sci-chemistry/ccpn: Version Bump, drop broken

Package-Manager: portage-2.2.0_alpha191/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

7 files changed, 27 insertions, 521 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 30bd6dc14578..62d15db9f448 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.112 2013/08/01 10:43:28 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.113 2013/08/08 06:51:10 jlec Exp $
+
+*ccpn-2.3.1 (08 Aug 2013)
+
+  08 Aug 2013; Justin Lecher <jlec@gentoo.org> -ccpn-2.3.0_p130705.ebuild,
+  -ccpn-2.3.0_p130709.ebuild, -ccpn-2.3.0_p130710.ebuild,
+  -ccpn-2.3.0_p130801.ebuild, +ccpn-2.3.1.ebuild, -files/2.3.0-parallel.patch,
+  +files/2.3.1-parallel.patch:
+  Version Bump, drop broken
 
 *ccpn-2.3.0_p130801 (01 Aug 2013)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 87f7f334942b..bc91c9a4b717 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -6,7 +6,7 @@ AUX 2.1.3_1-impl-dec.patch 2818 SHA256 f175a1b4a9cc4f1636bf36928883d37a266af8302
 AUX 2.1.3_1-parallel.patch 577 SHA256 7e650ef2fa1ff0626349affdf1bc9578fe1da3b8cee7dd9125d33a2164978b69 SHA512 c8a94fd6622dfdd90dc2f40ce2aea3440a1cb2c56e4143339675995e8cf29dfb73e4e501117db1e1f6c6cbcb62d49dd52a4c239680c2c4db6145f9bbbb2486af WHIRLPOOL f943d5bcef2ae2cdf969b15e03a50c5cb3cd640c6e7400657c78b2120aa0bf7847c93bc652dfc0510bee11b9c2d1a8cff9e8deb8946bf07be6055a6259458943
 AUX 2.2.1-parallel.patch 850 SHA256 318bbf3ae5b04e8cbe0e8e93a7e81a7e793fffa9a0d754464367092d6b79f04d SHA512 332815d3eec610eb2537c3bd803941bff06aa64dddbe730a53657be6139a4ef294995c0a1c962abddef7f45c756fdce4c21616cfee3222dd4005228021745da7 WHIRLPOOL fc97aa74630c0be0372b8c863fc985238cd16849c0f69cb60e483a88cfbe04faea1448ca656a83ed56c2599a45d36869dd293163e4faf240e75c1ffcfe54e204
 AUX 2.2.2-parallel.patch 850 SHA256 318bbf3ae5b04e8cbe0e8e93a7e81a7e793fffa9a0d754464367092d6b79f04d SHA512 332815d3eec610eb2537c3bd803941bff06aa64dddbe730a53657be6139a4ef294995c0a1c962abddef7f45c756fdce4c21616cfee3222dd4005228021745da7 WHIRLPOOL fc97aa74630c0be0372b8c863fc985238cd16849c0f69cb60e483a88cfbe04faea1448ca656a83ed56c2599a45d36869dd293163e4faf240e75c1ffcfe54e204
-AUX 2.3.0-parallel.patch 850 SHA256 38f796a18c75b2ffb1168d22d1e1453faa480e4c8b0e3d75db2b0603ac4d6788 SHA512 0597e21c03baa27e2342249814fc0700b73cf2800173468574ef704d48f7e6e042ac6ae552bbb9e27fd4baca36cfaf60a1eac9813354916b3e8295a35b64dcdf WHIRLPOOL 7fec03d065add264de91aa07c211003e2471e77035f36c497c325c4319e999d83c06ef6f496ebab966d0877c89101e26ec7ce86ea8b740973c0254ad118e3e26
+AUX 2.3.1-parallel.patch 850 SHA256 38f796a18c75b2ffb1168d22d1e1453faa480e4c8b0e3d75db2b0603ac4d6788 SHA512 0597e21c03baa27e2342249814fc0700b73cf2800173468574ef704d48f7e6e042ac6ae552bbb9e27fd4baca36cfaf60a1eac9813354916b3e8295a35b64dcdf WHIRLPOOL 7fec03d065add264de91aa07c211003e2471e77035f36c497c325c4319e999d83c06ef6f496ebab966d0877c89101e26ec7ce86ea8b740973c0254ad118e3e26
 AUX analysis 319 SHA256 0731b9a1624259b373c7163c6ad095c82f77965f0b61880e84bc8e3c30b83d6e SHA512 68f5f0973682ba0e32f400e5d9bb04edac895552f3bfcdbca3f2ac74ce1de49ab59dd88b6fcd9fd4e2c085fe2c0b4843a8f20556d05bfc8aa9c1bb6ca0fe46df WHIRLPOOL e262996c20d72976414a013d4a956c469c139b7bfffa9b2ee5772280853644be7fc61fd0a455915c2f2d367c63ec31fda50e62b2e5abdafec34f51d936b9cf69
 AUX dangle 315 SHA256 03101ba39fc9fef1380315c2c64f9d027fb95b79d82c35b9971445613ad5774d SHA512 4e5d254df831bad683770dbf8d0845ea64fe781c3f5f14301ded6dd4efcf3bef06327bd83f5f38d1b9cd2e1d04318cafbb6185d607617357df2256ef38cca1ad WHIRLPOOL 933787db14c1f3b98ceb347b991769f196bf8c34b87acdf73ba72c59c6aad2ce6a6926e153eeae0f86af60013a85632a7d54403979452729bd31cc8d44b55248
 AUX dataShifter 318 SHA256 891f87e2eaae88253ffddd4e71b060f8b8e7711d54a02492117500186f04f45d SHA512 63d4f12afabd94c7a11f930d13eb27e5c1273057cfecfd2350833782a0089e84977a086fed6ea2adbe704a55d1f5bbe3a5497d2b8ea6ec9dc1228067e7119034 WHIRLPOOL 7849869b0e761884ee8ac462acd666858244044c4866ab1db4d32287e8f7f342d4ef21d9307da7e2990da8f1c5cbf696fb59c3980a32ae4e3cfbd33b8d8a0f01
@@ -18,8 +18,7 @@ AUX pipe2azara 326 SHA256 8b17d8c11dcbfeac21da3ad927e2e8de73509d21e9250c328fbea1
 AUX xeasy2azara 324 SHA256 89945dae1c7bd78aefdd19c81c79571a13aaa149d6c50e12cc0ecd075930ed4c SHA512 de31df36c259fa58483c6a0e24bfa6ece3a86db5d556c5c99f610c7c2ff659742fcf319ef387538cc5a74444bf4be8ffff96da7ee819ac583e2605f4f90a5806 WHIRLPOOL 6a40d21fa7cef520de86f04282b5e26e3a8809c7a8caed8e19a0758419039358e1b1f33a53f956bc77a10cddda703cce8f21584d8e9e3648fccca3a486ab9be8
 DIST analysis2.1.3_1.tar.gz 18932918 SHA256 bbc1ba5434f896d38b6745c1dc9adc470a78d3be7b879160edcd635a19228b74 SHA512 ee95119a972ada7949d646e0fd634d1828bba7562d7ea3a3be1c2b17d22f194dbd1267716f21ce86fffb3eadec136b0b613705f862747ab7933cb2ad57e063b8 WHIRLPOOL 1fb19a4bc676955eca4168595fad0661054061e18fa6e25e7f4ed5026cf31faba75b7644a8e2e18ece10e9641efc81feaccf580d3c766bda1d5232a346d99133
 DIST analysis2.2.2.tar.gz 21044504 SHA256 8e46d12b8fb7763d282933e14ddfa9ce197954ed9fbfa2333e22602ac841b6e5 SHA512 efe8a82381521dbfb95b12dd553f401f200aee3763f9e739c37a9141a14bf038865b2a860b0353adc532582697b58079034386be42161aecbe231952b8abaac7 WHIRLPOOL c9d7fc936dc25b952e711e8fa439ada5a67e68497b6d4ad034586e604bcbd9d1ff7dd48d1a3baace347fc9bab5c17d2f7852906f921708a16ce8c8eb4a8659b9
-DIST analysis2.3.0.tar.gz 21638757 SHA256 4dc693ed2a11bf8707477b4ef21d53c29a9f10c4540f57b2945b9249206b0b50 SHA512 b51e82329e3ee88f7040a256dd8e40121f1f7bf000b98ea8304861bb29b6f0000b61d4f81f9725df3e56641004679105bfa9b3878c447ddde5acf1fd56d010c5 WHIRLPOOL c0041b2e03d3efb8675c119217a09d4495355ad2242d2f1ccf1cacdd77f0461a5a7139d48ed33e8d72e541013513f93e1cf4742f0e9c127f3006621a987dbbbe
-DIST analysis2.3.0r3.tar.gz 21638769 SHA256 e503b88ffc166f40841dd4b0c1ba2712d2dfeca32df0efd8dbf1906319060549 SHA512 da6e07bb10abed5380b23660c6e0394d8f468b7d62cfe3210172f9462d272e129ba04e618097369898c17744751fec4a69074667ee06945af68f6c21bb2c7ec0 WHIRLPOOL b6e1ed35b008864503b39733ed75f2fff972884ff8488ca721ebdf5f77e1cad618dc6c637e2ef898c07b7d10acd1fa2e895713fdd586263d07dd7b79a2a729fd
+DIST analysis2.3.1.tar.gz 21702376 SHA256 892df0e2d999a9cac75438c5357d8766c9aa5f7d0d575e798d92638df26165e6 SHA512 34a86020e764bed9e85870a55896f9aaafdab4b50be6fca17d35830d013a314fbdc3d1609024b1d5ce8bfa306a3e5a39af9c70a751823adc12d38a26a424ff3e WHIRLPOOL aa7b4a3fd9350c9b98fa9226547635692eaff4a311951b2e89b493b258c1dc8353b9945fde46fc0fee4990cb4caa5615326e81532c579db34807221bdcb72e20
 DIST ccpn-update-100806.patch.bz2 187965 SHA256 5cea7899edb96237a6674f04a1beee6ad7b309e12964ea8b25d9ea6ff752d0d4 SHA512 ab145f14137955bcb4dcc4d242eb718a806152bf3376e4cc9ff5e8186ed54812051ad07de1c9d2316ce3379c8c74db4af36f714aa3291ea7a1d11d4f432df06f WHIRLPOOL 2a0cbf62aca74e22fc0e00a0a91c3c185c10fb07277ba30791511565a2fa645b123a8c5164389eb9fb5a2d1f591e26c6416c46038acceefa2f1ecf347b631a66
 DIST ccpn-update-2.2.2-121125.patch.xz 223556 SHA256 996f453d7d6a143715a94b1201bd7b8b9c037f6d0baa342f5c0645d500aa5c79 SHA512 d213e072a63110ec478c3ee64792b01c818d3c9052ae6d7dac903508536f78c432c72d5a4756665045579d72f4f54ef5ac9db1fb02eb5ea3111eaa47e72866b0 WHIRLPOOL c268761e4d9cf4c845964c7c865e20439a9cacd00bc56d89d8558e0f601fc9840d4288307c4a4f47ba6d478eb9da9dacd1e149c657d2e6506ef5e32d6b0b75d1
 DIST ccpn-update-2.2.2-130110.patch.xz 226800 SHA256 6c0f4d71322e45ef24a15f1e26eb5d4104499fc2391660e575158dc08ae0380a SHA512 2fa7e782ca30402c91793032dc0d4555d9e866ba11b03f8f4b06891c8c80d256f5598bccfc99e9a97ae9b3618b1c24307814de4656087e2c0b40d378df743e47 WHIRLPOOL 5a49c0480328e7b03691a1e63fea339e2a9a29afd845babcce70e57b6e8d6ce21a5cb612d856c22bd3a9033a9ab565b0149e61435bc31ffdf02e247051e29d6d
@@ -39,26 +38,23 @@ EBUILD ccpn-2.2.2_p130318.ebuild 4647 SHA256 3d0ed95475a6b6b883f30e51ab9ffd706ce
 EBUILD ccpn-2.2.2_p130530.ebuild 4649 SHA256 71865dc944175d9c8d89841b4f6901f228500832b0b04d27b42cbc85c229dbb1 SHA512 12841f1ebbdffb965045bd8aafe61f6cbad80faf82289ea77b4a6a0feb5957485b8146d8bbbc8b6c021a0c26684db85f7227953f89bbbeba12c789ce12cd3f49 WHIRLPOOL d22902143e22969661581581e58a2854003aefaaa665d878d69ccb24672ec5e724ed3bd3e178442724a816f9d1d5b46f3f53b29abc4c2eca8da7df67e3049b64
 EBUILD ccpn-2.2.2_p130618.ebuild 4649 SHA256 b207878c8186f25add8b44b09e0565c0659a72d55a683ba542d09184c6cc108b SHA512 5fb2620d6b12e4a94ead6158538634c5a842b097dcfedaaf570135adcdfb2d5119539c8306abd5ef43293385cf1aacfdc6e8de7e2963ed4c25ccaa727dac4945 WHIRLPOOL ac4561982960cf8d02d864112b97b00ce6af4c0b6a1190a08330a9effab7b41629d1681bdc0bf090faf3d6266549a17e9790b86b4e749b3718717b676197c2eb
 EBUILD ccpn-2.2.2_p130705.ebuild 4649 SHA256 1b3a3af9673c488457fc4b62074178c04c6aa67ef7db4bf1be13c628e8103a06 SHA512 e763f62dc24f181831ca87e301b889e2308a2d3ab34aea5934978cf509a3bc8387c68055d4f18ddc4cebb3d149e0ff0d3650d3dd80d616b551906a5568fdf405 WHIRLPOOL 3d41deb0023bdda918f3745c10f107d787388c88b68e98ee224fcb840029700b01405b2d3185a24c87f695b9dac071c9894376b053cbf961cd3db28190e9a171
-EBUILD ccpn-2.3.0_p130705.ebuild 4717 SHA256 3791c502fab4c7dffd98eb18b41ae7642f687e2763ae9496dfe9927964bb8a03 SHA512 2b1a73869bb1bfd79522432395e3cefbde8fd5e6158d9a87ee8f5977beadefe1feffcd4256888a66baa4b41458a6e327b9ac935dad60779a51fc3d4c04a24d39 WHIRLPOOL 52e733e610056e39a04fe75f6d2baafaf07048044f329408dad336561b60286dbb2b3d84191ee306bea57011d8bffa1b5e43d2b9b5c11570e9565cf3acd97b5e
-EBUILD ccpn-2.3.0_p130709.ebuild 4717 SHA256 a6d50c3708a40d6dd9c513fa0f54b431166ddda300c7f2a0c4992a8f1968549f SHA512 97f2a5b2b43fc7973968bca51d53efa4c6756e868037947271da3f707106dfe93c36e1ac665b0cc49e0dcf010654d2fdaad6626ae9c0f96cee68d09e4c2203f9 WHIRLPOOL 3b1eafb4a19964b81874f2569fc24239cb4095e4a9d7a718917148e57906deb578a0fa6ce160bc351f4ae54acb655c0556e605ac3cbb7f9c2bcd90665670a1c3
-EBUILD ccpn-2.3.0_p130710.ebuild 4717 SHA256 b09001eee288136722cc618c24db605abfa2c96f25152a2b77e600421fd94c63 SHA512 1ee3cc63921ba85f50ec2b287a12f925a30da641affcc961b848b501c44539c3b393c51d7f5c461107dd8e9a8e699331a67fbe7a4a2621dc3eede8f9f3bc8975 WHIRLPOOL f653b1bb85689f331b8d201484f7134ae75840f779a7a61699a0a810c5a8e7859a554e30b325008f66e4f1e9bc42eae1563b3fd2289de248b138d34d946224ab
-EBUILD ccpn-2.3.0_p130801.ebuild 4690 SHA256 5aa7e80ea1e951d05b66dbf8e41bd19e143aad0704e6eef1b442da081741b94b SHA512 b47c57a93be782a5fdd32c1e0b31c673d83532018ee6878a4f0ed91412fc879e8a43cf08293aa8ecf5d47de14853a8bbb9e2ce7c85cc2ed73d6a1b0ec85464a5 WHIRLPOOL 5ff65334df73dda827254420fc2bba58a457d9d4913e2c4d65e27dc2ba80ed10b2d9f8188615f49c8921069eae9733b68b912114eaa8a72bebf99ba9699ddb64
-MISC ChangeLog 21744 SHA256 a29a9e7b93acc1736c0350e89c97c04ad2f01f49e557015297cff5249cc088ab SHA512 1165f1e74b6f8f95ae23d52401541d89ef905ac376e76abcd258b66ea2707bece29b77945fce153b9a118a393f4b154d9130baebc4cc9c77be6f3715cc336b02 WHIRLPOOL e517333044624940c35219b8f89eb3c40c914309e6953beacf1ff2d4b60ec72cb369543f665ae8a85d5c360fbf0c73ba8571bc29ee3a3f351ac3d63f709cab95
+EBUILD ccpn-2.3.1.ebuild 4709 SHA256 ee3050fc0fd62efdbb32fc84e89cd11bed3570f3021909490d1080f76fc260fe SHA512 a03d3c1a8f517b9be2e093872288e0a8a14a93b5131b3b1de7a2d20f3e9569c5d0887e268b8b6a182195b7f595e2ab05e4f77716351e4ef8d8375af325e71bd3 WHIRLPOOL 4f810a4c972bc77a08b18d816606844f5f58556dfda2045907b549165a0638f99b55281677d958e19c8e84d87a75f46e7df55998427e706d1fba9f71a6b95f94
+MISC ChangeLog 22043 SHA256 95acf0c123907360f2201b53ce3dd00c8895614493200cf1ba90b4d9314115bc SHA512 e930b5850cd2b421abb52ae30eeb7b7102d72f72fa4d38e68e120a467798cccf8cb55f3db91a595ba8c6844da057368d4abc3baa7bf80c389378bb60ea5ae179 WHIRLPOOL 75040b05d032dc2f6e03cebf4a416694d0bdece69d13ae77914d0bab2bf321a005f450f05d9f9a0a30e602195a5966ef13b755bd46ccf44ee424c183148e526a
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.3.0_p130709.ebuild b/sci-chemistry/ccpn/ccpn-2.3.0_p130709.ebuild
deleted file mode 100644
index 91575733e1e9..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.3.0_p130709.ebuild
+++ /dev/null
@@ -1,166 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.3.0_p130709.ebuild,v 1.1 2013/07/09 07:22:10 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_5,2_6,2_7} )
-PYTHON_REQ_USE="ssl,tk"
-
-inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
-
-#PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}r2.tar.gz -> analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] \
-	&& SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+opengl"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	dev-lang/tk[threads]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-tcltk/tix
-	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
-	sci-biology/psipred
-	x11-libs/libXext
-	x11-libs/libX11
-	opengl? (
-		media-libs/freeglut
-		dev-python/pyglet[${PYTHON_USEDEP}] )"
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2)
-
-src_prepare() {
-	[[ -n ${PATCHSET} ]] && \
-		epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
-	epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
-	append-lfs-flags
-
-	sed \
-		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
-		-e "s:weights_s:weights:g" \
-		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
-	local tk_ver
-	local myconf
-
-	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
-	if use opengl; then
-		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
-		IGNORE_GL_FLAG=""
-		GL_FLAG="-DUSE_GL_TRUE"
-		GL_DIR="${EPREFIX}/usr"
-		GL_LIB="-lglut -lGLU -lGL"
-		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
-		GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
-	else
-		IGNORE_GL_FLAG="-DIGNORE_GL"
-		GL_FLAG="-DUSE_GL_FALSE"
-	fi
-
-	GLUT_NOT_IN_GL=""
-	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
-	rm -rf data model doc license || die
-
-	sed \
-		-e "s|/usr|${EPREFIX}/usr|g" \
-		-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
-		-e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \
-		-e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
-		-e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
-		-e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
-		-e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
-		-e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
-		-e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
-		-e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
-		-e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
-		-e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
-		-e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TK_LIB =\).*|\1 -ltk|g" \
-		-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \
-		-e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \
-		c/environment_default.txt > c/environment.txt || die
-
-	sed \
-		-e 's:ln -s:cp -f:g' \
-		-i $(find python -name linkSharedObjs) || die
-}
-
-src_compile() {
-	emake -C c all
-	emake -C c links
-}
-
-src_install() {
-	local libdir
-	local tkver
-	local _wrapper
-
-	find . -name "*.pyc" -type f -delete || die
-
-	libdir=$(get_libdir)
-	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
-	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr"
-	for wrapper in ${_wrapper}; do
-		sed \
-			-e "s|gentoo_sitedir|$(python_get_sitedir)|g" \
-		   -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
-			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
-			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
-			-e "s|gentoopython|${EPYTHON}|g" \
-			-e "s|gentoousr|${EPREFIX}/usr|g" \
-			-e "s|//|/|g" \
-			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
-		dobin "${T}"/${wrapper}
-	done
-
-	local in_path=$(python_get_sitedir)/${PN}
-	local files
-	local pydocs
-
-	pydocs="$(find python -name doc -type d)"
-	rm -rf ${pydocs} || die
-
-	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
-	sed \
-		-e 's|#from __future__|from __future__|g' \
-		-i ${i} || die
-	done
-
-	dodir ${in_path#${EPREFIX}}/c
-
-	ebegin "Installing main files"
-		python_moduleinto ${PN}
-		python_domodule python
-	eend
-
-	ebegin "Adjusting permissions"
-	for _file in $(find "${ED}" -type f -name "*so"); do
-		chmod 755 ${_file}
-	done
-	eend
-	python_optimize
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.3.0_p130710.ebuild b/sci-chemistry/ccpn/ccpn-2.3.0_p130710.ebuild
deleted file mode 100644
index 2f29119c7ade..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.3.0_p130710.ebuild
+++ /dev/null
@@ -1,166 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.3.0_p130710.ebuild,v 1.1 2013/07/10 09:03:41 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_5,2_6,2_7} )
-PYTHON_REQ_USE="ssl,tk"
-
-inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
-
-#PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}r2.tar.gz -> analysis${MY_PV}.tar.gz"
-[[ -n ${PATCHSET} ]] \
-	&& SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+opengl"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	dev-lang/tk[threads]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-tcltk/tix
-	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
-	sci-biology/psipred
-	x11-libs/libXext
-	x11-libs/libX11
-	opengl? (
-		media-libs/freeglut
-		dev-python/pyglet[${PYTHON_USEDEP}] )"
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2)
-
-src_prepare() {
-	[[ -n ${PATCHSET} ]] && \
-		epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
-	epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
-	append-lfs-flags
-
-	sed \
-		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
-		-e "s:weights_s:weights:g" \
-		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
-	local tk_ver
-	local myconf
-
-	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
-	if use opengl; then
-		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
-		IGNORE_GL_FLAG=""
-		GL_FLAG="-DUSE_GL_TRUE"
-		GL_DIR="${EPREFIX}/usr"
-		GL_LIB="-lglut -lGLU -lGL"
-		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
-		GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
-	else
-		IGNORE_GL_FLAG="-DIGNORE_GL"
-		GL_FLAG="-DUSE_GL_FALSE"
-	fi
-
-	GLUT_NOT_IN_GL=""
-	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
-	rm -rf data model doc license || die
-
-	sed \
-		-e "s|/usr|${EPREFIX}/usr|g" \
-		-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
-		-e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \
-		-e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
-		-e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
-		-e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
-		-e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
-		-e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
-		-e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
-		-e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
-		-e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
-		-e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
-		-e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TK_LIB =\).*|\1 -ltk|g" \
-		-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \
-		-e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \
-		c/environment_default.txt > c/environment.txt || die
-
-	sed \
-		-e 's:ln -s:cp -f:g' \
-		-i $(find python -name linkSharedObjs) || die
-}
-
-src_compile() {
-	emake -C c all
-	emake -C c links
-}
-
-src_install() {
-	local libdir
-	local tkver
-	local _wrapper
-
-	find . -name "*.pyc" -type f -delete || die
-
-	libdir=$(get_libdir)
-	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
-	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr"
-	for wrapper in ${_wrapper}; do
-		sed \
-			-e "s|gentoo_sitedir|$(python_get_sitedir)|g" \
-		   -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
-			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
-			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
-			-e "s|gentoopython|${EPYTHON}|g" \
-			-e "s|gentoousr|${EPREFIX}/usr|g" \
-			-e "s|//|/|g" \
-			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
-		dobin "${T}"/${wrapper}
-	done
-
-	local in_path=$(python_get_sitedir)/${PN}
-	local files
-	local pydocs
-
-	pydocs="$(find python -name doc -type d)"
-	rm -rf ${pydocs} || die
-
-	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
-	sed \
-		-e 's|#from __future__|from __future__|g' \
-		-i ${i} || die
-	done
-
-	dodir ${in_path#${EPREFIX}}/c
-
-	ebegin "Installing main files"
-		python_moduleinto ${PN}
-		python_domodule python
-	eend
-
-	ebegin "Adjusting permissions"
-	for _file in $(find "${ED}" -type f -name "*so"); do
-		chmod 755 ${_file}
-	done
-	eend
-	python_optimize
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.3.0_p130801.ebuild b/sci-chemistry/ccpn/ccpn-2.3.0_p130801.ebuild
deleted file mode 100644
index 0f317d6a044f..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.3.0_p130801.ebuild
+++ /dev/null
@@ -1,166 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.3.0_p130801.ebuild,v 1.1 2013/08/01 10:43:28 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_5,2_6,2_7} )
-PYTHON_REQ_USE="ssl,tk"
-
-inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
-
-#PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}r3.tar.gz"
-[[ -n ${PATCHSET} ]] \
-	&& SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+opengl"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	dev-lang/tk[threads]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-tcltk/tix
-	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
-	sci-biology/psipred
-	x11-libs/libXext
-	x11-libs/libX11
-	opengl? (
-		media-libs/freeglut
-		dev-python/pyglet[${PYTHON_USEDEP}] )"
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2)
-
-src_prepare() {
-	[[ -n ${PATCHSET} ]] && \
-		epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
-	epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
-	append-lfs-flags
-
-	sed \
-		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
-		-e "s:weights_s:weights:g" \
-		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
-	local tk_ver
-	local myconf
-
-	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
-	if use opengl; then
-		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
-		IGNORE_GL_FLAG=""
-		GL_FLAG="-DUSE_GL_TRUE"
-		GL_DIR="${EPREFIX}/usr"
-		GL_LIB="-lglut -lGLU -lGL"
-		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
-		GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
-	else
-		IGNORE_GL_FLAG="-DIGNORE_GL"
-		GL_FLAG="-DUSE_GL_FALSE"
-	fi
-
-	GLUT_NOT_IN_GL=""
-	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
-	rm -rf data model doc license || die
-
-	sed \
-		-e "s|/usr|${EPREFIX}/usr|g" \
-		-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
-		-e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \
-		-e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
-		-e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
-		-e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
-		-e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
-		-e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
-		-e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
-		-e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
-		-e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
-		-e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
-		-e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(TK_LIB =\).*|\1 -ltk|g" \
-		-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
-		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \
-		-e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \
-		c/environment_default.txt > c/environment.txt || die
-
-	sed \
-		-e 's:ln -s:cp -f:g' \
-		-i $(find python -name linkSharedObjs) || die
-}
-
-src_compile() {
-	emake -C c all
-	emake -C c links
-}
-
-src_install() {
-	local libdir
-	local tkver
-	local _wrapper
-
-	find . -name "*.pyc" -type f -delete || die
-
-	libdir=$(get_libdir)
-	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
-	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr"
-	for wrapper in ${_wrapper}; do
-		sed \
-			-e "s|gentoo_sitedir|$(python_get_sitedir)|g" \
-		   -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
-			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
-			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
-			-e "s|gentoopython|${EPYTHON}|g" \
-			-e "s|gentoousr|${EPREFIX}/usr|g" \
-			-e "s|//|/|g" \
-			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
-		dobin "${T}"/${wrapper}
-	done
-
-	local in_path=$(python_get_sitedir)/${PN}
-	local files
-	local pydocs
-
-	pydocs="$(find python -name doc -type d)"
-	rm -rf ${pydocs} || die
-
-	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
-	sed \
-		-e 's|#from __future__|from __future__|g' \
-		-i ${i} || die
-	done
-
-	dodir ${in_path#${EPREFIX}}/c
-
-	ebegin "Installing main files"
-		python_moduleinto ${PN}
-		python_domodule python
-	eend
-
-	ebegin "Adjusting permissions"
-	for _file in $(find "${ED}" -type f -name "*so"); do
-		chmod 755 ${_file}
-	done
-	eend
-	python_optimize
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.3.0_p130705.ebuild b/sci-chemistry/ccpn/ccpn-2.3.1.ebuild
index d951d4a216ec..76147254c592 100644
--- a/sci-chemistry/ccpn/ccpn-2.3.0_p130705.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.3.1.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-chemistry/ccpn/ccpn-2.3.0_p130705.ebuild,v 1.1 2013/07/05 15:21:52 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.3.1.ebuild,v 1.1 2013/08/08 06:51:10 jlec Exp $
 
 EAPI=5
 
diff --git a/sci-chemistry/ccpn/files/2.3.0-parallel.patch b/sci-chemistry/ccpn/files/2.3.1-parallel.patch
index fcf44707e082..fcf44707e082 100644
--- a/sci-chemistry/ccpn/files/2.3.0-parallel.patch
+++ b/sci-chemistry/ccpn/files/2.3.1-parallel.patch