Version Bump, 338199

Package-Manager: portage-2.2_rc88/cvs/Linux x86_64

3 files changed, 79 insertions, 6 deletions

diff --git a/sci-biology/t-coffee/ChangeLog b/sci-biology/t-coffee/ChangeLog
index c193d433bd28..5394cbb39124 100644
--- a/sci-biology/t-coffee/ChangeLog
+++ b/sci-biology/t-coffee/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/t-coffee
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.42 2010/06/18 07:55:33 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.43 2010/10/03 11:11:56 jlec Exp $
+
+*t-coffee-8.93 (03 Oct 2010)
+
+  03 Oct 2010; Justin Lecher <jlec@gentoo.org> +t-coffee-8.93.ebuild:
+  Version Bump, 338199
 
   18 Jun 2010; Justin Lecher <jlec@gentoo.org> t-coffee-8.69.ebuild:
   Fix installation, #324307
diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest
index b59c3cfb7d74..d9281a1437a4 100644
--- a/sci-biology/t-coffee/Manifest
+++ b/sci-biology/t-coffee/Manifest
@@ -7,16 +7,18 @@ DIST T-COFFEE_distribution_Version_5.65.tar.gz 2892013 RMD160 50c04dfbda649ebbf0
 DIST T-COFFEE_distribution_Version_7.54.tar.gz 3968725 RMD160 d11964db5232d137bf0db8101dfb75b1fde25936 SHA1 a302954a10860455bc23f924628598757c39eb12 SHA256 9d7d56abc000b61b48908fa4f93fb382a35df11c883966a0119605cd16aa668e
 DIST T-COFFEE_distribution_Version_8.14.tar.gz 4202237 RMD160 b292e4d4dd6576ad10dacafbb19eaa4f9154b85c SHA1 0286f719569f6717f879b38af520939f4399ab07 SHA256 ffc527e65e81cabc912a2816895efd46fb28bbd45e50327cd7e5d01ba88bcb03
 DIST T-COFFEE_distribution_Version_8.69.tar.gz 4112765 RMD160 5a2e7e089a5d2cc536247b9b26c7b6c216d7ef03 SHA1 3db6557c40587dba005179c98cc5b63b6dca9e44 SHA256 f346376bf341ce30f30f8c077820da466bed3e560c02d0ddd1a992381855d0f5
+DIST T-COFFEE_distribution_Version_8.93.tar.gz 4129848 RMD160 e88c519f19755017f1ade2abb2d9f04dc59364b6 SHA1 1ac365f0e0829a3e6c12ad99f36e0d5a5c9e021a SHA256 a2567d01d683f3e7faad72cc0d4e1749fec97cb64092db50f3d6696f523d8f80
 EBUILD t-coffee-5.65.ebuild 1999 RMD160 7ae18da2d689343547258b54f1de66f289f47114 SHA1 6518aae4c5e8b9bc55eaff6c0e763ae22995c393 SHA256 25d353182a9e946df52ad7dea404800a169067c77441c8d2456042b0cbea4d25
 EBUILD t-coffee-7.54.ebuild 1857 RMD160 ee23165c9f4e40b608c960d6c14886b1a680a4e6 SHA1 eb77681d7a1facb7fdab7c0ca45fe6dc02b99e61 SHA256 3da47ef23cf41088177fe5c8b90f96627c0f29f777145e79bf28b7aab618f372
 EBUILD t-coffee-8.14.ebuild 1863 RMD160 9dcfe5c6bbd1cf21d9f0ed0c9bae2ffab4816b02 SHA1 67cfd906a72e472fbf83156d0d3ee5371ad8b6b1 SHA256 75e3382c765661e1aca0900fc389a04999b72c08ee650950d5c3c98d3d21378f
 EBUILD t-coffee-8.69.ebuild 1912 RMD160 12709f2c5d029c95218ad9e365c31460e742e5aa SHA1 e4b058868af8ee3337be9fb330a98320e2d19f5f SHA256 1aaafe514f188dbdabdc9cd88150ba4bde3c1711daef5a76d429d30426522c8f
-MISC ChangeLog 5676 RMD160 62f3d432c3c8803075964f1a5e351862958f2b87 SHA1 fd07de776d29d4b4966e35126d082e80d6a00688 SHA256 a2e2568d924d5ecdde6b000b5e872180d5e5c779ba43684dea1aafedb6d8d55e
+EBUILD t-coffee-8.93.ebuild 1898 RMD160 741c4b5b18ca69c3065866f574c8b864762cd9c5 SHA1 ea965774e95c94d748330a76c96bb14f70d910d0 SHA256 3c77e829bdb7bf982f2ac2f106d458351c88881fddccf961085bd342eedc1e0e
+MISC ChangeLog 5800 RMD160 012ac926a7c8730bd17405694811801ec4a1a00a SHA1 95627dadea149f350dc6acf309ff9333ecb3fb87 SHA256 2a4b3ed77d0ebe9c8ae2c0a5d535ebd65640a4c93a78372f11525aac26a3e8e3
 MISC metadata.xml 760 RMD160 b9b95d31917ca092fbc88aaf871ffc6c22746860 SHA1 ee9d60b1947e1fb1542488003713ec1bcf3f3b71 SHA256 9d60cbec2e12219f15e311a1e8cb694b77fd7897c98186be3012f815c0f7bd12
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.15 (GNU/Linux)
+Version: GnuPG v2.0.16 (GNU/Linux)
 
-iEYEARECAAYFAkwbJnsACgkQgAnW8HDreRachACfYKg1aDSAbSXgp1vTWLhmZgw7
-UoYAoJVcAU8sCCakuPa6baliRD6y4jsW
-=7nHE
+iEYEARECAAYFAkyoZQEACgkQgAnW8HDreRZyPQCgx+9CndA5zPS5Kxbj8d+L56SM
+RXsAoNCeUnLCyBElGNjEfJrLOleJ6zNR
+=vTA2
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/t-coffee/t-coffee-8.93.ebuild b/sci-biology/t-coffee/t-coffee-8.93.ebuild
new file mode 100644
index 000000000000..90a0f33bc8c9
--- /dev/null
+++ b/sci-biology/t-coffee/t-coffee-8.93.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2010 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 1.1 2010/10/03 11:11:56 jlec Exp $
+
+EAPI="2"
+
+inherit 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_${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="examples test"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="sci-biology/clustalw"
+DEPEND="${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
+}