QA: Removed unused versions.

Package-Manager: portage-2.1.2_pre2-r1

15 files changed, 70 insertions, 773 deletions

diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
index 4f5a75691825..bd4a32c11a10 100644
--- a/sci-chemistry/apbs/Manifest
+++ b/sci-chemistry/apbs/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX apbs-examples-gentoo.patch 1446 RMD160 f0468219d3295cbaf90de7c0e3489d443f1ea144 SHA1 906197ecc9ee745cb0573ed2798a671cccd7b5a4 SHA256 1b12fdf855c4e80bb6e88d6b9c433a4c18eb406a5a6d1671146be897452863d4
 MD5 43dd7c966e75cdbd40215b3616cfddf5 files/apbs-examples-gentoo.patch 1446
 RMD160 f0468219d3295cbaf90de7c0e3489d443f1ea144 files/apbs-examples-gentoo.patch 1446
@@ -6,27 +9,26 @@ AUX apbs-gcc4-gentoo.patch 1080 RMD160 88138dc27c2fa17e558dc3a5c8c41e52bd2f0309
 MD5 c54fdb174c6ca236268f3fb45c3c837e files/apbs-gcc4-gentoo.patch 1080
 RMD160 88138dc27c2fa17e558dc3a5c8c41e52bd2f0309 files/apbs-gcc4-gentoo.patch 1080
 SHA256 9077f4ffc41a2af28eed4193a2e56d20b668e2bc280ca2740d3a8803e28c48d6 files/apbs-gcc4-gentoo.patch 1080
-DIST apbs-0.3.2.tar.gz 6560956 RMD160 2482656dc7b81ac9551c5939edb1987669a0db36 SHA1 723460aecb1b1e8e03f30fe4761f9e2e1628137d SHA256 914a77f9b48e56fd761ec9bcda11e7ba44a5cde95e855a4891b3d19168ec1aa8
 DIST apbs-0.4.0.tar.gz 6490858 RMD160 259c89efed2296eb20af1f8076adc767ef35228c SHA1 f7a5aaefebb545b06f66cb11f229f959060e6c3f SHA256 d1f6637e10b3051e6f618abaa14063f8f9bafbbbad75058645866b606d708acc
-EBUILD apbs-0.3.2.ebuild 1591 RMD160 dcfc1d57d44ca4e83dec75311be034c5b49a96dc SHA1 60dcb4788b135f41202e2bf4d0b19f0f118c1962 SHA256 2a69f675e3303aea56133623b6c36abc9d4b9578fd35365079e0b87347807838
-MD5 401bb19a1a50e92cccd4580795528579 apbs-0.3.2.ebuild 1591
-RMD160 dcfc1d57d44ca4e83dec75311be034c5b49a96dc apbs-0.3.2.ebuild 1591
-SHA256 2a69f675e3303aea56133623b6c36abc9d4b9578fd35365079e0b87347807838 apbs-0.3.2.ebuild 1591
 EBUILD apbs-0.4.0.ebuild 2280 RMD160 277f2f795e1e720426557f7fa0ce35dd9e7d403e SHA1 8cfe3adf2e3dcb89dccea3dc680c16b4e0ab5d29 SHA256 973ed7316cc0c481ffee964f741d6ee70d266e339c5866eb6ab03066409402c4
 MD5 708463d3385a2b9abdc5785f59282394 apbs-0.4.0.ebuild 2280
 RMD160 277f2f795e1e720426557f7fa0ce35dd9e7d403e apbs-0.4.0.ebuild 2280
 SHA256 973ed7316cc0c481ffee964f741d6ee70d266e339c5866eb6ab03066409402c4 apbs-0.4.0.ebuild 2280
-MISC ChangeLog 1530 RMD160 cf953c82ce13a448e8c6f9d8c736f9e4236f6dcc SHA1 477847f685ff40cd129c42b7806903e2bd986109 SHA256 4d17f6a84e608d8d303884802b6aa27916ea1be59de95d4feab62c48c4861bb4
-MD5 fd860cf08ff122507684c965ee31d659 ChangeLog 1530
-RMD160 cf953c82ce13a448e8c6f9d8c736f9e4236f6dcc ChangeLog 1530
-SHA256 4d17f6a84e608d8d303884802b6aa27916ea1be59de95d4feab62c48c4861bb4 ChangeLog 1530
+MISC ChangeLog 1637 RMD160 f67fb69781ced9f445a900fd77db3b8fbe3f110f SHA1 ebdddd0fe5fca00a7b32172592f8bfb47baa90bd SHA256 5d33ab22d4afc9b3b40ccbe8e3071812cd559a00feac8edd8026adcb2933da18
+MD5 4a26c09ad1d66176b2fccfab82c07520 ChangeLog 1637
+RMD160 f67fb69781ced9f445a900fd77db3b8fbe3f110f ChangeLog 1637
+SHA256 5d33ab22d4afc9b3b40ccbe8e3071812cd559a00feac8edd8026adcb2933da18 ChangeLog 1637
 MISC metadata.xml 282 RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 SHA1 7f42dcea44641b8a77ab9644791344ec6ed6c327 SHA256 3c1785eb4ab63774ed3a6b1bddd602ef24cd6795f690bb3289d5a980bca06349
 MD5 cf7436fe44a27481d1001082eb06326e metadata.xml 282
 RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 metadata.xml 282
 SHA256 3c1785eb4ab63774ed3a6b1bddd602ef24cd6795f690bb3289d5a980bca06349 metadata.xml 282
-MD5 18456df38fc9fbeddd1d764d8b1d8f53 files/digest-apbs-0.3.2 235
-RMD160 e68e27e3c3b5ccb7a2eccab79aa43d6210087508 files/digest-apbs-0.3.2 235
-SHA256 fc5b16c201a07aa1d040346d5e2a3d05a213b3f2562a5629fa1bbbabfb7c94ea files/digest-apbs-0.3.2 235
 MD5 2ef0a41feb8be34beec568bf9fe062d6 files/digest-apbs-0.4.0 235
 RMD160 0606ae9bd4d8f291be73e669911da24e3cc0c457 files/digest-apbs-0.4.0 235
 SHA256 b0c6ba75ae65cac80987484dab6a0c0bb889d01b852c12dd7c4e59e6062f19f9 files/digest-apbs-0.4.0 235
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.4 (GNU/Linux)
+
+iD8DBQFFoCER5mJXAu5GbtIRAorcAJ9Mf/zBaBKgXlB+r6GJboKDB4IlaACdGnAe
+HQHZQltenOSbiRPvyFjwgMM=
+=ISMM
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/apbs/apbs-0.3.2.ebuild b/sci-chemistry/apbs/apbs-0.3.2.ebuild
deleted file mode 100644
index 2111417a608b..000000000000
--- a/sci-chemistry/apbs/apbs-0.3.2.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-0.3.2.ebuild,v 1.1 2005/10/20 01:22:57 ribosome Exp $
-
-inherit eutils fortran
-
-DESCRIPTION=" Software for evaluating the electrostatic properties of nanoscale biomolecular systems"
-LICENSE="GPL-2"
-HOMEPAGE="http://agave.wustl.edu/apbs/"
-SRC_URI="http://agave.wustl.edu/apbs/download/dist/${P}.tar.gz"
-
-SLOT="0"
-IUSE="blas"
-KEYWORDS="~x86"
-
-DEPEND="blas? ( virtual/blas )
-		sys-libs/readline
-		dev-libs/maloc"
-
-pkg_setup() {
-	need_fortran g77
-}
-
-src_compile() {
-	# use blas
-	use blas && local myconf="--with-blas=-lblas"
-
-	# configure 
-	econf ${myconf} || die "configure failed"
-
-	# build
-	make || die "make failed"
-}
-
-src_install() {
-
-	# install apbs binary
-	dobin bin/apbs || die "failed to install apbs binary"
-
-	# fix up and install examples
-	sed -e "s|\${bindir}|/usr/bin|" \
-		-i examples/ion-pmf/runme || \
-		die "failed fixing ion-pmf/runme file"
-
-	sed -e "s|bindir=''|bindir=/usr/bin|" \
-		-i examples/point-pmf/runme.sh || \
-		die "failed fixing point-pmf/runme.sh"
-
-	insinto /usr/share/doc/${PF}/examples
-	doins -r examples/* || die "failed to install examples"
-
-	# install docs
-	insinto /usr/share/doc/${PF}/html/programmer
-	doins doc/html/programmer/* || die "failed to install html docs"
-
-	insinto /usr/share/doc/${PF}/html/tutorial
-	doins doc/html/tutorial/* || die "failed to install html docs"
-
-	insinto /usr/share/doc/${PF}/html/user-guide
-	doins doc/html/user-guide/* || die "failed to install html docs"
-}
diff --git a/sci-chemistry/apbs/files/digest-apbs-0.3.2 b/sci-chemistry/apbs/files/digest-apbs-0.3.2
deleted file mode 100644
index 42e75a38f34f..000000000000
--- a/sci-chemistry/apbs/files/digest-apbs-0.3.2
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 b2a417c1d9c102157f45cf00fd0ae196 apbs-0.3.2.tar.gz 6560956
-RMD160 2482656dc7b81ac9551c5939edb1987669a0db36 apbs-0.3.2.tar.gz 6560956
-SHA256 914a77f9b48e56fd761ec9bcda11e7ba44a5cde95e855a4891b3d19168ec1aa8 apbs-0.3.2.tar.gz 6560956
diff --git a/sci-chemistry/caver/Manifest b/sci-chemistry/caver/Manifest
index 969e31aa7006..e7979aeea838 100644
--- a/sci-chemistry/caver/Manifest
+++ b/sci-chemistry/caver/Manifest
@@ -1,17 +1,14 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX caver-0.99.4-001.patch 1856 RMD160 4d2809d7ef0ba9a3205fca398ead887b4e104c67 SHA1 af85d449e94642b4b165507c2b699f3389430c29 SHA256 ebe19169d3db5b71a7c88dd2a22bae9f2095981b67cdd0308bfce4ed60b5c987
 MD5 c9ed0f57b4b34e1d99cf3a14709b59bd files/caver-0.99.4-001.patch 1856
 RMD160 4d2809d7ef0ba9a3205fca398ead887b4e104c67 files/caver-0.99.4-001.patch 1856
 SHA256 ebe19169d3db5b71a7c88dd2a22bae9f2095981b67cdd0308bfce4ed60b5c987 files/caver-0.99.4-001.patch 1856
 DIST caverPLUG_unix_v0.99.2.tar.gz 81270 RMD160 58a5b2b7a1efe41a86d507831f754419ae912b12 SHA256 5b7ca30f26023e2ed9eda6a5430ca5db0ebef7b34f7f8d2391a49182ec0663b1
 DIST caverPLUG_unix_v0.99.4.tar.gz 81732 RMD160 5d2488d64077cfac0e81fdef53074149929aa558 SHA1 586037ad17f505e6eba739c8167982178edd86dc SHA256 61ac38fe2e9ae15af568d6eed19d7410599bc570fb0494793dff625c469b5b69
-DIST caver_unix_v0.99.1.tar.gz 898765
 DIST caver_unix_v0.99.2.tar.gz 1152263 RMD160 01b877bef15d0f0e1ccce8a3dbcda83826ba76c5 SHA256 9934b5e80f375159132c5327df1fa8bd19ce90682c04c4cd9b91e62476e0f98b
 DIST caver_unix_v0.99.4.tar.gz 1084660 RMD160 c57c5b0c6259bb86fc844820d169a60d3895b2bd SHA1 b4a6a26651a20a1664ddfb96f36e89906dcc0bff SHA256 7aa8da882b8c7525164c4643e8feea2bb644bb5790400a21dcf8c70c40f0ea09
-DIST pymolplug.tar.gz 81137
-EBUILD caver-0.99.1.ebuild 1382 RMD160 93c178976bb98acebfaa94180d49e2b3e0d186c3 SHA1 2d7e2964f8952383a1f588c548521a1435b6f97b SHA256 eb2f5b4ee5f23c4a35ff3fceb4dd0cf75e134b06c1fa180121f14462391e2517
-MD5 bb4a1218e09746c04c1f3da50f76eb66 caver-0.99.1.ebuild 1382
-RMD160 93c178976bb98acebfaa94180d49e2b3e0d186c3 caver-0.99.1.ebuild 1382
-SHA256 eb2f5b4ee5f23c4a35ff3fceb4dd0cf75e134b06c1fa180121f14462391e2517 caver-0.99.1.ebuild 1382
 EBUILD caver-0.99.2.ebuild 1422 RMD160 4d85edc83a2a01c9aba938346f141a9b14d96192 SHA1 7d10a56a81423160d4ea8634774bd1bf8486eb4a SHA256 eb4bdbb7dc085a505d7ae28a46caa1a439bf6df5dd8d3a2ae785eeb4946599a3
 MD5 a3b6b6c7247d16b4692deb7fc149758e caver-0.99.2.ebuild 1422
 RMD160 4d85edc83a2a01c9aba938346f141a9b14d96192 caver-0.99.2.ebuild 1422
@@ -20,20 +17,24 @@ EBUILD caver-0.99.4.ebuild 1789 RMD160 92a237a30a9b776045ede92724b1a25b52e095e5
 MD5 2bbd0a1c0845d254b3191df1aa432e8d caver-0.99.4.ebuild 1789
 RMD160 92a237a30a9b776045ede92724b1a25b52e095e5 caver-0.99.4.ebuild 1789
 SHA256 6e7697af6564548a64229542721ddce55dda144fbe5548fc7ea98820ebd4d226 caver-0.99.4.ebuild 1789
-MISC ChangeLog 1662 RMD160 cb505b6f437a43df379cd88fd4d8ef9fc7bde5d1 SHA1 0c2d58853eaf4052f33c2f4a4b91a7e7685d4d62 SHA256 3726a8c826d8eea1d9a46967fd710b54f6b7997640d9ffc45a0fc05c94326ec5
-MD5 368d9f8b1be68c6a8b8d3ba6a369280e ChangeLog 1662
-RMD160 cb505b6f437a43df379cd88fd4d8ef9fc7bde5d1 ChangeLog 1662
-SHA256 3726a8c826d8eea1d9a46967fd710b54f6b7997640d9ffc45a0fc05c94326ec5 ChangeLog 1662
+MISC ChangeLog 1768 RMD160 92efafd610717fd8a3927ef327885999ec8c248f SHA1 d9af6ccd8e6d68db145b02a0e033b95a47cb0739 SHA256 53f60bf297850badc4bb75d2a203abf7249bd6fad0faa9fc84ef3cce0e1a9c75
+MD5 0ae07666aa1b7f44bcaf44d60d8a8262 ChangeLog 1768
+RMD160 92efafd610717fd8a3927ef327885999ec8c248f ChangeLog 1768
+SHA256 53f60bf297850badc4bb75d2a203abf7249bd6fad0faa9fc84ef3cce0e1a9c75 ChangeLog 1768
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
 SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 metadata.xml 166
-MD5 946c4f9350e2386e497befe7afbe9cc2 files/digest-caver-0.99.1 130
-RMD160 9ca2102fa7a9b2c5257ff4044202c040d82ce628 files/digest-caver-0.99.1 130
-SHA256 fb5d883d649a3227ef05372d785aa49851202133670d2199ac6aecdf11ecae08 files/digest-caver-0.99.1 130
 MD5 8524c8b5718aaac466fa34658468955a files/digest-caver-0.99.2 524
 RMD160 1e54afa8530246f319c0b0a235d9cce35dc050c4 files/digest-caver-0.99.2 524
 SHA256 e7815fe179e318f1f736e8f6cf473f92fb8df0aae52222de71f0ce2fc82c88cf files/digest-caver-0.99.2 524
 MD5 580598ccf83086e940e96aacebfc1b45 files/digest-caver-0.99.4 524
 RMD160 38ce776a94ca93dd15522a7b4a6aca8ca2ef5781 files/digest-caver-0.99.4 524
 SHA256 633b07a25c8619cdc5e96b7d99ab69706403a67a4e3b0bb803749fcc29359e43 files/digest-caver-0.99.4 524
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.4 (GNU/Linux)
+
+iD8DBQFFoCGL5mJXAu5GbtIRAjKYAJ9QerX0sF6TwK4I0kqVqyjFZQBujQCfZmSx
+ss/N3xXKKUI//V2/rLMl17U=
+=LL/6
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/caver/caver-0.99.1.ebuild b/sci-chemistry/caver/caver-0.99.1.ebuild
deleted file mode 100644
index 737c2859a97a..000000000000
--- a/sci-chemistry/caver/caver-0.99.1.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/caver/caver-0.99.1.ebuild,v 1.1 2005/12/20 03:56:38 spyderous Exp $
-
-inherit multilib python
-
-MY_PN="${PN}_unix"
-MY_P="${MY_PN}_v${PV}"
-DESCRIPTION="Rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures"
-HOMEPAGE="http://viper.chemi.muni.cz/caver/"
-SRC_URI="${MY_P}.tar.gz
-	pymol? ( pymolplug.tar.gz )"
-LICENSE="CAVER"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE="pymol"
-RDEPEND="media-libs/qhull
-	pymol? ( sci-chemistry/pymol )"
-DEPEND="${RDEPEND}"
-RESTRICT="fetch"
-S="${WORKDIR}/${MY_P}"
-
-pkg_nofetch() {
-	einfo "Download ${MY_P}.tar.gz"
-	if use pymol; then
-		einfo "and pymolplug.tar.gz"
-	fi
-	einfo "from ${HOMEPAGE}. This requires registration."
-	einfo "Place them in ${DISTDIR}."
-}
-
-src_install() {
-	make DESTDIR="${D}" install
-	if use pymol; then
-		python_version
-		sed -i \
-			-e "s:^\(CAVER_BINARY_LOCATION\).*:\1 = \"${ROOT}usr/bin/caver\":g" \
-			${WORKDIR}/pymolplug/caver.py
-		insinto /usr/$(get_libdir)/python${PYVER}/site-packages/pmg_tk/startup
-		doins ${WORKDIR}/pymolplug/caver.py
-	fi
-}
-
-pkg_postinst() {
-	if use pymol; then
-		python_mod_compile \
-		/usr/$(get_libdir)/python${PYVER}/site-packages/pmg_tk/startup/caver.py
-	fi
-}
diff --git a/sci-chemistry/caver/files/digest-caver-0.99.1 b/sci-chemistry/caver/files/digest-caver-0.99.1
deleted file mode 100644
index 80f3e372b61f..000000000000
--- a/sci-chemistry/caver/files/digest-caver-0.99.1
+++ /dev/null
@@ -1,2 +0,0 @@
-MD5 7dfc10f67d345d81fa74f0c2c8bbca8d caver_unix_v0.99.1.tar.gz 898765
-MD5 522581ce929adb5d3bef0fa540382362 pymolplug.tar.gz 81137
diff --git a/sci-chemistry/ccp4/Manifest b/sci-chemistry/ccp4/Manifest
index e8832515b164..2356a0664f5f 100644
--- a/sci-chemistry/ccp4/Manifest
+++ b/sci-chemistry/ccp4/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX 6.0.1-dont-make-dirs-in-configure.patch 2790 RMD160 904e37ab1ea20dda50f50ce8780268eb5fa52480 SHA1 f8989cb867c92def86ccd88b4d67f38578d5d80b SHA256 2dbf78513ef94d88e446042e969644ad8a8462a22e80105e7481af93003a18bf
 MD5 3dc230e3cc15f5cd2a19968e8f07a9f2 files/6.0.1-dont-make-dirs-in-configure.patch 2790
 RMD160 904e37ab1ea20dda50f50ce8780268eb5fa52480 files/6.0.1-dont-make-dirs-in-configure.patch 2790
@@ -72,28 +75,28 @@ EBUILD ccp4-6.0.1-r1.ebuild 14018 RMD160 885fa6e0e3ebd0c998d53a3af77cfed008631ec
 MD5 33a6ca0f3d9dcaa800a00f8920b1717f ccp4-6.0.1-r1.ebuild 14018
 RMD160 885fa6e0e3ebd0c998d53a3af77cfed008631ece ccp4-6.0.1-r1.ebuild 14018
 SHA256 e0f9c5442844ba02ba3e1194f5d11fe6dd9a686b3a42b1d3e6a3f6e921cd0fb8 ccp4-6.0.1-r1.ebuild 14018
-EBUILD ccp4-6.0.1.ebuild 13729 RMD160 5fe2a8f1d42a810e8fda14c61e970f9146ab0b96 SHA1 25638dfbe892e82daccc6f40af9479ae88d2386f SHA256 d3d7ea08c1260eff42b49ead37d935bf3c9e38eac6e8eeb4fa86b3962ed25c7c
-MD5 48bda08719da61345f9297bdecd1b975 ccp4-6.0.1.ebuild 13729
-RMD160 5fe2a8f1d42a810e8fda14c61e970f9146ab0b96 ccp4-6.0.1.ebuild 13729
-SHA256 d3d7ea08c1260eff42b49ead37d935bf3c9e38eac6e8eeb4fa86b3962ed25c7c ccp4-6.0.1.ebuild 13729
 EBUILD ccp4-6.0.2.ebuild 13483 RMD160 20043e32b6a1aae3e9431c2c5f793816ee754b7e SHA1 bdfadd46b8b9e75e3758a17d98a077b69035e167 SHA256 0f4bc1201162b9dce21254e2f9497bbc391dd3ad7bba30fd5cec8fd9376e587b
 MD5 26accaf55746435d81fb5c55d1f41114 ccp4-6.0.2.ebuild 13483
 RMD160 20043e32b6a1aae3e9431c2c5f793816ee754b7e ccp4-6.0.2.ebuild 13483
 SHA256 0f4bc1201162b9dce21254e2f9497bbc391dd3ad7bba30fd5cec8fd9376e587b ccp4-6.0.2.ebuild 13483
-MISC ChangeLog 2216 RMD160 cbdef48f6f45064fa21a7a1e57b580e3899dc108 SHA1 d4fb0a46ab1a6ef736be031530329fcbae78d583 SHA256 3afb703e3805ab9c3830fa4d468fda79c16094311602fa859e2ee089580b3410
-MD5 2ebc390cdd05eabb3257b6a7b77d2309 ChangeLog 2216
-RMD160 cbdef48f6f45064fa21a7a1e57b580e3899dc108 ChangeLog 2216
-SHA256 3afb703e3805ab9c3830fa4d468fda79c16094311602fa859e2ee089580b3410 ChangeLog 2216
+MISC ChangeLog 2320 RMD160 537d3dd2b0a3a884d94515bcc03fae7d5d72a30a SHA1 202a49913ebc60634afe923f72635ff6e1491abc SHA256 14f95030989e926616b097295b1b00ae99cf23549a31598556ff071b26bcc664
+MD5 8cac6c4b6e10943b1dc6efe44a83210f ChangeLog 2320
+RMD160 537d3dd2b0a3a884d94515bcc03fae7d5d72a30a ChangeLog 2320
+SHA256 14f95030989e926616b097295b1b00ae99cf23549a31598556ff071b26bcc664 ChangeLog 2320
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
 SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 metadata.xml 166
-MD5 af2485e5d663b3c625e3ee4f94748730 files/digest-ccp4-6.0.1 265
-RMD160 72caf22fe0480a8c577d84ff2ffb3bb3a6dcadd5 files/digest-ccp4-6.0.1 265
-SHA256 52ebe8c93194a9140171ac2e0d80b4750913b3e97ac1ee0f37c34ad9137deda8 files/digest-ccp4-6.0.1 265
 MD5 42c7b9d83453a9015d474ef4eaea76c1 files/digest-ccp4-6.0.1-r1 3286
 RMD160 9c65d5658b463f2aa751cb59c63d954c0b69568a files/digest-ccp4-6.0.1-r1 3286
 SHA256 3ccb5d939d1f0386093758fe8c5cfbb54be329869df7a77b85c0653d613f0a86 files/digest-ccp4-6.0.1-r1 3286
 MD5 4197e0ed0288c715e184aa7df8a4dbd6 files/digest-ccp4-6.0.2 265
 RMD160 b7b82a63b44e956b19cd49241a49565cac594d25 files/digest-ccp4-6.0.2 265
 SHA256 a9d7f019b604fd193ac9797e76d5c3058771a16866134bdbe9b94ca137405946 files/digest-ccp4-6.0.2 265
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diff --git a/sci-chemistry/ccp4/ccp4-6.0.1.ebuild b/sci-chemistry/ccp4/ccp4-6.0.1.ebuild
deleted file mode 100644
index d3a1e56b5431..000000000000
--- a/sci-chemistry/ccp4/ccp4-6.0.1.ebuild
+++ /dev/null
@@ -1,432 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ccp4-6.0.1.ebuild,v 1.1 2006/06/16 20:46:02 spyderous Exp $
-
-inherit fortran eutils gnuconfig toolchain-funcs
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-PATCH_TOT="0"
-#PATCH1=( src
-#	anisoanl.f-r1.22-r1.24.diff )
-#PATCH2=( src/sc_
-#	sc.f-r1.9-r1.9.2.1.diff )
-#PATCH3=( src/sc_
-#	setup.fh-r1.5-r1.5.2.1.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror stricter"
-SRC_URI="${SRC}/${PV}/packed/${P}-core-src.tar.gz"
-#	${SRC}/${PV}/patches/${PATCH1[1]}
-#	${SRC}/${PV}/patches/${PATCH2[1]}
-#	${SRC}/${PV}/patches/${PATCH3[1]}"
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~ppc ~x86"
-IUSE="X"
-# app-office/sc overlaps sc binary and man page
-# We can't rename ours since the automated ccp4i interface expects it there,
-# as do many scripts. app-office/sc can't rename its because that's the name
-# of the package.
-RDEPEND="X? (
-			|| (
-				(
-					x11-libs/libX11
-					x11-libs/libXt
-					x11-libs/libXaw
-				)
-				virtual/x11
-			)
-		)
-		>=dev-lang/tcl-8.3
-		>=dev-lang/tk-8.3
-		>=dev-tcltk/blt-2.4
-		virtual/lapack
-		virtual/blas
-		=sci-libs/fftw-2*
-		sci-chemistry/pdb-extract
-		sci-chemistry/rasmol
-		sci-libs/mccp4
-		|| ( app-shells/tcsh app-shells/csh )
-		!app-office/sc"
-# >=sys-apps/portage-2.1.1_pre1 for RESTRICT=stricter
-# Otherwise portage dies instead of fixing RPATHs
-DEPEND="${RDEPEND}
-		X? (
-			|| (
-				(
-					x11-misc/imake
-					x11-proto/inputproto
-					x11-proto/xextproto
-				)
-				virtual/x11
-			)
-		)
-		>=sys-apps/portage-2.1.1_pre1"
-
-S="${WORKDIR}/${PN}-${PV}"
-
-src_unpack() {
-	unpack ${A}
-	cd ${S}
-
-	einfo "Applying upstream patches ..."
-	for patch in $(seq $PATCH_TOT); do
-		base="PATCH${patch}"
-		dir=$(eval echo \${${base}[0]})
-		p=$(eval echo \${${base}[1]})
-		pushd ${dir} >& /dev/null
-		ccp_patch ${DISTDIR}/${p}
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	einfo "Applying Gentoo patches ..."
-	# These two only needed when attempting to install outside build dir via
-	# --bindir and --libdir instead of straight copying after build
-
-	# it attempts to install some libraries during the build
-	#ccp_patch ${FILESDIR}/${P}-install-libs-at-install-time.patch
-	# hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
-	# without this patch when --libdir is set
-	# Rotgen still needs more patching to find it
-	#ccp_patch ${FILESDIR}/add-xdl-libdir.patch
-
-	# it tries to create libdir, bindir etc on live system in configure
-	ccp_patch ${FILESDIR}/${PV}-dont-make-dirs-in-configure.patch
-
-	# We already have sci-chemistry/rasmol
-	ccp_patch ${FILESDIR}/dont-build-rasmol.patch
-
-	# We already have sci-chemistry/pdb-extract
-# Use configure option instead
-#	ccp_patch ${FILESDIR}/dont-build-pdb-extract.patch
-
-	ccp_patch ${FILESDIR}/create-mosflm-bindir.patch
-	ccp_patch ${FILESDIR}/make-mosflm-libdir.patch
-	ccp_patch ${FILESDIR}/make-mosflm-index-libdir.patch
-	ccp_patch ${FILESDIR}/make-mosflm-cbf-libdir.patch
-	ccp_patch ${FILESDIR}/make-ipmosflm-dir.patch
-
-# Don't use these when we aren't building phaser
-#	ccp_patch ${FILESDIR}/make-phaser-bindir.patch
-#	ccp_patch ${FILESDIR}/no-phaser-ld-assume-kernel.patch
-#	# scons config.py tries to chmod python on live system
-#	ccp_patch ${FILESDIR}/dont-chmod-python-binary.patch
-
-	# Don't use this when we aren't building clipper
-	# For some reason clipper check for $enableval even when --enable is passed
-	ccp_patch ${FILESDIR}/pass-clipper-enablevals.patch
-	ccp_patch ${FILESDIR}/clipper-find-mccp4-includes.patch
-
-	# Default to firefox browser, not 'netscape'
-	ccp_patch ${FILESDIR}/ccp4i-default-to-firefox.patch
-
-	# Also use -lpthread when linking blas and lapack
-	# We may need more fixing to use libcblas for the C files
-	ccp_patch ${FILESDIR}/check-blas-lapack-pthread.patch
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch ${FILESDIR}/${PV}-ppc-double-define-gerror.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "${FORTRANC}" = "ifc" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		${S}/include/ccp4.setup
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		${S}/configure
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
-		${S}/include/ccp4.setup*
-
-	# Set up variables for build
-	source ${S}/include/ccp4.setup
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=${FORTRANC}
-	export FOPTIM=${FFLAGS:- -O2}
-
-	# Add xdl libraries to library search path
-	# Note: some of configure attaches CCP4_LIB to -L, and other parts
-	# append libfoo.a immediately after it, so it can only be a single path.
-	export CCP4_LIB="${CCP4}/x-windows/xdl_view/src/.libs"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		$(use_enable X x) \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-pdb_extract \
-		--disable-cctbx \
-		--disable-phaser \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-# Only needed when using --bindir and --libdir
-	# Needed to avoid errors. Originally tried to make lib and bin
-	# in configure script, now patched out by dont-make-dirs-in-configure.patch
-#	dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-#	make install || die "install failed"
-	einstall || die "install failed"
-
-	# Fix env
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \
-		-e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
-		-e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
-		-e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
-		-e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \
-		-e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \
-		-e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \
-		-e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \
-		${S}/include/ccp4.setup*
-
-	# Get rid of S instances
-	# Also the main clipper library is built as libclipper-core, not libclipper
-	sed -i \
-		-e "s:${S}:${ROOT}usr:g" \
-		-e "s:lclipper :lclipper-core :g" \
-		${S}/bin/clipper-config
-#	sed -i \
-#		-e "s:${S}:${ROOT}usr:g" \
-#		${S}/$(get_libdir)/cctbx/cctbx_build/setpaths*
-
-	# Bins
-	EXEDESTTREE="/usr/bin" doexe ${S}/bin/*
-
-	# Libs
-	for file in ${S}/lib/*; do
-		if [[ -d ${file} ]]; then
-			continue
-		elif [[ -x ${file} ]]; then
-			dolib.so ${file}
-		else
-			INSDESTTREE="/usr/$(get_libdir)" doins ${file}
-		fi
-	done
-
-	# Fix libdir in all *.la files
-	sed -i \
-		-e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
-		${D}/usr/$(get_libdir)/*.la
-
-	# Library symlinks
-	local LIBNAMES="libclipper-ccp4.so.0.0.0
-		libclipper-cif.so.0.0.0
-		libclipper-contrib.so.0.0.0
-		libclipper-core.so.0.0.0
-		libclipper-minimol.so.0.0.0
-		libclipper-mmdbold.so.0.0.0
-		libclipper-mmdb.so.0.0.0
-		libclipper-mtz.so.1.0.0
-		libclipper-phs.so.0.0.0
-		libjwc_c.so.0.1.1
-		libjwc_f.so.0.1.1
-		libssm.so.0.0.0
-		libxdl_viewextra.so.0.0.0
-		libxdl_view.so.2.0.0"
-
-	for LIBNAME in ${LIBNAMES}; do
-		library_dosym ${LIBNAME}
-	done
-
-#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so
-#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0
-#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0.0
-#
-#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so
-#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0
-#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0.0
-#
-#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so
-#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0
-#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0.0
-#
-#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so
-#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0
-#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0.0
-#
-#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so
-#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0
-#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0.0
-#
-#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so
-#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0
-#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0.0
-#
-#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so
-#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0
-#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0.0
-#
-#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so
-#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1
-#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1.0
-#
-#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so
-#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0
-#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0.0
-#
-#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so
-#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0
-#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0.1
-#
-#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so
-#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0
-#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0.1
-#
-#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so
-#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0
-#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0.0
-#
-#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so
-#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0
-#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0.0
-#
-#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so
-#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2
-#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2.0
-
-	# Environment files, setup scripts, etc.
-	INSDESTTREE="/usr/share/ccp4/include" doins ${S}/include/*
-
-	# CCP4Interface - GUI
-	INSDESTTREE="/usr/$(get_libdir)/ccp4" doins -r ${S}/ccp4i
-	EXEDESTTREE="/usr/$(get_libdir)/ccp4/ccp4i/bin" doexe ${S}/ccp4i/bin/*
-
-	# Data
-	INSDESTTREE="/usr/share/ccp4" doins -r ${S}/lib/data
-
-	# Include files
-	for i in ccp4 clipper mmdb ssm; do
-		INSDESTTREE="/usr/include" doins -r ${S}/include/${i}
-	done
-
-	# Install docs and examples
-
-	doman ${S}/man/cat1/*
-
-	mv ${S}/manual/README ${S}/manual/README-manual
-	dodoc ${S}/manual/*
-
-	dodoc ${S}/README ${S}/CHANGES
-
-	dodoc ${S}/doc/*
-	rm ${D}/usr/share/doc/${PF}/GNUmakefile.gz
-	rm ${D}/usr/share/doc/${PF}/COPYING.gz
-
-	dohtml -r ${S}/html/*
-	dodoc ${S}/examples/README
-
-	# Fix wrongly installed HTML pages from clipper
-	dohtml "${D}"/usr/html/*
-	rm -rf "${D}"/usr/html
-
-	for i in data rnase toxd; do
-		DOCDESTTREE="examples/${i}" dodoc ${S}/examples/${i}/*
-	done
-
-	DOCDESTTREE="examples/tutorial" dohtml -r ${S}/examples/tutorial/html
-	DOCDESTTREE="examples/tutorial" dohtml examples/tutorial/tut.css
-	for i in data results; do
-		DOCDESTTREE="examples/tutorial/${i}" dodoc ${S}/examples/tutorial/${i}/*
-	done
-
-	for i in non-runnable runnable; do
-		DOCDESTTREE="examples/unix/${i}" dodoc ${S}/examples/unix/${i}
-	done
-
-	# Needed for ccp4i docs to work
-	dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html
-
-	# Fix overlaps with other packages
-	rm ${D}/usr/share/man/man1/rasmol.1.gz
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in /usr/share/ccp4/include/ccp4.setup* to modify this."
-
-	ewarn "Set your .bashrc or other shell login file to source"
-	ewarn "one of the ccp4.setup* files in ${ROOT}usr/share/ccp4/include."
-	ewarn "CCP4 will not work without this."
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
-
-# Links libname.so, libname.so.major and libname.so.major.minor
-# to libname.so.major.minor.micro
-library_dosym() {
-	local LIBNAME LIBDIR SUFFIX CORE_LIBNAME LIB_MAJOR LIB_MINOR LIB_VERSIONS
-
-	LIBNAME=${1}
-	LIBDIR=${2:-/usr/$(get_libdir)}
-
-	# Tag / on the end of libdir if needed
-	if [[ ${LIBDIR:$((${#LIBDIR}-1)):1} != "/" ]]; then
-		LIBDIR="${LIBDIR}/"
-	fi
-
-	if [[ "${LIBNAME}" != *.so.* ]]; then
-		msg="library_dosym() requires a shared, versioned library as an argument"
-		eerror "$msg"
-		die "$msg"
-	fi
-
-	SUFFIX=${LIBNAME##*so.}
-	CORE_LIBNAME=${LIBNAME%.so.*}
-	CORE_LIBNAME="${CORE_LIBNAME}.so"
-	LIB_MAJOR=${SUFFIX%%.*}
-	LIB_MINOR=${SUFFIX#*.}
-	LIB_MINOR=${SUFFIX%%.*}
-	LIB_VERSIONS="${LIB_MAJOR} ${LIB_MAJOR}.${LIB_MINOR}"
-	for LIB_SUFFIX in .${LIB_MAJOR} .${LIB_MAJOR}.${LIB_MINOR} ""; do
-		einfo "Calling dosym ${LIBNAME} ${LIBDIR} ${CORE_LIBNAME} ${LIB_SUFFIX}"
-		dosym ${LIBNAME} ${LIBDIR}${CORE_LIBNAME}${LIB_SUFFIX}
-	done
-}
diff --git a/sci-chemistry/ccp4/files/digest-ccp4-6.0.1 b/sci-chemistry/ccp4/files/digest-ccp4-6.0.1
deleted file mode 100644
index acc5dc94a96a..000000000000
--- a/sci-chemistry/ccp4/files/digest-ccp4-6.0.1
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 bd3ff43388b58841de79bcc23ebf81e3 ccp4-6.0.1-core-src.tar.gz 59311291
-RMD160 0f514fe30f22a4f6eb2e05c8bab567d2132e8fae ccp4-6.0.1-core-src.tar.gz 59311291
-SHA256 26a5704d707c3bc2fbe4c1d0804abccc1c50255005d26a8ec3a03fcba63335f2 ccp4-6.0.1-core-src.tar.gz 59311291
diff --git a/sci-chemistry/chemtool/Manifest b/sci-chemistry/chemtool/Manifest
index 812488abe054..f777eb1188a3 100644
--- a/sci-chemistry/chemtool/Manifest
+++ b/sci-chemistry/chemtool/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 DIST chemtool-1.6.7.tar.gz 427878
 DIST chemtool-1.6.9.tar.gz 430701 RMD160 9c156f91ab17721461d524f82f59b5d49cb46f7a SHA256 3a66286195e3e5a79000245c1c28eca6ef4deb0e19fe9c3b481bfbabb49a1a44
 EBUILD chemtool-1.6.7-r1.ebuild 1842 RMD160 b648f85ba9b4d8ac251707ba6c62a2974cbaad3e SHA1 f3e842f4ad834efad31a2ec08bc1d6e0ca56273d SHA256 963935fd998612bbf9b26361bb1fda72e131baac2dde3c6ab31150f30e174d4b
@@ -8,14 +11,10 @@ EBUILD chemtool-1.6.9-r1.ebuild 1543 RMD160 b7e098d427818200fd4435b31f510cae8420
 MD5 234c8c3f45ffcb7050d2a0ab22625c4d chemtool-1.6.9-r1.ebuild 1543
 RMD160 b7e098d427818200fd4435b31f510cae84203d57 chemtool-1.6.9-r1.ebuild 1543
 SHA256 5b25625f33a07739d8b19eed06ac955cdb123774ccc52bfa2641650c84879300 chemtool-1.6.9-r1.ebuild 1543
-EBUILD chemtool-1.6.9.ebuild 1838 RMD160 868a3c0a588c8d38837012916dafaed9ab6baa64 SHA1 bb4e6acf412d01c0ed3dd4718dff0faae05801b9 SHA256 c5b3728f413171489fd086d3b5d98e8e85d7eb8d3201f304293499c34a8b6a0a
-MD5 df713aa114e3f862645d7cc75b9142c7 chemtool-1.6.9.ebuild 1838
-RMD160 868a3c0a588c8d38837012916dafaed9ab6baa64 chemtool-1.6.9.ebuild 1838
-SHA256 c5b3728f413171489fd086d3b5d98e8e85d7eb8d3201f304293499c34a8b6a0a chemtool-1.6.9.ebuild 1838
-MISC ChangeLog 4470 RMD160 98d5ffb77779fc76b47455b534153712dae65fec SHA1 bca67670c36caf1a031f73f69b2156fdae17a370 SHA256 aa5381ff0287b484970f780cfb77133fc19795fe58892d067ecd3ed5717d0bea
-MD5 c7c69a0b874e3b3ae46e1924b4b8855d ChangeLog 4470
-RMD160 98d5ffb77779fc76b47455b534153712dae65fec ChangeLog 4470
-SHA256 aa5381ff0287b484970f780cfb77133fc19795fe58892d067ecd3ed5717d0bea ChangeLog 4470
+MISC ChangeLog 4578 RMD160 35cc1a46da36d2a2b289c991e30afba98452e286 SHA1 c6493ea6978c3fcddca1abbf6721a2f7eb63155a SHA256 aa60d79d537bbcbb77264186f9aff550758fd565875d192e770ead356c851371
+MD5 a271cd7ccfbb00203b2bd5755d017670 ChangeLog 4578
+RMD160 35cc1a46da36d2a2b289c991e30afba98452e286 ChangeLog 4578
+SHA256 aa60d79d537bbcbb77264186f9aff550758fd565875d192e770ead356c851371 ChangeLog 4578
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
@@ -23,9 +22,13 @@ SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 metadata
 MD5 27dfa5500bf82b518c1ea34ae01c73ee files/digest-chemtool-1.6.7-r1 66
 RMD160 93e302ce9ff961c5f736ba3c99b52e037a568e8b files/digest-chemtool-1.6.7-r1 66
 SHA256 7512af23329dd14888dd2d5c26975a686534a0cfd0819c35c73562ad95c63bf5 files/digest-chemtool-1.6.7-r1 66
-MD5 075095ee16bb9b7eb6b42fd3951d4cc1 files/digest-chemtool-1.6.9 244
-RMD160 1174eacda0ec031d30ef8d182dabb95c05a042e3 files/digest-chemtool-1.6.9 244
-SHA256 c2128857dbd6009fd89a12add147d9108707e619c1cc2b317d6cf4bb6611e9d9 files/digest-chemtool-1.6.9 244
 MD5 075095ee16bb9b7eb6b42fd3951d4cc1 files/digest-chemtool-1.6.9-r1 244
 RMD160 1174eacda0ec031d30ef8d182dabb95c05a042e3 files/digest-chemtool-1.6.9-r1 244
 SHA256 c2128857dbd6009fd89a12add147d9108707e619c1cc2b317d6cf4bb6611e9d9 files/digest-chemtool-1.6.9-r1 244
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.4 (GNU/Linux)
+
+iD8DBQFFoCJn5mJXAu5GbtIRAg+qAJ48cCoataNKStCui25mvzNUJC5P4QCeIhwM
+V78FyY817x45WJIaG8xWiNY=
+=mcEJ
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/chemtool/chemtool-1.6.9.ebuild b/sci-chemistry/chemtool/chemtool-1.6.9.ebuild
deleted file mode 100644
index 26bf4babb756..000000000000
--- a/sci-chemistry/chemtool/chemtool-1.6.9.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/chemtool/chemtool-1.6.9.ebuild,v 1.1 2006/04/08 11:31:39 markusle Exp $
-
-inherit eutils kde-functions
-
-DESCRIPTION="program for drawing organic molecules"
-HOMEPAGE="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/"
-SRC_URI="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86 ~amd64 ~ppc"
-IUSE="gnome kde nls"
-
-DEPEND=">=media-gfx/transfig-3.2.3d
-		=x11-libs/gtk+-2*
-		kde? ( kde-base/kdelibs )
-		x86? ( >=media-libs/libemf-1.0 )"
-
-src_compile() {
-	local config_opts
-	local mycppflags
-	if ! use kde; then
-		unset KDEDIR
-		config_opts="${config_opts} --without-kdedir"
-	else
-		set-kdedir
-		config_opts="${config_opts} --with-kdedir=${KDEDIR}"
-	fi
-	if [ ${ARCH} = "x86"  ]; then
-		config_opts="${config_opts} --enable-emf"
-		mycppflags="${mycppflags} -I /usr/include/libEMF"
-	fi
-
-	sed -e "s:\(^CPPFLAGS.*\):\1 ${mycppflags}:" -i Makefile.in || \
-		die "could not append cppflags"
-
-	if use gnome ; then
-		config_opts="${config_opts} --with-gnomedir=/usr" ;
-	else
-		config_opts="${config_opts} --without-gnomedir" ;
-	fi
-
-	econf ${config_opts} \
-		|| die "./configure failed"
-	emake || die "make failed"
-}
-
-src_install() {
-	local sharedirs="applnk/Graphics mimelnk/application icons/hicolor/32x32/mimetypes"
-	for dir in ${sharedirs}; do
-		dodir ${mykdedir}/share/${dir}
-	done
-	dodir /usr/share/mime-types
-	dodir /usr/share/pixmaps/mc
-
-	make DESTDIR="${D}" install || die "make install failed"
-
-	if ! use gnome; then
-		rm -rf ${D}/usr/share/pixmaps ${D}/usr/share/mime-types
-	fi
-
-	dodoc ChangeLog INSTALL README TODO
-	insinto /usr/share/${PN}/examples
-	doins ${S}/examples/*
-	if ! use nls; then rm -rf ${D}/usr/share/locale; fi
-}
diff --git a/sci-chemistry/chemtool/files/digest-chemtool-1.6.9 b/sci-chemistry/chemtool/files/digest-chemtool-1.6.9
deleted file mode 100644
index 5d40707f8c0c..000000000000
--- a/sci-chemistry/chemtool/files/digest-chemtool-1.6.9
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 d13b16c019a9912cf0c3de07ca5bcd29 chemtool-1.6.9.tar.gz 430701
-RMD160 9c156f91ab17721461d524f82f59b5d49cb46f7a chemtool-1.6.9.tar.gz 430701
-SHA256 3a66286195e3e5a79000245c1c28eca6ef4deb0e19fe9c3b481bfbabb49a1a44 chemtool-1.6.9.tar.gz 430701
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index 93541a95a55f..be23dec432e4 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -1,17 +1,15 @@
-DIST coot-0.1.2-pre-1.tar.gz 2759927 RMD160 e54818e72274288f125661e09e2a834f83230604 SHA1 94d5f4860b6d6d02e66dc69c0706fc8a7f170987 SHA256 32e370f7b55bdcfbb341fa6c631a9a485ce3e066ced96ddb27cbdc26d48d24cf
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 DIST coot-0.1.2.tar.gz 2704638 RMD160 bb0ff46297fc7135b1bf31159bf41b18462b916c SHA1 66f4b13f37cab6537b454a0ad23050044eb4a95f SHA256 fcd2e5862ef57baffc19aa30b1bb48b5271baf0667cc72bf5ecd8a02911fe22a
 EBUILD coot-0.1.2.ebuild 2320 RMD160 0e24f7c81f354b053a0df2ac5fe287d5f106917a SHA1 69dceaa6e8341e45ce22ec176b96d8ff89183f94 SHA256 fc8b3afb9aaf2fbf56787d827610f6d63f40d3d62288ec7bb1adcf9c735111aa
 MD5 60ed52e7a223c379c006c66e31f18b5e coot-0.1.2.ebuild 2320
 RMD160 0e24f7c81f354b053a0df2ac5fe287d5f106917a coot-0.1.2.ebuild 2320
 SHA256 fc8b3afb9aaf2fbf56787d827610f6d63f40d3d62288ec7bb1adcf9c735111aa coot-0.1.2.ebuild 2320
-EBUILD coot-0.1.2_pre1.ebuild 2309 RMD160 b77d269e0109eaf81385ab6032b1ee04f7edb341 SHA1 5dd2b129e5dc49004813794651467048b2d11beb SHA256 299ba3698340c81283ab20bcd1032e1fc9660293c820e6a046bc60b7df19a784
-MD5 20b825b7c7a8213e3e487a350627cb12 coot-0.1.2_pre1.ebuild 2309
-RMD160 b77d269e0109eaf81385ab6032b1ee04f7edb341 coot-0.1.2_pre1.ebuild 2309
-SHA256 299ba3698340c81283ab20bcd1032e1fc9660293c820e6a046bc60b7df19a784 coot-0.1.2_pre1.ebuild 2309
-MISC ChangeLog 1174 RMD160 7eb273b4a2bbbcdfdeec6be7825ae863fdb6c271 SHA1 1910ef5e9acbfa41620a9c5facd92c5444a94a88 SHA256 43bac004b32411424222b6b225fb898d03f2fbec2c0dfd1e35389a01b31dffed
-MD5 1f5e8cfaf931e04c1e9d061dcc42c61b ChangeLog 1174
-RMD160 7eb273b4a2bbbcdfdeec6be7825ae863fdb6c271 ChangeLog 1174
-SHA256 43bac004b32411424222b6b225fb898d03f2fbec2c0dfd1e35389a01b31dffed ChangeLog 1174
+MISC ChangeLog 1283 RMD160 0e780a0e215c5a59be3897ce93647401d0f6ce5a SHA1 9d4c816a0d4ccfa51fbd0de5b0efc09e9de39b2d SHA256 21e31185794d8a914196f0eafa1be87cc5486ad7caebd2ce09b33d7f2e8d20de
+MD5 27be0f40972adb86a91b60bf05f7e645 ChangeLog 1283
+RMD160 0e780a0e215c5a59be3897ce93647401d0f6ce5a ChangeLog 1283
+SHA256 21e31185794d8a914196f0eafa1be87cc5486ad7caebd2ce09b33d7f2e8d20de ChangeLog 1283
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
@@ -19,6 +17,10 @@ SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 metadata
 MD5 39d53022c73d281c3d319c2c0ba3f4c6 files/digest-coot-0.1.2 235
 RMD160 dc807e2c87756c2731686576e75db488978a78e9 files/digest-coot-0.1.2 235
 SHA256 19a197b638681d05d7847a3563ef6cea23606b94a6f3056043ea775fcb88d515 files/digest-coot-0.1.2 235
-MD5 4dbc02767e6b27d8f3569cf6af79cc21 files/digest-coot-0.1.2_pre1 253
-RMD160 d8011ba50b97f25d69286530859110d518c10fe2 files/digest-coot-0.1.2_pre1 253
-SHA256 620c6c8e0faf9a2566a468132cdabfdc7f90ccb1fb26a1d9a33f01c2f472f1ce files/digest-coot-0.1.2_pre1 253
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v1.4.4 (GNU/Linux)
+
+iD8DBQFFoCJw5mJXAu5GbtIRAt6JAJwNZYS/PRa2A1RvvKzoNeWiSYgegACfWjaj
+jFHqqaZfHuVootY40yiDahU=
+=v6JX
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/coot/coot-0.1.2_pre1.ebuild b/sci-chemistry/coot/coot-0.1.2_pre1.ebuild
deleted file mode 100644
index ab8bbe7b9f4e..000000000000
--- a/sci-chemistry/coot/coot-0.1.2_pre1.ebuild
+++ /dev/null
@@ -1,90 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.1.2_pre1.ebuild,v 1.2 2006/06/28 08:24:00 spyderous Exp $
-
-inherit autotools
-
-MY_PV=${PV/_pre/-pre-}
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~emsley/coot/"
-if [[ ${MY_PV} = *pre* ]]; then
-	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/pre-release/${MY_P}.tar.gz"
-else
-	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${MY_P}.tar.gz"
-fi
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~ppc ~x86"
-IUSE=""
-RDEPEND=">=sci-libs/gsl-1.3
-	=dev-libs/glib-1.2*
-	=x11-libs/gtkglarea-1.2*
-	x11-libs/gtkglext
-	virtual/glut
-	virtual/opengl
-	sci-chemistry/ccp4
-	dev-lang/python
-	x11-libs/gtk-canvas
-	dev-lang/python
-	x11-libs/guile-gtk
-	dev-scheme/guile-gui
-	dev-scheme/net-http
-	dev-scheme/goosh
-	dev-scheme/guile-www
-	sci-libs/coot-data
-	sci-chemistry/reduce
-	sci-chemistry/probe"
-DEPEND="${RDEPEND}"
-S="${WORKDIR}/${MY_P}"
-
-src_unpack() {
-	unpack ${A}
-
-	# Link against single-precision fftw
-	sed -i \
-		-e "s:lfttw:lsfttw:g" \
-		-e "s:lrfttw:lsrfttw:g" \
-		"${S}"/macros/clipper.m4
-
-	# Don't install setup scripts, they're only needed for nonstandard prefixes
-	sed -i \
-		-e "s:^\(setup.*\):#\1:g" \
-		-e "s:.*\(bin_.*\):\1:g" \
-		"${S}"/setup/Makefile.am
-
-	# Fix where it looks for some binaries
-	sed -i \
-		-e "s:/y/people/emsley/coot/Linux/bin/probe.2.11.050121.linux.RH9:${ROOT}usr/bin/probe:g" \
-		-e "s:/y/people/emsley/coot/Linux/bin/reduce.2.21.030604:${ROOT}usr/bin/reduce:g" \
-		"${S}"/scheme/group-settings.scm
-
-	cd "${S}"
-	AT_M4DIR="macros" eautoreconf
-}
-
-src_compile() {
-	# All the --with's are used to activate various parts.
-	# Yes, this is broken behavior.
-	econf \
-		--includedir='${prefix}/include/coot' \
-		--with-gtkcanvas-prefix=/usr \
-		--with-clipper-prefix=/usr \
-		--with-mmdb-prefix=/usr \
-		--with-ssmlib-prefix=/usr \
-		--with-guile=/usr \
-		--with-python=/usr \
-		|| die "econf failed"
-
-	# Parallel build's broken
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	make DESTDIR="${D}" install || die "install failed"
-
-	# Install misses this
-	insinto /usr/share/coot/python
-	doins "${S}"/src/coot.py
-}
diff --git a/sci-chemistry/coot/files/digest-coot-0.1.2_pre1 b/sci-chemistry/coot/files/digest-coot-0.1.2_pre1
deleted file mode 100644
index 7e8520a23e55..000000000000
--- a/sci-chemistry/coot/files/digest-coot-0.1.2_pre1
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 632cf09e08d037288a50a34beb442ab3 coot-0.1.2-pre-1.tar.gz 2759927
-RMD160 e54818e72274288f125661e09e2a834f83230604 coot-0.1.2-pre-1.tar.gz 2759927
-SHA256 32e370f7b55bdcfbb341fa6c631a9a485ce3e066ced96ddb27cbdc26d48d24cf coot-0.1.2-pre-1.tar.gz 2759927