNGKGywRAuT/AJ9IFuU9bRxxCo1YuekSqPJwo4RgjwCeKPdO
-+Yg3ijzwLwyMGPFkrkZPQWI=
-=Fp9g
------END PGP SIGNATURE-----
+MD5 fe9350ce7cf1797452952868faea7151 files/digest-t-coffee-5.31 307
+RMD160 9d2416b4ea4fc2378132dd1de79d72c4627c7e08 files/digest-t-coffee-5.31 307
+SHA256 06047962fa7669039b77027beb1762cc79e548bbcdc83d81392065fea7efdc50 files/digest-t-coffee-5.31 307
diff --git a/sci-biology/t-coffee/files/digest-t-coffee-5.31 b/sci-biology/t-coffee/files/digest-t-coffee-5.31
new file mode 100644
index 000000000000..e226a14a4f80
--- /dev/null
+++ b/sci-biology/t-coffee/files/digest-t-coffee-5.31
@@ -0,0 +1,3 @@
+MD5 3c5eea83be2c18f45b55a9afac643b25 T-COFFEE_distribution_Version_5.31.tar.gz 2857478
+RMD160 95cb261c57fe31b3c26bdac85c10a4609692c2eb T-COFFEE_distribution_Version_5.31.tar.gz 2857478
+SHA256 43a38a6e9d0dc4bd663704b69c94c3aefd15608e5113703fad8d42f8fdc1a615 T-COFFEE_distribution_Version_5.31.tar.gz 2857478
diff --git a/sci-biology/t-coffee/t-coffee-5.31.ebuild b/sci-biology/t-coffee/t-coffee-5.31.ebuild
new file mode 100644
index 000000000000..52c33eaff805
--- /dev/null
+++ b/sci-biology/t-coffee/t-coffee-5.31.ebuild
@@ -0,0 +1,67 @@
+# 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-5.31.ebuild,v 1.1 2007/12/07 05:53:05 je_fro 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_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."
+}