Switch to CPU_FLAGS_X86.

Package-Manager: portage-2.2.15/cvs/Linux x86_64
Manifest-Sign-Key: 0xEFB4464E!

13 files changed, 118 insertions, 74 deletions

diff --git a/sci-biology/fasttree/ChangeLog b/sci-biology/fasttree/ChangeLog
index f4cc081eadaf..5b063a229025 100644
--- a/sci-biology/fasttree/ChangeLog
+++ b/sci-biology/fasttree/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/fasttree
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/ChangeLog,v 1.4 2013/12/20 09:20:44 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/ChangeLog,v 1.5 2015/01/29 21:21:10 mgorny Exp $
+
+  29 Jan 2015; Michał Górny <mgorny@gentoo.org> fasttree-2.1.7.ebuild:
+  Switch to CPU_FLAGS_X86.
 
 *fasttree-2.1.7 (20 Dec 2013)
 
@@ -21,4 +24,3 @@
   10 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml,
   +fasttree-2.0.1.ebuild:
   New package, ebuild written by me
-
diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest
index b3bba794e926..40ba1459fdfa 100644
--- a/sci-biology/fasttree/Manifest
+++ b/sci-biology/fasttree/Manifest
@@ -1,5 +1,5 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
+Hash: SHA256
 
 AUX CMakeLists.txt 948 SHA256 60c21f04ea3ef04782dfc0328e317b6d04197a45af4d15c5c43f4f87a1f82c44 SHA512 9858800bfce8d256ccb834a06bad5a5230f90f025a9c9b3c9aafe7244d219d66810530f6688e02889cdb67d6a9459d8e26cd1a9fcf2e8825278b31d0e8d51ff3 WHIRLPOOL edc50a85eaec6161924f38569c33ccd35170f9ac89e17741e4a87ceb350b165fdf6e118c20bfd27a02ec1e01aa76be8665908f39c531a292d3d1b706e6c1b25a
 AUX fasttree-2.0.1-asneeded.patch 455 SHA256 f43ec50d2d4284d60b438e62a407686a5149a31e9c5e389744d894b9e55243eb SHA512 fdd5a0f475d7f00c266a35dfafe7b5131919e345e39b03f51f9ab4ef64ac7bbb5372b437354e5498a242805fb973e4357c1254148abbce64ff71c00b57610ad8 WHIRLPOOL 165ccae141b47231192c091c133a004fdeb3aadbf3539fc6abe7af2df388bedc1c9947e2c335a58aabb918f6baf921a03088d07b0e5c1335be36cfa3765fd371
@@ -8,23 +8,25 @@ DIST FastTreeUPGMA-2.1.7.c 95271 SHA256 199acc84910ca899dae9dd96d2ea133b651e76bb
 DIST MOTreeComparison-2.1.7.tar.gz 13523 SHA256 aea482d47aca528026cdf86fc96dc59b7a9f66ea33b9e974f5c007b46335d174 SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b WHIRLPOOL 7ed1009d622ce77c59cf79078a08a08dafb281e87a6ae99be7b7fba9451f2748bfd7a51036c041e3667ea8e29f7545276b799d708aabb7ea1988ea443f73f475
 DIST fasttree-2.0.1.tar.bz2 149279 SHA256 968a42f126c67f471a21c6ffe621cbedb3ed406838a3d80e799487aedc137fb4 SHA512 b6c7fb9f2eb3ac859164ce459da0a258827550020973e126b984c8f4f87a7f708f46731b6c6bb148cc3fe5cf5ddc19c7c1211b78c19880644fcfb05b65b42367 WHIRLPOOL 1aa3b811afb34b4331f411005fb7e2f9972fcefc022fa3bf68d0156f13be89ec969979c8431d0cd209f6994f8241698b10ef0599c5684e3f943edb61ae59b1bc
 EBUILD fasttree-2.0.1.ebuild 783 SHA256 61f547093efad5df2ca57caa7fa35cf9c2b194c8b677fac5a008aecd3d744548 SHA512 933be57dd573f7fc0dc3f1768fc8c2366fb92a5a8c0a66c3065ee4a2b19e804b62c9ebf7f48fb9ff19a03872d8fe419f16f43325373cd081d59ca9927cd970d9 WHIRLPOOL 78c6cacbefa6525423cd2d302a4ae73df14eca0255c254e689360ff2d68e596251965b642f1fb98d1b3caed7b31323532513536be3128f436ae71b9a4bf2bec4
-EBUILD fasttree-2.1.7.ebuild 1207 SHA256 ad7aec82fa695d183e48f412038cbd454a369b3a1cb7e4a2dae707262e0b307c SHA512 b413f7e050beba9ab0e2e0f8ed47f394de57a68d17cef71bce9bfaf56bdd95be4f235abcc528a077c42b60368ecc79536029556307cc0c7870d3bdefac96ee97 WHIRLPOOL 49b0d703766f4985b4571b1a184ecce2837cfef11ffe3c549aaa46fd3287915666fa63e5ef6b7edd2acec866346d939616aaea4c1cc58881cde4a080ae737d02
-MISC ChangeLog 881 SHA256 17ac691d005a56d796f7612bafcf9deb17c694e544af3fc1da4403cf56c5ce29 SHA512 b86539962779bf8b21e9c5735a60bbf7e981992780d50b1e8c4da0e318092fe17b398416fb3bad726ea41c7df108ff5fe4eb6815e2f23f4e3877ea6f7b7120a2 WHIRLPOOL 45ae9ce94e460066496c23116ac4368b21c6c863bde5a74654911ce5b062b3d46234695d6f49e0af4947101c27647f9fdf558a7df63232f9b7d7ae5e3cb477ce
+EBUILD fasttree-2.1.7.ebuild 1256 SHA256 a20e4010c320b3aca1eaa1f7f5576f50eff51c0c792bc0eb5086aecf4434ab63 SHA512 833d516d269442e8fba20e8bbc4830488f0b1cadf00f01b2a8f74167f2e5127c9d624113c7bb7988ded430714e2874574ae7f80965c78ba681eccb15d493dd45 WHIRLPOOL 16adf456eb617f92d74a691fe9f7c654a432a41716a4986eedd72564761f8c001c72556429269f31dccbce5f062116638e5393f65072a7de18ceebb4295e9741
+MISC ChangeLog 983 SHA256 ef7f629a57692cda21875e30160b719c0af84ca40a4e2c46613374c7d8dabd9f SHA512 9f2807c240927d362567a18593881b536ebb3e71626461ea33dda051df99e9a754fb530e2670a7b3d86017de714b6e4e19b1bb08392d3370a2030af1b924a8c4 WHIRLPOOL 3b75ef96f0cdc16343b93afa81e9565244e79843629febb4968197932dde9cc70cebd8cbcaf1e29d7107fb0858dc09717a6ba070e49754d2ee856acf98f5f036
 MISC metadata.xml 315 SHA256 3fb5d83ebb92699b2a8ef0efcd99ce41389b6561a22ca457b88745238a887dcd SHA512 4f3de85a5d5f6fac19f34a125ded80cbe4908ae8d3a385387b4742766bd6447c661d3d8df676c8642289a63ee646677c346687b9428153550f9e74e2fe961f80 WHIRLPOOL 4a28481b281c50749d53412ffd3de0c409b849678232662e9b6cb41661bcf946ac5daa0db8bb623985d46f8a6407e1afc0b573f2a39ca18c7b6d2c44278d3ac6
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-Version: GnuPG v2.0.22 (GNU/Linux)
+Version: GnuPG v2
 
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diff --git a/sci-biology/fasttree/fasttree-2.1.7.ebuild b/sci-biology/fasttree/fasttree-2.1.7.ebuild
index 80d666677e81..69375a55c1a1 100644
--- a/sci-biology/fasttree/fasttree-2.1.7.ebuild
+++ b/sci-biology/fasttree/fasttree-2.1.7.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/fasttree-2.1.7.ebuild,v 1.1 2013/12/20 09:20:44 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/fasttree-2.1.7.ebuild,v 1.2 2015/01/29 21:21:10 mgorny Exp $
 
 EAPI=5
 
@@ -17,9 +17,9 @@ SRC_URI="
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="double-precision openmp sse3"
+IUSE="double-precision openmp cpu_flags_x86_sse3"
 
-REQUIRED_USE="?? ( double-precision sse3 )"
+REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )"
 
 DOCS=( README )
 
@@ -38,7 +38,7 @@ src_prepare() {
 src_configure() {
 	local mycmakeargs=(
 		-DVERSION="${PV}"
-		$(cmake-utils_use_has sse3)
+		$(cmake-utils_use_has cpu_flags_x86_sse3 sse3)
 		$(cmake-utils_use_use openmp)
 		$(cmake-utils_use_use double-precision double)
 	)
diff --git a/sci-biology/hmmer/ChangeLog b/sci-biology/hmmer/ChangeLog
index 8c16ced781df..2e075ba33e1f 100644
--- a/sci-biology/hmmer/ChangeLog
+++ b/sci-biology/hmmer/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/hmmer
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.37 2014/10/19 03:59:06 patrick Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.38 2015/01/29 21:21:18 mgorny Exp $
+
+  29 Jan 2015; Michał Górny <mgorny@gentoo.org> hmmer-3.0.ebuild:
+  Switch to CPU_FLAGS_X86.
 
   19 Oct 2014; Patrick Lauer <patrick@gentoo.org> hmmer-3.0.ebuild:
   Fix header
diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest
index aafbbe62c4e2..16d8ffbc6e24 100644
--- a/sci-biology/hmmer/Manifest
+++ b/sci-biology/hmmer/Manifest
@@ -1,9 +1,31 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
 AUX hmmer-3.0-fix_tests.patch 873 SHA256 bcf31054c0b646973faa97c27c03dc80c335c43e5e07816a10a65bd596e65d44 SHA512 2b8e2856cfb91b382bfbb0eb290e647d62e6b3958cd013a34ad987b3d64c92485e45a51d35c82f0b6040b09cbf4142d1ba513ba3e1a4e3f750199a736b044a7f WHIRLPOOL a1a0e5437ce9df8a89158df48178edfe11b5f55f0f58c0891c87bd508cb70f6dd4d14f022200e386399afb85c1bfaea2f9c3389ff4224063fe9b7332b44f335e
 AUX hmmer-3.0-perl-5.16-2.patch 3751 SHA256 c0e2959cb6dc737b05260da6d9a28b466497c821a051d4bf031baab1b609c853 SHA512 33f39c00104cf3e78993ad5d915b181eee5a3a9193bc4d8211b15444a79c335ba97cab3da328483320f153f0b9164860d475ca34001515fff7b97e1c503f8145 WHIRLPOOL c9c52f74830d4f986bd89e027745256e82d9dc8a2df17d757e6ad13697203eabc96ff1c353b67e823004e5dbfeb2bde794c72694b8a6472310cd330fe8a3b6da
 DIST hmmer-2.3.2.tar.gz 1024933 SHA256 d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4
 DIST hmmer-3.0.tar.gz 3952015 SHA256 6977e6473fcb554b1d5a86dc9edffffa53918c1bd88d7fd20d7499f1ba719e83
 EBUILD hmmer-2.3.2-r1.ebuild 1167 SHA256 1271485785e17ec569eb0d365fba45c69b139b07cb10895915e9a5310d2ef670 SHA512 e5052196d46aea33e226e0415900fcd0199bafc541155703514ade71d023c7fd57e091a81e452f96da33b82d8b4bd9942606971d351363f65d1ab0aaac9c27d3 WHIRLPOOL 7e74318d70a6a5d31ae13b8d96b884a231f52ae3f3233b70c971b11bce16f14c79b9dca971a03779f9b1b8ea8c09342827523fc6a99f2eee7128698bc0e6abda
 EBUILD hmmer-2.3.2-r2.ebuild 1167 SHA256 c20259de9eaf43c769a1a6b84f10da749018e10e32ae2e04e51995f0b4fd00d9 SHA512 3bb066bdb150f24475fad61a006ca484e5b17e68ccfaf1afafce24188ba6be6ed1cbe9ae5c7514c260719d4010d0e0c313518dd6cdce8d3acfa2ca472215783e WHIRLPOOL f05db9dea180b4b63ac07f532dd40b5f6319c9f81409378d44b18bbb9dc0b2dccd536384eff88bac556f9d5aea024910654246c8913435e70279892fe463dc88
-EBUILD hmmer-3.0.ebuild 1005 SHA256 1cac35dfad5837d0f0b1922bc518051d402556e3c8df2b98dfa58a539aeeb347 SHA512 1e233b564e653f47a3b48bced6176e8645cb8b96e83fc1a02827188026c34a39aa40274dc5cc98fba2e4a16d91e10ba2121f172171c293796b15ae421ac0f837 WHIRLPOOL 2970e617fb385e6a17751b6327ebf3ccd817fb336ae6f2f1e03cc50f2c301d30d622fe756667b1083018871c9b0e6a6dd6101b4a5c6e8728743fe73a10ee4ff3
-MISC ChangeLog 5316 SHA256 7b611d0d972d8d15c90c37025d9a1a00ff66ee4330ae622fc51f802eeb6aadec SHA512 fb20db787f37c7de12ecd908912f7838d9fce51a4ac68767d355478c694b85619fcf7807bafd55ab8a892b5f192d1e5ddc5cda8eab79471d442f64b2277bc266 WHIRLPOOL f60a10b0ec12c8c000b93058b3d3f9aa369af7df4cfbfca8302a75d765ab17babf34b2101c15fb58c6293f7de33751d0c3d1ed7fb217a6ae650ed2888558eb2a
+EBUILD hmmer-3.0.ebuild 1036 SHA256 fe399426a9e5e0bc3446cdd7c62ba9adf99f30cb418d9be46c4716b010d4c1e8 SHA512 9cfeb676ef0e10e83929c4190b6f4edcac0eea7091bd9a6ac9460ddafdd0815fa6450bc1536d3a4f02070b0a3f7946e9395226c91cefd87263c5b213f6f01790 WHIRLPOOL 1b3d85eea643fde860a286c9236d8ea536f9e1f212645ce0c298516bcb782bf02b954d376ebb8f41b166b3ed4c51081e2d3e585b1c6153e846e966af11f9d7b2
+MISC ChangeLog 5411 SHA256 6c0efb04e2ef19c016477e9f09f43844dbfa6561d0a30017788970911add7c8d SHA512 119f27f43cb815065b027d436f8e8ef81633cfb918327ff989f60728442f116ce00609e2cb8d4842b1430dd7dbea04927edb1c736217a4c59470a09a65a5c07e WHIRLPOOL c4503f79cfeef60de665e55f3138c1e261073e5751842a4fc51b0a3c70f1d9302bfd51bc97a762a6723777f1737879caddef85f582a314310932cfdf447961b7
 MISC metadata.xml 280 SHA256 ad90b4124fcc2ef68ba69b1afc073dc2d3178bade4286b8fb83a90df6f0e9843 SHA512 2ddf9319b34233fe7124ed7148d1eb6ac34801efeaa3d3ce2d1ce83526fd86d0eea5e9e628ccb4de85bd492c1f513b43847308844aa41ce71745768ca8d51803 WHIRLPOOL a0cf35c0ca9480cabb8ab44e901c477f673601d255380fe5d97dc22a59f1192a3bd2e286d7b8fde40668f1820600ecee9f63b6562b8ca9e180c8dfebcb22e5fc
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diff --git a/sci-biology/hmmer/hmmer-3.0.ebuild b/sci-biology/hmmer/hmmer-3.0.ebuild
index 6d7a38c05831..1fad74a4c780 100644
--- a/sci-biology/hmmer/hmmer-3.0.ebuild
+++ b/sci-biology/hmmer/hmmer-3.0.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-3.0.ebuild,v 1.7 2014/10/19 03:59:06 patrick Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-3.0.ebuild,v 1.8 2015/01/29 21:21:18 mgorny Exp $
 
 EAPI=4
 
@@ -12,7 +12,7 @@ SRC_URI="ftp://selab.janelia.org/pub/software/hmmer3/${PV}/${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
-IUSE="+sse mpi +threads gsl static-libs"
+IUSE="+cpu_flags_x86_sse mpi +threads gsl static-libs"
 KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos"
 
 DEPEND="
@@ -28,7 +28,7 @@ src_prepare() {
 
 src_configure() {
 	econf \
-		$(use_enable sse) \
+		$(use_enable cpu_flags_x86_sse sse) \
 		$(use_enable mpi) \
 		$(use_enable threads) \
 		$(use_with gsl)
diff --git a/sci-biology/raxml/ChangeLog b/sci-biology/raxml/ChangeLog
index e09c69b0a742..3adbd6fe1357 100644
--- a/sci-biology/raxml/ChangeLog
+++ b/sci-biology/raxml/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/raxml
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/ChangeLog,v 1.9 2013/03/11 16:51:35 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/ChangeLog,v 1.10 2015/01/29 21:23:13 mgorny Exp $
+
+  29 Jan 2015; Michał Górny <mgorny@gentoo.org> metadata.xml,
+  raxml-7.2.6.ebuild:
+  Switch to CPU_FLAGS_X86.
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
@@ -45,4 +49,3 @@
   03 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml,
   +raxml-7.0.4.ebuild:
   New package, ebuild written by me
-
diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest
index 3a3fad5e9595..393b4f726494 100644
--- a/sci-biology/raxml/Manifest
+++ b/sci-biology/raxml/Manifest
@@ -4,13 +4,25 @@ Hash: SHA256
 AUX raxml-7.2.5-makefile.patch 1420 SHA256 f3c9d9eaacf7a7e0d1594e3d689f938ff82c2dbdb4c4c4f2ed81a861ebd7adb5 SHA512 f905bfb638396c81ccd5f66deaf39c574bb9d97a94ff78b786214390f2ac715b7d4e251ba5d13701805f3928f450b6affefce565e7c30544d32e33ed6e5f20ca WHIRLPOOL d26222d935a8462cf10b6244ed043f1437038039c24486993c022332a7148bdd759704a9698242a1bbd60053afde0061edc31684c022085eb0e041e38818c42f
 AUX raxml-7.2.6-makefile.patch 777 SHA256 0e87b5cd6375669e660ef6e3c37e51e751ea8846de6c52060f484380c28610d5 SHA512 0cc326e8fed0882c56193fef9d1c98577f2252acc4dc25e650e0806d89ded0e2911e6967272a6d101cf830cfe63a190a8f5220fd7573864f5fa60106069ad74f WHIRLPOOL 896bb8f27d458e1d555ffb462abf89f55c487e595a604b3446c579a2e95719cfdfb1911873ca2570a73c3299ef49f0c489ee0c127fcb6e1acdcf907c748459b0
 DIST RAxML-7.2.6.tar.bz2 202803 SHA256 d45bcbe45e3ed5f8d6ba3c99b9da9b202c72a9fb196a9d32d2961ee4cb791868
-EBUILD raxml-7.2.6.ebuild 1104 SHA256 6c141557e09ffaac2d2d46f20b485b2ecce7ff12e319f6a47ea40289cf278e1b SHA512 4e7698a094f2b38b24ea81f4ccabbdcf63dd5e252dca889bb4fe50ffd9cd2123ad2565e265cd4663472e2a285f1682c6fac55603ef4e52a2dcda8a3f57e65c0a WHIRLPOOL 0ec5e308140d97f52c350e6c9c7ea727452b6f02139f97bc06d4415aac6d0c2a6a2132d3181b6c7996e5b2620fa3de33825bb216de5fd97e334fde3ab7071943
-MISC ChangeLog 1610 SHA256 5a7bfd23287dfe8c01913a94b7bd97a87c732823b0cd782ee4c48fcb011021e7 SHA512 ba1badfb098010e4a3621030f5b8a337820768391f91dc3ce623513cd60714f50f8c9a852a1c44feb67d2fa9854460fcdb63161179858342b01cc96ff195ecab WHIRLPOOL da8ac212145c07d491292c6b30a7254f46bee14d2d9c027a0e983f2c06d2303b97116219a1e23f0d82e068db863a326f39371ed2ea030ca8b37082d3ae581c82
-MISC metadata.xml 255 SHA256 efef11e470e8a0b8f3c364f48d5882986ea851821f72b5e6405704064b78cff7 SHA512 5175ba8b0cd526f6e1bacc5ac869e01d722133b03994f4322def1b135b5ca780b9b0bebbed9934005164dcebc79375f490fbce93bd5dd297d1b123c659fbb4b5 WHIRLPOOL 4a41cd8d6ec7637797148a53dab83386ff9b715ff261e79d7c298f8248877b40a6123de45f30bee87703df74fa487308d4679eb66c8e5caca64dd5477312f524
+EBUILD raxml-7.2.6.ebuild 1148 SHA256 050c95bdbe3c44d67e2f8c7f0ee2e1f494a929a0ab60362f83e5b3795354c658 SHA512 d7a4ee0de7613b52be93ad0d3f00bcb34f42c95bd8e8147cdfe9bea3b7495c5a0f4985bc09136f2b2a9c0ebeb32ecb3b68e3488fe157ba169d4a316198e2a25a WHIRLPOOL cee4b3a75cd89f2f950201f3d5bda20b091529b5969da905eec882eb7f786d9d6c93bc90a54b798498a30471bf40563275023d18df3f0da6ac37c126cd5e45e7
+MISC ChangeLog 1726 SHA256 13b6ddaba0ea1291a0112f04757aabb0c22edb9c89f9a4dfaf5b57884aaf0a09 SHA512 6d39e961477e5bdce29f7ff0b76ea1130e8f4afa06853f30713d5c88dcf72a2bb9f2351b98cac6f2f1dc7c87ac5e35182ab77cca46f46ac428e1a94e7e50a9a2 WHIRLPOOL 58022cd1fbae658bdc3f722c138e497d27e0fcf52ee0dea3c1e9ee5e795a0f79c54e3ae240a48cf0f39132440c36a3ecbf3b27388bd411a02687d1e0883723a7
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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-Version: GnuPG v2.0.19 (GNU/Linux)
+Version: GnuPG v2
 
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+=ZrhK
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml
index a3e4f8598df9..f17a827e3101 100644
--- a/sci-biology/raxml/metadata.xml
+++ b/sci-biology/raxml/metadata.xml
@@ -2,7 +2,4 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
   <herd>sci-biology</herd>
-  <use>
-    <flag name="sse3">Enable optimization for SSE3 capable chips</flag>
-  </use>
 </pkgmetadata>
diff --git a/sci-biology/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-7.2.6.ebuild
index 6339dd23bc1c..c8e23c50ca8b 100644
--- a/sci-biology/raxml/raxml-7.2.6.ebuild
+++ b/sci-biology/raxml/raxml-7.2.6.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/raxml-7.2.6.ebuild,v 1.2 2013/02/18 12:20:50 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/raxml-7.2.6.ebuild,v 1.3 2015/01/29 21:23:13 mgorny Exp $
 
 EAPI=4
 
@@ -13,7 +13,7 @@ SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2"
 SLOT="0"
 LICENSE="GPL-2"
 KEYWORDS="~amd64 ~x86"
-IUSE="sse3 +threads"
+IUSE="cpu_flags_x86_sse3 +threads"
 
 # mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS
 DEPEND="" # mpi? ( virtual/mpi )"
@@ -22,13 +22,13 @@ RDEPEND="${DEPEND}"
 S="${WORKDIR}/RAxML-${PV}"
 
 pkg_pretend() {
-	use sse3 || die "This package needs sse3 support in your CPU"
+	use cpu_flags_x86_sse3 || die "This package needs sse3 support in your CPU"
 }
 
 src_prepare() {
 	epatch "${FILESDIR}"/${P}-makefile.patch
 
-	use sse3 && append-cflags -D__SIM_SSE3
+	use cpu_flags_x86_sse3 && append-cflags -D__SIM_SSE3
 	use threads && \
 		append-cflags -D_USE_PTHREADS && \
 		append-ldflags -pthread
diff --git a/sci-biology/shrimp/ChangeLog b/sci-biology/shrimp/ChangeLog
index 10e34284e59f..971488086dcf 100644
--- a/sci-biology/shrimp/ChangeLog
+++ b/sci-biology/shrimp/ChangeLog
@@ -1,6 +1,9 @@
 # ChangeLog for sci-biology/shrimp
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.23 2013/09/05 19:44:46 mgorny Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.24 2015/01/29 21:21:30 mgorny Exp $
+
+  29 Jan 2015; Michał Górny <mgorny@gentoo.org> shrimp-2.2.3.ebuild:
+  Switch to CPU_FLAGS_X86.
 
   05 Sep 2013; Michał Górny <mgorny@gentoo.org> shrimp-2.2.3.ebuild:
   Clean up PYTHON_COMPAT from old implementations.
diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest
index b4b6dd114bd9..2c1de37f96a2 100644
--- a/sci-biology/shrimp/Manifest
+++ b/sci-biology/shrimp/Manifest
@@ -4,25 +4,25 @@ Hash: SHA256
 DIST SHRiMP_2_0_1.src.tar.gz 158535 SHA256 62557cf256421aea17a2b221ef485410be177cfc777a6bb8a3de89718d186f63
 DIST SHRiMP_2_2_3.src.tar.gz 4596867 SHA256 a8bed999baeda2ae17ae5c128b2161b20b896228d754e6e446439c1040d6dd8c SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5 WHIRLPOOL 84325b9db3f2e10baa3db935d6e3e2ecae9fd0f47cf5666ea7493f7a975fcd31515f2c77dbe8fcf5cfa099ac2735973e791fa96f0fe8371c5279353bc3f9995a
 EBUILD shrimp-2.0.1.ebuild 1390 SHA256 1300b850c9856da0ec493c88e0701cba5269ed6966ec97f8cdd448e2b9c4320d SHA512 b52b2b0ea20fcd691d9f0b390232044ca571e724be2a910bbfaa75cd7e68adab1bcab6864b14fc7b4c4beec577d140afcbc2c5a287d2c2911a39428ce18c6bfe WHIRLPOOL 7c7cbb027c1c89506d30119f94b0ad92282d288a628d32990740c4a11e9f0cc92ce6be341f389b443fceac5734abeabd0aa6fd2a1351e9d856c38c6c4c761f09
-EBUILD shrimp-2.2.3.ebuild 1909 SHA256 8b1cadf98cf6d6e460d2092cc362ef1c35dc6140c9eecfd63fcf28cd1c8d4849 SHA512 a695c3d190ea4549f8fd10ad85bfc028a8a9fb5246b55db8a2d83026409a5ab27d54a972dc1285d74eebfa6210baa782929819d3c46902a57a64810e4a05b57d WHIRLPOOL 181919aadc5a596a5a3a435809d14525b0ad670b13de4561894f574266e883182f0fcf7610edba175ced6e77bd0a30f7c19bfc5036b795fb2ee2a552d5542edb
-MISC ChangeLog 3373 SHA256 28dae1845f732737a9b0505441b3426817dcfcd17a055f3343b7f272f6b711db SHA512 5fcda3cf8769b8468f4b89e44e2948000058765ec76bada1253bdc203362ca3ff3f4d6cdecacc273f15cd9c4d1aa01c69b7a7d5210effee2d8d8999f97d2024c WHIRLPOOL 902b797111e0871d42faf2f61335983d4272dc9c631edac268423679cfc690b9218a5f387f5b4ae80e5e3461d98624ec1d3da995deb77b803ea003842b0759e7
+EBUILD shrimp-2.2.3.ebuild 1937 SHA256 e221c8a90dce15f51a2bf6fa6676263ff80db9d30b9198882247d437c3512f85 SHA512 8c1621467101644b67fb1fa39b14554d07139f9d8137fb707366856fcbf739e0050162d9df8ea71fc95ee9268d1e071165d0341bf28f9c171e39dc24e9beb636 WHIRLPOOL 2603ec6cc8dbd15ff43ad64e17194931b46a91f3c156a015624808b4ab574c49dae843d1f9cc1bc415c7ce315476b797cefdfa13996d6bf2c84e502b7c0714e4
+MISC ChangeLog 3472 SHA256 ed452b13aed56d5dfa5d585bc00ba8a9f53762deddf52d93dbf94a5bf2f4e2b9 SHA512 45214449cbc70a56bd631e3c128c3d6a91f1807e8c5eda1c2002fa1577e62ce819ab942102acb218c9ea32787d348986b02bc43ecfd921778f082a87f2d1df2a WHIRLPOOL 2e23290cabc62c6e56cf684d9ebea02bbca1b44ec54096bc6e7572e22a3517cde539fd55a73e8ea55f3e366e44d96afc61f1286c54acdd70040b09f9e2bffeff
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild
index 85b72f77eb79..36748e7ed597 100644
--- a/sci-biology/shrimp/shrimp-2.2.3.ebuild
+++ b/sci-biology/shrimp/shrimp-2.2.3.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.2.3.ebuild,v 1.7 2013/09/05 19:44:46 mgorny Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.2.3.ebuild,v 1.8 2015/01/29 21:21:30 mgorny Exp $
 
 EAPI=5
 
@@ -17,7 +17,7 @@ SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.g
 LICENSE="shrimp"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="custom-cflags +sse2"
+IUSE="custom-cflags +cpu_flags_x86_sse2"
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
@@ -29,7 +29,7 @@ RDEPEND="${DEPEND}
 S=${WORKDIR}/SHRiMP_${MY_PV}
 
 pkg_pretend() {
-	use sse2 || die "This package needs sse2 support in your CPU"
+	use cpu_flags_x86_sse2 || die "This package needs sse2 support in your CPU"
 }
 
 pkg_setup() {