Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci

166 files changed, 3208 insertions, 2719 deletions

diff --git a/Documentation/wherearethefiles b/Documentation/wherearethefiles
deleted file mode 100644
index dafa14cc7..000000000
--- a/Documentation/wherearethefiles
+++ /dev/null
@@ -1 +0,0 @@
-moved to REPO_ROOT/scripts as they are scripts
diff --git a/dev-lang/icc/ChangeLog b/dev-lang/icc/ChangeLog
deleted file mode 100644
index eac7722d0..000000000
--- a/dev-lang/icc/ChangeLog
+++ /dev/null
@@ -1,22 +0,0 @@
-# ChangeLog for dev-lang/icc
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  17 Sep 2009; Sébastien Fabbro <bicatali@gentoo.org>
-  icc-11.1.046-r3.ebuild:
-  Added ROOTPATH in the env file, and change env file to 05icfc since this
-  is the same as ifc
-
-  05 Sep 2009; Sébastien Fabbro <bicatali@gentoo.org>
-  icc-11.1.046-r3.ebuild:
-  Fixed collision files with other Intel packages
-
-*icc-11.1.046-r3 (04 Sep 2009)
-
-  04 Sep 2009; Sébastien Fabbro <bicatali@gentoo.org>
-  +icc-11.1.046-r3.ebuild, +metadata.xml:
-  Revision bump. Complete rewrite: no more rpm dependency, used smaller
-  upstream tar balls, now include full suite apart from TBB (open source),
-  introducing mkl, idb and ipp USE flags. Test in science overlay before
-  main tree inclusion
-
diff --git a/dev-lang/icc/Manifest b/dev-lang/icc/Manifest
deleted file mode 100644
index cf9c2aeb4..000000000
--- a/dev-lang/icc/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-DIST l_cproc_p_11.1.046_ia32.tgz 713224821 RMD160 de7183db93dbc348561f131b68b8963d19ccf0bb SHA1 985b4d2b72f806d40389680a81b905b58a63b931 SHA256 e9c4f36b8eaee666ede6c8cfe694d153b7f23061c6085a8be1bdbe99e9629669
-DIST l_cproc_p_11.1.046_ia64.tgz 548695070 RMD160 49e98bf43077f039e55497ad0db5342c52210b57 SHA1 f858f1bedc2e2248720a34a4488f66a42b312c07 SHA256 9740a51c6c722b29cd57f8f8096a66564c100309241f66423b4c9e3925bfd21e
-DIST l_cproc_p_11.1.046_intel64.tgz 783691399 RMD160 53bb3581f34a0cd319f6ebc2200444e137deacd6 SHA1 c81307d9f95f6a126137ec5baf187f5a7595384a SHA256 51231e3f7f46372eddb721d9aac497e6ba824f86f7f220c34f4348ec65eeb25d
-EBUILD icc-11.1.046-r3.ebuild 3259 RMD160 35075069beac5c019070232740203f651f59cb55 SHA1 424107dbb6ab16bc6dd9e22b3d5c941073b6c051 SHA256 050debb773cd8e0ad777a9f5f8b2d8835647137a788f33fd5ae4ff572df649a6
-MISC ChangeLog 795 RMD160 11152aa5d0a9e1a6ee13551fdf39095156bebb48 SHA1 cfc6d896d7e1254ee0a7c3ddbdee1591e8278a49 SHA256 e177f4a1d2eb39ef28467ef37b77b2b172f4708fbbfde0cebc09077d8748ffb1
-MISC metadata.xml 978 RMD160 ca73ec402e36b4159530331ecb1e31e7d4f1812f SHA1 d1ba4a9828bb7939231d776f20e2298639d8f1ca SHA256 41938d9e4f3793fffc335074317c71bc396473e9244d0239fde1f2586f15b2e4
diff --git a/dev-lang/icc/icc-11.1.046-r3.ebuild b/dev-lang/icc/icc-11.1.046-r3.ebuild
deleted file mode 100644
index 4f4858c72..000000000
--- a/dev-lang/icc/icc-11.1.046-r3.ebuild
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=2
-
-inherit rpm versionator check-reqs
-
-PB=cproc
-PACKAGEID="l_${PB}_p_${PV}"
-RELEASE="$(get_version_component_range 1-2)"
-BUILD="$(get_version_component_range 3)"
-PID=1536
-
-DESCRIPTION="Intel compiler suite for Linux"
-HOMEPAGE="http://www.intel.com/software/products/compilers/clin/"
-SRC_COM="http://registrationcenter-download.intel.com/irc_nas/${PID}/${PACKAGEID}"
-SRC_URI="amd64? ( ${SRC_COM}_intel64.tgz )
-	ia64? ( ${SRC_COM}_ia64.tgz )
-	x86?  ( ${SRC_COM}_ia32.tgz )"
-
-LICENSE="Intel-SDP"
-SLOT="0"
-IUSE="+idb ipp mkl"
-KEYWORDS="~amd64 ~ia64 ~x86"
-
-RESTRICT="mirror strip binchecks"
-
-DEPEND=""
-RDEPEND="~virtual/libstdc++-3.3
-	amd64? ( app-emulation/emul-linux-x86-compat )"
-
-DESTINATION="opt/intel/Compiler/${RELEASE}/${BUILD}"
-
-pkg_setup() {
-	CHECKREQS_MEMORY=1024
-	CHECKREQS_DISK_BUILD=2048
-	use idb && use ipp && use mkl && CHECKREQS_DISK_BUILD=3072
-	check_reqs
-	IARCH=ia32
-	use amd64 && IARCH=intel64
-	use ia64 && IARCH=ia64
-}
-
-src_unpack() {
-	unpack ${A}
-	mv "${WORKDIR}"/l_* "${S}"
-	cd "${S}"
-	# tbb is open source, thus built from sources in dev-cpp/tbb
-	rm -f rpm/*tbb*.rpm
-	use idb || rm -f rpm/*idb*.rpm
-	use ipp || rm -f rpm/*ipp*.rpm
-	use mkl || rm -f rpm/*mkl*.rpm
-	if has_version "~dev-lang/ifc-${PV}"; then
-		rm -f rpm/*cprolib*.rpm
-		use idb && built_with_use dev-lang/ifc idb && rm -f rpm/*idb*.rpm
-		use mkl && built_with_use dev-lang/ifc mkl && rm -f rpm/*mkl*.rpm
-	fi
-	for x in rpm/intel*.rpm; do
-		einfo "Extracting $(basename ${x})..."
-		rpm_unpack ${x} || die "rpm_unpack ${x} failed"
-	done
-}
-
-src_prepare() {
-	# from the PURGE_UB804_FNP in pset/install_cc.sh
-	# rm -f "${DESTINATION}"/lib/*/*libFNP.so || die
-
-	# extract the tag function from the original install
-	sed -n \
-		-e "s|find \$DESTINATION|find ${DESTINATION}|g" \
-		-e "s|@\$DESTINATION|@${ROOT}${DESTINATION}|g" \
-		-e '/^UNTAG_CFG_FILES[[:space:]]*(/,/^}/p' \
-		pset/install_cc.sh > tag.sh || die
-	# fix world writeable files
-	[ -d ${DESTINATION}/mkl ]  && chmod 644 \
-		${DESTINATION}/mkl/tools/{environment,builder}/* \
-		${DESTINATION}/mkl/tools/plugins/*/*
-}
-
-src_install() {
-	einfo "Tagging"
-	. ./tag.sh
-	UNTAG_CFG_FILES
-
-	keepdir /opt/intel/licenses
-	einfo "Copying files"
-	dodir "${DESTINATION}"
-	cp -pPR \
-		${DESTINATION}/* \
-		"${D}"/${DESTINATION}/ \
-		|| die "Copying ${PN} failed"
-
-	if ! has_version "~dev-lang/ifc-${PV}"; then
-		cat > 05icfc <<-EOF
-			PATH="${ROOT}${DESTINATION}/bin/${IARCH}"
-			ROOTPATH="${ROOT}${DESTINATION}/bin/${IARCH}"
-			LDPATH="${ROOT}${DESTINATION}/lib/${IARCH}"
-			LIBRARY_PATH="${ROOT}${DESTINATION}/lib/${IARCH}"
-			NLSPATH="${ROOT}${DESTINATION}/lib/locale/en_US/%N"
-			MANPATH="${ROOT}${DESTINATION}/man/en_US"
-		EOF
-		doenvd 05icfc || die "doenvd 05icfc failed"
-	fi
-	[ -d ${DESTINATION}/idb ] && \
-		dosym ../../common/com.intel.debugger.help_1.0.0 \
-		${DESTINATION}/idb/gui/${IARCH}/plugins
-}
-
-pkg_postinst() {
-	elog "Make sure you have recieved the an Intel license."
-	elog "To receive a non-commercial license, you need to register at:"
-	elog "http://software.intel.com/en-us/articles/non-commercial-software-development/"
-	elog "Install the license file into ${ROOT}opt/intel/licenses."
-}
diff --git a/dev-lang/icc/metadata.xml b/dev-lang/icc/metadata.xml
deleted file mode 100644
index 3da1677ab..000000000
--- a/dev-lang/icc/metadata.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-
-<pkgmetadata>
-<herd>no-herd</herd>
-<maintainer>
-  <email>bicatali@gentoo.org</email>
-</maintainer>
-<maintainer>
-  <email>weaver@gentoo.org</email>
-  <name>Andrey Kislyuk</name>
-</maintainer>
-<longdescription lang="en">
-  The Intel® C++ Compiler is a full featured C/C++ compiler for Intel
-  based architectures. The compiler supports multi-threading, automatic
-  processor dispatch, vectorization, auto-parallelization, OpenMP, data
-  prefetching, loop unrolling. The package comes with extensive
-  documentation. The product can be installed as a non-commercial as
-  well. License, terms of qualifications can be found on the web site.
-</longdescription>
-<use>
-  <flag name='idb'>Install the Intel Debugger</flag>
-  <flag name='mkl'>Install the Intel Math Kernel Library</flag>
-  <flag name='ipp'>Install the Intel Integrated Primitive</flag>
-</use>
-</pkgmetadata>
diff --git a/dev-lang/idb/ChangeLog b/dev-lang/idb/ChangeLog
deleted file mode 100644
index 3fd058e14..000000000
--- a/dev-lang/idb/ChangeLog
+++ /dev/null
@@ -1,14 +0,0 @@
-# ChangeLog for dev-lang/idb
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  05 Sep 2009; Sébastien Fabbro <bicatali@gentoo.org> idb-11.1.046.ebuild:
-  Fixed collision files with other Intel packages
-
-*idb-11.1.046 (04 Sep 2009)
-
-  04 Sep 2009; Sébastien Fabbro <bicatali@gentoo.org> +idb-11.1.046.ebuild,
-  +metadata.xml:
-  Version bump. Complete rewrite due to upstream packaging system and use
-  EAPI2 use flag depedencies
-
diff --git a/dev-lang/idb/Manifest b/dev-lang/idb/Manifest
deleted file mode 100644
index 7c4fa381f..000000000
--- a/dev-lang/idb/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-EBUILD idb-11.1.046.ebuild 728 RMD160 e0a2a4a01eafbd08e60422815208580b35d2cb94 SHA1 80059082d2b82be1e500bcccf775eaabbdb207b4 SHA256 a3cb74134deab3e687f7ca085d6bda3a794ed9a78831a45e70b284449cb42e3a
-MISC ChangeLog 467 RMD160 a9ca1a47b9b149c6f56a73dfefeaecdf862e926c SHA1 22b93438304ebaafb518daaf0eddf8327b7f7e04 SHA256 1344df69db9e012d11b3431e7dd499cc7ea15d62c652982d772ba4a2cdc147f2
-MISC metadata.xml 769 RMD160 e0213bd0ec069c7680c5eb5fec1c48d8215cb358 SHA1 0e122fa202d2328569e188e4bfe68d637bdf86d6 SHA256 abf59ceaa7de63559560f96e05e6e667ba5684432dc79aa92d5f162b18b41241
diff --git a/dev-lang/idb/idb-11.1.046.ebuild b/dev-lang/idb/idb-11.1.046.ebuild
deleted file mode 100644
index a24840806..000000000
--- a/dev-lang/idb/idb-11.1.046.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=2
-inherit versionator
-
-RELEASE="$(get_version_component_range 1-2)"
-BUILD="$(get_version_component_range 3)"
-
-DESCRIPTION="Intel C/C++/FORTRAN debugger for Linux"
-HOMEPAGE="http://www.intel.com/software/products/compilers/"
-SRC_URI=""
-
-KEYWORDS="~amd64 ~ia64 ~x86"
-
-LICENSE="Intel-SDP"
-SLOT="0"
-IUSE=""
-
-DEPEND=""
-RDEPEND="|| ( ~dev-lang/icc-${PV}[idb] ~dev-lang/ifc-${PV}[idb] )
-	>=virtual/jre-1.5"
-
-DESTINATION="${ROOT}opt/intel/Compiler/${RELEASE}/${BUILD}"
-
-src_install() {
-	cat > 06idb <<-EOF
-		NLSPATH=${DESTINATION}/idb/${IARCH}/locale/%l_%t/%N
-	EOF
-	doenvd 06idb || die "doenvd 06idb failed"
-}
diff --git a/dev-lang/idb/metadata.xml b/dev-lang/idb/metadata.xml
deleted file mode 100644
index bbf112e1d..000000000
--- a/dev-lang/idb/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>no-herd</herd>
-<maintainer>
-<email>bicatali@gentoo.org</email>
-</maintainer>
-<longdescription lang="en">
-  The Intel® Debugger is a command line debugger for Intel based
-  architectures. It is well suited with the Intel C++ or Intel FORTRAN
-  compilers. It also comes also with a graphical interface and extensive
-  documentation. The package is bundled in either compiler tar ball, and
-  has been split to produce this one.
-  The product can be installed as a non-commercial as
-  well. License, terms of qualifications can be found on the web
-  site and follow the one received in the Intel compilers.
-</longdescription>
-</pkgmetadata>
-
diff --git a/dev-lang/ifc/ChangeLog b/dev-lang/ifc/ChangeLog
deleted file mode 100644
index b9a2ad36b..000000000
--- a/dev-lang/ifc/ChangeLog
+++ /dev/null
@@ -1,17 +0,0 @@
-# ChangeLog for dev-lang/ifc
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  17 Sep 2009; Sébastien Fabbro <bicatali@gentoo.org> ifc-11.1.046.ebuild:
-  Added ROOTPATH in the env file, and change env file to 05icfc since this
-  is the same as ifc
-
-  05 Sep 2009; Sébastien Fabbro <bicatali@gentoo.org> ifc-11.1.046.ebuild:
-  Fixed collision files with other Intel packages
-
-*ifc-11.1.046 (04 Sep 2009)
-
-  04 Sep 2009; Sébastien Fabbro <bicatali@gentoo.org> +ifc-11.1.046.ebuild,
-  +metadata.xml:
-  Version bump. Complete rewrite, now a compiler suite with mkl and debugger
-
diff --git a/dev-lang/ifc/Manifest b/dev-lang/ifc/Manifest
deleted file mode 100644
index 1eb9f2880..000000000
--- a/dev-lang/ifc/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-DIST l_cprof_p_11.1.046_ia32.tgz 274480154 RMD160 40a7ba9b40e5a4c1240812c9f02ef49117169f55 SHA1 c27e3aac41c3d4fc5f151c545716287de714b729 SHA256 bf35ef392d34344a5f63b92e97a9c6329a25e7e49942a0d20169864cafbf3e6d
-DIST l_cprof_p_11.1.046_ia64.tgz 314180894 RMD160 85fdb5a4d53344787e5c5ed5af5844273905c728 SHA1 e08ac3bf47151c6185dbc859b82368eecc891e85 SHA256 5fd0fa4f6d55ee7c1f9188eadf137f50f7e27635c68ae9dcf954dd25c87bbd6e
-DIST l_cprof_p_11.1.046_intel64.tgz 335932969 RMD160 19dd0f984e7fc3949f3d0d7ed15c45d851566e66 SHA1 3277f8ab66ddfc300f984679c4b32ccaf0c183c4 SHA256 ba405b576827ec15b19d5ccb63822b453075222352ae47094dd38401fcf44c9a
-EBUILD ifc-11.1.046.ebuild 3138 RMD160 73ea05780e3a868afe656f331a1d9f982e05d5ba SHA1 2bd71c35bc5ebb72a7b50f931e7115c6f76e834c SHA256 ab4baa122d86aaecb6ebca63b6871a961a44c666528d6d21f8a4dc31a235a71f
-MISC ChangeLog 614 RMD160 ca9dd3e2b929ace63b548970d3ab46dfbc58c6ed SHA1 9e5150af8126acac5316e228c63a9b66c33619c0 SHA256 5015bfc3d7f662d167ff971a4a597b89fc2014062000188b751c1566034f1977
-MISC metadata.xml 800 RMD160 9aa0b134326ad930fc30eca8d04a1b436ab28b09 SHA1 f41a78ef9756b681616a17af19acd74d3ae057f3 SHA256 0cd8e311615981457834b478c836a1eb0762439b76c267989dcf490db9c7a070
diff --git a/dev-lang/ifc/ifc-11.1.046.ebuild b/dev-lang/ifc/ifc-11.1.046.ebuild
deleted file mode 100644
index 062d28465..000000000
--- a/dev-lang/ifc/ifc-11.1.046.ebuild
+++ /dev/null
@@ -1,113 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=2
-
-inherit rpm versionator check-reqs
-
-PB=cprof
-PACKAGEID="l_${PB}_p_${PV}"
-RELEASE="$(get_version_component_range 1-2)"
-BUILD="$(get_version_component_range 3)"
-PID=1539
-
-DESCRIPTION="Intel FORTRAN compiler suite for Linux"
-HOMEPAGE="http://www.intel.com/software/products/compilers/clin/"
-SRC_COM="http://registrationcenter-download.intel.com/irc_nas/${PID}/${PACKAGEID}"
-SRC_URI="amd64? ( ${SRC_COM}_intel64.tgz )
-	ia64? ( ${SRC_COM}_ia64.tgz )
-	x86?  ( ${SRC_COM}_ia32.tgz )"
-
-LICENSE="Intel-SDP"
-SLOT="0"
-IUSE="idb +mkl"
-KEYWORDS="~amd64 ~ia64 ~x86"
-
-RESTRICT="mirror strip binchecks"
-
-DEPEND=""
-RDEPEND="~virtual/libstdc++-3.3
-	amd64? ( app-emulation/emul-linux-x86-compat )"
-
-DESTINATION="opt/intel/Compiler/${RELEASE}/${BUILD}"
-
-pkg_setup() {
-	CHECKREQS_MEMORY=1024
-	CHECKREQS_DISK_BUILD=1536
-	use idb && use mkl && CHECKREQS_DISK_BUILD=2048
-	check_reqs
-	IARCH=ia32
-	use amd64 && IARCH=intel64
-	use ia64 && IARCH=ia64
-}
-
-src_unpack() {
-	unpack ${A}
-	mv "${WORKDIR}"/l_* "${S}"
-	cd "${S}"
-	use idb || rm -f rpm/*idb*.rpm
-	use mkl || rm -f rpm/*mkl*.rpm
-	if has_version "~dev-lang/icc-${PV}"; then
-		rm -f rpm/*cprolib*.rpm
-		use idb && built_with_use dev-lang/icc idb && rm -f rpm/*idb*.rpm
-		use mkl && built_with_use dev-lang/icc mkl && rm -f rpm/*mkl*.rpm
-	fi
-	for x in rpm/intel*.rpm; do
-		einfo "Extracting $(basename ${x})..."
-		rpm_unpack ${x} || die "rpm_unpack ${x} failed"
-	done
-}
-
-src_prepare() {
-	# from the PURGE_UB804_FNP in pset/install_fc.sh
-	# rm -f "${DESTINATION}"/lib/*/*libFNP.so || die
-
-	# extract the tag function from the original install
-	sed -n \
-		-e "s|find \$DESTINATION|find ${DESTINATION}|g" \
-		-e "s|@\$DESTINATION|@${ROOT}${DESTINATION}|g" \
-		-e '/^UNTAG_CFG_FILES[[:space:]]*(/,/^}/p' \
-		pset/install_fc.sh > tag.sh || die
-	# fix world writeable files
-	[ -d ${DESTINATION}/mkl ]  && chmod 644 \
-		${DESTINATION}/mkl/tools/{environment,builder}/* \
-		${DESTINATION}/mkl/tools/plugins/*/*
-}
-
-src_install() {
-	einfo "Tagging"
-	. ./tag.sh
-	UNTAG_CFG_FILES
-
-	keepdir /opt/intel/licenses
-	einfo "Copying files"
-	dodir "${DESTINATION}"
-	cp -pPR \
-		${DESTINATION}/* \
-		"${D}"/${DESTINATION}/ \
-		|| die "Copying ${PN} failed"
-
-	if ! has_version "~dev-lang/icc-${PV}"; then
-		cat > 05icfc <<-EOF
-			PATH="${ROOT}${DESTINATION}/bin/${IARCH}"
-			ROOTPATH="${ROOT}${DESTINATION}/bin/${IARCH}"
-			LDPATH="${ROOT}${DESTINATION}/lib/${IARCH}"
-			LIBRARY_PATH="${ROOT}${DESTINATION}/lib/${IARCH}"
-			NLSPATH="${ROOT}${DESTINATION}/lib/locale/en_US/%N"
-			MANPATH="${ROOT}${DESTINATION}/man/en_US"
-		EOF
-		doenvd 05icfc || die "doenvd 05icfc failed"
-	fi
-
-	[ -d ${DESTINATION}/idb ] && \
-		dosym ../../common/com.intel.debugger.help_1.0.0 \
-		${DESTINATION}/idb/gui/${IARCH}/plugins
-}
-
-pkg_postinst() {
-	elog "Make sure you have recieved the an Intel license."
-	elog "To receive a non-commercial license, you need to register at:"
-	elog "http://software.intel.com/en-us/articles/non-commercial-software-development/"
-	elog "Install the license file into ${ROOT}opt/intel/licenses."
-}
diff --git a/dev-lang/ifc/metadata.xml b/dev-lang/ifc/metadata.xml
deleted file mode 100644
index 100431df0..000000000
--- a/dev-lang/ifc/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-
-<pkgmetadata>
-<herd>sci</herd>
-<longdescription lang="en">
-  The Intel® Fortran Compiler is a full featured FORTRAN 77/95 and
-  substantial FORTRAN 2003 compiler for Intel based architectures. The
-  compiler supports multi-threading with automatic processor dispatch,
-  vectorization, auto-parallelization, OpenMP, data prefetching, loop
-  unrolling. The package comes with extensive documentation.
-  The product can be installed as a non-commercial as well. License,
-  terms of qualifications can be found on the web site.
-</longdescription>
-<use>
-  <flag name='idb'>Install the Intel Debugger</flag>
-  <flag name='mkl'>Install the Intel Math Kernel Library</flag>
-</use>
-</pkgmetadata>
diff --git a/dev-python/aplpy/ChangeLog b/dev-python/aplpy/ChangeLog
index f468371b7..a63c03c59 100644
--- a/dev-python/aplpy/ChangeLog
+++ b/dev-python/aplpy/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*aplpy-0.9.4 (08 Oct 2009)
+
+  08 Oct 2009; Sébastien Fabbro <bicatali@gentoo.org> -aplpy-0.9.3.ebuild,
+  +aplpy-0.9.4.ebuild:
+  Version bump
+
 *aplpy-0.9.2 (26 Jun 2009)
 
   26 Jun 2009; Sébastien Fabbro <bicatali@gentoo.org> +aplpy-0.9.2.ebuild,
diff --git a/dev-python/aplpy/Manifest b/dev-python/aplpy/Manifest
index ac2ffbdf5..6ee353a87 100644
--- a/dev-python/aplpy/Manifest
+++ b/dev-python/aplpy/Manifest
@@ -1,4 +1,4 @@
-DIST APLpy-0.9.3.tar.gz 38032 RMD160 5718830e21853289e82149e29c8dfbac9425474f SHA1 48db82576b2e639344af9cbf3f1beef68fe7524b SHA256 f362f03c4d9424aff308f7fc194560e0c2d3afb2c77c84752b3eacdc8f6ea54d
-EBUILD aplpy-0.9.3.ebuild 580 RMD160 ab0103a68318d77813967d6d6e28a2d258477627 SHA1 aef25802748dcdc436037713455ac162efa369e3 SHA256 19a7026a4c26a2b30b312c59176b785f041afcc93a64079b5004e3a10ec340ba
-MISC ChangeLog 256 RMD160 778fbf138415a533ea753e900ce9dbe706dffdd5 SHA1 cafa8a36b0eccc28efef521d2b1f43c2c1d95f10 SHA256 a2a6457e948e215bc0a8fee214d904ae2e6ef3a915ef3e64910b3384d4f7a32a
+DIST APLpy-0.9.4.tar.gz 42909 RMD160 141f96398e86058601d697b6d81599bb3e55252f SHA1 3d7d5dd8aadf5a0e3732dbf0ed828688c79da091 SHA256 3ad49630e4ca226c0ddddaed2ea42a002c0ce8a04254db0ea146397c947fae87
+EBUILD aplpy-0.9.4.ebuild 575 RMD160 ac0688cbb5ae8517415e356dd3f0eb7f2aa02f66 SHA1 a9be7d21d0e7d9048610308b38f52d6f34d5319b SHA256 aa4fdd5dcf6cea90afe314e735a5812eda71410cbf29e04894c23edff98e8d2e
+MISC ChangeLog 399 RMD160 cc19256913a72e15a5ee624c053c5d6bcb77942f SHA1 aa4b531ea1c75e80a38b82975536b9040d906156 SHA256 7598356821550502b3b4d105f6b2525773fe9a1b2cd08c5fa774b63a8271f151
 MISC metadata.xml 512 RMD160 c5dd1e03db546106233618350a040fab77235884 SHA1 e8256b862e0bd613e7f8de90e7b04eed1fa3a096 SHA256 17b533970c1c70f93e3b04f126dc641e765944687bdfb0f58001eeb9010b7122
diff --git a/dev-python/aplpy/aplpy-0.9.3.ebuild b/dev-python/aplpy/aplpy-0.9.4.ebuild
index d1994213e..7ad743f84 100644
--- a/dev-python/aplpy/aplpy-0.9.3.ebuild
+++ b/dev-python/aplpy/aplpy-0.9.4.ebuild
@@ -13,7 +13,7 @@ HOMEPAGE="http://aplpy.sourceforge.net/"
 SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.gz"
 
 RDEPEND=">=dev-python/numpy-1.3
-	>=dev-python/matplotlib-0.98.5.2
+	>=dev-python/matplotlib-0.99
 	>=dev-python/pyfits-2.1
 	>=dev-python/pywcs-1.5.1
 	>=sci-libs/scipy-0.7"
@@ -26,4 +26,3 @@ KEYWORDS="~amd64 ~x86"
 LICENSE="GPL-3"
 
 S="${WORKDIR}/${MYP}"
-
diff --git a/dev-python/atpy/ChangeLog b/dev-python/atpy/ChangeLog
index 032725b9e..396614866 100644
--- a/dev-python/atpy/ChangeLog
+++ b/dev-python/atpy/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*atpy-0.9.1 (08 Oct 2009)
+
+  08 Oct 2009; Sébastien Fabbro <bicatali@gentoo.org> -atpy-0.9.0.ebuild,
+  +atpy-0.9.1.ebuild, metadata.xml:
+  Version bump
+
 *atpy-0.9.0 (21 Jul 2009)
 
   21 Jul 2009; Sébastien Fabbro <bicatali@gentoo.org> +atpy-0.9.0.ebuild,
diff --git a/dev-python/atpy/Manifest b/dev-python/atpy/Manifest
index ebd38ec66..51e2bc759 100644
--- a/dev-python/atpy/Manifest
+++ b/dev-python/atpy/Manifest
@@ -1,4 +1,4 @@
-DIST ATpy-0.9.0.tar.gz 467393 RMD160 1f564ed9a13352b098324c0e150562a46ad60ab1 SHA1 9e652c69bdb871d06b5565ec982ba2aaedc2a6ed SHA256 408e08d83b0974f433145e8c8e6033e19d1f2b2a2b44936767c875d5a8e008d3
-EBUILD atpy-0.9.0.ebuild 755 RMD160 bde20b82c673b4b2cead96631b975214f0c36eed SHA1 82b9f6b9f2a58cb1fc542ca58d07262f6cdcd51e SHA256 25f135603405b34cbc4459adc68e94f24a9010afb09fb74b437c1a40d4864ae7
-MISC ChangeLog 253 RMD160 c70bf0db426274a001e44fa3f6086123171c4526 SHA1 16fb51364f96ffd5c1ff99aa25d4322b6b7a2027 SHA256 40fcf5bae519f753097044ad5b8efbe8e14b7615d3ee8ff99398f3f0199f5443
-MISC metadata.xml 987 RMD160 ad736cb072a2c9a08f53119d274f21eda0a08e2c SHA1 bbcab187910606001226ae89252d6d69f9ac8eac SHA256 b1c1d5a5d2f8639ca72f762d92339b7934facdf7e05c8df9c0d1e945d14b5795
+DIST ATpy-0.9.1.tar.gz 468439 RMD160 0d8ef2a11ce2acf331aa9c3bb659f5fcabfc30a9 SHA1 b30bfe2f87e50e95fd930984371d9ac4ddbbf46c SHA256 702bf9a07b990c8d49532bd6f9f60798bc00d841e10464c1817f178398d7c2e9
+EBUILD atpy-0.9.1.ebuild 751 RMD160 e6c5b5f607c2974100c1b6967cfc0e435cace834 SHA1 310037aec8e1f369b677ac830db525f6e1d808bd SHA256 d76a26eba365888cb398b3e049c98e4ad9fa10c6bb1e5a3cbf85ce12473c856c
+MISC ChangeLog 407 RMD160 85317d881b13dfdce490fa88830fec0afd0106dd SHA1 0d38e33bca459b48be1d87c053e4e65a8dbd738c SHA256 8021229f4660b69e6d2c4edfcdf47015db5b1d2ad4cf736e22465472a12367ee
+MISC metadata.xml 990 RMD160 a2d6e525f6ac1f63f58cd6aea51e15e27e3bb393 SHA1 efafdba2cbb91071dc99e510c43e2fc9f9c83d08 SHA256 b848a506f5c41178669501433f524e28a6975fecbbb0e82b425f5e48486624c4
diff --git a/dev-python/atpy/atpy-0.9.0.ebuild b/dev-python/atpy/atpy-0.9.1.ebuild
index c46c73046..8407bc278 100644
--- a/dev-python/atpy/atpy-0.9.0.ebuild
+++ b/dev-python/atpy/atpy-0.9.1.ebuild
@@ -15,7 +15,7 @@ SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.gz"
 RDEPEND=">=dev-python/numpy-1.3
 	fits? ( >=dev-python/pyfits-2.1 )
 	mysql? ( dev-python/mysql-python )
-	postgres? ( dev-python/pygresql )
+	postgres? ( dev-db/pygresql )
 	sqlite? ( dev-python/pysqlite )
 	votable? ( >=dev-python/vo-0.3 )"
 
diff --git a/dev-python/atpy/metadata.xml b/dev-python/atpy/metadata.xml
index d931601a8..173cba328 100644
--- a/dev-python/atpy/metadata.xml
+++ b/dev-python/atpy/metadata.xml
@@ -17,7 +17,7 @@
   <flag name="fits">
     Enable support for reading and FITS with <pkg>dev-python/pyfits</pkg>.
   </flag>
-  <flag name="fits">
+  <flag name="votable">
     Enable support for reading and VOTABLE with <pkg>dev-python/vo</pkg>.
   </flag>
 </use>
diff --git a/dev-python/vo/ChangeLog b/dev-python/vo/ChangeLog
index 6310f7fb3..540e03805 100644
--- a/dev-python/vo/ChangeLog
+++ b/dev-python/vo/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*vo-0.4 (08 Oct 2009)
+
+  08 Oct 2009; Sébastien Fabbro <bicatali@gentoo.org> -vo-0.3.1.ebuild,
+  +vo-0.4.ebuild:
+  Version bump
+
 *vo-0.3.1 (21 Jul 2009)
 
   21 Jul 2009; Sébastien Fabbro <bicatali@gentoo.org> +vo-0.3.1.ebuild,
diff --git a/dev-python/vo/Manifest b/dev-python/vo/Manifest
index 6b3ae658e..9eeff6746 100644
--- a/dev-python/vo/Manifest
+++ b/dev-python/vo/Manifest
@@ -1,5 +1,5 @@
 AUX vo-0.3.1-docs.patch 1499 RMD160 5aa6f16abedfd8af700a9fc729c55a026d381551 SHA1 c79e4232b1fb2cfe19567a06b7e1750adbbd1bcf SHA256 bf551b3008332af20fdebe1f22c84835dbad11745c00db65c3eca8d15f7fb72e
-DIST vo-0.3.1.tar.gz 989913 RMD160 3c63a3acd409a62e31d23ab05f15db31d8cc1784 SHA1 d3fd1bf58eded61ec4ee8a3dc8f4e43f1bff6d5b SHA256 ef30f36d9c5dfa49bbc4212f183648393ac48f73d711f8ea24c151300de16ef7
-EBUILD vo-0.3.1.ebuild 889 RMD160 220c2a101e7ac52396adfa4eee337edc5f7279e9 SHA1 1c624c11f8d7d4aed8e59124dbe3967c872c0a0e SHA256 41446739231c5108ec37468abd12af031756e0876d2842f4cc49877ea0d563ef
-MISC ChangeLog 275 RMD160 7445b76e6fea6ca0ad8aa7df027a55f874c07a71 SHA1 1c3c12ad1722580a3d0d40366623897004fd4aa9 SHA256 97b15abf17eaf33876aa50b2dddf062c7d7d88b6fcb4bac21d6bf5e2f9015033
+DIST vo-0.4.tar.gz 995064 RMD160 8973a0929046d3cfea49f77eebbb2aad40cf3b2f SHA1 8979d6baa4aa1fc757001133704855c59181f071 SHA256 c5cd6d3837ce1e293950315d65afdcbe08d35430bc58de8eec7b4cebb607c370
+EBUILD vo-0.4.ebuild 896 RMD160 1759cf3028ee9ae431e3a8b92e8f10853e801ad8 SHA1 7d9c63b7d44b0741489ec3a75e519937d3e6b694 SHA256 9e829f011531602c014e25794cc29acfbeb782849cfbc1206efdbfeb5192f26c
+MISC ChangeLog 405 RMD160 8d8d7d0c14cdddcfe349919fd0b2e2d07b720c73 SHA1 0aa2f80d0f0927184ce1fa753e2f0d402ce2ea2a SHA256 c41a3085023e577fafb8b455c4e6f93d5d8ddea24cb733d0f0099e0d44b6ff60
 MISC metadata.xml 478 RMD160 a115ae6d3b7da632887d7443ee1a85b6ae9b322a SHA1 e42c2e82e7fa028662ef7cb77691ba2ab0c1c9a4 SHA256 d68f25e4c06961ecaa6d08df19e1cf671a592c5f1de97fb1cd780f6722cf793f
diff --git a/dev-python/vo/vo-0.3.1.ebuild b/dev-python/vo/vo-0.4.ebuild
index 8add5b316..8ed1f14c1 100644
--- a/dev-python/vo/vo-0.3.1.ebuild
+++ b/dev-python/vo/vo-0.4.ebuild
@@ -20,7 +20,7 @@ LICENSE="AURA"
 RESTRICT=test
 
 src_prepare() {
-	epatch "${FILESDIR}"/${P}-docs.patch
+	epatch "${FILESDIR}"/${PN}-0.3.1-docs.patch
 }
 
 src_compile() {
diff --git a/docs/proj/blas-lapack.xml b/docs/proj/blas-lapack.xml
new file mode 100644
index 000000000..2b931fc49
--- /dev/null
+++ b/docs/proj/blas-lapack.xml
@@ -0,0 +1,509 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE guide SYSTEM "/dtd/guide.dtd">
+<!-- $Header: /var/cvsroot/gentoo/xml/htdocs/proj/en/science/blas-lapack.xml,v 1.3 2007/12/27 19:35:25 bicatali Exp $ -->
+
+<guide link="/proj/en/science/blas-lapack.xml">
+<title>Using multiple versions of BLAS and LAPACK with Gentoo/Linux</title>
+
+<author title="Author">
+  <mail link="bicatali@gentoo.org">Sébastien Fabbro</mail>
+</author>
+<author title="Author">
+  <mail link="markusle@gentoo.org">Markus Dittrich</mail>
+</author>
+<author title="Editor">
+  <mail link="nightmorph@gentoo.org">Joshua Saddler</mail>
+</author>
+
+<abstract>
+This guide explains the use of the different implementations of the BLAS
+and LAPACK libraries that are available via Portage.
+</abstract>
+
+<!-- The content of this document is licensed under the CC-BY-SA license -->
+<!-- See http://creativecommons.org/licenses/by-sa/2.5 -->
+<license/>
+
+<version>1.0</version>
+<date>2007-10-22</date>
+
+<chapter>
+<title>Introduction</title>
+<section>
+<body>
+
+<p>
+The Basic Linear Algebra Subroutines (BLAS) and Linear Algebra PACKage (LAPACK)
+are well designed linear algebra software libraries developed by the
+High Performance Computing (HPC) community. BLAS
+implements dense matrix and vectors products, while LAPACK provides routines for 
+solving systems of linear equations. Both are widely used in
+many scientific applications and it is, therefore, important to 
+have efficient implementations available.
+</p>
+
+<p>
+Originally written in FORTRAN 77, a number of additional language
+wrappers have been developed for languages like C, C++, FORTRAN 95, and others.
+The following legacy libraries are available via the reference ebuilds:
+</p>
+
+<ul>
+  <li>
+    <uri link="http://netlib.org/blas">BLAS</uri>: FORTRAN 77 implementation of
+    BLAS
+  </li>
+  <li>
+    <uri link="http://netlib.org/blas">CBLAS</uri>: C implementation of BLAS
+  </li>
+  <li>
+    <uri link="http://netlib.org/lapack">LAPACK</uri>: FORTRAN 77 implementation
+    of LAPACK
+  </li>
+</ul>
+
+<p>
+In addition, Gentoo provides a number of optimized BLAS and LAPACK implementations
+that will be described below. Different implementations are bundled together with
+Gentoo's <c>eselect</c> system and the widely used <c>pkg-config</c> tool.
+</p>
+
+<p> It is important to note that if you require, e.g., a well performing 
+BLAS implementation, simply emerging X over Y often is not enough. Rather, you will have
+to carefully benchmark your applications since performance may depend 
+on many factors,
+such as hardware or network.
+If you are simply looking for a well performing and well tested
+implementation, the reference ebuilds will likely be your best choice.
+</p>
+
+
+</body>
+</section>
+</chapter>
+
+<chapter>
+<title>For Users</title>
+<section>
+<title>Installing</title>
+<body>
+
+<p>
+If best possible performance is not of paramount importance for you 
+and you simply
+need BLAS and/or LAPACK, just emerge the virtual packages:
+</p>
+
+<pre caption="Installing">
+# <i>emerge blas cblas lapack</i>
+</pre>
+
+<p>
+These will install the reference legacy	packages from
+<uri>http://netlib.org</uri>. They are well tested, easy to debug
+implementations. They should satisfy most users; if they're all you need, you're
+done reading.
+</p>
+
+<p>
+However, if:
+</p>
+
+<ul>
+  <li>BLAS/LAPACK are critical for the speed of your applications</li>
+  <li>you absolutely need to build the fastest computer</li>
+  <li>you want to help Gentoo sci project to improve their packages</li>
+</ul>
+
+<p>
+... then read on, and be sure to file bugs both to Gentoo and upstream.
+</p>
+
+<p>
+There is a number of optimized implementations of these libraries in the Portage
+tree:
+</p>
+
+<ul>
+  <li>
+   <uri link="http://math-atlas.sourceforge.net">ATLAS</uri>: Automatically
+   Tuned Linear Algebra Software is an open-source package that empirically
+   tunes the library to the machine it is being compiled on. It provides BLAS
+   (FORTRAN 77 and C), and LAPACK implementations on various architectures.
+  </li>
+  <li>
+   <uri
+   link="http://www.tacc.utexas.edu/resources/software/software.php">GotoBLAS</uri>:
+   Goto BLAS provide open-source, free for academic use, hand-coded
+   machine language, processor optimized versions of the FORTRAN 77 BLAS
+   routines. Claims to be the fastest BLAS.
+  </li>
+  <li>
+    <uri link="http://developer.amd.com/acml.jsp">ACML</uri>: AMD Core Math
+    Library is a closed-source but free package containing BLAS (FORTRAN 77
+    only) and LAPACK for x86 and amd64 architectures, but also other math tools
+    such as statistical libraries and FFTs.
+  </li>
+  <li>
+    <uri link="http://developer.intel.com/software/products/mkl/">MKL</uri>:
+    Intel® Math Kernel Library is a closed-source but free package for
+    non-commercial use containing BLAS (FORTRAN 77 and C), LAPACK optimized for
+    Intel® based architectures: x86, amd64 and ia64.
+  </li>
+</ul>
+
+<p>
+Usually performance gain is noticeable mainly with BLAS, since LAPACK routines
+depend on BLAS kernels.
+</p>
+
+</body>
+</section>
+<section>
+<title>Compiling and linking with installed libraries</title>
+<body>
+
+<p>
+We took great care to make sure that each package provides consistent pkg-config files.
+Hence, compiling and linking with BLAS/LAPACK should be simple and straightforward:
+</p>
+
+<pre caption="Compiling and linking BLAS/LAPACK">
+# <i>pkg-config --libs blas</i>    <comment>(To link with FORTRAN 77 BLAS library)</comment>
+# <i>pkg-config --cflags cblas</i> <comment>(To compile against C BLAS library)</comment>
+# <i>pkg-config --libs cblas</i>   <comment>(To link with C BLAS library)</comment>
+# <i>pkg-config --libs lapack</i>  <comment>(To link with FORTRAN 77 LAPACK library)</comment>
+</pre>
+
+<p>
+<c>pkg-config</c> files are available for whichever implementation you select with <c>eselect</c>.
+More information on using <c>pkg-config</c> can be obtained with <c>man pkg-config</c>. 
+</p>
+
+</body>
+</section>
+<section>
+<title>Choosing libraries</title>
+<body>
+
+<p>
+You can easily switch BLAS, CBLAS and LAPACK implementations with
+<c>eselect</c>. At this point, you probably have <c>eselect-blas</c>,
+<c>eselect-cblas</c> and <c>eselect-lapack</c> installed. If you do not,
+install them now! Using eselect, you can view which implementations of CBLAS
+are available.
+</p>
+
+<pre caption="Viewing available implementations">
+# <i>eselect cblas list</i>
+Installed CBLAS for library directory lib64
+[1]   atlas
+[2]   atlas-threads
+[3]   gsl
+[4]   mkl-threads *
+[5]   reference
+</pre>
+
+<p>
+The implementation marked with an asterisk (*) is the currently
+selected implementation. To switch implementations, run:
+</p>
+
+<pre caption="Switching to the ATLAS implementation of LAPACK">
+# <i>eselect lapack set atlas</i>
+</pre>
+
+<p>
+To learn more about the <c>eselect</c> tool, visit the 
+<uri link="http://www.gentoo.org/proj/en/eselect/user-guide.xml">eselect guide</uri>
+</p>
+
+<p>
+When selecting blas, cblas or lapack profiles try to avoid mixing
+different implementations since we don't have any mechanism to enforce
+reasonable profiles. However, here is a list of well performing
+profile combinations that have been used successfully in the past:
+</p>
+<ul>
+  <li> Most CPUs:
+    <ul>
+      <li>blas,cblas: atlas (or atlas-threads with multi-processor)</li>
+      <li>lapack:atlas</li>
+    </ul>
+  </li>
+  <li> Most CPUs:
+    <ul>
+      <li>blas: goto </li>
+      <li>cblas,lapack: reference</li>
+    </ul>
+  </li>
+  <li> AMD based CPUs:
+    <ul>
+      <li>blas,lapack: acml-gfortran (or acml-gfortran-openmp with
+	multi-processors) </li>
+      <li>cblas: reference</li>
+    </ul>
+  </li>
+  <li> Intel based CPUs:
+    <ul>
+      <li>blas,cblas,lapack: mkl-threads</li>
+    </ul>
+  </li>
+</ul>
+
+</body>
+</section>
+
+<section>
+<title>Choosing a compiler</title>
+<body>
+
+<p>
+Most of the libraries can compile with both the GNU compiler collection and the
+Intel® compilers on the x86, amd64 and ia64 architectures. By default, you are
+probably using <c>gcc</c>. You can also compile the <c>*-reference</c> packages
+with <c>ifort</c> and <c>icc</c>. To do this, you need to define the F77
+environment variable and don't forget the FFLAGS.
+</p>
+
+<pre caption="Using non-GCC compilers">
+# <i>F77=ifort FFLAGS="-O2 -mp" emerge blas-reference</i>
+</pre>
+
+<p>
+Depending on your hardware, a small performance gain can be noticed thanks to
+vectorization. The <c>-mp</c> flag maintains floating-point precision, since by
+default ifort is pretty aggressive on floating point arithmetic, and we are
+actually compiling a math package. Try <c>man ifort</c> to see additional flags
+to fit your hardware.
+</p>
+
+<p>
+Some of the implementations let you specify the Intel® C compiler as
+well. Please beware that not all libraries compile with all
+combinations.  You should receive an error during the emerge in case you have
+chosen an incompatible combination.
+</p>
+
+<p>
+As usual for Gentoo, there are many combinations of USE flags and
+compilers with which you could compile a package. Unfortunately
+switching compilers between BLAS and LAPACK might not be always
+compatible. For example: 
+</p>
+
+<pre caption="Incompatible combinations">
+# <i>F77=ifort FFLAGS="-O2 -mp" USE="openmp" emerge =acml-3.6.0-r1</i>
+# <i>eselect blas set acml-ifort-openmp</i>
+# <i>F77=gfortran FFLAGS="-O2" emerge lapack-reference</i>
+</pre>
+
+<p>
+This will most likely break things or not even compile.
+</p>
+
+<p>
+Try to be consistent in your choice. Stay with the GCC most of the time will
+avoid you some trouble, unless you want to use the MKL, in which case the Intel®
+C and FORTRAN compilers make a good combination.
+</p>
+
+</body>
+</section>
+<section>
+<title>Documentation</title>
+<body>
+
+<p>
+If you need BLAS or LAPACK to develop your own programs, the documentation
+becomes pretty handy. Setting the USE="doc" flag for the corresponding BLAS or
+LAPACK package will install man pages and quick reference sheets from the
+<c>app-doc/blas-docs</c> and <c>app-doc/lapack-docs</c> packages. They are
+standard and valid for all implementations. For optimized packages, the
+USE="doc" flags will usually install extra doc in PDF or HTML format.
+</p>
+
+</body>
+</section>
+</chapter>
+
+<chapter>
+<title>For Developers</title>
+<section>
+<title>Providing new implementations</title>
+<body>
+
+<p>
+The Portage tree contains many ebuilds that depend on the BLAS/CBLAS/LAPACK
+libraries. As there is more than one possible implementation, the Gentoo
+Scientific Project reorganized all the packages to provide <c>virtual/blas</c>,
+<c>virtual/cblas</c>, and <c>virtual/lapack</c>. All ebuilds using BLAS should
+depend on this virtual package, unless it is explicitly known to break with
+different BLAS implementations.
+</p>
+
+<p>
+To work with Gentoo's configuration tools
+<c>app-admin/eselect-{blas,cblas,lapack}</c>, and the virtual, every ebuild that
+installs a BLAS implementation must fulfill following requirements:
+</p>
+
+<ol>
+  <li>
+    The ebuild must install an eselect file for each profile it provides. The
+    libraries should link to the ones in <path>/usr/$(get_libdir)</path>
+    directories and the include files in <path>/usr/include</path>:
+    <ul>
+      <li>
+	<path>libblas.so[.0]</path> - Shared object for FORTRAN BLAS
+	applications
+      </li>
+      <li>
+        <path>libblas.a</path> - Static library for FORTRAN BLAS applications
+      </li>
+      <li>
+        <path>libcblas.so[.0]</path> - Shared object for C/C++ CBLAS applications
+      </li>
+      <li>
+        <path>libcblas.a</path> - Static library for C/C++ CBLAS applications
+      </li>
+      <li><path>cblas.h</path> - Include header for C/C++ applications</li>
+      <li>
+        <path>liblapack.so[.0]</path> - Shared object for FORTRAN LAPACK
+	applications
+      </li>
+      <li>
+        <path>liblapack.a</path> - Static library for FORTRAN LAPACK applications
+      </li>
+    </ul>
+  </li>
+  <li>
+    The ebuild must install a <path>blas.pc</path>, <path>cblas.pc</path> and/or
+    <path>lapack.pc</path> pkg-config file and therefore RDEPEND on
+    <c>dev-util/pkgconfig</c>.  They should also be included in the eselect
+    files, and link to the <path>/usr/$(get_libdir)/pkgconfig</path> directory:
+    <ul>
+      <li><path>blas.pc</path> - BLAS pkg-config file</li>
+      <li><path>cblas.pc</path> - CBLAS pkg-config file</li>
+      <li><path>lapack.pc</path> - LAPACK pkg-config file</li>
+    </ul>
+  </li>
+  <li>Be included in the virtual package as a possible provider:
+    <ul>
+      <li><c>virtual/blas</c> - BLAS virtual package</li>
+      <li><c>virtual/cblas</c> - CBLAS virtual package</li>
+      <li><c>virtual/lapack</c> - LAPACK virtual package</li>
+    </ul>
+  </li>
+</ol>
+ 
+<p>
+The easiest way of understanding all this is probably getting inspiration from
+one of the available packages.  Currently the Portage tree provide the following
+virtuals:
+</p>
+
+<table>
+<tr>
+  <th>Package name</th>
+  <th>virtual/blas</th>
+  <th>virtual/cblas</th>
+  <th>virtual/lapack</th>
+</tr>
+<tr>
+  <ti><c>sci-libs/acml</c></ti>
+  <ti>*</ti>
+  <ti></ti>
+  <ti>*</ti>
+</tr>
+<tr>
+  <ti><c>sci-libs/blas-atlas</c></ti>
+  <ti>*</ti>
+  <ti>*</ti>
+  <ti></ti>
+</tr>
+<tr>
+  <ti><c>sci-libs/blas-goto</c></ti>
+  <ti>*</ti>
+  <ti></ti>
+  <ti></ti>
+</tr>
+<tr>
+  <ti><c>sci-libs/blas-reference</c></ti>
+  <ti>*</ti>
+  <ti></ti>
+  <ti></ti>
+</tr>
+<tr>
+  <ti><c>sci-libs/cblas-reference</c></ti>
+  <ti></ti>
+  <ti>*</ti>
+  <ti></ti>
+</tr>
+<tr>
+  <ti><c>sci-libs/gsl</c></ti>
+  <ti></ti>
+  <ti>*</ti>
+  <ti></ti>
+</tr>
+<tr>
+  <ti><c>sci-libs/lapack-atlas</c></ti>
+  <ti></ti>
+  <ti></ti>
+  <ti>*</ti>
+</tr>
+<tr>
+  <ti><c>sci-libs/lapack-reference</c></ti>
+  <ti></ti>
+  <ti></ti>
+  <ti>*</ti>
+</tr>
+<tr>
+  <ti><c>sci-libs/mkl</c></ti>
+  <ti>*</ti>
+  <ti>*</ti>
+  <ti>*</ti>
+</tr>
+</table>
+
+</body>
+</section>
+<section>
+<title>Packages with BLAS/LAPACK dependencies</title>
+<body>
+
+<p>
+Simply use <c>virtual/{blas,cblas,lapack}</c> as a [R]DEPEND. To build some
+packages, you might need to use the pkg-config tool. If you are lucky, the
+package uses autotools together with common BLAS and LAPACK M4 macros.In this
+case, the configuration step becomes simple. For example:
+</p>
+
+<pre caption="Sample package configuration">
+<keyword>econf</keyword> --with-blas="<var>$(pkg-config --libs blas)</var>"
+</pre>
+
+<impo>
+Don't forget to add <c>dev-util/pkgconfig</c> in DEPEND.
+</impo>
+
+</body>
+</section>
+</chapter>
+
+<chapter>
+<title>In the near future</title>
+<section>
+<body>
+
+<p>
+We plan to include more standard BLAS, LAPACK libraries: BLAS 95, LAPACK 95,
+Sparse BLAS, ScaLAPACK. If you feel inclined to write an ebuild for these, you
+are more than welcomed to file it on our <uri
+link="http://bugs.gentoo.org">Bugzilla</uri>.
+</p>
+
+</body>
+</section>
+</chapter>
+</guide>
diff --git a/docs/proj/contrib.xml b/docs/proj/contrib.xml
new file mode 100644
index 000000000..fd474808b
--- /dev/null
+++ b/docs/proj/contrib.xml
@@ -0,0 +1,182 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE guide SYSTEM "/dtd/guide.dtd">
+<guide link="/doc/en/" lang="en">
+
+  <title>Contributing to the Scientific Project</title>
+
+  <author title="Author">
+    <mail link="bicatali@gentoo.org">Sébastien Fabbro</mail>
+    <!-- others add your name here -->
+  </author>
+
+  <abstract>
+    This document provides information on how one can get involved and 
+    help out with the Gentoo Scientific Project
+  </abstract>
+
+  <!-- The content of this document is licensed under the CC-BY-SA license -->
+  <!-- See http://creativecommons.org/licenses/by-sa/2.5 -->
+  <license/>
+
+  <version>0.1</version>
+  <date>2009-01-21</date>
+
+  <chapter>
+    <title>Overview</title>
+    <section>
+      <body>
+        <p>
+          This document aims to provide information on how one can get
+          involved and help out with the Gentoo Scientific Project.
+	  Scientific packages are very diverse and many of us want our
+          pet application in the main tree for easy installation. Due to
+          the small size of our team, we can not implement all of
+          them, so we really appreciate any contribution.
+        </p>
+	<p>
+	  There are few obvious areas where one can help as we
+	  describe below. The Scientific Project tends to set strong
+	  requirements on testing, especially on core packages.
+	  Comments, thoughts, and feedback is greatly welcomed!
+	</p>
+      </body>
+    </section>
+  </chapter>
+
+  <chapter>
+    <title>Bugs</title>
+    <section>
+      <title>Reporting</title>
+      <body>
+        <p>
+          All good software has bugs. They are too many combinations of
+          compilers, USE flags and versions to test them all. So if
+          you find the time to report them, we would love to hear
+          about it. We have the standard bugzilla system for
+          this. Don't be afraid of all these fields to fill in, it's
+          not that bad!
+        </p>
+      </body>
+    </section>
+    <section>
+      <title>Resolving</title>
+      <body>
+        <p>
+	  The Scientific Team in Gentoo has always had a high number of
+	  bugs. Fortunately, many of them are new packages. Any help in resolving
+	  issues, improving submitted ebuilds is greatly appreciated.
+        </p>
+        <p>
+	  <uri link="http://tinyurl.com/2qxmvu">Bugs for the Scientific Team.</uri>
+	  <uri link="http://tinyurl.com/2nm6ag">Bugs for the Biology Team.</uri>
+	  <uri link="http://tinyurl.com/368f2d">Bugs for the Chemistry Team.</uri>
+	  <uri link="http://tinyurl.com/2lknlo">Bugs for the Electronics Team.</uri>
+	  <uri link="http://tinyurl.com/2pcntk">Bugs for the Mathematics Team.</uri>
+	  <uri link="http://tinyurl.com/3789aa">Bugs for the Physics Team.</uri>
+        </p>
+      </body>
+    </section>
+  </chapter>
+
+  <chapter>
+    <title>Writing ebuilds</title>
+    <section>
+      <body>
+        <p>
+	  You don't see your application in the main tree or in the
+	  overlays and you don't want to wait for someone else to
+	  create the ebuilds? The most obvious solution is to develop
+	  your own ebuilds. If you do so, it's always nice to share
+	  them. You can post them to our bugzilla system and then one
+	  of our devs will comment out. The <uri link="http://overlays.gentoo.org/proj/sunrise">sunrise
+	  overlay</uri> allows you more directly to commit your
+	  ebuilds if you don't want to wait for science access.
+	</p>
+      </body>
+    </section>
+  </chapter>
+
+  <chapter>
+    <title>Communication</title>
+    <section>
+      <title>Mailing List</title>
+      <body>
+        <p>
+          Join our
+          <uri link="http://www.gentoo.org/main/en/lists.xml"> gentoo-science mailing list
+          </uri> and asking/answering questions. 
+        </p>
+      </body>
+    </section>
+    <section>
+      <title>IRC</title>
+      <body>
+        <p>
+          Meet some of us in #gentoo-science. It is a fairly quiet
+          channel, but slowly growing and we are responsive. We can
+          answer your questions, help you developing your ebuilds,
+          share ideas, etc...
+        </p>
+      </body>
+    </section>
+      <title>Direct emails</title>
+      <body>
+        <p>
+	  If you feel your questions are more private and don't need
+	  to be known from the rest of the world, you can always
+	  directly send an email to our developers
+	  listed <uri link="http://www.gentoo.org/main/en/proj/science/index.xml">here</uri>
+	  and the listed sub-projects. If you want to mail all of us, send a mail to the herd.
+        </p>
+      </body>
+  </chapter>
+
+  <chapter>
+    <title>Writing Documentation</title>
+      <body>
+	<section>
+          <p>
+	    You may not be interested in fixing ebuilds and testing
+	    packages, but want to share your knowledge about some
+	    software, configuration or tips and tricks. The best way to
+	    do this is to write some documentation. You can even write
+	    official Gentoo documentation such as our
+	    <uri link="http://www.gentoo.org/main/en/proj/science/blas-lapack.xml">blas/lapack
+	      guide</uri>.
+	  </p>
+	</section>
+      </body>
+  </chapter>
+
+  <chapter>
+    <title>Seriously getting involved</title>
+    <section>
+      <body>
+        <p>
+          If you would like to join our team of volunteers and become
+          an official Gentoo Developer, show activity in anywhere you
+          can: bugzilla, overlays, mailing lists, irc, forums,...
+	  Please refer to
+	  <uri link="http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=1&amp;chap=2">
+	  Becoming a Developer</uri> in the
+	  <uri link="http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml">
+	  Gentoo Developer Handbook</uri>.
+        </p>
+	<p> 
+	  Benefits are huge :-) :
+          <dl>
+            <dd>
+              <ul>
+		<li>Receive a warm welcome from us</li>
+		<li>Impress your geek friends</li>
+		<!--<li>Loose your social life, but</li>-->
+		<li>Get a free beer first time we meet in person!</li>
+              </ul>
+            </dd>
+          </dl>	  
+	</p>
+
+      </body>
+    </section>
+  </chapter>
+</guide>
diff --git a/docs/proj/index.xml b/docs/proj/index.xml
new file mode 100644
index 000000000..aa5398556
--- /dev/null
+++ b/docs/proj/index.xml
@@ -0,0 +1,101 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?xml-stylesheet href="/xsl/project.xsl" type="text/xsl"?>
+<?xml-stylesheet href="/xsl/guide.xsl" type="text/xsl"?>
+<!DOCTYPE project SYSTEM "/dtd/project.dtd"> 
+
+<project>
+  <name>Science</name>
+  <longname>The Gentoo Scientific Project</longname>
+  <date>2009-01-21</date>
+  <author title="author">
+    <mail link="sci@gentoo.org">Science Team</mail>
+  </author>
+    
+  <description>
+    The Gentoo Scientific Project handles all Gentoo related Math and Science items.
+  </description>
+
+  <longdescription>
+    <p>
+      The Gentoo Scientific Project handles math and science related activities in Gentoo.
+      This includes maintaining packages that belong to various math
+      and science related herds, fortran compilers, documentations and communications.
+    </p>
+  </longdescription>
+
+  <goals>
+    <p>
+      The goals of Scientific Gentoo are to provide a simple but optimal
+      installation and configuration of a wide variety of math and
+      science applications. Scientific computing is an area where custom optimization
+      provides great benefit. We also provide tools to easily switch configurations, and relevant
+      documentations. We give special attention to ways to test the
+      packages, through regression suites, and benchmarks.
+    </p>
+  </goals>
+
+
+  <!-- Staff -->	
+  <dev role="my role in the science project" description="what i do mainly">dev-name</dev>
+  <dev role="my role in the science project" description="what i do mainly">dev-name</dev>
+  <dev role="my role in the science project" description="what i do mainly">dev-name</dev>
+
+  <!-- Subprojects 
+  <subproject ref="/proj/en/science/astronomy/index.xml" />
+  <subproject ref="/proj/en/science/biology/index.xml" />
+  <subproject ref="/proj/en/science/chemistry/index.xml" />
+  <subproject ref="/proj/en/science/electronics/index.xml" />
+  <subproject ref="/proj/en/science/math/index.xml" />
+  <subproject ref="/proj/en/science/physics/index.xml" />
+  -->
+
+  <resource link="blas-lapack.xml">Guide on using BLAS/LAPACK</resource>
+  <resource link="contrib.xml">Guide on contributing to the science project</resource>
+  <resource link="http://overlays.gentoo.org/proj/science">Official overlay</resource>
+  <resource link="http://news.gmane.org/gmane.linux.gentoo.science/">Mailing list archives</resource>
+  <resource link="irc://irc.freenode.net/gentoo-science">#gentoo-science IRC Channel</resource>
+
+<extrachapter position="bottom">
+<title>The Science Overlay</title>
+<section>
+<body>
+<p>
+  New packages and more complex version bumps are held in
+  an <uri link="http://overlays.gentoo.org/proj/science/">Overlay</uri>. They
+  help both the science and hp-cluster team and the wiki contains some
+  temporary information.
+</p>
+</body>
+</section>
+</extrachapter>
+
+<recruitment>
+  <job>
+    <summary>Scientific package maintainer</summary>
+    <details>
+      The sci team and its various subprojects are always looking for a
+      general package maintainer to help our understaffed
+      team. Tasks are troubleshooting, version bumping and
+      stabilizing, new ebuilds and eclassed introduction.
+    </details>
+    <requirements>
+      Experience with Linux, various package build systems (autotools, cmake)
+      and makefiles, and bash.
+    </requirements>
+    <contact>sci</contact>
+  </job>
+  <job>
+    <summary>CAD Programs</summary>
+    <details>
+      Computer Aided Design open source programs are getting more popular
+      and yet to have decent support in Gentoo. We need to put an end
+      on this.
+    </details>
+    <requirements>
+      Knowledge of a few CAD programs and good ebuild skills.
+    </requirements>
+    <contact>sci</contact>
+  </job>
+</recruitment>
+
+</project>
diff --git a/eclass/octave-forge.eclass b/eclass/octave-forge.eclass
index b6377761d..5341e77bc 100644
--- a/eclass/octave-forge.eclass
+++ b/eclass/octave-forge.eclass
@@ -219,7 +219,7 @@ octave-forge_src_unpack() {
 	if [[ -n "${PATCHES}" ]]; then
 		unpack "${A}"
 		pushd "${S}" >& /dev/null
-		for patch in "${PATCHES}"; do
+		for patch in "${PATCHES[@]}"; do
 			epatch "${FILESDIR}/${patch}"
 		done
 		popd >& /dev/null
diff --git a/eclass/openib.eclass b/eclass/openib.eclass
index 8f8d843ba..2be0a2fd8 100644
--- a/eclass/openib.eclass
+++ b/eclass/openib.eclass
@@ -69,7 +69,7 @@ S="${WORKDIR}/${MY_PN}-${MY_PV}"
 # This function will unpack OFED packages
 openib_src_unpack() {
 	unpack ${A}
-	rpm_unpack "OFED-${OFED_VER}/SRPMS/${MY_PN}-${MY_PV}-${OFED_SUFFIX}.src.rpm"
+	rpm_unpack "./OFED-${OFED_VER}/SRPMS/${MY_PN}-${MY_PV}-${OFED_SUFFIX}.src.rpm"
 	case ${MY_PN} in
 		rds-tools)
 			MY_PV="${PV}-${OFED_SUFFIX}"
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
index 52a96e5f9..a96b4508a 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -1,4 +1,16 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 DIST fasta-35.3.6.tar.gz 614606 RMD160 f0d8a5514a430d592a030afd69348413d1ac8c63 SHA1 335f2f3732f9b03ba0d6102fd94674f5ac616297 SHA256 4525232e2a1a42388921760d75c5ece6e058d9ce2c35cba074ce544d6e56df15
+DIST fasta-35.4.8.tar.gz 630387 RMD160 9504f8924594cfa2fc8c7d21dd7da2e80ff678f4 SHA1 f076dde53c4f59887828bf919e3060831912aea9 SHA256 2347ca3af2c9f3ee43148852cd31dc7a89a2cb5d130280d0ec0d3287cb833d33
 EBUILD fasta-35.3.6.ebuild 1171 RMD160 058a268f6e8f9d2dcf4f4479303d6b328d5f1a05 SHA1 446781c0ce28898309b77c1311f83580f16a5537 SHA256 2456a736004083126ac3041773810bc612b66e3af0f77fd3bed85467000fcc3c
+EBUILD fasta-35.4.8.ebuild 1171 RMD160 058a268f6e8f9d2dcf4f4479303d6b328d5f1a05 SHA1 446781c0ce28898309b77c1311f83580f16a5537 SHA256 2456a736004083126ac3041773810bc612b66e3af0f77fd3bed85467000fcc3c
 MISC ChangeLog 237 RMD160 a2ce23a123f5d353398a267d84bc81663f034abc SHA1 103e50d0f241a7e4d467f627cf98983056e640b8 SHA256 002d044f54613ed80b5b8e261d91f0d56f90cb42745a044560090dc1d3749b80
-MISC metadata.xml 307 RMD160 0993f9568f191dc314f2f742417cca45456af8ff SHA1 94fe99112096a2e23c199fbf22aa8ad8be475b7e SHA256 e998d3ee356e25351b86abf709647bde3856ccceafce876ff17dbd8ea0a8d41b
+MISC metadata.xml 382 RMD160 75d40acc3b5a8fb8ea656817aa204cc524ef7059 SHA1 7c7a5b42930a24b3fb2609716b7238ba3193e18d SHA256 2d9cc9ccec1bcd41294ff75ff29b4b449868a1dc2cd763ac28ee946a90611185
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.11 (GNU/Linux)
+
+iEYEARECAAYFAkrIgqMACgkQ5BmOA85PVLhRQwCfRToNdFo9NiY3eWV0G2vzEdv6
+a90An21LUcNlDzhQOwVpMCnVIczyun/v
+=Kuxa
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/fasta/metadata.xml b/sci-biology/fasta/metadata.xml
index 736e60fbb..7bf7a49aa 100644
--- a/sci-biology/fasta/metadata.xml
+++ b/sci-biology/fasta/metadata.xml
@@ -8,5 +8,8 @@
 	</maintainer>
 	<longdescription lang="en">
 	</longdescription>
+	<use>
+		<flag name='icc'>Use intel compiler instead of gcc</flag>
+	</use>
 </pkgmetadata>
 
diff --git a/sci-biology/foldingathome/ChangeLog b/sci-biology/foldingathome/ChangeLog
new file mode 100644
index 000000000..7c1beaf4e
--- /dev/null
+++ b/sci-biology/foldingathome/ChangeLog
@@ -0,0 +1,238 @@
+# ChangeLog for sci-biology/foldingathome
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/foldingathome/ChangeLog,v 1.27 2008/11/30 19:46:50 je_fro Exp $
+
+*foldingathome-6.24 (04 Oct 2009)
+
+  04 Oct 2009; Alexey Shvetsov <alexxy@gentoo.org> +files/6.24/fah-init,
+  +foldingathome-6.24.ebuild, +files/6.24/folding-conf.d,
+  +files/6.24/initfolding, +metadata.xml:
+  Version bump
+
+  30 Nov 2008; Jeff Gardner <je_fro@gentoo.org> files/6.02/folding-conf.d:
+  Removing smp from default opts to hopefully fix bug #248896
+  Thanks to Vladimir Berezhnoy.
+
+  22 Nov 2008; Jeff Gardner <je_fro@gentoo.org>
+  foldingathome-6.02-r1.ebuild:
+  Add shameless plug for my folding group.
+
+*foldingathome-6.02-r1 (22 Nov 2008)
+
+  22 Nov 2008; Jeff Gardner <je_fro@gentoo.org> -foldingathome-6.02.ebuild,
+  +foldingathome-6.02-r1.ebuild:
+  Bumping for init script fix and add back ~x86.
+
+  22 Nov 2008; Jeff Gardner <je_fro@gentoo.org> files/6.02/fah-init:
+  Changing to use init script from Constantin Baranov on bug #218331
+
+  03 Aug 2008; Jeff Gardner <je_fro@gentoo.org> -files/6.02_beta1/fah-init,
+  -files/6.02_beta1/folding-conf.d, -files/6.02_beta1/initfolding,
+  -foldingathome-6.02_beta1.ebuild:
+  remove dead beta
+
+*foldingathome-6.02 (03 Aug 2008)
+
+  03 Aug 2008; Jeff Gardner <je_fro@gentoo.org> +files/6.02/fah-init,
+  +files/6.02/folding-conf.d, +files/6.02/initfolding,
+  +foldingathome-6.02.ebuild:
+  Latest version, thanks to Nicolas Schlumberger, closes bug #233751
+
+  15 Jun 2008; Jeff Gardner <je_fro@gentoo.org>
+  files/6.02_beta1/folding-conf.d:
+  Add smp option thanks to Timon Van Overveldt in bug #194423
+
+*foldingathome-6.02_beta1 (14 Jun 2008)
+
+  14 Jun 2008; Jeff Gardner <je_fro@gentoo.org> -files/5.91_beta/fah-init,
+  -files/5.91_beta/initfolding, -files/5.91_beta/folding-conf.d,
+  +files/6.02_beta1/fah-init, +files/6.02_beta1/folding-conf.d,
+  +files/6.02_beta1/initfolding, -foldingathome-5.91_beta.ebuild,
+  +foldingathome-6.02_beta1.ebuild:
+  Latest beta client
+
+  12 Jul 2007; Christoph Mende <angelos@gentoo.org>
+  foldingathome-5.0.2-r5.ebuild:
+  Stable on amd64 wrt bug #164823
+
+  12 Jul 2007; Christian Faulhammer <opfer@gentoo.org>
+  foldingathome-5.0.2-r5.ebuild:
+  stable x86, bug 164823
+
+  03 Jul 2007; Jeff Gardner <je_fro@gentoo.org>
+  foldingathome-5.91_beta.ebuild:
+  foldingathome-5.91_beta has expired. Removing KEYWORDS until the next
+  release arrives.
+
+  02 Jul 2007; Piotr Jaroszyński <peper@gentoo.org>
+  foldingathome-5.0.2-r3.ebuild, foldingathome-5.0.2-r5.ebuild:
+  (QA) RESTRICT clean up.
+
+  21 Apr 2007; Jeff Gardner <je_fro@gentoo.org>
+  foldingathome-5.0.2-r3.ebuild, foldingathome-5.0.2-r5.ebuild:
+  Use newconfd wrt bug #174266
+
+  11 Apr 2007; Jeff Gardner <je_fro@gentoo.org>
+  foldingathome-5.91_beta.ebuild:
+  Fixed to better install files under /etc.
+
+*foldingathome-5.91_beta (10 Apr 2007)
+
+  10 Apr 2007; Jeff Gardner <je_fro@gentoo.org> +files/5.91_beta/fah-init,
+  +files/5.91_beta/folding-conf.d, +files/5.91_beta/initfolding,
+  +foldingathome-5.91_beta.ebuild:
+  Adding the amd64-smp client for testing. Thanks to John Gibson.
+
+  03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> -files/init-5.0.2-r4,
+  -foldingathome-5.0.2-r4.ebuild:
+  Pruned old version.
+
+*foldingathome-5.0.2-r5 (16 Jun 2006)
+
+  16 Jun 2006; Patrick Kursawe <phosphan@gentoo.org> +files/init-5.0.2-r5,
+  +foldingathome-5.0.2-r5.ebuild:
+  Adding --chdir to start-stop-daemon because of bug #109707
+
+*foldingathome-5.0.2-r4 (14 Aug 2005)
+
+  14 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +files/init-5.0.2-r4,
+  +foldingathome-5.0.2-r4.ebuild:
+  Fixed bug #95697: license is now correct and the binaries are no longer
+  stripped since we are not allowed to modify them. Thanks to Ian Kelly
+  <kellyia@udel.edu>. Fixed bugs #90247 and #93047: Foldingathome init script
+  now uses start-stop-daemon. Thanks to James Lademann
+  <jwlademann@myrealbox.com>.
+
+  22 Apr 2005; Danny van Dyk <kugelfang@gentoo.org>
+  foldingathome-5.0.2-r3.ebuild:
+  Marked stable on amd64.
+
+  03 Mar 2005; Brandon Low <lostlogic@gentoo.org> -files/folding-conf.d,
+  -files/folding-init.d, -files/folding-init.d-r1, -files/folding-init.d-r3,
+  -files/folding.sh, files/init-5.0.2-r3, -files/initfolding,
+  -files/initfolding-r1, -foldingathome-4.0.0-r2.ebuild,
+  -foldingathome-4.0.0.ebuild:
+  Fix bug 82345, nice 20 doesn't exist.
+  Remove old ebuilds and files.
+
+  08 Feb 2005; Brandon Low <lostlogic@gentoo.org>
+  foldingathome-5.0.2-r3.ebuild:
+  Mark stable on x86
+
+  05 Feb 2005; Brandon Low <lostlogic@gentoo.org> -files/copy_client_config,
+  -files/folding-init.d-r2, -files/folding-init.d-r4, -files/init-5.0.2-r1,
+  -files/init-5.0.2-r2, -foldingathome-5.0.2-r1.ebuild,
+  -foldingathome-5.0.2-r2.ebuild, -foldingathome-5.0.2.ebuild:
+  Clean up some cruft
+
+*foldingathome-5.0.2-r3 (05 Feb 2005)
+
+  05 Feb 2005; Brandon Low <lostlogic@gentoo.org> +files/init-5.0.2-r3,
+  +foldingathome-5.0.2-r3.ebuild:
+  Fix bug #80778
+
+*foldingathome-5.0.2-r2 (04 Feb 2005)
+
+  04 Feb 2005; Brandon Low <lostlogic@gentoo.org> +files/init-5.0.2-r2,
+  +foldingathome-5.0.2-r2.ebuild:
+  Fix bug #79574. Add unitinfo target to initscript to get the status of each
+  core on the system. Thanks to Yosef Meller <yosefm@gmail.com> for the idea
+  and initial patch
+
+*foldingathome-5.0.2-r1 (03 Feb 2005)
+
+  03 Feb 2005; Brandon Low <lostlogic@gentoo.org>
+  +files/copy_client_config-5.0.2-r1, +files/init-5.0.2-r1,
+  +foldingathome-5.0.2-r1.ebuild:
+  Fix bug 71700 hopefully. Use bash not python for copy_client_config. Update
+  the init script to do more sane things and not fail to stop on multi-cpu
+  systems.
+
+*foldingathome-4.0.0-r2 (23 Dec 2004)
+
+  23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +files/copy_client_config, +files/folding-conf.d, +files/folding-conf.d-r1,
+  +files/folding-init.d, +files/folding-init.d-r1, +files/folding-init.d-r2,
+  +files/folding-init.d-r3, +files/folding-init.d-r4, +files/folding.sh,
+  +files/initfolding, +files/initfolding-r1, +files/initfolding-r2,
+  +foldingathome-4.0.0-r2.ebuild, +foldingathome-4.0.0.ebuild,
+  +foldingathome-5.0.2.ebuild:
+  Moved from app-sci/foldingathome to sci-biology/foldingathome.
+
+  13 Dec 2004; Patrick Kursawe <phosphan@gentoo.org>
+  -foldingathome-4.0.0-r1.ebuild:
+  Cleanup
+
+*foldingathome-5.0.2 (09 Nov 2004)
+
+  09 Nov 2004; Steve Arnold <nerdboy@gentoo.org> +files/copy_client_config,
+  +files/folding-conf.d-r1, +files/folding-init.d-r4, +files/initfolding-r2,
+  +foldingathome-5.0.2.ebuild:
+  bumped to current version (bug 60318) with ebuild from Gregory P. Smith
+  <greg-gentoo@electricrain.com>.  Gentoo team config.
+
+  12 Jun 2004; Danny van Dyk <kugelfang@gentoo.org>
+  foldingathome-4.0.0-r2.ebuild:
+  Marked ~amd64.
+
+*foldingathome-4.0.0-r2 (07 Jun 2004)
+
+  07 Jun 2004; Patrick Kursawe <phosphan@gentoo.org>
+  foldingathome-3.24-r1.ebuild, foldingathome-3.24.ebuild,
+  foldingathome-4.0.0-r2.ebuild, files/folding-init.d-r3:
+  No longer redirecting output to a redundand log file, see bug #51489
+  Cleanup, removing 3.x versions.
+
+  23 Apr 2004; David Holm <dholm@gentoo.org> foldingathome-4.0.0-r1.ebuild:
+  Added to ~ppc.
+
+*foldingathome-4.0.0-r1 (22 Apr 2004)
+
+  22 Apr 2004; Patrick Kursawe <phosphan@gentoo.org>
+  foldingathome-4.0.0-r1.ebuild, files/folding-conf.d,
+  files/folding-init.d-r2, files/initfolding-r1:
+  Added support to run multiple clients for those with multiprocessors
+  and the ability to pass options to the Folding clients.
+  Based on bug #47526 (by Mike Caley <mjcaley@darkarctic.com>)
+
+  26 Mar 2004; Patrick Kursawe <phosphan@gentoo.org>
+  foldingathome-3.14.ebuild, foldingathome-3.24-r1.ebuild,
+  foldingathome-3.24.ebuild, foldingathome-4.0.0.ebuild:
+  Setting IUSE, removing S= where not necessary, declaring 4.0.0 stable for x86
+
+  09 Mar 2004; Daniel Ahlberg <aliz@gentoo.org> foldingathome-4.0.0.ebuild:
+  Adding amd64 keyword. Closing #43779.
+
+*foldingathome-4.0.0 (03 Mar 2004)
+
+  03 Mar 2004; Patrick Kursawe <phosphan@gentoo.org>
+  foldingathome-4.0.0.ebuild:
+  Version bump inspired by bug #34859
+
+*foldingathome-3.24-r1 (01 Mar 2004)
+
+  01 Mar 2004; Patrick Kursawe <phosphan@gentoo.org>
+  foldingathome-3.24-r1.ebuild, files/folding-init.d-r1, files/folding.sh,
+  files/initfolding:
+  Running as seperate user now.
+
+  05 May 2003; Daniel Ahlberg <aliz@gentoo.org> files/folding-init.d :
+  Fixed stop() in init script. Fix by 
+  Roderick van Domburg <r.s.a.vandomburg@student.utwente.nl> in #20327.
+
+  23 Apr 2003; Daniel Ahlberg <aliz@gentoo.org> foldingathome-3.2.4.ebuild, files/folding-init.d :
+  Now has the version number in SRC_URI and also uses the newer client if we're running >=glibc-2.3.0. 
+  Also updated init script. Closes #19709 and #17715.
+
+*foldingathome-3.24 (27 Feb 2003)
+
+  27 Feb 2003; Daniel Ahlberg <aliz@gentoo.org> foldingathome-3.24.ebuild :
+  Version bump.
+
+  27 Feb 2003; Daniel Ahlberg <aliz@gentoo.org> files/folding-init.d :
+  Start the daemon with nice, closes #12950.
+  
+*foldingathome-3.14 (04 Nov 2002)
+
+  04 Nov 2002; Daniel Ahlberg <aliz@gentoo.org> :
+  Initial import. Ebuild contributed by Ryan Shaw <ryan.shaw@stanfordalumni.org> in #9535.
diff --git a/sci-biology/foldingathome/Manifest b/sci-biology/foldingathome/Manifest
new file mode 100644
index 000000000..6228c0669
--- /dev/null
+++ b/sci-biology/foldingathome/Manifest
@@ -0,0 +1,17 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 6.24/fah-init 802 RMD160 7c15544374e4adb9d8351a478f3551bcebd665ab SHA1 af814b258f67fcaf6bc6a5519c886895c31208fe SHA256 94e35a7aabfb0b2f10f5c8a6f28adca543dedaa51d4e737f4abffeef46a09323
+AUX 6.24/folding-conf.d 854 RMD160 c705e87e36b32b764eba185c2916a81a929e8c16 SHA1 6b29cac64993d9518fbefa8a61f09e07e6d44562 SHA256 815559a3c30858d47836dcb9244f8a42799630c88ac013e50f19fd74cca33c8c
+AUX 6.24/initfolding 125 RMD160 70e92fa4aa493fdf362e98c88850008a2d9aa226 SHA1 27838b24f2f12b51212fa1845c210a1443911dfc SHA256 8bada0baf3b0835774c472e0e2e05e7cebfa675a77c15ebdf75fee6d80a95f8b
+DIST FAH6.24beta-Linux.tgz 444667 RMD160 925d7686f42e7c39c00efc4afae534080072cf73 SHA1 609cc62ea65e0be9e1dbcd0ac62628b2b2689f93 SHA256 0b8ea7e824331f7b54323a756f5f8ea91365614d2f74079f8c3fdcfcf073ac49
+EBUILD foldingathome-6.24.ebuild 1591 RMD160 81efd5e8da212430462708e724b5c9463f1e20ba SHA1 ad463f8a0aa00093619f9332595ad4f1227420d1 SHA256 87c14f45a04b7789245c4de9484c20ab2a021b833db6d23b4cc4b7d47bafc8f1
+MISC ChangeLog 9195 RMD160 5b93b8cc0ae95d83c93d4bc9b1fb74c03c927369 SHA1 e18145b24646a2eea9f8e7eef5878cf8b291e57f SHA256 66ddd7945a2669209fc5a6ce8d4dd28c15f1ba964ef51e014d76552f5383b7c7
+MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.11 (GNU/Linux)
+
+iEYEARECAAYFAkrJGS0ACgkQ5BmOA85PVLjisgCfUmot5mH1tPVILlQ3X2n6Twm+
+mmwAnAsXKSpRSD+3h1jGUhEtcTgWe989
+=Ftkn
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/foldingathome/files/6.24/fah-init b/sci-biology/foldingathome/files/6.24/fah-init
new file mode 100644
index 000000000..70424cac1
--- /dev/null
+++ b/sci-biology/foldingathome/files/6.24/fah-init
@@ -0,0 +1,27 @@
+#!/sbin/runscript
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/foldingathome/files/6.02/fah-init,v 1.3 2008/11/22 21:31:26 je_fro Exp $
+
+opts="${opts} unitinfo"
+
+unitinfo() {
+	einfo "$(head -n1 /opt/foldingathome/unitinfo.txt):"
+	sed -e '1,2d' /opt/foldingathome/unitinfo.txt
+}
+
+start() {
+	ebegin "Starting Folding@Home"
+	cd /opt/foldingathome
+	start-stop-daemon --chdir ${PWD} --chuid foldingathome --nicelevel 19 \
+		--make-pidfile --pidfile "${PIDFILE}" \
+		--start --background --exec ./fah6 -- ${FOLD_OPTS}
+	eend $?
+}
+
+stop() {
+	ebegin "Stopping Folding@Home"
+	start-stop-daemon --stop --user foldingathome --pidfile "${PIDFILE}"
+	eend $?
+	killall --user foldingathome --signal SIGKILL
+}
diff --git a/sci-biology/foldingathome/files/6.24/folding-conf.d b/sci-biology/foldingathome/files/6.24/folding-conf.d
new file mode 100644
index 000000000..af99fc1d6
--- /dev/null
+++ b/sci-biology/foldingathome/files/6.24/folding-conf.d
@@ -0,0 +1,21 @@
+# Config file for /etc/init.d/foldingathome
+#
+# The f@h client configuration can be found in /opt/foldingathome/client.cfg
+# Run /opt/foldingathome/initfolding to reconfigure that.
+#
+# Enter options here to be passed to the Folding client:
+#
+#  -oneunit	Instruct the client to quit following the completion of one work unit.
+#  -verbosity x Sets the output level, from 1 to 9 (max). The default is 3
+#  -forceasm    Force core assembly optimizations to be used if available
+#  -advmethods  Request to be assigned any new Cores or work units.
+#  -smp		Set the client to run in SMP mode (multicore)
+#
+# A full listing of options can be found here:
+# http://www.stanford.edu/group/pandegroup/folding/console-userguide.html
+# But use of other options are not recommended when using the Folding client
+# as a service.
+#
+FOLD_OPTS=""
+PIDFILE=/var/run/folding
+
diff --git a/sci-biology/foldingathome/files/6.24/initfolding b/sci-biology/foldingathome/files/6.24/initfolding
new file mode 100644
index 000000000..3f760a1e6
--- /dev/null
+++ b/sci-biology/foldingathome/files/6.24/initfolding
@@ -0,0 +1,6 @@
+#!/bin/sh
+
+cd /opt/foldingathome
+/opt/foldingathome/fah6 -configonly
+/bin/chown -R foldingathome:nogroup /opt/foldingathome
+
diff --git a/sci-biology/foldingathome/foldingathome-6.24.ebuild b/sci-biology/foldingathome/foldingathome-6.24.ebuild
new file mode 100644
index 000000000..4c0685ce9
--- /dev/null
+++ b/sci-biology/foldingathome/foldingathome-6.24.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/foldingathome/foldingathome-6.24beta.ebuild,v 1.0 2009/05/10 splat Exp $
+
+I="/opt/foldingathome"
+
+inherit eutils
+
+DESCRIPTION="Folding@Home is a distributed computing project for protein folding."
+HOMEPAGE="http://folding.stanford.edu/FAQ-SMP.html"
+SRC_URI="http://www.stanford.edu/group/pandegroup/folding/release/FAH6.24beta-Linux.tgz"
+
+LICENSE="folding-at-home"
+SLOT="0"
+
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=sys-libs/glibc-2.3.0
+		amd64? ( app-emulation/emul-linux-x86-baselibs )"
+
+RDEPEND=""
+
+S="${WORKDIR}"
+
+src_install() {
+	exeinto ${I}
+	newexe "${FILESDIR}"/${PV}/initfolding initfolding
+	doexe fah6 mpiexec
+	newconfd "${FILESDIR}"/${PV}/folding-conf.d foldingathome
+	newinitd "${FILESDIR}"/${PV}/fah-init foldingathome
+}
+
+pkg_preinst() {
+	# the bash shell is important for "su -c" in init script
+	enewuser foldingathome -1 /bin/bash /opt/foldingathome
+}
+
+pkg_postinst() {
+	chown -R foldingathome:nogroup /opt/foldingathome
+	einfo "To run Folding@home in the background at boot:"
+	einfo " rc-update add foldingathome default"
+	einfo ""
+	einfo "Please run ${I}/initfolding to configure your client"
+	einfo "and edit /etc/conf.d/foldingathome for options"
+	einfo ""
+	einfo "I encourage you to acquire a username and join team 36480."
+	einfo "http://folding.stanford.edu/English/Download#ntoc2"
+	einfo ""
+}
+
+pkg_postrm() {
+	einfo "Folding@home data files were not removed."
+	einfo " Remove them manually from ${I}"
+	einfo ""
+}
diff --git a/sci-visualization/opendx-samples/metadata.xml b/sci-biology/foldingathome/metadata.xml
index b229aec85..34294c65c 100644
--- a/sci-visualization/opendx-samples/metadata.xml
+++ b/sci-biology/foldingathome/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
+<herd>sci-biology</herd>
 </pkgmetadata>
diff --git a/sci-chemistry/autodock/ChangeLog b/sci-chemistry/autodock/ChangeLog
new file mode 100644
index 000000000..27432b1ce
--- /dev/null
+++ b/sci-chemistry/autodock/ChangeLog
@@ -0,0 +1,36 @@
+# 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
new file mode 100644
index 000000000..544b9c849
--- /dev/null
+++ b/sci-chemistry/autodock/Manifest
@@ -0,0 +1,6 @@
+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
new file mode 100644
index 000000000..cf5e3a312
--- /dev/null
+++ b/sci-chemistry/autodock/autodock-4.0.1-r2.ebuild
@@ -0,0 +1,76 @@
+# 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 "${S}/autogrid/Tests"
+	python test_autogrid4.py || die "AutoGrid tests failed."
+}
+
+pkg_postinst() {
+	einfo "The AutoDock development team requests all users to fill out the"
+	einfo "registration form at:"
+	einfo
+	einfo "\thttp://autodock.scripps.edu/downloads/autodock-registration"
+	einfo
+	einfo "The number of unique users of AutoDock is used by Prof. Arthur J."
+	einfo "Olson and the Scripps Research Institude to support grant"
+	einfo "applications."
+}
diff --git a/sci-chemistry/autodock/files/4.0.1-gcc-4.3.patch b/sci-chemistry/autodock/files/4.0.1-gcc-4.3.patch
new file mode 100644
index 000000000..b9eb3c409
--- /dev/null
+++ b/sci-chemistry/autodock/files/4.0.1-gcc-4.3.patch
@@ -0,0 +1,10 @@
+--- autodocksuite-4.0.1.orig/src/autogrid/check_size.cpp	2008-08-04 22:44:46.000000000 -0700
++++ autodocksuite-4.0.1/src/autogrid/check_size.cpp	2008-08-04 22:45:12.000000000 -0700
+@@ -27,6 +27,7 @@
+ 
+ #include <iostream>
+ #include <math.h>
++#include <cstdlib>
+ #include "autogrid.h"
+ 
+ 
diff --git a/sci-chemistry/autodock/files/4.0.1-respect-flags.patch b/sci-chemistry/autodock/files/4.0.1-respect-flags.patch
new file mode 100644
index 000000000..b622192c3
--- /dev/null
+++ b/sci-chemistry/autodock/files/4.0.1-respect-flags.patch
@@ -0,0 +1,40 @@
+--- src/autogrid/Makefile.am	2007-05-17 22:53:30.000000000 +0200
++++ src/autogrid/Makefile.am.new	2009-10-07 19:48:52.000000000 +0200
+@@ -78,9 +78,9 @@
+             util.h \
+             version.h
+ 
+-AM_CFLAGS = -Wall -O3 # All warnings, Agressive optimization
++#AM_CFLAGS = -Wall -O3 # All warnings, Agressive optimization
+ 
+-AM_CXXFLAGS = -Wall -O3 # All warnings, Agressive optimization
++#AM_CXXFLAGS = -Wall -O3 # All warnings, Agressive optimization
+ 
+ AM_CPPFLAGS = -I$(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
new file mode 100644
index 000000000..e42d0af60
--- /dev/null
+++ b/sci-chemistry/autodock/metadata.xml
@@ -0,0 +1,5 @@
+<?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/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index a998f4d68..f9ed525ad 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*ccpn-2.1.0-r2 (09 Oct 2009)
+
+  09 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +ccpn-2.1.0-r2.ebuild:
+  Started to include upstreams online patching into releases
+
 *ccpn-2.1.0-r1 (18 Sep 2009)
 
   18 Sep 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 8ae8271e5..d0c56d2d8 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -6,8 +6,10 @@ AUX formatConverter 317 RMD160 a0f3424901c96bfffd01e8b8a667357b6a29f78a SHA1 cff
 AUX pipe2azara 321 RMD160 c6ca09d178507af6dd2bff4bc8ad6765f4586b62 SHA1 96900b029b8bcdcc414b8e57877cac81d9aef95d SHA256 15fa8d6717e10e3e65d90d1bd89b81fb49a6b218923dc7d70234157c63286b0b
 DIST analysis2.0.7.1.tar.gz 18142642 RMD160 b345c8c8a3cbee549f0ddffbe76d208aa0a93b42 SHA1 f1cade41ce9d488926873bbc6f83fa79af7d9623 SHA256 8d37aa12a3e18a875dcce8689751144c5a949e3431395d00fdef49fbbb0f4d69
 DIST analysis2.1.0.tar.gz 18962012 RMD160 3997fe7deafd50142f60d036e82f436519efe1d0 SHA1 df86d54a13fa1c955f47889f1310b62edfd9dc09 SHA256 132ab4a39fdeedde24385b0c976adea43efd512fefcff7dd973790e9faaf9d95
+DIST update-091009.patch.bz2 34169 RMD160 b37270eeaaa20bb7adb30bcf8049668f753d74fb SHA1 e846a7a43c72b3daaaf018f44914e6d784f4c6e8 SHA256 0b5e642314fc80c6cc082cfd0de3a7a99285d666cb4ee168053ea12baf691e29
 EBUILD ccpn-2.0.7.1-r2.ebuild 4550 RMD160 4adb7d8e25ae01b7c390475fa253e3408425e5fd SHA1 a177bc13e9f9da9f82e86acc6579ef3d11d227ff SHA256 e7f5ad42f1a095259c37ce9a6fe45a462fd105971b90719b3ad66cebe7e82865
 EBUILD ccpn-2.1.0-r1.ebuild 4020 RMD160 266630e5c59e305654c8945de40cf5505b054b13 SHA1 4b9922f385b8df068f37fbdbb5c1c5828ef086c9 SHA256 21dd4e262ddd5c361900828561f20aa0777895d5a2c9f35d4d72f4208c39cb09
+EBUILD ccpn-2.1.0-r2.ebuild 4167 RMD160 c3bb757cbf4865d2fc133b2b5afee6964ad1948e SHA1 050f55e463f1597a5fb9c269cf8284d6233e7894 SHA256 3d6d1c4bad3c325d80ac474a05b1be12806d025477018bb466afb78fcc480027
 EBUILD ccpn-2.1.0.ebuild 4546 RMD160 86a4d9260ca3aa7a401e5b311bc336794d14f311 SHA1 1220889c05b6e9ba814ffa32d83360ed3eccf471 SHA256 afc425f1e75a995322972a51f899d52d69610953d5e59cdb968277695b54ab87
-MISC ChangeLog 3319 RMD160 d6edf93c4b7738600640a1497ccd4198291b2306 SHA1 432d135a08b5833d14678229af67ee174f28f1f9 SHA256 64019e9ff1f1bbd5ac6460f50da1ba51dd10c4fad718ce3353187f2642ace041
+MISC ChangeLog 3493 RMD160 53047c4fb2967d3bcbfb63fb80e713d43b03652c SHA1 c9f4f9302a385608e8ba796b1481a41a4d695874 SHA256 7f2f02b06550012f1bd31cbf6362a0dc2f24593eb3dca4acb727a3062d31119b
 MISC metadata.xml 339 RMD160 2e62dd84c66f8229f9f75832b91b3921a23386c9 SHA1 3252b1e326b3ba201266861d6461bcc069ad770e SHA256 bbb58d377587da3e6a2d4a742829e24b2c840be26d8e8da2d3f6fbf26c0143ec
diff --git a/sci-chemistry/ccpn/ccpn-2.1.0-r2.ebuild b/sci-chemistry/ccpn/ccpn-2.1.0-r2.ebuild
new file mode 100644
index 000000000..a0a221f6f
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.1.0-r2.ebuild
@@ -0,0 +1,167 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+NEED_PYTHON=2.5
+PYTHON_MODNAME="${PN}"
+PYTHON_USE_WITH="ssl tk"
+PATCHSET="091009"
+EAPI="2"
+
+inherit distutils portability python toolchain-funcs versionator
+
+MY_PN="${PN}mr"
+
+DESCRIPTION="The Collaborative Computing Project for NMR"
+SRC_URI="
+	http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${PV}.tar.gz
+	http://dev.gentooexperimental.org/~jlec/distfiles/update-${PATCHSET}.patch.bz2"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc +opengl"
+
+RDEPEND="
+	dev-lang/tk
+	dev-python/elementtree
+	dev-python/numpy
+	dev-tcltk/tix
+	virtual/glut"
+DEPEND="${RDEPEND}"
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
+
+pkg_setup() {
+	python_version
+}
+
+src_prepare() {
+	epatch "${WORKDIR}"/update-${PATCHSET}.patch
+
+	local tk_ver
+	local myconf
+
+	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
+
+	if use opengl; then
+		if has_version media-libs/freeglut; then
+			GLUT_NEED_INIT="-DNEED_GLUT_INIT"
+		else
+			GLUT_NEED_INIT=""
+		fi
+
+		IGNORE_GL_FLAG=""
+		GL_FLAG="-DUSE_GL_FALSE"
+		GL_DIR="/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)"
+
+	sed \
+		-e "s:^\(CC = \).*:\1$(tc-getCC):g" \
+		-e "s:^\(OPT_FLAG = \).*:\1${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:^\(GLUT_NEED_INIT = \).*:\1${GLUT_NEED_INIT}:g" \
+		-e "s:^\(GLUT_NOT_IN_GL = \).*:\1:g" \
+		-e "s:^\(X11_LIB_FLAGS = \).*:\1-L/usr/$(get_libdir):g" \
+		-e "s:^\(TCL_LIB_FLAGS = \).*:\1-L/usr/$(get_libdir):g" \
+		-e "s:^\(TK_LIB_FLAGS = \).*:\1-L/usr/$(get_libdir):g" \
+		-e "s:^\(PYTHON_INCLUDE_FLAGS = \).*:\1-I\$(PYTHON_DIR)/include/python${PYVER}:g" \
+		-e "s:^\(GL_LIB_FLAGS = \).*:\1-L/usr/$(get_libdir):g" \
+		c/environment_default.txt > c/environment.txt
+}
+
+src_compile() {
+	emake \
+		-C c \
+		all links || \
+		die "failed to compile"
+}
+
+src_install() {
+
+	local in_path
+	local gentoo_sitedir
+	local libdir
+	local files
+	local tkver
+
+	in_path=$(python_get_sitedir)/${PN}
+	gentoo_sitedir=$(python_get_sitedir)
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	for wrapper in analysis dangle dataShifter eci formatConverter pipe2azara; do
+		sed -e "s:gentoo_sitedir:${gentoo_sitedir}:g" \
+		    -e "s:libdir:${libdir}:g" \
+			-e "s:tkver:${tkver}:g" \
+		    "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+		dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
+	done
+
+	use doc && treecopy $(find . -name doc) "${D}"usr/share/doc/${PF}/html/
+
+	ebegin "Removing unneeded docs"
+	find . -name doc -exec rm -rf '{}' \; 2> /dev/null
+	eend
+
+	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
+		sed \
+			-e 's:#from __future__:from __future__:g' \
+			-i ${i}
+	done
+
+	insinto ${in_path}
+
+	ebegin "Installing main files"
+	doins -r data model python || die "main files installation failed"
+	eend
+
+	einfo "Adjusting permissions"
+
+	files="ccpnmr/c/ContourFile.so
+		ccpnmr/c/ContourLevels.so
+		ccpnmr/c/ContourStyle.so
+		ccpnmr/c/PeakList.so
+		ccpnmr/c/SliceFile.so
+		ccpnmr/c/WinPeakList.so
+		ccpnmr/c/AtomCoordList.so
+		ccpnmr/c/AtomCoord.so
+		ccpnmr/c/Bacus.so
+		ccpnmr/c/CloudUtil.so
+		ccpnmr/c/DistConstraintList.so
+		ccpnmr/c/DistConstraint.so
+		ccpnmr/c/DistForce.so
+		ccpnmr/c/Dynamics.so
+		ccpnmr/c/Midge.so
+		ccp/c/StructAtom.so
+		ccp/c/StructBond.so
+		ccp/c/StructStructure.so
+		ccp/c/StructUtil.so
+		memops/c/BlockFile.so
+		memops/c/FitMethod.so
+		memops/c/GlHandler.so
+		memops/c/MemCache.so
+		memops/c/PdfHandler.so
+		memops/c/PsHandler.so
+		memops/c/ShapeFile.so
+		memops/c/StoreFile.so
+		memops/c/StoreHandler.so
+		memops/c/TkHandler.so"
+
+	for FILE in ${files}; do
+		fperms 755 ${in_path}/python/${FILE}
+	done
+}
diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index be5aaeebe..8cb1ef61c 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,15 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> coot-0.5.2.ebuild,
+  coot-9999.ebuild:
+  econf dies itself
+
+  03 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> ChangeLog:
+  as-needed patch not needed anymore
+  fixes for reduce not needed anymore
+  rappermc fix included
+
   20 Sep 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> coot-9999.ebuild:
   upstream fixes COOT_TEST_DATA_DIR and included our patch for tests
 
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index 1f9d06a8c..e86f28cfe 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -5,8 +5,10 @@ AUX 0.6_pre1-as-needed.patch 18539 RMD160 2596dac3eb33e1704f84a11613fdc52c42fe87
 AUX 0.6_pre1-gcc4.4.patch 299 RMD160 75374bd38981d4383d926a3b6529ef955a18e893 SHA1 e05d1caeb3dd13d101d417e7f2613402b6712005 SHA256 02c18e695086d70152b923af5d0aecd334bc18f1b6b955d3133c2ae7b6f218af
 AUX 0.6_pre1-test-rama.patch 497 RMD160 6db4732c088d6435dfa1eab0b036f5d37cf13df4 SHA1 dea0505ccdfae27c5632c1c57ce889024a8681bc SHA256 13eed941e596f5a8f1a7a266f8f7c44a359ab35d7df1dad6cae1d91461a7f3bf
 AUX 9999-as-needed.patch 18539 RMD160 2596dac3eb33e1704f84a11613fdc52c42fe8765 SHA1 b6d932312e38d7822866df6449226d90ea1c38c3 SHA256 1646003be0db635ff9b9ef7726adb06f4da8de8a4dbe77baa5074ec8a2faa68a
+AUX 9999-as-needed2.patch 18539 RMD160 2596dac3eb33e1704f84a11613fdc52c42fe8765 SHA1 b6d932312e38d7822866df6449226d90ea1c38c3 SHA256 1646003be0db635ff9b9ef7726adb06f4da8de8a4dbe77baa5074ec8a2faa68a
 AUX 9999-check-include.patch 833 RMD160 7b877f8973b06119779518b433b607665930a382 SHA1 c8a0c80d3a3f5e85592c9925b35c6d5462fc36ad SHA256 98a6c8ef47953501e360b1bdd568ac99d5a53749738d940939e9f6a47cf85cd1
 AUX 9999-gcc4.4.patch 299 RMD160 75374bd38981d4383d926a3b6529ef955a18e893 SHA1 e05d1caeb3dd13d101d417e7f2613402b6712005 SHA256 02c18e695086d70152b923af5d0aecd334bc18f1b6b955d3133c2ae7b6f218af
+AUX 9999-rappermc.patch 552 RMD160 66feba0ce4e6539ef67ab69e5b6d1bed448e18db SHA1 1806984097fde639a282a27c3de60945daeb1e6d SHA256 01ada3aac5413acfa9328e6235dc6d3e7fa7dc08455c560e97d498e5adea9523
 AUX 9999-test-rama.patch 497 RMD160 6db4732c088d6435dfa1eab0b036f5d37cf13df4 SHA1 dea0505ccdfae27c5632c1c57ce889024a8681bc SHA256 13eed941e596f5a8f1a7a266f8f7c44a359ab35d7df1dad6cae1d91461a7f3bf
 AUX fix-namespace-error.patch 1081 RMD160 ebecd51b87c39dc2c37e565f18fc88b7aa837d05 SHA1 f732df5f4795e728bdf217aac9c9f53952e2890c SHA256 fd271dd22eec5725fcbd20c68b57008eed0f435d1e0ac212fbfd389a0a970beb
 AUX glib.m4 8444 RMD160 f3f4b2987796f16d17758f2af3459279351d6f2c SHA1 201eb58c2b3f3c5395dacd3913a4fb9d950d3276 SHA256 ada4a0a46bd00eda39afe77f675b721f60cd20c0080170848f4d7e92b4ba4dc8
@@ -16,9 +18,9 @@ AUX imlib.m4 11371 RMD160 4470d0cf2d0f8298bea6565069acda8a44e1cd9d SHA1 c983c372
 AUX link-against-guile-gtk-properly.patch 800 RMD160 4215ea41c02e7db2c04dda191e0200cc1704d43c SHA1 5bd24ab8c651a147076289098956f545c6e431d6 SHA256 7805cdf4e34c532899a8c37eb19664fc95fc8bc440e770db7c87373a94e1fb2d
 DIST coot-0.5.2.tar.gz 10160364 RMD160 5cee5e8da6e4d2ce06016f6f8935b395e65ddbf9 SHA1 041cc947a68296701deb153c0932ee20a3437323 SHA256 6245f85dfb796ee7f3488c0790531f8d5e29a9f6ea18411ae539e3993e4ed2d6
 DIST coot-0.6-pre-1-revision-2312.tar.gz 11014498 RMD160 d509629d4a4aaa042699b255270d02f19af5c1e7 SHA1 4502d18aa14eb1f0f2725e877b7ddfab8a145efd SHA256 9ac5076502c1cb0a45e3dd6c59ef9f39e2732bdfca5441bf59f0af398ca1be85
-DIST greg-data.tar.gz 7853711 RMD160 3d736f3dfd0ad1a1fbe857ae3b6d412106375e6d SHA1 639db46bbd8ee5ff9764a011873ca635bc3c9351 SHA256 6ccdbec91c098b4e89666259cb93acec4dc0213e9762e5d3d3e9a8b96d9f0fcc
-EBUILD coot-0.5.2.ebuild 3238 RMD160 80d71146f3b11a4283494bfb95e77667a5128c1f SHA1 72f982f9a9fa8bc22688f5a5bbae9488b3e5dafb SHA256 582a0d78796e8666825befbc2fe5a4256ea5a5512cded142480f70f14bca2e74
+DIST greg-data.tar.gz 7853712 RMD160 9dc7f9dc65786e3aa4ebdc58c280fffa32ed07d3 SHA1 eff196da7da65e4265cc289aba4c7717f5600916 SHA256 ce0c5ae438dcb14771f3339fe57d3b40bb8cd0a8cb37a237eeecc0bb69fb3e5d
+EBUILD coot-0.5.2.ebuild 3212 RMD160 485b95eb31d4b25fed8a4952b79a7ee9a6157bb1 SHA1 3922d0d186ccbb8e401c552742f8cd64e7ba7536 SHA256 05082d1ea84b06462833194940ba5a7c608485e16586c75727b1ce88aa94df7a
 EBUILD coot-0.6_pre1-r2312.ebuild 4318 RMD160 8164ef691b3ef718bdd0aad743789624d7021239 SHA1 e725804986286fb50de2def68b7218a2f5f8b4ee SHA256 81fef115c1b7972482bf6f578f0350abbbc68a685673bdbceb4fcde50d67a0ff
-EBUILD coot-9999.ebuild 4194 RMD160 025e880a348a1c856de8d1130cecb6179acffa51 SHA1 89413c8a0c9d2b516c6c0158beed5503e499f7fa SHA256 36de50557b876646276acbb7167b7ae4af291c4c662f189d7a5eef99d795e78f
-MISC ChangeLog 6038 RMD160 44f05c3a14daf55c3b4f14f710790e7b83e4e83b SHA1 5c1d78bdb14cb3e748336c91d44bd746091b958f SHA256 58bb9a17e32402179e269cadb493468c519e96b5972f75a369db731ab89d9245
+EBUILD coot-9999.ebuild 3931 RMD160 6259e74fa4df12126ca55f667533cf78b51b0221 SHA1 bda7534813d2c3e39a181d5b821e674c3be268e9 SHA256 2a953f46663c1b98278b37cebd57dc9503b577c89b81693156a9e2797be1b17e
+MISC ChangeLog 6323 RMD160 0e60847ef994e7cbbf2028f270cac668e8d7913f SHA1 af8f517f6ef640eeb5391eccbd573f1363232043 SHA256 069c46e345e102923526a11604ed534bc0698e0d33cf8487d7077a0c5fea0238
 MISC metadata.xml 316 RMD160 845cc100ac244efa5f02595717b5da635f87d2f1 SHA1 c870d2c52c44dee3bab8623e5b6095266f400813 SHA256 64f6dbcd3bb41b26fd7897089cd60ddb93f1ea7d75f9531bca94f28b07e21b2f
diff --git a/sci-chemistry/coot/coot-0.5.2.ebuild b/sci-chemistry/coot/coot-0.5.2.ebuild
index 3761537bc..348d1df99 100644
--- a/sci-chemistry/coot/coot-0.5.2.ebuild
+++ b/sci-chemistry/coot/coot-0.5.2.ebuild
@@ -100,8 +100,7 @@ src_compile() {
 		--with-python=/usr \
 		--with-guile-gtk \
 		--with-gtk2 \
-		--with-pygtk \
-		|| die "econf failed"
+		--with-pygtk
 
 	# Regenerate wrappers, otherwise at least gtk-2 build fails
 	pushd src
diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 72ec9f637..834f832c8 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -60,7 +60,7 @@ DEPEND="${RDEPEND}
 S="${WORKDIR}"
 
 PATCHES=(
-	"${FILESDIR}"/${PV}-as-needed.patch
+	"${FILESDIR}"/${PV}-rappermc.patch
 	"${FILESDIR}"/link-against-guile-gtk-properly.patch
 	"${FILESDIR}"/fix-namespace-error.patch
 	)
@@ -79,12 +79,6 @@ src_prepare() {
 		-e "s:lrfftw:lsrfftw:g" \
 		"${S}"/macros/clipper.m4
 
-	# Fix where it looks for some binaries
-	sed -i \
-		-e "s:/y/people/emsley/coot/Linux/bin/probe.2.11.050121.linux.RH9:/usr/bin/probe:g" \
-		-e "s:/y/people/emsley/coot/Linux/bin/reduce.2.21.030604:/usr/bin/reduce:g" \
-		"${S}"/scheme/group-settings.scm
-
 	# So we don't need to depend on crazy old gtk and friends
 	cp "${FILESDIR}"/*.m4 "${S}"/macros/
 
@@ -114,25 +108,24 @@ src_configure() {
 		--with-python=/usr \
 		--with-guile-gtk \
 		--with-gtk2 \
-		--with-pygtk \
-		|| die "econf failed"
+		--with-pygtk
 }
 
 src_compile() {
-	# Regenerate wrappers, otherwise at least gtk-2 build fails
-	pushd src
-	rm -f coot_wrap_python.cc coot_wrap_python_pre.cc \
-		&& emake coot_wrap_python.cc \
-		|| die "failed to regenerate python wrapper"
-
-	rm -f coot_wrap_guile.cc coot_wrap_guile_pre.cc \
-		&& emake coot_wrap_guile.cc \
-		||die "failed to regenerate guile wrapper"
-	popd
-
+#	# Regenerate wrappers, otherwise at least gtk-2 build fails
+#	pushd src
+#	rm -f coot_wrap_python.cc coot_wrap_python_pre.cc \
+#		&& emake coot_wrap_python.cc \
+#		|| die "failed to regenerate python wrapper"
+#
+#	rm -f coot_wrap_guile.cc coot_wrap_guile_pre.cc \
+#		&& emake coot_wrap_guile.cc \
+#		||die "failed to regenerate guile wrapper"
+#	popd
+#
 	emake || die "emake failed"
 
-	cp "${S}"/src/coot.py python/
+	cp "${S}"/src/coot.py python/ || die
 }
 
 src_test() {
diff --git a/sci-chemistry/coot/files/9999-as-needed2.patch b/sci-chemistry/coot/files/9999-as-needed2.patch
new file mode 100644
index 000000000..0cfce54dd
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-as-needed2.patch
@@ -0,0 +1,481 @@
+Index: mini-mol/Makefile.am
+===================================================================
+--- mini-mol/Makefile.am	(revision 2293)
++++ mini-mol/Makefile.am	(working copy)
+@@ -35,8 +35,9 @@
+ testminimol_SOURCES = testminimol.cc
+ 
+ libcoot_mini_mol_la_SOURCES =  mini-mol.cc mini-mol-utils.cc atom-quads.cc
++libcoot_mini_mol_la_LIBADD = \
++	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
++	$(CLIPPER_LIBS)
+ 
+ testminimol_LDADD = libcoot-mini-mol.la \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+-	$(top_builddir)/coot-utils/libcoot-utils.la \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
++	$(MMDB_LIBS)
+Index: coords/Makefile.am
+===================================================================
+--- coords/Makefile.am	(revision 2293)
++++ coords/Makefile.am	(working copy)
+@@ -40,3 +40,7 @@
+ 		 mmdb-extras.cc utils.cc mmdb.cc mmdb-crystal.cc \
+ 		 Bond_lines_ext.cc coot-close.cc
+ 
++libcoot_coords_la_LIBADD = \
++	$(top_builddir)/coot-utils/libcoot-shelx.la \
++	$(top_builddir)/mini-mol/libcoot-mini-mol.la
++
+Index: ligand/Makefile.am
+===================================================================
+--- ligand/Makefile.am	(revision 2293)
++++ ligand/Makefile.am	(working copy)
+@@ -49,6 +49,17 @@
+ 	torsion-general.cc rotamer-tables.cc primitive-chi-angles.cc dipole.cc\
+         base-pairing.cc backrub-rotamer.cc
+ 
++libcoot_ligand_la_LIBADD = \
++	$(top_builddir)/ideal/libcoot-ideal.la       \
++	$(top_builddir)/coords/libcoot-coords.la           \
++	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
++	$(top_builddir)/coot-utils/libcoot-map-utils.la    \
++	$(top_builddir)/db-main/libcoot-db-main.la         \
++	$(top_builddir)/coot-utils/libcoot-shelx.la        \
++	$(top_builddir)/geometry/libcoot-geometry.la       \
++	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
++	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la
++
+ AM_CXXFLAGS = \
+ 	-DPKGDATADIR='"$(pkgdatadir)"' \
+ 	$(COOT_WINDOWS_CFLAGS)
+@@ -68,7 +79,6 @@
+ 
+ test_random_LDADD = \
+ 	./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.la       \
+ 	$(top_builddir)/coords/libcoot-coords.la           \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+ 	$(top_builddir)/coot-utils/libcoot-map-utils.la    \
+@@ -85,31 +95,14 @@
+ 
+ test_ligand_LDADD = \
+ 	./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.la       \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la \
+-	$(top_builddir)/coords/libcoot-coords.la           \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la    \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la        \
+-	$(top_builddir)/geometry/libcoot-geometry.la       \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la        \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la    \
+ 	$(top_builddir)/compat/libcoot-compat.la           \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+ test_helix_placement_LDADD = \
+ 	./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.la       \
+-	$(top_builddir)/coords/libcoot-coords.la           \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la    \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la        \
+-	$(top_builddir)/geometry/libcoot-geometry.la       \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la        \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la    \
+@@ -120,18 +113,9 @@
+ 
+ test_fffear_in_coot_LDADD = \
+ 	./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.la            \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coords/libcoot-coords.la          \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+-	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/coot-utils/libcoot-map-heavy.la   \
+-	$(top_builddir)/db-main/libcoot-db-main.la        \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+@@ -143,23 +127,13 @@
+ 
+ findligand_real_LDADD = \
+ 	./libcoot-ligand.la                                \
+-	$(top_builddir)/ideal/libcoot-ideal.la             \
+-	$(top_builddir)/geometry/libcoot-geometry.la       \
+-	$(top_builddir)/coords/libcoot-coords.la           \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la    \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la    \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la        \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la        \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
+ 	$(top_builddir)/compat/libcoot-compat.la           \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+ findwaters_real_LDADD = \
+ 	./libcoot-ligand.la                                \
+-	$(top_builddir)/ideal/libcoot-ideal.la             \
+ 	$(top_builddir)/geometry/libcoot-geometry.la       \
+ 	$(top_builddir)/coords/libcoot-coords.la           \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la    \
+@@ -190,16 +164,7 @@
+ testdunbrack_SOURCES = testdunbrack.cc
+ 
+ testdunbrack_LDADD = ./libcoot-ligand.la \
+-	$(top_builddir)/ideal/libcoot-ideal.la       \
+-	$(top_builddir)/geometry/libcoot-geometry.la \
+-	$(top_builddir)/coords/libcoot-coords.la           \
+-	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la    \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+-	$(top_builddir)/db-main/libcoot-db-main.la         \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la        \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la \
+         $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
+ 
+Index: analysis/Makefile.am
+===================================================================
+--- analysis/Makefile.am	(revision 2293)
++++ analysis/Makefile.am	(working copy)
+@@ -9,6 +9,7 @@
+ 	$(MMDB_CXXFLAGS)
+ 
+ libcoot_analysis_la_SOURCES = bfkurt.cc
++libcoot_analysis_la_LIBADD = $(top_builddir)/coot-utils/libcoot-coord-utils.la
+ 
+ bin_PROGRAMS = bfactan
+ 
+@@ -16,7 +17,6 @@
+ 
+ bfactan_LDADD = \
+ 	libcoot-analysis.la 					\
+-	$(top_builddir)/coot-utils/libcoot-coord-utils.la 	\
+ 	$(top_builddir)/coot-utils/libcoot-utils.la 		\
+ 	$(top_builddir)/geometry/libcoot-geometry.la    	\
+ 	$(CLIPPER_LIBS) 	\
+Index: skeleton/Makefile.am
+===================================================================
+--- skeleton/Makefile.am	(revision 2293)
++++ skeleton/Makefile.am	(working copy)
+@@ -39,8 +39,8 @@
+ 
+ 
+ libcoot_skeleton_la_SOURCES = $(libskeleton_a_sources)
++libcoot_skeleton_la_LIBADD = ../atom-utils/libcoot-atomutils.la
+ 
+-
+ # bin_PROGRAMS = ncssearch test_various test_torsion test_theta_2
+ 
+ # ncssearch_SOURCES = ncs-search.cc ncs-search.h
+Index: coot-surface/Makefile.am
+===================================================================
+--- coot-surface/Makefile.am	(revision 2293)
++++ coot-surface/Makefile.am	(working copy)
+@@ -25,3 +25,4 @@
+ 
+ libcoot_surface_la_SOURCES = \
+ 	 coot-surface.cc coot-surface.hh rgbreps.cc rgbreps.h
++libcoot_surface_la_LIBADD = $(top_builddir)/surface/libccp4mg-surface.la
+Index: high-res/Makefile.am
+===================================================================
+--- high-res/Makefile.am	(revision 2293)
++++ high-res/Makefile.am	(working copy)
+@@ -39,13 +39,16 @@
+ 
+ libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \
+ 	sequence-assignment.cc
++libcoot_high_res_la_LIBADD = \
++	$(top_builddir)/ligand/libcoot-ligand.la \
++	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ check_PROGRAMS = testatomgraph tracehighres testseqalign testseqassignment globularize_protein
+ 
+ testatomgraph_SOURCES = test-atom-graph.cc
+ 
+ testatomgraph_LDADD =  libcoot-high-res.la                \
+-	$(top_builddir)/ligand/libcoot-ligand.la          \
+ 	$(top_builddir)/db-main/libcoot-db-main.la        \
+ 	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+@@ -53,71 +56,60 @@
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+ 	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+-	$(GSL_LIBS)			                  \
+-	$(CLIPPER_LIBS)
++	$(GSL_LIBS)
+ 
+ testseqassignment_SOURCES = testseqassignment.cc
+ testseqassignment_LDADD = libcoot-high-res.la             \
+-	$(top_builddir)/ligand/libcoot-ligand.la          \
+ 	$(top_builddir)/db-main/libcoot-db-main.la        \
+ 	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/coords/libcoot-coords.la          \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+-	$(GSL_LIBS)				          \
+-	$(CLIPPER_LIBS)
++	$(GSL_LIBS)
+ 
+ # tracehighres_LDFLAGS = -static 
+ tracehighres_SOURCES = trace-high-res.cc
+ tracehighres_LDADD = libcoot-high-res.la                  \
+-	$(top_builddir)/ligand/libcoot-ligand.la          \
+ 	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/db-main/libcoot-db-main.la        \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/coords/libcoot-coords.la          \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+-	$(GSL_LIBS)				          \
+-	$(CLIPPER_LIBS)
++	$(GSL_LIBS)
+ 
+ 
+ testseqalign_SOURCES = testseqalign.cc
+ 
+ # why do we need to link with all this (junk)?
+ testseqalign_LDADD = libcoot-high-res.la                  \
+-	$(top_builddir)/ligand/libcoot-ligand.la          \
+ 	$(top_builddir)/ideal/libcoot-ideal.la            \
+ 	$(top_builddir)/db-main/libcoot-db-main.la        \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/coords/libcoot-coords.la          \
+ 	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+ 	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+-	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+ 	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la       \
+ 	$(top_builddir)/ccp4mg-utils/libccp4mg-utils.la   \
+ 	$(top_builddir)/compat/libcoot-compat.la          \
+-	$(GSL_LIBS)				          \
+-	$(CLIPPER_LIBS)
++	$(GSL_LIBS)
+ 
+ 
+ globularize_protein_SOURCES = globularize.cc
+Index: cootaneer/Makefile.am
+===================================================================
+--- cootaneer/Makefile.am	(revision 2293)
++++ cootaneer/Makefile.am	(working copy)
+@@ -34,6 +34,7 @@
+ 	buccaneer-sequence.cpp cootaneer-sequence.cpp \
+ 	buccaneer-lib.h buccaneer-prot.h \
+ 	buccaneer-sequence.h cootaneer-sequence.h
++libcootaneer_la_LIBADD = $(CLIPPER_LIBS)
+ 
+ subpkgdatadir = $(pkgdatadir)
+ subpkgdata_DATA = cootaneer-llk-2.40.dat 
+Index: geometry/Makefile.am
+===================================================================
+--- geometry/Makefile.am	(revision 2293)
++++ geometry/Makefile.am	(working copy)
+@@ -35,6 +35,9 @@
+ #	-DHAVE_SYS_STDTYPES_H
+ 
+ libcoot_geometry_la_SOURCES = protein-geometry.cc protein-geometry-mmdb.cc 
++libcoot_geometry_la_LIBADD = \
++	$(top_builddir)/coot-utils/libcoot-utils.la \
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ # libcoot_geometry_la_CXXFLAGS = -g -O1
+ 
+@@ -44,12 +47,7 @@
+ 
+ test_read_components_SOURCES = test-read-components.cc test-read-components.hh
+ 
+-test_geometry_LDADD = ./libcoot-geometry.la         \
+-        $(top_builddir)/coot-utils/libcoot-utils.la \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
++test_geometry_LDADD = ./libcoot-geometry.la
++ 
++test_read_components_LDADD = ./libcoot-geometry.la
+ 
+-test_read_components_LDADD =  \
+-	./libcoot-geometry.la \
+-        $(top_builddir)/coot-utils/libcoot-utils.la   \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
+-
+Index: ideal/Makefile.am
+===================================================================
+--- ideal/Makefile.am	(revision 2293)
++++ ideal/Makefile.am	(working copy)
+@@ -54,6 +54,12 @@
+ 
+ 
+ libcoot_ideal_la_SOURCES = simple-restraint.cc  pepflip.cc regularize-minimol.cc lograma.cpp
++libcoot_ideal_la_LIBADD = \
++	$(top_builddir)/coot-utils/libcoot-utils.la       \
++	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
++	$(top_builddir)/coot-utils/libcoot-shelx.la       \
++	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
++	$(GSL_LIBS)
+ 
+ 
+ noinst_PROGRAMS = test-indexing with-geometry with-map logramatest
+@@ -75,12 +81,8 @@
+         ./libcoot-ideal.la                                \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+ 	$(top_builddir)/coords/libcoot-coords.la          \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la       \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+-	$(top_builddir)/coot-utils/libcoot-utils.la       \
+-	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ # add libcoot-map-utils for  the debugging density_around_point function
+ with_map_LDADD =  \
+@@ -88,22 +90,16 @@
+ 	$(top_builddir)/geometry/libcoot-geometry.la       \
+ 	$(top_builddir)/coords/libcoot-coords.la           \
+ 	$(top_builddir)/coot-utils/libcoot-map-utils.la   \
+-	$(top_builddir)/coot-utils/libcoot-shelx.la        \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la  \
+ 	$(top_builddir)/coot-utils/libcoot-utils.la        \
+-        $(top_builddir)/compat/libcoot-compat.la           \
+-	$(top_builddir)/mini-mol/libcoot-mini-mol.la       \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
++	$(top_builddir)/compat/libcoot-compat.la           \
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ test_indexing_LDADD = \
+         ./libcoot-ideal.la                                \
+ 	$(top_builddir)/geometry/libcoot-geometry.la      \
+-	$(top_builddir)/mini-mol/libcoot-mini-mol.la      \
+-	$(top_builddir)/coot-utils/libcoot-coord-extras.la \
+ 	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
+-	$(top_builddir)/coot-utils/libcoot-utils.la       \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
++	$(CLIPPER_LIBS) $(MMDB_LIBS)
+ 
+ # Why do I need all these libraries to simply link a trivial test program?
+ # Badness....
+Index: tw/Makefile.am
+===================================================================
+--- tw/Makefile.am	(revision 2293)
++++ tw/Makefile.am	(working copy)
+@@ -39,14 +39,15 @@
+ include_HEADERS = coot-tw.hh
+ 
+ libcoot_tw_la_SOURCES = tw.cc
++libcoot_tw_la_LIBADD = \
++	$(GTKCANVAS_LIBS) \
++	@GTK_LIBS@
+ 
+ noinst_PROGRAMS = coot-tiddly
+ 
+ coot_tiddly_SOURCES = tiddly.cc
+ 
+-coot_tiddly_LDADD = libcoot-tw.la \
+-	$(GTKCANVAS_LIBS) \
+-	@GTK_LIBS@
++coot_tiddly_LDADD = libcoot-tw.la
+ 
+ 
+ # cootsound_LDADD = -L/sw/lib -lvorbisfile -logg -lao
+Index: coot-utils/Makefile.am
+===================================================================
+--- coot-utils/Makefile.am	(revision 2293)
++++ coot-utils/Makefile.am	(working copy)
+@@ -49,6 +49,7 @@
+ # for simple things:
+ libcoot_utils_la_SOURCES = coot-utils.cc coot-fasta.cc atomic-numbers.cc \
+ 	gdk-keysyms.cc
++libcoot_coord_utils_la_LIBADD = $(CLIPPER_LIBS) libcoot-utils.la
+ 
+ # for pure coordinates (mmdb) things
+ libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc \
+@@ -56,6 +57,7 @@
+ 
+ # shelx
+ libcoot_shelx_la_SOURCES = coot-shelx-ins.cc
++libcoot_shelx_la_LIBADD = $(MMDB_LIBS) libcoot-coord-utils.la
+ 
+ # for non-simple coordinates things
+ libcoot_coord_extras_la_SOURCES = coot-coord-extras.cc coot-coord-lsq.cc \
+@@ -63,24 +65,23 @@
+ 
+ # for (map) things that need to link mmdb and clipper:
+ libcoot_map_utils_la_SOURCES = coot-map-utils.cc peak-search.cc trim.cc xmap-stats.cc
++libcoot_map_utils_la_LIBADD = $(CLIPPER_LIBS)
+ 
+ # for map things that need mmdb, clipper, gsl and other things
+ libcoot_map_heavy_la_SOURCES = coot-map-heavy.cc coot-fffear.cc
++libcoot_map_heavy_la_LIBADD = $(GSL_LIBS)
+ 
+ noinst_PROGRAMS = testshelxreader testcootutils
+ 
+ testshelxreader_SOURCES = test-shelx-reader.cc
+ testshelxreader_LDADD = \
+ 	./libcoot-shelx.la \
+-	./libcoot-coord-utils.la \
+ 	./libcoot-utils.la \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
++	$(MMDB_LIBS)
+ 
+ testcootutils_SOURCES = test-utils.cc
+ testcootutils_LDADD = \
+ 	./libcoot-shelx.la \
+-	./libcoot-coord-utils.la \
+ 	./libcoot-utils.la \
+-	$(CLIPPER_LIBS) $(MMDB_LIBS)
++  $(MMDB_LIBS)
+ 
+-
+Index: Makefile.am
+===================================================================
+--- Makefile.am	(revision 2293)
++++ Makefile.am	(working copy)
+@@ -25,10 +25,10 @@
+ 
+ # see configure.in for po intl 
+ SUBDIRS = auxil scheme python macros compat coot-utils surface coot-surface \
+-	skeleton ccp4mg-utils density-contour coords angles \
+-	mini-mol db-main  geometry  \
++	atom-utils skeleton ccp4mg-utils density-contour mini-mol coords angles \
++	db-main geometry  \
+ 	ideal ligand high-res build greg-tests python-tests \
+-	analysis sequence-view tw atom-utils cootaneer src rama-data doc 
++	analysis sequence-view tw cootaneer src rama-data doc 
+ 
+ # po, no po today.
+ 
diff --git a/sci-chemistry/coot/files/9999-rappermc.patch b/sci-chemistry/coot/files/9999-rappermc.patch
new file mode 100644
index 000000000..1ecd9c529
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-rappermc.patch
@@ -0,0 +1,15 @@
+Index: /data/svn-src/coot/trunk/python/a_rapper_gui.py
+===================================================================
+--- /data/svn-src/coot/trunk/python/a_rapper_gui.py	(revision 2398)
++++ /data/svn-src/coot/trunk/python/a_rapper_gui.py	(working copy)
+@@ -20,8 +20,8 @@
+     home_dir = os.getenv('COOT_HOME')
+ else:
+     home_dir = os.getenv('HOME')
+-rapper_dir = os.path.join(os.path.normpath(home_dir), "rappermc")
+-rapper_command = "rapper"
++rapper_dir = "/usr/share/rapper"
++rapper_command = "rappermc"
+ 
+ def rapper_process():
+     #needed?
diff --git a/sci-chemistry/mgltools-autodocktools/ChangeLog b/sci-chemistry/mgltools-autodocktools/ChangeLog
index 54a5bd39e..36113fc69 100644
--- a/sci-chemistry/mgltools-autodocktools/ChangeLog
+++ b/sci-chemistry/mgltools-autodocktools/ChangeLog
@@ -2,6 +2,18 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*mgltools-autodocktools-1.5.4-r1 (07 Oct 2009)
+
+  07 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  -mgltools-autodocktools-1.5.4.ebuild,
+  +mgltools-autodocktools-1.5.4-r1.ebuild:
+  EAPI=2
+  added dev-lang/python[tk] to depend
+
+  07 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  mgltools-autodocktools-1.5.4.ebuild:
+  Added sci-chemistry/mgltools-support to RDEPEND
+
 *mgltools-autodocktools-1.5.4 (18 May 2009)
 
   18 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/mgltools-autodocktools/Manifest b/sci-chemistry/mgltools-autodocktools/Manifest
index 1e7a939fe..1fbe53b90 100644
--- a/sci-chemistry/mgltools-autodocktools/Manifest
+++ b/sci-chemistry/mgltools-autodocktools/Manifest
@@ -1,4 +1,5 @@
 DIST mgltools_source_1.5.4.tar.gz 21591865 RMD160 faa158477c4e9156ee5fd23b89251e5bedbd689d SHA1 3b3056a75cd944a4aa46771e09916a4e85052b88 SHA256 d0c614e167512bd19127c741cb2d9860443c097f7ccf0bbe244c0b155e59a9c2
-EBUILD mgltools-autodocktools-1.5.4.ebuild 1125 RMD160 f3c33750f901bb33518c6d0a3892f74fda4d0d7c SHA1 e21175aac0d17833641cf5f42cc96d33c817b4ae SHA256 26fadb1f13466ee0a780f1d2053777cbbf198aab02ff289a0a78ba7b64b45057
-MISC ChangeLog 313 RMD160 f01fac2447bb1a6a38ae2779352206f4c0f3adc6 SHA1 d457936e2c06368d9ff7402edf5e5ed3f64be823 SHA256 d43e9e1d333e4fb53019563e3f22b07aa28f1bb82ebde002ea03190ba125a1fd
+EBUILD mgltools-autodocktools-1.5.4-r1.ebuild 1206 RMD160 11eabf254efd6493e9b9c0f6e27ac146b9bbbfa5 SHA1 f8acab1f1c270264bb9ec16b96d209312421c773 SHA256 728d77aa8af793ce4e66dd4affba61668d95119d68c84445a76868e701791ea1
+MISC ChangeLog 696 RMD160 e24161391a7429a1ca006fc769fb0bb638f1a1ce SHA1 45b60509dc7f0d2b30cffd7defc7b7458aeaeee7 SHA256 56df4489525358534080928defde7538adddcb8f62151d49589c0d4bdd0b240a
 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
+MISC mvAll.log.py 3230 RMD160 35ced7c61ed318ceab337dd0b958084f36b65f95 SHA1 b5c4ad6c363eef046172fa96295e0e71bc5b6da7 SHA256 f4dd1c686797f608f60fadea40af0815ae05dde78609331a65a0af9c16b3ea42
diff --git a/sci-chemistry/mgltools-autodocktools/mgltools-autodocktools-1.5.4.ebuild b/sci-chemistry/mgltools-autodocktools/mgltools-autodocktools-1.5.4-r1.ebuild
index b66e7d0e7..59ea2edbb 100644
--- a/sci-chemistry/mgltools-autodocktools/mgltools-autodocktools-1.5.4.ebuild
+++ b/sci-chemistry/mgltools-autodocktools/mgltools-autodocktools-1.5.4-r1.ebuild
@@ -2,6 +2,8 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
+EAPI="2"
+
 inherit distutils
 
 MY_P="AutoDockTools-${PV}"
@@ -16,7 +18,9 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-RDEPEND=""
+RDEPEND="
+	sci-chemistry/mgltools-support
+	dev-lang/python[tk]"
 DEPEND="${RDEPEND}
 	dev-lang/swig"
 
@@ -27,7 +31,9 @@ DOCS="AutoDockTools/RELNOTES"
 src_unpack() {
 	tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV}/MGLPACKS/${MY_P}.tar.gz
 	tar xzpf mgltools_source_${PV}/MGLPACKS/${MY_P}.tar.gz
+}
 
+src_prepare() {
 	find "${S}" -name CVS -type d -exec rm -rf '{}' \; >& /dev/null
 	find "${S}" -name LICENSE -type f -exec rm -f '{}' \; >& /dev/null
 
diff --git a/sci-chemistry/mgltools-autodocktools/mvAll.log.py b/sci-chemistry/mgltools-autodocktools/mvAll.log.py
new file mode 100644
index 000000000..1329a1894
--- /dev/null
+++ b/sci-chemistry/mgltools-autodocktools/mvAll.log.py
@@ -0,0 +1,51 @@
+# Pmv version 1.5.4 revision 24
+self.GUI.setGeom(397, 100, 704, 660)
+self.browseCommands('autotors4Commands', commands=None, log=0, package='AutoDockTools')
+self.browseCommands('autoflex4Commands', commands=None, log=0, package='AutoDockTools')
+self.browseCommands('colorCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('editCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('colorCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('editCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('colorCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('editCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('autogpf4Commands', commands=None, log=0, package='AutoDockTools')
+self.browseCommands('labelCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('displayCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('hbondCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('displayCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('bondsCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('fileCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('labelCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('autostart4Commands', commands=None, log=0, package='AutoDockTools')
+self.browseCommands('WebServices', commands=None, log=0, package='AutoDockTools')
+self.browseCommands('labelCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('displayCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('hbondCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('autoanalyze4Commands', commands=None, log=0, package='AutoDockTools')
+self.browseCommands('autotors41Commands', commands=None, log=0, package='AutoDockTools')
+self.browseCommands('autoflex41Commands', commands=None, log=0, package='AutoDockTools')
+self.browseCommands('autogpf41Commands', commands=None, log=0, package='AutoDockTools')
+self.browseCommands('displayCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('bondsCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('fileCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('autodpf41Commands', commands=None, log=0, package='AutoDockTools')
+self.browseCommands('autostart41Commands', commands=None, log=0, package='AutoDockTools')
+self.browseCommands('WebServices', commands=None, log=0, package='AutoDockTools')
+self.browseCommands('labelCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('displayCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('hbondCommands', commands=None, log=0, package='Pmv')
+self.browseCommands('autoanalyze41Commands', commands=None, log=0, package='AutoDockTools')
+self.ADTSetMode('AD4.2', log=0)
+self.browseCommands('selectionCommands', commands=None, log=0, package='Pmv')
+##
+## Saving Vision networks
+##
+self.browseCommands('visionCommands', commands=('vision',))
+from NetworkEditor.net import Network
+self.vision.ed.deleteNetwork(self.vision.ed.networks['Network 0'])
+pmv = self
+self = pmv.vision.ed
+self = pmv
+##
+## Vision networks are saved
+##
diff --git a/sci-chemistry/molrep/ChangeLog b/sci-chemistry/molrep/ChangeLog
index 43913ea38..8f6a39989 100644
--- a/sci-chemistry/molrep/ChangeLog
+++ b/sci-chemistry/molrep/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*molrep-10.2.34 (02 Oct 2009)
+
+  02 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/10.2.34-respect-FLAGS.patch, +molrep-10.2.34.ebuild:
+  version bump
+
 *molrep-10.2.33 (29 Jul 2009)
 
   29 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/molrep/Manifest b/sci-chemistry/molrep/Manifest
index b3f13048b..a57945607 100644
--- a/sci-chemistry/molrep/Manifest
+++ b/sci-chemistry/molrep/Manifest
@@ -1,11 +1,14 @@
 AUX 10.2.27-respect-FLAGS.patch 2376 RMD160 d11071cc402375b2376b6202f960b6f909d1b8df SHA1 7c1ea85188776bbf1054ef18efd55c04343ba187 SHA256 30b55e61663e217c1ee5ef12fe9954046016e303f77f9ff52caa6959c3e3eaa5
 AUX 10.2.32-respect-FLAGS.patch 2368 RMD160 4f24b345f0c78de0c0222abfef987d61fe1356d0 SHA1 bc445d646208de7e879a5989b66296fd89b2fc96 SHA256 809d9f290a1eb59b8fc5904328e72c30b65d3be821a61a1bff050bc446bdc991
 AUX 10.2.33-respect-FLAGS.patch 2368 RMD160 4f24b345f0c78de0c0222abfef987d61fe1356d0 SHA1 bc445d646208de7e879a5989b66296fd89b2fc96 SHA256 809d9f290a1eb59b8fc5904328e72c30b65d3be821a61a1bff050bc446bdc991
+AUX 10.2.34-respect-FLAGS.patch 2368 RMD160 4f24b345f0c78de0c0222abfef987d61fe1356d0 SHA1 bc445d646208de7e879a5989b66296fd89b2fc96 SHA256 809d9f290a1eb59b8fc5904328e72c30b65d3be821a61a1bff050bc446bdc991
 DIST molrep-10.2.27.tar.gz 3595088 RMD160 6e36b6bf992fb306b67de6e483a3487c5fc21da3 SHA1 04d1ecdbd62498703d3c9f3a7d31659074f75c66 SHA256 85c15c827936540134ab65ea9de5a13faa789edeea0f39f65ec1b319ca43c42a
 DIST molrep-10.2.32.tar.gz 3601054 RMD160 bc71b85de92871d540073b1df48e4df7be843a5a SHA1 514a902306bfdb606a4975f95a31859392ff51f7 SHA256 d6736d11cef2638eb4534d65c31871396d3404c8a3011d55bad81fecd810a8b7
 DIST molrep-10.2.33.tar.gz 3601162 RMD160 c75d3512b070c6cff186c8faf93c02a927c0f314 SHA1 1ae001f9fa07c11487ff9c0d9f7f393f119d58a5 SHA256 3df04892a46e21061b9138dd57879741abecddf18bef45c9a98391a8739d589a
+DIST molrep-10.2.34.tar.gz 3601494 RMD160 099dbd8a24204957cdf6432f55de392a5951f667 SHA1 ee089279324e3eeb21044a7e61c4850650c659a8 SHA256 44aae53a61b70bb5c780a0a1ffeff25cc5b1e73387b1fbff9ef88646e2fd78e7
 EBUILD molrep-10.2.27.ebuild 1160 RMD160 b1f07fbe73c3b00b494fc18e1b9a267e2c575a3d SHA1 4c134783e6212b7d36a90d8f8237b71bc54ee31e SHA256 81e4901a4e5fb86e1af154de28eac6be0c4c142b4d145a9e4c054ac2b342e15b
 EBUILD molrep-10.2.32.ebuild 1160 RMD160 760335990f17b01524937e009f6841c452cce60b SHA1 fbcb65b2d613ce8e6e2b3e224155ef34c8e938a9 SHA256 d064d9b69c369a810330bad8c1e549649d0c35799082f3f14f2ec93a45389d4a
 EBUILD molrep-10.2.33.ebuild 1160 RMD160 760335990f17b01524937e009f6841c452cce60b SHA1 fbcb65b2d613ce8e6e2b3e224155ef34c8e938a9 SHA256 d064d9b69c369a810330bad8c1e549649d0c35799082f3f14f2ec93a45389d4a
-MISC ChangeLog 906 RMD160 af014fc3f74207f9a300ee38ab04f4460b20e4f9 SHA1 b41c11693f389c22a3f45baf87ce577cceac842a SHA256 100b2461cebffec629cf7e576dfebe3834e09273baf90e3eb2c1a7a1354026a8
+EBUILD molrep-10.2.34.ebuild 1160 RMD160 760335990f17b01524937e009f6841c452cce60b SHA1 fbcb65b2d613ce8e6e2b3e224155ef34c8e938a9 SHA256 d064d9b69c369a810330bad8c1e549649d0c35799082f3f14f2ec93a45389d4a
+MISC ChangeLog 1072 RMD160 9fb300247187f1548ad6030710393b8adaa868ba SHA1 f77ff1e63c800af725d1fb3bf45b77e3332baee5 SHA256 59997de176ea3121cf1efdcc4a4824ae7e58f593350837711ac7c64a57517ef3
 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-chemistry/molrep/files/10.2.34-respect-FLAGS.patch b/sci-chemistry/molrep/files/10.2.34-respect-FLAGS.patch
new file mode 100644
index 000000000..d81ec793b
--- /dev/null
+++ b/sci-chemistry/molrep/files/10.2.34-respect-FLAGS.patch
@@ -0,0 +1,61 @@
+--- src/makefile	2009-02-27 16:51:46.492890717 +0100
++++ src/makefile.new	2009-02-27 16:52:18.295619642 +0100
+@@ -5,8 +5,8 @@
+ 
+ BIN = $(MOLREP)/bin
+ 
+-OBJS =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym.o molrep_unix.o
+-OBJSL =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym.o molrep_unix.o
++OBJS =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym_ccp4.o molrep_unix_ccp4.o
++OBJSL =  main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym_ccp4.o molrep_unix_ccp4.o
+ 
+ 
+ all: molrep
+@@ -19,31 +19,31 @@
+ # -----------------------------
+ 
+ molrep.o: molrep.f 
+-	$(MR_FORT) -c molrep.f 
++	$(MR_FORT) $(FFLAGS) -c molrep.f
+ molrep1.o: molrep1.f 
+-	$(MR_FORT) -c molrep1.f 
++	$(MR_FORT) $(FFLAGS) -c molrep1.f
+ molrep2.o: molrep2.f 
+-	$(MR_FORT) -c molrep2.f 
++	$(MR_FORT) $(FFLAGS) -c molrep2.f
+ molrep3.o: molrep3.f 
+-	$(MR_FORT) -c molrep3.f 
++	$(MR_FORT) $(FFLAGS) -c molrep3.f
+ molrep_prog.o: molrep_prog.f 
+-	$(MR_FORT) -c molrep_prog.f 
++	$(MR_FORT) $(FFLAGS) -c molrep_prog.f
+ molrep_prog1.o: molrep_prog1.f 
+-	$(MR_FORT) -c molrep_prog1.f 
++	$(MR_FORT) $(FFLAGS) -c molrep_prog1.f
+ molrep_prog2.o: molrep_prog2.f 
+-	$(MR_FORT) -c molrep_prog2.f 
++	$(MR_FORT) $(FFLAGS) -c molrep_prog2.f
+ molrep_subr.o: molrep_subr.f  
+-	$(MR_FORT) -c molrep_subr.f 
+-molrep_sym.o: molrep_sym.f  
+-	$(MR_FORT) -c molrep_sym.f 
++	$(MR_FORT) $(FFLAGS) -c molrep_subr.f
++molrep_sym_ccp4.o: molrep_sym.f  
++	$(MR_FORT) $(FFLAGS) -c molrep_sym_ccp4.f 
+ main_molrep_mtz.o: main_molrep_mtz.f molrep_version.fh molrep_keywords.fh 
+-	$(MR_FORT) -c main_molrep_mtz.f 
+-molrep_unix.o: molrep_unix.f 
+-	$(MR_FORT) -c molrep_unix.f 
++	$(MR_FORT) $(FFLAGS) -c main_molrep_mtz.f 
++molrep_unix_ccp4.o: molrep_unix.f 
++	$(MR_FORT) $(FFLAGS) -c molrep_unix_ccp4.f 
+ molrep_dummy.o: molrep_dummy.f 
+-	$(MR_FORT) -c molrep_dummy.f 
++	$(MR_FORT) $(FFLAGS) -c molrep_dummy.f 
+ 
+ molrep: $(OBJS)
+-	$(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
++	$(MR_FORT) $(FFLAGS) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY)
+ 
+ # --------------------------------
+
diff --git a/sci-chemistry/molrep/molrep-10.2.34.ebuild b/sci-chemistry/molrep/molrep-10.2.34.ebuild
new file mode 100644
index 000000000..09be4f2a0
--- /dev/null
+++ b/sci-chemistry/molrep/molrep-10.2.34.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+inherit base multilib toolchain-funcs
+
+DESCRIPTION="molecular replacement program"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html"
+SRC_URI="http://dev.gentooexperimental.org/~jlec/science-dist/${P}.tar.gz"
+
+LICENSE="ccp4"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE=""
+RDEPEND=">=sci-libs/ccp4-libs-6.1.1
+	virtual/lapack"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${PN}"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-respect-FLAGS.patch
+	)
+
+src_compile() {
+	cd "${S}"/src
+	emake \
+		MR_FORT=$(tc-getFC) \
+		FFLAGS="${FFLAGS}" \
+		LDFLAGS="${LDFLAGS}" \
+		MR_LIBRARY="-L/usr/$(get_libdir) -lccp4f -lccp4c -lmmdb -lccif -llapack -lstdc++ -lm" \
+	|| die
+}
+
+src_test() {
+	ewarn "Can take a long, long time ..."
+	ewarn "Go, take a coffee, lunch, go to sleep and have breakfast ..."
+	cd molrep_check && \
+		sed 's:\.\.:\.:g' -i em.bat && \
+		mkdir out && \
+		mkdir scr && \
+		MR_TEST="${S}/bin" bash em.bat && \
+		MR_TEST="${S}/bin" bash mr.bat || \
+		die "test failed"
+}
+
+src_install() {
+	dobin bin/${PN} || die
+
+	dodoc readme doc/${PN}.rtf || die
+}
diff --git a/sci-chemistry/pointless/ChangeLog b/sci-chemistry/pointless/ChangeLog
index 9521e075c..5b4e017d2 100644
--- a/sci-chemistry/pointless/ChangeLog
+++ b/sci-chemistry/pointless/ChangeLog
@@ -2,6 +2,17 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*pointless-1.3.12 (08 Oct 2009)
+
+  08 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/1.3.12-gcc4.4.patch, -pointless-1.3.9.ebuild,
+  +pointless-1.3.12.ebuild, -pointless-1.3.14.ebuild,
+  -files/1.3.13-gcc4.4.patch, -pointless-1.3.13.ebuild,
+  pointless-1.3.15.ebuild, -files/1.3.14-gcc4.4.patch,
+  -pointless-1.3.10.ebuild:
+  removed old versions
+  mirrored the 1.3.15 source on gentooexperimental
+
 *pointless-1.3.15 (08 Sep 2009)
 
   08 Sep 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/pointless/Manifest b/sci-chemistry/pointless/Manifest
index ea7aa925f..07201f9d6 100644
--- a/sci-chemistry/pointless/Manifest
+++ b/sci-chemistry/pointless/Manifest
@@ -1,15 +1,8 @@
-AUX 1.3.13-gcc4.4.patch 274 RMD160 142a4073fcd2afb6ebe9ea666a5ef2026abe5015 SHA1 896bc4fef788e3c23022f937507e888e45b04bae SHA256 54256e3ac934da2429b08fb009f51495c6ead14ed2bc5cb58ef30f13cc67bdc9
-AUX 1.3.14-gcc4.4.patch 274 RMD160 142a4073fcd2afb6ebe9ea666a5ef2026abe5015 SHA1 896bc4fef788e3c23022f937507e888e45b04bae SHA256 54256e3ac934da2429b08fb009f51495c6ead14ed2bc5cb58ef30f13cc67bdc9
+AUX 1.3.12-gcc4.4.patch 274 RMD160 142a4073fcd2afb6ebe9ea666a5ef2026abe5015 SHA1 896bc4fef788e3c23022f937507e888e45b04bae SHA256 54256e3ac934da2429b08fb009f51495c6ead14ed2bc5cb58ef30f13cc67bdc9
 AUX 1.3.15-gcc4.4.patch 274 RMD160 142a4073fcd2afb6ebe9ea666a5ef2026abe5015 SHA1 896bc4fef788e3c23022f937507e888e45b04bae SHA256 54256e3ac934da2429b08fb009f51495c6ead14ed2bc5cb58ef30f13cc67bdc9
-DIST pointless-1.3.10.tar.gz 298000 RMD160 f1b488f536a82fcd2636b25a525adc56309c8598 SHA1 82355e2b887fd48ef203f6c8573e6a65cf7f04d1 SHA256 1125053ea1c5fe7208f61364bc7594531e159f05ffa79b0bf1545831556a30b6
-DIST pointless-1.3.13.tar.gz 299153 RMD160 25cef7d043d340bf80847bbfacd301e4ed4a04cf SHA1 6615d7154b2a21c6c4a6a99b965194544864dc2c SHA256 9367825d7b4e495f86481ee7ad9a1835a5c3aefd35d7500bf2d0950cc5209cf6
-DIST pointless-1.3.14.tar.gz 299533 RMD160 9a6fe839de75817fffe4caeac648f4deecc3a1b9 SHA1 1abc6db23909c0c347158687c34c11895148e70f SHA256 f78e816f9ad1caeaa799a01d5c64bced21cec60d52021a29678e69af89d40436
+DIST pointless-1.3.12.tar.gz 298024 RMD160 84ebf9e2fb87a175b3220e66da4e5829e519b3ec SHA1 6a9fced0be22afe2a4ed02a6f98edaf8ebe41cf2 SHA256 94d1f01d956c28b3378e9e894ff4b201c4391ac19f61b19bb61b6e93d8930a59
 DIST pointless-1.3.15.tar.gz 299592 RMD160 c81e71a0dfad52828f1a57f625127115a574667a SHA1 b86831406fb3a8ed5930612b9859d3c40777e49c SHA256 335b0e66be2356b2ab0db8bda65a4f990932c82322d158f84230fe8a54aa4975
-DIST pointless-1.3.9.tar.gz 297655 RMD160 dc710ea3cef779bd15d0f4cf03e479de148b3b5e SHA1 80c39791812a0c2534d9dbbd3d28be6ff9539590 SHA256 deb7ad5bae99bae7a532e8626228a45222a9e5ba68838c05062ccc7e4de79f27
-EBUILD pointless-1.3.10.ebuild 1381 RMD160 a49fdd7eabbb5c754270414bccd9abf49daf82f2 SHA1 da216e968ed39f04d21537b814082d3247e0740f SHA256 c4b2d1127e894a1b2757a80e6fed24dad2a98342cf18e4335e9425f2c2deb2d9
-EBUILD pointless-1.3.13.ebuild 1439 RMD160 c2e3e52abf6f4cffac60405f44a7e8351e5d583d SHA1 21c19882f01914004344883fc75cc39960b04fc9 SHA256 d64d47b73643e7fe75a2c50d80a58b4d99cdcf52b770b96fa0d6678faaab2a13
-EBUILD pointless-1.3.14.ebuild 1439 RMD160 c2e3e52abf6f4cffac60405f44a7e8351e5d583d SHA1 21c19882f01914004344883fc75cc39960b04fc9 SHA256 d64d47b73643e7fe75a2c50d80a58b4d99cdcf52b770b96fa0d6678faaab2a13
-EBUILD pointless-1.3.15.ebuild 1439 RMD160 c2e3e52abf6f4cffac60405f44a7e8351e5d583d SHA1 21c19882f01914004344883fc75cc39960b04fc9 SHA256 d64d47b73643e7fe75a2c50d80a58b4d99cdcf52b770b96fa0d6678faaab2a13
-EBUILD pointless-1.3.9.ebuild 1381 RMD160 a49fdd7eabbb5c754270414bccd9abf49daf82f2 SHA1 da216e968ed39f04d21537b814082d3247e0740f SHA256 c4b2d1127e894a1b2757a80e6fed24dad2a98342cf18e4335e9425f2c2deb2d9
-MISC ChangeLog 1124 RMD160 bb1ff6d2a6d658996b069225c76aff76f8aba630 SHA1 2603c61d9815b20ab1fcc4e392b4cb14defa108d SHA256 1305a0f70a6fe929875fa969c73fdc284f9c1c448941729e2328649a0e7fe8d7
+EBUILD pointless-1.3.12.ebuild 1439 RMD160 c2e3e52abf6f4cffac60405f44a7e8351e5d583d SHA1 21c19882f01914004344883fc75cc39960b04fc9 SHA256 d64d47b73643e7fe75a2c50d80a58b4d99cdcf52b770b96fa0d6678faaab2a13
+EBUILD pointless-1.3.15.ebuild 1512 RMD160 7ad60272615db3263535ad1441f8ca54a684ac8b SHA1 07dcae15d271010e26c8d5be6f27544bbf372d06 SHA256 8fd8579bd8f45d3e719bee71c889a52b14a572b04ee419070b8d759dc65d0b15
+MISC ChangeLog 1537 RMD160 3e89bdabbbfe1a62c6a4ac9ee70dd399e1e9bb77 SHA1 75b32c12e7a12a1a907a890efca1342ec64bdd70 SHA256 6eddbdea9c8c8470c9e2aa17ecab1e097e3856f3f711cc58c8f537a085b2ce02
 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-chemistry/pointless/files/1.3.13-gcc4.4.patch b/sci-chemistry/pointless/files/1.3.12-gcc4.4.patch
index 153fe8829..153fe8829 100644
--- a/sci-chemistry/pointless/files/1.3.13-gcc4.4.patch
+++ b/sci-chemistry/pointless/files/1.3.12-gcc4.4.patch
diff --git a/sci-chemistry/pointless/files/1.3.14-gcc4.4.patch b/sci-chemistry/pointless/files/1.3.14-gcc4.4.patch
deleted file mode 100644
index 153fe8829..000000000
--- a/sci-chemistry/pointless/files/1.3.14-gcc4.4.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- Errors.cpp	2009-07-28 11:24:49.000000000 +0200
-+++ Errors.cpp.new	2009-08-03 21:32:12.000000000 +0200
-@@ -2,6 +2,7 @@
- //(c) 2000-2005 Cambridge University Technical Services Ltd
- //All rights reserved
- #include "Errors.hh"
-+#include <cstdio>
- 
- namespace phaser_io {
- 
diff --git a/sci-chemistry/pointless/pointless-1.3.10.ebuild b/sci-chemistry/pointless/pointless-1.3.10.ebuild
deleted file mode 100644
index f79da0359..000000000
--- a/sci-chemistry/pointless/pointless-1.3.10.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit toolchain-funcs multilib
-
-DESCRIPTION="Scores crystallographic Laue and space groups"
-HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html"
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="sci-chemistry/ccp4
-	>=sci-libs/ccp4-libs-6.1.1-r5
-	sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-S=${WORKDIR}
-
-src_compile() {
-	# Fails to link against my libcctbx
-	# Tried stealing autotools from ccp4 but that breaks differently with a weird boost error.
-	emake  \
-		-f Makefile.make \
-		CC=$(tc-getCC) \
-		CXX=$(tc-getCXX) \
-		CFLAGS="${CFLAGS}" \
-		CXXFLAGS="${CXXFLAGS}" \
-		LFLAGS="${LDFLAGS}" \
-		CLIB="/usr/$(get_libdir)" \
-		CCTBX_sources=/usr/$(get_libdir)/cctbx/cctbx_sources \
-		CCTBX_VERSION=2009 \
-		ICCP4=-I/usr/include/ccp4 \
-		ICLPR="-I/usr/include -I/usr/$(get_libdir)/cctbx/cctbx_sources -I/usr/$(get_libdir)/cctbx/cctbx_build/include" \
-		LTBX="-L/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \
-		|| die
-#		LCCP4=" $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -L/usr/$(get_libdir) -lgfortran -lgfortranbegin -lccp4c -lccp4f -lm" \
-#		LCCP4="-L/usr/$(get_libdir) -lccp4c -lccp4f -lm" \
-}
-
-src_install() {
-	dobin pointless othercell || die
-}
diff --git a/sci-chemistry/pointless/pointless-1.3.13.ebuild b/sci-chemistry/pointless/pointless-1.3.12.ebuild
index adcdead68..adcdead68 100644
--- a/sci-chemistry/pointless/pointless-1.3.13.ebuild
+++ b/sci-chemistry/pointless/pointless-1.3.12.ebuild
diff --git a/sci-chemistry/pointless/pointless-1.3.14.ebuild b/sci-chemistry/pointless/pointless-1.3.14.ebuild
deleted file mode 100644
index adcdead68..000000000
--- a/sci-chemistry/pointless/pointless-1.3.14.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit base toolchain-funcs multilib
-
-DESCRIPTION="Scores crystallographic Laue and space groups"
-HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html"
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="sci-chemistry/ccp4-apps
-	>=sci-libs/ccp4-libs-6.1.1-r5
-	sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-S=${WORKDIR}
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-gcc4.4.patch
-	)
-
-src_compile() {
-	# Fails to link against my libcctbx
-	# Tried stealing autotools from ccp4 but that breaks differently with a weird boost error.
-	emake  \
-		-f Makefile.make \
-		CC=$(tc-getCC) \
-		CXX=$(tc-getCXX) \
-		CFLAGS="${CFLAGS}" \
-		CXXFLAGS="${CXXFLAGS}" \
-		LFLAGS="${LDFLAGS}" \
-		CLIB="/usr/$(get_libdir)" \
-		CCTBX_sources=/usr/$(get_libdir)/cctbx/cctbx_sources \
-		CCTBX_VERSION=2009 \
-		ICCP4=-I/usr/include/ccp4 \
-		ICLPR="-I/usr/include -I/usr/$(get_libdir)/cctbx/cctbx_sources -I/usr/$(get_libdir)/cctbx/cctbx_build/include" \
-		LTBX="-L/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \
-		|| die
-#		LCCP4=" $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -L/usr/$(get_libdir) -lgfortran -lgfortranbegin -lccp4c -lccp4f -lm" \
-#		LCCP4="-L/usr/$(get_libdir) -lccp4c -lccp4f -lm" \
-}
-
-src_install() {
-	dobin pointless othercell || die
-}
diff --git a/sci-chemistry/pointless/pointless-1.3.15.ebuild b/sci-chemistry/pointless/pointless-1.3.15.ebuild
index adcdead68..9430800a9 100644
--- a/sci-chemistry/pointless/pointless-1.3.15.ebuild
+++ b/sci-chemistry/pointless/pointless-1.3.15.ebuild
@@ -6,7 +6,8 @@ inherit base toolchain-funcs multilib
 
 DESCRIPTION="Scores crystallographic Laue and space groups"
 HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html"
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
+#SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
+SRC_URI="http://dev.gentooexperimental.org/~jlec/distfiles/${P}.tar.gz"
 
 SLOT="0"
 LICENSE="ccp4"
diff --git a/sci-chemistry/pointless/pointless-1.3.9.ebuild b/sci-chemistry/pointless/pointless-1.3.9.ebuild
deleted file mode 100644
index f79da0359..000000000
--- a/sci-chemistry/pointless/pointless-1.3.9.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit toolchain-funcs multilib
-
-DESCRIPTION="Scores crystallographic Laue and space groups"
-HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html"
-SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="sci-chemistry/ccp4
-	>=sci-libs/ccp4-libs-6.1.1-r5
-	sci-libs/cctbx"
-DEPEND="${RDEPEND}"
-
-S=${WORKDIR}
-
-src_compile() {
-	# Fails to link against my libcctbx
-	# Tried stealing autotools from ccp4 but that breaks differently with a weird boost error.
-	emake  \
-		-f Makefile.make \
-		CC=$(tc-getCC) \
-		CXX=$(tc-getCXX) \
-		CFLAGS="${CFLAGS}" \
-		CXXFLAGS="${CXXFLAGS}" \
-		LFLAGS="${LDFLAGS}" \
-		CLIB="/usr/$(get_libdir)" \
-		CCTBX_sources=/usr/$(get_libdir)/cctbx/cctbx_sources \
-		CCTBX_VERSION=2009 \
-		ICCP4=-I/usr/include/ccp4 \
-		ICLPR="-I/usr/include -I/usr/$(get_libdir)/cctbx/cctbx_sources -I/usr/$(get_libdir)/cctbx/cctbx_build/include" \
-		LTBX="-L/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \
-		|| die
-#		LCCP4=" $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -L/usr/$(get_libdir) -lgfortran -lgfortranbegin -lccp4c -lccp4f -lm" \
-#		LCCP4="-L/usr/$(get_libdir) -lccp4c -lccp4f -lm" \
-}
-
-src_install() {
-	dobin pointless othercell || die
-}
diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index 079c53a25..bad05d05b 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*refmac-5.5.0105 (05 Oct 2009)
+
+  05 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  -refmac-5.5.0104.ebuild, +refmac-5.5.0105.ebuild:
+  version bump
+  5.5.104 segf but 5.5.105 fixes it
+
 *refmac-5.5.0102 (07 Jul 2009)
 
   07 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
index 02afcc277..23161b833 100644
--- a/sci-chemistry/refmac/Manifest
+++ b/sci-chemistry/refmac/Manifest
@@ -8,10 +8,10 @@ AUX test.log.patch 1146 RMD160 0ea6293e8ecde3b9ae12658a523e3c30a5c9f01b SHA1 d02
 AUX twin.inp 91 RMD160 0848ddf8ebdb6e0dd327f9d01d89f86007ac1859 SHA1 bdef4076010499cae0d0c886138e2230b835481a SHA256 172706f6ef1b7a85636a176d18e73611406f29ca8d84f1d82a6120daa8f956e6
 DIST refmac5.6_source_v5.6.0041.tar.gz 1487802 RMD160 575b0152c2c8c941f46acd8bf30ebf2ce7bf1f23 SHA1 6e1b68159597167b5167966ebf80a68064bcb90b SHA256 e8074bb2e86d9b9af698939acce6d81ea5a2ae7bb895585574e4b77787d39e8e
 DIST refmac_5.5.0102.tar.gz 1298285 RMD160 0a33e10ad498f9d516aa174ceddf8f860ec1711f SHA1 b6291eb524b419434cd851d8b3b6e9ef6845695f SHA256 435614b4aa946fa4e982237d76f814ac6459e5de7db003009563b8d6a2e3aa9f
-DIST refmac_5.5.0104.tar.gz 1298444 RMD160 b4c679194ed8de2041d991cf727df6214cb46c52 SHA1 e77134088683641a3e4c7997e3015040a72f8fbd SHA256 87e621722d69081daea334a8a84087830588c99d97e6e76b495f8bfb80d0da2c
+DIST refmac_5.5.0105.tar.gz 1326340 RMD160 648bca2961ec45a944b5e8c329abdce144157056 SHA1 3e653a1d9b16e333bb836e534bd4cfb3f7c67606 SHA256 9dc238ac9f2fc62c5f1b108e52a5fc0c9b3e847e73c4ca738e8297dd9660f195
 DIST test-framework.tar.gz 130939944 RMD160 ab9dbb0ad1b86dbedf3633742b252c2cc8aa4541 SHA1 2d5f9857fd2cfcd40e79e4ab48f3cd7d2ced1117 SHA256 8b56ade3423bc4c04495241b972d7591a980b32bf09d3c296db5fdd2f5db5229
 EBUILD refmac-5.5.0102.ebuild 1569 RMD160 a8bb80cb3cfaef17e83fcd23a348d145783c7021 SHA1 847ea6af6c6144fa23112d60c9bb2ece077dd3e7 SHA256 5307b738af874fb6f041b542ab1b505ef706fff0b6c405b67f9a99f7874bf230
-EBUILD refmac-5.5.0104.ebuild 1569 RMD160 a8bb80cb3cfaef17e83fcd23a348d145783c7021 SHA1 847ea6af6c6144fa23112d60c9bb2ece077dd3e7 SHA256 5307b738af874fb6f041b542ab1b505ef706fff0b6c405b67f9a99f7874bf230
+EBUILD refmac-5.5.0105.ebuild 1569 RMD160 a8bb80cb3cfaef17e83fcd23a348d145783c7021 SHA1 847ea6af6c6144fa23112d60c9bb2ece077dd3e7 SHA256 5307b738af874fb6f041b542ab1b505ef706fff0b6c405b67f9a99f7874bf230
 EBUILD refmac-5.6.0041.ebuild 1548 RMD160 79e91e75bdf73967395030a2149aa70bffda520c SHA1 dd9c28c314428b7a855a7e78e4dddf16610a939c SHA256 e996414bb81928536d97e17c580317b84d97beda5710441170c790dfcded771f
-MISC ChangeLog 6848 RMD160 f7fb30e4d11c5fc70407aeba5d1824ab594d88d4 SHA1 9cb68e238a46574a3a486e393690f90cea15cafc SHA256 4f5e7be5c0c746bdafe75ca2c242063cc7f5dcb23af076fc3b6db41656e2e09e
+MISC ChangeLog 7041 RMD160 3c695f769e623956dfed0333bf5c10f92dfac32b SHA1 002e00a4f6c62ee4b4a51cb98f99cb3b97edf70f SHA256 60537e21e62e4143b35053b3238c0ace5bf7e3f13314d0bd00f7527c5aeeb22e
 MISC metadata.xml 314 RMD160 d8922635160b6047732051715291e8553b513bba SHA1 b53fc6fb6cf908093794b876e729606c00351937 SHA256 50a519ddbcef4ad4f76175df36849a076d20adbb6340fdba292175b70c0d9719
diff --git a/sci-chemistry/refmac/refmac-5.5.0104.ebuild b/sci-chemistry/refmac/refmac-5.5.0105.ebuild
index 68b90a568..68b90a568 100644
--- a/sci-chemistry/refmac/refmac-5.5.0104.ebuild
+++ b/sci-chemistry/refmac/refmac-5.5.0105.ebuild
diff --git a/sci-libs/ipp/ChangeLog b/sci-libs/ipp/ChangeLog
deleted file mode 100644
index 944b0de29..000000000
--- a/sci-libs/ipp/ChangeLog
+++ /dev/null
@@ -1,14 +0,0 @@
-# ChangeLog for sci-libs/ipp
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  05 Sep 2009; Sébastien Fabbro <bicatali@gentoo.org> ipp-6.1.1.042.ebuild:
-  Fixed collision files with other Intel packages
-
-*ipp-6.1.1.042 (04 Sep 2009)
-
-  04 Sep 2009; Sébastien Fabbro <bicatali@gentoo.org>
-  +ipp-6.1.1.042.ebuild, +metadata.xml:
-  Version bump. Complete rewrite due to upstream packaging system and use
-  EAPI2 use flag depedencies
-
diff --git a/sci-libs/ipp/Manifest b/sci-libs/ipp/Manifest
deleted file mode 100644
index 704e263ec..000000000
--- a/sci-libs/ipp/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-EBUILD ipp-6.1.1.042.ebuild 971 RMD160 116e25e05ad389644217af359fd449256a729925 SHA1 80993d8690bc5fec2d4326bdb3c69a60dc7fa807 SHA256 bf3c3dac486b6e3df87a388bd9c16644f807d0044f843695ef82e6d5a89d4691
-MISC ChangeLog 470 RMD160 13f5045278f7f1b26507e7bed352988f90ca17b6 SHA1 f09f764f5fb0d75a8b3d653267740e9a3ed93e83 SHA256 ba2dee45fb2526cf03bec759748dcb28cc5e54ae61144487e819c14af02904a4
-MISC metadata.xml 395 RMD160 78b7bbaa8672c1e40aa66668551f7209a878771e SHA1 b38ff0f64254815e4b834d780a24a94fce4a5b56 SHA256 9dbb41576b70408e22cc1d2154666cd92af74d2ffed3801b29f3131da6edc370
diff --git a/sci-libs/ipp/ipp-6.1.1.042.ebuild b/sci-libs/ipp/ipp-6.1.1.042.ebuild
deleted file mode 100644
index 619bf7fbc..000000000
--- a/sci-libs/ipp/ipp-6.1.1.042.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ipp/ipp-6.0.1.071.ebuild,v 1.3 2009/01/31 12:07:10 bicatali Exp $
-
-EAPI=2
-inherit versionator
-RELEASE="$(get_version_component_range 1-2)"
-BUILD="$(get_version_component_range 3)"
-
-DESCRIPTION="Intel(R) Integrated Performance Primitive library for multimedia and data processing"
-HOMEPAGE="http://developer.intel.com/software/products/ipp/"
-SRC_URI=""
-
-KEYWORDS="~amd64 ~x86 ~ia64"
-SLOT="0"
-LICENSE="Intel-SDP"
-
-IUSE=""
-
-DEPEND=""
-RDEPEND="~dev-lang/icc-${PV}[ipp]"
-
-DESTINATION="${ROOT}opt/intel/Compiler/${RELEASE}/${BUILD}"
-
-src_install() {
-	cat > 36ipp <<-EOF
-		IPPROOT=${DESTINATION}/ipp/${IARCH/intel64/em64t}
-		LDPATH=\${IPPROOT}/sharedlib
-		LIB=\${IPPROOT}/lib
-		LIBRARY_PATH=\${IPPROOT}/lib
-		CPATH=\${IPPROOT}/include
-		NLSPATH=\${IPPROOT}/lib/locale/%l_%t/%N
-	EOF
-	doenvd 36ipp || die "doenvd 36ipp failed"
-}
diff --git a/sci-libs/ipp/metadata.xml b/sci-libs/ipp/metadata.xml
deleted file mode 100644
index 50b197d0e..000000000
--- a/sci-libs/ipp/metadata.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<longdescription lang="en">
-  Intel(R) Integrated Performance Primitives (Intel(R) IPP) is a
-  library of multi-core-ready, optimized software functions for
-  multimedia data processing, and communications applications.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-libs/lwpr/ChangeLog b/sci-libs/lwpr/ChangeLog
new file mode 100644
index 000000000..482884f03
--- /dev/null
+++ b/sci-libs/lwpr/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-libs/lwpr
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*lwpr-1.2.2 (09 Oct 2009)
+
+  09 Oct 2009; Sébastien Fabbro <bicatali@gentoo.org> +lwpr-1.2.2.ebuild,
+  +files/lwpr-1.2.2-setup.py.patch, +metadata.xml:
+  Initial import, ebuild based on bug #288032, initially submitted by
+  Florent Teichteil
+
diff --git a/sci-libs/lwpr/Manifest b/sci-libs/lwpr/Manifest
new file mode 100644
index 000000000..78c168892
--- /dev/null
+++ b/sci-libs/lwpr/Manifest
@@ -0,0 +1,5 @@
+AUX lwpr-1.2.2-setup.py.patch 517 RMD160 8c7e6bd38cff80d779b04d6147943bb960ba8c90 SHA1 591763838ec6359704e2d7ef18fb99131c345b48 SHA256 5b77f2f9a17b7759948c04c903ea12ada65cc3904f87d7ca0015edeb8d3260c2
+DIST lwpr-1.2.2.tar.gz 723920 RMD160 055f6c437e7e310b6f2ae77946443ee280c1334d SHA1 9e60bae960831f669701e106c276a3a4bea81b27 SHA256 a55d0ca8b66d4b62d07767ade714f545cf24d933b37d58613d8a79882afcf918
+EBUILD lwpr-1.2.2.ebuild 1687 RMD160 b9477ab966c593446092e578bf59cc9d3db5339b SHA1 f01e738c82f3247626195be1d88367012ec69cc3 SHA256 810a58edbc2e3cfbd11cd01e414938e7c5ba1add5632d1a103a24be6a0973a01
+MISC ChangeLog 358 RMD160 4b5b12ed86ac9fad77040e4e52424906b9b31cae SHA1 a1f62fb9c48ae2987272671fa4c9a82efc897d74 SHA256 7e122a6a311f4569158be0b1f3a93e038e80174208e4cc85f134005694c03d33
+MISC metadata.xml 731 RMD160 6398d7c8274b3b5086055ec1d934c88a73419127 SHA1 b1d63222eceb214ca91c49547ee3b59c6feadf15 SHA256 9c6fbc1c2093d759fd0d0564d6d037249f7902ba7451a1278099e05f43889596
diff --git a/sci-libs/lwpr/files/lwpr-1.2.2-setup.py.patch b/sci-libs/lwpr/files/lwpr-1.2.2-setup.py.patch
new file mode 100644
index 000000000..d560d164f
--- /dev/null
+++ b/sci-libs/lwpr/files/lwpr-1.2.2-setup.py.patch
@@ -0,0 +1,12 @@
+--- python/setup.py.orig	2009-10-09 21:53:17.000000000 +0100
++++ python/setup.py	2009-10-09 21:53:54.000000000 +0100
+@@ -5,7 +5,8 @@
+ module = Extension('lwpr',
+                     include_dirs = ['../include', 
+                        os.path.join(get_python_lib(),'numpy','core','include')],
+-                    libraries = ['lwpr'],    
++                    libraries = ['lwpr'],
++                   library_dirs=['../src/.libs'],
+                     sources = ['lwprmodule.c'])
+ 
+ setup (name = 'LWPR Module',
diff --git a/sci-libs/lwpr/lwpr-1.2.2.ebuild b/sci-libs/lwpr/lwpr-1.2.2.ebuild
new file mode 100644
index 000000000..12686852c
--- /dev/null
+++ b/sci-libs/lwpr/lwpr-1.2.2.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=2
+inherit eutils distutils
+
+DESCRIPTION="The Locally Weighted Projection Regression Library"
+HOMEPAGE="http://www.ipab.inf.ed.ac.uk/slmc/software/lwpr/"
+SRC_URI="http://www.ipab.inf.ed.ac.uk/slmc/software/${PN}/${P}.tar.gz"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc examples octave python"
+
+RDEPEND="octave? ( >=sci-mathematics/octave-3 )
+	python? ( dev-python/numpy )"
+DEPEND="${RDEPEND}
+	doc? ( app-doc/doxygen )"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-setup.py.patch
+}
+
+src_configure() {
+	econf $(use_with octave octave "$(octave-config -p PREFIX)")
+	# threads buggy
+	#	$(use_enable threads threads X) \
+}
+
+src_compile() {
+	emake || die "emake failed"
+	if use doc; then
+		doxygen Doxyfile || die "doxygen failed"
+	fi
+	if use python; then
+		cd  python
+		distutils_src_compile
+	fi
+}
+
+src_test() {
+	emake check || die "emake test failed"
+	if use python; then
+		cd python
+		LD_LIBRARY_PATH=../src/.libs \
+			PYTHONPATH=$(dir -d build/lib*) \
+			"${python}" test.py || die "python test failed"
+	fi
+}
+
+src_install() {
+	emake DESTDIR="${D}" \
+		mexflags="-DMATLAB -I../include -L./.libs -llwproctave" \
+		install || die "emake install failed"
+	dodoc README.TXT
+	if use doc; then
+		insinto /usr/share/doc/${PF}
+		doins doc/lwpr_doc.pdf
+		dohtml html/* || die
+	fi
+	if use examples ; then
+		insinto /usr/share/doc/${PF}/examples
+		doins example_c/cross.c example_cpp/cross.cc || die
+	fi
+	if use octave; then
+		insinto /usr/share/octave/packages/${P}
+		doins matlab/*.m || die
+	fi
+	if use python; then
+		cd python
+		distutils_src_install
+	fi
+}
diff --git a/sci-libs/lwpr/metadata.xml b/sci-libs/lwpr/metadata.xml
new file mode 100644
index 000000000..dbae229f0
--- /dev/null
+++ b/sci-libs/lwpr/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription>
+  Locally Weighted Projection Regression (LWPR) is a recent algorithm
+  that achieves nonlinear function approximation in high dimensional spaces
+  with redundant and irrelevant input dimensions. At its core, it uses
+  locally linear models, spanned by a small number of univariate regressions in
+  selected directions in input space. A locally weighted variant of
+  Partial Least Squares (PLS) is employed for doing the dimensionality
+  reduction. 
+</longdescription>
+<use>
+  <flag name='octave'>Add <pkg>sci-mathematics/octave</pkg> support</flag>
+</use>
+</pkgmetadata>
diff --git a/sci-mathematics/octave-forge-linear-algebra/ChangeLog b/sci-mathematics/octave-forge-linear-algebra/ChangeLog
index 793cd1459..1d234ed63 100644
--- a/sci-mathematics/octave-forge-linear-algebra/ChangeLog
+++ b/sci-mathematics/octave-forge-linear-algebra/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-mathematics/octave-forge-linear-algebra
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-linear-algebra-1.0.8 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  +octave-forge-linear-algebra-1.0.8.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-linear-algebra-1.0.4.ebuild,
   +octave-forge-linear-algebra-1.0.6.ebuild:
diff --git a/sci-mathematics/octave-forge-linear-algebra/Manifest b/sci-mathematics/octave-forge-linear-algebra/Manifest
index 0d1524b37..22efc355d 100644
--- a/sci-mathematics/octave-forge-linear-algebra/Manifest
+++ b/sci-mathematics/octave-forge-linear-algebra/Manifest
@@ -1,4 +1,6 @@
 DIST linear-algebra-1.0.6.tar.gz 85234 RMD160 65d5c9b590d4939e5f3f3ef091c837b8d476944f SHA1 8568da55da8910632218c8d4e675e6dd99ac4213 SHA256 605c0315b7e4fa77f8d5b00786bfdaa8738ec3662e062fbb2e556a3fb89d6b14
+DIST linear-algebra-1.0.8.tar.gz 85039 RMD160 e19b067efb39afa244a27c0442af650bf588f72b SHA1 08332368e1d7f933802320fae22c4ed7ab72a9b2 SHA256 8cae5b7e9079414bc3974004d07fa8885e8bd4ace7ff6070d11c90c34d3efcc0
 EBUILD octave-forge-linear-algebra-1.0.6.ebuild 523 RMD160 7afe772659c73c82d9c81757404ac79bd6dc3c5c SHA1 7c96437b77a3c29b50f89863202cc28031fad49d SHA256 ea5276dd50331c69152bee1fd8c382d5ca377ebcda8bcdf13580cae13f3d67f5
-MISC ChangeLog 919 RMD160 d6267d933be2cb9714dd25572efdacf52e60a31d SHA1 2704ff876585d8f5278f06628dd74183a9cac086 SHA256 bace46c28666fed95ea4b12bc171c307d038ff56fd88bf7d907458c52113358e
+EBUILD octave-forge-linear-algebra-1.0.8.ebuild 523 RMD160 347d2747d45870657c3057485a9bd3df419bc5a4 SHA1 d5504597e6bc9a86f2e3cc3fac5cc9fd31d5255f SHA256 79db3ecbfb50c063f91f0b1469a8059f721fef37b9f13c1a870fccd0a176b4c0
+MISC ChangeLog 1084 RMD160 8d09dc8337e688092fc405c6a40b63c0ebe1d9db SHA1 24914749e784085c5b1a5dbe5859ae7d86176a63 SHA256 8bfeee47b4eb7e1fb1c443aa340f15e754049c6b02976eba59a8315fd5691765
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-linear-algebra/octave-forge-linear-algebra-1.0.8.ebuild b/sci-mathematics/octave-forge-linear-algebra/octave-forge-linear-algebra-1.0.8.ebuild
new file mode 100644
index 000000000..c6c833924
--- /dev/null
+++ b/sci-mathematics/octave-forge-linear-algebra/octave-forge-linear-algebra-1.0.8.ebuild
@@ -0,0 +1,14 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
+
+inherit octave-forge
+
+DESCRIPTION="Additional linear algebra code, including general SVD and matrix functions."
+LICENSE="GPL-2"
+HOMEPAGE="http://octave.sourceforge.net/linear-algebra/index.html"
+SRC_URI="mirror://sourceforge/octave/${OCT_PKG}.tar.gz"
+SLOT="0"
+
+IUSE=""
+KEYWORDS="~amd64 ~x86"
diff --git a/sci-mathematics/octave-forge-nnet/ChangeLog b/sci-mathematics/octave-forge-nnet/ChangeLog
index 6927072d6..5e5f506dc 100644
--- a/sci-mathematics/octave-forge-nnet/ChangeLog
+++ b/sci-mathematics/octave-forge-nnet/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-mathematics/octave-forge-nnet
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-nnet-0.1.10 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-nnet-0.1.7.ebuild, +octave-forge-nnet-0.1.10.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-nnet-0.1.6.ebuild, +octave-forge-nnet-0.1.8.ebuild:
   Version bump.
diff --git a/sci-mathematics/octave-forge-nnet/Manifest b/sci-mathematics/octave-forge-nnet/Manifest
index 3a3ff2115..72cae03d4 100644
--- a/sci-mathematics/octave-forge-nnet/Manifest
+++ b/sci-mathematics/octave-forge-nnet/Manifest
@@ -1,6 +1,6 @@
-DIST nnet-0.1.7.tar.gz 193343 RMD160 88af1458faeca9f6ffa3aa290db74d6d73b1a3b4 SHA1 1a9c1ad5552d436c421930de570ced3cbc3b7758 SHA256 b81f813c916cbc8aeac0c874f1af8f6711111b2fd0d52c89cab662394caad2d4
+DIST nnet-0.1.10.tar.gz 218230 RMD160 df59efda0597d2eace9112c19ec036d3e907f65a SHA1 a3bdd6914268f70dbfc8d30d001014cb8783861a SHA256 83a1599af06a41e4a0539ca6b0e1d3cce11ff114dd8bfa9218c6d8b88625d15f
 DIST nnet-0.1.8.tar.gz 194947 RMD160 4ff8c10c70805627a979142c3e0b7b8e7eafa1ce SHA1 48cab72ea7582de5a9eaf50678462e326c877010 SHA256 14dfa3006e1f139923c251298eecb5c6e42b6a3a841478376a5b5ea2737f86a9
-EBUILD octave-forge-nnet-0.1.7.ebuild 480 RMD160 d47b497c7a935078d1cf66aa215f6c883fccd383 SHA1 ed04966d5329206be3537983dac0a3024a0ff8d8 SHA256 17b2ed774199dffd0ab98b169b346f78cadc1023775378842b6be080a6db2aa7
+EBUILD octave-forge-nnet-0.1.10.ebuild 480 RMD160 de6c9b24603bdf1db265548dee62eaf5e616371f SHA1 2724ec20f5715c730d124c2fd648dc60d21388ea SHA256 9ab96dbabbd1b2d660eaeec8f9ce13fe39d608b30ac2cbd3da7854f53c516fd7
 EBUILD octave-forge-nnet-0.1.8.ebuild 480 RMD160 d47b497c7a935078d1cf66aa215f6c883fccd383 SHA1 ed04966d5329206be3537983dac0a3024a0ff8d8 SHA256 17b2ed774199dffd0ab98b169b346f78cadc1023775378842b6be080a6db2aa7
-MISC ChangeLog 833 RMD160 9d0ab22a1ea01b6704f021ea79c0c1a9d1f8c491 SHA1 0101669720cb9ae76bd1986a1c22789d506f6959 SHA256 7ce02d613e94eb76213b3aa799d2f5ae8ef90e3873773c16d33bb8024fe5e402
+MISC ChangeLog 1013 RMD160 409d62970f2ec7cd6e9c0449da434398052389bf SHA1 db074a014143a70380aace9ef1ebc9252dff873f SHA256 bae4562352878e89a68e30bd5fd79a11c0c482a0b4fc11b13605f14ba647becb
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-nnet/octave-forge-nnet-0.1.7.ebuild b/sci-mathematics/octave-forge-nnet/octave-forge-nnet-0.1.10.ebuild
index 45e7e5109..c43405810 100644
--- a/sci-mathematics/octave-forge-nnet/octave-forge-nnet-0.1.7.ebuild
+++ b/sci-mathematics/octave-forge-nnet/octave-forge-nnet-0.1.10.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
diff --git a/sci-mathematics/octave-forge-octcdf/ChangeLog b/sci-mathematics/octave-forge-octcdf/ChangeLog
index 2926f8377..a6be230da 100644
--- a/sci-mathematics/octave-forge-octcdf/ChangeLog
+++ b/sci-mathematics/octave-forge-octcdf/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-mathematics/octave-forge-octcdf
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-octcdf-1.0.13 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-octcdf-1.0.9.ebuild, +octave-forge-octcdf-1.0.13.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-octcdf-1.0.8.ebuild, +octave-forge-octcdf-1.0.11.ebuild:
   Version bump.
diff --git a/sci-mathematics/octave-forge-octcdf/Manifest b/sci-mathematics/octave-forge-octcdf/Manifest
index c9ca0c35d..8b13002f6 100644
--- a/sci-mathematics/octave-forge-octcdf/Manifest
+++ b/sci-mathematics/octave-forge-octcdf/Manifest
@@ -1,6 +1,6 @@
 DIST octcdf-1.0.11.tar.gz 88683 RMD160 7a1a502fb8dd98af3358457669e83c9b8890142a SHA1 c2cd06683fffd40424dfccfed56ead6ffb901b46 SHA256 cc7717bd0cbd07b86d3175555da726f315c972dd43d68e69cb4cd196a296e948
-DIST octcdf-1.0.9.tar.gz 88299 RMD160 db00a30bd9cd90fd2829b9ac9823f09aeefa23ba SHA1 f5360dcba1b3919df84823d4742a861373963d44 SHA256 5a575ff9a796da51053936c2a3c64adecbd124d31b571b5bf092f0589b05b523
+DIST octcdf-1.0.13.tar.gz 89656 RMD160 570cd84e7ddc833ff6850134c5e661afc2bae55d SHA1 a74e9233f8309a7e39171aed552e8160eff04090 SHA256 8e4520f3935e6ab556ee5c93cc41b39f7f285dc359157f66860028d117a584d7
 EBUILD octave-forge-octcdf-1.0.11.ebuild 496 RMD160 20da5697e6533f125916e344d8ec40b3c3b796aa SHA1 2557dbc7c1a32677bf061bc96101ba7cdfde96bd SHA256 86e962e4a4f600017cd9cce30759f0a37c3a30d39794199c0aa6fd43847c6916
-EBUILD octave-forge-octcdf-1.0.9.ebuild 496 RMD160 20da5697e6533f125916e344d8ec40b3c3b796aa SHA1 2557dbc7c1a32677bf061bc96101ba7cdfde96bd SHA256 86e962e4a4f600017cd9cce30759f0a37c3a30d39794199c0aa6fd43847c6916
-MISC ChangeLog 850 RMD160 82e3e458fbfaf2303af8599221824c5f1eff35d5 SHA1 c7626e1b93bacb863b3ca43698ea70c13d109b5e SHA256 6d316645e91365be6514ed9d3daeaaf1100c895eb6075be366b749269f385651
+EBUILD octave-forge-octcdf-1.0.13.ebuild 496 RMD160 5d9f49e42eeb794fb40a88223278b4f1271edb98 SHA1 7097f6ed1fae245120c789170f426826c3834a7b SHA256 5a2dfb72f00a5a9bc09e140cae6ae90a0db436435433e04d0956e4c6e431ee14
+MISC ChangeLog 1036 RMD160 b4f2dcb3ab579fbfc914a3c5e307672c48448997 SHA1 6f08ea7b8790e5ef3ff929b5ecf15d7379af9aa6 SHA256 5404804d0c5eaa177184d63caabda20ea2dc25eaf4c6f1647106fc80dcd191fc
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-octcdf/octave-forge-octcdf-1.0.9.ebuild b/sci-mathematics/octave-forge-octcdf/octave-forge-octcdf-1.0.13.ebuild
index a3e0025a8..edfe1f884 100644
--- a/sci-mathematics/octave-forge-octcdf/octave-forge-octcdf-1.0.9.ebuild
+++ b/sci-mathematics/octave-forge-octcdf/octave-forge-octcdf-1.0.13.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
diff --git a/sci-mathematics/octave-forge-octgpr/ChangeLog b/sci-mathematics/octave-forge-octgpr/ChangeLog
index 39494fae3..34f01aa8a 100644
--- a/sci-mathematics/octave-forge-octgpr/ChangeLog
+++ b/sci-mathematics/octave-forge-octgpr/ChangeLog
@@ -1,7 +1,13 @@
-# ChangeLog for sci-mathematics/octave-forge-time
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# ChangeLog for sci-mathematics/octave-forge-octgpr
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-octgpr-1.1.5 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-octgpr-1.1.3.ebuild, +octave-forge-octgpr-1.1.5.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-octgpr-1.1.1.ebuild, +octave-forge-octgpr-1.1.4.ebuild:
   Version bump.
diff --git a/sci-mathematics/octave-forge-octgpr/Manifest b/sci-mathematics/octave-forge-octgpr/Manifest
index b59186b37..9447d049c 100644
--- a/sci-mathematics/octave-forge-octgpr/Manifest
+++ b/sci-mathematics/octave-forge-octgpr/Manifest
@@ -1,5 +1,5 @@
-DIST octgpr-1.1.3.tar.gz 71040 RMD160 5da82c1369ad147e2c0444869eb9497388ecf2e2 SHA1 a6bc24a0b64de6459a9dda540f34474299c8b730 SHA256 331f464ff8de2530ff9e7abcece3b6dca9900416bd9df57eaca592c434fff777
 DIST octgpr-1.1.4.tar.gz 71991 RMD160 30f67c5d3dc35700ebdd35fe3e861bde45d649fa SHA1 6fb12c7b85c81a75e7cdf5bfc9bd5fa41f276938 SHA256 79231d085612b4981894165f1a760e62bb1bead709bdccd50d40c4fc08974a3b
-EBUILD octave-forge-octgpr-1.1.3.ebuild 539 RMD160 dc6f99839d60514e2cdd45e7df7e0d79c1b08703 SHA1 76782737beb6f5f8f40024c787ffa99cf07db3ef SHA256 b14c437449c1f006bf81c02b2726aa6b4afd88adb87994e0f28b0ee9423c4b2b
+DIST octgpr-1.1.5.tar.gz 72121 RMD160 a2f00d22db3d0721a15c98c4dbd3f533f5709f99 SHA1 3777006e1634c6829a1b4a038ce5cc709168d421 SHA256 0972235bbf10784b1f807f5367235c79fe5e5b794ff06d24dee274f988606853
 EBUILD octave-forge-octgpr-1.1.4.ebuild 539 RMD160 dc6f99839d60514e2cdd45e7df7e0d79c1b08703 SHA1 76782737beb6f5f8f40024c787ffa99cf07db3ef SHA256 b14c437449c1f006bf81c02b2726aa6b4afd88adb87994e0f28b0ee9423c4b2b
-MISC ChangeLog 489 RMD160 077111d6d379c043a6785c28765d0e09973a2ec1 SHA1 3ae0ef1f4ad356b5a64b40d61db6604c46fd418b SHA256 af21b2454e1b2bf9efcb94059e031c13b651a067aacb0739e61a7732aee0be5a
+EBUILD octave-forge-octgpr-1.1.5.ebuild 539 RMD160 5cb62195b84d1a847c065d748f507f504b04d8c7 SHA1 bfc8ab7043b80ac7fd277d9ad33a9de98847ace9 SHA256 269f169497887c33491a704da23f812d08ad5c3c9bffb8a43ad9a59e618ed8be
+MISC ChangeLog 675 RMD160 a4b11b439fc1a136abd6147512f39e182cd105fe SHA1 29a319936bc01d726637b3c24f14b52e40709f85 SHA256 d574f5acc179c989fb998d0e1d22b288c2fb03858a5f6fb8b370f2d20d7b0b66
diff --git a/sci-mathematics/octave-forge-octgpr/octave-forge-octgpr-1.1.3.ebuild b/sci-mathematics/octave-forge-octgpr/octave-forge-octgpr-1.1.5.ebuild
index 9a777aed4..885f7b8d2 100644
--- a/sci-mathematics/octave-forge-octgpr/octave-forge-octgpr-1.1.3.ebuild
+++ b/sci-mathematics/octave-forge-octgpr/octave-forge-octgpr-1.1.5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
diff --git a/sci-mathematics/octave-forge-odebvp/ChangeLog b/sci-mathematics/octave-forge-odebvp/ChangeLog
index b89f11385..89bc9d709 100644
--- a/sci-mathematics/octave-forge-odebvp/ChangeLog
+++ b/sci-mathematics/octave-forge-odebvp/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-mathematics/octave-forge-odebvp
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-odebvp-1.0.6 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  +octave-forge-odebvp-1.0.6.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-odebvp-1.0.3.ebuild, +octave-forge-odebvp-1.0.5.ebuild:
   Version bump.
diff --git a/sci-mathematics/octave-forge-odebvp/Manifest b/sci-mathematics/octave-forge-odebvp/Manifest
index 06d592928..2252aaef1 100644
--- a/sci-mathematics/octave-forge-odebvp/Manifest
+++ b/sci-mathematics/octave-forge-odebvp/Manifest
@@ -1,4 +1,6 @@
 DIST odebvp-1.0.5.tar.gz 17536 RMD160 46a215e2a3a211a4f7dce694c6f3717bdd4ca692 SHA1 b4d53de50b3a3ae625d1b4a99854a8d75f75e824 SHA256 90aad420c2af1deb3bdd3a737f8c0f42123d945a26888c6ec6b8e67161a1d700
+DIST odebvp-1.0.6.tar.gz 17562 RMD160 f8542decb4d7e3b7852ceb806aa1310367de8c18 SHA1 c20253c62838c610c8da1b984554a5aa031262a1 SHA256 36f924e58d80b8f23852a1d4ef8486eba2975e6d20dd00bd4ce3307586eb3f67
 EBUILD octave-forge-odebvp-1.0.5.ebuild 528 RMD160 02664fc7f464e1a415651e31bfeb1ae2aba48ce3 SHA1 1677fbc746b58b428303cfb07bd65d480ecace18 SHA256 2841af220a779e3d17720ab0388a60357b25e6d8dd2b66774113d590afbea43a
-MISC ChangeLog 849 RMD160 65a117e3335a53c006c0bcdfb40ce240a4253938 SHA1 bc1d1b1f10dc6b4b74e7fd3e913e18285d7aa690 SHA256 440e7ccd1dd08920bdfdf610c623d960fdf00abb41e50806283ca25b9110f3eb
+EBUILD octave-forge-odebvp-1.0.6.ebuild 528 RMD160 528171e6f7e2bc2f66d05777fb72f7bdd30eda5e SHA1 fd593468ac77754eb6fb1e08a6b8ef96f72599ce SHA256 61fd86e21929a09829166c9ff49c586f667348bb82696a4bccc1bb770c94a459
+MISC ChangeLog 998 RMD160 3faf614f287d21de0ceed0780087bd7b547a7959 SHA1 8fd67fcf4502368a78163e7e91af6855ee3243c9 SHA256 fdaf87960ccfcc4092425db0f4202fde889f55de3afe7bbe1176bcf3c9b78cc1
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-odebvp/octave-forge-odebvp-1.0.6.ebuild b/sci-mathematics/octave-forge-odebvp/octave-forge-odebvp-1.0.6.ebuild
new file mode 100644
index 000000000..c8905d2dc
--- /dev/null
+++ b/sci-mathematics/octave-forge-odebvp/octave-forge-odebvp-1.0.6.ebuild
@@ -0,0 +1,14 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
+
+inherit octave-forge
+
+DESCRIPTION="Approximate the solution of boundary-value problem by the linear finite-diffence method."
+LICENSE="GPL-2"
+HOMEPAGE="http://octave.sourceforge.net/odebvp/index.html"
+SRC_URI="mirror://sourceforge/octave/${OCT_PKG}.tar.gz"
+SLOT="0"
+
+IUSE=""
+KEYWORDS="~amd64 ~x86"
diff --git a/sci-mathematics/octave-forge-odepkg/ChangeLog b/sci-mathematics/octave-forge-odepkg/ChangeLog
index 85d5aa0e4..8435f33ac 100644
--- a/sci-mathematics/octave-forge-odepkg/ChangeLog
+++ b/sci-mathematics/octave-forge-odepkg/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-mathematics/octave-forge-odepkg
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-odepkg-0.6.7 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-odepkg-0.6.0.ebuild, +octave-forge-odepkg-0.6.7.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-odepkg-0.4.1.ebuild, +octave-forge-odepkg-0.6.4.ebuild:
   Version bump.
diff --git a/sci-mathematics/octave-forge-odepkg/Manifest b/sci-mathematics/octave-forge-odepkg/Manifest
index 6b37f425b..0f516af5c 100644
--- a/sci-mathematics/octave-forge-odepkg/Manifest
+++ b/sci-mathematics/octave-forge-odepkg/Manifest
@@ -1,6 +1,6 @@
-DIST odepkg-0.6.0.tar.gz 782201 RMD160 7c84c290c0f091d0f4ddcdf9ab2ce4a6311b5dc9 SHA1 3ba961d40fee046ca135e765f72b536de335cb47 SHA256 936c0041b7c3f0fe0787b1df9a4a73caf823c3f13e40e5e0af551f9c4493ffc4
 DIST odepkg-0.6.4.tar.gz 786912 RMD160 28c901f0dacad3eb502170e4dd6712744735e601 SHA1 0796a69e123d44e05dbb633beac08447ede9eb60 SHA256 d2840d1ae6c58ca5b19bfd8c301ed06b92968a96767c9deb9613f1879d2eaee5
-EBUILD octave-forge-odepkg-0.6.0.ebuild 503 RMD160 15102a72a0ae461b05120382d1ddfa9cfb23b9c5 SHA1 7d95fa6b3a42a691192f536e6dca046dfd6e52b4 SHA256 073570455ea8007d549d0375a4585880baa8fafbec3962abbb10fa661f62a7ac
+DIST odepkg-0.6.7.tar.gz 786747 RMD160 fe85f5a64058ef67e5e65b5b89773685275b68ff SHA1 d050dce3a043bd74c5143c6602e8d67af6a5e22d SHA256 22643c29a278f04f519d8c6d6947a3cec34e2c0bbfab9e20e777cbaf4d779dce
 EBUILD octave-forge-odepkg-0.6.4.ebuild 503 RMD160 15102a72a0ae461b05120382d1ddfa9cfb23b9c5 SHA1 7d95fa6b3a42a691192f536e6dca046dfd6e52b4 SHA256 073570455ea8007d549d0375a4585880baa8fafbec3962abbb10fa661f62a7ac
-MISC ChangeLog 849 RMD160 bd7145e1d7fcfdc585c69be0b08a6cc04b01af79 SHA1 91e458e5a3e4e0721f15ae4c7b1b5809a4f594ee SHA256 3c19825099b227e8863ac4d4c7743230bad3cb9176a19964589b7f6c23797372
+EBUILD octave-forge-odepkg-0.6.7.ebuild 503 RMD160 6c498a3ed3d8a191b2b30f1e86fe4a126b0b7757 SHA1 80584eec648fa12678ac86ec5c6adb12b4c073db SHA256 cf052e166368bc3c2c52a8828eafe2ae84f04b3c6a3549d6a60073338561e276
+MISC ChangeLog 1033 RMD160 e349156af85d3b728d7e4ad5ae4e432c65e9a816 SHA1 cd6e66434819be11a394a8ae8273de07567e2983 SHA256 f716b331081933cd72b1275001b43561caee37685443bb08a79eb098ada3bae1
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-odepkg/octave-forge-odepkg-0.6.0.ebuild b/sci-mathematics/octave-forge-odepkg/octave-forge-odepkg-0.6.7.ebuild
index 385823c72..6a8366903 100644
--- a/sci-mathematics/octave-forge-odepkg/octave-forge-odepkg-0.6.0.ebuild
+++ b/sci-mathematics/octave-forge-odepkg/octave-forge-odepkg-0.6.7.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
diff --git a/sci-mathematics/octave-forge-optiminterp/ChangeLog b/sci-mathematics/octave-forge-optiminterp/ChangeLog
index 37ebeb537..e95a5de1a 100644
--- a/sci-mathematics/octave-forge-optiminterp/ChangeLog
+++ b/sci-mathematics/octave-forge-optiminterp/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-mathematics/octave-forge-optiminterp
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-optiminterp-0.3.2 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-optiminterp-0.2.7.ebuild,
+  +octave-forge-optiminterp-0.3.2.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-optiminterp-0.2.6.ebuild,
   +octave-forge-optiminterp-0.3.1.ebuild:
diff --git a/sci-mathematics/octave-forge-optiminterp/Manifest b/sci-mathematics/octave-forge-optiminterp/Manifest
index 98558d087..d24f4610e 100644
--- a/sci-mathematics/octave-forge-optiminterp/Manifest
+++ b/sci-mathematics/octave-forge-optiminterp/Manifest
@@ -1,6 +1,6 @@
-DIST optiminterp-0.2.7.tar.gz 66606 RMD160 fa2299f04304d3af258ae0c6d6488a23019eeb63 SHA1 58e70077d497489e48286f5dd7c3d8f6db124790 SHA256 1651c74f9ae215623fab9724de26628851fea827065b9e1b4acea2c8315cdd5b
 DIST optiminterp-0.3.1.tar.gz 67109 RMD160 a573f96d10c6d076759847c4521301baad03ed81 SHA1 ce9e23d857d150b5a07c5c35f8e309d41abfc442 SHA256 bd7db18a17f0368d76e9884d8a45d9b92ff4fa810bb409df6ea7cf38bef706d4
-EBUILD octave-forge-optiminterp-0.2.7.ebuild 489 RMD160 aa4ffbc891914160fc2ea38b5fb2f691a25e2e19 SHA1 72ab4dad08e2504d675892553e9c669aefa09565 SHA256 02634e2ad2db8b7c748d967f21c5cbfcff384d3196329bd02d738f9a85628401
+DIST optiminterp-0.3.2.tar.gz 67135 RMD160 ccf8119ab8c05bb072bf45f1ddf1fd1ddc281794 SHA1 2f59d8cf5acda824fb09823ef27a6a109db0b4ec SHA256 6f3ad34ffa85ca9423582557389b6fb1fe131b9c946ed7307061d38663a5d2fb
 EBUILD octave-forge-optiminterp-0.3.1.ebuild 489 RMD160 aa4ffbc891914160fc2ea38b5fb2f691a25e2e19 SHA1 72ab4dad08e2504d675892553e9c669aefa09565 SHA256 02634e2ad2db8b7c748d967f21c5cbfcff384d3196329bd02d738f9a85628401
-MISC ChangeLog 895 RMD160 a7af478cd79072bf6e495483bb26164a497f5c63 SHA1 34ad622ff1c464600584037883590ece24fa83e9 SHA256 21de6e86cddd66a1325f6ded8c97ed1e22130b139f674f473a2cc35ba4a0892f
+EBUILD octave-forge-optiminterp-0.3.2.ebuild 489 RMD160 7bbc41c837847ab95c6ae9b9d4231d28d3d0c378 SHA1 c8a68e6c25f772c726c3bf594848618be251e88a SHA256 4f3bd3186e4aaac00bacd0ad0da2f48c1468c20654b60e4d60374fd6da60659c
+MISC ChangeLog 1096 RMD160 3565eeeb6df4743a4a95b3380775180cee4f64eb SHA1 4956f62978032a1fb906ff4087f14fede00f1160 SHA256 04c77de8ed6707fa24ec97868b097d7355ab31d8394dc94b9791fbc12c8a4a14
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-optiminterp/octave-forge-optiminterp-0.2.7.ebuild b/sci-mathematics/octave-forge-optiminterp/octave-forge-optiminterp-0.3.2.ebuild
index 0586d9998..3b57e0a08 100644
--- a/sci-mathematics/octave-forge-optiminterp/octave-forge-optiminterp-0.2.7.ebuild
+++ b/sci-mathematics/octave-forge-optiminterp/octave-forge-optiminterp-0.3.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
diff --git a/sci-mathematics/octave-forge-outliers/ChangeLog b/sci-mathematics/octave-forge-outliers/ChangeLog
index 765623b0c..c5d67a824 100644
--- a/sci-mathematics/octave-forge-outliers/ChangeLog
+++ b/sci-mathematics/octave-forge-outliers/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-mathematics/octave-forge-outliers
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-outliers-0.13.9 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-outliers-0.13.7.ebuild,
+  +octave-forge-outliers-0.13.9.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-outliers-0.13.6.ebuild,
   +octave-forge-outliers-0.13.8.ebuild:
diff --git a/sci-mathematics/octave-forge-outliers/Manifest b/sci-mathematics/octave-forge-outliers/Manifest
index 0f0fc3c22..b95d558ac 100644
--- a/sci-mathematics/octave-forge-outliers/Manifest
+++ b/sci-mathematics/octave-forge-outliers/Manifest
@@ -1,6 +1,6 @@
-DIST outliers-0.13.7.tar.gz 34155 RMD160 d9ec29df37026b2ba188352407042268bf8c1a0e SHA1 a0c4490f33b254e1a839d6d70ddcaadad5af1b87 SHA256 b074e1426b6a225e8fd76c92ffe8b9b7c168ab0529f4fac2985700fc50a412a0
 DIST outliers-0.13.8.tar.gz 34440 RMD160 764be9515bb24cfcf3f06d13c547ae7b9a8ba1e5 SHA1 4aa2331da37263dccd66c98a7efe7ebefa90d0c6 SHA256 bde6fe6b45ffc29e0073a0b9bf6d50731ad01e5b0d1ee0480ede40c8d9b74b3a
-EBUILD octave-forge-outliers-0.13.7.ebuild 531 RMD160 2d049d23e18536082ed56effe23e1d928b111697 SHA1 5320f224e5b60bcbd041a8ad05fb05922bc24605 SHA256 fe5ae7d6f2e514118b5238ab24bb1bae54f5548db330aa419e39bc4e8eec5909
+DIST outliers-0.13.9.tar.gz 34369 RMD160 dcbac14d3a09b71828ee72d3de3598bfbfa52851 SHA1 3589598382fbddbb0771a54b90272be63bdd2e44 SHA256 075c69c4a1793c1fabc87fcc3ad69803faf9625c6d9c2dc8f9811969d0f68045
 EBUILD octave-forge-outliers-0.13.8.ebuild 531 RMD160 2d049d23e18536082ed56effe23e1d928b111697 SHA1 5320f224e5b60bcbd041a8ad05fb05922bc24605 SHA256 fe5ae7d6f2e514118b5238ab24bb1bae54f5548db330aa419e39bc4e8eec5909
-MISC ChangeLog 878 RMD160 db4cb23c82a7c1ca654b0753f3258307d98cf4e8 SHA1 0a695b43fa984ab296562868144e3080c4eded18 SHA256 e67d0a85955679f1eafa32db625901f88f12c6da5b908a78a3882cc62b706a11
+EBUILD octave-forge-outliers-0.13.9.ebuild 531 RMD160 578e82c0b456798aa5aa7a519223a644577bfa5e SHA1 35b3ef06133ec2faab729580792b9d1922658b44 SHA256 9acd9032d317be3a3b861737e47a94d4e08a77901d75858fa96aa5b8bd4cd641
+MISC ChangeLog 1073 RMD160 b994318da3c5f99563d6fd45000618e5cbef0e88 SHA1 4e344374882f33c5a6f27313dda9365d6c56839a SHA256 465ddd0cd93f267fb27331bf0df61b63391f23cec8782df7df143b1a977f5860
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-outliers/octave-forge-outliers-0.13.7.ebuild b/sci-mathematics/octave-forge-outliers/octave-forge-outliers-0.13.9.ebuild
index 698ecc563..6abe20cf9 100644
--- a/sci-mathematics/octave-forge-outliers/octave-forge-outliers-0.13.7.ebuild
+++ b/sci-mathematics/octave-forge-outliers/octave-forge-outliers-0.13.9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
diff --git a/sci-mathematics/octave-forge-parallel/ChangeLog b/sci-mathematics/octave-forge-parallel/ChangeLog
index e35d5ca22..badf61a65 100644
--- a/sci-mathematics/octave-forge-parallel/ChangeLog
+++ b/sci-mathematics/octave-forge-parallel/ChangeLog
@@ -1,7 +1,15 @@
 # ChangeLog for sci-mathematics/octave-forge-parallel
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-parallel-2.0.0 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-parallel-1.0.6.ebuild, +octave-forge-parallel-2.0.0.ebuild
+  +files/octave-forge-parallel-2.0.0-octave-3.2.patch
+  +files/octave-forge-parallel-2.0.0-description.patch:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-parallel-1.0.5.ebuild, +octave-forge-parallel-1.0.7.ebuild:
   Version bump.
diff --git a/sci-mathematics/octave-forge-parallel/Manifest b/sci-mathematics/octave-forge-parallel/Manifest
index 91b6a01c6..8a66fc42b 100644
--- a/sci-mathematics/octave-forge-parallel/Manifest
+++ b/sci-mathematics/octave-forge-parallel/Manifest
@@ -1,6 +1,8 @@
-DIST parallel-1.0.6.tar.gz 35471 RMD160 9786a6cb8e0389005503a4244fda2088edf2b6dd SHA1 57706906089cd24c854a5ee29bb0bd02b65eea69 SHA256 7a278c5f60af9de16e0211a9e6f7fa5848416b240c5aea840ed4da332d7e0504
+AUX octave-forge-parallel-2.0.0-description.patch 841 RMD160 38d77b97722a19cbc03169abf94f715b2cd9152c SHA1 e02a5b5c641b5ab64a69e97dfcbf8567ce4359f2 SHA256 31dd9f47b6e5dd89964f707bc57e436f2d0b5885bcb64cc76a90539960dc88ef
+AUX octave-forge-parallel-2.0.0-octave-3.2.patch 7070 RMD160 9f25612477a97ca1c78c81f19ec7cb629a7b27f3 SHA1 d57878c28817a1e8d93ffe1cbbbf0f76e0a73564 SHA256 c7d73305ec27ed9ca61fb9b328a720bf19838a726a8cf7fcc56ecbe24b0b26da
 DIST parallel-1.0.7.tar.gz 35684 RMD160 d30484a76c5aa676b4c0e5ee16233220c3eaea68 SHA1 df4c61e1fe6b64d220824469bc3ba126931d2337 SHA256 39aa3e5edbf1c332290ab3682c7c3ce126aae0d674ebc9201e70e1e40d867fcf
-EBUILD octave-forge-parallel-1.0.6.ebuild 491 RMD160 e8a28ed4e1137bdf81f71ecd344be7d3869d2381 SHA1 846a8a50641b4fa63636c2d9a000a9e87d51be72 SHA256 193d7fbbca6bebe0f0515970464f68697c8f7d7c62d52d57c633ff217211de56
+DIST parallel-2.0.0.tar.gz 60316 RMD160 10556901eae3cfd57622f55aae06d7bea1c853c6 SHA1 f0bfde75c677cf4dca1a1a1dfa6c1233bc7bcb68 SHA256 405ab438aa35866515044abfacf9cb31bd7729563bc831fabff50689f3c0a5ed
 EBUILD octave-forge-parallel-1.0.7.ebuild 491 RMD160 e8a28ed4e1137bdf81f71ecd344be7d3869d2381 SHA1 846a8a50641b4fa63636c2d9a000a9e87d51be72 SHA256 193d7fbbca6bebe0f0515970464f68697c8f7d7c62d52d57c633ff217211de56
-MISC ChangeLog 865 RMD160 42b8eefa1b75c78851c0ae956b5232eddbaa3215 SHA1 8430f0fce0b32f311da50e9936709d7d27b4c164 SHA256 7d4cbefd3ba61ec1738f8349a148d1334de7beffb675295149c8767de1b9ee73
+EBUILD octave-forge-parallel-2.0.0.ebuild 599 RMD160 44b0c9583a94ba1c47de4d75778b285fcd2c3050 SHA1 43a831434507f32be8e321c832e139c9ef4821df SHA256 73756af69a3bed7c1e0202d9efde522a86c30bd58d8d7e9bc81cbc3f1731e09a
+MISC ChangeLog 1164 RMD160 5840c6f98cc281419d6c71fe3f581d07838d1624 SHA1 7290fae94805e05067fffb7bb7502f30953233f1 SHA256 6513caefab5a094f5b3a33264c03eee1c5c5079ca7f4721d80804de5ca0dfcae
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-parallel/files/octave-forge-parallel-2.0.0-description.patch b/sci-mathematics/octave-forge-parallel/files/octave-forge-parallel-2.0.0-description.patch
new file mode 100644
index 000000000..7dd383b22
--- /dev/null
+++ b/sci-mathematics/octave-forge-parallel/files/octave-forge-parallel-2.0.0-description.patch
@@ -0,0 +1,14 @@
+diff -Naur parallel-2.0.0/DESCRIPTION parallel-2.0.0.new/DESCRIPTION
+--- parallel-2.0.0/DESCRIPTION	2009-05-08 09:17:57.000000000 -0400
++++ parallel-2.0.0.new/DESCRIPTION	2009-10-04 10:41:06.000000000 -0400
+@@ -4,9 +4,7 @@
+ Author: Hayato Fujiwara and Olaf Till <olaf.till@uni-jena.de>
+ Maintainer: Hayato Fujiwara and Olaf Till <olaf.till@uni-jena.de>
+ Title: Parallel Computing.
+-Description: Parallel execution package for cluster computers. For
+- parallel execution on a single machine see e.g. function parcellfun
+- (author: Jaroslav Hajek) in package general.
++Description: Parallel execution package for cluster computers. For parallel execution on a single machine see e.g. function parcellfun (author Jaroslav Hajek) in package general.
+ Depends: octave (>= 3.0.0)
+ Autoload: yes
+ License: GPL, see individual files for GPL version
diff --git a/sci-mathematics/octave-forge-parallel/files/octave-forge-parallel-2.0.0-octave-3.2.patch b/sci-mathematics/octave-forge-parallel/files/octave-forge-parallel-2.0.0-octave-3.2.patch
new file mode 100644
index 000000000..6bf3cba87
--- /dev/null
+++ b/sci-mathematics/octave-forge-parallel/files/octave-forge-parallel-2.0.0-octave-3.2.patch
@@ -0,0 +1,236 @@
+diff -Naur parallel-2.0.0/src/__bw_prcv__.cc parallel-2.0.0.new/src/__bw_prcv__.cc
+--- parallel-2.0.0/src/__bw_prcv__.cc	2009-05-08 09:17:57.000000000 -0400
++++ parallel-2.0.0.new/src/__bw_prcv__.cc	2009-10-04 07:25:32.000000000 -0400
+@@ -20,7 +20,7 @@
+ #include <octave/oct-stream.h>
+ #include <octave/oct-map.h>
+ 
+-DEFUN_DLD (__bw_prcv__, args, nargout, "prcv (pd)\n\
++DEFUN_DLD (__bw_prcv__, args, nargout, "__bw_prcv__ (pd)\n\
+ Reads one variable from pipe stream 'pd'.\n\
+ The variable must have been coded in Octaves binary format,\n\
+ including a header. This can be done by 'psend ()'.\n\
+@@ -29,8 +29,8 @@
+ call 'feof ()' afterwards. If EOF is met later in reading,\n\
+ it causes an error.\n\
+ Normally, a structure is returned with the variable under its name\n\
+-in a single field. With no output arguments, the variable is installed\n\
+-into memory.\n\
++in a single field. Originally, with no output arguments, the variable was\n\
++installed into memory, but this has been disabled.\n\
+ \n\
+ This function may change and is internal to the parallel package.\n")
+ {
+@@ -38,10 +38,10 @@
+ 	Octave_map retstruct;
+ 
+ 	if (args.length () != 1) {
+-		error ("prcv: exactly one argument required\n");
++		error ("__bw_prcv__: exactly one argument required\n");
+ 		return retval;
+ 	}
+-	octave_stream is = octave_stream_list::lookup (args(0), "prcv");
++	octave_stream is = octave_stream_list::lookup (args(0), "__bw_prcv__");
+ 	if (error_state) return retval;
+ 
+ 	if (is.is_open ()) {
+@@ -49,7 +49,7 @@
+ 		// 114: "r", 43: "+"
+ 		if (! strchr (mode.c_str (), 114) &&
+ 		    ! strchr (mode.c_str (), 43)) {
+-			error ("prcv: stream not readable\n");
++			error ("__bw_prcv__: stream not readable\n");
+ 			return retval;
+ 		}
+ #ifdef PATCHED_PIPE_CODE
+@@ -59,13 +59,13 @@
+ 
+ 		// 98: "b"
+ 		if (! strchr (mode.c_str (), 98)) {
+-			error ("prcv: stream not binary\n");
++			error ("__bw_prcv__: stream not binary\n");
+ 			return retval;
+ 		}
+ #endif
+ 	}
+ 	else {
+-		error ("prcv: stream not open\n");
++		error ("__bw_prcv__: stream not open\n");
+ 		return retval;
+ 	}
+ 
+@@ -100,50 +100,17 @@
+ 	// after the header exactly one variable is expected. This
+ 	// is mended by asking for EOF here.
+ 	if (ps.eof () || error_state || name.empty ()) {
+-		error ("prcv: error in reading variable data\n");
++		error ("__bw_prcv__: error in reading variable data\n");
+ 		return retval;
+ 	}
+ 	if  (! tc.is_defined ()) {
+ 		// What means this?
+-		error ("prcv: error in reading variable\n");
++		error ("__bw_prcv__: error in reading variable\n");
+ 		return retval;
+ 	}
+ 
+-	if (nargout == 1) {
+-		retstruct.assign(name, tc);
+-		retval = retstruct;
+-	}
+-	else {
+-		// install_loaded_variable () is static ... here the
+-		// code equivalent to
+-		//
+-		// install_loaded_variable (true, name, tc, global, doc);
+-		//
+-		// is duplicated (except one error check) ...
+-
+-		symbol_record *lsr = curr_sym_tab->lookup (name);
+-
+-		bool is_undefined = true;
+-		bool is_variable = false;
+-
+-		if (lsr) {
+-			is_undefined = ! lsr->is_defined ();
+-			is_variable = lsr->is_variable ();
+-		}
+-
+-		symbol_record *sr = 0;
++	retstruct.assign(name, tc);
++	retval = retstruct;
+ 
+-		if (! global && (is_variable || is_undefined)) {
+-			lsr = curr_sym_tab->lookup (name, true);
+-			sr = lsr;
+-		}
+-		else {
+-			lsr = curr_sym_tab->lookup (name, true);
+-			link_to_global_variable (lsr);
+-			sr = lsr;
+-		}
+-		sr->define (tc);
+-		sr->document (doc);
+-	}
+ 	return retval;
+ }
+diff -Naur parallel-2.0.0/src/__bw_psend__.cc parallel-2.0.0.new/src/__bw_psend__.cc
+--- parallel-2.0.0/src/__bw_psend__.cc	2009-05-08 09:17:57.000000000 -0400
++++ parallel-2.0.0.new/src/__bw_psend__.cc	2009-10-04 07:25:36.000000000 -0400
+@@ -19,72 +19,31 @@
+ #include <octave/ls-oct-binary.h>
+ #include <octave/oct-stream.h>
+ 
+-DEFUN_DLD (__bw_psend__, args, , "psend (pd, name[, value])\n\
+-Sends variable named in 'name' through pipe stream 'pd'.\n\
+-With 'value' given and having boolean value 'true', the\n\
+-contents of the second argument itself is sent under the name\n\
+-'psend_var'.\n\
++DEFUN_DLD (__bw_psend__, args, , "psend (pd, var)\n\
++The contents of 'var' is sent through the pipe stream 'pd'\n\
++under the name 'psend_var'.\n\
+ The variable is coded in Octaves binary format,\n\
+ a header is included. It can be read by 'prcv ()'.\n\
+ \n\
+ This function may change and is internal to the parallel package.\n")
+ {
+-	std::string name;
+-	std::string help;
+-	int global;
+ 	octave_value retval;
+ 	octave_value tc;
+-	bool contents;
+ 
+-	if (args.length () == 2) 
+-		contents = false;
+-	else if (args.length () == 3) {
+-		if (! args(2).is_real_scalar ()) {
+-			error ("psend: third variable, if given, must be a real scalar.\n");
+-			return retval;
+-		}
+-		contents = args(2).scalar_value ();
+-	} else {
+-		error ("psend: two or three arguments required\n");
++	if (args.length () != 2) {
++		error ("__bw_psend__: two arguments required\n");
+ 		return retval;
+ 	}
+ 
+-	if (contents) {
+-		name = "psend_var";
+-		tc = args(1);
+-		help = "";
+-		global = false;
+-	}
+-	else {
+-		if (args(1).is_string ()) name = args(1).string_value ();
+-		else {
+-			error ("psend: if named variable is to be sent, second argument must be a string\n");
+-			return retval;
+-		}
+-		symbol_record *var = curr_sym_tab->lookup (name);
+-	        if (! var) {
+-			error ("psend: no such variable %s\n", name.c_str ());
+-			return retval;
+-		}
+-		tc = var->def ();
+-		help = var->help ();
+-		global = var->is_linked_to_global ();
+-	}
+-	if (! tc.is_defined ()) {
+-		// What means this?
+-		error ("psend: variable not defined\n");
+-		return retval;
+-	}
+-		
+-	octave_stream os = octave_stream_list::lookup (args(0), "psend");
++	octave_stream os = octave_stream_list::lookup (args(0), "__bw_psend__");
+ 	if (error_state) {
+-		error ("psend: no valid file id\n");
++		error ("__bw_psend__: no valid file id\n");
+ 		return retval;
+ 	}
+ 	if (os.is_open ()) {
+ 		std::string mode = os.mode_as_string (os.mode ());
+ 		if (mode == "r" || mode == "rb") {
+-			error ("psend: stream not writable\n");
++			error ("__bw_psend__: stream not writable\n");
+ 			return retval;
+ 		}
+ #ifdef PATCHED_PIPE_CODE_15TH_JUNE_07
+@@ -94,20 +53,20 @@
+ 
+ 		// 98: "b"
+ 		if (! strchr (mode.c_str (), 98)) {
+-			error ("psend: stream not binary\n");
++			error ("__bw_psend__: stream not binary\n");
+ 			return retval;
+ 		}
+ #endif
+ 	}
+ 	else {
+-		error ("psend: stream not open\n");
++		error ("__bw_psend__: stream not open\n");
+ 		return retval;
+ 	}
+ 
+ 	std::ostream *tps = os.output_stream ();
+ 	std::ostream& ps = *tps;
+ 	write_header (ps, LS_BINARY);
+-	save_binary_data (ps, tc, name, help, global, false);
++	save_binary_data (ps, args(1), "psend_var", "", false, false);
+ 
+ 	return retval;
+ }
+diff -Naur parallel-2.0.0/src/pserver.cc parallel-2.0.0.new/src/pserver.cc
+--- parallel-2.0.0/src/pserver.cc	2009-05-08 09:17:57.000000000 -0400
++++ parallel-2.0.0.new/src/pserver.cc	2009-10-04 07:25:27.000000000 -0400
+@@ -58,6 +58,8 @@
+ #include <setjmp.h>
+ #include <netinet/in.h>
+ 
++#include <iostream>
++
+ // SSIZE_MAX might be for 64-bit. Limit to 2^31-1
+ #define BUFF_SIZE 2147483647
+ 
diff --git a/sci-mathematics/octave-forge-parallel/octave-forge-parallel-1.0.6.ebuild b/sci-mathematics/octave-forge-parallel/octave-forge-parallel-2.0.0.ebuild
index ad2d666b3..35cbeb910 100644
--- a/sci-mathematics/octave-forge-parallel/octave-forge-parallel-1.0.6.ebuild
+++ b/sci-mathematics/octave-forge-parallel/octave-forge-parallel-2.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
@@ -12,3 +12,6 @@ SLOT="0"
 
 IUSE=""
 KEYWORDS="~amd64 ~x86"
+
+PATCHES=("octave-forge-parallel-2.0.0-octave-3.2.patch"
+		"octave-forge-parallel-2.0.0-description.patch")
diff --git a/sci-mathematics/octave-forge-physicalconstants/ChangeLog b/sci-mathematics/octave-forge-physicalconstants/ChangeLog
index 742eb31f6..b3d9c790f 100644
--- a/sci-mathematics/octave-forge-physicalconstants/ChangeLog
+++ b/sci-mathematics/octave-forge-physicalconstants/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-mathematics/octave-forge-physicalconstants
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-physicalconstants-0.1.7 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-physicalconstants-0.1.5.ebuild,
+  +octave-forge-physicalconstants-0.1.7.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-physicalconstants-0.1.4.ebuild,
   +octave-forge-physicalconstants-0.1.6.ebuild:
diff --git a/sci-mathematics/octave-forge-physicalconstants/Manifest b/sci-mathematics/octave-forge-physicalconstants/Manifest
index 21b7accd2..3f13d050e 100644
--- a/sci-mathematics/octave-forge-physicalconstants/Manifest
+++ b/sci-mathematics/octave-forge-physicalconstants/Manifest
@@ -1,6 +1,6 @@
-DIST physicalconstants-0.1.5.tar.gz 38749 RMD160 5da394ed7d3595071c3130cc5aebf75e70af8124 SHA1 7acd53ccea20afc1760a2cef9b1d2ee245d86158 SHA256 91fa8bbf30e24253d3ca2fa378d47244e12be96012ccb97cfbd52766dcbfeabc
 DIST physicalconstants-0.1.6.tar.gz 38964 RMD160 d0d1804b5536d3e3f235c728e4ef901b432ae301 SHA1 4f5fb293245801853023e8578bb3794b0bb74e21 SHA256 a27bb10eae673647bf67e0e40f99cc173871fc7aa975c182042854eab9d1032a
-EBUILD octave-forge-physicalconstants-0.1.5.ebuild 529 RMD160 3716b696ef45b481bf1012106bf20cc6c973f736 SHA1 dccd637fbda017b99918af23adf35153cd24ae73 SHA256 5ff4d04feeccd1823096c64d82e55f14b6572d39b2e7af5ab4bb417f6077c64e
+DIST physicalconstants-0.1.7.tar.gz 39654 RMD160 8d5b85066e3f65f1e49cc723bf249c880e7d41a6 SHA1 58a3a4627de5b1c5a185ee1331aec1d310a05e01 SHA256 40e784569dc4f4632311fbb589ede356cb6bc67b28586fececa19e88114d29a0
 EBUILD octave-forge-physicalconstants-0.1.6.ebuild 529 RMD160 3716b696ef45b481bf1012106bf20cc6c973f736 SHA1 dccd637fbda017b99918af23adf35153cd24ae73 SHA256 5ff4d04feeccd1823096c64d82e55f14b6572d39b2e7af5ab4bb417f6077c64e
-MISC ChangeLog 943 RMD160 ea6d575eb344c1ea71b0fa8513d427b522b62b3d SHA1 aa5640c7f43e77fc4510ac007b168580587c8982 SHA256 aeb981e866ccd9eb905879f0501a75705722bfdbfa601c6e61595c223b6da44d
+EBUILD octave-forge-physicalconstants-0.1.7.ebuild 529 RMD160 2f01b13196d59b0f441861a72d01df2913cf30bf SHA1 8a5e68f82552dd79600fb85b1a1de48674ac8ad5 SHA256 8d52c8c6eb2ce6721fd95bbd625165b7418df91a2ad68baa5256fe83f7c571dc
+MISC ChangeLog 1162 RMD160 b5f6decd664ac1e7cb739b304f50bd8cac35624b SHA1 0f7baa660c362975c33ad1aab30e8f9bbba49c15 SHA256 421b5219c0a26ff661311b14670516dc455a30962c4bcd4b5196c1849ee8391b
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-physicalconstants/octave-forge-physicalconstants-0.1.5.ebuild b/sci-mathematics/octave-forge-physicalconstants/octave-forge-physicalconstants-0.1.7.ebuild
index 9f00d55ad..e4bb890b6 100644
--- a/sci-mathematics/octave-forge-physicalconstants/octave-forge-physicalconstants-0.1.5.ebuild
+++ b/sci-mathematics/octave-forge-physicalconstants/octave-forge-physicalconstants-0.1.7.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
diff --git a/sci-mathematics/octave-forge-plot/ChangeLog b/sci-mathematics/octave-forge-plot/ChangeLog
index b65aaf19b..5bfe54c6f 100644
--- a/sci-mathematics/octave-forge-plot/ChangeLog
+++ b/sci-mathematics/octave-forge-plot/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-mathematics/octave-forge-plot
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-plot-1.0.7 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-plot-1.0.5.ebuild, +octave-forge-plot-1.0.7.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-plot-1.0.4.ebuild, +octave-forge-plot-1.0.6.ebuild:
   Version bump.
diff --git a/sci-mathematics/octave-forge-plot/Manifest b/sci-mathematics/octave-forge-plot/Manifest
index 129dd74b5..313b5f307 100644
--- a/sci-mathematics/octave-forge-plot/Manifest
+++ b/sci-mathematics/octave-forge-plot/Manifest
@@ -1,6 +1,6 @@
-DIST plot-1.0.5.tar.gz 47426 RMD160 c9cc9d60c9bc8406b568f538b1c159df1bf1e843 SHA1 a58ddaed14dc782c9d53d68cd136b56011f785d0 SHA256 8780f0db8835e0bd548700e0ec12158cf0f1bf4958a857e65e7612d73e13003d
 DIST plot-1.0.6.tar.gz 48135 RMD160 312a7339b13a466bd631c831c815572013852302 SHA1 d4094ed0afac84a6eb46ec5b2da5e05f37ed49ea SHA256 ae2fb61cabdb581d97546377d62b557efbc8fe1618d7ca507bd47636c4db5a13
-EBUILD octave-forge-plot-1.0.5.ebuild 475 RMD160 70b0f79670889c6a10afab816cd9f7580162a00c SHA1 a5bb063da036358dc11a3303a34d8f4a231f8400 SHA256 727346d29ceaad079c2ff5e2aaccbba5a0c84a300803756d9e101aa4e870c647
+DIST plot-1.0.7.tar.gz 47956 RMD160 421fa29e2448e150dec179f5ffc60f2ea1753dba SHA1 a0fa23a77791e7df90ba587c0ddbec62d16adfe1 SHA256 cecb0ca065452ac1c39502f0980f88f0a690ba803fe42e8b9c8248538d69ca3e
 EBUILD octave-forge-plot-1.0.6.ebuild 475 RMD160 70b0f79670889c6a10afab816cd9f7580162a00c SHA1 a5bb063da036358dc11a3303a34d8f4a231f8400 SHA256 727346d29ceaad079c2ff5e2aaccbba5a0c84a300803756d9e101aa4e870c647
-MISC ChangeLog 833 RMD160 6cf6081c18b1fdf9cddcb8b091719033ae1e9e21 SHA1 38cf68b12bfb32d560190c7d9bddb9ea787c2741 SHA256 0802261a84dc43a382c7b8729fa8d039e6ae57014bec025c0cf28eac1d42f1b8
+EBUILD octave-forge-plot-1.0.7.ebuild 475 RMD160 1ad58de9423f0b6e12fa98596651682dd6bacf66 SHA1 65c2f1bb1a59dd0dee7a5d5b4825014b3efd2c7d SHA256 434eda6b8ab3c1d436bdb9c9c26e534db9794594f00b917f5e450ba2f412da19
+MISC ChangeLog 1011 RMD160 30691715e48d9ab20b0d6bfaf777cd5925830885 SHA1 3bba582e8154be0fedba6aa6fc2f054277bb6340 SHA256 7fe83850680c1563536e52df1e14efe2c9b6d795da3cfe56df8433476280a99f
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-plot/octave-forge-plot-1.0.5.ebuild b/sci-mathematics/octave-forge-plot/octave-forge-plot-1.0.7.ebuild
index 95cba0fa8..2a26ab2cd 100644
--- a/sci-mathematics/octave-forge-plot/octave-forge-plot-1.0.5.ebuild
+++ b/sci-mathematics/octave-forge-plot/octave-forge-plot-1.0.7.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
diff --git a/sci-mathematics/octave-forge-special-matrix/ChangeLog b/sci-mathematics/octave-forge-special-matrix/ChangeLog
index 826e2fa3f..5249d8acc 100644
--- a/sci-mathematics/octave-forge-special-matrix/ChangeLog
+++ b/sci-mathematics/octave-forge-special-matrix/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-mathematics/octave-forge-special-matrix
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-special-matrix-1.0.7 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-special-matrix-1.0.5.ebuild,
+  +octave-forge-special-matrix-1.0.7.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-special-matrix-1.0.4.ebuild,
   +octave-forge-special-matrix-1.0.6.ebuild:
diff --git a/sci-mathematics/octave-forge-special-matrix/Manifest b/sci-mathematics/octave-forge-special-matrix/Manifest
index 69f05dad6..c277aef24 100644
--- a/sci-mathematics/octave-forge-special-matrix/Manifest
+++ b/sci-mathematics/octave-forge-special-matrix/Manifest
@@ -1,6 +1,6 @@
-DIST special-matrix-1.0.5.tar.gz 8237 RMD160 c64fa883f2d9e7618b9e99bc0faa2497d3ca598e SHA1 2ce7a7a88774570272498ea0cd5031101d530664 SHA256 05deca3fc8cd9937e4c72f5dc0c9640b843c37bf3fe53f671f7fdf86a1a77dda
 DIST special-matrix-1.0.6.tar.gz 8458 RMD160 6df7c89ab9e998e1b268aaf1f653f4674b0debea SHA1 a00bcdeceec4e27a43012fa45962a5ab0f76514c SHA256 5180645a2b65067035a3b7b064fbb9ce5c1b9d4b33fa80dea7d3abaab42edcb5
-EBUILD octave-forge-special-matrix-1.0.5.ebuild 487 RMD160 1f4f43118a55025074bb97f6068ff6ff1e300252 SHA1 52a950fcdd858ec042fb4099ee276f9b4c5512f5 SHA256 737429f91da4e4a8662f22089fd21153070326328993889023955fb3726f3989
+DIST special-matrix-1.0.7.tar.gz 8371 RMD160 dfac40b0aa692dbf6221829ffac9f895bb0620b2 SHA1 6c9f36a45071ecbb4c75d8084d3bee70652cd4f6 SHA256 1e936b5951343729f638f91172e7033491fdd03ab30bf9ee7529dc9c04780222
 EBUILD octave-forge-special-matrix-1.0.6.ebuild 487 RMD160 1f4f43118a55025074bb97f6068ff6ff1e300252 SHA1 52a950fcdd858ec042fb4099ee276f9b4c5512f5 SHA256 737429f91da4e4a8662f22089fd21153070326328993889023955fb3726f3989
-MISC ChangeLog 919 RMD160 fed76e5fc89ff2e69a0cfbed75bafa6f494b642f SHA1 2e32b14fbcf914489cb6d416329d44cc4f830532 SHA256 2f9f4b0b7be2a082981cf48fb488a7a4935f661f9dc803593d024c85df3b9aa4
+EBUILD octave-forge-special-matrix-1.0.7.ebuild 487 RMD160 469239af842e96df668cafe02b6f804b7962facc SHA1 6f125a770287c35d916ba6e37a072fc9bff565d9 SHA256 a57d603fc9ba752dd4981f079099c09f2d81eeecae0bf6adb7b447eaf7128c22
+MISC ChangeLog 1129 RMD160 33be55c4d394120feeee9d2477f368ccaea7aa22 SHA1 e5e7233f25594599f5ab8a5dcf64635cc89ae5cc SHA256 41f07c49d532ff1399f904337f1e10dd0c65e4c53166b712d94c7d4421ab335c
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-special-matrix/octave-forge-special-matrix-1.0.5.ebuild b/sci-mathematics/octave-forge-special-matrix/octave-forge-special-matrix-1.0.7.ebuild
index 8b93db538..6ac8737fe 100644
--- a/sci-mathematics/octave-forge-special-matrix/octave-forge-special-matrix-1.0.5.ebuild
+++ b/sci-mathematics/octave-forge-special-matrix/octave-forge-special-matrix-1.0.7.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
diff --git a/sci-mathematics/octave-forge-splines/ChangeLog b/sci-mathematics/octave-forge-splines/ChangeLog
index 187a0d650..a7e61054f 100644
--- a/sci-mathematics/octave-forge-splines/ChangeLog
+++ b/sci-mathematics/octave-forge-splines/ChangeLog
@@ -1,7 +1,13 @@
-# ChangeLog for sci-mathematics/octave-forge-time
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# ChangeLog for sci-mathematics/octave-forge-splines
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-splines-1.0.7 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-splines-1.0.5.ebuild, +octave-forge-splines-1.0.7.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-splines-1.0.4.ebuild, +octave-forge-splines-1.0.6.ebuild:
   Version bump.
diff --git a/sci-mathematics/octave-forge-splines/Manifest b/sci-mathematics/octave-forge-splines/Manifest
index 6211b0df4..330ab83e0 100644
--- a/sci-mathematics/octave-forge-splines/Manifest
+++ b/sci-mathematics/octave-forge-splines/Manifest
@@ -1,5 +1,5 @@
-DIST splines-1.0.5.tar.gz 34141 RMD160 b44511d69ee17cd264ac3b1d91750612531caf42 SHA1 c1ef7554db7c23c8d5f3dd22b6fd34cd8191d664 SHA256 d68eee1b5f5e60f337230b66402ac85c19751bda2653d036e3c38b7aa075b7cd
 DIST splines-1.0.6.tar.gz 34662 RMD160 f8e2f78bf804cf9956373c9a22d50dc886bd8a8c SHA1 47a2ba341f16d03cc66fa056887931928d554c4d SHA256 aff9a00ac7242993a3b5f2f1914160e785f8eb53b30beebba60cc6d65514622f
-EBUILD octave-forge-splines-1.0.5.ebuild 478 RMD160 80f7e03c98d5c3052ece49150374a598808307f0 SHA1 91bc20c5ef96983b05dc0fae422130b3e2c877dd SHA256 c2858f7e4df06101b4b6a0a0c282f0f318b808e6f36d0fd600e2c17845f78ec0
+DIST splines-1.0.7.tar.gz 34486 RMD160 f66e5c5b69b4f4aef67d00b0a412a63a21418dd5 SHA1 f972b7224ed896e1bee8df3f41938dd01c488a0c SHA256 f4ee402de031333cdacfe1dc8218fc25b717387c1a31180ca4cd9e31810b8289
 EBUILD octave-forge-splines-1.0.6.ebuild 478 RMD160 80f7e03c98d5c3052ece49150374a598808307f0 SHA1 91bc20c5ef96983b05dc0fae422130b3e2c877dd SHA256 c2858f7e4df06101b4b6a0a0c282f0f318b808e6f36d0fd600e2c17845f78ec0
-MISC ChangeLog 493 RMD160 18695fa31886f5c8810d7c788b1ffbb7ae7281d6 SHA1 f692bfe51669f4baaab60762e005e8b9007e4584 SHA256 80d7f41ebea84760bd479963e89193d68817838ad3853b1d8bdf6180c9b1e01e
+EBUILD octave-forge-splines-1.0.7.ebuild 478 RMD160 5db05516d8dfb52e1ac353eca5dc71d7f3e29a62 SHA1 e9b88f962ed61ec3742adc2bc6a1187f1b1a72bd SHA256 8eb1a3540bcdda2bfc2849f431672349cac7f1321a746676c5ed1c9049ecc17a
+MISC ChangeLog 683 RMD160 f10ba78396dd08e524450d891d68b9d92c355008 SHA1 14d024db841f8b678cae18903c4a4d90ef17ee9e SHA256 eb61df543d09bebfbb1da3e59d62082d82f32f623a6233668acdf6b1b4dbef69
diff --git a/sci-mathematics/octave-forge-splines/octave-forge-splines-1.0.5.ebuild b/sci-mathematics/octave-forge-splines/octave-forge-splines-1.0.7.ebuild
index 6253b2cfb..c4751c56f 100644
--- a/sci-mathematics/octave-forge-splines/octave-forge-splines-1.0.5.ebuild
+++ b/sci-mathematics/octave-forge-splines/octave-forge-splines-1.0.7.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
diff --git a/sci-mathematics/octave-forge-statistics/ChangeLog b/sci-mathematics/octave-forge-statistics/ChangeLog
index 843626a7f..2bae70996 100644
--- a/sci-mathematics/octave-forge-statistics/ChangeLog
+++ b/sci-mathematics/octave-forge-statistics/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-mathematics/octave-forge-statistics
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-statistics-1.0.9 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-statistics-1.0.6.ebuild,
+  +octave-forge-statistics-1.0.9.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-statistics-1.0.5.ebuild,
   +octave-forge-statistics-1.0.7.ebuild:
diff --git a/sci-mathematics/octave-forge-statistics/Manifest b/sci-mathematics/octave-forge-statistics/Manifest
index 95cec2354..e39f9aa6d 100644
--- a/sci-mathematics/octave-forge-statistics/Manifest
+++ b/sci-mathematics/octave-forge-statistics/Manifest
@@ -1,6 +1,6 @@
-DIST statistics-1.0.6.tar.gz 71449 RMD160 ac42bc168c2cbef195b82ce2b4091cf7bb772968 SHA1 a65774d7cd380bf9ef50e787aaf84a76471a13e1 SHA256 03e99cb092a838e85a93fa635f466e75bcf4bff98d5829a982ec9bbaad627916
 DIST statistics-1.0.7.tar.gz 78129 RMD160 3f3adec1e8ccb6f90d5cf8bfd48d177788135c44 SHA1 da5ce1827b0f4318c0335d6b385b3fc25e17258b SHA256 2cff2b80f40e6ebe35fff6d0592497640a8279988fd6aed00443a9545d540d59
-EBUILD octave-forge-statistics-1.0.6.ebuild 487 RMD160 1939c9a0ab0dce7ad14a31fe22aa6d8264c04464 SHA1 c869d2093201b302255388c181bf6c516a7c1200 SHA256 683aa6e3a02c0727fe8390b4b868e81697be42dd5b8dbee71838726201883803
+DIST statistics-1.0.9.tar.gz 89539 RMD160 3f5895975e4fe45c2bd32567400547dc73754163 SHA1 45763558c7b57d41c4b36f0c715770c9d3d5e6bc SHA256 0fe6bb405e65310537e4a45a61346483bbca7c420d013ddca492592e44e32c6f
 EBUILD octave-forge-statistics-1.0.7.ebuild 487 RMD160 1939c9a0ab0dce7ad14a31fe22aa6d8264c04464 SHA1 c869d2093201b302255388c181bf6c516a7c1200 SHA256 683aa6e3a02c0727fe8390b4b868e81697be42dd5b8dbee71838726201883803
-MISC ChangeLog 887 RMD160 b289c1c2a4539133d1b23c0ed836b00bf5a28ec6 SHA1 fc86dc3a3fd57163ca9387807a9154ae34e26da3 SHA256 b6e0acb64af49abb580f2e98c283ca1d0b804da66c248f65130307f0616ea5af
+EBUILD octave-forge-statistics-1.0.9.ebuild 540 RMD160 7a27ceeac967adc9c3cd928080fda7babc854937 SHA1 edecc532b4e827c5aaf34d609c90b33d324c1a12 SHA256 fa3980e69157bdeab2b299329c9fa1e87f823358b6ab0375f1c20c660051ef95
+MISC ChangeLog 1085 RMD160 6a5f70453c625dea93d9b207e40e06368276a20e SHA1 e2970d558807f357cac48ca6947c59e55fc6b929 SHA256 43c8f859924dfce98bf71e728a899edcc9422cbd9dc92c58c86319231bdd377b
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-statistics/octave-forge-statistics-1.0.6.ebuild b/sci-mathematics/octave-forge-statistics/octave-forge-statistics-1.0.9.ebuild
index 9b47c5bef..f87115c52 100644
--- a/sci-mathematics/octave-forge-statistics/octave-forge-statistics-1.0.6.ebuild
+++ b/sci-mathematics/octave-forge-statistics/octave-forge-statistics-1.0.9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
@@ -12,3 +12,5 @@ SLOT="0"
 
 IUSE=""
 KEYWORDS="~amd64 ~x86"
+
+DEPEND="sci-mathematics/octave-forge-miscellaneous"
diff --git a/sci-mathematics/octave-forge-strings/ChangeLog b/sci-mathematics/octave-forge-strings/ChangeLog
index e281c71a3..ea314a438 100644
--- a/sci-mathematics/octave-forge-strings/ChangeLog
+++ b/sci-mathematics/octave-forge-strings/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-mathematics/octave-forge-strings
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-strings-1.0.7 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-strings-1.0.5.ebuild, +octave-forge-strings-1.0.7.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-strings-1.0.4.ebuild, octave-forge-strings-1.0.5.ebuild,
   +octave-forge-strings-1.0.6.ebuild:
diff --git a/sci-mathematics/octave-forge-strings/Manifest b/sci-mathematics/octave-forge-strings/Manifest
index 9f3508e2f..b7c0064ab 100644
--- a/sci-mathematics/octave-forge-strings/Manifest
+++ b/sci-mathematics/octave-forge-strings/Manifest
@@ -1,6 +1,6 @@
-DIST strings-1.0.5.tar.gz 70616 RMD160 fe99320f7f09514692b84677d90199c5439bd160 SHA1 1ba64a6670ef7bd2fca51c68d6c9db84faea9310 SHA256 d05c907dd90f97e2305fb67a14666c6b4ed649dbaead0743be36c46ec97c9f48
 DIST strings-1.0.6.tar.gz 70996 RMD160 611715700f7dd9dcbe89ed5b65cf38d03dd4f7e4 SHA1 3cf635b5db2d51d23f9a88d72b0e870b68b04746 SHA256 df4895b560dce3c17f71b376be45bdb9e79cbfab40e15ca8893342c0e593662f
-EBUILD octave-forge-strings-1.0.5.ebuild 501 RMD160 461a0e0fed78c2f5e7e73c138a63b56d345a01d3 SHA1 8264eaedf8ed07e4e0ca5ba3ff4dfd91dfbe5b2c SHA256 4a597ea013bec35b33a35e8faa1e69a989906ccf6f5f0808710aee3d6ba4d15d
+DIST strings-1.0.7.tar.gz 71481 RMD160 a33812368f8f257f0646fe5499cbf9d55cba312c SHA1 ab6a49f72b925cba7a5b3e8bf5fc5850484abc42 SHA256 22f84d3fb6333abdbce5ab77c7b3a2e98db5b46ab4561c57f74f0f3b7b478ea1
 EBUILD octave-forge-strings-1.0.6.ebuild 501 RMD160 461a0e0fed78c2f5e7e73c138a63b56d345a01d3 SHA1 8264eaedf8ed07e4e0ca5ba3ff4dfd91dfbe5b2c SHA256 4a597ea013bec35b33a35e8faa1e69a989906ccf6f5f0808710aee3d6ba4d15d
-MISC ChangeLog 923 RMD160 ef1a76244a2802c0fa2db8246ad733a538de3a77 SHA1 f572976f3cc9811af3210ca0da7caccf68826b40 SHA256 dd52d9fe33d61fe1674b2520cc2f7a6e88075a42dd20f71ec74c842c0cf823f1
+EBUILD octave-forge-strings-1.0.7.ebuild 501 RMD160 63c3c5f24a3df85f5e0af8835e1b7333107f2412 SHA1 aa9d5d05e8fb1236be1cb47ffa407f28377db1aa SHA256 aa7b88bf315352ad9daf0a9aa76edcb793ff9ffa9d8d96a29ce7e3b96ee7ab3a
+MISC ChangeLog 1110 RMD160 6bcbf2eb83e972f690d4c6b6c0132f462b717f8d SHA1 733b730247003c51683b24beddd2213f4b2cac76 SHA256 cf93916e8d609969b93badfed806a006f90032884a25101a10f3acd68710fec6
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-strings/octave-forge-strings-1.0.5.ebuild b/sci-mathematics/octave-forge-strings/octave-forge-strings-1.0.7.ebuild
index dd4983d2d..edece2947 100644
--- a/sci-mathematics/octave-forge-strings/octave-forge-strings-1.0.5.ebuild
+++ b/sci-mathematics/octave-forge-strings/octave-forge-strings-1.0.7.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
diff --git a/sci-mathematics/octave-forge-struct/ChangeLog b/sci-mathematics/octave-forge-struct/ChangeLog
index 129db527a..9a48d4068 100644
--- a/sci-mathematics/octave-forge-struct/ChangeLog
+++ b/sci-mathematics/octave-forge-struct/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-mathematics/octave-forge-struct
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-struct-1.0.7 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-struct-1.0.5.ebuild, +octave-forge-struct-1.0.7.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-struct-1.0.4.ebuild, +octave-forge-struct-1.0.6.ebuild:
   Version bump.
diff --git a/sci-mathematics/octave-forge-struct/Manifest b/sci-mathematics/octave-forge-struct/Manifest
index 0d4b93641..e157eae89 100644
--- a/sci-mathematics/octave-forge-struct/Manifest
+++ b/sci-mathematics/octave-forge-struct/Manifest
@@ -1,6 +1,6 @@
-DIST struct-1.0.5.tar.gz 34143 RMD160 048de3a0f33d307829f87dd9020a3872f5895652 SHA1 a43e6fdeaed6fa93345b508293a1bde4a2e0f556 SHA256 928178ea43cae5cda52d9d38d779496b9a7ee2c065ebcba5d58a4fcaa5114a52
 DIST struct-1.0.6.tar.gz 34353 RMD160 821d44091ae499482ef924911c7d755ae491e503 SHA1 e66eaf9631a5921004f280bd00d40d1031e18cfc SHA256 c84fca5fb3278e038b2cb6aa01666b1a58888c467693f625627e1e6b893287dc
-EBUILD octave-forge-struct-1.0.5.ebuild 485 RMD160 c132fccc0a842431ef181a4edba57a8714f599f9 SHA1 b76ec502eaa752058584effb760437babd843b98 SHA256 751652bb6c6ba843c5cdaa2de892550b45e2fee017a1c8f23af36682f7901088
+DIST struct-1.0.7.tar.gz 34188 RMD160 d082d047117a5bccbf2e4b64c2d5035a7d6ceeb9 SHA1 55f232a95f015347875a2e64830d8ff8588f9967 SHA256 57ab4487b948d1a11a8d6efe432e60067ef866fa9e4ae5b56cb7f18d4cdf451d
 EBUILD octave-forge-struct-1.0.6.ebuild 485 RMD160 c132fccc0a842431ef181a4edba57a8714f599f9 SHA1 b76ec502eaa752058584effb760437babd843b98 SHA256 751652bb6c6ba843c5cdaa2de892550b45e2fee017a1c8f23af36682f7901088
-MISC ChangeLog 849 RMD160 98f63e6e0e24f9b90920d2d4b47cec578bed91ef SHA1 2ec4df283d6c09789778d139f21c2901b59a125e SHA256 dfd7da27bb643b4c059fa92dea0d255bfd206e95de99c310ab49baab57671e24
+EBUILD octave-forge-struct-1.0.7.ebuild 485 RMD160 831a31a29c11146b4e7ce55e24756b3494b9130f SHA1 299d3a4591bb73e0f6a17a6f5db8bf5510a6f9a8 SHA256 5ce1bbad5ef26961d725a8a3f881f4ad30984d824927e52d22b04d2266e133fe
+MISC ChangeLog 1033 RMD160 53a7aca7679fc3eb1722c5e986974caca80a3457 SHA1 9e875506d44a9bb30e655076e1914de8091475b0 SHA256 8d24ebd7e8ea780409cf2846d120158db546143942b644ecf2695b131bb6f76b
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-struct/octave-forge-struct-1.0.5.ebuild b/sci-mathematics/octave-forge-struct/octave-forge-struct-1.0.7.ebuild
index dbbb77669..48b502435 100644
--- a/sci-mathematics/octave-forge-struct/octave-forge-struct-1.0.5.ebuild
+++ b/sci-mathematics/octave-forge-struct/octave-forge-struct-1.0.7.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
diff --git a/sci-mathematics/octave-forge-symbolic/ChangeLog b/sci-mathematics/octave-forge-symbolic/ChangeLog
index ecc2712c9..19f4f722c 100644
--- a/sci-mathematics/octave-forge-symbolic/ChangeLog
+++ b/sci-mathematics/octave-forge-symbolic/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-mathematics/octave-forge-symbolic
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-symbolic-1.0.9 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-symbolic-1.0.6.ebuild, +octave-forge-symbolic-1.0.9.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-symbolic-1.0.5.ebuild, +octave-forge-symbolic-1.0.7.ebuild:
   Version bump.
diff --git a/sci-mathematics/octave-forge-symbolic/Manifest b/sci-mathematics/octave-forge-symbolic/Manifest
index bc4c472dd..c2aec2890 100644
--- a/sci-mathematics/octave-forge-symbolic/Manifest
+++ b/sci-mathematics/octave-forge-symbolic/Manifest
@@ -1,6 +1,6 @@
-DIST symbolic-1.0.6.tar.gz 85711 RMD160 03043ccadee3cf7125e1801c07fcc10f39510b19 SHA1 b50215f07639d6dd0b3742374f422479fbfde2b5 SHA256 95edc9ca1dfcfd85e58778fcef2d0fcfd22fe3e899c8e0a0d28b9736e796d2ba
 DIST symbolic-1.0.7.tar.gz 80658 RMD160 1dbe3cf254d3d0f18cff47b879a41250d7bd3df4 SHA1 0bd9b1462ee884b0de78cc2523623a756d9e8022 SHA256 0566c0ce9b0b7b1488b369629562dc2ac8d5d8213b05afc86e9781da82a77a03
-EBUILD octave-forge-symbolic-1.0.6.ebuild 514 RMD160 12e22e4653faf4b7963da153de2c2b757ffa0892 SHA1 8a9aafc99a88be2319340e815d6f5d6d82b7ca50 SHA256 b91a141538ad432a018c1e13f27298ad6aaf7f17f572e3cb96208e17b3aa2ca3
+DIST symbolic-1.0.9.tar.gz 82695 RMD160 f5ae1b1647734b7a04cdaa30121bf9390a4a6e22 SHA1 4f005ed4970e37652da4b77ababaf9b57d343a8a SHA256 eee6ef61ca92d9033c9aeffaf5383adbeb623de039085fea22f9d02c7e718fb0
 EBUILD octave-forge-symbolic-1.0.7.ebuild 514 RMD160 12e22e4653faf4b7963da153de2c2b757ffa0892 SHA1 8a9aafc99a88be2319340e815d6f5d6d82b7ca50 SHA256 b91a141538ad432a018c1e13f27298ad6aaf7f17f572e3cb96208e17b3aa2ca3
-MISC ChangeLog 865 RMD160 f7c859217dedc23d62a7dc63ba2aa12e64cec309 SHA1 f229910946c213514169246880840b19318d3c81 SHA256 a28e563c5826359c531b83947d3ac4212d1f2b101b47cc1b4affaa766015c94c
+EBUILD octave-forge-symbolic-1.0.9.ebuild 514 RMD160 80f232d625811e90b0afa44abda909c23e23efb3 SHA1 92f719a8fc799ee6d33f9cfb64356899a1a2a878 SHA256 16174f31e630c0c4cb8e9851c3c514b491c372bae98323a4b1bc6b3e39898952
+MISC ChangeLog 1055 RMD160 47cb968851cf2ec61697b1466dc975895633e553 SHA1 28b768d5af6cac6a4c850b99b3ba6227c48bd7fc SHA256 e82991e7519acf75cd63435e6668b55594250d072f8f70f1f984b93db3ae02df
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-symbolic/octave-forge-symbolic-1.0.6.ebuild b/sci-mathematics/octave-forge-symbolic/octave-forge-symbolic-1.0.9.ebuild
index c7805179a..3e8c1e963 100644
--- a/sci-mathematics/octave-forge-symbolic/octave-forge-symbolic-1.0.6.ebuild
+++ b/sci-mathematics/octave-forge-symbolic/octave-forge-symbolic-1.0.9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
diff --git a/sci-mathematics/octave-forge-vrml/ChangeLog b/sci-mathematics/octave-forge-vrml/ChangeLog
index ac6395d62..da5f9d525 100644
--- a/sci-mathematics/octave-forge-vrml/ChangeLog
+++ b/sci-mathematics/octave-forge-vrml/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-mathematics/octave-forge-vrml
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-vrml-1.0.10 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-vrml-1.0.6.ebuild, +octave-forge-vrml-1.0.10.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-vrml-1.0.5.ebuild, +octave-forge-vrml-1.0.8.ebuild:
   Version bump.
diff --git a/sci-mathematics/octave-forge-vrml/Manifest b/sci-mathematics/octave-forge-vrml/Manifest
index cc325bb7d..7742efbcd 100644
--- a/sci-mathematics/octave-forge-vrml/Manifest
+++ b/sci-mathematics/octave-forge-vrml/Manifest
@@ -1,6 +1,6 @@
-DIST vrml-1.0.6.tar.gz 1503168 RMD160 730e909e0debb8daf57c0198dba73d92fcd0d1f5 SHA1 275cc101a5ee6228b7593df69c47ae370c562d0a SHA256 d4f2905f302b74a58ec71793e2077d1f7d4c15da338f854feeb3dfc012d4f069
+DIST vrml-1.0.10.tar.gz 1498723 RMD160 b90f289b0a99c6b53c9d898bc7ad1dc808c56fba SHA1 3967cec848d38fa411534b1642bdce57836b0caa SHA256 015ab05d181d8394a02d9296b080c1286f6267768307204c7ea5403ae50a37aa
 DIST vrml-1.0.8.tar.gz 1503883 RMD160 7fdc089ceffc2c72c70d572391e0434b364bc4e9 SHA1 70db2337a69b5a92182d2946cd8f65eb4bed9e31 SHA256 20af764305fee8507d9f1a690876d496c1f9897d960c91d03d35bffd84d5495c
-EBUILD octave-forge-vrml-1.0.6.ebuild 482 RMD160 fef797f0090f9eb9fb326465367ceb5caf2a55a2 SHA1 10e82adbf4b4c97b9a250c0152e96a6ea0bc5b15 SHA256 f98b94bb8bd3b9ca4979c59cd78b50c9750f08c71ed91a89bfa7fec7bf09d59f
+EBUILD octave-forge-vrml-1.0.10.ebuild 607 RMD160 f0cfa86caa150207b6802145870503025d1b3846 SHA1 ecc2b4de3d219916ac31120e1c6bf7b1344ecc49 SHA256 7a6836159162e3f1b666239b79b0ddafc6bc340827559704a8ae455dac96cbef
 EBUILD octave-forge-vrml-1.0.8.ebuild 482 RMD160 fef797f0090f9eb9fb326465367ceb5caf2a55a2 SHA1 10e82adbf4b4c97b9a250c0152e96a6ea0bc5b15 SHA256 f98b94bb8bd3b9ca4979c59cd78b50c9750f08c71ed91a89bfa7fec7bf09d59f
-MISC ChangeLog 833 RMD160 762c3145cd7ba72ca2cee14984280976b4c04bf0 SHA1 1da71c86d904b765799a634e580afe08c7f7e564 SHA256 b5c8d5f2a3968a29f874afece229042577173d1d331585a0695a55365ff79a73
+MISC ChangeLog 1013 RMD160 ec1fdbee444803805ebe185523eadd62d070cbb7 SHA1 3ef47b29019ec8a4effa6e1cd98ee0089105a33e SHA256 976c6fe77541539b19593ab16b42e6d8cab599474d2c57e21a07dc786216c286
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-vrml/octave-forge-vrml-1.0.6.ebuild b/sci-mathematics/octave-forge-vrml/octave-forge-vrml-1.0.10.ebuild
index 9bd95bf81..9d8db72bd 100644
--- a/sci-mathematics/octave-forge-vrml/octave-forge-vrml-1.0.6.ebuild
+++ b/sci-mathematics/octave-forge-vrml/octave-forge-vrml-1.0.10.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
@@ -13,4 +13,7 @@ SLOT="0"
 IUSE=""
 KEYWORDS="~x86"
 
-DEPEND="media-gfx/freewrl"
+DEPEND="media-gfx/freewrl
+		sci-mathematics/octave-forge-miscellaneous
+		sci-mathematics/octave-forge-struct
+		sci-mathematics/octave-forge-statistics"
diff --git a/sci-mathematics/octave-forge-zenity/ChangeLog b/sci-mathematics/octave-forge-zenity/ChangeLog
index c00ba4ff4..f997bdd75 100644
--- a/sci-mathematics/octave-forge-zenity/ChangeLog
+++ b/sci-mathematics/octave-forge-zenity/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-mathematics/octave-forge-zenity
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*octave-forge-zenity-0.5.7 (04 Oct 2009)
+
+  04 Oct 2009; Markus Dittrich <markusle@gentoo.org>
+  -octave-forge-zenity-0.5.5.ebuild, +octave-forge-zenity-0.5.7.ebuild:
+  Version bump.
+
   30 Sep 2008; Markus Dittrich <markusle@gentoo.org>
   -octave-forge-zenity-0.5.4.ebuild, +octave-forge-zenity-0.5.6.ebuild:
   Version bump.
diff --git a/sci-mathematics/octave-forge-zenity/Manifest b/sci-mathematics/octave-forge-zenity/Manifest
index 4c04f3dc2..d18cd1715 100644
--- a/sci-mathematics/octave-forge-zenity/Manifest
+++ b/sci-mathematics/octave-forge-zenity/Manifest
@@ -1,6 +1,6 @@
-DIST zenity-0.5.5.tar.gz 27000 RMD160 2776576e6dd944327130f52ed514dc892aaf53e5 SHA1 67553b7e02d7c8202b475995710ff6bf4c6c36c4 SHA256 291905fa990b75b9a6b988027826c644d8ec4edeefd8add26256652e747dd9dc
 DIST zenity-0.5.6.tar.gz 27286 RMD160 39e5932b9e677f0a3da593cc5c22542186816e1d SHA1 1acb159459c8a11ae8acf4b1ac960cea5840b294 SHA256 d255fbee107ed72e0faeb61c09face258b67f61029b05ee8143b06baa73a1e65
-EBUILD octave-forge-zenity-0.5.5.ebuild 534 RMD160 c95694661eb7faa9696f6afdb05ce5b10dbd737d SHA1 82db6bde73694fd94b39f892f49fcfda79873030 SHA256 e99321198ea04a042d5c92a3529c2c3d6da479db77016ab3df0f533c8c4ce00c
+DIST zenity-0.5.7.tar.gz 27225 RMD160 f4c7eeacbdc5a0de24398fd09b1b39d9fb42bd83 SHA1 bc24b583385a3d4d6f438361334be530e38752c7 SHA256 cd1a6fe127b4a96f18cc25a4981537a279ad8f1b877287049b11d9afd2a0bd59
 EBUILD octave-forge-zenity-0.5.6.ebuild 534 RMD160 c95694661eb7faa9696f6afdb05ce5b10dbd737d SHA1 82db6bde73694fd94b39f892f49fcfda79873030 SHA256 e99321198ea04a042d5c92a3529c2c3d6da479db77016ab3df0f533c8c4ce00c
-MISC ChangeLog 849 RMD160 42548c34a43ac993857206fcc3c1f3c3e443f831 SHA1 2734bad788a65dcd96f8dfcffbb6f5c4c7d1eb6c SHA256 bd8cf432e4a1ea17a33415a142aa1146d4d578008fc1378d676b49ee5249cc41
+EBUILD octave-forge-zenity-0.5.7.ebuild 534 RMD160 d45529d9ae51c7b7aa48b799c6c0620a66f0575e SHA1 a9dab88789b08be5bc408146c9c1b7271fe41bff SHA256 cd541559e8e33081f0293af540c1b0a2fd5e5803a6fa8d8b1e8f2c9b82e71d80
+MISC ChangeLog 1033 RMD160 0d2923f095517a4b9c1c4ac9e0df369307dd9936 SHA1 7088f437f95a8a63edfa9a32a7451993d0286b0e SHA256 f2bd1eca47563a49b5bfea6ae79c732a580900dd37343cbb4b1e5fa5e431f460
 MISC metadata.xml 169 RMD160 034a084ee31c755155956712517306aad3d81298 SHA1 8fc92d7ea9b5520d0781291e752b5ab4f278bf4c SHA256 cd9ff49ab9a91cae923683a6693ca676e0f6495822404d8dd69629881069d863
diff --git a/sci-mathematics/octave-forge-zenity/octave-forge-zenity-0.5.5.ebuild b/sci-mathematics/octave-forge-zenity/octave-forge-zenity-0.5.7.ebuild
index 177f7c652..9515247b8 100644
--- a/sci-mathematics/octave-forge-zenity/octave-forge-zenity-0.5.5.ebuild
+++ b/sci-mathematics/octave-forge-zenity/octave-forge-zenity-0.5.7.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-mathematics/octave/octave-2.1.73-r1.ebuild,v 1.2 2006/11/03 15:44:39 markusle Exp $
 
diff --git a/sci-visualization/ferret-bin/ChangeLog b/sci-visualization/ferret-bin/ChangeLog
index c812a7919..a587745d3 100644
--- a/sci-visualization/ferret-bin/ChangeLog
+++ b/sci-visualization/ferret-bin/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*ferret-bin-6.3 (04 Oct 2009)
+
+  04 Oct 2009; Tim Cera <timcera@earthlink.net> +ferret-bin-6.3.ebuild:
+  Version bump to 6.3.
+
 *ferret-bin-6.2 (16 Sep 2009)
 
   16 Sep 2009; Tim Cera <timcera@earthlink.net> files/99ferret,
diff --git a/sci-visualization/ferret-bin/Manifest b/sci-visualization/ferret-bin/Manifest
index c838d5f6f..1a353f95a 100644
--- a/sci-visualization/ferret-bin/Manifest
+++ b/sci-visualization/ferret-bin/Manifest
@@ -1,12 +1,15 @@
 AUX 99ferret 635 RMD160 bfa4ed3209b39803d04b6e875f18477a6c5a33ed SHA1 7475b300aea68c3372811a1d1f8e43bd971db7a4 SHA256 5bba5c50d06399720e8030efa5f4db344928d8fc855f20b0b7db25b78e66c38b
 DIST fer_dsets.tar.gz 39991296 RMD160 dc3c8c67d86bcddad6bf1d984b524e1121ea5286 SHA1 4e0f514b7ae1441597e0f06fd06eda5797025ce6 SHA256 094645b275520321940002d286e792877a4867e2576832e246ab3d3f113425f3
 DIST fer_environment.v62.tar.gz 7833080 RMD160 92b71efc6ce4b820d6a54e21274e8462c69eb2fa SHA1 06f1a660f0c93c946d55922f831bf2a28ca50f5b SHA256 1844d0f13f3d3a53d110a3d12f72b707e33837cab02906512f4913560774a6ed
+DIST fer_environment.v63.tar.gz 7909512 RMD160 e04a46862e3ae60b06b72c55734b519663162dd7 SHA1 373df55bd96f991580697e6fd53bd50e280757e0 SHA256 3dab28c1e8951a582da1bda18cdb517e68348fbc692c97c30444ed8f4dead74b
 DIST fer_environment_x86.61.tar.Z 10514543 RMD160 47505dac54b16e75ae5610931193168f183102dd SHA1 19c31f210fd88d61b1f5c0989a117fd7443657a1 SHA256 e2050eca0b903df58f07319651aae1e3e9d5fc3cb8d21bdd91ea228b0e55bc8b
 DIST fer_environment_x86_64.61.tar.Z 10511779 RMD160 870059554f90a0b60128ff605cab8f12ff250366 SHA1 ee9d696100fd72429fa90496f0a4c597b5663ac8 SHA256 c28b337628e8d33f6e8dd79de6960797594df8c9f8272cfaa50569a5ca178999
 DIST fer_executables.v62.tar.gz 5819789 RMD160 049eb3e3e8530a5638d2c45294225373fbb68344 SHA1 ed1181dde5255b29f6570a6634b08258d5b6352b SHA256 66ab638dc8ebad905c5a7fccba9bd5b4cf21380c0c81108ea24a54c77ba8c6d7
+DIST fer_executables.v63.tar.gz 6436465 RMD160 4e8347a015bc10ad23faf48a4e094bf5d5afbf2a SHA1 8e8b6f63254d6f32a0b225605ad183df73accd83 SHA256 b41d65f491db62a876f8a4bd0ee44e9359e2563fcfb5c6f647beae4d2b988fde
 DIST fer_executables_x86.61.tar.Z 9310457 RMD160 13eff5eded02582abe8958793b2d753b556e08de SHA1 fcaed69892cd3f934684c969d0808f5c62c837c0 SHA256 dde20aa1164f12a22be67aaafd521653f40bbec62871e6ff176ae5233cc92b66
 DIST fer_executables_x86_64.61.tar.Z 9077769 RMD160 cbc6b8737da64611aeda11db113fd580492ed16b SHA1 d2815fbda1b3efc7fef25e89183eebec3f312203 SHA256 bcb1e9d523bcf8009718954c18a77e94e440c3f664a9dc11fb90aa64aeb74ff5
 EBUILD ferret-bin-6.1.ebuild 1626 RMD160 dda17227198aac344e4db5196565262715afb1b7 SHA1 a5714a26a2fc86efa691a55063cfe3a4ce5b3442 SHA256 00d4ebc26953728a3781e840aaf4f53fbe32489a5798282456ca6684ea86f0d5
 EBUILD ferret-bin-6.2.ebuild 1299 RMD160 affb667d0b88e126db48fc9f5789b2925cf8b885 SHA1 4f73923ec77f1cb859373248d9df3586d821ab02 SHA256 070788bc2c89d56f3d0c50d189af615f8c46db86857954c487a18bb81b19c92c
-MISC ChangeLog 374 RMD160 9c2ef8c105fc125585fa65b444128c3dc8bb3144 SHA1 e46a3f84730ac10a3a1c5ca9efbc58cbbf631732 SHA256 ca4fd60e497c52c4dfdbcb4f06030b1f91a76b82723328f6db5e663d8e816cc9
+EBUILD ferret-bin-6.3.ebuild 1299 RMD160 affb667d0b88e126db48fc9f5789b2925cf8b885 SHA1 4f73923ec77f1cb859373248d9df3586d821ab02 SHA256 070788bc2c89d56f3d0c50d189af615f8c46db86857954c487a18bb81b19c92c
+MISC ChangeLog 674 RMD160 9f1ebe1c56ef1963cab3c981f76107b872d1f1d7 SHA1 2ba0ab5d43a44e7b4fa3ac4f11a938d62de520dc SHA256 125551d10681fb5474c8de62b0de72cc1792e80a105bc08e4fe6893b6c34bccc
 MISC metadata.xml 362 RMD160 81d21aa9fb0e54a53c2db8ea0965a59a633417fa SHA1 8e0c5a42c19d225c6b0087173dfd3498fb6098ad SHA256 114c2d067f3f6e4e809739707c042f4a2959895fe4f8dfdd86f52857d6e4532a
diff --git a/sci-visualization/ferret-bin/ferret-bin-6.3.ebuild b/sci-visualization/ferret-bin/ferret-bin-6.3.ebuild
new file mode 100644
index 000000000..e87c28215
--- /dev/null
+++ b/sci-visualization/ferret-bin/ferret-bin-6.3.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+MY_PV=${PV/\./}
+
+MY_FER_ENV="fer_environment.v${MY_PV}.tar.gz"
+MY_FER_EXE="fer_executables.v${MY_PV}.tar.gz"
+
+DESCRIPTION="Ferret is an interactive computer visualization and analysis environment"
+HOMEPAGE="http://ferret.pmel.noaa.gov/Ferret/"
+SRC_URI="ftp://ftp.pmel.noaa.gov/ferret/pub/data/fer_dsets.tar.gz
+	amd64? ( ftp://ftp.pmel.noaa.gov/ferret/pub/x86_64-linux/${MY_FER_ENV}
+	         ftp://ftp.pmel.noaa.gov/ferret/pub/x86_64-linux/${MY_FER_EXE} )
+	x86? ( ftp://ftp.pmel.noaa.gov/ferret/pub/linux_32/${MY_FER_ENV}
+	       ftp://ftp.pmel.noaa.gov/ferret/pub/linux_32/${MY_FER_EXE} )"
+
+LICENSE="PMEL-FERRET"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	>=app-crypt/mit-krb5-1.6.3-r6
+	x11-base/xorg-server
+	~virtual/libstdc++-3.3"
+
+BASEDIR="/opt/ferret-bin"
+
+
+src_unpack() {
+	mkdir "${S}"
+	cd "${S}"
+	unpack "${MY_FER_ENV}"
+	cd "${S}"/bin
+	unpack "${MY_FER_EXE}"
+	cd "${S}"
+	mkdir data
+	cd data
+	unpack "fer_dsets.tar.gz"
+}
+
+
+src_install() {
+	mkdir -p ext_func/libs
+	mv bin/*.so ext_func/libs
+
+	mkdir -p "${D}/${BASEDIR}"
+	mv "${S}"/* "${D}/${BASEDIR}"
+
+	doenvd "${FILESDIR}"/99ferret
+}
+
+
+pkg_postinst() {
+	env-update
+}
+
+
+pkg_postrm() {
+	env-update
+}
+
diff --git a/sci-visualization/opendx-samples/ChangeLog b/sci-visualization/opendx-samples/ChangeLog
deleted file mode 100644
index f0cdfe6a2..000000000
--- a/sci-visualization/opendx-samples/ChangeLog
+++ /dev/null
@@ -1,56 +0,0 @@
-# ChangeLog for sci-visualization/opendx-samples
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-visualization/opendx-samples/ChangeLog,v 1.8 2008/01/21 16:27:07 spock Exp $
-
-*opendx-samples-4.4.0-r1 (11 May 2009)
-
-  11 May 2009; François Bissey <f.r.bissey@massey.ac.nz>
-  +opendx-samples-4.4.0-r1.ebuild,
-  +files/opendx-samples-4.4.0-install.patch,
-  +files/opendx-samples-4.4.0-nojava.patch, +metadata.xml:
-  initial import in the science overlay. Release needed to match the new
-  file location in opendx-4.4.4-r2. Got rid of the ugly installation hack 
-  in favor of a (big) patch.
-
-*opendx-samples-4.4.0 (21 Jan 2008)
-
-  21 Jan 2008; Michał Januszewski <spock@gentoo.org>
-  +opendx-samples-4.4.0.ebuild:
-  Version bump.
-
-  22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog:
-  Redigest for Manifest2
-
-  22 Apr 2006; Mark Loeser <halcy0n@gentoo.org> opendx-samples-4.3.2.ebuild:
-  Stable on x86; bug #129411
-
-  10 Apr 2006; Stephanie Lockwood-Childs <wormo@gentoo.org>
-  opendx-samples-4.3.2.ebuild:
-  stable on ppc (bug #129411)
-
-  09 Apr 2006; Marcus D. Hanwell <cryos@gentoo.org>
-  opendx-samples-4.3.2.ebuild:
-  Stable on amd64.
-
-  29 Jan 2006; Marcus D. Hanwell <cryos@gentoo.org>
-  opendx-samples-4.3.2.ebuild:
-  Fix broken DEPEND from the move, bug 120870.
-
-  29 Jan 2006; Marcus D. Hanwell <cryos@gentoo.org> +metadata.xml,
-  +opendx-samples-4.3.2.ebuild:
-  Moved from media-gfx/opendx-samples to sci-visualization/opendx-samples.
-
-  15 Jan 2006; Marcus D. Hanwell <cryos@gentoo.org>
-  opendx-samples-4.3.2.ebuild:
-  Marked ~amd64, bug 118683.
-
-  20 Aug 2005; Michael Hanselmann <hansmi@gentoo.org>
-  opendx-samples-4.3.2.ebuild:
-  Added to ~ppc (#101951).
-
-*opendx-samples-4.3.2 (08 Aug 2005)
-
-  08 Aug 2005; Patrick Kursawe <phosphan@gentoo.org>
-  +opendx-samples-4.3.2.ebuild:
-  Initial import, mainly provided in bug #22217 and demanded again in #54047.
-
diff --git a/sci-visualization/opendx-samples/Manifest b/sci-visualization/opendx-samples/Manifest
deleted file mode 100644
index 80f1f50bf..000000000
--- a/sci-visualization/opendx-samples/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-AUX opendx-samples-4.4.0-install.patch 28807 RMD160 f46ede3e551d02738fcac8f027658a026409a251 SHA1 3e0b1ee5d8149f8a088a93a927197b58324ff1b0 SHA256 5a89c8eb378998b46dd1d1000bd2246d4802b95467a1472484ed805b7e7eda82
-AUX opendx-samples-4.4.0-nojava.patch 1744 RMD160 ee0b9eb8e24166c8012406f3dc6487eda6cf61b9 SHA1 83b67669460c4bf3f26f2902203b16e12e0b544d SHA256 c69345e77d3698719e315deeae68d3c033ed7f085c1785f573d4c66046a526ef
-DIST dxsamples-4.4.0.tar.gz 7791659 RMD160 3d5f09c48452374ec25099bd7a894859fe34fba9 SHA1 24a8981312c3a2564623acb85538d9935e5c2469 SHA256 ec2277facc8cf0f095a7fc4cb58391e053d5fd26c90d4711c927d2897dc455d9
-EBUILD opendx-samples-4.4.0-r1.ebuild 981 RMD160 5b9ad9ef5e84b228f484075b1952e84efe96e777 SHA1 05b77ca50130ee5d056ef32c6df7dee5529c53e3 SHA256 1144d2c0855c5e790f3361245dc8e2beba11bf77c3fa99978bea476140fcc973
-MISC ChangeLog 1942 RMD160 5983812639a0f202f882a58ab24ba67cf1d1f443 SHA1 4ba4319271134fe383b09bfa0510cd22e7414fc4 SHA256 de014562cc8e2458acceb9c86cd9094685685d096d18960f92140d29847df2fb
-MISC metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 SHA1 da2b240a255820145b7c83a5c48e45b96b7e9ee6 SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900
diff --git a/sci-visualization/opendx-samples/files/opendx-samples-4.4.0-install.patch b/sci-visualization/opendx-samples/files/opendx-samples-4.4.0-install.patch
deleted file mode 100644
index 833a6faf6..000000000
--- a/sci-visualization/opendx-samples/files/opendx-samples-4.4.0-install.patch
+++ /dev/null
@@ -1,515 +0,0 @@
---- dxsamples-4.4.0/supervise/simpledemo/Makefile.am.r	2003-06-19 16:55:12.000000000 +0200
-+++ dxsamples-4.4.0/supervise/simpledemo/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -3,7 +3,7 @@
- 
- SUBDIRS =  interactors
- 
--datadir = $(prefix)/dx/samples/supervise/simpledemo
-+datadir = @libdir@/dx/samples/supervise/simpledemo
- 
- data_DATA =  README demo demo.cfg demo.net
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/supervise/simpledemo/interactors/Makefile.am.r	2000-02-14 23:27:50.000000000 +0100
-+++ dxsamples-4.4.0/supervise/simpledemo/interactors/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/supervise/simpledemo/interactors
-+datadir = @libdir@/dx/samples/supervise/simpledemo/interactors
- 
- data_DATA =  Makefile_alphax Makefile_hp700 Makefile_ibm6000 Makefile_sgi Makefile_solaris interactors.c module_make Makefile
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/supervise/interactors/Makefile.am.r	2003-06-19 16:53:34.000000000 +0200
-+++ dxsamples-4.4.0/supervise/interactors/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/supervise/interactors
-+datadir = @libdir@/dx/samples/supervise/interactors
- 
- data_DATA =  Makefile_alphax Makefile_aviion Makefile_hp700 Makefile_ibm6000 Makefile_sgi Makefile_solaris Makefile_sun4 README myinteractors.c module_make Makefile 
- 
---- dxsamples-4.4.0/supervise/mediumdemo/Makefile.am.r	2003-06-19 16:54:13.000000000 +0200
-+++ dxsamples-4.4.0/supervise/mediumdemo/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -3,7 +3,7 @@
- 
- SUBDIRS =  interactors
- 
--datadir = $(prefix)/dx/samples/supervise/mediumdemo
-+datadir = @libdir@/dx/samples/supervise/mediumdemo
- 
- data_DATA =  README demo
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/supervise/mediumdemo/interactors/Makefile.am.r	2000-02-01 21:33:38.000000000 +0100
-+++ dxsamples-4.4.0/supervise/mediumdemo/interactors/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/supervise/mediumdemo/interactors
-+datadir = @libdir@/dx/samples/supervise/mediumdemo/interactors
- 
- data_DATA =  Makefile_alphax Makefile_hp700 Makefile_ibm6000 Makefile_sgi Makefile_solaris interactors.c module_make Makefile
- 
---- dxsamples-4.4.0/supervise/imagedemo/Makefile.am.r	2003-06-19 16:51:48.000000000 +0200
-+++ dxsamples-4.4.0/supervise/imagedemo/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/supervise/imagedemo
-+datadir = @libdir@/dx/samples/supervise/imagedemo
- 
- data_DATA =  README demo demo.cfg demo.net demo1 demo1.cfg demo1.net
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/supervise/complexdemo/Makefile.am.r	2003-06-19 16:50:04.000000000 +0200
-+++ dxsamples-4.4.0/supervise/complexdemo/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -3,7 +3,7 @@
- 
- SUBDIRS =  data interactors nets
- 
--datadir = $(prefix)/dx/samples/supervise/complexdemo
-+datadir = @libdir@/dx/samples/supervise/complexdemo
- 
- data_DATA =  README demo
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/supervise/complexdemo/data/Makefile.am.r	1999-05-06 00:02:17.000000000 +0200
-+++ dxsamples-4.4.0/supervise/complexdemo/data/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/supervise/complexdemo/data
-+datadir = @libdir@/dx/samples/supervise/complexdemo/data
- 
- data_DATA =  frags.dx
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/supervise/complexdemo/nets/Makefile.am.r	1999-05-06 00:02:17.000000000 +0200
-+++ dxsamples-4.4.0/supervise/complexdemo/nets/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/supervise/complexdemo/nets
-+datadir = @libdir@/dx/samples/supervise/complexdemo/nets
- 
- data_DATA =  ShowSelected.net hiliteObject.net peruDX.cfg peruDX.net
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/supervise/complexdemo/interactors/Makefile.am.r	2000-02-01 21:33:35.000000000 +0100
-+++ dxsamples-4.4.0/supervise/complexdemo/interactors/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/supervise/complexdemo/interactors
-+datadir = @libdir@/dx/samples/supervise/complexdemo/interactors
- 
- data_DATA =  Makefile_alphax Makefile_hp700 Makefile_ibm6000 Makefile_sgi Makefile_solaris interactors.c module_make Makefile
- 
---- dxsamples-4.4.0/data/Makefile.am.r	2003-06-19 07:09:12.000000000 +0200
-+++ dxsamples-4.4.0/data/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/data
-+datadir = @libdir@/dx/samples/data
- 
--data_DATA =  2D2ormorevarnotseries.data 2D2ormorevarnotseries.general 3D2ormorevarnotseries.data 3D2ormorevarnotseries.general CO2.general CO2.lis CO2fragment.lis FacesLoopsEdges.dx FacesLoopsEdges_hole.dx MOS_key.txt MOS_lookup.txt MOS_state_order.txt MOS_states.dx MOS_zips.dx MRI.data Polylines.dx ROM_ozone.dx README background.tiff block_example.data block_example.general blue_yellow.cm categorical.data categorical.data1 census.general census.spreadsheet census.tab census_normalized.dx cloudwater.dx colo_elev.general colorado.tiff colorado_elev.vit cyan_red.cm cylinder.rgb cylinder.size cylinder.tiff datadepconnections.dx datawithattribute.dx deformedregular.dx dx_logo.gif dx_logo2.tif dx_logo.tiff external.data externalfilter externalfilter.c externalfilter_alphax externalfilter_hp700 externalfilter_ibm6000 externalfilter_sgi externalfilter_solaris fontlayout.dx general.exampledata general.exampleheader griddeddata.data grocery.txt group.dx head_slice.dx heat.cm homeown.txt hyper.dx image.dx image.general imide.rgb imide.size imide_potential.dx invalid_field.bin invalid_field.dx irregirreg2.bin irregirreg2.dx irregular.dx labelled_series.dx labels.dx magnetism.dx majority.data mixed_freq.cm mri.general multigrid1.dx multigrid2.dx multigrid3.dx npp.dx oriented_labels.dx pos_conn.data product1.dx product2.dx rain.cm rainwater.dx record_datafile record_deformed record_deformed.general record_depconnections record_depconnections.general record_multiscalar record_multiscalar.general record_multiscalardepconn record_multiscalardepconn.general record_multiscalarmixed record_multiscalarmixed.general record_scalar record_scalar.general record_scalarvector1 record_scalarvector1.general record_scalarvector2 record_scalarvector2.general record_scattered.general record_series record_series.general record_vectordata1 record_vectordata1.general record_vectordata2 record_vectordata2.general record_withheader record_withheader.general regseries.dx regular.dx regularskewed.dx salesdata.data salesdata.txt sampletext.dx segmented_black-red.cm segmented_green-white.cm segmented_high-freq.cm segmented_hue.cm segmented_low-freq.cm series.dx seriesdata.dx solid.dx southeastern_topo.dx spreadsheet_2var spreadsheet_2var.general spreadsheet_deformed spreadsheet_deformed.general spreadsheet_layout.general spreadsheet_scattered.general spreadsheet_series.general storm_data.dx temp_wind.general temp_wind.lis temperature.dx test.hdf topo_one_deg.dx topography_km-gray.cm topography_km.cm topography_m-gray.cm topography_m.cm velocity.dx violet_to_white.cm watermolecule.dx wind.dx windbarbs.dx windbarbsdata.dx zipcode.data
-+data_DATA =  2D2ormorevarnotseries.data 2D2ormorevarnotseries.general 3D2ormorevarnotseries.data 3D2ormorevarnotseries.general CO2.general CO2.lis CO2fragment.lis FacesLoopsEdges.dx FacesLoopsEdges_hole.dx MOS_key.txt MOS_lookup.txt MOS_state_order.txt MOS_states.dx MOS_zips.dx MRI.data Polylines.dx ROM_ozone.dx README background.tiff block_example.data block_example.general blue_yellow.cm categorical.data categorical.data1 census.general census.spreadsheet census.tab census_normalized.dx cloudwater.dx colo_elev.general colorado.tiff colorado_elev.vit cyan_red.cm cylinder.rgb cylinder.size cylinder.tiff datadepconnections.dx datawithattribute.dx deformedregular.dx dx_logo.gif dx_logo2.tif dx_logo.tiff external.data externalfilter.c fontlayout.dx general.exampledata general.exampleheader griddeddata.data grocery.txt group.dx head_slice.dx heat.cm homeown.txt hyper.dx image.dx image.general imide.rgb imide.size imide_potential.dx invalid_field.bin invalid_field.dx irregirreg2.bin irregirreg2.dx irregular.dx labelled_series.dx labels.dx magnetism.dx majority.data mixed_freq.cm mri.general multigrid1.dx multigrid2.dx multigrid3.dx npp.dx oriented_labels.dx pos_conn.data product1.dx product2.dx rain.cm rainwater.dx record_datafile record_deformed record_deformed.general record_depconnections record_depconnections.general record_multiscalar record_multiscalar.general record_multiscalardepconn record_multiscalardepconn.general record_multiscalarmixed record_multiscalarmixed.general record_scalar record_scalar.general record_scalarvector1 record_scalarvector1.general record_scalarvector2 record_scalarvector2.general record_scattered.general record_series record_series.general record_vectordata1 record_vectordata1.general record_vectordata2 record_vectordata2.general record_withheader record_withheader.general regseries.dx regular.dx regularskewed.dx salesdata.data salesdata.txt sampletext.dx segmented_black-red.cm segmented_green-white.cm segmented_high-freq.cm segmented_hue.cm segmented_low-freq.cm series.dx seriesdata.dx solid.dx southeastern_topo.dx spreadsheet_2var spreadsheet_2var.general spreadsheet_deformed spreadsheet_deformed.general spreadsheet_layout.general spreadsheet_scattered.general spreadsheet_series.general storm_data.dx temp_wind.general temp_wind.lis temperature.dx test.hdf topo_one_deg.dx topography_km-gray.cm topography_km.cm topography_m-gray.cm topography_m.cm velocity.dx violet_to_white.cm watermolecule.dx wind.dx windbarbs.dx windbarbsdata.dx zipcode.data
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/programs/SIMPLE/Makefile.am.r	2004-04-26 23:43:18.000000000 +0200
-+++ dxsamples-4.4.0/programs/SIMPLE/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/SIMPLE
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/SIMPLE
- 
- LINKLIST = \
-          Arrange.cfg\
---- dxsamples-4.4.0/programs/SCATTERED/Makefile.am.r	2002-04-30 20:53:08.000000000 +0200
-+++ dxsamples-4.4.0/programs/SCATTERED/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/SCATTERED
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/SCATTERED
- 
- LINKLIST = \
-          AnnotationGlyphs.cfg\
---- dxsamples-4.4.0/programs/Makefile.am.r	2004-04-26 23:42:18.000000000 +0200
-+++ dxsamples-4.4.0/programs/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -6,7 +6,7 @@
-     IMAGE_PROCESSING IMPORTING INTERFACE_CONTROL LOOPING MISC PLOTTING \
-     PROBES RENDERING SCATTERED SEQUENCER SIMPLE SUPERVISE
- 
--datadir = $(prefix)/dx/samples/programs
-+datadir = @libdir@/dx/samples/programs
- 
- data_DATA =  $(DATA1) $(DATA2)
- 
---- dxsamples-4.4.0/programs/DATA_DRIVEN_INTERACTORS/Makefile.am.r	2002-04-30 20:53:22.000000000 +0200
-+++ dxsamples-4.4.0/programs/DATA_DRIVEN_INTERACTORS/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/DATA_DRIVEN_INTERACTORS
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/DATA_DRIVEN_INTERACTORS
- 
- LINKLIST = \
-          DataDrivenInteractors.cfg\
---- dxsamples-4.4.0/programs/LOOPING/Makefile.am.r	2002-04-30 20:53:17.000000000 +0200
-+++ dxsamples-4.4.0/programs/LOOPING/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/LOOPING
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/LOOPING
- 
- LINKLIST = \
-          Accumulate.cfg\
---- dxsamples-4.4.0/programs/CATEGORICAL/Makefile.am.r	2002-04-30 20:53:24.000000000 +0200
-+++ dxsamples-4.4.0/programs/CATEGORICAL/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/CATEGORICAL
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/CATEGORICAL
- 
- LINKLIST = \
-          Categorical.cfg\
---- dxsamples-4.4.0/programs/SUPERVISE/Makefile.am.r	2002-04-30 20:53:01.000000000 +0200
-+++ dxsamples-4.4.0/programs/SUPERVISE/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/SUPERVISE
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/SUPERVISE
- 
- LINKLIST = \
-          Image_wo_UI.cfg\
---- dxsamples-4.4.0/programs/PROBES/Makefile.am.r	2002-04-30 20:53:11.000000000 +0200
-+++ dxsamples-4.4.0/programs/PROBES/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/PROBES
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/PROBES
- 
- LINKLIST = \
-          PlotLine2.cfg\
---- dxsamples-4.4.0/programs/ANNOTATION/Makefile.am.r	2002-04-30 20:53:25.000000000 +0200
-+++ dxsamples-4.4.0/programs/ANNOTATION/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/ANNOTATION
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/ANNOTATION
- 
- LINKLIST = \
-          AnnotationGlyphs.cfg\
---- dxsamples-4.4.0/programs/3D_DATA/Makefile.am.r	2002-04-30 20:53:26.000000000 +0200
-+++ dxsamples-4.4.0/programs/3D_DATA/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/3D_DATA
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/3D_DATA
- 
- LINKLIST = \
-          AnnotationGlyphs.cfg\
---- dxsamples-4.4.0/programs/IMAGE_PROCESSING/Makefile.am.r	2002-04-30 20:53:20.000000000 +0200
-+++ dxsamples-4.4.0/programs/IMAGE_PROCESSING/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/IMAGE_PROCESSING
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/IMAGE_PROCESSING
- 
- LINKLIST = \
-          FFT.cfg\
---- dxsamples-4.4.0/programs/DEBUGGING/Makefile.am.r	2002-04-30 20:53:21.000000000 +0200
-+++ dxsamples-4.4.0/programs/DEBUGGING/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/DEBUGGING
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/DEBUGGING
- 
- LINKLIST = \
-          Verify.cfg\
---- dxsamples-4.4.0/programs/COLORMAP_EDITOR/Makefile.am.r	2002-04-30 20:53:23.000000000 +0200
-+++ dxsamples-4.4.0/programs/COLORMAP_EDITOR/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/COLORMAP_EDITOR
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/COLORMAP_EDITOR
- 
- LINKLIST = \
-          DataDrivenInteractors.cfg\
---- dxsamples-4.4.0/programs/COMPUTE/Makefile.am.r	2002-04-30 20:53:23.000000000 +0200
-+++ dxsamples-4.4.0/programs/COMPUTE/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/COMPUTE
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/COMPUTE
- 
- LINKLIST = \
-          Bounce.cfg\
---- dxsamples-4.4.0/programs/RENDERING/Makefile.am.r	2002-04-30 20:53:10.000000000 +0200
-+++ dxsamples-4.4.0/programs/RENDERING/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/RENDERING
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/RENDERING
- 
- LINKLIST = \
-          FatLines.cfg\
---- dxsamples-4.4.0/programs/2D_DATA/Makefile.am.r	2002-04-30 20:53:26.000000000 +0200
-+++ dxsamples-4.4.0/programs/2D_DATA/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/2D_DATA
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/2D_DATA
- 
- LINKLIST = \
-          AlternateVisualizations.cfg\
---- dxsamples-4.4.0/programs/MISC/Makefile.am.r	2002-04-30 20:53:13.000000000 +0200
-+++ dxsamples-4.4.0/programs/MISC/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/MISC
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/MISC
- 
- LINKLIST = \
-          CensusData.cfg\
---- dxsamples-4.4.0/programs/SEQUENCER/Makefile.am.r	2002-04-30 20:53:07.000000000 +0200
-+++ dxsamples-4.4.0/programs/SEQUENCER/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/SEQUENCER
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/SEQUENCER
- 
- LINKLIST = \
-          ContoursAndCaption.cfg\
---- dxsamples-4.4.0/programs/PLOTTING/Makefile.am.r	2002-04-30 20:53:12.000000000 +0200
-+++ dxsamples-4.4.0/programs/PLOTTING/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/PLOTTING
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/PLOTTING
- 
- LINKLIST = \
-          Categorical.cfg\
---- dxsamples-4.4.0/programs/DISTRIBUTED_PROCESSING/Makefile.am.r	2002-04-30 20:53:20.000000000 +0200
-+++ dxsamples-4.4.0/programs/DISTRIBUTED_PROCESSING/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/DISTRIBUTED_PROCESSING
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/DISTRIBUTED_PROCESSING
- 
- LINKLIST = \
-          Distributed.cfg\
---- dxsamples-4.4.0/programs/INTERFACE_CONTROL/Makefile.am.r	2002-04-30 20:53:18.000000000 +0200
-+++ dxsamples-4.4.0/programs/INTERFACE_CONTROL/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/INTERFACE_CONTROL
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/INTERFACE_CONTROL
- 
- LINKLIST = \
-          DialogStyle.cfg\
---- dxsamples-4.4.0/programs/IMPORTING/Makefile.am.r	2002-04-30 20:53:19.000000000 +0200
-+++ dxsamples-4.4.0/programs/IMPORTING/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--sampleprogdir = $(prefix)/dx/samples/programs/IMPORTING
-+sampleprogdir = $(DESTDIR)@libdir@/dx/samples/programs/IMPORTING
- 
- LINKLIST = \
-          Categorical.cfg\
---- dxsamples-4.4.0/dxlink/Makefile.am.r	2003-10-20 05:28:44.000000000 +0200
-+++ dxsamples-4.4.0/dxlink/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/dxlink
-+datadir = @libdir@/dx/samples/dxlink
- 
- data_DATA =  CensusData150.rgb CensusData150.size Imide_potential150.rgb \
- 	Imide_potential150.size Makefile_alphax Makefile_aviion Makefile_hp700 \
---- dxsamples-4.4.0/scripts/Makefile.am.r	2003-06-19 16:58:07.000000000 +0200
-+++ dxsamples-4.4.0/scripts/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/scripts
-+datadir = @libdir@/dx/samples/scripts
- 
- data_DATA =  AmbientLight Append Arrange Attribute AutoAxes AutoCamera AutoColor \
- 	AutoGlyph AutoGrayScale Band Camera Caption ClipBox ClipPlane Collect \
---- dxsamples-4.4.0/stereo/src/Makefile.am.r	2005-02-01 07:20:27.000000000 +0100
-+++ dxsamples-4.4.0/stereo/src/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--datadir = $(prefix)/dx/samples/stereo/src
-+datadir = @libdir@/dx/samples/stereo/src
- 
- data_DATA =  mymodes.c mycams.c
- 
---- dxsamples-4.4.0/stereo/Makefile.am.r	2001-06-21 23:30:41.000000000 +0200
-+++ dxsamples-4.4.0/stereo/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -2,7 +2,7 @@
- 
- SUBDIRS = src 
- 
--datadir = $(prefix)/dx/samples/stereo
-+datadir = @libdir@/dx/samples/stereo
- 
- data_DATA = StereoMacro.net StereoState.net TestStereo.cfg TestStereo.net stereo.html
- 
---- dxsamples-4.4.0/user/Makefile.am.r	2003-06-19 07:09:14.000000000 +0200
-+++ dxsamples-4.4.0/user/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/user
-+datadir = @libdir@/dx/samples/user
- 
- data_DATA =  Makefile_inboard_alphax Makefile_inboard_aviion Makefile_inboard_hp700 Makefile_inboard_ibm6000 Makefile_inboard_ibmpvs Makefile_inboard_intelnt Makefile_inboard_sgi Makefile_inboard_solaris Makefile_inboard_sun4 Makefile_intelnt Makefile_loadable_alphax Makefile_loadable_hp700 Makefile_loadable_ibm6000 Makefile_loadable_intelnt Makefile_loadable_sgi Makefile_loadable_solaris Makefile_os2 Makefile_outboard_alphax Makefile_outboard_aviion Makefile_outboard_hp700 Makefile_outboard_ibm6000 Makefile_outboard_ibmpvs Makefile_outboard_intelnt Makefile_outboard_sgi Makefile_outboard_solaris Makefile_outboard_sun4 README add.c hello.c hello_loadable.mdf makex.c user_inboard.mdf user_loadable.mdf user_outboard.mdf
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/program_guide/Makefile.am.r	2005-02-01 07:19:50.000000000 +0100
-+++ dxsamples-4.4.0/program_guide/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--datadir = $(prefix)/dx/samples/program_guide
-+datadir = @libdir@/dx/samples/program_guide
- 
- data_DATA =  README add.c add.cfg add.mb add.mdf add.net add2.c add2.cfg \
- 	     add2.mb add2.mdf add2.net add2_invalid.cfg add2_invalid.net \
---- dxsamples-4.4.0/macros/Makefile.am.r	1999-05-06 00:02:05.000000000 +0200
-+++ dxsamples-4.4.0/macros/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/macros
-+datadir = @libdir@/dx/samples/macros
- 
- data_DATA =  ArrangeMemberMacro.net AutoScaleMacro.net BandColorsMacro.net BarChartMacro.net CappedIsoMacro.net ClipSurfaceMacro.net ClipVolumeMacro.net ConvertColorNameListMacro.net DrapeMacro.net ExportVRML.net FactorialMacro.net FormatListMacro.net GetCategoricalLabelsMacro.net GetEventsMacro.net Image2Macro.net InsetImageMacro.net InterpolateCameraMacro.net InterpolatePositionsMacro.net KeyFrameCameraMacro.net MOS_statesMacro.net Make3DFieldMacro.net MakeLineMacro.net MapOnStatesMacro.net MatteMacro.net PickPlotMacro.net UnsquishGlyphMacro.net WindBarbsMacro.net
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/tutorial/Makefile.am.r	1999-05-06 00:02:19.000000000 +0200
-+++ dxsamples-4.4.0/tutorial/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/tutorial
-+datadir = @libdir@/dx/samples/tutorial
- 
- data_DATA =  Animate.cfg Animate.net AutoColor.cfg AutoColor.net AutoColor2D.cfg AutoColor2D.net AutoGlyph2DScalar.cfg AutoGlyph2DScalar.net AutoGlyph2DVector.cfg AutoGlyph2DVector.net AutoGlyph3DScalar.cfg AutoGlyph3DScalar.net AutoGlyph3DVector.cfg AutoGlyph3DVector.net Caption.cfg Caption.net Color2D.cfg Color2D.net Compute.cfg Compute.net Connect.cfg Connect.net DataDrivenColormap.cfg DataDrivenColormap.net DataDrivenScalar.cfg DataDrivenScalar.net DataDrivenSelector.cfg DataDrivenSelector.net DataDrivenSequencer.cfg DataDrivenSequencer.net ImageProcessing.cfg ImageProcessing.net Isosurface2D.cfg Isosurface2D.net Isosurface3D.cfg Isosurface3D.net Map.cfg Map.net MapToPlane.cfg MapToPlane.net Plot.cfg Plot.net Regrid.cfg Regrid.net RubberSheet.cfg RubberSheet.net SampleMacro.net Slab.cfg Slab.net Streamlines2D.cfg Streamlines2D.net Streamlines3D.cfg Streamlines3D.net Switch.cfg Switch.net UseSampleMacro.cfg UseSampleMacro.net VolumeRendering.cfg VolumeRendering.net WarpedGrid.cfg WarpedGrid.net batch_script example.general example1.cfg example1.net external.data spreadsheet.data view_isosurfaces.cfg view_isosurfaces.net
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/outboard/Makefile.am.r	2004-05-25 00:21:27.000000000 +0200
-+++ dxsamples-4.4.0/outboard/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/outboard
-+datadir = @libdir@/dx/samples/outboard
- 
- data_DATA =  Makefile_alphax Makefile_aviion Makefile_hp700 Makefile_ibm6000 Makefile_ibmpvs Makefile_intelnt Makefile_linux Makefile_os2 Makefile_sgi Makefile_solaris Makefile_sun4 README async.c async.mdf dummy.c hello.c hello.mdf makedata my_simulation.c socket.c watchfile.c watchfile.mdf watchsocket.c watchsocket.cfg watchsocket.mdf watchsocket.net
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/callmodule/Makefile.am.r	2005-02-01 07:19:17.000000000 +0100
-+++ dxsamples-4.4.0/callmodule/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--datadir = $(prefix)/dx/samples/callmodule
-+datadir = @libdir@/dx/samples/callmodule
- 
- data_DATA = README Simple.c ThunderStreamlines.c renderimage.c xapp_supervise.c
- 
---- dxsamples-4.4.0/util/Makefile.am.r	2002-11-11 05:55:54.000000000 +0100
-+++ dxsamples-4.4.0/util/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -3,7 +3,7 @@
- 
- SUBDIRS =  dxf fluent mpeg plot3d biorad-pic
- 
--datadir = $(prefix)/dx/samples/util
-+datadir = @libdir@/dx/samples/util
- 
- data_DATA =  Makefile.sample
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/util/fluent/Makefile.am.r	1999-05-06 00:02:21.000000000 +0200
-+++ dxsamples-4.4.0/util/fluent/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/util/fluent
-+datadir = @libdir@/dx/samples/util/fluent
- 
- data_DATA =  Fluent2DX.c README
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/util/dxf/Makefile.am.r	1999-05-06 00:02:21.000000000 +0200
-+++ dxsamples-4.4.0/util/dxf/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/util/dxf
-+datadir = @libdir@/dx/samples/util/dxf
- 
- data_DATA =  MANIFEST Makefile.sample README balloon.dxf colors.c common.c dx.c dxf.c dxf.h dxf_r12.txt entity.c entity.h header.c ignored.c output_funcs.c read.c snag_funcs.c table.c tree.c x29.dxf
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/util/plot3d/Makefile.am.r	1999-05-06 00:02:21.000000000 +0200
-+++ dxsamples-4.4.0/util/plot3d/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/util/plot3d
-+datadir = @libdir@/dx/samples/util/plot3d
- 
- data_DATA =  Plot3DtoDX.c README
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/util/biorad-pic/Makefile.am.r	2002-11-11 05:55:35.000000000 +0100
-+++ dxsamples-4.4.0/util/biorad-pic/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--datadir = $(prefix)/dx/samples/util/biorad-pic
-+datadir = @libdir@/dx/samples/util/biorad-pic
- 
- data_DATA =  PIC2dx.c README
- EXTRA_DIST = $(data_DATA)
---- dxsamples-4.4.0/util/mpeg/Makefile.am.r	1999-05-06 00:02:21.000000000 +0200
-+++ dxsamples-4.4.0/util/mpeg/Makefile.am	2006-09-03 01:38:54.000000000 +0200
-@@ -1,7 +1,7 @@
- ## Process this file with automake to produce Makefile.in
- 
- 
--datadir = $(prefix)/dx/samples/util/mpeg
-+datadir = @libdir@/dx/samples/util/mpeg
- 
- data_DATA =  README default.param write_yuv.cfg write_yuv.net
- EXTRA_DIST = $(data_DATA)
diff --git a/sci-visualization/opendx-samples/files/opendx-samples-4.4.0-nojava.patch b/sci-visualization/opendx-samples/files/opendx-samples-4.4.0-nojava.patch
deleted file mode 100644
index 984f84a10..000000000
--- a/sci-visualization/opendx-samples/files/opendx-samples-4.4.0-nojava.patch
+++ /dev/null
@@ -1,50 +0,0 @@
---- dxsamples-4.4.0/Makefile.am.nojava	2002-01-28 21:53:08.000000000 +0100
-+++ dxsamples-4.4.0/Makefile.am	2006-09-03 01:40:26.000000000 +0200
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--SUBDIRS = callmodule data dxlink java macros \
-+SUBDIRS = callmodule data dxlink macros \
- 	  outboard program_guide programs scripts \
- 	  supervise tutorial user util stereo
- 
---- dxsamples-4.4.0/configure.ac-orig	2009-05-03 14:30:59.000000000 +1200
-+++ dxsamples-4.4.0/configure.ac	2009-05-03 14:31:44.000000000 +1200
-@@ -25,11 +25,6 @@ AC_SUBST(RTL_LIBS)
- 
- SHELL=/bin/sh
- 
--AC_ARG_WITH(javadx,
--              [  --with-javadx           enable JAVADX (default is yes)],
--              [with_javadx=$withval],
--              [with_javadx='yes'])
--
- AC_PROG_INSTALL
- if test -z "$LN_S" ; then
-     AC_PROG_LN_S
-@@ -40,25 +35,8 @@ DX_GET_PREFIX
- DX_GET_ARCH
- DX_ARCH_SPECIFIC
- 
--MAKE_JAVADX_SAMPLES=""
--if test "with_javadx" != 'no' ; then
--  failed=0;
--  passed=0;
--  DX_PROG_JAVAC(passed=`expr $passed + 1`,failed=`expr $failed + 1`)
--  DX_PROG_JAR(passed=`expr $passed + 1`,failed=`expr $failed + 1`)
--
--  if test $failed -eq 0 ; then
--     DX_JAVADX_SETUP(passed=`expr $passed + 1`,failed=`expr $failed + 1`)
--     if test $failed -eq 0 ; then
--       MAKE_JAVADX_SAMPLES=samples
--     fi
--  fi
--fi
--
- AC_OUTPUT( Makefile callmodule/Makefile callmodule/localmk \
- 	data/Makefile dxlink/Makefile dxlink/dxlink_make \
--	java/samples/Makefile java/Makefile java/userdata/Makefile  \
--	java/usermacros/Makefile  java/nets/Makefile  java/makes/Makefile  \
- 	macros/Makefile outboard/Makefile \
- 	program_guide/Makefile program_guide/localmk program_guide/guidemake \
- 	programs/2D_DATA/Makefile programs/3D_DATA/Makefile \
diff --git a/sci-visualization/opendx-samples/opendx-samples-4.4.0-r1.ebuild b/sci-visualization/opendx-samples/opendx-samples-4.4.0-r1.ebuild
deleted file mode 100644
index ab905cdd0..000000000
--- a/sci-visualization/opendx-samples/opendx-samples-4.4.0-r1.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=2
-
-inherit eutils multilib autotools
-
-MY_PN="dxsamples"
-MY_P="${MY_PN}-${PV}"
-DESCRIPTION="Samples for IBM Data Explorer"
-HOMEPAGE="http://www.opendx.org/"
-SRC_URI="http://opendx.sdsc.edu/source/${MY_P}.tar.gz"
-LICENSE="IPL-1"
-SLOT="0"
-
-S="${WORKDIR}/${MY_P}"
-
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE=""
-
-RDEPEND=">=sci-visualization/opendx-4.4.4-r2"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-
-	epatch "${FILESDIR}/${P}-nojava.patch"
-#	absolutely no javadx for now
-	epatch "${FILESDIR}/${P}-install.patch"
-
-	eautoreconf
-}
-
-src_configure() {
-	econf "--libdir=/usr/$(get_libdir)"
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die
-}
-
-pkg_postinst() {
-	elog "This version of the opendx-samples ebuild is still under development."
-	elog "suggestions, comments and offer of help welcome"
-	elog "post a message in gentoo-science or pop up on irc on #gentoo-science"
-}
diff --git a/sci-visualization/opendx/ChangeLog b/sci-visualization/opendx/ChangeLog
deleted file mode 100644
index 7c1468dbe..000000000
--- a/sci-visualization/opendx/ChangeLog
+++ /dev/null
@@ -1,164 +0,0 @@
-# ChangeLog for sci-visualization/opendx
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-visualization/opendx/ChangeLog,v 1.15 2008/09/14 11:25:38 spock Exp $
-
-  14 Jun 2009; François Bissey <f.r.bissey@massey.ac.nz>
-  opendx-4.4.4-r2.ebuild, +files/opendx-4.4.4-szip.patch:
-  Patch configure.ac to make szip a proper configure option
-
-  12 May 2009; François Bissey <f.r.bissey@massey.ac.nz>
-  files/opendx-4.4.4-concurrent-make-fix.patch:
-  make sure the concurent make fix _always_ works.
-
-*opendx-4.4.4-r2 (11 May 2009)
-
-  11 May 2009; François Bissey <f.r.bissey@massey.ac.nz>
-  opendx-4.4.4-r1.ebuild, +opendx-4.4.4-r2.ebuild,
-  +files/opendx-4.4.4-install.patch, +files/opendx-4.4.4-xdg.patch:
-  small clean up in opendx-4.4.4-r1, in r2 new layout for the installation
-  and replaced call to netscape/lynx etc... with xdg-open
-
-  19 Apr 2009; François Bissey <f.r.bissey@massey.ac.nz>
-  +files/opendx-4.4.4-dx-errno.patch,
-  +files/opendx-4.4.4-gcc43-fedora.patch, +files/opendx-4.4.4-open.patch,
-  -files/dx-errno.patch, -files/dx-gcc43-fedora.patch, -files/dx-open.patch,
-  opendx-4.4.4-r1.ebuild:
-  rename patches to something nicer. some cleaning of the ebuild structure.
-  introduce the smp keyword and simplify greatly the associated logic.
-
-*opendx-4.4.4-r1 (17 Apr 2009)
-
-  17 Apr 2009; François Bissey <f.r.bissey@massey.ac.nz>
-  +files/20-opendx-revdep, +files/opendx-4.3.2-sys.h.patch,
-  +files/opendx-4.4.4-concurrent-make-fix.patch,
-  +files/opendx-4.4.4-libtool.patch, +files/dx-errno.patch,
-  +files/dx-gcc43-fedora.patch, +files/dx-open.patch,
-  +files/opendx-compressed-man.patch, +metadata.xml,
-  +opendx-4.4.4-r1.ebuild:
-  Initial import in the overlay from the main tree. *port to EAPI2 *updated
-  gcc43 patch to upstream/fedora level *added an upstream patch to fix bug
-  #261438 *added a fedora patch to solve a problem dx use all CPU after
-  exiting *updated the source url to a working one
-
-  14 Sep 2008; Michał Januszewski <spock@gentoo.org>
-  +files/opendx-4.4.4-concurrent-make-fix.patch, opendx-4.4.4.ebuild:
-  Fix concurrent make (bug #230535).
-
-  06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml:
-  Add USE flag description to metadata wrt GLEP 56.
-
-  29 Jun 2008; Markus Dittrich <markusle@gentoo.org>
-  +files/opendx-4.4.4-libtool.patch, opendx-4.4.4.ebuild:
-  Added libtool-2.2* compatibility patch (fixes bug #229901).
-
-  18 May 2008; Michał Januszewski <spock@gentoo.org>
-  +files/opendx-4.4.4-gcc43.patch, opendx-4.4.4.ebuild:
-  Add a patch to allow compilation with GCC 4.3.
-
-  05 Apr 2008; Markus Dittrich <markusle@gentoo.org> opendx-4.3.2-r1.ebuild,
-  opendx-4.4.4.ebuild:
-  Need to call linux-info_pkg_setup to pick up the correct environment
-  variables (fixed bug #216243).
-
-  26 Mar 2008; Markus Dittrich <markusle@gentoo.org> opendx-4.3.2-r1.ebuild,
-  opendx-4.4.4.ebuild:
-  Added check for imagemagick's hdri useflag which breaks compilation 
-  (see bug #214058).
-
-  28 Feb 2008; Markus Dittrich <markusle@gentoo.org>
-  +files/20-opendx-revdep, opendx-4.3.2-r1.ebuild, opendx-4.4.4.ebuild:
-  Added file to make revdep-rebuild aware of opendx binary paths 
-  (see bug #211553).
-
-*opendx-4.4.4 (21 Jan 2008)
-
-  21 Jan 2008; Michał Januszewski <spock@gentoo.org>
-  +files/opendx-compressed-man.patch, +opendx-4.4.4.ebuild:
-  Version bump.
-
-  22 Jul 2007; Donnie Berkholz <dberkholz@gentoo.org>;
-  opendx-4.3.2-r1.ebuild:
-  Drop virtual/x11 references.
-
-  19 Jul 2007; Jeff Gardner <je_fro@gentoo.org>
-  +files/opendx-4.3.2-sys.h.patch, -files/opendx-sys.h.patch,
-  opendx-4.3.2-r1.ebuild:
-  Fix patch name.
-
-  19 Jul 2007; Jeff Gardner <je_fro@gentoo.org> +files/opendx-sys.h.patch,
-  opendx-4.3.2-r1.ebuild:
-  Add patch to fix compilation with >=linux headers-2.6.19. See bug 185828.
-
-  22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog:
-  Redigest for Manifest2
-
-  09 Apr 2006; Marcus D. Hanwell <cryos@gentoo.org> -opendx-4.3.2.ebuild:
-  Prune old version.
-
-  29 Jan 2006; Marcus D. Hanwell <cryos@gentoo.org> +metadata.xml,
-  +opendx-4.3.2.ebuild, +opendx-4.3.2-r1.ebuild:
-  Moved from media-gfx/opendx to sci-visualization/opendx.
-
-  26 Jan 2006; Karol Wojtaszek <sekretarz@gentoo.org>
-  opendx-4.3.2-r1.ebuild:
-  Stable on amd64, bug #118683
-
-  14 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>;
-  opendx-4.3.2-r1.ebuild:
-  Add modular X dependencies.
-
-  28 Aug 2005; Simon Stelling <blubb@gentoo.org> ChangeLog:
-  added ~amd64 keyword
-
-  20 Aug 2005; Michael Hanselmann <hansmi@gentoo.org>
-  opendx-4.3.2-r1.ebuild:
-  Stable on ppc (bug #101923).
-
-  25 Jul 2005; Donnie Berkholz <spyderous@gentoo.org>;
-  opendx-4.3.2-r1.ebuild:
-  Stable on x86.
-
-  25 Jul 2005; Donnie Berkholz <spyderous@gentoo.org>;
-  opendx-4.3.2-r1.ebuild:
-  Update to use linux-info.eclass and to check for SMP properly.
-
-  24 May 2005; Donnie Berkholz <spyderous@gentoo.org>;
-  opendx-4.3.2-r1.ebuild:
-  (#82672) Filter -finline-functions and -O3.
-
-  28 Dec 2004; Olivier Fisette <ribosome@gentoo.org> :
-  Dependency update: dev-libs/szip -> sci-libs/szip.
-
-  28 Dec 2004; Olivier Fisette <ribosome@gentoo.org> :
-  Dependency update: dev-libs/szip -> sci-libs/szip.
-
-  28 Dec 2004; Olivier Fisette <ribosome@gentoo.org> opendx-4.3.2-r1.ebuild:
-  Dependency update: dev-libs/szip -> sci-libs/szip.
-
-  28 Dec 2004; Olivier Fisette <ribosome@gentoo.org> opendx-4.3.2.ebuild:
-  Dependency update: dev-libs/szip -> sci-libs/szip.
-
-  28 Dec 2004; Olivier Fisette <ribosome@gentoo.org> opendx-4.3.2-r1.ebuild:
-  Dependency update: dev-libs/hdf -> sci-libs/hdf.
-
-  28 Dec 2004; Olivier Fisette <ribosome@gentoo.org> opendx-4.3.2.ebuild:
-  Dependency update: dev-libs/hdf -> sci-libs/hdf.
-
-*opendx-4.3.2-r1 (24 May 2004)
-
-  24 May 2004; Patrick Kursawe <phosphan@gentoo.org> opendx-4.3.2-r1.ebuild:
-  Making szip dependency optional
-
-  16 Mar 2004; Patrick Kursawe <phosphan@gentoo.org> opendx-4.3.2.ebuild:
-  Fixing bug #44727 by adding szip as dependency.
-
-  15 Mar 2004; David Holm <dholm@gentoo.org> opendx-4.3.2.ebuild:
-  Added to ~ppc.
-
-*opendx-4.3.2 (14 Mar 2004)
-
-  14 Mar 2004; Donnie Berkholz <spyderous@gentoo.org>; metadata.xml,
-  opendx-4.3.2.ebuild:
-  Initial commit to close #22217. Ebuild by myself and Patrick Kursawe
-  <phosphan@gentoo.org>.
-
diff --git a/sci-visualization/opendx/Manifest b/sci-visualization/opendx/Manifest
deleted file mode 100644
index e49a49180..000000000
--- a/sci-visualization/opendx/Manifest
+++ /dev/null
@@ -1,16 +0,0 @@
-AUX 20-opendx-revdep 44 RMD160 9b68b96b8f513a78a51249c7705d93d665bb3d2b SHA1 9389ea70249fe8149a33944a07466dddc9c1ae8d SHA256 fa96c22f9e7870a60c27c02cceb6bb3782d40c07ac53f19d7be7941a12347a01
-AUX opendx-4.3.2-sys.h.patch 1200 RMD160 f3658ac7fd0582b69ab32df5cc23d77f8d5364c8 SHA1 b4eed91d8ad2df57241a74d4ef8452ad0d171296 SHA256 919299f0fbb6e9891a8792641ea58720ae6bb95d4ffc3f6a20cae7b8e2d1729b
-AUX opendx-4.4.4-concurrent-make-fix.patch 2388 RMD160 b30b7aa12a3d8c36b90e7d0fd4eb653a828203ee SHA1 786d37fda67bc4cb0ef96f2fbaac927123432658 SHA256 7ce46d4fe5dda470d4a165409de8c69c1bcda1a065ecf782dbe8e1b28ee88dcf
-AUX opendx-4.4.4-dx-errno.patch 340 RMD160 39928c8d031394cf59dd6dd06d25f26cd56482b7 SHA1 7be653fb8303a49a5788dee27323192c2127d199 SHA256 046fdd113d0c3c48b2c0efabe11423539e0ab8b0d567df2acfff93f5864ea7e4
-AUX opendx-4.4.4-gcc43-fedora.patch 13310 RMD160 b98f8034d26db8440be8c8e02a06aaf24fb7030a SHA1 513a64535c04da9ab65db6b89318002171ef2e4c SHA256 8ca2296f7c36f0dd7dbaf185b3fdf68ea40a09695aaca6c0f65d3970286d225d
-AUX opendx-4.4.4-install.patch 11982 RMD160 2136aca79e909dc28cc18c6fd821014e777c96ea SHA1 7a86aec33dc1d23ab9700dcd6f8cb9d7d08c512d SHA256 75f9ee934b19f9f67fdbfd16b9d52fb692bb4db3d1a1fc8cc666c7ac5c5e447f
-AUX opendx-4.4.4-libtool.patch 319 RMD160 2b501064b72e84f791ee3c3b3ac3bd83d6fd0de7 SHA1 6548dae81cb9fdf83f2a0a1095851ef40578de0e SHA256 1bde8364f7a40322f9812f0fbb0403ab8f52f946318bd548e7fa63dd887c291f
-AUX opendx-4.4.4-open.patch 1671 RMD160 9c4ba9d2735049c841c32ab2efa2d778ce80044a SHA1 f59ba51b5e301f4bf20512835adadd3c65f2fd29 SHA256 0b0cbc06ecc8e44d32f16000c6ee2c09b70b7cfbf44ee71a50165dad19314403
-AUX opendx-4.4.4-szip.patch 1482 RMD160 67bef3dade274ac78011bc23913dd8b7724ee13d SHA1 edfb38bb5c73d340716dc6e8ccd01eea0ee5de1a SHA256 c330e0fc642d4f5004fd3173532e2f7223499dc612be298a53b41f423b021a23
-AUX opendx-4.4.4-xdg.patch 785 RMD160 ee1a8bce4a352c7bf3335f5e13bd81664f3fd7c3 SHA1 001cb1ee444631926b43857aac137ce2d9336ba2 SHA256 93e50b0da16f3d28c016fa95ee49530322e83f8527b45abd7415bb14365600c1
-AUX opendx-compressed-man.patch 496 RMD160 670de4ea728a3f9b5c02f7950ce88c58d1073a7b SHA1 56dd8a6d9710264ae3b45358ad2eb48ad00d6d98 SHA256 2877bd95b592548c1a0a532b49131b84f5ab1077714ef16d768f3e33f50d6aab
-DIST dx-4.4.4.tar.gz 9676049 RMD160 db4cff78c9712a6e1e19265b0f42fdb87ab5ff7b SHA1 c8e4d72d169675c66acd2135599b211d80810f76 SHA256 a9915e17d49c5499edd3df69ffeac0b7ba24f8b38ddf7509712b48eb3c21f1ff
-EBUILD opendx-4.4.4-r1.ebuild 2403 RMD160 b3949b577be1888d71ea220e111da11fe59fa4d2 SHA1 6392a006d33e9205fbed11408a458c97c1a37360 SHA256 788ab5b20cd81b19b4c34cce650dac91a4eff4ea12a31b750cae08d527716203
-EBUILD opendx-4.4.4-r2.ebuild 2349 RMD160 c41235566ae47fe6d9617b8f8ce4dcf92cb4c9df SHA1 c1ef20ad2a60e2121cd400886239c9ecfc208df3 SHA256 6624f2e8169e4cecc5373be1449130a42c7ec3597ef1f9facc7096aa87996d1d
-MISC ChangeLog 6270 RMD160 186702f315f64b27d685b4186ef19d8b3e3f5a00 SHA1 59d356e5e22e987907129f6c6a0575affdda75b1 SHA256 41c2438f61abb39ef9715845fad8340f548c3c01f44e364442282f53afa83033
-MISC metadata.xml 361 RMD160 404d4eb0602277959498f65685d76eb4350a470d SHA1 f683e24f437dc6a5254d2d4c814c48cfd7d3740e SHA256 1be0f8158e35295c498714d8ad1b780a6fc749bee37bdbb13ad9eb163bbf38f0
diff --git a/sci-visualization/opendx/files/20-opendx-revdep b/sci-visualization/opendx/files/20-opendx-revdep
deleted file mode 100644
index f1d735116..000000000
--- a/sci-visualization/opendx/files/20-opendx-revdep
+++ /dev/null
@@ -1 +0,0 @@
-SEARCH_DIRS="/usr/dx/bin /usr/dx/bin_linux"
diff --git a/sci-visualization/opendx/files/opendx-4.3.2-sys.h.patch b/sci-visualization/opendx/files/opendx-4.3.2-sys.h.patch
deleted file mode 100644
index 93bf18efb..000000000
--- a/sci-visualization/opendx/files/opendx-4.3.2-sys.h.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-diff -aurN dx-4.3.2-orig/configure.ac dx-4.3.2/configure.ac
---- dx-4.3.2-orig/configure.ac	2007-07-19 00:59:55.000000000 -0500
-+++ dx-4.3.2/configure.ac	2007-07-19 01:02:34.000000000 -0500
-@@ -1004,7 +1004,7 @@
-   Xm/ScrolledWP.h Xm/SelectioB.h Xm/SeparatoG.h Xm/SeparatoGP.h Xm/Separator.h \
-   Xm/Text.h Xm/TextF.h Xm/ToggleB.h Xm/ToggleBG.h Xm/Xm.h Xm/XmP.h Xm/XmStrDefs.h \
-   gl.h gl/device.h gl/gl.h invent.h iop/afb.h iop/mov.h iop/pfs.h license.h \
--  linux/kernel.h linux/sys.h math.h mingw32/dir.h mon.h net/if_arp.h net/route.h \
-+  linux/kernel.h math.h mingw32/dir.h mon.h net/if_arp.h net/route.h \
-   os2.h setjmp.h starbase.c.h stddef.h stdio.h synch.h sys/access.h \
-   sys/ipc.h sys/m88kbcs.h sys/mman.h sys/mode.h sys/pstat.h sys/resource.h \
-   sys/svs.h sys/sysconfig.h sys/syslimits.h sys/sysmacros.h ulocks.h x11/xlibxtra.h \
-diff -aurN dx-4.3.2-orig/src/exec/libdx/memory.c dx-4.3.2/src/exec/libdx/memory.c
---- dx-4.3.2-orig/src/exec/libdx/memory.c	2007-07-19 00:59:54.000000000 -0500
-+++ dx-4.3.2/src/exec/libdx/memory.c	2007-07-19 01:01:57.000000000 -0500
-@@ -66,7 +66,6 @@
- 
- #if linux
- #include <linux/kernel.h>
--#include <linux/sys.h>
- #include <sys/sysinfo.h>
- #endif
- 
diff --git a/sci-visualization/opendx/files/opendx-4.4.4-concurrent-make-fix.patch b/sci-visualization/opendx/files/opendx-4.4.4-concurrent-make-fix.patch
deleted file mode 100644
index ba2c9c8c4..000000000
--- a/sci-visualization/opendx/files/opendx-4.4.4-concurrent-make-fix.patch
+++ /dev/null
@@ -1,66 +0,0 @@
-diff -Nuarp dx-4.4.4-orig/src/exec/dxmods/local.mk dx-4.4.4/src/exec/dxmods/local.mk
---- dx-4.4.4-orig/src/exec/dxmods/local.mk	2008-09-11 22:31:38.000000000 +0200
-+++ dx-4.4.4/src/exec/dxmods/local.mk	2008-09-11 22:33:44.000000000 +0200
-@@ -14,15 +14,15 @@ user.c:  dx.mdf
- 
- dxcm.mdf:  ${srcdir}/dxmdf.src
- 	-rm -f dxcm.mdf
--	cp ${srcdir}/dxmdf.src tmp.c
--	$(CPP) $(INCLUDES) $(MDF) $(DEFS) tmp.c > dxcm.mdf
--	-rm -f tmp.c
-+	cp ${srcdir}/dxmdf.src tmp-dxcm.c
-+	$(CPP) $(INCLUDES) $(MDF) $(DEFS) tmp-dxcm.c > dxcm.mdf
-+	-rm -f tmp-dxcm.c
- 
- dx.mdf:  ${srcdir}/dxmdf.src
- 	echo MYINC: $(MYINC)
- 	-rm -f dx.mdf
--	cp ${srcdir}/dxmdf.src tmp.c
--	$(CPP) $(INCLUDES) $(MYINC) $(MDF) $(DEFS) -DCPLUSPLUS_UI -DEXECUTIVE_MODS tmp.c > dx.mdf
-+	cp ${srcdir}/dxmdf.src tmp-dx.c
-+	$(CPP) $(INCLUDES) $(MYINC) $(MDF) $(DEFS) -DCPLUSPLUS_UI -DEXECUTIVE_MODS tmp-dx.c > dx.mdf
- 	@echo '/^ *$$/{' > stripl.sed
- 	@echo 'N' >> stripl.sed
- 	@echo '/^ *\\n *$$/D' >> stripl.sed
-@@ -30,7 +30,7 @@ dx.mdf:  ${srcdir}/dxmdf.src
- 	cat dx.mdf |sed '/^#/d' > tmp.mdf
- 	cat tmp.mdf |sed -f stripl.sed > dx.mdf
- 	@rm -f stripl.sed tmp.mdf
--	-rm -f tmp.c
-+	-rm -f tmp-dx.c
- 
- .y.h:
- 	$(YACC) $(YFLAGS) -d ${srcdir}/$*.y
-diff -Nuarp dx-4.4.4-orig/src/exec/dxmods/local.mk dx-4.4.4/src/exec/dxmods/local.mk
---- dx-4.4.4-orig/src/exec/dxmods/local.mk.in	2008-09-11 22:31:38.000000000 +0200
-+++ dx-4.4.4/src/exec/dxmods/local.mk.in	2008-09-11 22:33:44.000000000 +0200
-@@ -14,15 +14,15 @@ user.c:  dx.mdf
- 
- dxcm.mdf:  ${srcdir}/dxmdf.src
- 	-rm -f dxcm.mdf
--	cp ${srcdir}/dxmdf.src tmp.c
--	$(CPP) $(INCLUDES) $(MDF) $(DEFS) tmp.c > dxcm.mdf
--	-rm -f tmp.c
-+	cp ${srcdir}/dxmdf.src tmp-dxcm.c
-+	$(CPP) $(INCLUDES) $(MDF) $(DEFS) tmp-dxcm.c > dxcm.mdf
-+	-rm -f tmp-dxcm.c
- 
- dx.mdf:  ${srcdir}/dxmdf.src
- 	echo MYINC: $(MYINC)
- 	-rm -f dx.mdf
--	cp ${srcdir}/dxmdf.src tmp.c
--	$(CPP) $(INCLUDES) $(MYINC) $(MDF) $(DEFS) -DCPLUSPLUS_UI -DEXECUTIVE_MODS tmp.c > dx.mdf
-+	cp ${srcdir}/dxmdf.src tmp-dx.c
-+	$(CPP) $(INCLUDES) $(MYINC) $(MDF) $(DEFS) -DCPLUSPLUS_UI -DEXECUTIVE_MODS tmp-dx.c > dx.mdf
- 	@echo '/^ *$$/{' > stripl.sed
- 	@echo 'N' >> stripl.sed
- 	@echo '/^ *\\n *$$/D' >> stripl.sed
-@@ -30,7 +30,7 @@ dx.mdf:  ${srcdir}/dxmdf.src
- 	cat dx.mdf |sed '/^#/d' > tmp.mdf
- 	cat tmp.mdf |sed -f stripl.sed > dx.mdf
- 	@rm -f stripl.sed tmp.mdf
--	-rm -f tmp.c
-+	-rm -f tmp-dx.c
- 
- .y.h:
- 	$(YACC) $(YFLAGS) -d ${srcdir}/$*.y
diff --git a/sci-visualization/opendx/files/opendx-4.4.4-dx-errno.patch b/sci-visualization/opendx/files/opendx-4.4.4-dx-errno.patch
deleted file mode 100644
index 70c1b28f0..000000000
--- a/sci-visualization/opendx/files/opendx-4.4.4-dx-errno.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-diff -up dx-4.4.4/src/exec/dpexec/lex.c.errno dx-4.4.4/src/exec/dpexec/lex.c
---- dx-4.4.4/src/exec/dpexec/lex.c.errno	2006-01-09 23:57:34.000000000 +0100
-+++ dx-4.4.4/src/exec/dpexec/lex.c	2009-01-26 19:16:20.000000000 +0100
-@@ -504,6 +504,7 @@ int yylex(YYSTYPE *lvalp)
-     for (;;)
-     {
- 	yyleng = 0;
-+	errno = 0;
-  
- 	c = input();
-  
diff --git a/sci-visualization/opendx/files/opendx-4.4.4-gcc43-fedora.patch b/sci-visualization/opendx/files/opendx-4.4.4-gcc43-fedora.patch
deleted file mode 100644
index 64a3d91fe..000000000
--- a/sci-visualization/opendx/files/opendx-4.4.4-gcc43-fedora.patch
+++ /dev/null
@@ -1,315 +0,0 @@
-diff -up dx-4.4.4/src/uipp/startup/StartupApplication.C.gcc43 dx-4.4.4/src/uipp/startup/StartupApplication.C
---- dx-4.4.4/src/uipp/startup/StartupApplication.C.gcc43	2005-11-10 20:48:22.000000000 +0100
-+++ dx-4.4.4/src/uipp/startup/StartupApplication.C	2008-01-07 21:55:03.000000000 +0100
-@@ -117,7 +117,7 @@ InitializeSignals(void)
- #endif       
- }            
- 
--boolean StartupApplication::initialize(unsigned int* argcp,
-+boolean StartupApplication::initialize(int*  argcp,
- 			       char**        argv)
- {
-     ASSERT(argcp);
-diff -up dx-4.4.4/src/uipp/startup/StartupApplication.h.gcc43 dx-4.4.4/src/uipp/startup/StartupApplication.h
---- dx-4.4.4/src/uipp/startup/StartupApplication.h.gcc43	2003-09-20 07:33:56.000000000 +0200
-+++ dx-4.4.4/src/uipp/startup/StartupApplication.h	2008-01-07 21:50:47.000000000 +0100
-@@ -84,7 +84,7 @@ class StartupApplication : public IBMApp
-     // Overrides the Application class version:
-     //   Initializes Xt Intrinsics with option list (switches).
-     //
--    virtual boolean initialize(unsigned int* argcp, char**argv);
-+    virtual boolean initialize(int* argcp, char**argv);
- 
-     CommandScope       *commandScope;   // command scope
- 
-diff -up dx-4.4.4/src/uipp/startup/Main.C.gcc43 dx-4.4.4/src/uipp/startup/Main.C
---- dx-4.4.4/src/uipp/startup/Main.C.gcc43	2000-05-16 20:53:07.000000000 +0200
-+++ dx-4.4.4/src/uipp/startup/Main.C	2008-01-07 19:57:58.000000000 +0100
-@@ -14,7 +14,7 @@
- extern "C" void HCLXmInit();
- #endif
- 
--int main(unsigned int argc,
-+int main( int          argc,
- 	  char**       argv)
- {
- #if defined(HAVE_HCLXMINIT)
-diff -up dx-4.4.4/src/uipp/base/Application.C.gcc43 dx-4.4.4/src/uipp/base/Application.C
---- dx-4.4.4/src/uipp/base/Application.C.gcc43	2005-11-09 19:56:17.000000000 +0100
-+++ dx-4.4.4/src/uipp/base/Application.C	2008-01-07 22:39:15.000000000 +0100
-@@ -136,7 +136,7 @@ void Application::installDefaultResource
-     //this->setDefaultResources(baseWidget, Application::DefaultResources);
- }
- 
--boolean Application::initializeWindowSystem(unsigned int *argcp, char **argv) 
-+boolean Application::initializeWindowSystem(int *argcp, char **argv) 
- {
- 
-     //
-@@ -149,7 +149,7 @@ boolean Application::initializeWindowSys
- 	     NULL,			// command line options table
- 	     0,				// number of entries in options table
- #if XtSpecificationRelease > 4
--	     (int*)argcp,
-+	     argcp,
- #else
- 	     argcp,
- #endif
-@@ -235,7 +235,7 @@ boolean Application::initializeWindowSys
-     return TRUE;
- }
- 
--void Application::parseCommand(unsigned int* argcp, char** argv,
-+void Application::parseCommand(int* argcp, char** argv,
-                                XrmOptionDescList optlist, int optlistsize)
- {
-     char res_file[256];
-@@ -280,7 +280,7 @@ void Application::parseCommand(unsigned 
-     //
- }
- 
--boolean Application::initialize(unsigned int* argcp, char** argv)
-+boolean Application::initialize(int* argcp, char** argv)
- {
-     //
-     // Initialize the window system if not done already.
-diff -up dx-4.4.4/src/uipp/base/Application.h.gcc43 dx-4.4.4/src/uipp/base/Application.h
---- dx-4.4.4/src/uipp/base/Application.h.gcc43	2005-11-09 19:26:29.000000000 +0100
-+++ dx-4.4.4/src/uipp/base/Application.h	2008-01-07 21:49:49.000000000 +0100
-@@ -49,7 +49,7 @@ class Application : public UIComponent, 
-     //
-     // The main program needs to access protected member functions.
-     //
--    friend int main(unsigned int argc,
-+    friend int main( int          argc,
- 		     char**       argv);
- 
- 
-@@ -71,9 +71,9 @@ class Application : public UIComponent, 
-     //
-     // Initialize the window system.
-     //
--    virtual boolean initializeWindowSystem(unsigned int *argcp, char **argv);
-+    virtual boolean initializeWindowSystem(int *argcp, char **argv);
- 
--    virtual void parseCommand(unsigned int* argcp, char** argv,
-+    virtual void parseCommand(int* argcp, char** argv,
- 			       XrmOptionDescList optlist, int optlistsize);
- 
-     //
-@@ -145,7 +145,7 @@ class Application : public UIComponent, 
-     // Initializes any Application specfic state.  This routine should 
-     // be called by main() or subclasses only.
-     //
--    virtual boolean initialize(unsigned int* argcp, char** argv);
-+    virtual boolean initialize(int* argcp, char** argv);
- 
-     //
-     // Allow others to access our event processing mechanism
-diff -up dx-4.4.4/src/uipp/base/IBMApplication.C.gcc43 dx-4.4.4/src/uipp/base/IBMApplication.C
---- dx-4.4.4/src/uipp/base/IBMApplication.C.gcc43	2004-04-02 22:32:43.000000000 +0200
-+++ dx-4.4.4/src/uipp/base/IBMApplication.C	2008-01-07 21:53:29.000000000 +0100
-@@ -349,7 +349,7 @@ int status;
- }
- 
- 
--boolean IBMApplication::initializeWindowSystem(unsigned int *argcp, char **argv)
-+boolean IBMApplication::initializeWindowSystem(int *argcp, char **argv)
- {
- 
-     if (!this->Application::initializeWindowSystem(argcp, argv))
-@@ -375,7 +375,7 @@ boolean IBMApplication::initializeWindow
-     return TRUE;
- }
- 
--boolean IBMApplication::initialize(unsigned int* argcp,
-+boolean IBMApplication::initialize(int*          argcp,
- 				   char**        argv)
- {
-     if (!this->Application::initialize(argcp,argv))
-diff -up dx-4.4.4/src/uipp/base/IBMApplication.h.gcc43 dx-4.4.4/src/uipp/base/IBMApplication.h
---- dx-4.4.4/src/uipp/base/IBMApplication.h.gcc43	2003-09-20 07:35:22.000000000 +0200
-+++ dx-4.4.4/src/uipp/base/IBMApplication.h	2008-01-07 21:50:19.000000000 +0100
-@@ -77,7 +77,7 @@ class IBMApplication : public Applicatio
-     //
-     // Initialize the window system.
-     //
--    virtual boolean initializeWindowSystem(unsigned int *argcp, char **argv);
-+    virtual boolean initializeWindowSystem(int *argcp, char **argv);
- 
-     //
-     // Protected member data:
-@@ -88,7 +88,7 @@ class IBMApplication : public Applicatio
- 
-     HelpWin		*helpWindow;
- 
--    boolean initialize(unsigned int* argcp, char** argv);
-+    boolean initialize(int* argcp, char** argv);
- 
-     //
-     // Load application specific action routines
-diff -up dx-4.4.4/src/uipp/tutor/TutorApplication.h.gcc43 dx-4.4.4/src/uipp/tutor/TutorApplication.h
---- dx-4.4.4/src/uipp/tutor/TutorApplication.h.gcc43	1999-05-10 17:46:30.000000000 +0200
-+++ dx-4.4.4/src/uipp/tutor/TutorApplication.h	2008-01-07 21:49:29.000000000 +0100
-@@ -69,7 +69,7 @@ class TutorApplication : public IBMAppli
-     // Overrides the Application class version:
-     //   Initializes Xt Intrinsics with option list (switches).
-     //
--    virtual boolean initialize(unsigned int* argcp,
-+    virtual boolean initialize(int*       argcp,
- 			    char**        argv);
- 
-     //
-diff -up dx-4.4.4/src/uipp/tutor/Main.C.gcc43 dx-4.4.4/src/uipp/tutor/Main.C
---- dx-4.4.4/src/uipp/tutor/Main.C.gcc43	2000-05-16 20:53:15.000000000 +0200
-+++ dx-4.4.4/src/uipp/tutor/Main.C	2008-01-07 19:57:39.000000000 +0100
-@@ -31,7 +31,7 @@ extern "C" void HCLXmInit();
- //
- const char *AssertMsgString = "Internal error detected at \"%s\":%d.\n";
-  
--int main(unsigned int argc,
-+int main( int          argc,
- 	  char**       argv)
- {
- #if defined(HAVE_HCLXMINIT)
-diff -up dx-4.4.4/src/uipp/tutor/TutorApplication.C.gcc43 dx-4.4.4/src/uipp/tutor/TutorApplication.C
---- dx-4.4.4/src/uipp/tutor/TutorApplication.C.gcc43	2006-05-08 18:20:14.000000000 +0200
-+++ dx-4.4.4/src/uipp/tutor/TutorApplication.C	2008-01-07 21:56:09.000000000 +0100
-@@ -196,7 +196,7 @@ InitializeSignals(void)
- #endif       
- }            
- 
--boolean TutorApplication::initialize(unsigned int* argcp,
-+boolean TutorApplication::initialize(int*    argcp,
- 			       char**        argv)
- {
-     ASSERT(argcp);
-diff -up dx-4.4.4/src/uipp/widgets/MultiText.h.gcc43 dx-4.4.4/src/uipp/widgets/MultiText.h
---- dx-4.4.4/src/uipp/widgets/MultiText.h.gcc43	2006-01-03 01:12:34.000000000 +0100
-+++ dx-4.4.4/src/uipp/widgets/MultiText.h	2008-01-07 19:06:27.000000000 +0100
-@@ -91,7 +91,7 @@ typedef struct _XmMultiTextClassRec* XmM
- #define XmNsmoothScroll		"smoothScroll"
- #define XmNwaitCursorCount	"waitCursorCount"
- 
--#if !(defined(_Xm_h) || defined(XM_H))
-+#if !(defined(_Xm_h) || defined(XM_H) || defined(_XM_XM_H))
- #define XmNmarginHeight		"marginHeight"
- #define XmNmarginWidth		"marginWidth"
- #define XmNwordWrap		"wordWrap"
-@@ -109,7 +109,7 @@ typedef struct _XmMultiTextClassRec* XmM
- #define XmCSmoothScroll		"SmoothScroll"
- #define XmCWaitCursorCount	"WaitCursorCount"
- 
--#if !(defined(_Xm_h) || defined(XM_H))
-+#if !(defined(_Xm_h) || defined(XM_H) || defined(_XM_XM_H))
- #define XmCMarginHeight		"MarginHeight"
- #define XmCMarginWidth		"MarginWidth"
- #define XmCWordWrap		"WordWrap"
-diff -up dx-4.4.4/src/uipp/dxui/Main.C.gcc43 dx-4.4.4/src/uipp/dxui/Main.C
---- dx-4.4.4/src/uipp/dxui/Main.C.gcc43	2005-12-07 18:50:53.000000000 +0100
-+++ dx-4.4.4/src/uipp/dxui/Main.C	2008-01-07 19:57:21.000000000 +0100
-@@ -48,7 +48,7 @@ extern unsigned long _etext;
- //
- const char *AssertMsgString = "Internal error detected at \"%s\":%d.\n";
-  
--int main(unsigned int argc,
-+int main( int          argc,
- 	  char**       argv)
- {
- #if defined(HAVE_HCLXMINIT)
-diff -up dx-4.4.4/src/uipp/prompter/GARApplication.h.gcc43 dx-4.4.4/src/uipp/prompter/GARApplication.h
---- dx-4.4.4/src/uipp/prompter/GARApplication.h.gcc43	2003-09-20 07:33:21.000000000 +0200
-+++ dx-4.4.4/src/uipp/prompter/GARApplication.h	2008-01-07 21:49:05.000000000 +0100
-@@ -129,7 +129,7 @@ class GARApplication : public IBMApplica
-     // Overrides the Application class version:
-     //   Initializes Xt Intrinsics with option list (switches).
-     //
--    virtual boolean initialize(unsigned int* argcp,
-+    virtual boolean initialize(int*       argcp,
- 			    char**        argv);
- 
-     CommandScope       *commandScope;   // command scope
-diff -up dx-4.4.4/src/uipp/prompter/Main.C.gcc43 dx-4.4.4/src/uipp/prompter/Main.C
---- dx-4.4.4/src/uipp/prompter/Main.C.gcc43	2000-05-16 20:52:59.000000000 +0200
-+++ dx-4.4.4/src/uipp/prompter/Main.C	2008-01-07 19:57:01.000000000 +0100
-@@ -17,7 +17,7 @@ extern "C" void HCLXmInit();
- #endif
- 
- 
--int main(unsigned int argc,
-+int main( int          argc,
- 	  char**       argv)
- {
- #if defined(HAVE_HCLXMINIT)
-diff -up dx-4.4.4/src/uipp/prompter/GARApplication.C.gcc43 dx-4.4.4/src/uipp/prompter/GARApplication.C
---- dx-4.4.4/src/uipp/prompter/GARApplication.C.gcc43	2006-05-08 18:20:13.000000000 +0200
-+++ dx-4.4.4/src/uipp/prompter/GARApplication.C	2008-01-07 21:54:28.000000000 +0100
-@@ -198,7 +198,7 @@ InitializeSignals(void)
-     }
- }            
- 
--boolean GARApplication::initialize(unsigned int* argcp,
-+boolean GARApplication::initialize(int*      argcp,
- 			       char**        argv)
- {
-     ASSERT(argcp);
-diff -up dx-4.4.4/src/uipp/dxuilib/DXApplication.h.gcc43 dx-4.4.4/src/uipp/dxuilib/DXApplication.h
---- dx-4.4.4/src/uipp/dxuilib/DXApplication.h.gcc43	2006-05-08 18:20:10.000000000 +0200
-+++ dx-4.4.4/src/uipp/dxuilib/DXApplication.h	2008-01-07 21:14:12.000000000 +0100
-@@ -372,7 +372,7 @@ class DXApplication : public IBMApplicat
-     // Overrides the Application class version:
-     //   Initializes Xt Intrinsics with option list (switches).
-     //
--    virtual boolean initialize(unsigned int* argcp,
-+    virtual boolean initialize(int*       argcp,
- 			    char**        argv);
- 
-     //
-diff -up dx-4.4.4/src/uipp/dxuilib/DXApplication.C.gcc43 dx-4.4.4/src/uipp/dxuilib/DXApplication.C
---- dx-4.4.4/src/uipp/dxuilib/DXApplication.C.gcc43	2006-06-22 21:45:34.000000000 +0200
-+++ dx-4.4.4/src/uipp/dxuilib/DXApplication.C	2008-01-07 21:32:56.000000000 +0100
-@@ -2248,7 +2248,7 @@ void DXApplication::installDefaultResour
-     this->setDefaultResources(baseWidget, _defaultDXResources);
-     this->IBMApplication::installDefaultResources(baseWidget);
- }
--boolean DXApplication::initialize(unsigned int* argcp,
-+boolean DXApplication::initialize(int* argcp,
- 								  char**        argv)
- {
- 	boolean wasSetBusy = FALSE;
-diff -up dx-4.4.4/src/uipp/mb/Main.C.gcc43 dx-4.4.4/src/uipp/mb/Main.C
---- dx-4.4.4/src/uipp/mb/Main.C.gcc43	2000-05-20 19:49:40.000000000 +0200
-+++ dx-4.4.4/src/uipp/mb/Main.C	2008-01-07 19:56:41.000000000 +0100
-@@ -22,7 +22,7 @@ extern "C" void HCLXmInit();
- //
- const char *AssertMsgString = "Internal error detected at \"%s\":%d.\n";
- 
--int main(unsigned int argc,
-+int main( int          argc,
- 	  char**       argv)
- {
- #if defined(HAVE_HCLXMINIT)
-diff -up dx-4.4.4/src/uipp/mb/MBApplication.C.gcc43 dx-4.4.4/src/uipp/mb/MBApplication.C
---- dx-4.4.4/src/uipp/mb/MBApplication.C.gcc43	2006-05-08 18:20:13.000000000 +0200
-+++ dx-4.4.4/src/uipp/mb/MBApplication.C	2008-01-07 21:51:15.000000000 +0100
-@@ -117,7 +117,7 @@ InitializeSignals(void)
- #endif       
- }            
- 
--boolean MBApplication::initialize(unsigned int* argcp,
-+boolean MBApplication::initialize(int*       argcp,
- 			       char**        argv)
- {
-     ASSERT(argcp);
-diff -up dx-4.4.4/src/uipp/mb/MBApplication.h.gcc43 dx-4.4.4/src/uipp/mb/MBApplication.h
---- dx-4.4.4/src/uipp/mb/MBApplication.h.gcc43	1999-05-10 17:46:25.000000000 +0200
-+++ dx-4.4.4/src/uipp/mb/MBApplication.h	2008-01-07 21:48:38.000000000 +0100
-@@ -51,7 +51,7 @@ class MBApplication : public IBMApplicat
-     // Overrides the Application class version:
-     //   Initializes Xt Intrinsics with option list (switches).
-     //
--    virtual boolean initialize(unsigned int* argcp,
-+    virtual boolean initialize(int*       argcp,
- 			    char**        argv);
- 
-     static MBResource	resource;
diff --git a/sci-visualization/opendx/files/opendx-4.4.4-install.patch b/sci-visualization/opendx/files/opendx-4.4.4-install.patch
deleted file mode 100644
index 342f6f88b..000000000
--- a/sci-visualization/opendx/files/opendx-4.4.4-install.patch
+++ /dev/null
@@ -1,330 +0,0 @@
-diff -up dx-4.4.4/bin/dx.in.r dx-4.4.4/bin/dx.in
---- dx-4.4.4/bin/dx.in.r	2004-05-31 18:12:05.000000000 +0200
-+++ dx-4.4.4/bin/dx.in	2009-01-26 23:57:11.000000000 +0100
-@@ -60,14 +60,7 @@ exit 1
- #
- longhelp() {
- 
--if test -f "$dxroot/man/catl/dx.l" ; then
--    more "$dxroot/man/catl/dx.l"
--else
--    echo "cannot find $dxroot/man/catl/dx.l"
--    echo "set the DXROOT environment variable to the root of the"
--    echo "dx installation tree and try again."
--fi
--exit 1
-+man dx
- 
- cat << EOFlonghelp
- command line parameters:
-@@ -286,7 +279,7 @@ fi
- 
- 
- if [ -z "$DXROOT" ]; then
--  prefix=@prefix@
-+  prefix=@libdir@
-   DXROOT=$prefix/dx
- fi
- export DXROOT
-@@ -507,7 +507,7 @@ export DXARCH
- 
- # default to running locally, from @prefix@/dx  
- exhost=$thishost
--dxroot=@prefix@/dx
-+dxroot=@libdir@/dx
- startup=1   # run the startup window by default
- 
- 
-diff -up dx-4.4.4/bin/Makefile.am.r dx-4.4.4/bin/Makefile.am
---- dx-4.4.4/bin/Makefile.am.r	2003-07-12 02:11:37.000000000 +0200
-+++ dx-4.4.4/bin/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--dxbindir = $(prefix)/dx/bin
-+dxbindir = $(libdir)/dx/bin
- bindir = $(prefix)/bin
- 
- EXTRA_SCRIPTS = mdf2c dx
-diff -up dx-4.4.4/bin/mdf2c.in.r dx-4.4.4/bin/mdf2c.in
---- dx-4.4.4/bin/mdf2c.in.r	1999-12-14 05:13:04.000000000 +0100
-+++ dx-4.4.4/bin/mdf2c.in	2009-01-26 23:57:11.000000000 +0100
-@@ -1,6 +1,6 @@
- #!/bin/sh
- # Configure is looking for the following line
--prefix=@prefix@
-+prefix=@libdir@
- DFLTROOT=$prefix/dx
- root=${DXROOT=${DXEXECROOT=$DFLTROOT}}
- 
-diff -up dx-4.4.4/doc/Makefile.am.r dx-4.4.4/doc/Makefile.am
---- dx-4.4.4/doc/Makefile.am.r	1999-04-05 13:57:03.000000000 +0200
-+++ dx-4.4.4/doc/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--docdir = $(prefix)/dx/doc
-+docdir = $(datadir)/dx/doc
- 
- doc_DATA = \
- 	README README_SMP README_alphax README_aviion README_hp700 \
-diff -up dx-4.4.4/fonts/Makefile.am.r dx-4.4.4/fonts/Makefile.am
---- dx-4.4.4/fonts/Makefile.am.r	2003-07-12 02:11:37.000000000 +0200
-+++ dx-4.4.4/fonts/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--fontdir = $(prefix)/dx/fonts
-+fontdir = $(libdir)/dx/fonts
- 
- font_DATA = \
- 	README area.dx cyril_d.dx \
-diff -up dx-4.4.4/help/Makefile.am.r dx-4.4.4/help/Makefile.am
---- dx-4.4.4/help/Makefile.am.r	2003-07-12 02:11:37.000000000 +0200
-+++ dx-4.4.4/help/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--helpdir = $(prefix)/dx/help
-+helpdir = $(libdir)/dx/help
- 
- EXTRA_DIST = $(helpfiles1) $(helpfiles2) $(helpfiles3) $(helpfiles4) $(helpfiles5)  \
- 	$(helpfiles6) $(helpfiles7) $(helpfiles8) $(helpfiles9) $(helpfiles10)  \
-diff -up dx-4.4.4/html/images/Makefile.am.r dx-4.4.4/html/images/Makefile.am
---- dx-4.4.4/html/images/Makefile.am.r	2002-04-01 10:51:13.000000000 +0200
-+++ dx-4.4.4/html/images/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,5 +1,5 @@
- 
--imagesdir = $(prefix)/dx/html/images
-+imagesdir = $(libdir)/dx/html/images
- 
- images1 = \
- 	3dcurs.gif adctlpt.gif arch.gif autoax.gif autoexp.gif		\
-diff -up dx-4.4.4/html/Makefile.am.r dx-4.4.4/html/Makefile.am
---- dx-4.4.4/html/Makefile.am.r	2003-07-12 02:11:39.000000000 +0200
-+++ dx-4.4.4/html/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--htmldir = $(prefix)/dx/html
-+htmldir = $(libdir)/dx/html
- 
- SUBDIRS = pages images
- 
-diff -up dx-4.4.4/html/pages/Makefile.am.r dx-4.4.4/html/pages/Makefile.am
---- dx-4.4.4/html/pages/Makefile.am.r	2002-06-20 06:38:03.000000000 +0200
-+++ dx-4.4.4/html/pages/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,4 +1,4 @@
--pagesdir = $(prefix)/dx/html/pages
-+pagesdir = $(libdir)/dx/html/pages
- 
- pages1 = \
- 	insgu002.htm insgu003.htm insgu004.htm insgu005.htm insgu006.htm \
-diff -up dx-4.4.4/include/dx/Makefile.am.r dx-4.4.4/include/dx/Makefile.am
---- dx-4.4.4/include/dx/Makefile.am.r	1999-05-26 01:35:16.000000000 +0200
-+++ dx-4.4.4/include/dx/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--dxincdir = $(prefix)/dx/include/dx
-+dxincdir = $(prefix)/include/dx
-  
- dxinc_HEADERS = \
- 	UserInteractors.h advanced.h arch.h array.h arrayhandles.h \
-diff -up dx-4.4.4/include/Makefile.am.r dx-4.4.4/include/Makefile.am
---- dx-4.4.4/include/Makefile.am.r	2006-04-09 05:44:49.000000000 +0200
-+++ dx-4.4.4/include/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,4 +1,4 @@
--dxincdir = $(prefix)/dx/include
-+dxincdir = $(prefix)/include
- SUBDIRS = dx
- dxinc_HEADERS = dxl.h dxstereo.h
- nodist_dxinc_HEADERS = dxconfig.h
-diff -up dx-4.4.4/lib/Makefile.am.r dx-4.4.4/lib/Makefile.am
---- dx-4.4.4/lib/Makefile.am.r	2003-08-22 01:22:13.000000000 +0200
-+++ dx-4.4.4/lib/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,4 +1,4 @@
--libsdir = $(prefix)/dx/lib
-+libsdir = $(libdir)/dx/lib
- 
- libs_DATA = colors.txt dxexec.def dxexec.exp dxexec.imp dxexec.ifs \
- 	dxfSaveCurrentImage.net dxrc mdf2c.awk messages outboard.c
-diff -up dx-4.4.4/man/Makefile.am.r dx-4.4.4/man/Makefile.am
---- dx-4.4.4/man/Makefile.am.r	1999-04-03 18:31:28.000000000 +0200
-+++ dx-4.4.4/man/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,4 +1,4 @@
- ## Process this file with automake to produce Makefile.in
- 
--SUBDIRS = manl catl
-+SUBDIRS = manl
- 
-diff -up dx-4.4.4/man/manl/Makefile.am.r dx-4.4.4/man/manl/Makefile.am
---- dx-4.4.4/man/manl/Makefile.am.r	2002-05-20 06:47:06.000000000 +0200
-+++ dx-4.4.4/man/manl/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--mandir = $(prefix)/dx/man
-+mandir = $(prefix)/man
- 
- man_MANS = dx.l
- EXTRA_DIST = $(man_MANS)
-diff -up dx-4.4.4/src/exec/dxexec/Makefile.am.r dx-4.4.4/src/exec/dxexec/Makefile.am
---- dx-4.4.4/src/exec/dxexec/Makefile.am.r	2006-01-11 17:24:39.000000000 +0100
-+++ dx-4.4.4/src/exec/dxexec/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -9,7 +9,7 @@ noinst_LTLIBRARIES = libDXEXEC.la
- libDXEXEC_la_SOURCES = main.c
- libDXEXEC_la_CFLAGS = $(AM_CFLAGS)
- 
--bindir = $(prefix)/dx/bin_@ARCH@
-+bindir = $(libdir)/dx/bin_@ARCH@
- bin_PROGRAMS = dxexec
- 
- dxexec_LDADD = ../dpexec/libDPEXEC.la ../dxmods/libDXMODS.la ../dxmods/user.lo \
-diff -up dx-4.4.4/src/exec/dxmods/Makefile.am.r dx-4.4.4/src/exec/dxmods/Makefile.am
---- dx-4.4.4/src/exec/dxmods/Makefile.am.r	2003-08-19 00:51:10.000000000 +0200
-+++ dx-4.4.4/src/exec/dxmods/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,8 +1,8 @@
- ## Process this file with automake to produce Makefile.in
- 
- INCLUDES = -I${top_srcdir}/include -I${srcdir}/../dpexec -I$(BUILDBASE)/include -D@ARCH@
- 
--dxmdfdir = $(prefix)/dx/lib
-+dxmdfdir = $(libdir)/dx/lib
- noinst_LTLIBRARIES = libDXMODS.la libusercm.la libuser.la libDXMODSN.la
- SUFFIXES = .c .y .c .s .h .o 
- 
-@@ -13,6 +14,8 @@ DISTCLEANFILES = dx.mdf dxcm.mdf user.c 
- 
- dxmdf_DATA = dx.mdf
- 
-+user.c: dx.mdf
-+
- _complex.o: _compparse.h
- 
- HEADERS1 = \
-diff -up dx-4.4.4/src/exec/libdx/Makefile.am.r dx-4.4.4/src/exec/libdx/Makefile.am
---- dx-4.4.4/src/exec/libdx/Makefile.am.r	2006-03-27 20:56:53.000000000 +0200
-+++ dx-4.4.4/src/exec/libdx/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -7,7 +7,7 @@ MICRO_VERSION=@MICRO_VERSION@
- #INCLUDES = -I../../../include  -D@ARCH@
- INCLUDES = -I${top_srcdir}/include  -D@ARCH@
- 
--dxlibdir = $(prefix)/dx/lib_@ARCH@
-+dxlibdir = $(libdir)/dx/lib_@ARCH@
- 
- noinst_LTLIBRARIES = libLIBDX.la libcallm.la libmem.la
- #dxlib_LIBRARIES = libDXlite.a 
-diff -up dx-4.4.4/src/exec/Makefile.am.r dx-4.4.4/src/exec/Makefile.am
---- dx-4.4.4/src/exec/Makefile.am.r	2003-09-17 00:40:40.000000000 +0200
-+++ dx-4.4.4/src/exec/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,6 +1,6 @@
- SUBDIRS = libdx dxmods hwrender dpexec dxexec
- 
--dxlibdir = $(prefix)/dx/lib_@ARCH@
-+dxlibdir = $(libdir)/dx/lib_@ARCH@
- 
- MAJOR_VERSION=@MAJOR_VERSION@
- MINOR_VERSION=@MINOR_VERSION@
-diff -up dx-4.4.4/src/misc/Makefile.am.r dx-4.4.4/src/misc/Makefile.am
---- dx-4.4.4/src/misc/Makefile.am.r	2003-07-12 02:12:13.000000000 +0200
-+++ dx-4.4.4/src/misc/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -4,7 +4,7 @@ INCLUDES = -I${top_srcdir}/include -D@AR
- 
- dxbindir = $(prefix)/bin
- noinst_PROGRAMS = dxlocal
--archmakdir = $(prefix)/dx/lib_$(ARCH)
-+archmakdir = $(libdir)/dx/lib_$(ARCH)
- archmak_DATA = arch.mak
- 
- dxlocal_SOURCES = dx.c utils.c
-@@ -15,5 +15,5 @@ install-exec-local: 
- 	if test ! -z "@INSTALL_BIN_PROGRAM@" ; then		         \
- 		$(mkinstalldirs) $(prefix)/bin ;                	         \
- 		$(INSTALL) dxlocal@EXEEXT@ 				         \
--		$(prefix)/dx/bin_$(ARCH)/@INSTALL_BIN_PROGRAM@@EXEEXT@ ; \
-+		$(libdir)/dx/bin_$(ARCH)/@INSTALL_BIN_PROGRAM@@EXEEXT@ ; \
- 	fi
-diff -up dx-4.4.4/src/uipp/dxl/Makefile.am.r dx-4.4.4/src/uipp/dxl/Makefile.am
---- dx-4.4.4/src/uipp/dxl/Makefile.am.r	2003-07-12 02:12:16.000000000 +0200
-+++ dx-4.4.4/src/uipp/dxl/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -7,7 +7,7 @@ MICRO_VERSION=@MICRO_VERSION@
- 
- INCLUDES = -I${top_srcdir}/include  -D@ARCH@
- 
--dxlibdir = $(prefix)/dx/lib_@ARCH@
-+dxlibdir = $(libdir)/dx/lib_@ARCH@
- 
- noinst_HEADERS = \
- 	dxlP.h \
-diff -up dx-4.4.4/src/uipp/dxui/Makefile.am.r dx-4.4.4/src/uipp/dxui/Makefile.am
---- dx-4.4.4/src/uipp/dxui/Makefile.am.r	2003-07-12 02:12:17.000000000 +0200
-+++ dx-4.4.4/src/uipp/dxui/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -2,7 +2,7 @@
- 
- INCLUDES = -I${srcdir}/../base -I${top_srcdir}/include -I${srcdir}/../dxuilib -D@ARCH@
- 
--dxbindir = $(prefix)/dx/bin_@ARCH@
-+dxbindir = $(libdir)/dx/bin_@ARCH@
- dxbin_PROGRAMS = dxui
- 
- 
-diff -up dx-4.4.4/src/uipp/mb/Makefile.am.r dx-4.4.4/src/uipp/mb/Makefile.am
---- dx-4.4.4/src/uipp/mb/Makefile.am.r	2003-08-20 16:21:33.000000000 +0200
-+++ dx-4.4.4/src/uipp/mb/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -2,7 +2,7 @@
- 
- INCLUDES = -I${top_srcdir}/include -I${srcdir}/../base -I${srcdir}/../widgets -D@ARCH@
- 
--dxbindir = $(prefix)/dx/bin_@ARCH@
-+dxbindir = $(libdir)/dx/bin_@ARCH@
- 
- dxbin_PROGRAMS = builder
- 
-diff -up dx-4.4.4/src/uipp/prompter/Makefile.am.r dx-4.4.4/src/uipp/prompter/Makefile.am
---- dx-4.4.4/src/uipp/prompter/Makefile.am.r	2003-11-04 05:20:14.000000000 +0100
-+++ dx-4.4.4/src/uipp/prompter/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -2,7 +2,7 @@
- 
- INCLUDES =  -I${srcdir}/../base -I${top_srcdir}/include -D@ARCH@
- 
--dxbindir = $(prefix)/dx/bin_@ARCH@
-+dxbindir = $(libdir)/dx/bin_@ARCH@
- 
- dxbin_PROGRAMS = prompter
- 
-diff -up dx-4.4.4/src/uipp/startup/Makefile.am.r dx-4.4.4/src/uipp/startup/Makefile.am
---- dx-4.4.4/src/uipp/startup/Makefile.am.r	2003-07-12 02:12:29.000000000 +0200
-+++ dx-4.4.4/src/uipp/startup/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -2,7 +2,7 @@
- 
- INCLUDES =  -I${top_srcdir}/include -I${srcdir}/../base -D@ARCH@
- 
--dxbindir = $(prefix)/dx/bin_@ARCH@
-+dxbindir = $(libdir)/dx/bin_@ARCH@
- 
- dxbin_PROGRAMS = startupui
- 
-diff -up dx-4.4.4/src/uipp/tutor/Makefile.am.r dx-4.4.4/src/uipp/tutor/Makefile.am
---- dx-4.4.4/src/uipp/tutor/Makefile.am.r	2003-07-12 02:12:29.000000000 +0200
-+++ dx-4.4.4/src/uipp/tutor/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -2,7 +2,7 @@
- 
- INCLUDES = -I${top_srcdir}/include -I${srcdir}/../base -D@ARCH@
- 
--dxbindir = $(prefix)/dx/bin_@ARCH@
-+dxbindir = $(libdir)/dx/bin_@ARCH@
- 
- dxbin_PROGRAMS = tutor
- 
-diff -up dx-4.4.4/src/uipp/ui/Makefile.am.r dx-4.4.4/src/uipp/ui/Makefile.am
---- dx-4.4.4/src/uipp/ui/Makefile.am.r	2001-04-12 16:29:02.000000000 +0200
-+++ dx-4.4.4/src/uipp/ui/Makefile.am	2009-01-26 23:57:11.000000000 +0100
-@@ -1,6 +1,6 @@
- ## Process this file with automake to produce Makefile.in
- 
--uidatadir = $(prefix)/dx/ui
-+uidatadir = $(libdir)/dx/ui
- 
- DATA1 = \
- 	icon50.dat icon50.xpm logo.dat logo.xpm ui.mdf Basic2D.cfg Basic2D.net \
diff --git a/sci-visualization/opendx/files/opendx-4.4.4-libtool.patch b/sci-visualization/opendx/files/opendx-4.4.4-libtool.patch
deleted file mode 100644
index 2a5aad6d4..000000000
--- a/sci-visualization/opendx/files/opendx-4.4.4-libtool.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-diff -Naur dx-4.4.4/configure.ac dx-4.4.4.new/configure.ac
---- dx-4.4.4/configure.ac	2006-08-21 17:56:08.000000000 -0400
-+++ dx-4.4.4.new/configure.ac	2008-06-29 07:31:08.000000000 -0400
-@@ -10,6 +10,7 @@
- AM_INIT_AUTOMAKE
- AC_DISABLE_SHARED
- AC_PROG_LIBTOOL
-+AC_PROG_CXX
- 
- VERSION_STRING="04.4.4000"
- MAJOR_VERSION=4
diff --git a/sci-visualization/opendx/files/opendx-4.4.4-open.patch b/sci-visualization/opendx/files/opendx-4.4.4-open.patch
deleted file mode 100644
index b62ebd094..000000000
--- a/sci-visualization/opendx/files/opendx-4.4.4-open.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-diff -up dx-4.4.4/src/exec/libdx/fileio.c.open dx-4.4.4/src/exec/libdx/fileio.c
---- dx-4.4.4/src/exec/libdx/fileio.c.open	2006-01-05 23:55:47.000000000 +0100
-+++ dx-4.4.4/src/exec/libdx/fileio.c	2008-09-24 19:16:30.000000000 +0200
-@@ -263,7 +263,7 @@ Error _dxffile_open(char *name, int rw)
- 	case 2:/* read/write */
- 		fd = open(name, O_RDWR);
- 		if (fd < 0) {
--			fd = open(name, O_WRONLY | O_CREAT);
-+			fd = open(name, O_WRONLY | O_CREAT, S_IRUSR | S_IWUSR);
- 			if (fd < 0) {
- 				DXSetError(ERROR_DATA_INVALID, 
- 				"can't open/create file '%s'", name);
-diff -up dx-4.4.4/src/exec/libdx/plock.c.open dx-4.4.4/src/exec/libdx/plock.c
---- dx-4.4.4/src/exec/libdx/plock.c.open	2002-07-17 06:48:18.000000000 +0200
-+++ dx-4.4.4/src/exec/libdx/plock.c	2008-09-24 19:16:30.000000000 +0200
-@@ -37,7 +37,8 @@ struct seminfo *__buf;      /* buffer fo
- 
- #define SEM_FLAGS  	 (IPC_CREAT | S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH)
- #define SHM_FLAGS  	 (IPC_CREAT | S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH)
--#define OPEN_FLAGS 	 (O_CREAT | S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH)
-+#define OPEN_FLAGS	 (O_CREAT)
-+#define OPEN_MODE 	 (S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH)
- #define IS_MINE(a)	 (locks->_owner[a] == getpid())
- #define SET_OWNER(a)	 (locks->_owner[a] = getpid())
- #define CLEAR_OWNER(a)	 (locks->_owner[a] = 0)
-@@ -268,7 +269,7 @@ PLockInit()
- 
-     if (stat(LOCKFILE, &statbuf))
-     {
--        int fd = open(LOCKFILE, OPEN_FLAGS);
-+        int fd = open(LOCKFILE, OPEN_FLAGS, OPEN_MODE);
- 	if (fd < 0)
- 	{
- 	    fprintf(stderr, "initLocks: error accessing locks shared block: open\n");
diff --git a/sci-visualization/opendx/files/opendx-4.4.4-szip.patch b/sci-visualization/opendx/files/opendx-4.4.4-szip.patch
deleted file mode 100644
index 5e63d4e6b..000000000
--- a/sci-visualization/opendx/files/opendx-4.4.4-szip.patch
+++ /dev/null
@@ -1,55 +0,0 @@
---- configure.ac.orig	2009-06-14 22:10:24.000000000 +1200
-+++ configure.ac	2009-06-14 22:26:29.000000000 +1200
-@@ -148,6 +148,12 @@ AC_ARG_WITH(netcdf,
- 	      [with_netcdf=$withval],
- 	      [with_netcdf='yes'])
- 
-+# Enable szip.
-+AC_ARG_WITH(szlib,
-+	      [  --with-szlib            Use szlib library for external szlib I/O (default is yes)],
-+	      [with_szlib=$withval],
-+	      [with_szlib='yes'])
-+
- # Enable 64-bit arenas, if supported
- AC_ARG_WITH(large-arenas,
-               [  --with-large-arenas     enable 64-bit arenas, when available (default is no)],
-@@ -790,6 +796,39 @@ fi
- 
- 
- #
-+# Check for szlib
-+#
-+have_szlib='no'
-+LIB_SZLIB=''
-+if test "$with_szlib" != 'no'
-+then
-+    AS_MESSAGE([checking for szlib ......])
-+    failed=0;
-+    passed=0;
-+    AC_CHECK_HEADERS(szlib.h, passed=`expr $passed + 1`,failed=`expr $failed + 1`)
-+    AC_CHECK_LIB(sz, SZ_BufftoBuffCompress,passed=`expr $passed + 1`,failed=`expr $failed + 1`,)
-+    AC_MSG_CHECKING(if szlib package is complete)
-+    if test $passed -gt 0
-+    then
-+    if test $failed -gt 0
-+    then
-+	AC_MSG_RESULT(no -- some components failed test)
-+        have_szlib='no (failed tests)'
-+    else
-+	LIB_SZLIB='-lsz'
-+	LIBS="$LIB_SZLIB $LIBS"
-+	FMT_LIBS="$FMT_LIBS libsz.a"
-+	AC_DEFINE(HAVE_LIBSZIP, 1, [Define to 1 if you have the SZLIB libraries])
-+	AC_MSG_RESULT(yes)
-+        have_szlib='yes'
-+    fi
-+    else
-+        AC_MSG_RESULT(no)
-+    fi
-+fi
-+
-+
-+#
- # Check for IMAGEMAGICK
- #
- have_magick='no'
diff --git a/sci-visualization/opendx/files/opendx-4.4.4-xdg.patch b/sci-visualization/opendx/files/opendx-4.4.4-xdg.patch
deleted file mode 100644
index c5b38f274..000000000
--- a/sci-visualization/opendx/files/opendx-4.4.4-xdg.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-diff -up bin/url_handler.sh.orig bin/url_handler.sh
---- bin/url_handler.sh.orig	2009-05-02 23:21:08.000000000 +1200
-+++ bin/url_handler.sh	2009-05-02 23:24:25.000000000 +1200
-@@ -27,21 +27,7 @@ case $method in
- 	mailto)	mutt `echo "$url" | sed 's;^[^:]*:\(.*\);\1;'`
- 		;;
- 
--        *)      use_xbrowser=n
--		case "$DISPLAY" in
--                   :0)       use_xbrowser=y
--                             ;;
--                   :0.*)     use_xbrowser=y
--                             ;;
--                   unix:0.*) use_xbrowser=y
--                             ;;
--                esac
--		if [ $use_xbrowser = n ]; then
--			lynx "$url" 
--		else
--			netscape -remote "openURL($url)" 2> /dev/null || \
--			(netscape "$url" &)
--                fi
-+        *) xdg-open "$url"
- 		;;
- esac
- 
diff --git a/sci-visualization/opendx/files/opendx-compressed-man.patch b/sci-visualization/opendx/files/opendx-compressed-man.patch
deleted file mode 100644
index c7535ccb5..000000000
--- a/sci-visualization/opendx/files/opendx-compressed-man.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff -Naurp dx-4.4.4-orig/bin/dx.in dx-4.4.4/bin/dx.in
---- dx-4.4.4-orig/bin/dx.in	2008-01-21 17:04:51.000000000 +0100
-+++ dx-4.4.4/bin/dx.in	2008-01-21 17:05:14.000000000 +0100
-@@ -60,8 +60,8 @@ exit 1
- #
- longhelp() {
- 
--if test -f "$dxroot/man/catl/dx.l" ; then
--    more "$dxroot/man/catl/dx.l"
-+if test -f "$dxroot"/man/catl/dx.l* ; then
-+    man "$dxroot"/man/catl/dx.l*
- else
-     echo "cannot find $dxroot/man/catl/dx.l"
-     echo "set the DXROOT environment variable to the root of the"
diff --git a/sci-visualization/opendx/metadata.xml b/sci-visualization/opendx/metadata.xml
deleted file mode 100644
index 016c1159b..000000000
--- a/sci-visualization/opendx/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<use>
-  <flag name='cdf'>Add support for <pkg>sci-libs/cdf</pkg> data exchange
-    format</flag>
-  <flag name='hdf'>Add support for the Hierarchical Data Format
-    (<pkg>sci-libs/hdf</pkg>)</flag>
-</use>
-</pkgmetadata>
diff --git a/sci-visualization/opendx/opendx-4.4.4-r1.ebuild b/sci-visualization/opendx/opendx-4.4.4-r1.ebuild
deleted file mode 100644
index c87e01a3b..000000000
--- a/sci-visualization/opendx/opendx-4.4.4-r1.ebuild
+++ /dev/null
@@ -1,102 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-# Set SMP="no" to force disable of SMP compilation.
-# Set SMP="yes" to force enable of SMP compilation.
-# Otherwise it will be autodetected from /usr/src/linux.
-
-EAPI=2
-
-inherit eutils flag-o-matic autotools
-
-DESCRIPTION="A 3D data visualization tool"
-HOMEPAGE="http://www.opendx.org/"
-SRC_URI="http://opendx.sdsc.edu/source/${P/open}.tar.gz"
-
-LICENSE="IPL-1"
-SLOT="0"
-
-KEYWORDS="~amd64 ~ppc ~x86"
-
-IUSE="hdf cdf netcdf tiff imagemagick szip smp"
-
-DEPEND="x11-libs/libXmu
-	x11-libs/libXi
-	x11-libs/libXp
-	x11-libs/libXpm
-	x11-libs/openmotif
-	szip? ( sci-libs/szip )
-	hdf? ( sci-libs/hdf )
-	cdf? ( sci-libs/cdf )
-	netcdf? ( sci-libs/netcdf )
-	tiff? ( media-libs/tiff )
-	imagemagick? ( >=media-gfx/imagemagick-5.3.4[-hdri] )"
-
-RDEPEND="${DEPEND}"
-# waiting on bug #36349 for media-libs/jasper in imagemagick
-
-S="${WORKDIR}/${P/open}"
-
-src_prepare() {
-
-	epatch "${FILESDIR}/${PN}-4.3.2-sys.h.patch"
-	epatch "${FILESDIR}/${PN}-compressed-man.patch"
-	epatch "${FILESDIR}/${P}-gcc43-fedora.patch"
-	epatch "${FILESDIR}/${P}-dx-errno.patch"
-	epatch "${FILESDIR}/${P}-libtool.patch"
-	epatch "${FILESDIR}/${P}-concurrent-make-fix.patch"
-	epatch "${FILESDIR}/${P}-open.patch"
-
-	eautoreconf
-}
-
-src_configure() {
-	# check flag filtering
-	# with gcc 3.3.2 I had an infinite loop on src/exec/libdx/zclipQ.c
-	append-flags -fno-strength-reduce
-
-	# (#82672)
-	filter-flags -finline-functions
-	replace-flags -O3 -O2
-
-	# opendx uses this variable
-	local GENTOOARCH="${ARCH}"
-	unset ARCH
-
-	local morelibs=""
-	use szip && morelibs="-lsz"
-	econf LIBS="${morelibs}" \
-		"--with-x" \
-		$(use_with cdf) \
-		$(use_with netcdf) \
-		$(use_with hdf) \
-		$(use_with tiff) \
-		$(use_with imagemagick magick) \
-		$(use_enable smp smp-linux)
-
-	ARCH="${GENTOOARCH}"
-#	javadx is currently broken. we may try to fix it someday.
-}
-
-src_compile() {
-	local GENTOOARCH="${ARCH}"
-	unset ARCH
-
-	emake || die
-	ARCH="${GENTOOARCH}"
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die
-
-	# inform revdep-rebuild about binary locations
-	insinto /etc/revdep-rebuild
-	doins "${FILESDIR}"/20-${PN}-revdep
-}
-
-pkg_postinst() {
-	elog "This version of the opendx ebuild is still under development."
-	elog "suggestions, comments and offer of help welcome"
-	elog "post a message in gentoo-science or pop up on irc on #gentoo-science"
-}
diff --git a/sci-visualization/opendx/opendx-4.4.4-r2.ebuild b/sci-visualization/opendx/opendx-4.4.4-r2.ebuild
deleted file mode 100644
index 39acb57ca..000000000
--- a/sci-visualization/opendx/opendx-4.4.4-r2.ebuild
+++ /dev/null
@@ -1,100 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=2
-
-inherit eutils flag-o-matic autotools multilib
-
-DESCRIPTION="A 3D data visualization tool"
-HOMEPAGE="http://www.opendx.org/"
-SRC_URI="http://opendx.sdsc.edu/source/${P/open}.tar.gz"
-
-LICENSE="IPL-1"
-SLOT="0"
-
-KEYWORDS="~amd64 ~ppc ~x86"
-
-IUSE="hdf cdf netcdf tiff imagemagick szip smp"
-
-DEPEND="x11-libs/libXmu
-	x11-libs/libXi
-	x11-libs/libXp
-	x11-libs/libXpm
-	x11-libs/openmotif
-	szip? ( sci-libs/szip )
-	hdf? ( sci-libs/hdf )
-	cdf? ( sci-libs/cdf )
-	netcdf? ( sci-libs/netcdf )
-	tiff? ( media-libs/tiff )
-	imagemagick? ( >=media-gfx/imagemagick-5.3.4[-hdri] )"
-
-RDEPEND="${DEPEND}"
-# waiting on bug #36349 for media-libs/jasper in imagemagick
-
-S="${WORKDIR}/${P/open}"
-
-src_prepare() {
-
-	epatch "${FILESDIR}/${PN}-4.3.2-sys.h.patch"
-	epatch "${FILESDIR}/${P}-install.patch"
-	epatch "${FILESDIR}/${P}-xdg.patch"
-	epatch "${FILESDIR}/${P}-gcc43-fedora.patch"
-	epatch "${FILESDIR}/${P}-dx-errno.patch"
-	epatch "${FILESDIR}/${P}-libtool.patch"
-	epatch "${FILESDIR}/${P}-concurrent-make-fix.patch"
-	epatch "${FILESDIR}/${P}-open.patch"
-	epatch "${FILESDIR}/${P}-szip.patch"
-
-	eautoreconf
-}
-
-src_configure() {
-	# check flag filtering
-	# with gcc 3.3.2 I had an infinite loop on src/exec/libdx/zclipQ.c
-	append-flags -fno-strength-reduce
-
-	# (#82672)
-	filter-flags -finline-functions
-	replace-flags -O3 -O2
-
-	# opendx uses this variable
-	local GENTOOARCH="${ARCH}"
-	unset ARCH
-
-	econf \
-		"--libdir=/usr/$(get_libdir)" \
-		"--with-x" \
-		"--without-javadx" \
-		$(use_with szip szlib) \
-		$(use_with cdf) \
-		$(use_with netcdf) \
-		$(use_with hdf) \
-		$(use_with tiff) \
-		$(use_with imagemagick magick) \
-		$(use_enable smp smp-linux)
-
-	ARCH="${GENTOOARCH}"
-#	javadx is currently broken. we may try to fix it someday.
-}
-
-src_compile() {
-	local GENTOOARCH="${ARCH}"
-	unset ARCH
-
-	emake || die
-	ARCH="${GENTOOARCH}"
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die
-
-	newicon "src/uipp/ui/icon50.xpm" "${PN}.xpm"
-	make_desktop_entry dx "openDX" "${PN}.xpm" "DataVisualization;Education;Science;"
-}
-
-pkg_postinst() {
-	elog "This version of the opendx ebuild is still under development."
-	elog "suggestions, comments and offer of help welcome"
-	elog "post a message in gentoo-science or pop up on irc on #gentoo-science"
-}
diff --git a/sys-cluster/mpich2/Manifest b/sys-cluster/mpich2/Manifest
index 75a90a2ba..1582d7ef2 100644
--- a/sys-cluster/mpich2/Manifest
+++ b/sys-cluster/mpich2/Manifest
@@ -8,7 +8,9 @@ AUX mpich2-1.0.8-mpdconf-env.patch 5355 RMD160 26ffada537073676553fdc4a9ee6a02f1
 AUX mpich2-1.0.8-pkgconfig.patch 928 RMD160 5ce7a800423f250dba0dd69560abebf845e7e556 SHA1 afba6883d1204a4b7c082af7e976186153263d64 SHA256 7f8dcafcb0d138130a684284d9bca86e4834f74a5132f0fef4556391abf43f8e
 DIST mpich2-1.0.8.tar.gz 17237476 RMD160 646cf50fbdc60a49809f4d0a6bcaf2835844db1f SHA1 41d6f6ce1034ecec5c14fb03592730ae2dd071e5 SHA256 7551ce20f3ef366567c566d08782323360b5dbd2d15d816e41c10b5f96eaf369
 DIST mpich2-1.1.1p1.tar.gz 18343542 RMD160 efa469c42306f3c4ce1d38d09da7c793c55ae03d SHA1 053fadf971f93fd023fae1e762f801f1d08d76e3 SHA256 10badc5afe55998f7be90f569447ce1b56c42ed0248c3a925090ad1e6a5d800f
+DIST mpich2-1.2.tar.gz 17245392 RMD160 fdf9f578817750be52e0d46c9dbc47fd8cbd925f SHA1 48502bf0acd6f877503b7f7756d51b63989e4fdd SHA256 b9d6d830864a940eead0e48965e5258f07190446eb511c14f5d567b2acfcdf44
 EBUILD mpich2-1.0.8-r1.ebuild 5240 RMD160 f1d871778940074334539cd4f9ef11749fba6eb8 SHA1 36e38cde4a648a31e3e413b6521508a948a18209 SHA256 c9d014301a1c6f6498fab873055bb9f038f2d3890b997aa9d2a4815b20152dca
 EBUILD mpich2-1.1.1_p1.ebuild 5114 RMD160 6b8ac2836241a7a7d446305d059a251ec9d55683 SHA1 07f58de02c5a6ddafa9abf22f8977c8229a1d07e SHA256 7e7218c778df0d67646d98489003dabb4bf62d6cb62e9ffd9eae8248b7d32d7a
+EBUILD mpich2-1.2.ebuild 5114 RMD160 6b8ac2836241a7a7d446305d059a251ec9d55683 SHA1 07f58de02c5a6ddafa9abf22f8977c8229a1d07e SHA256 7e7218c778df0d67646d98489003dabb4bf62d6cb62e9ffd9eae8248b7d32d7a
 MISC ChangeLog 1551 RMD160 282e5347dafc004d7faa0dc62dd78e7adf8e8a98 SHA1 79d79e69594fc934b6a6377f43221cea2fc7ce35 SHA256 b578b4b142c1dbdbb031c84e7738828c1202488b92eb88caa6d272b4d0fce536
 MISC metadata.xml 468 RMD160 98d955b7fd33a5b54c618424df4bc1237bb91a21 SHA1 eb055936e1a4ecafa846c1b7be6bc8c96d503ba1 SHA256 9516aa2c4536c5bc0555b42af1019a82e0f027ba8e52c0c46bcb5ee3fff8a765
diff --git a/sys-cluster/mpich2/mpich2-1.2.ebuild b/sys-cluster/mpich2/mpich2-1.2.ebuild
new file mode 100644
index 000000000..fc33a78bd
--- /dev/null
+++ b/sys-cluster/mpich2/mpich2-1.2.ebuild
@@ -0,0 +1,198 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=1
+inherit eutils fortran mpi
+
+MY_PV=${PV/_/}
+DESCRIPTION="MPICH2 - A portable MPI implementation"
+HOMEPAGE="http://www-unix.mcs.anl.gov/mpi/mpich2"
+SRC_URI="http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/${MY_PV}/${PN}-${MY_PV}.tar.gz"
+
+LICENSE="as-is"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
+IUSE="+cxx debug doc fortran pvfs2 threads romio mpi-threads"
+
+MPI_UNCLASSED_BLOCKERS="media-sound/mpd"
+
+COMMON_DEPEND="dev-lang/perl
+	>=dev-lang/python-2.3
+	romio? ( net-fs/nfs-utils )
+	pvfs2? ( >=sys-cluster/pvfs2-2.7.0 )
+	dev-libs/libaio
+	$(mpi_imp_deplist)"
+
+DEPEND="${COMMON_DEPEND}
+	sys-devel/libtool"
+
+RDEPEND="${COMMON_DEPEND}
+	net-misc/openssh"
+
+S="${WORKDIR}"/${PN}-${MY_PV}
+
+pkg_setup() {
+	MPI_ESELECT_FILE="eselect.mpi.mpich2"
+
+	if [ -n "${MPICH_CONFIGURE_OPTS}" ]; then
+	    elog "User-specified configure options are ${MPICH_CONFIGURE_OPTS}."
+	else
+	    elog "User-specified configure options are not set."
+	    elog "If needed, see the docs and set MPICH_CONFIGURE_OPTS."
+	fi
+
+	if use fortran ; then
+		FORTRAN="g77 gfortran ifort ifc"
+		fortran_pkg_setup
+	fi
+
+	if use mpi-threads && ! use threads; then
+		die "USE=mpi-threads requires USE=threads"
+	fi
+
+	if mpi_classed; then
+		MPD_CONF_FILE_DIR=/etc/$(mpi_class)
+	else
+		MPD_CONF_FILE_DIR=/etc/${PN}
+	fi
+}
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	# A lot of these patches touch Makefile.in and configure files.
+	# While it would be nice to regenerate everything, mpich2 uses
+	# simplemake instead of automake, so we're doing this for now
+	# and hoping for a receptive upstream.
+
+	# #220877
+	sed -i 's/-fpic/-fPIC/g' \
+		$(grep -lr -e '-fpic' "${S}"/) || die "failed to change -fpic to -fPIC"
+
+	# TODO: None of this has been sent upstream yet.
+	epatch "${FILESDIR}"/0001-MPD_CONF_FILE-should-be-readable.patch
+	epatch "${FILESDIR}"/0002-mpd_conf_file-search-order.patch
+	epatch "${FILESDIR}"/0003-Fix-pkgconfig-for-mpich2-ch3.patch
+
+	# We need f90 to include the directory with mods, and to
+	# fix hardcoded paths for src_test()
+	sed -i \
+		-e "s,F90FLAGS\( *\)=,F90FLAGS\1?=," \
+		-e "s,\$(bindir)/,${S}/bin/,g" \
+		-e "s,@MPIEXEC@,${S}/bin/mpiexec,g" \
+		$(find ./test/ -name 'Makefile.in') || die
+
+	if ! use romio; then
+		# These tests in errhan/ rely on MPI::File ...which is in romio
+		echo "" > test/mpi/errors/cxx/errhan/testlist
+	fi
+}
+
+src_compile() {
+	local c="${MPICH_CONFIGURE_OPTS} --enable-sharedlibs=gcc"
+	local romio_conf
+
+	# The configure statements can be somewhat confusing, as they
+	# don't all show up in the top level configure, however, they
+	# are picked up in the children directories.
+
+	use debug && c="${c} --enable-g=all --enable-debuginfo"
+
+	if use threads ; then
+	    c="${c} --with-thread-package=pthreads"
+	else
+	    c="${c} --with-thread-package=none"
+	fi
+
+	# enable f90 support for appropriate compilers
+	case "${FORTRANC}" in
+	    gfortran|if*)
+			c="${c} --enable-f77 --enable-f90";;
+	    g77)
+			c="${c} --enable-f77 --disable-f90";;
+	esac
+
+	if use mpi-threads; then
+		c="${c} --enable-threads=default"
+	else
+		c="${c} --enable-threads=single"
+	fi
+
+	if use pvfs2; then
+		# nfs and ufs are defaults in 1.0.8 at least.
+	    romio_conf="--with-file-system=pvfs2+nfs+ufs --with-pvfs2=/usr"
+	fi
+
+	! mpi_classed && c="${c} --sysconfdir=/etc/${PN}"
+	econf $(mpi_econf_args) ${c} ${romio_conf} \
+		--docdir=$(mpi_root)/usr/share/doc/${PF} \
+		--with-pm=mpd:gforker \
+		--disable-mpe \
+		$(use_enable romio) \
+		$(use_enable cxx) \
+		|| die
+	# Oh, the irony.
+	# http://wiki.mcs.anl.gov/mpich2/index.php/Frequently_Asked_Questions#Q:_The_build_fails_when_I_use_parallel_make.
+	# https://trac.mcs.anl.gov/projects/mpich2/ticket/297
+	emake -j1 || die
+}
+
+src_test() {
+	local rc
+
+	cp "${FILESDIR}"/mpd.conf "${T}"/mpd.conf || die
+	chmod 600 "${T}"/mpd.conf
+	export MPD_CONF_FILE="${T}/mpd.conf"
+	"${S}"/bin/mpd --daemon --pid="${T}"/mpd.pid
+
+	make \
+		CC="${S}"/bin/mpicc \
+		CXX="${S}"/bin/mpicxx \
+		FC="${S}"/bin/mpif77 \
+		F90="${S}"/bin/mpif90 \
+		F90FLAGS="${F90FLAGS} -I${S}/src/binding/f90/" \
+		testing
+	rc=$?
+
+	"${S}"/bin/mpdallexit || kill $(<"${T}"/mpd.pid)
+	return ${rc}
+}
+
+src_install() {
+	local d=$(mpi_root)
+
+	emake DESTDIR="${D}" install || die
+
+	dodir ${MPD_CONF_FILE_DIR}
+	insinto ${MPD_CONF_FILE_DIR}
+	doins "${FILESDIR}"/mpd.conf || die
+
+	mpi_dodir /usr/share/doc/${PF}
+	mpi_dodoc COPYRIGHT README CHANGES RELEASE_NOTES || die
+	mpi_newdoc src/pm/mpd/README README.mpd || die
+	if use romio; then
+		mpi_newdoc src/mpi/romio/README README.romio || die
+	fi
+
+	if ! use doc; then
+		rm -rf "${D}"/${d}/usr/share/doc/www*
+	else
+		mpi_dodir /usr/share/doc/${PF}/www
+		mv "${D}"/${d}/usr/share/doc/www*/* "${D}"/${d}/usr/share/doc/${PF}/www/
+	fi
+
+	mpi_imp_add_eselect
+}
+
+pkg_postinst() {
+	# Here so we can play with ebuild commands as a normal user
+	chown root:root "${ROOT}"${MPD_CONF_FILE_DIR}/mpd.conf
+	chmod 600 "${ROOT}"${MPD_CONF_FILE_DIR}/mpd.conf
+
+	elog ""
+	elog "MPE2 has been removed from this ebuild and now stands alone"
+	elog "as sys-cluster/mpe2."
+	elog ""
+}