sci-biology/mafft: Drop old; Bump version

Package-Manager: portage-2.2.0_alpha186/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

11 files changed, 16 insertions, 434 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/Manifest b/sci-biology/mafft/Manifest
index ce1fcdcc906b..1220c7b0b57d 100644
--- a/sci-biology/mafft/Manifest
+++ b/sci-biology/mafft/Manifest
@@ -4,30 +4,14 @@ Hash: SHA512
 AUX 6.811-respect.patch 6327 SHA256 3d527220ce3fb90e4fa2dd2f41bca1f2684bb03f0de94313d7aea432b955e37c SHA512 0e7e829cc95fcf218fbdf9763983ee6d6ecfb6153201c302fb18ef05818ee19b3b7852c1f85162d2eb2055869033f759cdb3fdbc98cfe4d30ee3607148290e6c WHIRLPOOL ae5c596613dab72df381f849cff927a44dd7f1d9281564fa51f019f38e7435175293674390418f19bbd7305fe4a4748db87abd83cc49a67954ae2a05a6747efb
 AUX mafft-6.240-mktemp.patch 6497 SHA256 783f6f5678781dff1fafece92f37688698052fe1e0bfa13850443a0f8cc91533 SHA512 ade9d0f296a70324f4847763d03585b29cea6bd4a81fa04868eb92df56da40f9df0877f9b310de925c257baaac50208ca17f406639a87cd10c2c83361463b571 WHIRLPOOL af88a170882c110e44026f3402a8d1192264865e1f028725eb1d4d3e94bf7793c4190c53437d1e29e3a57d29e4e08cf8c10db517641f2c809c862a300a27ef0e
 AUX mafft-7.037-respect.patch 7463 SHA256 eeedc574ad5977661ea879eefaa1c4b4d428384f25af891c1fcef16e6bfc6293 SHA512 ba706bc83b1c249c08fa7e39d6b80df42be058ea2e68baf1028125dcad289764ead3a6269e557bffc62da87a7ac2ff9856a602e20ca5eae052060d44b431994b WHIRLPOOL cf340ae92dec7ac35099706e5f2a31ac123b341391d2ebe25d4050fc470bbc295ab51c26612c4cc6c659abfba48c355df170b5352b2a6b6a04e8eeca6f453bb5
-DIST mafft-6.240-src.tgz 657197 SHA256 d0183ab1d6a5e0d1132b95cb917fedb3b6dc16c38d3fde35d7140ecdca555e8f SHA512 271b1ceed17e4a877183fff309370a94a96c59600221c902b0bea49725147552d21d2b4e661feb7672e54a0908e6b8549c0ec32d191f64210890192c9cbefe90 WHIRLPOOL 3edbf726073448e7eccebdf7bc1898c852743b947c171edbaf6d9b3666d70dbdc6fd73ea586fc1be672405fa5d4e2107dfdd1a14d7e079b2f563bd58f603162d
-DIST mafft-6.707-without-extensions-src.tgz 455884 SHA256 08789aa9351128e32b0003cb524668c3f2e35aec7ea9f834047f0780851989a0 SHA512 67c9cc1effef41a6d08428cf50ddd9e1ff5fe0ef27e496aee21a283601ee68088df88fc0412ae2c1bc6d0b8d9a621cd9c339261708fe948aaeae8a36dbce1e62 WHIRLPOOL ac54823f0918dc381d7d40dca26e1d5a3c1e9f12b4b0d5c1169c3d1c26a9bd45ee72fd0bfcdfa0511c63099ba59089404672c40e912def2317d052c6064ffe65
-DIST mafft-6.811-without-extensions-src.tgz 500063 SHA256 a99b57444787b2e910b0b56a5cc8c69949dc987b7ff12995650a1dd0be065c43 SHA512 c50296209e09e0c4dfe4cf68956c470970462497c0ddb5a1af51f075e83ea84ab3c271c7651ac44018375a41f119619b0263f9d4c155364d647ee9571a18f940 WHIRLPOOL 3b1c3fe990e78dfc971f49e6db77e6c166ab8ba599a0cb6ce979c22294cad0110e14089faa9cfc5648f9e0c21528d70e344518508e52ef005df72e7a36ca867a
-DIST mafft-7.037-without-extensions-src.tgz 371344 SHA256 9c4688e55d8f47202ea8fd100753970dfe7c8c349f855f54bf5af4a90ee9d9dd SHA512 c32cf15a7ef935c5f78ce2d6472eba062e14ed5d49fcc3dff86f293223dfb79183fecef7e519b3116a16076f0f1f32d88233c0e85f64fbffeef2ad9cd06c9740 WHIRLPOOL 950049ad719f0ee6eb4abb7578a87752ac8c2dc419089c49122f929841918d79e5fb995b7ac324fb88617d8a4b8daa4ce8c9fce4c5b7fb4a2bd95c37e12fdfa7
-DIST mafft-7.040-without-extensions-src.tgz 373505 SHA256 3c2014c49d31c9f435bb14ce06381f915cd36ec4407c3975e0469ed2fdcee0f8 SHA512 4a1579d1030c2ede68111cc6e39749dfbb6e392278c41d4ea8219d9821ccc1fa458940feca0e8c40761a97116df6b5da97a4690666a6a61bf6cc470caa49edf5 WHIRLPOOL f022e9439043a268ceb83e073ac035623ed0918cf486a3a38dcc27da6ac55dfe97b6683fb55be71d5e41eeb9bcda6433cd822eeba692ed961328b432c51e7ca6
-DIST mafft-7.043-without-extensions-src.tgz 379777 SHA256 cb0dcf9988732ddd4510eb310e63c0b481bb09e90c91d4624e566edc23dca0ad SHA512 ab7527a1decdb528d7b61f454d5d5564b0a1fbf0f54f03f9d59c264c9bcabb689ba51fbf1c82e9578eae5b5463edb901999f89e5eabf6926689b320c20bdcdfa WHIRLPOOL c2e12afd8d3c89585fcb7abe3537558856e3fb25cf03a3c231c446cc5110a1da9cc192fb9d15918f0ed380ba49fef67c8e9e358a2e892c7975da6b510d318455
-DIST mafft-7.045-without-extensions-src.tgz 380217 SHA256 afcd4c13ebd4cde3e6890c5fc5098922e3312e21096d5a62df32bfcdf48b4cdb SHA512 6d0466c2a0d7813503c5c05e33cc59cb8fde3f9efc5b58b8bcf92bf82c964a5cbb6f140134c9080ed684b64643f410735073d37a19b812806268837d280b8f0c WHIRLPOOL 2f02668901c829b1731ceb67ab4365bed204025f6ffa7f0f60a7e57d7a90ce31dc835856e947f7b2b3d0ed6067add69964c081092fed638c1a6f6518597e6b17
-DIST mafft-7.046-without-extensions-src.tgz 380226 SHA256 01eba5cfd8bb37dc6830b4cd3b7bb74c2892d3d06f8b2da23886ef5c27404b3e SHA512 305f7ae0d110364e8197be2c8fa87094df062cbdf9726d32ce96ded2122a51ffe3ac6359bbf45cfc57bd13f55c0a02a06eac757eed860317ff27358c393cf77e WHIRLPOOL de67470bd0e0c295459364e858b7b80b6d1532b57cb8d4913296ac6c75580f01b247d936aa198a8346aaa9859fb3122d29c486fa89e8f707c7599ba3d7ec82f2
-DIST mafft-7.047-without-extensions-src.tgz 379835 SHA256 f59a95a5e27386aaf9c6a087d34bd17dda7e57728fd2f5d9b099c268fe0a20e7 SHA512 10b8d2822f8829fce4f233866bf38aecca2b7b8ec3b0364050a2cbb91c5b4e4f49ae9fc43bab2901a3390ca9ecf3e2355b66071398df50721c139a0a91238f2c WHIRLPOOL d0e841e5bf535358fb59f6a96194103f8e2a670196cc2869e26b26359ffca79ec93b588ea154a8faf2faa8e0b75f4b036b4f7778766efa3b8bb97b407f34fa60
-EBUILD mafft-6.240-r1.ebuild 1004 SHA256 70cb92f9d6a0a9e6dab1e5bae147191ffbe54c4517df9d2efd859cceb6df41e6 SHA512 40ddd365b68b82446ba3931525ad1d1d91a1e442af2d0e8efa20448b69b3d79b0fb8c24adffadd5cbd2e1e10ff32643af7eb6058a53a9b28bfbaa17f97f1ca2f WHIRLPOOL d2d0a212d863f125bd866de9003c05ad3f5a92434550cd75567ce572cc50c25d12bbb18019040be2f6a686d28ce609e27537038198f678eb60186a80a06a7fe1
-EBUILD mafft-6.707.ebuild 998 SHA256 ca548edebc7b720371b27b456d63c806141c2d6337d1436cd973b6c5261581bc SHA512 b8067e0e56d0bec8a2f2af3d11d03cd92db1432f1c1b6bfe680ee7d9958a537b3f6f60219c813b74c753d7d7f353495164c947fe953f9113997aedd03a2ca8f6 WHIRLPOOL a0781c7b82d4fb07837ff00526cc748c4102492166449b6b0274381a42f364236efbce58c46561fdf120a81c0d4bd0a7b94a761034c6c2ec6128a1ae1858070d
-EBUILD mafft-6.811.ebuild 1166 SHA256 a83f99b61abe2933ec68b7f0bc65708c36670b658dc225e470a693817e73fdfa SHA512 ab298b855b637f183f7f5869fe528cca32e9dfda5fe978fe7d6e189141aed5a1cfcbf0cd803cda98b747c35d8366376d03ec548ef8db0f41780b550a774bc86f WHIRLPOOL f1bbe9eceb8d495b1cfad1069c7531b3c528934d456b225583c36ef357dcbfe5b8b941315c20a98d1675cf46b1b1916ec1eb9c3fb56d0b53e406f861f823b20b
-EBUILD mafft-7.037.ebuild 1188 SHA256 9db220c35a72637ffe20a1d0f26d15877036ee25be224217ac10cd7f6130cfd2 SHA512 ecf630a87220647e438136751db6f680cc5f058cff221323e5aaa3226fb2b901310ab00e0ad7d20e0be4aa817a74d78a2ad2f7d8586f39d8d3389f5ec67ba235 WHIRLPOOL d9b5503c02bb793a3d9e02faf97a25bd8c9a486339eea992c4e07067326e750c1d36bcb4f13db917e8c1a90a2db4d689936a243e2e2ede62df13e7170ce031c1
-EBUILD mafft-7.040.ebuild 1840 SHA256 e32d74d2f1d05672daac4e8b5eb05dd27086d85cd3c1dcdbe960ea04d5c34c7a SHA512 14038c3c70103aa69393344c6e486d288b9750c83dcac16789253557d9ed2cd5aea1c56bb80960bf0c4a5a43641f9f3b937c7a0a8fd713892ebc5d04e57337cd WHIRLPOOL acb0279404cd71a3caa8458881b9fe9de1c828ebf17819cdf6d1ff47603440b5fc4dbbdb4664ba2511498fa35c99dd1d2b9d0321a454a65d39d8903d1252a7e4
-EBUILD mafft-7.043.ebuild 1843 SHA256 50105f72dea8b0ea4d21e88a2e24f30d192ccaed5723e2c5d0455bc1034a379f SHA512 2e1544da85dfa08ec63c02e1a8efd842388a92e4aad0dc07dae0b86e9560d893bb7aa6f3355b08c13ed3070bbd22aa8dcc85b48a646dafef8aae84901867b5fd WHIRLPOOL cdbe60eee4f932d8252bbd4e324e159d248f24694cd6af84d98b4f8b6b9e1e3b1741c635a63c4b78490e24303806fa980dc455031da76588f4b950b00785d023
-EBUILD mafft-7.045.ebuild 1881 SHA256 547f1942e788f73bd77e06186e9e346c23e83a60c331d107e4bb388f04918dee SHA512 fed739530adc0e6702bbe6897c2ebb1f031d92e964e17adbb2417ee00f2d9bfe19322bc44d947eecfdeb939e787716619df4f1fa5f0e36474eed4bb47be2731a WHIRLPOOL 53c0245cd106eaa88e0b2c046b01e0588f08b422323bf40fc38ee661231a47118e389acc74c3848b557af7a9f9cfba4b5ef03ce8e0ba5653bdfe902fc4376af5
-EBUILD mafft-7.046.ebuild 1881 SHA256 975f6ef7ab7ce88af52fda3e12f74772a70cfc77d485a3c002a2fc92cb958bdf SHA512 fd5638a81afa72f94b03c3686d5e09b902c15d593eaa7da9f3f6395bf3a51057724d45c2688bbadfbd59a6666a22b12dbdc99f07ddda15344a9eda7999e9d68b WHIRLPOOL 77dfa0f72d0debf2818f03f731bbf6edcda69393f870238defba98c00d0ca0f6d7e6d0a2367bae78432ea71176321f4cbdb6fab8b36c2d389a7aeb86636edc3c
-EBUILD mafft-7.047.ebuild 1881 SHA256 e5bf00d7985394a08e0887428833aae47afc9bbd057c54b46161c098da4f6745 SHA512 134e98d312c948d9c33ab91f5356f978d0d7c0888d166869b919bb27d1d52009236092ca1ffa1d871e08c61106114608e3953bedfa3c69399d42b58efe54d5c6 WHIRLPOOL a949300bc643f2b15630ebaf1c3df90f8cfed1feda9485fad7cfb941144dd883abfe4f4dec295b5612a05c77c0f33cab49d0a32119deadd7f9dc35b67b6075c2
-MISC ChangeLog 3110 SHA256 2535d3715d157c0a1e94bc8e35c612f7bcd10e9087df75e79c065a6ee24a60f4 SHA512 6a3002070aef81f4d67022c45fb58e510fd6fc7448dff34592235ec6157c9f444e6158fffb900c7e12f2bc8bc9048a6145a20fdca06509cc4201c874c05fea67 WHIRLPOOL 01ac73b9f6e81aac7651b2c9edea7421fb560b7b9e02d0ea93a4150bdea5bcd67ca5f9d60fc56ba7b7ef165d002e8eb293fd874a357f5a11e0ed3b4896658390
+DIST mafft-7.050-without-extensions-src.tgz 380375 SHA256 29ddb276bfca24f5815acc41f1e640a705bb12c9d29b7c74902ebca68cece7bc SHA512 ffddedcd03f37241b1493a62bf843eb23caa04089bd0182006aa7669f74de27204d324817e22fec1cb4ae11c4c226db5b725d03ba9f73b30a71ca3d38368d73e WHIRLPOOL d46d7d4dfe453bfb54b9e418308772fb063bffce1d6d45d92262bee45504301daff9a6e57ecde41912a6c11852bb64510fb5ba6df04c7e79dc671e7a31444d49
+EBUILD mafft-7.050.ebuild 1881 SHA256 4de7e20747102f9318e6d1be6113b2b560d8fb61326400bdc16f1fe9fb6609fb SHA512 954f776452db3260985ec837959d2d099fdeb6a85c80bad17e8522a10f5a8418b705661d0abc8f3af1a518f06c07e3cac7bf990b4c55c41e1b24853a2481e90c WHIRLPOOL db6d1961d6379010b7d98a282fe3518c99813ada06091a85b8f017f57215a99ecbbc75b8d91487b7b7633591c8c70c7935489c93003f9bdae9ddddb3f0592438
+MISC ChangeLog 3430 SHA256 678ea06ddf0a830a4b67800d8462854eb22b243d3e3ba7110a951f16e65d7e0a SHA512 51b70e0c426838d72eea1bfd1e74df22b81013e63b6060cd3e3868488eb51fe6e69205d3f5d78f2b48f2755b3650984e29829344a320fa0fd36b674098e5abfa WHIRLPOOL d86581f97f441f2d1a8cd52468a33cd927a454b483c1b53edefb955c6b10ee21129eee08923fc36dce16225c73580d6c6f0e19f1d7f2e1bc79757af8bc095d3c
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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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