InCvs

10 files changed, 0 insertions, 234 deletions

diff --git a/sci-chemistry/autodock/ChangeLog b/sci-chemistry/autodock/ChangeLog
deleted file mode 100644
index 27432b1ce..000000000
--- a/sci-chemistry/autodock/ChangeLog
+++ /dev/null
@@ -1,36 +0,0 @@
-# ChangeLog for sci-chemistry/autodock
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/autodock/ChangeLog,v 1.6 2009/03/24 21:39:42 ribosome Exp $
-
-*autodock-4.0.1-r2 (07 Oct 2009)
-
-  07 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +autodock-4.0.1-r2.ebuild, +files/4.0.1-gcc-4.3.patch,
-  +files/4.0.1-respect-flags.patch, +metadata.xml:
-  Respect CFLAGS now
-  QA on ebuild
-
-  24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
-  Giving up maintainership of this package.
-
-  05 Aug 2008; Donnie Berkholz <dberkholz@gentoo.org>;
-  +files/4.0.1-gcc-4.3.patch, autodock-4.0.1-r1.ebuild:
-  Fix for gcc 4.3.
-
-*autodock-4.0.1-r1 (26 Jun 2007)
-
-  26 Jun 2007; Olivier Fisette <ribosome@gentoo.org>
-  +autodock-4.0.1-r1.ebuild:
-  Install documentation and parameter files. Added test suite. Ebuild clean-up.
-
-  21 Jun 2007; Olivier Fisette <ribosome@gentoo.org> autodock-4.0.1.ebuild:
-  Added a notice and URL to encourage Gentoo users to register as AutoDock
-  users for grant application purposes.
-
-*autodock-4.0.1 (19 Jun 2007)
-
-  19 Jun 2007; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
-  +autodock-4.0.1.ebuild:
-  Initial import. Thanks to Luc Grenier <lgrenier@rsvs.ulaval.ca> for his
-  ebuild and for testing the package.
-
diff --git a/sci-chemistry/autodock/Manifest b/sci-chemistry/autodock/Manifest
deleted file mode 100644
index 544b9c849..000000000
--- a/sci-chemistry/autodock/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-AUX 4.0.1-gcc-4.3.patch 288 RMD160 baa74a563ff1307f10f7a8231884004c62f42598 SHA1 7316ded087e79b04a9c5cd0437ef07d7bc10a83f SHA256 1bbd84b47a93856245103e2c6ab3ed4932ab0d8909010f2e43fd62bdf680936c
-AUX 4.0.1-respect-flags.patch 1661 RMD160 498b0284288dbe6b88e71d812d6c61c41e5f7127 SHA1 c0409c6e18e1fb09c9d65fe7a8b428f3a35621e7 SHA256 aa4dd797009002f9a1805dec715c23849a5a8a7bfc2fec9c5dcc8e7a982760dc
-DIST autodocksuite-4.0.1-src.tar.gz 1898212 RMD160 af2709277c1e9d36602c7100091b707937aa32d8 SHA1 3c43d9cf67790b47803a37e9e8ace893018cf874 SHA256 8265e313c575dbb4e284dab90af2ed9b8f34dfdeb45508e652ca5fa9a09dc11b
-EBUILD autodock-4.0.1-r2.ebuild 1722 RMD160 8504ab3132e5ca654d307f9fa72afa1dfd8897ae SHA1 de49d9e86e90f1259b1912e4f62931ea128a7e64 SHA256 ad0de26b73ad55982cb49ddb859406b3432a37729b74787c1c678509b6f96922
-MISC ChangeLog 1325 RMD160 ae44fba838b9753e0e25a179495d66b2fa857e8d SHA1 709aeb6604cee407bf64601be64b907c66b4d522 SHA256 85ccb4637f1d44eab41eb045b0c2561e16b0fcde5b5bf9e63ed92e2f0cf288a6
-MISC metadata.xml 167 RMD160 ea4003a55d6e2079381a540c441fc59cde29025a SHA1 3bc6dc4dd68f7de22828138e62aa117387b1765d SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8
diff --git a/sci-chemistry/autodock/autodock-4.0.1-r2.ebuild b/sci-chemistry/autodock/autodock-4.0.1-r2.ebuild
deleted file mode 100644
index cf5e3a312..000000000
--- a/sci-chemistry/autodock/autodock-4.0.1-r2.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit autotools eutils
-
-MY_PN="autodocksuite"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="A suite of automated docking tools"
-HOMEPAGE="http://autodock.scripps.edu/"
-SRC_URI="mirror://gentoo/${MY_PN}/${MY_P}-src.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-S="${WORKDIR}/${MY_P}/src"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-gcc-4.3.patch \
-		"${FILESDIR}"/${PV}-respect-flags.patch
-
-	for i in autodock autogrid; do
-		pushd $i
-		eautoreconf
-		popd
-	done
-}
-
-src_configure() {
-	for i in autodock autogrid; do
-		pushd $i
-		econf || die "AutoDock econf failed."
-		popd
-	done
-}
-
-src_compile() {
-	emake -C autodock || die
-	emake -C autogrid || die
-}
-
-src_install() {
-	dobin "${S}"/autodock/autodock4 "${S}"/autogrid/autogrid4 \
-		|| die "Failed to install autodock binary."
-
-	insinto "/usr/share/autodock"
-	doins "${S}"/autodock/{AD4_parameters.dat,AD4_PARM99.dat} \
-		 || die "Failed to install shared files."
-
-	dodoc "${S}"/autodock/{AUTHORS,ChangeLog,NEWS,README} \
-		|| die "Failed to install documentation."
-}
-
-src_test() {
-	cd "${S}/autodock/Tests"
-	python test_autodock4.py || die "AutoDock tests failed."
-	cd "${S}/autogrid/Tests"
-	python test_autogrid4.py || die "AutoGrid tests failed."
-}
-
-pkg_postinst() {
-	einfo "The AutoDock development team requests all users to fill out the"
-	einfo "registration form at:"
-	einfo
-	einfo "\thttp://autodock.scripps.edu/downloads/autodock-registration"
-	einfo
-	einfo "The number of unique users of AutoDock is used by Prof. Arthur J."
-	einfo "Olson and the Scripps Research Institude to support grant"
-	einfo "applications."
-}
diff --git a/sci-chemistry/autodock/files/4.0.1-gcc-4.3.patch b/sci-chemistry/autodock/files/4.0.1-gcc-4.3.patch
deleted file mode 100644
index b9eb3c409..000000000
--- a/sci-chemistry/autodock/files/4.0.1-gcc-4.3.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- autodocksuite-4.0.1.orig/src/autogrid/check_size.cpp	2008-08-04 22:44:46.000000000 -0700
-+++ autodocksuite-4.0.1/src/autogrid/check_size.cpp	2008-08-04 22:45:12.000000000 -0700
-@@ -27,6 +27,7 @@
- 
- #include <iostream>
- #include <math.h>
-+#include <cstdlib>
- #include "autogrid.h"
- 
- 
diff --git a/sci-chemistry/autodock/files/4.0.1-respect-flags.patch b/sci-chemistry/autodock/files/4.0.1-respect-flags.patch
deleted file mode 100644
index b622192c3..000000000
--- a/sci-chemistry/autodock/files/4.0.1-respect-flags.patch
+++ /dev/null
@@ -1,40 +0,0 @@
---- src/autogrid/Makefile.am	2007-05-17 22:53:30.000000000 +0200
-+++ src/autogrid/Makefile.am.new	2009-10-07 19:48:52.000000000 +0200
-@@ -78,9 +78,9 @@
-             util.h \
-             version.h
- 
--AM_CFLAGS = -Wall -O3 # All warnings, Agressive optimization
-+#AM_CFLAGS = -Wall -O3 # All warnings, Agressive optimization
- 
--AM_CXXFLAGS = -Wall -O3 # All warnings, Agressive optimization
-+#AM_CXXFLAGS = -Wall -O3 # All warnings, Agressive optimization
- 
- AM_CPPFLAGS = -I$(srcdir)/../autodock-4.0.1
- 
---- src/autodock/Makefile.am	2007-05-12 06:51:41.000000000 +0200
-+++ src/autodock/Makefile.am.new	2009-10-07 19:48:01.000000000 +0200
-@@ -244,7 +244,7 @@
- 		writePDBQT.h
- 
- 
--AM_CXXFLAGS = -Wall -O3 # All warnings, Agressive optimization
-+#AM_CXXFLAGS = -Wall -O3 # All warnings, Agressive optimization
- #AM_CXXFLAGS = -Wall -O3 -ftree-vectorize # All warnings, Agressive optimization + GCC vectorization # MacOSX only?
- 
- AM_CPPFLAGS = -DNOSQRT \
---- src/autogrid/Makefile.am	2009-10-07 19:58:04.000000000 +0200
-+++ src/autogrid/Makefile.am.new	2009-10-07 20:00:17.000000000 +0200
-@@ -84,10 +84,10 @@
- 
- AM_CPPFLAGS = -I$(srcdir)/../autodock-4.0.1
- 
--autogrid4_CFLAGS = -Wall -O3 # All warnings, Agressive optimization
-+autogrid4_CFLAGS = # All warnings, Agressive optimization
- # autogrid4_CFLAGS = -Wall -O3 -ftree-vectorize # All warnings, Agressive optimization, GCC vectorization in Mac OS X
- 
--autogrid4_CXXFLAGS = -Wall -O3 # All warnings, Agressive optimization
-+autogrid4_CXXFLAGS = # All warnings, Agressive optimization
- # autogrid4_CXXFLAGS = -Wall -O3 -ftree-vectorize # All warnings, Agressive optimization, GCC vectorization in Mac OS X
- 
- 
diff --git a/sci-chemistry/autodock/metadata.xml b/sci-chemistry/autodock/metadata.xml
deleted file mode 100644
index e42d0af60..000000000
--- a/sci-chemistry/autodock/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci-chemistry</herd>
-</pkgmetadata>
diff --git a/sci-chemistry/autodock_vina/ChangeLog b/sci-chemistry/autodock_vina/ChangeLog
deleted file mode 100644
index 8d4dac031..000000000
--- a/sci-chemistry/autodock_vina/ChangeLog
+++ /dev/null
@@ -1,10 +0,0 @@
-# ChangeLog for sci-chemistry/autodock_vina
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*autodock_vina-1.0.3 (04 Feb 2010)
-
-  04 Feb 2010; Alexey Shvetsov <alexxy@gentoo.org>
-  +autodock_vina-1.0.3.ebuild, +metadata.xml:
-  Initial import per bug #282682
-
diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest
deleted file mode 100644
index ee486663c..000000000
--- a/sci-chemistry/autodock_vina/Manifest
+++ /dev/null
@@ -1,14 +0,0 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-DIST autodock_vina_1_0_3_linux_i386.tar.gz 807351 RMD160 463563f57a5c9892ffd6631b4fe19033997c52a5 SHA1 45419a5ab1e279ef8ce11b7201f0990d6e254898 SHA256 07b1f0b56d7d72c240f2b3bb89d2076e79a6f412d9d8207a7b2be0b5b3ce4aed
-EBUILD autodock_vina-1.0.3.ebuild 783 RMD160 e64278ecf88de24efe12f4087da757dda0f94041 SHA1 4805d53f155da7e8c6b336617f9a9cad5167966b SHA256 c58031fdc69e90379d1aaa47b0cb016ecf5788b21a5802a1f1ca5ac37e723814
-MISC ChangeLog 295 RMD160 99a9c97f2a09c6f4847d6fa555ec27445e1dbadc SHA1 4fbf1f23badf3902886ea7ec63b2bf1779d5888f SHA256 a161eba92bb51b0e5bbefec09246a5f51adb0893cb56b1c8236d2ccb4e2c617b
-MISC metadata.xml 167 RMD160 ea4003a55d6e2079381a540c441fc59cde29025a SHA1 3bc6dc4dd68f7de22828138e62aa117387b1765d SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.14 (GNU/Linux)
-
-iEYEARECAAYFAktqwjsACgkQ5BmOA85PVLga6gCgjeBVVn9vZwPRkXp3CbjBwRXm
-xJkAn2jTa/gN/zCZnwBBFNULgifW4nHQ
-=PJ5g
------END PGP SIGNATURE-----
diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.0.3.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.0.3.ebuild
deleted file mode 100644
index 15672b80f..000000000
--- a/sci-chemistry/autodock_vina/autodock_vina-1.0.3.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-DESCRIPTION="AutoDock Vina is a new program for drug discovery and molecular docking"
-HOMEPAGE="http://vina.scripps.edu/"
-MY_PN="${PN}_${PV//./_}_linux_i386"
-SRC_URI="http://vina.scripps.edu/download/${MY_PN}.tar.gz"
-MY_S="${PN}_${PV//./_}_linux_i386"
-
-LICENSE="vina_license"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="amd64? (
-				app-emulation/emul-linux-x86-baselibs
-				app-emulation/emul-linux-x86-compat
-		)"
-
-src_unpack() {
-	unpack ${A}
-	cd "${MY_S}"
-	header=`grep --binary-files=text "header_length=" install.sh | cut -d "=" -f2`
-	tail -n+${header} install.sh | tar -xz
-}
-
-src_install() {
-	dobin	${MY_S}/vina
-	dobin	${MY_S}/vina_split
-}
diff --git a/sci-chemistry/autodock_vina/metadata.xml b/sci-chemistry/autodock_vina/metadata.xml
deleted file mode 100644
index e42d0af60..000000000
--- a/sci-chemistry/autodock_vina/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci-chemistry</herd>
-</pkgmetadata>