Merge branch 'master' of https://github.com/TheChymera/sci

Conflicts:
	sci-libs/scikits_image/scikits_image-9999.ebuild

69 files changed, 840 insertions, 2225 deletions

diff --git a/dev-lang/vtune/ChangeLog b/dev-lang/vtune/ChangeLog
index 78878803f..3c6e77648 100644
--- a/dev-lang/vtune/ChangeLog
+++ b/dev-lang/vtune/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  24 Jul 2013; Justin Lecher <jlec@gentoo.org> -vtune-13.1.4.270817.ebuild,
+  -vtune-13.1.9.295420.ebuild, +vtune-13.1.10.298370.ebuild:
+  Version BUmp and fix missing libs, #472572
+
 *vtune-13.1.9.295420 (14 Jul 2013)
 
   14 Jul 2013; Justin Lecher <jlec@gentoo.org> +vtune-13.1.9.295420.ebuild:
diff --git a/dev-lang/vtune/Manifest b/dev-lang/vtune/Manifest
index d99d3ff30..2f10fbcf3 100644
--- a/dev-lang/vtune/Manifest
+++ b/dev-lang/vtune/Manifest
@@ -1,6 +1 @@
-DIST parallel_studio_xe_2013_update2.tgz 2152945149 SHA256 e8ddf6141f7d84c1f242891fabe0882c40269c358c0b946fee22ee6caa37121c SHA512 633370f58bd9fc14140912d5b3dd251ca4819a926b004a8053f92c83de6f9fdfdad192b425c5224d8b5aee47042a1a99d49628e6e2bb53e623ae429eefcfaac4 WHIRLPOOL 5b4a7c0c9cab758885ccffab25f1aaf64a6f5576d02df81a4797a2b9ae2151efb5e564e43397a2b61040d4af66024107a5a9c537982d3e17723655414dcba166
-DIST parallel_studio_xe_2013_update2_ia32.tgz 1190613262 SHA256 13063ea9c47c781ea8f368566d328434351002e7321b2021b5f04ff741a5d55f SHA512 1488a1b8c9b84881041ccf42d9f856d44aa0654ce3171b0f92114a3408d8cb1f1a18a6d488db6bbfd7322d5a230748612b53378b6ac01b8b7b3e66b3b8f94333 WHIRLPOOL f7d2b307d2f4e226004ddfcf073db087fff6d68e94f849e85350dc18894db884b62362bb3929076fdd531e29f5c49e2cd94eba8685b13fc52e293226516d909d
-DIST parallel_studio_xe_2013_update2_intel64.tgz 1488277925 SHA256 6136774de466de19f4024eeb5a8176ffbf559143b048fecc83848c27008361d6 SHA512 8260ab223d9a959089ae66c8948d90ce119cceeb719ef18c1a9d258ccd77e9b6a67af1a3e203d96a1c3c774def9a6fc302c126001072b7c5aa2bb3cdc68bc4dd WHIRLPOOL 006dc0e925c8265abf174682cd54f2c2fc4c4f1e059e045407d523b3e3b659cadc47da005126236a8b01b882fd0b4dfa7dadce0c52f640d5c0ada8122a9d6d08
-DIST parallel_studio_xe_2013_update4.tgz 2184817121 SHA256 55d549fc34f7a9eb96951c7be3216b68f9f960edfdc0997cf8dcffe5c78d66c8 SHA512 84ea227fdca2c427996b0c4d17a0bad6c289a6fbfc267c19f54ebee875e11e6e8d14bb3103599e3b89331c34a153b0a63a5ca8c12f4619420f78f8c4b0c2da96 WHIRLPOOL 6bedfdbcad7f0d7ad4681d51ad865db247d5f264f5fa33e7136fc64c5e83eee30bb2611f39bd7f31b790432e314a7dbea755297ae3fd2b90ccecb7beffb20d79
-DIST parallel_studio_xe_2013_update4_ia32.tgz 1220177902 SHA256 5bd75b2747f4b787b8128a83914b060d156ecdc41236f4100363b7ab4f9f6859 SHA512 968db307e08cd31450200abd41ade1f2b2855f4b5cb19911d03c1cd357cab11cbba814db354452496fcf66fc3fad1423b24f428bd4db07402f12bd63e4d34247 WHIRLPOOL f2b03ebb78960718a15fc69be814eeb7996fdd7575720f4b09cb915086cc757fea188ef5ceb7e37ed00c995e11ae544d8bd55aba8ab2d12530e26b3d23362f3e
-DIST parallel_studio_xe_2013_update4_intel64.tgz 1520767493 SHA256 31383f357b9b7d9c76e727e63427387d9ee42358f5b5df75a0d8766cd318a11d SHA512 497ad8f3473e1d11cdd31dff340a8e6ec1f012e731def084b2072146b5d11db906f85ace53b2223c3fbef949222f73f36783fd697eb7809464f4403c0ac8744a WHIRLPOOL d08447f27aee0f088797968d541fe98e3813a1daf5b87024d37493663238594c3e4e75a8d9636a4059191782f5eae9065d45b7ad2c27e1f73fc74eb110ad399f
+DIST vtune_amplifier_xe_2013_update10.tar.gz 203822924 SHA256 66a4cc9d036925cf631849702033c9820eff88cea5b99e7f4708d8fa2e4cb86f SHA512 377d3b3e4fdcff2b27a15c3c064de513e71ff18b467984a8d815f8bb50b725b24a673046b9b4b912c4bfd1fce7a88e07e6c41df221bdd9cb3cc09a527526e4af WHIRLPOOL fc2d1943ff0fcc8841fbc96d672c5bd4cf26182c9157ada99752157658b1a8f5c6a4046167a49d5e3a13b7931046042548ddf8a50e18379baf5b653d6d7a9a65
diff --git a/dev-lang/vtune/vtune-13.1.4.270817.ebuild b/dev-lang/vtune/vtune-13.1.10.298370.ebuild
index 4a1e08952..79f7915da 100644
--- a/dev-lang/vtune/vtune-13.1.4.270817.ebuild
+++ b/dev-lang/vtune/vtune-13.1.10.298370.ebuild
@@ -4,10 +4,12 @@
 
 EAPI=5
 
-INTEL_DPN=parallel_studio_xe
-INTEL_DID=2987
-INTEL_DPV=2013_update2
+INTEL_DPN=vtune_amplifier_xe
+INTEL_DID=3290
+INTEL_DPV=2013_update10
 INTEL_SUBDIR=vtune_amplifier_xe
+INTEL_TARX=tar.gz
+INTEL_SINGLE_ARCH=false
 
 inherit intel-sdp multilib
 
@@ -17,22 +19,16 @@ HOMEPAGE="http://software.intel.com/en-us/articles/intel-vtune-amplifier-xe/"
 IUSE=""
 KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
 
-INTEL_BIN_RPMS="vtune-amplifier-xe-gui"
-INTEL_DAT_RPMS="vtune-amplifier-xe-gui-common"
-#INTEL_RPMS_DIRS="rpm CLI_install/rpm"
-
-create_bin_symlink() {
-	_libdir=$(get_libdir)
-	_arch=${_libdir/lib/}
-	dosym /${INTEL_SDP_DIR}/bin${_arch}/${1} /opt/bin/${1}
-}
+INTEL_BIN_RPMS="vtune-amplifier-xe-gui CLI_install/rpm/intel-vtune-amplifier-xe-cli"
+INTEL_DAT_RPMS="vtune-amplifier-xe-gui-common CLI_install/rpm/intel-vtune-amplifier-xe-cli-common"
 
 src_install() {
 	intel-sdp_src_install
 
-	# Create symbolic links
-	create_bin_symlink amplxe-gui
-	create_bin_symlink amplxe-configurator
+	cat >> "${T}"/50vtune <<- EOF
+	PATH=${INTEL_SDP_EDIR}/bin64:${INTEL_SDP_EDIR}/bin32
+	EOF
+	doenvd "${T}"/50vtune
 
 	make_desktop_entry amplxe-gui "VTune Amplifier XE" "" "Development;Debugger"
 }
diff --git a/dev-lang/vtune/vtune-13.1.9.295420.ebuild b/dev-lang/vtune/vtune-13.1.9.295420.ebuild
deleted file mode 100644
index 3d441a198..000000000
--- a/dev-lang/vtune/vtune-13.1.9.295420.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-INTEL_DPN=parallel_studio_xe
-INTEL_DID=3266
-INTEL_DPV=2013_update4
-INTEL_SUBDIR=vtune_amplifier_xe
-
-inherit intel-sdp multilib
-
-DESCRIPTION="Intel VTune Amplifier XE"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-vtune-amplifier-xe/"
-
-IUSE=""
-KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-INTEL_BIN_RPMS="vtune-amplifier-xe-gui"
-INTEL_DAT_RPMS="vtune-amplifier-xe-gui-common"
-#INTEL_RPMS_DIRS="rpm CLI_install/rpm"
-
-create_bin_symlink() {
-	_libdir=$(get_libdir)
-	_arch=${_libdir/lib/}
-	dosym /${INTEL_SDP_DIR}/bin${_arch}/${1} /opt/bin/${1}
-}
-
-src_install() {
-	intel-sdp_src_install
-
-	# Create symbolic links
-	create_bin_symlink amplxe-gui
-	create_bin_symlink amplxe-configurator
-
-	make_desktop_entry amplxe-gui "VTune Amplifier XE" "" "Development;Debugger"
-}
diff --git a/eclass/intel-sdp.eclass b/eclass/intel-sdp.eclass
index 6e715b314..f5f01d8d8 100644
--- a/eclass/intel-sdp.eclass
+++ b/eclass/intel-sdp.eclass
@@ -102,6 +102,11 @@
 #
 # e.g. CLI_install/rpm/intel-vtune-amplifier-xe-cli-common
 
+# @ECLASS-VARIABLE: INTEL_SINGLE_ARCH
+# @DESCRIPTION:
+# Unset, if only the multilib package will be provided by intel
+: ${INTEL_SINGLE_ARCH:=true}
+
 # @ECLASS-VARIABLE: INTEL_SDP_DB
 # @DESCRIPTION:
 # Full path to intel registry db
@@ -115,10 +120,14 @@ _INTEL_PV3=$(get_version_component_range 3)
 _INTEL_PV4=$(get_version_component_range 4)
 _INTEL_URI="http://registrationcenter-download.intel.com/irc_nas/${INTEL_DID}/${INTEL_DPN}"
 
-SRC_URI="
-	amd64? ( multilib? ( ${_INTEL_URI}_${INTEL_DPV}.${INTEL_TARX} ) )
-	amd64? ( !multilib? ( ${_INTEL_URI}_${INTEL_DPV}_intel64.${INTEL_TARX} ) )
-	x86?	( ${_INTEL_URI}_${INTEL_DPV}_ia32.${INTEL_TARX} )"
+if [ ${INTEL_SINGLE_ARCH} == true ]; then
+	SRC_URI="
+		amd64? ( multilib? ( ${_INTEL_URI}_${INTEL_DPV}.${INTEL_TARX} ) )
+		amd64? ( !multilib? ( ${_INTEL_URI}_${INTEL_DPV}_intel64.${INTEL_TARX} ) )
+		x86?	( ${_INTEL_URI}_${INTEL_DPV}_ia32.${INTEL_TARX} )"
+else
+	SRC_URI="${_INTEL_URI}_${INTEL_DPV}.${INTEL_TARX}"
+fi
 
 LICENSE="Intel-SDP"
 # Future work, #394411
@@ -340,13 +349,13 @@ intel-sdp_pkg_setup() {
 	INTEL_RPMS=()
 	INTEL_RPMS_FULL=()
 	for p in ${INTEL_BIN_RPMS}; do
-		if [ ${p} == $(basename ${p}) ]; then
-			for a in ${arch}; do
+		for a in ${arch}; do
+			if [ ${p} == $(basename ${p}) ]; then
 				INTEL_RPMS+=( intel-${p}-${_INTEL_PV4}-${_INTEL_PV1}.${_INTEL_PV2}-${_INTEL_PV3}.${a}.rpm )
-			done
-		else
-			INTEL_RPMS_FULL+=( ${p}-${_INTEL_PV4}-${_INTEL_PV1}.${_INTEL_PV2}-${_INTEL_PV3}.${a}.rpm )
-		fi
+			else
+				INTEL_RPMS_FULL+=( ${p}-${_INTEL_PV4}-${_INTEL_PV1}.${_INTEL_PV2}-${_INTEL_PV3}.${a}.rpm )
+			fi
+		done
 	done
 	for p in ${INTEL_DAT_RPMS}; do
 		if [ ${p} == $(basename ${p}) ]; then
diff --git a/profiles/package.mask b/profiles/package.mask
index 4edd6951d..230760bc6 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -122,11 +122,6 @@ sci-visualization/vtkPOFFReader
 # new blas/lapack framework
 =sci-libs/blas-reference-20070226*
 
-# Francois Bissey (kiwifb) (29 Oct 2010)
-# f.r.bissey@massey.ac.nz
-# mask paraview-3.8.* as there are no stable versions in the tree
-# Avoid accidental upgrade
->=sci-visualization/paraview-3.8.0
 
 # Justin Lecher <jlec@gentoo.org> (11 May 2009)
 # work in progress 
diff --git a/sci-biology/psychopy/Manifest b/sci-biology/psychopy/Manifest
index ced74875f..96fc24a59 100644
--- a/sci-biology/psychopy/Manifest
+++ b/sci-biology/psychopy/Manifest
@@ -1 +1,2 @@
 DIST PsychoPy-1.75.01.zip 3512277 SHA256 c86c617bcd9a215f1fe3d1420563a9bc1c8c6707b477481f885437a68a56d211 SHA512 3a57dcff426d9bbeeababd7699d2fe99fc36025d45b4f52abb8ae4544454314dacb00b52b16f94168c86a255f9ac469fad297590b6e466931d5de12e7520f684 WHIRLPOOL a0f258c293937efbd6cbbc325663a1de93961de349e0113562c20d54a957c686590256d7c7a2e0ebea7a497090569ba0e2b777165e9cfe908af82a90991bb939
+DIST PsychoPy-1.77.02.zip 6313389 SHA256 37313ca13e6062146979dbc79dde79306377a08958b47ea1477957373914f1a1 SHA512 11c305d69763c7eca236c53ccef56780637ad2d53801764dada52565a4e07949422722cf7d8691b615d515c6eeee1c29e2ec44fc312fb299fc2bea17b5a15b44 WHIRLPOOL 568cd06a9ad511ceeb0f0293296d4a98549855960be82e25de57b576bbf6614f37253358dcc44909570a73b298df0651920ab2378e0145eb8bd69186922a745c
diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 80bd47e8c..795df1197 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  24 Jul 2013; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild:
+  Fx stupid argparse import
+
   26 Jun 2013; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild:
   Update repo uri
 
diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild
index 57b5715bd..4d5a6bdac 100644
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ b/sci-chemistry/pymol/pymol-9999.ebuild
@@ -46,6 +46,7 @@ python_prepare_all() {
 	sed \
 		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
 		-e "/ext_comp_args/s:=\[.*\]$:= \[\]:g" \
+		-e "/import/s:argparse:argparseX:g" \
 		-i setup.py || die
 
 	rm ./modules/pmg_tk/startup/apbs_tools.py || die
diff --git a/sci-libs/avogadro-libs/ChangeLog b/sci-libs/avogadro-libs/ChangeLog
new file mode 100644
index 000000000..6afd3fb7b
--- /dev/null
+++ b/sci-libs/avogadro-libs/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-libs/avogadro-libs
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*avogadro-libs-0.6.0 (23 Jul 2013)
+
+  23 Jul 2013; Justin Lecher <jlec@gentoo.org> +avogadro-libs-0.6.0.ebuild,
+  +metadata.xml:
+  New addition written by me
+
diff --git a/sci-libs/avogadro-libs/Manifest b/sci-libs/avogadro-libs/Manifest
new file mode 100644
index 000000000..bd4c7ba99
--- /dev/null
+++ b/sci-libs/avogadro-libs/Manifest
@@ -0,0 +1 @@
+DIST avogadrolibs-0.6.0.tar.gz 459937 SHA256 9a524eb122358231cc76a0f4efd0fb9313608598af6a105c92c045ec026fbde1 SHA512 fbcf8f07de32ca7f6f0fab32b96a288e7e6a19e7a00b3ed08290b6d9b4efb4284d8f60d18bf26334a4266afd15aefbf9faf1740e6f752b4cea4c183e89e7bc29 WHIRLPOOL ffb04d0e04891bee4eb9deda5dd6da5973fc7dbd222e9acb2acc52ec04610f4953bc83623a456e8f4a7e6b7f9b51e95295af6a8fe989c5cc2dde5bbd5e59573f
diff --git a/sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild b/sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild
new file mode 100644
index 000000000..a6bdff287
--- /dev/null
+++ b/sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cmake-utils versionator
+
+MY_PN="${PN/-/}"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="Advanced molecule editor and visualizer 2"
+HOMEPAGE="http://www.openchemistry.org/"
+SRC_URI="http://openchemistry.org/files/v$(get_version_component_range 1-2)/${MY_P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc opengl qt4 test vtk"
+
+RDEPEND="
+	sci-chemistry/molequeue
+	sci-libs/chemkit
+	"
+DEPEND="${RDEPEND}
+"
+
+S="${WORKDIR}"/${MY_P}
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_STATIC_PLUGINS=OFF
+		-DUSE_PROTOCALL=OFF
+		$(cmake-utils_use_build doc DOCUMENTATION)
+		$(cmake-utils_use_use opengl OPENGL)
+		$(cmake-utils_use_enable test TESTING)
+		$(cmake-utils_use_use qt4 QT)
+		$(cmake-utils_use_use vtk VTK)
+		)
+	cmake-utils_src_configure
+}
diff --git a/sci-libs/avogadro-libs/metadata.xml b/sci-libs/avogadro-libs/metadata.xml
new file mode 100644
index 000000000..dbe5682b6
--- /dev/null
+++ b/sci-libs/avogadro-libs/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+  </maintainer>
+  <use>
+    <flag name="vtk">include vtk support</flag>
+  </use>
+</pkgmetadata>
diff --git a/sci-libs/chemkit/ChangeLog b/sci-libs/chemkit/ChangeLog
new file mode 100644
index 000000000..62d386007
--- /dev/null
+++ b/sci-libs/chemkit/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-libs/chemkit
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*chemkit-0.1 (22 Jul 2013)
+
+  22 Jul 2013; Justin Lecher <jlec@gentoo.org> +chemkit-0.1.ebuild,
+  +metadata.xml:
+  New addition written by me
+
diff --git a/sci-libs/chemkit/Manifest b/sci-libs/chemkit/Manifest
new file mode 100644
index 000000000..13f90d9ca
--- /dev/null
+++ b/sci-libs/chemkit/Manifest
@@ -0,0 +1 @@
+DIST chemkit-0.1.tar.gz 5842235 SHA256 bec718ce4ae2fcb4cda63004d05a6e6bf65c1887179f665fcee118cbe7bec11b SHA512 0273f8735333000b04007ccd7adc58f0c4809a570fa5a72e4161652d72e8953bf89cad0893c20ecbb3484d6c13a8828c92f12366dddeedaf591815c35f6ef011 WHIRLPOOL 30c73d5d2bb7e946204d3dcdd87b82fa3e5278e799b06df523557f46ca4c71ae7d5b9c37d82af8dcdee48bb83f8840c5f2900b4331c3cf643c323ef20abc1883
diff --git a/sci-libs/chemkit/chemkit-0.1.ebuild b/sci-libs/chemkit/chemkit-0.1.ebuild
new file mode 100644
index 000000000..8f17cdd6c
--- /dev/null
+++ b/sci-libs/chemkit/chemkit-0.1.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit cmake-utils multilib
+
+DESCRIPTION="Library for chemistry applications"
+HOMEPAGE="http://www.chemkit.org/"
+SRC_URI="mirror://sourceforge/project/${PN}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="applications examples python test"
+
+RDEPEND="${PYTHON_DEPS}
+	dev-libs/boost
+	dev-cpp/eigen:3
+	examples? (
+		x11-libs/libX11
+		x11-libs/libXext
+	)"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${PN}
+
+src_prepare() {
+	sed \
+		-e "/install/s:lib:$(get_libdir):g" \
+		-i CMakeLists.txt src/CMakeLists.txt src/plugins/CMakeLists.txt || die
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCHEMKIT_BUILD_PLUGIN_BABEL=on
+		$(cmake-utils_use applications CHEMKIT_BUILD_APPS)
+		$(cmake-utils_use applications CHEMKIT_BUILD_QT_DESIGNER_PLUGINS)
+		$(cmake-utils_use examples CHEMKIT_BUILD_EXAMPLES)
+		$(cmake-utils_use examples CHEMKIT_BUILD_DEMOS)
+		$(cmake-utils_use python CHEMKIT_BUILD_BINDINGS_PYTHON)
+		$(cmake-utils_use test CHEMKIT_BUILD_TESTS)
+	)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	use examples && dobin demos/*-viewer/*-viewer examples/uff-energy/uff-energy
+
+	cmake-utils_src_install
+}
diff --git a/sci-libs/chemkit/metadata.xml b/sci-libs/chemkit/metadata.xml
new file mode 100644
index 000000000..200ba799f
--- /dev/null
+++ b/sci-libs/chemkit/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+  </maintainer>
+  <use>
+    <flag name="applications">Build also applications not only the libraries</flag>
+  </use>
+</pkgmetadata>
diff --git a/sci-libs/dealii/Manifest b/sci-libs/dealii/Manifest
new file mode 100644
index 000000000..fd3018c89
--- /dev/null
+++ b/sci-libs/dealii/Manifest
@@ -0,0 +1,2 @@
+DIST deal.II-8.0.0.tar.gz 15212414 SHA256 2bf7443cb16b5fc39fe6d70b07071d731de9ac415a90658ec4d2197d40513738 SHA512 fb6c79cc7ab18dbb579a2a5dd8144c71f37b36170a9653f805b753fd69ebb66f98c866d7811c5daf24a99cb107ab1f59a7edb18ed9d9597cba566cd04753b3d7 WHIRLPOOL ac63e12431613a59275b39284da1bc6a5cbc52a36c7de2a86845202cbdbccd0d296165f57a3cecba85f2e1ccb4741292ed5770cb2afd0d1c0c4c2f42787a5345
+DIST deal.offlinedoc-8.0.0.tar.gz 90684547 SHA256 7af02e32f691dba950d78f39c227bc22863c5d882cb83665eb639f4aadea9009 SHA512 47b959d976908c5a49d957fcf8a48e53db047e0aa6d8cf2b299f5e91d82c384b48fe326399f5e78146d80ad6ca39b1a305334086730b61d9c5c6975e91641529 WHIRLPOOL 16fa92f65e45a771c1ecafe7bc29b707f38930da9c7b8b423ed933b63ecc5c58f16d25c600c19636c59e9f6b1f8b42e69f485e912ff788de5de67d35cd76ac5c
diff --git a/sci-libs/dealii/dealii-8.0.0.ebuild b/sci-libs/dealii/dealii-8.0.0.ebuild
new file mode 120000
index 000000000..9860d7b9f
--- /dev/null
+++ b/sci-libs/dealii/dealii-8.0.0.ebuild
@@ -0,0 +1 @@
+dealii-9999.ebuild
\ No newline at end of file
diff --git a/sci-libs/dealii/dealii-9999.ebuild b/sci-libs/dealii/dealii-9999.ebuild
new file mode 100644
index 000000000..1b08288dd
--- /dev/null
+++ b/sci-libs/dealii/dealii-9999.ebuild
@@ -0,0 +1,128 @@
+# Copyright 2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+if [[ ${PV} == "9999" ]] ; then
+	inherit cmake-utils subversion eutils multilib
+else
+	inherit cmake-utils eutils multilib
+fi
+
+DESCRIPTION="library for solving partial differential equations with the finite element method"
+HOMEPAGE="http://www.dealii.org/"
+
+if [[ ${PV} == "9999" ]] ; then
+	ESVN_REPO_URI="https://svn.dealii.org/trunk/deal.II"
+	ESVN_OPTIONS="--trust-server-cert --non-interactive"
+	KEYWORDS=""
+else
+	SRC_URI="https://dealii.googlecode.com/files/deal.II-${PV}.tar.gz
+		doc? ( https://dealii.googlecode.com/files/deal.offlinedoc-${PV}.tar.gz )"
+	S="${WORKDIR}/deal.II"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+LICENSE="LGPL-2.1+"
+SLOT="0"
+IUSE="arpack avx +debug doc +examples hdf5 +lapack mesh_converter metis mpi mumps netcdf p4est parameter_gui petsc +sparse sse2 static-libs +tbb trilinos +zlib"
+# TODO: add slepc use flag once slepc is packaged for gentoo-science
+REQUIRED_USE="
+	mumps? ( mpi lapack )
+	p4est? ( mpi )
+	trilinos? ( mpi )
+"
+
+RDEPEND="
+	dev-libs/boost
+	arpack? ( sci-libs/arpack[mpi=] )
+	doc? ( app-doc/doxygen[dot] dev-lang/perl )
+	hdf5? ( sci-libs/hdf5[mpi=] )
+	lapack? ( virtual/lapack )
+	metis? ( >=sci-libs/parmetis-4 )
+	mpi? ( virtual/mpi )
+	mumps? ( sci-libs/mumps[mpi] )
+	netcdf? ( || ( <sci-libs/netcdf-4.2[cxx] sci-libs/netcdf-cxx ) )
+	p4est? ( sci-libs/p4est[mpi] )
+	parameter_gui? ( dev-qt/qtgui )
+	petsc? ( sci-mathematics/petsc[mpi=] )
+	sparse? ( sci-libs/umfpack )
+	tbb? ( dev-cpp/tbb )
+	trilinos? ( sci-libs/trilinos )
+	zlib? ( sys-libs/zlib )
+"
+
+DEPEND="
+	${RDEPEND}
+	virtual/pkgconfig
+"
+
+src_configure() {
+
+	if [[ ${PV} == "9999" ]] ; then
+		subversion_wc_info
+		local live_version="-DDEAL_II_PACKAGE_VERSION=99.99.svn${ESVN_WC_REVISION}"
+	fi
+
+	if use debug; then
+		CMAKE_BUILD_TYPE="DebugRelease"
+	else
+		CMAKE_BUILD_TYPE="Release"
+	fi
+
+	local mycmakeargs=(
+		${live_version}
+		"-DDEAL_II_ALLOW_AUTODETECTION=OFF"
+		"-DDEAL_II_ALLOW_BUNDLED=OFF"
+		"-DDEAL_II_ALLOW_PLATFORM_INTROSPECTION=OFF"
+		$(cmake-utils_use arpack DEAL_II_WITH_ARPACK)
+		$(cmake-utils_use avx DEAL_II_HAVE_AVX)
+		$(cmake-utils_use doc DEAL_II_COMPONENT_DOCUMENTATION)
+		$(cmake-utils_use examples DEAL_II_COMPONENT_EXAMPLES)
+		$(cmake-utils_use hdf5 DEAL_II_WITH_HDF5)
+		$(cmake-utils_use lapack DEAL_II_WITH_LAPACK)
+		$(cmake-utils_use mesh_converter DEAL_II_COMPONENT_MESH_CONVERTER)
+		$(cmake-utils_use metis DEAL_II_WITH_METIS)
+		$(cmake-utils_use mpi DEAL_II_WITH_MPI)
+		$(cmake-utils_use mumps DEAL_II_WITH_MUMPS)
+		$(cmake-utils_use netcdf DEAL_II_WITH_NETCDF)
+		$(cmake-utils_use p4est DEAL_II_WITH_P4EST)
+		$(cmake-utils_use parameter_gui DEAL_II_COMPONENT_PARAMETER_GUI)
+		$(cmake-utils_use petsc DEAL_II_WITH_PETSC)
+		$(cmake-utils_use sparse DEAL_II_WITH_UMFPACK)
+		$(cmake-utils_use sse2 DEAL_II_HAVE_SSE2)
+		$(cmake-utils_use !static-libs BUILD_SHARED_LIBS)
+		$(cmake-utils_use static-libs DEAL_II_PREFER_STATIC_LIBS)
+		$(cmake-utils_use tbb DEAL_II_WITH_THREADS)
+		$(cmake-utils_use trilinos DEAL_II_WITH_TRILINOS)
+		$(cmake-utils_use zlib DEAL_II_WITH_ZLIB)
+		"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=OFF"
+		"-DDEAL_II_COMPONENT_COMPAT_FILES=OFF"
+		"-DDEAL_II_CMAKE_MACROS_RELDIR=share/${PN}/cmake/macros"
+		"-DDEAL_II_DOCHTML_RELDIR=share/doc/${PF}/html"
+		"-DDEAL_II_DOCREADME_RELDIR=share/doc/${PF}/"
+		"-DDEAL_II_EXAMPLES_RELDIR=share/doc/${PF}/examples"
+		"-DDEAL_II_LIBRARY_RELDIR=$(get_libdir)"
+		)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	dodoc README
+
+	if use doc; then
+		if [[ ${PV} != "9999" ]] ; then
+			# copy missing images to the build directory:
+			cp -r "${WORKDIR}"/doc/doxygen/deal.II/images "${BUILD_DIR}"/doc/doxygen/deal.II
+			# replace links:
+			sed -i \
+				's#"http://www.dealii.org/images/steps/developer/\(step-.*\)"#"images/\1"#g' \
+				"${BUILD_DIR}"/doc/doxygen/deal.II/step_*.html || die "sed failed"
+		fi
+	fi
+	cmake-utils_src_install
+
+	# unpack the installed example sources:
+	use examples && docompress -x /usr/share/doc/${PF}/examples
+}
diff --git a/sci-libs/dealii/metadata.xml b/sci-libs/dealii/metadata.xml
new file mode 100644
index 000000000..65475b58a
--- /dev/null
+++ b/sci-libs/dealii/metadata.xml
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+  <email>tamiko+GENTOO@kyomu.43-1.org</email>
+  <name>Matthias Maier</name>
+</maintainer>
+<longdescription lang="en">
+  deal.II is a C++ program library targeted at the computational solution
+  of partial differential equations using adaptive finite elements. It uses
+  state-of-the-art programming techniques to offer you a modern interface
+  to the complex data structures and algorithms required.
+</longdescription>
+<use>
+  <flag name="arpack">Adds support for ARPACK (<pkg>sci-libs/arpack</pkg>)</flag>
+  <flag name="avx">Use Advanced Vector Extensions for AVX capable chips</flag>
+  <flag name="debug">Build an additional debug library with extra debug codepaths, like asserts and extra output. If you want to get meaningful backtraces see &lt;http://www.gentoo.org/proj/en/qa/backtraces.xml&gt;</flag>
+  <flag name="mesh_converter">Build and install the mesh_converter executable</flag>
+  <flag name="metis">Add support for metis (<pkg>sci-libs/metis</pkg>)</flag>
+  <flag name="mumps">Add support for mumps (<pkg>sci-libs/mumps</pkg>)</flag>
+  <flag name="p4est">Add support for p4est (<pkg>sci-mathematics/p4est</pkg>)</flag>
+  <flag name="parameter_gui">Build and install the parameter_gui executable</flag>
+  <flag name="petsc">Add support for petsc (<pkg>sci-libs/petsc</pkg>)</flag>
+  <flag name="tbb">Add threading support with the help of the tbb library (<pkg>dev-cpp/tbb</pkg>)</flag>
+  <flag name="trilinos">Add support for trilinos (<pkg>sci-libs/trilinos</pkg>)</flag>
+</use>
+</pkgmetadata>
diff --git a/sci-libs/nibabel/nibabel-9999.ebuild b/sci-libs/nibabel/nibabel-9999.ebuild
new file mode 100644
index 000000000..dc69d022e
--- /dev/null
+++ b/sci-libs/nibabel/nibabel-9999.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="5"
+
+PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} )
+
+inherit distutils-r1 git-2
+
+DESCRIPTION="Access a cacophony of neuro-imaging file formats"
+HOMEPAGE="http://http://nipy.org/nibabel/"
+EGIT_REPO_URI="https://github.com/nipy/nibabel.git"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE="dicom doc test"
+
+COMMONDEP="
+	>=dev-python/numpy-1.2[${PYTHON_USEDEP}]
+	>=sci-libs/scipy-0.7.0[${PYTHON_USEDEP}]
+	>=dev-python/nose-0.11[${PYTHON_USEDEP}]
+	dicom? ( 
+		sci-libs/pydicom[${PYTHON_USEDEP}]
+		virtual/python-imaging[${PYTHON_USEDEP}] )"	
+
+DEPEND="
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	test? ( ${COMMONDEP} )
+	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )"
+
+RDEPEND="
+	${COMMONDEP}"
+
+python_test() {
+	distutils_install_for_testing
+	cd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die
+	echo "backend: Agg" > matplotlibrc
+	MPLCONFIGDIR=. nosetests-"${EPYTHON}" || die
+}
\ No newline at end of file
diff --git a/sci-libs/nipy/Manifest b/sci-libs/nipy/Manifest
new file mode 100644
index 000000000..e2730eee9
--- /dev/null
+++ b/sci-libs/nipy/Manifest
@@ -0,0 +1 @@
+DIST nipy-0.3.0.tar.gz 2143887 SHA256 74fef65c832795a35e1757d8bd852177fae190517a964afcb0812cfc1107d155 SHA512 3eaab4628bfa1706c99d516242387e1a27330bbf03b5b79da80d9a5e697b4e779f8f059e6f7bcc4253c5ad7af1bf6c600bcc5bd87db95d2e38f445d1f4416106 WHIRLPOOL 8a27c42abd8c7ae5ce66b8cfb0686b79e3208950107fcc5090d88fa2c23bf15d4ce4ae5b598f6f51c6e70122c40a343b9b7b2950ef09aefaeb22e24efd854af0
diff --git a/sci-libs/nipy/nipy-0.3.0.ebuild b/sci-libs/nipy/nipy-0.3.0.ebuild
new file mode 100644
index 000000000..24754ae1a
--- /dev/null
+++ b/sci-libs/nipy/nipy-0.3.0.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="5"
+
+PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} )
+DISTUTILS_NO_PARALLEL_BUILD=true
+
+inherit distutils-r1 eutils multilib flag-o-matic
+
+MY_P="nipy-${PV}"
+
+DESCRIPTION="Neuroimaging tools for Python"
+HOMEPAGE="http://nipy.org/"
+SRC_URI="https://pypi.python.org/packages/source/n/nipy/nipy-0.3.0.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+	>=dev-python/numpy-1.2[${PYTHON_USEDEP}]
+	>=sci-libs/scipy-0.7.0[${PYTHON_USEDEP}]
+	>=dev-python/sympy-0.6.6[${PYTHON_USEDEP}]
+	>=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]"
+DEPEND="
+	"
+
+python_prepare_all() {
+	# bug #397605
+	[[ ${CHOST} == *-darwin* ]] \
+		&& append-ldflags -bundle "-undefined dynamic_lookup" \
+		|| append-ldflags -shared
+
+	# nipy uses the horrible numpy.distutils automagic
+}
\ No newline at end of file
diff --git a/sci-libs/nipy/nipy-9999.ebuild b/sci-libs/nipy/nipy-9999.ebuild
new file mode 100644
index 000000000..87902deec
--- /dev/null
+++ b/sci-libs/nipy/nipy-9999.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_image/scikits_image-0.8.2.ebuild,v 1.3 2013/06/18 04:33:25 patrick Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} )
+DISTUTILS_NO_PARALLEL_BUILD=true
+
+inherit distutils-r1 multilib git-2 flag-o-matic
+
+DESCRIPTION="Neuroimaging tools for Python"
+HOMEPAGE="http://nipy.org/"
+EGIT_REPO_URI="https://github.com/nipy/nipy"
+
+LICENSE="BSD"
+SLOT="0"
+
+RDEPEND="
+	>=dev-python/numpy-1.2[${PYTHON_USEDEP}]
+	>=sci-libs/scipy-0.7.0[${PYTHON_USEDEP}]
+	>=dev-python/sympy-0.6.6[${PYTHON_USEDEP}]
+	>=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]"
+DEPEND="
+	"
+
+python_prepare_all() {
+	# bug #397605
+	[[ ${CHOST} == *-darwin* ]] \
+		&& append-ldflags -bundle "-undefined dynamic_lookup" \
+		|| append-ldflags -shared
+
+	# nipy uses the horrible numpy.distutils automagic
+}
\ No newline at end of file
diff --git a/sci-libs/nipype/nipype-9999.ebuild b/sci-libs/nipype/nipype-9999.ebuild
new file mode 100644
index 000000000..8abf2e1c0
--- /dev/null
+++ b/sci-libs/nipype/nipype-9999.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_image/scikits_image-0.8.2.ebuild,v 1.3 2013/06/18 04:33:25 patrick Exp $
+
+EAPI=5
+
+# pyamg missing py3 support
+# PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} )
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1 git-2
+
+DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
+HOMEPAGE="http://nipy.sourceforge.net/nipype/"
+EGIT_REPO_URI="https://github.com/nipy/nipype"
+
+LICENSE="BSD"
+SLOT="0"
+
+RDEPEND="
+	>=sci-libs/scipy-0.7.0[${PYTHON_USEDEP}]
+	>=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]
+	dev-python/traits[${PYTHON_USEDEP}]
+	dev-python/networkx[${PYTHON_USEDEP}]"
+DEPEND="
+	"
diff --git a/sci-libs/openblas/ChangeLog b/sci-libs/openblas/ChangeLog
index 73db9ea66..80ed3d883 100644
--- a/sci-libs/openblas/ChangeLog
+++ b/sci-libs/openblas/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*openblas-0.2.7 (24 Jul 2013)
+
+  24 Jul 2013; Sébastien Fabbro <bicatali@gentoo.org> +openblas-0.2.7.ebuild,
+  -files/openblas-aliasing.patch, -files/openblas-sharedlibs-0.2.patch,
+  -openblas-0.2.6.ebuild, metadata.xml, openblas-9999.ebuild:
+  sci-libs/openblas: Version bump. Rewrote ebuild to try to follow upstream
+  closer
+
 *openblas-0.2.6 (03 Mar 2013)
 
   03 Mar 2013; Sébastien Fabbro <bicatali@gentoo.org> +openblas-0.2.6.ebuild,
diff --git a/sci-libs/openblas/Manifest b/sci-libs/openblas/Manifest
index 2035709d0..4383aa606 100644
--- a/sci-libs/openblas/Manifest
+++ b/sci-libs/openblas/Manifest
@@ -1 +1,2 @@
-DIST openblas-0.2.6.tar.gz 3259286 SHA256 f14fed709343a40d32bdfe2c1a0b2e874ef7514661930a20afe8e7e2436b4440 SHA512 794fc44f81b09afc8ff4529386a721ce2a04371752ad84a9c71d9956c6a7dbbd6f0af390be4acaa35454cf5fba77b61925de660ca1a9cfc5950ad89fb5f9608a WHIRLPOOL e418dbacaf78c620e31e6263224fa87bbf612f34d97407684f19a8a1f5a07f668785c2f728706b239dae14b07a1aa920d5b63fa52751d1f6f306e37e38b8e10e
+DIST openblas-0.2.7.tar.gz 9470019 SHA256 6be05c1cbaaa463d8758e2a0b5968b6b7e0a9a3780d0bd3727ea3cb86c3a40f0 SHA512 0ac6e2bf85cec34fc5ee8b6a28178c5d3083528d73d607031b7e680ec490458da53e353fe94c22b0f9f4d446cd82dab34d2c0b71d2f572659b61d6e24fa3c264 WHIRLPOOL 933f39bb78b35b4d514288a28cea977b037f3d7cfe031df893d73ce941d2b53ca094bd63354f805bbf487d89812a946482dbd77311e579ae2ca5aed08f73cc32
+DIST openblas-gentoo.patch 252572 SHA256 284ff5a5d89cdf80688d923a54ca78fb714063ec49388853145acde606d255e9 SHA512 36b090bec3572af06c506ef92b93bc70f1a81e63d9dbf7babef518af70aff75022c34156ac62792193a1d90bbcc2789eb806f0d05f1f1fb03cd18006bab55e33 WHIRLPOOL f2a09aa4e7166cff158ff0863a176fb1521ba00e4b4bc826d750ff9c7350b04342a15750c8b9d5b34eec2f3aed75d27c4a03e6885af42f04200b2403eadd7100
diff --git a/sci-libs/openblas/files/openblas-aliasing.patch b/sci-libs/openblas/files/openblas-aliasing.patch
deleted file mode 100644
index 8c59b1c63..000000000
--- a/sci-libs/openblas/files/openblas-aliasing.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- driver/others/init.c.orig	2011-05-31 18:59:24.000000000 +0100
-+++ driver/others/init.c	2011-05-31 20:18:51.000000000 +0100
-@@ -261,7 +261,7 @@
-   for (node = 0; node < MAX_NODES; node ++) common -> node_info[node] = 0;
- 
-   while ((dir = readdir(dp)) != NULL) {
--    if (*(unsigned int *) dir -> d_name == 0x065646f6eU) {
-+    if (*(char *) dir -> d_name == 0x065646f6eU) {
- 
-       node = atoi(&dir -> d_name[4]);
- 
diff --git a/sci-libs/openblas/files/openblas-sharedlibs-0.2.patch b/sci-libs/openblas/files/openblas-sharedlibs-0.2.patch
deleted file mode 100644
index a66b31457..000000000
--- a/sci-libs/openblas/files/openblas-sharedlibs-0.2.patch
+++ /dev/null
@@ -1,45 +0,0 @@
---- exports/Makefile.orig	2012-06-26 10:24:20.154182394 -0700
-+++ exports/Makefile	2012-06-26 10:28:59.894394334 -0700
-@@ -106,9 +106,9 @@
- so : ../$(LIBSONAME)
- 
- ../$(LIBSONAME) : ../$(LIBNAME) linux.def linktest.c
--	$(CC) $(CFLAGS) -shared -o ../$(LIBSONAME) \
-+	$(CC) $(LDFLAGS) -shared \
- 	-Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive \
--	-Wl,--retain-symbols-file=linux.def -Wl,-soname,$(LIBPREFIX).so.$(MAJOR_VERSION) $(EXTRALIB)
-+	-Wl,--retain-symbols-file=linux.def -Wl,-soname,$(LIBSONAME) $(EXTRALIB) -o ../$(LIBSONAME)
- 	$(CC) $(CFLAGS) -w -o linktest linktest.c ../$(LIBSONAME) $(FEXTRALIB) && echo OK.
- 	rm -f linktest
- 
-@@ -119,9 +119,9 @@
- so : ../$(LIBSONAME)
- 
- ../$(LIBSONAME) : ../$(LIBNAME) linux.def linktest.c
--	$(CC) $(CFLAGS)  -shared -o ../$(LIBSONAME) \
-+	$(CC) $(LDFLAGS)  -shared \
- 	-Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive \
--	-Wl,--retain-symbols-file=linux.def $(FEXTRALIB) $(EXTRALIB)
-+	-Wl,--soname=$(LIBSONAME) -Wl,--retain-symbols-file=linux.def $(FEXTRALIB) $(EXTRALIB) -o ../$(LIBSONAME)
- 	$(CC) $(CFLAGS) -w -o linktest linktest.c ../$(LIBSONAME) $(FEXTRALIB) && echo OK.
- 	rm -f linktest
- 
-@@ -132,14 +132,15 @@
- so : ../$(LIBSONAME)
- 
- ../$(LIBSONAME) :
--	$(CC) -shared -o ../$(LIBSONAME) ../$(LIBNAME)
-+	$(CC) -shared ../$(LIBNAME) -o ../$(LIBSONAME)
- endif
- 
- ifeq ($(OSNAME), SunOS)
- 
- so : ../$(LIBSONAME)
--	$(CC) $(CFLAGS)  -shared -o ../$(LIBSONAME) \
--	-Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive $(EXTRALIB)
-+	$(CC) $(LDFLAGS)  -shared  \
-+	-Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive -Wl,--soname=$\(LIBSONAME) $(EXTRALIB) \
-+	-o ../$(LIBSONAME)
- 	$(CC) $(CFLAGS) -w -o linktest linktest.c ../$(LIBSONAME) $(FEXTRALIB) && echo OK.
- 	rm -f linktest
- 
diff --git a/sci-libs/openblas/metadata.xml b/sci-libs/openblas/metadata.xml
index fd35350ed..67a10b4bd 100644
--- a/sci-libs/openblas/metadata.xml
+++ b/sci-libs/openblas/metadata.xml
@@ -8,7 +8,6 @@
 </longdescription>
 <use>
   <flag name='int64'>Build the 64 bits integer library</flag>
-  <flag name='incblas'>Build the CBLAS interface</flag>
   <flag name='dynamic'>Build dynamic architecture detection at run time (for multi targets)</flag>
 </use>
 </pkgmetadata>
diff --git a/sci-libs/openblas/openblas-0.2.6.ebuild b/sci-libs/openblas/openblas-0.2.6.ebuild
deleted file mode 120000
index 2381753b7..000000000
--- a/sci-libs/openblas/openblas-0.2.6.ebuild
+++ /dev/null
@@ -1 +0,0 @@
-openblas-9999.ebuild
\ No newline at end of file
diff --git a/sci-libs/openblas/openblas-0.2.7.ebuild b/sci-libs/openblas/openblas-0.2.7.ebuild
new file mode 100644
index 000000000..30e5918ee
--- /dev/null
+++ b/sci-libs/openblas/openblas-0.2.7.ebuild
@@ -0,0 +1,127 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils toolchain-funcs alternatives-2 multilib fortran-2
+
+DESCRIPTION="Optimized BLAS library based on GotoBLAS2"
+HOMEPAGE="http://xianyi.github.com/OpenBLAS/"
+SRC_URI="http://github.com/xianyi/OpenBLAS/tarball/v${PV} -> ${P}.tar.gz
+	http://dev.gentoo.org/~bicatali/distfiles/${PN}-gentoo.patch"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos ~ppc-macos ~x64-macos"
+
+LICENSE="BSD"
+SLOT="0"
+
+IUSE="int64 dynamic openmp static-libs threads"
+
+RDEPEND=""
+DEPEND="${RDEPEND}"
+
+src_unpack() {
+	default
+	find "${WORKDIR}" -maxdepth 1 -type d -name \*OpenBLAS\* && \
+		mv "${WORKDIR}"/*OpenBLAS* "${S}"
+}
+
+src_prepare() {
+	# openblas already does multi-jobs
+	MAKEOPTS+=" -j1"
+	cd "${S}"
+	epatch "${DISTDIR}"/${PN}-gentoo.patch
+}
+
+src_configure() {
+	# lapack and lapacke are not modified from upstream lapack
+	sed -i \
+		-e "s:^#\s*\(CC\)\s*=.*:\1=$(tc-getCC):" \
+		-e "s:^#\s*\(FC\)\s*=.*:\1=$(tc-getFC):" \
+		-e "s:^#\s*\(COMMON_OPT\)\s*=.*:\1=${CFLAGS}:" \
+		-e "s:^#\s*\(NO_LAPACK\)\s*=.*:\1=1:" \
+		-e "s:^#\s*\(NO_LAPACKE\)\s*=.*:\1=1:" \
+		Makefile.rule || die
+}
+
+openblas_compile() {
+	local profname=$1
+	einfo "Compiling profile ${profname}"
+	# cflags already defined twice
+	unset CFLAGS
+	emake clean
+	emake libs shared ${openblas_flags}
+	mkdir -p libs && mv lib* libs/
+	# avoid pic when compiling static libraries, so re-compiling
+	if use static-libs; then
+		emake clean
+		emake libs ${openblas_flags} NO_SHARED=1 NEED_PIC=
+		mv lib* libs/
+	fi
+	cat <<-EOF > ${profname}.pc
+		prefix=${EPREFIX}/usr
+		libdir=\${prefix}/$(get_libdir)
+		includedir=\${prefix}/include
+		Name: ${PN}
+		Description: ${DESCRIPTION}
+		Version: ${PV}
+		URL: ${HOMEPAGE}
+		Libs: -L\${libdir} -lopenblas
+		Libs.private: -lm
+		Cflags: -I\${includedir}/${PN}
+	EOF
+}
+
+src_compile() {
+	openblas_flags=""
+	use dynamic && \
+		openblas_flags+=" DYNAMIC_ARCH=1 TARGET=GENERIC NUM_THREADS=64 NO_AFFINITY=1"
+	use int64 && \
+		openblas_flags+=" INTERFACE64=1"
+
+	# choose posix threads over openmp when the two are set
+	# yet to see the need of having the two profiles simultaneously
+	if use threads; then
+		openblas_flags+=" USE_THREAD=1 USE_OPENMP=0"
+	elif use openmp; then
+		openblas_flags+=" USE_THREAD=0 USE_OPENMP=1"
+	fi
+	openblas_compile openblas
+	mv libs/lib* . || die
+}
+
+src_test() {
+	emake tests ${openblas_flags}
+}
+
+src_install() {
+	local pcfile
+	for pcfile in *.pc; do
+		local profname=${pcfile%.pc}
+		emake install \
+			PREFIX="${ED}"usr ${openblas_flags} \
+			OPENBLAS_INCLUDE_DIR="${ED}"usr/include/${PN} \
+			OPENBLAS_LIBRARY_DIR="${ED}"usr/$(get_libdir)
+		use static-libs || rm "${ED}"usr/$(get_libdir)/lib*.a
+		alternatives_for blas ${profname} 0 \
+			/usr/$(get_libdir)/pkgconfig/blas.pc ${pcfile}
+		alternatives_for cblas ${profname} 0 \
+			/usr/$(get_libdir)/pkgconfig/cblas.pc ${pcfile} \
+			/usr/include/cblas.h ${PN}/cblas.h
+		insinto /usr/$(get_libdir)/pkgconfig
+		doins ${pcfile}
+	done
+
+	dodoc GotoBLAS_{01Readme,03FAQ,04FAQ,05LargePage,06WeirdPerformance}.txt
+	dodoc *md Changelog.txt
+
+	if [[ ${CHOST} == *-darwin* ]] ; then
+		cd "${ED}"/usr/$(get_libdir)
+		local d
+		for d in *.dylib ; do
+			ebegin "Correcting install_name of ${d}"
+			install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/${d}" "${d}"
+			eend $?
+		done
+	fi
+}
diff --git a/sci-libs/openblas/openblas-9999.ebuild b/sci-libs/openblas/openblas-9999.ebuild
index 008e107d2..f9834f69e 100644
--- a/sci-libs/openblas/openblas-9999.ebuild
+++ b/sci-libs/openblas/openblas-9999.ebuild
@@ -4,96 +4,56 @@
 
 EAPI=5
 
-if [[ ${PV} == "9999" ]] ; then
-	_SCM=git-2
-	EGIT_REPO_URI="https://github.com/xianyi/OpenBLAS.git"
-	SRC_URI=""
-	KEYWORDS=""
-else
-	SRC_URI="http://github.com/xianyi/OpenBLAS/tarball/v${PV} -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos ~ppc-macos ~x64-macos"
-fi
-
-inherit eutils toolchain-funcs alternatives-2 multilib fortran-2 ${_SCM}
+EGIT_REPO_URI="https://github.com/xianyi/OpenBLAS.git"
+EGIT_MASTER="develop"
+
+inherit eutils toolchain-funcs alternatives-2 multilib fortran-2 git-2
 
 DESCRIPTION="Optimized BLAS library based on GotoBLAS2"
 HOMEPAGE="http://xianyi.github.com/OpenBLAS/"
+KEYWORDS=""
+SRC_URI="http://dev.gentoo.org/~bicatali/distfiles/${PN}-gentoo.patch"
 
 LICENSE="BSD"
 SLOT="0"
 
-IUSE="+incblas int64 dynamic openmp static-libs threads"
+IUSE="int64 dynamic openmp static-libs threads"
 
 RDEPEND=""
 DEPEND="${RDEPEND}"
 
-src_unpack() {
-	unpack ${A}
-	mv "${WORKDIR}"/*OpenBLAS* "${S}" || die
-}
-
 src_prepare() {
-	epatch "${FILESDIR}"/${PN}-{sharedlibs-0.2,aliasing}.patch
-	# respect LDFLAGS
-	sed -i -e '/^LDFLAGS\s*=/d' Makefile.* || die
-	# respect CFLAGS only if dynamic flag not enabled
-	if ! use dynamic; then
-		sed -i \
-			-e "/^COMMON_OPT/s/-O2/${CFLAGS}/" \
-			Makefile.rule || die
-	fi
-	# fix executable stacks
-	local i
-	for i in $(find . -name \*.S); do
-		cat >> ${i} <<-EOF
-			#if defined(__ELF__)
-			.section .note.GNU-stack,"",%progbits
-			#endif
-		EOF
-	done
+	# openblas already does multi-jobs
+	MAKEOPTS+=" -j1"
+	cd "${S}"
+	epatch "${DISTDIR}"/${PN}-gentoo.patch
 }
 
 src_configure() {
-	local use_openmp=$(use openmp && echo 1)
-	use threads && use openmp && use_openmp="" && \
-		einfo "openmp and threads enabled: using threads"
+	# lapack and lapacke are not modified from upstream lapack
 	sed -i \
-		-e "s:^#\s*\(NO_LAPACK\)\s*=.*:\1=1:" \
-		-e "s:^#\s*\(NO_LAPACKE\)\s*=.*:\1=1:" \
 		-e "s:^#\s*\(CC\)\s*=.*:\1=$(tc-getCC):" \
 		-e "s:^#\s*\(FC\)\s*=.*:\1=$(tc-getFC):" \
-		-e "s:^#\s*\(USE_THREAD\)\s*=.*:\1=$(use threads && echo 1 || echo 0):" \
-		-e "s:^#\s*\(USE_OPENMP\)\s*=.*:\1=${use_openmp}:" \
-		-e "s:^#\s*\(DYNAMIC_ARCH\)\s*=.*:\1=$(use dynamic && echo 1):" \
-		-e "s:^#\s*\(INTERFACE64\)\s*=.*:\1=$(use int64 && echo 1):" \
-		-e "s:^#\s*\(NO_CBLAS\)\s*=.*:\1=$(use incblas || echo 1):" \
+		-e "s:^#\s*\(COMMON_OPT\)\s*=.*:\1=${CFLAGS}:" \
+		-e "s:^#\s*\(NO_LAPACK\)\s*=.*:\1=1:" \
+		-e "s:^#\s*\(NO_LAPACKE\)\s*=.*:\1=1:" \
 		Makefile.rule || die
 }
 
-src_compile() {
-	mkdir solibs
-	emake libs shared && mv *$(get_libname) solibs/
-	use static-libs && emake clean && emake libs NEED_PIC=
-}
-
-src_test() {
-	emake tests
-}
-
-src_install() {
-	local profname=${PN} threads
-	use int64 && profname=${profname}-int64
-	if use threads; then
-		threads="-pthread"
-		profname=${profname}-threads
-	elif use openmp; then
-		profname=${profname}-openmp
+openblas_compile() {
+	local profname=$1
+	einfo "Compiling profile ${profname}"
+	# cflags already defined twice
+	unset CFLAGS
+	emake clean
+	emake libs shared ${openblas_flags}
+	mkdir -p libs && mv lib* libs/
+	# avoid pic when compiling static libraries, so re-compiling
+	if use static-libs; then
+		emake clean
+		emake libs ${openblas_flags} NO_SHARED=1 NEED_PIC=
+		mv lib* libs/
 	fi
-
-	dolib.so solibs/lib*$(get_libname)
-	use static-libs && dolib.a lib*.a
-
-	# create pkg-config file and associated eselect file
 	cat <<-EOF > ${profname}.pc
 		prefix=${EPREFIX}/usr
 		libdir=\${prefix}/$(get_libdir)
@@ -103,27 +63,57 @@ src_install() {
 		Version: ${PV}
 		URL: ${HOMEPAGE}
 		Libs: -L\${libdir} -lopenblas
-		Libs.private: -lm ${threads}
+		Libs.private: -lm
+		Cflags: -I\${includedir}/${PN}
 	EOF
+}
+
+src_compile() {
+	openblas_flags=""
+	use dynamic && \
+		openblas_flags+=" DYNAMIC_ARCH=1 TARGET=GENERIC NUM_THREADS=64 NO_AFFINITY=1"
+	use int64 && \
+		openblas_flags+=" INTERFACE64=1"
+
+	# choose posix threads over openmp when the two are set
+	# yet to see the need of having the two profiles simultaneously
+	if use threads; then
+		openblas_flags+=" USE_THREAD=1 USE_OPENMP=0"
+	elif use openmp; then
+		openblas_flags+=" USE_THREAD=0 USE_OPENMP=1"
+	fi
+	openblas_compile openblas-int64
+	mv libs/lib* . || die
+}
 
-	alternatives_for blas ${profname} 0 \
-		/usr/$(get_libdir)/pkgconfig/blas.pc ${profname}.pc
+src_test() {
+	emake tests ${openblas_flags}
+}
 
-	if use incblas; then
-		echo >> ${profname}.pc "Cflags: -I\${includedir}/${PN}"
-		insinto /usr/include/${PN}
-		doins cblas.h common*.h config.h param.h
+src_install() {
+	local pcfile
+	for pcfile in *.pc; do
+		local profname=${pcfile%.pc}
+		emake install \
+			PREFIX="${ED}"usr ${openblas_flags} \
+			OPENBLAS_INCLUDE_DIR="${ED}"usr/include/${PN} \
+			OPENBLAS_LIBRARY_DIR="${ED}"usr/$(get_libdir)
+		use static-libs || rm "${ED}"usr/$(get_libdir)/lib*.a
+		alternatives_for blas ${profname} 0 \
+			/usr/$(get_libdir)/pkgconfig/blas.pc ${pcfile}
 		alternatives_for cblas ${profname} 0 \
-			/usr/$(get_libdir)/pkgconfig/cblas.pc ${profname}.pc \
+			/usr/$(get_libdir)/pkgconfig/cblas.pc ${pcfile} \
 			/usr/include/cblas.h ${PN}/cblas.h
-	fi
+		insinto /usr/$(get_libdir)/pkgconfig
+		doins ${pcfile}
+	done
 
-	insinto /usr/$(get_libdir)/pkgconfig
-	doins ${profname}.pc
 	dodoc GotoBLAS_{01Readme,03FAQ,04FAQ,05LargePage,06WeirdPerformance}.txt
+	dodoc *md Changelog.txt
 
 	if [[ ${CHOST} == *-darwin* ]] ; then
 		cd "${ED}"/usr/$(get_libdir)
+		local d
 		for d in *.dylib ; do
 			ebegin "Correcting install_name of ${d}"
 			install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/${d}" "${d}"
diff --git a/sci-libs/p4est/Manifest b/sci-libs/p4est/Manifest
new file mode 100644
index 000000000..12a3a3354
--- /dev/null
+++ b/sci-libs/p4est/Manifest
@@ -0,0 +1 @@
+DIST p4est-0.3.4.1.tar.gz 1789020 SHA256 752df2868362e2d6bb984a10ad71ca3f8079972b48d444865d1ea231bd6336fa SHA512 497ee1d2f963227bc4dd60de5a63b9e9065200a9322b65b491a044b27c2fcc35ef6aa24082c3f304b8ac127dbece506de6a6913852f4bea5824cd2903888f1ee WHIRLPOOL 896e5e8cd894d9cb807367a1c1bb203f6d32de447c5d6905a62711c26dfaebce96bae6578f8f4a58ac24c80a8bf695f9dd15b3404cf879d35e67c9dd6d746ea5
diff --git a/sci-libs/p4est/files/p4est-libtool-fix.patch b/sci-libs/p4est/files/p4est-libtool-fix.patch
new file mode 100644
index 000000000..a484694d4
--- /dev/null
+++ b/sci-libs/p4est/files/p4est-libtool-fix.patch
@@ -0,0 +1,59 @@
+--- a/src/Makefile.am   2013-07-25 23:49:48.949442972 +0200
++++ b/src/Makefile.am   2013-07-25 23:50:23.255540853 +0200
+@@ -49,17 +49,6 @@
+ endif
+ P4EST_CPPFLAGS =
+ 
+-# build static library
+-lib_LIBRARIES += src/libp4est.a
+-src_libp4est_a_SOURCES = \
+-        $(libp4est_installed_headers) \
+-        $(libp4est_internal_headers) \
+-        $(libp4est_compiled_sources)
+-src_libp4est_a_CPPFLAGS = $(AM_CPPFLAGS) $(P4EST_CPPFLAGS)
+-src_libp4est_a_DEPENDENCIES = @P4EST_DEPENDENCIES@
+-
+-# build shared library
+-if P4EST_ENABLE_SHARED
+ lib_LTLIBRARIES += src/libp4est.la
+ src_libp4est_la_SOURCES = \
+         $(libp4est_internal_headers) \
+@@ -67,9 +56,6 @@
+ src_libp4est_la_CPPFLAGS = $(AM_CPPFLAGS) $(P4EST_CPPFLAGS)
+ src_libp4est_la_DEPENDENCIES = @P4EST_DEPENDENCIES@
+ LDADD += @top_builddir@/src/libp4est.la @P4EST_SC_LDADD@
+-else
+-LDADD += @top_builddir@/src/libp4est.a @P4EST_SC_LDADD@
+-endif
+ 
+ nodist_include_HEADERS += $(libp4est_generated_headers)
+ include_HEADERS += $(libp4est_installed_headers)
+--- a/sc/src/Makefile.am  2013-07-25 23:54:46.330624131 +0200
++++ a/sc/src/Makefile.am  2013-07-25 23:55:12.516935722 +0200
+@@ -35,26 +35,12 @@
+         src/sc_builtin/zlib.h src/sc_builtin/zconf.h
+ LIBSC_CPPFLAGS =
+ 
+-# build static library
+-lib_LIBRARIES += src/libsc.a
+-src_libsc_a_SOURCES = \
+-        $(libsc_installed_headers) \
+-        $(libsc_internal_headers) \
+-        $(libsc_compiled_sources)
+-src_libsc_a_CPPFLAGS = $(AM_CPPFLAGS) $(LIBSC_CPPFLAGS)
+-
+-# build shared library
+-if SC_ENABLE_SHARED
+ lib_LTLIBRARIES += src/libsc.la
+ src_libsc_la_SOURCES = \
+         $(libsc_internal_headers) \
+         $(libsc_compiled_sources)
+ src_libsc_la_CPPFLAGS = $(AM_CPPFLAGS) $(LIBSC_CPPFLAGS)
+ LDADD += @top_builddir@/src/libsc.la
+-else
+-LDADD += @top_builddir@/src/libsc.a
+-endif
+-LDADD_STATIC += @top_builddir@/src/libsc.a
+ 
+ nodist_include_HEADERS += $(libsc_generated_headers)
+ include_HEADERS += $(libsc_installed_headers)
diff --git a/sci-libs/p4est/metadata.xml b/sci-libs/p4est/metadata.xml
new file mode 100644
index 000000000..592c6fc09
--- /dev/null
+++ b/sci-libs/p4est/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+  <email>tamiko+GENTOO@kyomu.43-1.org</email>
+  <name>Matthias Maier</name>
+</maintainer>
+<longdescription lang="en">
+  The p4est software library enables the dynamic management of a collection
+  of adaptive octrees, conveniently called a forest of octrees. p4est is
+  designed to work in parallel and scale to hundreds of thousands of
+  processor cores.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-libs/p4est/p4est-0.3.4.1.ebuild b/sci-libs/p4est/p4est-0.3.4.1.ebuild
new file mode 100644
index 000000000..9df1e73fd
--- /dev/null
+++ b/sci-libs/p4est/p4est-0.3.4.1.ebuild
@@ -0,0 +1,71 @@
+# Copyright 2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+WANT_AUTOMAKE=1.11
+
+inherit autotools-utils toolchain-funcs eutils multilib
+
+DESCRIPTION="Scalable Algorithms for Parallel Adaptive Mesh Refinement on Forests of Octrees"
+HOMEPAGE="http://www.p4est.org/"
+SRC_URI="http://burstedde.ins.uni-bonn.de/release/p4est-${PV}.tar.gz"
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+LICENSE="GPL-2+"
+SLOT="0"
+
+IUSE="debug doc examples mpi romio static-libs"
+REQUIRED_USE="romio? ( mpi )"
+
+RDEPEND="
+	dev-lang/lua
+	sys-apps/util-linux
+	sys-libs/zlib
+	virtual/blas
+	virtual/lapack
+	mpi? ( virtual/mpi[romio?] )"
+
+DEPEND="
+    ${RDEPEND}
+    virtual/pkgconfig"
+
+DOCS=(AUTHORS ChangeLog NEWS README)
+
+PATCHES=( "${FILESDIR}/${PN}-libtool-fix.patch" )
+AUTOTOOLS_AUTORECONF=true
+
+src_configure() {
+	local myeconfargs=(
+        $(use_enable debug)
+		$(use_enable mpi)
+		$(use_enable romio mpiio)
+		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)"
+		--with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)"
+	)
+	autotools-utils_src_configure
+}
+
+src_install() {
+	autotools-utils_src_install
+
+	use doc && dodoc -r doc/*
+
+	if use examples
+	then
+		docinto examples
+		dodoc -r example/*
+		docompress -x /usr/share/doc/${PF}/examples
+	else
+		# Remove the compiled example binaries in case of -examples:
+		rm -r "${ED}"/usr/bin || die "rm failed"
+	fi
+
+	# Fix up some wrong installation pathes:
+	dodir /usr/share/p4est
+	mv "${ED}"/usr/share/data "${ED}"/usr/share/p4est/data
+	mv "${ED}"/etc/* "${ED}"/usr/share/p4est
+	rmdir "${ED}"/etc/
+}
diff --git a/sci-libs/scikits_image/scikits_image-9999.ebuild b/sci-libs/scikits_image/scikits_image-9999.ebuild
index 951583432..9c92ac4bf 100644
--- a/sci-libs/scikits_image/scikits_image-9999.ebuild
+++ b/sci-libs/scikits_image/scikits_image-9999.ebuild
@@ -42,9 +42,13 @@ S="${WORKDIR}/${MYPN}-${PV}"
 DOCS=( CONTRIBUTORS.txt DEPENDS.txt RELEASE.txt TASKS.txt )
 
 python_test() {
+<<<<<<< HEAD
 	distutils_install_for_testing.py \
 		install --root="${T}/test-${EPYTHON}" \
 		--no-compile || die "install test failed"
+=======
+	distutils_install_for_testing.py
+>>>>>>> e20cf96b7230e5bd7e2d5a7531754a84ba6a67df
 	cd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die
 	echo "backend: Agg" > matplotlibrc
 	MPLCONFIGDIR=. PYTHONPATH=. nosetests-"${EPYTHON}" || die
diff --git a/sci-visualization/paraview/ChangeLog b/sci-visualization/paraview/ChangeLog
deleted file mode 100644
index df874d135..000000000
--- a/sci-visualization/paraview/ChangeLog
+++ /dev/null
@@ -1,156 +0,0 @@
-# ChangeLog for sci-visualization/paraview
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  03 Mar 2013; Justin Lecher <jlec@gentoo.org> paraview-3.10.1.ebuild,
-  paraview-3.12.0.ebuild, paraview-3.14.1-r4.ebuild, metadata.xml:
-  Update to new qt deps names
-
-  19 Dec 2012; François Bissey <francois.bissey@canterbury.ac.nz>
-  paraview-3.14.1-r4.ebuild, files/paraview-3.14.1-vtknetcd.patch:
-  Fix forgotten instances of vtkNetCDF
-
-  17 Dec 2012; François Bissey <francois.bissey@canterbury.ac.nz>
-  paraview-3.14.1-r4.ebuild:
-  sort webkit dependencies
-
-*paraview-3.14.1-r4 (20 Sep 2012)
-
-  20 Sep 2012; François Bissey <francois.bissey@canterbury.ac.nz>
-  -paraview-3.14.1-r3.ebuild, +paraview-3.14.1-r4.ebuild, metadata.xml:
-  change postscript useflag to gl2ps as in opencascade
-
-*paraview-3.14.1-r3 (16 Sep 2012)
-
-  16 Sep 2012; François Bissey <francois.bissey@canterbury.ac.nz>
-  -paraview-3.14.1-r2.ebuild, +paraview-3.14.1-r3.ebuild:
-  add a ps useflags for gl2ps
-
-*paraview-3.14.1-r2 (31 Aug 2012)
-
-  31 Aug 2012; François Bissey <francois.bissey@canterbury.ac.nz>
-  -paraview-3.14.1-r1.ebuild, +paraview-3.14.1-r2.ebuild,
-  +files/paraview-3.14.1-vtknetcd.patch:
-  netcdf dealt with
-
-*paraview-3.14.1-r1 (30 Aug 2012)
-
-  30 Aug 2012; François Bissey <francois.bissey@canterbury.ac.nz>
-  -paraview-3.14.1.ebuild, +paraview-3.14.1-r1.ebuild,
-  +files/paraview-3.14.1-gcc-4.7.patch, +files/paraview-3.14.1-mpi4py.patch,
-  +files/paraview-3.14.1-python-exit.patch,
-  +files/paraview-3.14.1-removesqlite.patch:
-  fix a number of things
-
-*paraview-3.14.1 (28 Aug 2012)
-
-  28 Aug 2012; François Bissey <francois.bissey@canterbury.ac.nz>
-  +paraview-3.14.1.ebuild, +files/paraview-3.14.1-ffmpeg-noinstall.patch,
-  +files/paraview-3.14.1-xdmf-linking.patch, +files/vtk-5.6.0-odbc.patch,
-  +files/vtk-5.6.1-ffmpeg.patch, +files/vtk-boost1.49.patch,
-  +files/vtk-5.6.1-libav-0.8.patch:
-  3.14.1
-
-  09 Feb 2012; François Bissey <francois.bissey@canterbury.ac.nz>
-  paraview-3.12.0.ebuild, files/paraview-3.12.0-protobuf.patch:
-  clean up protobuf mess, go to EAPI 3 (for python QA)
-
-*paraview-3.12.0 (07 Feb 2012)
-
-  07 Feb 2012; François Bissey <francois.bissey@canterbury.ac.nz>
-  +paraview-3.12.0.ebuild, +files/paraview-3.12.0-gcc46.patch,
-  +files/paraview-3.12.0-protobuf.patch:
-  introducing paraview-3.12.0
-
-  24 Aug 2011; Kacper Kowalik <xarthisius@gentoo.org> -paraview-3.8.1.ebuild,
-  paraview-3.10.1.ebuild, +files/paraview-3.10.1-gcc46.patch:
-  Drop old, fix building with gcc-4.6, add missing dependency on PyQt4
-
-*paraview-3.10.1 (16 Jun 2011)
-
-  16 Jun 2011; François Bissey <francois.bissey@canterbury.ac.nz>
-  +paraview-3.10.1.ebuild, metadata.xml:
-  New paraview ebuild for 3.10.1
-
-  13 Apr 2011; Justin Lecher <jlec@gentoo.org> paraview-3.8.1.ebuild:
-  Fix for python ABI stuff
-
-  09 Mar 2011; Oliver Borm (boroli) <oli.borm@web.de> paraview-3.8.1.ebuild:
-  sci-visualization/paraview: removed OFF patch as this is now an external
-  plugin
-
-  07 Mar 2011; Justin Lecher <jlec@gentoo.org> paraview-3.8.1.ebuild:
-  Correct Slots for gtk 3 introduction to tree
-
-  01 Feb 2011; François Bissey <francois.bissey@canterbury.ac.nz>
-  paraview-3.8.1.ebuild:
-  Resolve file collisions with vtk.
-
-  31 Jan 2011; François Bissey <francois.bissey@canterbury.ac.nz>
-  paraview-3.8.1.ebuild:
-  General scrubbing, add plugin development files.
-
-  10 Jan 2011; Oliver Borm (boroli) <oli.borm@web.de> paraview-3.8.1.ebuild:
-  added second python path as this seems to be needed for the compile *.so
-  files
-
-  29 Dec 2010; François Bissey <f.r.bissey@massey.ac.nz>
-  -paraview-3.8.0.ebuild, paraview-3.8.1.ebuild:
-  "patch" for python-2.7, add pkg_postrm to deal with left over python files,
-  drop old.
-
-  03 Dec 2010; Oliver Borm (boroli) <oli.borm@web.de> paraview-3.8.1.ebuild:
-  sci-visualization/paraview: fixed python path
-
-  30 Nov 2010; Oliver Borm (boroli) <oli.borm@web.de> paraview-3.8.1.ebuild:
-  sci-visualization/paraview: added new OpenFOAM patch
-
-  09 Nov 2010; François Bissey <f.r.bissey@massey.ac.nz>
-  paraview-3.8.0.ebuild, paraview-3.8.1.ebuild:
-  migrate to virtual/jpeg
-
-  29 Oct 2010; François Bissey <f.r.bissey@massey.ac.nz>
-  +paraview-3.8.0.ebuild:
-  Restore paraview-3.8.0 while working on several issues with 3.8.1
-
-  27 Oct 2010; François Bissey <f.r.bissey@massey.ac.nz>
-  paraview-3.8.1.ebuild:
-  Fix installation of copies of Qt and ffmpeg and so on.
-
-*paraview-3.8.1 (27 Oct 2010)
-
-  27 Oct 2010; François Bissey <f.r.bissey@massey.ac.nz>
-  -paraview-3.8.0.ebuild, +paraview-3.8.1.ebuild:
-  Bump to version 3.8.1
-
-  12 Oct 2010; François Bissey <f.r.bissey@massey.ac.nz>
-  paraview-3.8.0.ebuild:
-  Move to qt4-r2 eclass
-
-  12 Oct 2010; François Bissey <f.r.bissey@massey.ac.nz>
-  paraview-3.8.0.ebuild:
-  fix conditional boost dependency problem.
-
-  30 Jul 2010; François Bissey <f.r.bissey@massey.ac.nz>
-  paraview-3.8.0.ebuild:
-  Correct SRC_URI.
-
-  11 Jul 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de>
-  metadata.xml:
-  Silenced repoman.
-
-  20 Jun 2010; François Bissey <f.r.bissey@massey.ac.nz>
-  paraview-3.8.0.ebuild, +files/paraview-3.8.0-h5part.patch:
-  Added a fix for mpi in h5part - hopefully.
-
-*paraview-3.8.0 (11 Jun 2010)
-
-  11 Jun 2010; François Bissey <f.r.bissey@massey.ac.nz>
-  +paraview-3.8.0.ebuild, +files/paraview-3.8.0-installpath.patch,
-  +files/paraview-3.8.0-pointsprite-example.patch,
-  +files/paraview-3.8.0-pointsprite-example-install.patch,
-  +files/paraview-3.8.0-xdmf-bc.patch,
-  +files/paraview-3.8.0-xdmf-cstring.patch, +files/vtk-5.6.0-cg-path.patch,
-  +files/vtk-5.6.0-libpng14.patch, +metadata.xml:
-  Importing paraview-3.8.0 in the overelay.
-
diff --git a/sci-visualization/paraview/Manifest b/sci-visualization/paraview/Manifest
deleted file mode 100644
index 16fa3fc2a..000000000
--- a/sci-visualization/paraview/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST ParaView-3.10.1.tar.gz 40696006 SHA256 453deee23b6fa62ecb010d951adbc49e740dcb8875680725f93b8f76b9df5cfc SHA512 7110fd549db8b40067f4f8e5951df17067d7b8ad05a73fdbe1bb36d55ac9c25059c643dcb3c7b7cc07619b5dc6eb52a2084e14a17527edcf99fd313e7be10b79 WHIRLPOOL cf92a55eddfe7c4807d200371165a8c949aea6fd7db2016b0f5e17ea5dab1a6fc4f18d9efe14d16db97d7678d4b2df94786f71158aaea564e39912517298c8b7
-DIST ParaView-3.12.0.tar.gz 37510144 SHA256 357a8cc27d4c8fb40ec9f508000edaa802e2a8528bfc61564e2d0bb033041658 SHA512 20f844b75e1a4f8581e213d24ddeefe2404676f86368506c6bf76f1d68cf4d757f137119c8ace16dd322d8411f3b4f8e2201857aee0ec5c483d369040ac896c0 WHIRLPOOL 70f2019fbbd588a2d344ee4ea7a62a69c1cf09f49b8a470c47c622b775c8b898ca7ffea48333c8f02c314ca9afaabf3bb316f86202c3f56a650d748932164d75
-DIST ParaView-3.14.1-Source.tar.gz 41471770 SHA256 84499b2775b2159a6f9afed43e7e48ecde998d094a0afe5e2a97db04e359b6f1 SHA512 9459cf896cc7e188c1b6bdeb567d0ed9edebb708fcce6268bf84d3cd2860a4a25747a85256cd6a5dff7c297ac1941258375238f74169a143031b176a7161873e WHIRLPOOL 4c36e3c5e1cb87a9a1ee06326754578f805e55fa4e6746ad06de28644f2c3d8055541478b7b6cca2d0b39412fdac2121e192fad7679420efafeed6d0f81adf53
diff --git a/sci-visualization/paraview/files/paraview-3.10.1-gcc46.patch b/sci-visualization/paraview/files/paraview-3.10.1-gcc46.patch
deleted file mode 100644
index 20be721ec..000000000
--- a/sci-visualization/paraview/files/paraview-3.10.1-gcc46.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- a/VTK/Utilities/vtkmetaio/metaUtils.cxx
-+++ b/VTK/Utilities/vtkmetaio/metaUtils.cxx
-@@ -29,6 +29,7 @@
- #include <arpa/inet.h>
- #endif
- 
-+#include <stddef.h>
- #include <stdlib.h>
- #include <string.h>
- #include <string>
---- a/VTK/Wrapping/Python/PyVTKObject.cxx
-+++ b/VTK/Wrapping/Python/PyVTKObject.cxx
-@@ -33,6 +33,7 @@
- #include "vtkObjectBase.h"
- #include "vtkDataArray.h"
- 
-+#include <vtksys/cstddef>
- #include <vtksys/ios/sstream>
- 
- //--------------------------------------------------------------------
diff --git a/sci-visualization/paraview/files/paraview-3.12.0-gcc46.patch b/sci-visualization/paraview/files/paraview-3.12.0-gcc46.patch
deleted file mode 100644
index 15ff5d00c..000000000
--- a/sci-visualization/paraview/files/paraview-3.12.0-gcc46.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/VTK/Utilities/vtkmetaio/metaUtils.cxx
-+++ b/VTK/Utilities/vtkmetaio/metaUtils.cxx
-@@ -29,6 +29,7 @@
- #include <arpa/inet.h>
- #endif
- 
-+#include <stddef.h>
- #include <stdlib.h>
- #include <string.h>
- #include <string>
diff --git a/sci-visualization/paraview/files/paraview-3.12.0-protobuf.patch b/sci-visualization/paraview/files/paraview-3.12.0-protobuf.patch
deleted file mode 100644
index fe8f4b4a0..000000000
--- a/sci-visualization/paraview/files/paraview-3.12.0-protobuf.patch
+++ /dev/null
@@ -1,53 +0,0 @@
---- CMake/ParaViewCommon.cmake.orig	2012-02-03 15:31:08.531644115 +1300
-+++ CMake/ParaViewCommon.cmake	2012-02-03 15:30:36.420633741 +1300
-@@ -526,13 +526,13 @@
- 
- #########################################################################
- # Configure protobuf
--SET (PROTOBUF_INSTALL_BIN_DIR ${PV_INSTALL_BIN_DIR})
--SET (PROTOBUF_INSTALL_LIB_DIR ${PV_INSTALL_LIB_DIR})
--SET (PROTOBUF_INSTALL_EXPORT_NAME ${PV_INSTALL_EXPORT_NAME})
--IF (NOT PV_INSTALL_NO_LIBRARIES)
--  SET_PROPERTY(GLOBAL APPEND PROPERTY VTK_TARGETS protobuf)
--ENDIF (NOT PV_INSTALL_NO_LIBRARIES)
--ADD_SUBDIRECTORY(Utilities/protobuf)
-+# SET (PROTOBUF_INSTALL_BIN_DIR ${PV_INSTALL_BIN_DIR})
-+# SET (PROTOBUF_INSTALL_LIB_DIR ${PV_INSTALL_LIB_DIR})
-+# SET (PROTOBUF_INSTALL_EXPORT_NAME ${PV_INSTALL_EXPORT_NAME})
-+# IF (NOT PV_INSTALL_NO_LIBRARIES)
-+#   SET_PROPERTY(GLOBAL APPEND PROPERTY VTK_TARGETS protobuf)
-+# ENDIF (NOT PV_INSTALL_NO_LIBRARIES)
-+# ADD_SUBDIRECTORY(Utilities/protobuf)
- 
- #########################################################################
- # Configure mpeg2 encoding
---- CMake/ParaViewMacros.cmake.orig	2012-02-09 13:12:07.518350208 +1300
-+++ CMake/ParaViewMacros.cmake	2012-02-09 13:12:16.863356368 +1300
-@@ -214,6 +214,6 @@
-     COMMAND protoc_compiler
-       --cpp_out=dllexport_decl=VTK_PROTOBUF_EXPORT:${CMAKE_CURRENT_BINARY_DIR}
-       --proto_path ${path} ${absolute}
--    DEPENDS ${in_proto_file} protoc_compiler
-+    DEPENDS ${in_proto_file}
-   )
- ENDFUNCTION (protobuf_generate)
---- ParaViewCore/ServerImplementation/CMakeLists.txt.orig	2012-02-09 13:14:15.230434986 +1300
-+++ ParaViewCore/ServerImplementation/CMakeLists.txt	2012-02-09 13:15:04.214467797 +1300
-@@ -86,7 +86,7 @@
- #------------------------------------------------------------------------------
- # Compile protobuf resources.
- # run it from a script so we can set necessary paths.
--get_target_property(PROTOC_LOCATION protoc_compiler LOCATION)
-+SET(PROTOC_LOCATION ${SYSTEM_PB})
- if (WIN32)
-   get_filename_component(PROTOC_DIR ${PROTOC_LOCATION} PATH)
-   get_filename_component(PROTOC_PDIR ${PROTOC_DIR} PATH)
-@@ -101,7 +101,7 @@
-            ${CMAKE_CURRENT_BINARY_DIR}/vtkPVMessage.pb.cc
-     COMMAND ${CMAKE_COMMAND}
-     ARGS    -DOutDir=${CMAKE_CFG_INTDIR} -P ${CMAKE_CURRENT_BINARY_DIR}/ExecuteProtoC.cmake
--    DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/Resources/vtkPVMessage.proto protoc_compiler ${ParaView_CMAKE_DIR}/ExecuteProtoC.cmake.in
-+    DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/Resources/vtkPVMessage.proto ${ParaView_CMAKE_DIR}/ExecuteProtoC.cmake.in
-     WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- )
- 
diff --git a/sci-visualization/paraview/files/paraview-3.14.1-ffmpeg-noinstall.patch b/sci-visualization/paraview/files/paraview-3.14.1-ffmpeg-noinstall.patch
deleted file mode 100644
index 915725253..000000000
--- a/sci-visualization/paraview/files/paraview-3.14.1-ffmpeg-noinstall.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- CommandLineExecutables/CMakeLists.txt.orig	2012-08-28 14:29:41.472454000 +1200
-+++ CommandLineExecutables/CMakeLists.txt	2012-08-28 14:30:07.959473756 +1200
-@@ -69,15 +69,15 @@
- 
- #------------------------------------------------------------------------
- # Install ffmpeg, if used.
--IF (VTK_USE_FFMPEG_ENCODER)
--  FOREACH(fmpglib avcodec avformat avutil)
--    IF (FFMPEG_${fmpglib}_LIBRARY)
--      pv_install_library(${FFMPEG_${fmpglib}_LIBRARY}
--        ${PV_INSTALL_LIB_DIR}
--        BrandedRuntime)
--    ENDIF(FFMPEG_${fmpglib}_LIBRARY)
--  ENDFOREACH(fmpglib)
--ENDIF (VTK_USE_FFMPEG_ENCODER)
-+#IF (VTK_USE_FFMPEG_ENCODER)
-+#  FOREACH(fmpglib avcodec avformat avutil)
-+#    IF (FFMPEG_${fmpglib}_LIBRARY)
-+#      pv_install_library(${FFMPEG_${fmpglib}_LIBRARY}
-+#        ${PV_INSTALL_LIB_DIR}
-+#        BrandedRuntime)
-+#    ENDIF(FFMPEG_${fmpglib}_LIBRARY)
-+#  ENDFOREACH(fmpglib)
-+#ENDIF (VTK_USE_FFMPEG_ENCODER)
- 
- IF (NOT PV_INSTALL_NO_RUNTIME)
-   INSTALL(TARGETS smTestDriver
diff --git a/sci-visualization/paraview/files/paraview-3.14.1-gcc-4.7.patch b/sci-visualization/paraview/files/paraview-3.14.1-gcc-4.7.patch
deleted file mode 100644
index 0da9aab78..000000000
--- a/sci-visualization/paraview/files/paraview-3.14.1-gcc-4.7.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-Description: fix FTBFS with gcc-4.7
-Author: Mathieu Malaterre <malat@debian.org>
-Origin: http://anonscm.debian.org/gitweb/?p=collab-maint/vtk.git;a=commitdiff;h=428e763c995bb303805e07da70c1a34fc103d208
-Reviewed-by: Anton Gladky <gladky.anton@gmail.com>
-Last-Update: 2012-05-08
-
---- a/VTK/Rendering/vtkFreeTypeTools.cxx
-+++ b/VTK/Rendering/vtkFreeTypeTools.cxx
-@@ -35,6 +35,8 @@
- using namespace ftgl;
- #endif
- 
-+#include <stdint.h>
-+
- // Print debug info
- #define VTK_FTFC_DEBUG 0
- #define VTK_FTFC_DEBUG_CD 0
---- a/VTK/Rendering/vtkFreeTypeUtilities.cxx
-+++ b/VTK/Rendering/vtkFreeTypeUtilities.cxx
-@@ -36,6 +36,8 @@
- using namespace ftgl;
- #endif
- 
-+#include <stdint.h>
-+
- // Print debug info
- 
- #define VTK_FTFC_DEBUG 0
diff --git a/sci-visualization/paraview/files/paraview-3.14.1-mpi4py.patch b/sci-visualization/paraview/files/paraview-3.14.1-mpi4py.patch
deleted file mode 100644
index 95a0d7ac8..000000000
--- a/sci-visualization/paraview/files/paraview-3.14.1-mpi4py.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- CMake/ParaViewCommon.cmake.orig	2012-08-29 13:38:19.392381797 +1200
-+++ CMake/ParaViewCommon.cmake	2012-08-29 13:38:47.271407061 +1200
-@@ -497,9 +497,9 @@
- 
- #########################################################################
- # Configure mpi4py
--IF(PARAVIEW_ENABLE_PYTHON AND PARAVIEW_USE_MPI)
--  ADD_SUBDIRECTORY(Utilities/mpi4py)
--ENDIF(PARAVIEW_ENABLE_PYTHON AND PARAVIEW_USE_MPI)
-+#IF(PARAVIEW_ENABLE_PYTHON AND PARAVIEW_USE_MPI)
-+#  ADD_SUBDIRECTORY(Utilities/mpi4py)
-+#ENDIF(PARAVIEW_ENABLE_PYTHON AND PARAVIEW_USE_MPI)
- 
- 
- 
diff --git a/sci-visualization/paraview/files/paraview-3.14.1-python-exit.patch b/sci-visualization/paraview/files/paraview-3.14.1-python-exit.patch
deleted file mode 100644
index 03ae27ae5..000000000
--- a/sci-visualization/paraview/files/paraview-3.14.1-python-exit.patch
+++ /dev/null
@@ -1,46 +0,0 @@
---- ParaViewCore/ClientServerCore/vtkPythonProgrammableFilter.cxx.orig	2012-08-28 15:42:34.410099857 +1200
-+++ ParaViewCore/ClientServerCore/vtkPythonProgrammableFilter.cxx	2012-08-28 15:45:25.731279418 +1200
-@@ -80,6 +80,16 @@
- }
- 
- //----------------------------------------------------------------------------
-+void vtkPythonProgrammableFilter::DeleteGlobalPythonInterpretor()
-+{
-+  if(GlobalPipelineInterpretor)
-+    {
-+    GlobalPipelineInterpretor->Delete();
-+    GlobalPipelineInterpretor = 0;
-+    }
-+}
-+
-+//----------------------------------------------------------------------------
- vtkPythonProgrammableFilter::vtkPythonProgrammableFilter() :
-   Implementation(new vtkPythonProgrammableFilterImplementation())
- {
---- ParaViewCore/ClientServerCore/vtkPythonProgrammableFilter.h.orig	2012-08-28 15:42:45.892355278 +1200
-+++ ParaViewCore/ClientServerCore/vtkPythonProgrammableFilter.h	2012-08-28 15:45:54.883213682 +1200
-@@ -102,6 +102,7 @@
- //BTX
-   static vtkPVPythonInterpretor* GetGlobalPipelineInterpretor();
- //ETX
-+static void DeleteGlobalPythonInterpretor();
- protected:
-   vtkPythonProgrammableFilter();
-   ~vtkPythonProgrammableFilter();
---- Utilities/VTKPythonWrapping/paraview/servermanager.py.orig	2012-08-28 15:47:14.611830975 +1200
-+++ Utilities/VTKPythonWrapping/paraview/servermanager.py	2012-08-28 15:48:11.995520340 +1200
-@@ -40,7 +40,7 @@
- #     PURPOSE.  See the above copyright notice for more information.
- #
- #==============================================================================
--import paraview, re, os, os.path, new, sys, vtk
-+import paraview, re, os, os.path, new, sys, atexit, vtk
- 
- if not paraview.compatibility.minor:
-     paraview.compatibility.major = 3
-@@ -3027,3 +3027,5 @@
- 
- def GetNumberOfConnections():
-    return len(MultiServerConnections)
-+
-+atexit.register(vtkPythonProgrammableFilter.DeleteGlobalPythonInterpretor)
diff --git a/sci-visualization/paraview/files/paraview-3.14.1-removesqlite.patch b/sci-visualization/paraview/files/paraview-3.14.1-removesqlite.patch
deleted file mode 100644
index 3467fa965..000000000
--- a/sci-visualization/paraview/files/paraview-3.14.1-removesqlite.patch
+++ /dev/null
@@ -1,526 +0,0 @@
-Description: Import patch from VTK to remove sqlite
-Author: Mathieu Malaterre <mathieu.malaterre@gmail.com>
-Last-Update: 2011-09-07
-
---- a/VTK/IO/vtkSQLiteDatabase.cxx
-+++ b/VTK/IO/vtkSQLiteDatabase.cxx
-@@ -29,7 +29,7 @@
- #include <vtksys/ios/fstream>
- #include <vtksys/ios/sstream>
- 
--#include <vtksqlite/vtk_sqlite3.h>
-+#include <sqlite3.h>
- 
- vtkStandardNewMacro(vtkSQLiteDatabase);
- 
-@@ -307,15 +307,15 @@
-       }
-     }
- 
--  int result = vtk_sqlite3_open(this->DatabaseFileName, & (this->SQLiteInstance));
-+  int result = sqlite3_open(this->DatabaseFileName, & (this->SQLiteInstance));
- 
--  if (result != VTK_SQLITE_OK)
-+  if (result != SQLITE_OK)
-     {
-     vtkDebugMacro(<<"SQLite open() failed.  Error code is "
-                   << result << " and message is "
--                  << vtk_sqlite3_errmsg(this->SQLiteInstance) );
-+                  << sqlite3_errmsg(this->SQLiteInstance) );
- 
--    vtk_sqlite3_close(this->SQLiteInstance);
-+    sqlite3_close(this->SQLiteInstance);
-     return false;
-     }
-   else
-@@ -334,8 +334,8 @@
-     }
-   else
-     {
--    int result = vtk_sqlite3_close(this->SQLiteInstance);
--    if (result != VTK_SQLITE_OK)
-+    int result = sqlite3_close(this->SQLiteInstance);
-+    if (result != SQLITE_OK)
-       {
-       vtkWarningMacro(<< "Close(): SQLite returned result code " << result);
-       }
-@@ -374,7 +374,7 @@
-   if (!status)
-     {
-     vtkErrorMacro(<< "GetTables(): Database returned error: "
--                  << vtk_sqlite3_errmsg(this->SQLiteInstance) );
-+                  << sqlite3_errmsg(this->SQLiteInstance) );
-     query->Delete();
-     return this->Tables;
-     }
-@@ -403,7 +403,7 @@
-   if (!status)
-     {
-     vtkErrorMacro(<< "GetRecord(" << table << "): Database returned error: "
--                  << vtk_sqlite3_errmsg(this->SQLiteInstance) );
-+                  << sqlite3_errmsg(this->SQLiteInstance) );
-     query->Delete();
-     return NULL;
-     }
-@@ -467,10 +467,10 @@
- // ----------------------------------------------------------------------
- bool vtkSQLiteDatabase::HasError()
- {
--  return (vtk_sqlite3_errcode(this->SQLiteInstance)!=VTK_SQLITE_OK);
-+  return (sqlite3_errcode(this->SQLiteInstance)!=SQLITE_OK);
- }
- 
- const char* vtkSQLiteDatabase::GetLastErrorText()
- {
--  return vtk_sqlite3_errmsg(this->SQLiteInstance);
-+  return sqlite3_errmsg(this->SQLiteInstance);
- }
---- a/VTK/IO/vtkSQLiteQuery.cxx
-+++ b/VTK/IO/vtkSQLiteQuery.cxx
-@@ -25,7 +25,7 @@
- #include "vtkVariant.h"
- #include "vtkVariantArray.h"
- 
--#include <vtksqlite/vtk_sqlite3.h>
-+#include <sqlite3.h>
- 
- #include <assert.h>
- 
-@@ -43,7 +43,7 @@
- {
-   this->Statement = NULL;
-   this->InitialFetch = true;
--  this->InitialFetchResult=VTK_SQLITE_DONE;
-+  this->InitialFetchResult=SQLITE_DONE;
-   this->LastErrorText = NULL;
-   this->TransactionInProgress = false;
- }
-@@ -61,7 +61,7 @@
-     {
-     if (this->Database != NULL)
-       {
--      vtk_sqlite3_finalize(this->Statement);
-+      sqlite3_finalize(this->Statement);
-       this->Statement = NULL;
-       }
-     }
-@@ -131,8 +131,8 @@
-   if (this->Statement)
-     {
-     vtkDebugMacro(<<"Finalizing old statement");
--    int finalizeStatus = vtk_sqlite3_finalize(this->Statement);
--    if (finalizeStatus != VTK_SQLITE_OK)
-+    int finalizeStatus = sqlite3_finalize(this->Statement);
-+    if (finalizeStatus != SQLITE_OK)
-       {
-       vtkWarningMacro(<<"SetQuery(): Finalize returned unexpected code "
-                       << finalizeStatus);
-@@ -151,19 +151,19 @@
-       return false;
-       }
-     
--    vtk_sqlite3 *db = dbContainer->SQLiteInstance;
-+    sqlite3 *db = dbContainer->SQLiteInstance;
-     const char *unused_statement;
-     
--    int prepareStatus = vtk_sqlite3_prepare_v2(db, 
-+    int prepareStatus = sqlite3_prepare_v2(db, 
-                                                this->Query,
-                                                static_cast<int>(strlen(this->Query)),
-                                                &this->Statement,
-                                                &unused_statement);
-     
--    if (prepareStatus != VTK_SQLITE_OK)
-+    if (prepareStatus != SQLITE_OK)
-       {
--      this->SetLastErrorText(vtk_sqlite3_errmsg(db));
--      vtkWarningMacro(<<"SetQuery(): vtk_sqlite3_prepare_v2() failed with error message "
-+      this->SetLastErrorText(sqlite3_errmsg(db));
-+      vtkWarningMacro(<<"SetQuery(): sqlite3_prepare_v2() failed with error message "
-                     << this->GetLastErrorText()
-                     << " on statement: '"
-                     << this->Query << "'");
-@@ -194,31 +194,31 @@
-     }
-   else
-     {
--    vtk_sqlite3_reset(this->Statement);
-+    sqlite3_reset(this->Statement);
-     }
- 
-   vtkDebugMacro(<<"Execute(): Query ready to execute.");
- 
-   this->InitialFetch = true;
--  int result = vtk_sqlite3_step(this->Statement);
-+  int result = sqlite3_step(this->Statement);
-   this->InitialFetchResult = result;
- 
--  if (result == VTK_SQLITE_DONE)
-+  if (result == SQLITE_DONE)
-     {
-     this->SetLastErrorText(NULL);
-     this->Active = true;
-     return true;
-     }
--  else if (result != VTK_SQLITE_ROW)
-+  else if (result != SQLITE_ROW)
-     {
-     vtkSQLiteDatabase *dbContainer = 
-       vtkSQLiteDatabase::SafeDownCast(this->Database);
-     assert(dbContainer != NULL);
-     
--    vtk_sqlite3 *db = dbContainer->SQLiteInstance;
-+    sqlite3 *db = dbContainer->SQLiteInstance;
- 
--    this->SetLastErrorText(vtk_sqlite3_errmsg(db));
--    vtkDebugMacro(<< "Execute(): vtk_sqlite3_step() returned error message "
-+    this->SetLastErrorText(sqlite3_errmsg(db));
-+    vtkDebugMacro(<< "Execute(): sqlite3_step() returned error message "
-                   << this->GetLastErrorText());
-     this->Active = false;
-     return false;
-@@ -239,7 +239,7 @@
-     }
-   else
-     {
--    return vtk_sqlite3_column_count(this->Statement);
-+    return sqlite3_column_count(this->Statement);
-     }
- }
- 
-@@ -259,7 +259,7 @@
-     }
-   else
-     {
--    return vtk_sqlite3_column_name(this->Statement, column);
-+    return sqlite3_column_name(this->Statement, column);
-     }
- }
- 
-@@ -279,22 +279,22 @@
-     }
-   else
-     {
--    switch (vtk_sqlite3_column_type(this->Statement, column))
-+    switch (sqlite3_column_type(this->Statement, column))
-       {
--      case VTK_SQLITE_INTEGER:
-+      case SQLITE_INTEGER:
-         return VTK_INT; 
--      case VTK_SQLITE_FLOAT:
-+      case SQLITE_FLOAT:
-         return VTK_FLOAT;
--      case VTK_SQLITE_TEXT:
-+      case SQLITE_TEXT:
-         return VTK_STRING;
--      case VTK_SQLITE_BLOB:
-+      case SQLITE_BLOB:
-         return VTK_STRING; // until we have a BLOB type of our own
--      case VTK_SQLITE_NULL:
-+      case SQLITE_NULL:
-         return VTK_VOID; // ??? what makes sense here?
-       default:
-       {
-       vtkErrorMacro(<<"GetFieldType(): Unknown data type " 
--                    << vtk_sqlite3_column_type(this->Statement, column)
-+                    << sqlite3_column_type(this->Statement, column)
-                     <<" from SQLite.");
-       return VTK_VOID;
-       }
-@@ -315,7 +315,7 @@
-     {
-     vtkDebugMacro(<<"NextRow(): Initial fetch being handled.");
-     this->InitialFetch = false;
--    if (this->InitialFetchResult == VTK_SQLITE_DONE)
-+    if (this->InitialFetchResult == SQLITE_DONE)
-       {
-       return false;
-       }
-@@ -326,12 +326,12 @@
-     }
-   else
-     {
--    int result = vtk_sqlite3_step(this->Statement);
--    if (result == VTK_SQLITE_DONE)
-+    int result = sqlite3_step(this->Statement);
-+    if (result == SQLITE_DONE)
-       {
-       return false;
-       }
--    else if (result == VTK_SQLITE_ROW)
-+    else if (result == SQLITE_ROW)
-       {
-       return true;
-       }
-@@ -339,8 +339,8 @@
-       {
-       vtkSQLiteDatabase *dbContainer = vtkSQLiteDatabase::SafeDownCast( this->Database );
-       assert(dbContainer != NULL);
--      vtk_sqlite3 *db = dbContainer->SQLiteInstance;
--      this->SetLastErrorText(vtk_sqlite3_errmsg(db));
-+      sqlite3 *db = dbContainer->SQLiteInstance;
-+      this->SetLastErrorText(sqlite3_errmsg(db));
-       vtkErrorMacro(<<"NextRow(): Database returned error code " 
-                     << result << " with the following message: "
-                     << this->GetLastErrorText());
-@@ -366,33 +366,33 @@
-     }
-   else
-     {
--    switch (vtk_sqlite3_column_type(this->Statement, column))
-+    switch (sqlite3_column_type(this->Statement, column))
-       {
--      case VTK_SQLITE_INTEGER:
--        return vtkVariant(vtk_sqlite3_column_int(this->Statement, column));
-+      case SQLITE_INTEGER:
-+        return vtkVariant(sqlite3_column_int(this->Statement, column));
- 
--      case VTK_SQLITE_FLOAT:
--        return vtkVariant(vtk_sqlite3_column_double(this->Statement, column));
-+      case SQLITE_FLOAT:
-+        return vtkVariant(sqlite3_column_double(this->Statement, column));
- 
--      case VTK_SQLITE_TEXT:
-+      case SQLITE_TEXT:
-       {
-       vtksys_ios::ostringstream str;
--      str << vtk_sqlite3_column_text(this->Statement, column);
-+      str << sqlite3_column_text(this->Statement, column);
-       return vtkVariant(vtkStdString(str.str()));
-       }
- 
--      case VTK_SQLITE_BLOB:
-+      case SQLITE_BLOB:
-       {
-       // This is a hack ... by passing the BLOB to vtkStdString with an explicit
-       // byte count, we ensure that the string will store all of the BLOB's bytes,
-       // even if there are NULL values.
- 
-       return vtkVariant(vtkStdString(
--        static_cast<const char*>(vtk_sqlite3_column_blob(this->Statement, column)),
--        vtk_sqlite3_column_bytes(this->Statement, column)));
-+        static_cast<const char*>(sqlite3_column_blob(this->Statement, column)),
-+        sqlite3_column_bytes(this->Statement, column)));
-       }
-       
--      case VTK_SQLITE_NULL:
-+      case SQLITE_NULL:
-       default:
-         return vtkVariant();
-       }
-@@ -423,11 +423,11 @@
-   vtkSQLiteDatabase *dbContainer = vtkSQLiteDatabase::SafeDownCast( this->Database );
-   assert(dbContainer != NULL);
- 
--  vtk_sqlite3 *db = dbContainer->SQLiteInstance;
-+  sqlite3 *db = dbContainer->SQLiteInstance;
-   char *errorMessage = NULL;
--  int result = vtk_sqlite3_exec(db, BEGIN_TRANSACTION, NULL, NULL, &errorMessage);
-+  int result = sqlite3_exec(db, BEGIN_TRANSACTION, NULL, NULL, &errorMessage);
- 
--  if (result == VTK_SQLITE_OK)
-+  if (result == SQLITE_OK)
-     {
-     this->TransactionInProgress = true;
-     this->SetLastErrorText(NULL);
-@@ -451,7 +451,7 @@
- {
-   if (this->Statement)
-     {
--    vtk_sqlite3_finalize(this->Statement);
-+    sqlite3_finalize(this->Statement);
-     this->Statement = NULL;
-     }
- 
-@@ -463,11 +463,11 @@
-   
-   vtkSQLiteDatabase *dbContainer = vtkSQLiteDatabase::SafeDownCast( this->Database );
-   assert(dbContainer != NULL);
--  vtk_sqlite3 *db = dbContainer->SQLiteInstance;
-+  sqlite3 *db = dbContainer->SQLiteInstance;
-   char *errorMessage = NULL;
--  int result = vtk_sqlite3_exec(db, COMMIT_TRANSACTION, NULL, NULL, &errorMessage);
-+  int result = sqlite3_exec(db, COMMIT_TRANSACTION, NULL, NULL, &errorMessage);
- 
--  if (result == VTK_SQLITE_OK)
-+  if (result == SQLITE_OK)
-     {
-     this->TransactionInProgress = false;
-     this->SetLastErrorText(NULL);
-@@ -499,11 +499,11 @@
- 
-   vtkSQLiteDatabase *dbContainer = vtkSQLiteDatabase::SafeDownCast( this->Database );
-   assert(dbContainer != NULL);
--  vtk_sqlite3 *db = dbContainer->SQLiteInstance;
-+  sqlite3 *db = dbContainer->SQLiteInstance;
-   char *errorMessage = NULL;
--  int result = vtk_sqlite3_exec(db, ROLLBACK_TRANSACTION, NULL, NULL, &errorMessage);
-+  int result = sqlite3_exec(db, ROLLBACK_TRANSACTION, NULL, NULL, &errorMessage);
- 
--  if (result == VTK_SQLITE_OK)
-+  if (result == SQLITE_OK)
-     {
-     this->TransactionInProgress = false;
-     this->SetLastErrorText(NULL);
-@@ -647,11 +647,11 @@
-   if (this->Active)
-     {
-     this->Active = false;
--    vtk_sqlite3_reset(this->Statement);
-+    sqlite3_reset(this->Statement);
-     }
--  int status = vtk_sqlite3_bind_int(this->Statement, index+1, value);
-+  int status = sqlite3_bind_int(this->Statement, index+1, value);
- 
--  if (status != VTK_SQLITE_OK)
-+  if (status != SQLITE_OK)
-     {
-     vtksys_ios::ostringstream errormessage;
-     errormessage << "sqlite_bind_int returned error: " << status;
-@@ -676,11 +676,11 @@
-   if (this->Active)
-     {
-     this->Active = false;
--    vtk_sqlite3_reset(this->Statement);
-+    sqlite3_reset(this->Statement);
-     }
--  int status = vtk_sqlite3_bind_int(this->Statement, index+1, static_cast<vtk_sqlite_int64>(value));
-+  int status = sqlite3_bind_int(this->Statement, index+1, static_cast<sqlite_int64>(value));
- 
--  if (status != VTK_SQLITE_OK)
-+  if (status != SQLITE_OK)
-     {
-     vtksys_ios::ostringstream errormessage;
-     errormessage << "sqlite_bind_int64 returned error: " << status;
-@@ -705,12 +705,12 @@
-   if (this->Active)
-     {
-     this->Active = false;
--    vtk_sqlite3_reset(this->Statement);
-+    sqlite3_reset(this->Statement);
-     }
- 
--  int status = vtk_sqlite3_bind_double(this->Statement, index+1, value);
-+  int status = sqlite3_bind_double(this->Statement, index+1, value);
- 
--  if (status != VTK_SQLITE_OK)
-+  if (status != SQLITE_OK)
-     {
-     vtksys_ios::ostringstream errormessage;
-     errormessage << "sqlite_bind_double returned error: " << status;
-@@ -734,12 +734,12 @@
-   if (this->Active)
-     {
-     this->Active = false;
--    vtk_sqlite3_reset(this->Statement);
-+    sqlite3_reset(this->Statement);
-     }
-   
--  int status = vtk_sqlite3_bind_text(this->Statement, index+1, value, length, VTK_SQLITE_TRANSIENT);
-+  int status = sqlite3_bind_text(this->Statement, index+1, value, length, SQLITE_TRANSIENT);
- 
--  if (status != VTK_SQLITE_OK)
-+  if (status != SQLITE_OK)
-     {
-     vtksys_ios::ostringstream errormessage;
-     errormessage << "sqlite_bind_text returned error: " << status;
-@@ -763,17 +763,17 @@
-   if (this->Active)
-     {
-     this->Active = false;
--    vtk_sqlite3_reset(this->Statement);
-+    sqlite3_reset(this->Statement);
-     }
-   
-   int status = 
--    vtk_sqlite3_bind_blob(this->Statement, 
-+    sqlite3_bind_blob(this->Statement, 
-                           index+1, 
-                           data, 
-                           length, 
--                          VTK_SQLITE_TRANSIENT);
-+                          SQLITE_TRANSIENT);
- 
--  if (status != VTK_SQLITE_OK)
-+  if (status != SQLITE_OK)
-     {
-     vtksys_ios::ostringstream errormessage;
-     errormessage << "sqlite_bind_blob returned error: " << status;
-@@ -797,12 +797,12 @@
-   if (this->Active)
-     {
-     this->Active = false;
--    vtk_sqlite3_reset(this->Statement);
-+    sqlite3_reset(this->Statement);
-     }
- 
--  int status = vtk_sqlite3_clear_bindings(this->Statement);
-+  int status = sqlite3_clear_bindings(this->Statement);
-   
--  if (status != VTK_SQLITE_OK)
-+  if (status != SQLITE_OK)
-     {
-     vtksys_ios::ostringstream errormessage;
-     errormessage << "sqlite_clear_bindings returned error: " << status;
---- a/VTK/IO/vtkSQLiteDatabase.h
-+++ b/VTK/IO/vtkSQLiteDatabase.h
-@@ -48,7 +48,7 @@
- class vtkSQLQuery;
- class vtkSQLiteQuery;
- class vtkStringArray;
--struct vtk_sqlite3;
-+struct sqlite3;
- 
- class VTK_IO_EXPORT vtkSQLiteDatabase : public vtkSQLDatabase
- {
-@@ -146,7 +146,7 @@
-   virtual bool ParseURL(const char* url);
- 
- private:
--  vtk_sqlite3 *SQLiteInstance;
-+  sqlite3 *SQLiteInstance;
-   
-   // We want this to be private, a user of this class
-   // should not be setting this for any reason
---- a/VTK/IO/vtkSQLiteQuery.h
-+++ b/VTK/IO/vtkSQLiteQuery.h
-@@ -46,7 +46,7 @@
- class vtkSQLiteDatabase;
- class vtkVariant;
- class vtkVariantArray;
--struct vtk_sqlite3_stmt;
-+struct sqlite3_stmt;
- 
- class VTK_IO_EXPORT vtkSQLiteQuery : public vtkSQLQuery
- {
-@@ -154,7 +154,7 @@
-   vtkSQLiteQuery(const vtkSQLiteQuery &); // Not implemented.
-   void operator=(const vtkSQLiteQuery &); // Not implemented.
- 
--  vtk_sqlite3_stmt *Statement;
-+  sqlite3_stmt *Statement;
-   bool InitialFetch;
-   int InitialFetchResult;
-   char *LastErrorText;
---- a/VTK/Utilities/CMakeLists.txt
-+++ b/VTK/Utilities/CMakeLists.txt
-@@ -55,7 +55,7 @@
-     SET_PROPERTY(GLOBAL APPEND PROPERTY VTK_TARGETS vtkmetaio)
-   ENDIF(NOT VTK_INSTALL_NO_LIBRARIES)
- ENDIF(VTK_USE_METAIO)
--ADD_SUBDIRECTORY(vtksqlite)
-+#ADD_SUBDIRECTORY(vtksqlite)
- 
- IF(VTK_HAS_EXODUS)
-   ADD_SUBDIRECTORY(vtkexodus2)
---- a/VTK/IO/CMakeLists.txt
-+++ b/VTK/IO/CMakeLists.txt
-@@ -19,7 +19,7 @@
- SET(KIT_JAVA_LIBS vtkFilteringJava)
- SET(KIT_INTERFACE_LIBRARIES vtkFiltering)
- SET(KIT_LIBS vtkDICOMParser vtkNetCDF vtkNetCDF_cxx LSDyna
--  ${_VTK_METAIO_LIB} vtksqlite
-+  ${_VTK_METAIO_LIB} sqlite3
-   ${VTK_PNG_LIBRARIES} ${VTK_ZLIB_LIBRARIES} ${VTK_JPEG_LIBRARIES}
-   ${VTK_TIFF_LIBRARIES} ${VTK_EXPAT_LIBRARIES} ${VTK_OGGTHEORA_LIBRARIES}
-   ${KWSYS_NAMESPACE})
diff --git a/sci-visualization/paraview/files/paraview-3.14.1-vtknetcd.patch b/sci-visualization/paraview/files/paraview-3.14.1-vtknetcd.patch
deleted file mode 100644
index f6f9e4e45..000000000
--- a/sci-visualization/paraview/files/paraview-3.14.1-vtknetcd.patch
+++ /dev/null
@@ -1,97 +0,0 @@
---- VTK/Utilities/CMakeLists.txt.orig	2012-08-31 13:55:56.616827748 +1200
-+++ VTK/Utilities/CMakeLists.txt	2012-08-31 13:56:43.487830247 +1200
-@@ -47,7 +47,7 @@
- SET( verdict_INSTALL_LIB_DIR ${VTK_INSTALL_LIB_DIR_CM24})
- ADD_SUBDIRECTORY(verdict)
- 
--ADD_SUBDIRECTORY(vtknetcdf)
-+#ADD_SUBDIRECTORY(vtknetcdf)
- IF(VTK_USE_METAIO)
-   SET(METAIO_FOR_VTK 1)
-   ADD_SUBDIRECTORY(vtkmetaio)
---- VTK/Utilities/vtk_netcdf.h.orig	2012-08-31 13:57:25.704832693 +1200
-+++ VTK/Utilities/vtk_netcdf.h	2012-08-31 13:57:59.823834877 +1200
-@@ -16,6 +16,6 @@
- #define __vtk_netcdf_h
- 
- /* Use the netcdf library configured for VTK.  */
--#include <vtknetcdf/include/netcdf.h>
-+#include <netcdf.h>
- 
- #endif
---- VTK/Utilities/vtk_netcdfcpp.h.orig	2012-08-31 13:58:48.800838210 +1200
-+++ VTK/Utilities/vtk_netcdfcpp.h	2012-08-31 13:59:31.223841343 +1200
-@@ -16,6 +16,6 @@
- #define __vtk_netcdfcpp_h
- 
- /* Use the netcdf library configured for VTK.  */
--#include <vtknetcdf/cxx/netcdfcpp.h>
-+#include <netcdfcpp.h>
- 
- #endif
---- VTK/Utilities/vtkexodus2/CMakeLists.txt.orig	2012-08-31 14:01:26.536856845 +1200
-+++ VTK/Utilities/vtkexodus2/CMakeLists.txt	2012-08-31 14:02:11.503872711 +1200
-@@ -241,7 +241,7 @@
- 
- 
- VTK_ADD_LIBRARY(vtkexoIIc ${cbind_SRCS})
--TARGET_LINK_LIBRARIES(vtkexoIIc vtkNetCDF)
-+TARGET_LINK_LIBRARIES(vtkexoIIc netcdf)
- 
- # Apply user-defined properties to the library target.
- IF(VTK_LIBRARY_PROPERTIES)
---- VTK/Utilities/vtkexodus2/test/CMakeLists.txt.orig	2012-08-31 14:02:39.696882673 +1200
-+++ VTK/Utilities/vtkexodus2/test/CMakeLists.txt	2012-08-31 14:02:59.743889790 +1200
-@@ -21,7 +21,7 @@
-   )
- 
- ADD_EXECUTABLE( ExoIICTests ${ExoIICTests} )
--TARGET_LINK_LIBRARIES( ExoIICTests vtkCommon vtkexoIIc vtkNetCDF )
-+TARGET_LINK_LIBRARIES( ExoIICTests vtkCommon vtkexoIIc netcdf )
- 
- SET( TestsToRun ${ExoIICTests} )
- REMOVE( TestsToRun ExoIICTests.cxx )
---- VTK/IO/CMakeLists.txt.orig	2012-08-31 14:05:00.657933170 +1200
-+++ VTK/IO/CMakeLists.txt	2012-08-31 14:06:18.024961299 +1200
-@@ -18,7 +18,7 @@
- SET(KIT_PYTHON_LIBS vtkFilteringPythonD)
- SET(KIT_JAVA_LIBS vtkFilteringJava)
- SET(KIT_INTERFACE_LIBRARIES vtkFiltering)
--SET(KIT_LIBS vtkDICOMParser vtkNetCDF vtkNetCDF_cxx LSDyna
-+SET(KIT_LIBS vtkDICOMParser netcdf netcdf_c++ LSDyna
-   ${_VTK_METAIO_LIB} sqlite3
-   ${VTK_PNG_LIBRARIES} ${VTK_ZLIB_LIBRARIES} ${VTK_JPEG_LIBRARIES}
-   ${VTK_TIFF_LIBRARIES} ${VTK_EXPAT_LIBRARIES} ${VTK_OGGTHEORA_LIBRARIES}
---- VTK/vtkIncludeDirectories.cmake.orig	2012-08-31 15:36:06.599955661 +1200
-+++ VTK/vtkIncludeDirectories.cmake	2012-08-31 15:37:35.759045094 +1200
-@@ -193,7 +193,7 @@
- VTK_THIRD_PARTY_INCLUDE2(TIFF)
- VTK_THIRD_PARTY_INCLUDE2(EXPAT)
- VTK_THIRD_PARTY_INCLUDE2(LIBXML2)
--VTK_THIRD_PARTY_INCLUDE(NETCDF vtknetcdf/include)
-+#VTK_THIRD_PARTY_INCLUDE(NETCDF vtknetcdf/include)
- VTK_THIRD_PARTY_INCLUDE2(Exodus2)
- IF(VTK_USE_GL2PS)
-   VTK_THIRD_PARTY_INCLUDE2(GL2PS)
---- Plugins/StreamingView/VTK/CMakeLists.txt.orig	2012-12-20 09:43:26.858734060 +1300
-+++ Plugins/StreamingView/VTK/CMakeLists.txt	2012-12-20 09:44:49.472845455 +1300
-@@ -10,7 +10,7 @@
- INCLUDE ( ${VTK_USE_FILE} )
- 
- SET ( VTK_LINK_LIBRARIES
--  vtkRendering vtkGraphics vtkFiltering vtkCommon vtkIO vtkImaging vtkNetCDF)
-+  vtkRendering vtkGraphics vtkFiltering vtkCommon vtkIO vtkImaging netcdf)
- 
- INCLUDE_DIRECTORIES(${VTKNETCDF_BINARY_DIR})
- 
---- Utilities/VisItBridge/databases/CMakeLists.txt.orig	2012-12-20 09:43:39.257750799 +1300
-+++ Utilities/VisItBridge/databases/CMakeLists.txt	2012-12-20 09:45:45.321920591 +1300
-@@ -163,7 +163,7 @@
- #build all the readers into a single library
- vtk_add_library(vtk${KIT} ${Kit_SRCS} ${VISIT_DB_SOURCES})
- 
--target_link_libraries(vtk${KIT} vtkVisItAVTAlgorithms vtkNetCDF) 
-+target_link_libraries(vtk${KIT} vtkVisItAVTAlgorithms netcdf) 
- if(PARAVIEW_HDF5_LIBRARIES)
-   target_link_libraries(vtk${KIT} ${PARAVIEW_HDF5_LIBRARIES})
- endif(PARAVIEW_HDF5_LIBRARIES)  
diff --git a/sci-visualization/paraview/files/paraview-3.14.1-xdmf-linking.patch b/sci-visualization/paraview/files/paraview-3.14.1-xdmf-linking.patch
deleted file mode 100644
index 115793158..000000000
--- a/sci-visualization/paraview/files/paraview-3.14.1-xdmf-linking.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Description: rusr/lib/paraview/libvtkXdmf.so contains an unresolvable 
- reference to symbol XtDispatchEvent.
-Author: Mathieu Malaterre <mathieu.malaterre@gmail.com>
-Bug: http://paraview.org/Bug/view.php?id=12576
-Last-Update: 2011-09-07
-
---- a/Utilities/Xdmf2/vtk/CMakeLists.txt
-+++ b/Utilities/Xdmf2/vtk/CMakeLists.txt
-@@ -105,6 +105,7 @@
-   ELSE(VTK_USE_PARALLEL)
-     TARGET_LINK_LIBRARIES(vtkXdmf vtkIO Xdmf vtkRendering)
-   ENDIF(VTK_USE_PARALLEL)
-+  TARGET_LINK_LIBRARIES(${X11_Xt_LIB})
- 
-   IF (VTK_USE_MPI)
-     # Needed for mpich 2
diff --git a/sci-visualization/paraview/files/paraview-3.8.0-h5part.patch b/sci-visualization/paraview/files/paraview-3.8.0-h5part.patch
deleted file mode 100644
index 59f27d0bb..000000000
--- a/sci-visualization/paraview/files/paraview-3.8.0-h5part.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur ParaView3/Plugins/H5PartReader/H5Part/src/H5PartTypes.h ParaView3.new/Plugins/H5PartReader/H5Part/src/H5PartTypes.h
---- ParaView3/Plugins/H5PartReader/H5Part/src/H5PartTypes.h	2009-10-01 15:19:59.000000000 -0400
-+++ ParaView3.new/Plugins/H5PartReader/H5Part/src/H5PartTypes.h	2010-01-30 09:40:22.000000000 -0500
-@@ -17,7 +17,7 @@
- #endif
-  ;
- 
--#ifndef H5PART_HAS_MPI
-+#if !defined(H5PART_HAS_MPI) && !defined(MPI_BOTTOM)
- typedef int  MPI_Comm;
- #endif
- 
diff --git a/sci-visualization/paraview/files/paraview-3.8.0-installpath.patch b/sci-visualization/paraview/files/paraview-3.8.0-installpath.patch
deleted file mode 100644
index f59cbfaf2..000000000
--- a/sci-visualization/paraview/files/paraview-3.8.0-installpath.patch
+++ /dev/null
@@ -1,33 +0,0 @@
---- Applications/AdaptiveParaView/CMakeLists.txt.orig	2010-06-04 22:40:43.973547693 +1200
-+++ Applications/AdaptiveParaView/CMakeLists.txt	2010-06-04 22:41:37.889549494 +1200
-@@ -45,6 +45,8 @@
-     ${CMAKE_CURRENT_SOURCE_DIR}/CustomResources/CustomFilters.xml
-     ${CMAKE_CURRENT_SOURCE_DIR}/CustomResources/CustomSources.xml
-   SOURCES ${Application_SOURCE_FILES}
-+  INSTALL_BIN_DIR "${PV_INSTALL_BIN_DIR}"
-+  INSTALL_LIB_DIR "${PV_INSTALL_LIB_DIR}"
- )
- 
- ADD_EXECUTABLE(ppRawStridedReader2 ppRawStridedReader2.cxx)
---- Applications/ParaView/CMakeLists.txt.orig	2010-06-04 22:42:36.500548837 +1200
-+++ Applications/ParaView/CMakeLists.txt	2010-06-04 22:43:21.355548188 +1200
-@@ -63,6 +63,8 @@
-       ${PARAVIEW_EXTRA_GUI_RESOURCES} # Add any compiled in GUI configuration xmls
-     COMPRESSED_HELP_FILE "${ParaView_BINARY_DIR}/Documentation/paraview.qch"
-     SOURCES ${ParaView_SOURCE_FILES}
-+    INSTALL_BIN_DIR "${PV_INSTALL_BIN_DIR}"
-+    INSTALL_LIB_DIR "${PV_INSTALL_LIB_DIR}"
- )
- 
- # Configure the ".plugins" configuration xml for making paraview aware of the
---- Applications/StreamingParaView/CMakeLists.txt.orig	2010-06-04 22:43:46.287547403 +1200
-+++ Applications/StreamingParaView/CMakeLists.txt	2010-06-04 22:44:44.047547909 +1200
-@@ -45,6 +45,8 @@
-     ${CMAKE_CURRENT_SOURCE_DIR}/CustomResources/CustomFilters.xml
-     ${CMAKE_CURRENT_SOURCE_DIR}/CustomResources/CustomSources.xml
-   SOURCES ${Application_SOURCE_FILES}
-+  INSTALL_BIN_DIR "${PV_INSTALL_BIN_DIR}"
-+  INSTALL_LIB_DIR "${PV_INSTALL_LIB_DIR}"
- )
- 
- IF(FALSE)#BUILD_TESTING)
diff --git a/sci-visualization/paraview/files/paraview-3.8.0-pointsprite-example-install.patch b/sci-visualization/paraview/files/paraview-3.8.0-pointsprite-example-install.patch
deleted file mode 100644
index 9a8ab2103..000000000
--- a/sci-visualization/paraview/files/paraview-3.8.0-pointsprite-example-install.patch
+++ /dev/null
@@ -1,9 +0,0 @@
---- Plugins/PointSprite/Examples/Rendering/Cxx/CMakeLists.txt.orig	2010-06-11 22:54:37.423952532 +1200
-+++ Plugins/PointSprite/Examples/Rendering/Cxx/CMakeLists.txt	2010-06-11 22:55:07.546951156 +1200
-@@ -6,5 +6,5 @@
- target_link_libraries(${exe} PointSprite_Rendering vtkIO)
- 
- install(TARGETS ${exe} 
--    RUNTIME DESTINATION ${PROJECT_BINARY_DIR}
-+    RUNTIME DESTINATION ${PV_INSTALL_BIN_DIR}
- )
diff --git a/sci-visualization/paraview/files/paraview-3.8.0-pointsprite-example.patch b/sci-visualization/paraview/files/paraview-3.8.0-pointsprite-example.patch
deleted file mode 100644
index b88351a07..000000000
--- a/sci-visualization/paraview/files/paraview-3.8.0-pointsprite-example.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- Plugins/PointSprite/CMakeLists.txt.orig
-+++ Plugins/PointSprite/CMakeLists.txt
-@@ -56,11 +56,17 @@ add_subdirectory(Graphics)
- # -----------------------------------------------------------------------------
- # Build the tests
- # -----------------------------------------------------------------------------
--set(PointSpritePlugin_BUILD_EXAMPLES ON CACHE BOOL "Build the example.")
--if(PointSpritePlugin_BUILD_EXAMPLES)
--    add_subdirectory(Examples)
--endif(PointSpritePlugin_BUILD_EXAMPLES)
--mark_as_advanced(PointSpritePlugin_BUILD_EXAMPLES)
-+IF (DEFINED BUILD_EXAMPLES)
-+  IF (BUILD_EXAMPLES)
-+      add_subdirectory(Examples)
-+  ENDIF (BUILD_EXAMPLES)
-+ELSE (DEFINED BUILD_EXAMPLES)
-+  set(PointSpritePlugin_BUILD_EXAMPLES ON CACHE BOOL "Build the example.")
-+  IF(PointSpritePlugin_BUILD_EXAMPLES)
-+      add_subdirectory(Examples)
-+  ENDIF(PointSpritePlugin_BUILD_EXAMPLES)
-+  mark_as_advanced(PointSpritePlugin_BUILD_EXAMPLES)
-+ENDIF (DEFINED BUILD_EXAMPLES)
- # -----------------------------------------------------------------------------
- # Build the Paraview plugins
- # -----------------------------------------------------------------------------
\ No newline at end of file
diff --git a/sci-visualization/paraview/files/paraview-3.8.0-xdmf-bc.patch b/sci-visualization/paraview/files/paraview-3.8.0-xdmf-bc.patch
deleted file mode 100644
index 99c1ad7f9..000000000
--- a/sci-visualization/paraview/files/paraview-3.8.0-xdmf-bc.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- Utilities/Xdmf2/libsrc/CMakeLists.txt.orig	2010-06-05 23:02:46.495999925 +1200
-+++ Utilities/Xdmf2/libsrc/CMakeLists.txt	2010-06-07 21:57:25.261616104 +1200
-@@ -503,8 +503,8 @@
-       RENAME Xdmf.py) # always named the same regardless of build with or without mpi
- 
-   # Compile Byte Code
--  INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} ${Xdmf_SOURCE_DIR}/CMake/CompileXdmfByteCode.py 
--    ${CMAKE_INSTALL_PREFIX}/${XDMF_WRAP_PYTHON_INSTALL_PY_DIR})")
-+#  INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} ${Xdmf_SOURCE_DIR}/CMake/CompileXdmfByteCode.py
-+#    ${XDMF_WRAP_PYTHON_INSTALL_DIR})")
-   
- ENDIF(XDMF_WRAP_PYTHON)
- 
diff --git a/sci-visualization/paraview/files/paraview-3.8.0-xdmf-cstring.patch b/sci-visualization/paraview/files/paraview-3.8.0-xdmf-cstring.patch
deleted file mode 100644
index da0647618..000000000
--- a/sci-visualization/paraview/files/paraview-3.8.0-xdmf-cstring.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- Utilities/Xdmf2/libsrc/XdmfObject.h.orig	2010-06-01 18:41:14.006986954 +1200
-+++ Utilities/Xdmf2/libsrc/XdmfObject.h	2010-06-01 18:42:48.257851302 +1200
-@@ -82,6 +82,7 @@
- # ifdef UNIX
- #  include "sys/file.h"
- #  include "strings.h"
-+#  include <cstring>
- #  define STRCASECMP strcasecmp
- #  define STRNCASECMP strncasecmp
- #  define STRCMP strcmp
diff --git a/sci-visualization/paraview/files/vtk-5.6.0-cg-path.patch b/sci-visualization/paraview/files/vtk-5.6.0-cg-path.patch
deleted file mode 100644
index 984bf5008..000000000
--- a/sci-visualization/paraview/files/vtk-5.6.0-cg-path.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-diff --git a/CMake/FindCg.cmake b/CMake/FindCg.cmake
-index ceb41de..5eb6003 100644
---- a/CMake/FindCg.cmake
-+++ b/CMake/FindCg.cmake
-@@ -82,6 +82,7 @@ ELSE (APPLE)
-     FIND_PROGRAM( CG_COMPILER cgc
-       /usr/bin
-       /usr/local/bin
-+      /opt/nvidia-cg-toolkit/bin
-       DOC "The Cg Compiler"
-       )
-     GET_FILENAME_COMPONENT(CG_COMPILER_DIR "${CG_COMPILER}" PATH)
-@@ -89,6 +90,7 @@ ELSE (APPLE)
-     FIND_PATH( CG_INCLUDE_PATH Cg/cg.h
-       /usr/include
-       /usr/local/include
-+      /opt/nvidia-cg-toolkit/include
-       ${CG_COMPILER_SUPER_DIR}/include
-       DOC "The directory where Cg/cg.h resides"
-       )
-@@ -98,6 +100,7 @@ ELSE (APPLE)
-       /usr/lib
-       /usr/local/lib64
-       /usr/local/lib
-+      /opt/nvidia-cg-toolkit/lib
-       ${CG_COMPILER_SUPER_DIR}/lib64
-       ${CG_COMPILER_SUPER_DIR}/lib
-       DOC "The Cg runtime library"
-@@ -108,6 +111,7 @@ ELSE (APPLE)
-       /usr/lib
-       /usr/local/lib64
-       /usr/local/lib
-+      /opt/nvidia-cg-toolkit/lib
-       ${CG_COMPILER_SUPER_DIR}/lib64
-       ${CG_COMPILER_SUPER_DIR}/lib
-       DOC "The Cg runtime library"
diff --git a/sci-visualization/paraview/files/vtk-5.6.0-libpng14.patch b/sci-visualization/paraview/files/vtk-5.6.0-libpng14.patch
deleted file mode 100644
index db1f87d3a..000000000
--- a/sci-visualization/paraview/files/vtk-5.6.0-libpng14.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/IO/vtkPNGReader.cxx b/IO/vtkPNGReader.cxx
-index d1f5c2f..0bf00e4 100644
---- a/IO/vtkPNGReader.cxx
-+++ b/IO/vtkPNGReader.cxx
-@@ -116,7 +116,7 @@ void vtkPNGReader::ExecuteInformation()
-   // minimum of a byte per pixel
-   if (color_type == PNG_COLOR_TYPE_GRAY && bit_depth < 8) 
-     {
--    png_set_gray_1_2_4_to_8(png_ptr);
-+    png_set_expand_gray_1_2_4_to_8(png_ptr);
-     }
- 
-   // add alpha if any alpha found
-@@ -225,7 +225,7 @@ void vtkPNGReaderUpdate2(vtkPNGReader *self, OT *outPtr,
-   // minimum of a byte per pixel
-   if (color_type == PNG_COLOR_TYPE_GRAY && bit_depth < 8) 
-     {
--    png_set_gray_1_2_4_to_8(png_ptr);
-+    png_set_expand_gray_1_2_4_to_8(png_ptr);
-     }
- 
-   // add alpha if any alpha found
diff --git a/sci-visualization/paraview/files/vtk-5.6.0-odbc.patch b/sci-visualization/paraview/files/vtk-5.6.0-odbc.patch
deleted file mode 100644
index be24af11a..000000000
--- a/sci-visualization/paraview/files/vtk-5.6.0-odbc.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur CMake/FindODBC.cmake.orig CMake/FindODBC.cmake
---- CMake/FindODBC.cmake.orig	2008-10-08 13:51:36.000000000 -0400
-+++ CMake/FindODBC.cmake	2010-01-21 22:11:26.000000000 -0500
-@@ -30,7 +30,7 @@
- )
- 
- FIND_LIBRARY( ODBC_LIBRARY 
--  NAMES iodbc unixodbc
-+  NAMES iodbc unixodbc odbc
-   PATHS
-   /usr/lib
-   /usr/lib/odbc
diff --git a/sci-visualization/paraview/files/vtk-5.6.1-ffmpeg.patch b/sci-visualization/paraview/files/vtk-5.6.1-ffmpeg.patch
deleted file mode 100644
index 34ec52885..000000000
--- a/sci-visualization/paraview/files/vtk-5.6.1-ffmpeg.patch
+++ /dev/null
@@ -1,42 +0,0 @@
- CMake/vtkFFMPEGTestAvAlloc.cxx   |    2 +-
- CMake/vtkFFMPEGTestURLFClose.cxx |    2 +-
- IO/vtkFFMPEGWriter.cxx           |    2 +-
- 3 files changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/CMake/vtkFFMPEGTestAvAlloc.cxx b/CMake/vtkFFMPEGTestAvAlloc.cxx
-index ad691e3..32489d5 100644
---- a/CMake/vtkFFMPEGTestAvAlloc.cxx
-+++ b/CMake/vtkFFMPEGTestAvAlloc.cxx
-@@ -1,6 +1,6 @@
- extern "C" {
- #ifdef HAS_OLD_HEADER
--# include <ffmpeg/avformat.h>
-+# include <libavformat/avformat.h>
- #else
- # include <libavformat/avformat.h>
- #endif
-diff --git a/CMake/vtkFFMPEGTestURLFClose.cxx b/CMake/vtkFFMPEGTestURLFClose.cxx
-index 0bf4314..1c10a93 100644
---- a/CMake/vtkFFMPEGTestURLFClose.cxx
-+++ b/CMake/vtkFFMPEGTestURLFClose.cxx
-@@ -1,6 +1,6 @@
- extern "C" {
- #ifdef HAS_OLD_HEADER
--# include <ffmpeg/avformat.h>
-+# include <libavformat/avformat.h>
- #else
- # include <libavformat/avformat.h>
- #endif
-diff --git a/IO/vtkFFMPEGWriter.cxx b/IO/vtkFFMPEGWriter.cxx
-index 52673ef..ffbb78f 100644
---- a/IO/vtkFFMPEGWriter.cxx
-+++ b/IO/vtkFFMPEGWriter.cxx
-@@ -22,7 +22,7 @@
- 
- extern "C" {
- #ifdef VTK_FFMPEG_HAS_OLD_HEADER
--# include <ffmpeg/avformat.h>
-+# include <libavformat/avformat.h>
- #else
- # include <libavformat/avformat.h>
- #endif
diff --git a/sci-visualization/paraview/files/vtk-5.6.1-libav-0.8.patch b/sci-visualization/paraview/files/vtk-5.6.1-libav-0.8.patch
deleted file mode 100644
index 523919d6f..000000000
--- a/sci-visualization/paraview/files/vtk-5.6.1-libav-0.8.patch
+++ /dev/null
@@ -1,66 +0,0 @@
-Description: Upstream changes introduced in version 5.6.1-6.1
- This patch has been created by dpkg-source during the package build.
- Here's the last changelog entry, hopefully it gives details on why
- those changes were made:
- .
- vtk (5.6.1-6.1) unstable; urgency=low
- .
-   [ Michael Schutte ]
-   * Non-maintainer upload.
-   * Remove absolute paths to required libraries from
-     /usr/lib/vtk-5.6/VTKLibraryDepends.cmake after building, closes:
-     #506992.  Due to the multiarch transition, the original behavior
-     frequently causes reverse build-deps to FTBFS.  This change should
-     probably be reverted once all required libraries are multiarched.
- .
-   [ Steve M. Robbins ]
-   * Override lintian diagnostic about embedded libraries ftgl and sqlite.
-   * IO/vtkFFMPEGWriter.cxx: Applied fix from #638246 to build with libav
-     0.7.
- .
- The person named in the Author field signed this changelog entry.
-Author: Steve M. Robbins <smr@debian.org>
-Bug-Debian: http://bugs.debian.org/506992
-
----
-The information above should follow the Patch Tagging Guidelines, please
-checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
-are templates for supplementary fields that you might want to add:
-
-Origin: <vendor|upstream|other>, <url of original patch>
-Bug: <url in upstream bugtracker>
-Bug-Debian: http://bugs.debian.org/<bugnumber>
-Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
-Forwarded: <no|not-needed|url proving that it has been forwarded>
-Reviewed-By: <name and email of someone who approved the patch>
-Last-Update: <YYYY-MM-DD>
-
---- vtk-5.6.1.orig/IO/vtkFFMPEGWriter.cxx
-+++ vtk-5.6.1/IO/vtkFFMPEGWriter.cxx
-@@ -123,7 +123,7 @@ int vtkFFMPEGWriterInternal::Start()
-     }
- 
-   //choose avi media file format
--  this->avOutputFormat = guess_format("avi", NULL, NULL);
-+  this->avOutputFormat = av_guess_format("avi", NULL, NULL);
-   if (!this->avOutputFormat) 
-     {
-     vtkGenericWarningMacro (<< "Could not open the avi media file format.");
-@@ -150,7 +150,7 @@ int vtkFFMPEGWriterInternal::Start()
-   //Set up the codec.
-   AVCodecContext *c = this->avStream->codec;
-   c->codec_id = (CodecID)this->avOutputFormat->video_codec;
--  c->codec_type = CODEC_TYPE_VIDEO;
-+  c->codec_type = AVMEDIA_TYPE_VIDEO;
-   c->width = this->Dim[0];
-   c->height = this->Dim[1];
-   c->pix_fmt = PIX_FMT_YUVJ420P;
-@@ -329,7 +329,7 @@ int vtkFFMPEGWriterInternal::Write(vtkIm
-     pkt.stream_index = this->avStream->index;
-     if (cc->coded_frame->key_frame) //treat keyframes well
-       {
--      pkt.flags |= PKT_FLAG_KEY;
-+      pkt.flags |= AV_PKT_FLAG_KEY;
-       }
-     pkt.duration = 0; //presentation duration in time_base units or 0 if NA
-     pkt.pos = -1; //byte position in stream or -1 if NA
diff --git a/sci-visualization/paraview/files/vtk-boost1.49.patch b/sci-visualization/paraview/files/vtk-boost1.49.patch
deleted file mode 100644
index b04d3917c..000000000
--- a/sci-visualization/paraview/files/vtk-boost1.49.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-Description: fix FTBFS with boost 1.49
-Author: Dominique Belhachemi <domibel@debian.org>
-Origin: http://anonscm.debian.org/gitweb/?p=collab-maint/vtk.git;a=commitdiff;h=55084a11b450e53b2e8786e23dd64a6a6b846e6b
-Last-Update: 2012-05-07
-
---- a/VTK/Infovis/vtkBoostBreadthFirstSearchTree.cxx
-+++ b/VTK/Infovis/vtkBoostBreadthFirstSearchTree.cxx
-@@ -49,11 +49,17 @@
- 
- #if BOOST_VERSION >= 104800      // Boost 1.48.x
- namespace {
--  vtkIdType unwrap_edge_id(vtkEdgeType const &e) {
-+  vtkIdType unwrap_edge_id(vtkEdgeType const &e) 
-+  {
-     return e.Id;
-   }
--  vtkIdType unwrap_edge_id(boost::detail::reverse_graph_edge_descriptor<vtkEdgeType> const &e) {
-+  vtkIdType unwrap_edge_id(boost::detail::reverse_graph_edge_descriptor<vtkEdgeType> const &e) 
-+  {
-+# if BOOST_VERSION == 104800
-     return e.underlying_desc.Id;
-+# else
-+    return e.underlying_descx.Id;
-+# endif
-   }
- }
- #endif
diff --git a/sci-visualization/paraview/metadata.xml b/sci-visualization/paraview/metadata.xml
deleted file mode 100644
index 38ea062d7..000000000
--- a/sci-visualization/paraview/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci</herd>
-  <maintainer>
-    <email>markusle@gentoo.org</email>
-    <name>Markus Dittrich</name>
-  </maintainer>
-  <use>
-    <flag name="plugins">Build and install additional plugins</flag>
-    <flag name="gui">Build paraview's gui not just the server</flag>
-    <flag name="cg">Add support for nvidia's cg shaders</flag>
-    <flag name="boost">Add support for boost</flag>
-    <flag name="streaming">Enable streaming paraview application</flag>
-    <flag name="adaptive">Enable the adaptive paraview application</flag>
-    <flag name="mysql">Build support for MySQL data item in the XDMF format</flag>
-    <flag name="nvcontrol">Add NVCONTROL support for OpenGL options</flag>
-    <flag name="webkit">Built support for qt-webkit in vtk</flag>
-    <flag name="gl2ps">Enables gl2ps PostScript printing library</flag>
-    <flag name="coprocessing">Enable the coprocessing infrastructure which is mainly useful in the context of clusters</flag>
-  </use>
-</pkgmetadata>
diff --git a/sci-visualization/paraview/paraview-3.10.1.ebuild b/sci-visualization/paraview/paraview-3.10.1.ebuild
deleted file mode 100644
index ec894f308..000000000
--- a/sci-visualization/paraview/paraview-3.10.1.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=2
-
-PYTHON_DEPEND="python? 2:2.6"
-
-inherit cmake-utils eutils flag-o-matic multilib python qt4-r2 toolchain-funcs versionator
-
-MAIN_PV=$(get_major_version)
-MAJOR_PV=$(get_version_component_range 1-2)
-MY_P="ParaView-${PV}"
-
-DESCRIPTION="ParaView is a powerful scientific data visualization application"
-HOMEPAGE="http://www.paraview.org"
-SRC_URI="http://www.paraview.org/files/v${MAJOR_PV}/${MY_P}.tar.gz"
-RESTRICT="mirror"
-
-LICENSE="paraview GPL-2"
-KEYWORDS="~x86 ~amd64"
-SLOT="0"
-IUSE="adaptive cg -coprocessing doc examples +gui mpi mysql nvcontrol plugins +python streaming webkit"
-
-RDEPEND="
-	sci-libs/hdf5[mpi=]
-	mpi? ( virtual/mpi[cxx,romio] )
-	gui? (
-		dev-qt/qtgui:4
-		dev-qt/qt3support:4
-		dev-qt/qtopengl:4
-		|| ( >=dev-qt/qthelp-4.7.0:4[compat] <dev-qt/qthelp-4.7.0:4 )
-		dev-qt/qtsql:4
-		webkit? ( dev-qt/qtwebkit:4 ) )
-	adaptive? (
-		dev-qt/qtgui:4
-		dev-qt/qt3support:4
-		dev-qt/qtopengl:4
-		dev-qt/qthelp:4
-		webkit? ( dev-qt/qtwebkit:4 ) )
-	mysql? ( virtual/mysql )
-	coprocessing? ( plugins? ( dev-qt/qtgui:4 ) )
-	python? (
-		dev-python/sip
-		dev-python/PyQt4
-	)
-	dev-libs/libxml2:2
-	media-libs/libpng
-	virtual/jpeg
-	media-libs/tiff
-	dev-libs/expat
-	sys-libs/zlib
-	media-libs/freetype
-	>=app-admin/eselect-opengl-1.0.6-r1
-	virtual/opengl
-	sci-libs/netcdf
-	x11-libs/libXmu"
-DEPEND="${RDEPEND}
-		doc? ( app-doc/doxygen )
-		>=dev-util/cmake-2.6.4"
-
-PVLIBDIR=$(get_libdir)/${PN}-${MAJOR_PV}
-S=${WORKDIR}/${MY_P}
-
-pkg_setup() {
-	use python && python_set_active_version 2
-}
-
-src_prepare() {
-	# gcc header fix
-	epatch "${FILESDIR}"/${PN}-3.8.0-xdmf-cstring.patch
-	# disable automatic byte compiling that act directly on the live system
-	epatch "${FILESDIR}"/${PN}-3.8.0-xdmf-bc.patch
-	# Install properly pointspritedemo without duplicate DESTDIR
-	epatch "${FILESDIR}"/${PN}-3.8.0-pointsprite-example-install.patch
-	# mpi + hdf5 fix
-	#epatch "${FILESDIR}"/${PN}-3.8.0-h5part.patch
-	# gcc fix for vtk
-	epatch "${FILESDIR}"/${P}-gcc46.patch
-
-	# lib64 fixes
-	sed -i "s:/usr/lib:/usr/$(get_libdir):g" \
-		Utilities/Xdmf2/libsrc/CMakeLists.txt || die
-	sed -i "s:\/lib\/python:\/$(get_libdir)\/python:g" \
-		Utilities/Xdmf2/CMake/setup_install_paths.py || die
-
-	# Install internal vtk binaries inside /usr/${PVLIBDIR}
-	sed -e 's:VTK_INSTALL_BIN_DIR \"/${PV_INSTALL_BIN_DIR}\":VTK_INSTALL_BIN_DIR \"/${PV_INSTALL_LIB_DIR}\":' \
-		-i CMake/ParaViewCommon.cmake || die "failed to patch vtk install location"
-
-	cd VTK
-	epatch "${FILESDIR}"/vtk-5.6.0-cg-path.patch
-
-	# help vtk to find PyQT4 sip if required
-	sed -e 's:/usr/share/sip/PyQt4:/usr/share/sip:' \
-		-i GUISupport/Qt/CMakeLists.txt
-}
-
-src_configure() {
-	mycmakeargs=(
-		-DPV_INSTALL_LIB_DIR="${PVLIBDIR}"
-		-DCMAKE_INSTALL_PREFIX=/usr
-		-DPV_INSTALL_DOC_DIR="/usr/share/doc/${PF}"
-		-DEXPAT_INCLUDE_DIR=/usr/include
-		-DEXPAT_LIBRARY=/usr/$(get_libdir)/libexpat.so
-		-DOPENGL_gl_LIBRARY=/usr/$(get_libdir)/libGL.so
-		-DOPENGL_glu_LIBRARY=/usr/$(get_libdir)/libGLU.so
-		-DCMAKE_SKIP_RPATH=YES
-		-DVTK_USE_RPATH=OFF
-		-DBUILD_SHARED_LIBS=ON
-		-DVTK_USE_SYSTEM_FREETYPE=ON
-		-DVTK_USE_SYSTEM_JPEG=ON
-		-DVTK_USE_SYSTEM_PNG=ON
-		-DVTK_USE_SYSTEM_TIFF=ON
-		-DVTK_USE_SYSTEM_ZLIB=ON
-		-DVTK_USE_SYSTEM_EXPAT=ON
-		-DPARAVIEW_USE_SYSTEM_HDF5=ON
-		-DCMAKE_VERBOSE_MAKEFILE=ON
-		-DCMAKE_COLOR_MAKEFILE=TRUE
-		-DVTK_USE_SYSTEM_LIBXML2=ON
-		-DVTK_USE_OFFSCREEN=TRUE
-		-DCMAKE_USE_PTHREADS=ON
-		-DBUILD_TESTING=OFF
-		-DVTK_USE_FFMPEG_ENCODER=OFF
-		-DPARAVIEW_INSTALL_THIRD_PARTY_LIBRARIES=OFF)
-
-	# use flag triggered options
-	mycmakeargs+=(
-		$(cmake-utils_use gui PARAVIEW_BUILD_QT_GUI)
-		$(cmake-utils_use gui VTK_USE_QVTK)
-		$(cmake-utils_use gui VTK_USE_QVTK_QTOPENGL)
-		$(cmake-utils_use mpi PARAVIEW_USE_MPI)
-		$(cmake-utils_use mpi PARAVIEW_USE_MPI_SSEND)
-		$(cmake-utils_use python PARAVIEW_ENABLE_PYTHON)
-		$(cmake-utils_use python VTK_WRAP_PYTHON_SIP)
-		$(cmake-utils_use python XDMF_WRAP_PYTHON)
-		$(cmake-utils_use doc BUILD_DOCUMENTATION)
-		$(cmake-utils_use examples BUILD_EXAMPLES)
-		$(cmake-utils_use cg VTK_USE_CG_SHADERS)
-		$(cmake-utils_use nvcontrol VTK_USE_NVCONTROL)
-		$(cmake-utils_use adaptive PARAVIEW_BUILD_AdaptiveParaView)
-		$(cmake-utils_use streaming PARAVIEW_BUILD_StreamingParaView)
-		$(cmake-utils_use mysql XDMF_USE_MYSQL)
-		$(cmake-utils_use coprocessing PARAVIEW_ENABLE_COPROCESSING))
-
-	if ( use gui || use adaptive ); then
-		mycmakeargs+=(-DVTK_INSTALL_QT_DIR=/${PVLIBDIR}/plugins/designer
-			$(cmake-utils_use webkit VTK_QT_USE_WEBKIT))
-		if use python ; then
-			# paraview cannot guess sip directory right probably because a path is not propagated properly
-			mycmakeargs+=(-DSIP_INCLUDE_DIR=$(python_get_includedir))
-		fi
-	fi
-
-	# the rest of the plugins
-	mycmakeargs+=(
-		$(cmake-utils_use plugins PARAVIEW_INSTALL_DEVELOPMENT)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_ClientChartView)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_CosmoFilters)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_H5PartReader)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_Moments)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_PointSprite)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_Prism)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_SLACTools)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_AnalyzeNIfTIReaderWriter)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_SurfaceLIC)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_EyeDomeLighting)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_ForceTime)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_SierraPlotTools)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_StreamingView)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_VisTrailPlugin))
-
-	if use python; then
-		mycmakeargs+=($(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_pvblot))
-	fi
-
-	if use coprocessing; then
-		mycmakeargs+=($(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_CoProcessingScriptGenerator))
-	fi
-
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	# set up the environment
-	echo "LDPATH=/usr/${PVLIBDIR}" >> "${T}"/40${PN}
-	echo "PYTHONPATH=/usr/${PVLIBDIR}:/usr/${PVLIBDIR}/site-packages" >> "${T}"/40${PN}
-	doenvd "${T}"/40${PN}
-
-	# last but not least lets make a desktop entry
-	newicon "${S}"/Applications/ParaView/pvIcon.png paraview.png \
-		|| die "Failed to create paraview icon."
-	make_desktop_entry paraview "Paraview" paraview \
-		|| die "Failed to install Paraview desktop entry"
-
-}
-
-pkg_postinst() {
-	# with Qt4.5 there seem to be issues reading data files
-	# under certain locales. Setting LC_ALL=C should fix these.
-	echo
-	elog "If you experience data corruption during parsing of"
-	elog "data files with paraview please try setting your"
-	elog "locale to LC_ALL=C."
-	echo
-}
-
-pkg_postrm() {
-	if use python ; then
-		python_mod_cleanup /usr/$(get_libdir)/"${PN}-${MAJOR_PV}"/site-packages
-	fi
-}
diff --git a/sci-visualization/paraview/paraview-3.12.0.ebuild b/sci-visualization/paraview/paraview-3.12.0.ebuild
deleted file mode 100644
index d8bb82697..000000000
--- a/sci-visualization/paraview/paraview-3.12.0.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-PYTHON_DEPEND="python? 2:2.6"
-
-inherit cmake-utils eutils flag-o-matic multilib python qt4-r2 toolchain-funcs versionator
-
-MAIN_PV=$(get_major_version)
-MAJOR_PV=$(get_version_component_range 1-2)
-MY_P="ParaView-${PV}"
-
-DESCRIPTION="ParaView is a powerful scientific data visualization application"
-HOMEPAGE="http://www.paraview.org"
-SRC_URI="http://www.paraview.org/files/v${MAJOR_PV}/${MY_P}.tar.gz"
-RESTRICT="mirror"
-
-LICENSE="paraview GPL-2"
-KEYWORDS="~x86 ~amd64"
-SLOT="0"
-IUSE="adaptive cg -coprocessing doc examples +gui mpi mysql nvcontrol plugins +python streaming webkit"
-
-RDEPEND="
-	sci-libs/hdf5[mpi=]
-	mpi? ( virtual/mpi[cxx,romio] )
-	gui? (
-		dev-qt/qtgui:4
-		dev-qt/qt3support:4
-		dev-qt/qtopengl:4
-		|| ( >=dev-qt/qthelp-4.7.0:4[compat] <dev-qt/qthelp-4.7.0:4 )
-		dev-qt/qtsql:4
-		webkit? ( dev-qt/qtwebkit:4 ) )
-	adaptive? (
-		dev-qt/qtgui:4
-		dev-qt/qt3support:4
-		dev-qt/qtopengl:4
-		dev-qt/qthelp:4
-		webkit? ( dev-qt/qtwebkit:4 ) )
-	mysql? ( virtual/mysql )
-	coprocessing? ( plugins? ( dev-qt/qtgui:4 ) )
-	python? (
-		dev-python/sip
-		dev-python/PyQt4
-	)
-	dev-libs/libxml2:2
-	media-libs/libpng
-	virtual/jpeg
-	media-libs/tiff
-	dev-libs/expat
-	sys-libs/zlib
-	media-libs/freetype
-	>=app-admin/eselect-opengl-1.0.6-r1
-	virtual/opengl
-	sci-libs/netcdf
-	x11-libs/libXmu"
-DEPEND="${RDEPEND}
-		doc? ( app-doc/doxygen )
-		dev-libs/protobuf
-		>=dev-util/cmake-2.6.4"
-
-PVLIBDIR=$(get_libdir)/${PN}-${MAJOR_PV}
-S=${WORKDIR}/${MY_P}
-
-pkg_setup() {
-	use python && python_set_active_version 2
-}
-
-src_prepare() {
-	# gcc header fix
-	epatch "${FILESDIR}"/${PN}-3.8.0-xdmf-cstring.patch
-	# disable automatic byte compiling that act directly on the live system
-	epatch "${FILESDIR}"/${PN}-3.8.0-xdmf-bc.patch
-	# mpi + hdf5 fix
-	#epatch "${FILESDIR}"/${PN}-3.8.0-h5part.patch
-	# gcc fix for vtk
-	epatch "${FILESDIR}"/${P}-gcc46.patch
-	# use system provided protobuf and avoid http://paraview.org/Bug/view.php?id=12852
-	epatch "${FILESDIR}"/${P}-protobuf.patch
-
-	# lib64 fixes
-	sed -i "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \
-		Utilities/Xdmf2/libsrc/CMakeLists.txt || die
-	sed -i "s:\/lib\/python:\/$(get_libdir)\/python:g" \
-		Utilities/Xdmf2/CMake/setup_install_paths.py || die
-
-	# Install internal vtk binaries inside /usr/${PVLIBDIR}
-	sed -e 's:VTK_INSTALL_BIN_DIR \"/${PV_INSTALL_BIN_DIR}\":VTK_INSTALL_BIN_DIR \"/${PV_INSTALL_LIB_DIR}\":' \
-		-i CMake/ParaViewCommon.cmake || die "failed to patch vtk install location"
-
-	cd VTK
-	epatch "${FILESDIR}"/vtk-5.6.0-cg-path.patch
-}
-
-src_configure() {
-	mycmakeargs=(
-		-DPV_INSTALL_LIB_DIR="${PVLIBDIR}"
-		-DCMAKE_INSTALL_PREFIX="${EPREFIX}"/usr
-		-DPV_INSTALL_DOC_DIR="${EPREFIX}/usr/share/doc/${PF}"
-		-DEXPAT_INCLUDE_DIR="${EPREFIX}"/usr/include
-		-DEXPAT_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libexpat.so
-		-DOPENGL_gl_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libGL.so
-		-DOPENGL_glu_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libGLU.so
-		-DCMAKE_SKIP_RPATH=YES
-		-DVTK_USE_RPATH=OFF
-		-DBUILD_SHARED_LIBS=ON
-		-DVTK_USE_SYSTEM_FREETYPE=ON
-		-DVTK_USE_SYSTEM_JPEG=ON
-		-DVTK_USE_SYSTEM_PNG=ON
-		-DVTK_USE_SYSTEM_TIFF=ON
-		-DVTK_USE_SYSTEM_ZLIB=ON
-		-DVTK_USE_SYSTEM_EXPAT=ON
-		-DPARAVIEW_USE_SYSTEM_HDF5=ON
-		-DCMAKE_VERBOSE_MAKEFILE=ON
-		-DCMAKE_COLOR_MAKEFILE=TRUE
-		-DVTK_USE_SYSTEM_LIBXML2=ON
-		-DVTK_USE_OFFSCREEN=TRUE
-		-DCMAKE_USE_PTHREADS=ON
-		-DBUILD_TESTING=OFF
-		-DVTK_USE_FFMPEG_ENCODER=OFF
-		-DPARAVIEW_INSTALL_THIRD_PARTY_LIBRARIES=OFF
-		-DSYSTEM_PB=$(which protoc))
-
-	# use flag triggered options
-	mycmakeargs+=(
-		$(cmake-utils_use gui PARAVIEW_BUILD_QT_GUI)
-		$(cmake-utils_use gui VTK_USE_QVTK)
-		$(cmake-utils_use gui VTK_USE_QVTK_QTOPENGL)
-		$(cmake-utils_use mpi PARAVIEW_USE_MPI)
-		$(cmake-utils_use mpi PARAVIEW_USE_MPI_SSEND)
-		$(cmake-utils_use python PARAVIEW_ENABLE_PYTHON)
-		$(cmake-utils_use python VTK_WRAP_PYTHON_SIP)
-		$(cmake-utils_use python XDMF_WRAP_PYTHON)
-		$(cmake-utils_use doc BUILD_DOCUMENTATION)
-		$(cmake-utils_use examples BUILD_EXAMPLES)
-		$(cmake-utils_use cg VTK_USE_CG_SHADERS)
-		$(cmake-utils_use nvcontrol VTK_USE_NVCONTROL)
-		$(cmake-utils_use adaptive PARAVIEW_BUILD_AdaptiveParaView)
-		$(cmake-utils_use streaming PARAVIEW_BUILD_StreamingParaView)
-		$(cmake-utils_use mysql XDMF_USE_MYSQL)
-		$(cmake-utils_use coprocessing PARAVIEW_ENABLE_COPROCESSING))
-
-	if ( use gui || use adaptive ); then
-		mycmakeargs+=(-DVTK_INSTALL_QT_DIR=/${PVLIBDIR}/plugins/designer
-			$(cmake-utils_use webkit VTK_QT_USE_WEBKIT))
-		if use python ; then
-			# paraview cannot guess sip directory right probably because a path is not propagated properly
-			mycmakeargs+=(
-				-DSIP_PYQT_DIR="${EPREFIX}/usr/share/sip"
-				-DSIP_INCLUDE_DIR="${EPREFIX}$(python_get_includedir)")
-		fi
-	fi
-
-	# the rest of the plugins
-	mycmakeargs+=(
-		$(cmake-utils_use plugins PARAVIEW_INSTALL_DEVELOPMENT)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_ClientChartView)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_CosmoFilters)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_H5PartReader)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_Moments)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_PointSprite)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_Prism)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_SLACTools)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_AnalyzeNIfTIReaderWriter)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_SurfaceLIC)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_EyeDomeLighting)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_ForceTime)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_SierraPlotTools)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_StreamingView)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_VisTrailPlugin))
-
-	if use python; then
-		mycmakeargs+=($(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_pvblot))
-	fi
-
-	if use coprocessing; then
-		mycmakeargs+=($(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_CoProcessingScriptGenerator))
-	fi
-
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	# set up the environment
-	echo "LDPATH=${EPREFIX}/usr/${PVLIBDIR}" >> "${T}"/40${PN}
-	echo "PYTHONPATH="${EPREFIX}"/usr/${PVLIBDIR}:/usr/${PVLIBDIR}/site-packages" >> "${T}"/40${PN}
-	doenvd "${T}"/40${PN}
-
-	# last but not least lets make a desktop entry
-	newicon "${S}"/Applications/ParaView/pvIcon.png paraview.png \
-		|| die "Failed to create paraview icon."
-	make_desktop_entry paraview "Paraview" paraview \
-		|| die "Failed to install Paraview desktop entry"
-
-}
-
-pkg_postinst() {
-	# with Qt4.5 there seem to be issues reading data files
-	# under certain locales. Setting LC_ALL=C should fix these.
-	echo
-	elog "If you experience data corruption during parsing of"
-	elog "data files with paraview please try setting your"
-	elog "locale to LC_ALL=C."
-	echo
-}
-
-pkg_postrm() {
-	if use python ; then
-		python_mod_cleanup "${EPREFIX}"/usr/$(get_libdir)/"${PN}-${MAJOR_PV}"/site-packages
-	fi
-}
diff --git a/sci-visualization/paraview/paraview-3.14.1-r4.ebuild b/sci-visualization/paraview/paraview-3.14.1-r4.ebuild
deleted file mode 100644
index 4d13a8703..000000000
--- a/sci-visualization/paraview/paraview-3.14.1-r4.ebuild
+++ /dev/null
@@ -1,254 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-PYTHON_DEPEND="python? 2:2.6"
-
-inherit cmake-utils eutils flag-o-matic multilib python qt4-r2 toolchain-funcs versionator
-
-MAIN_PV=$(get_major_version)
-MAJOR_PV=$(get_version_component_range 1-2)
-MY_P="ParaView-${PV}-Source"
-
-DESCRIPTION="ParaView is a powerful scientific data visualization application"
-HOMEPAGE="http://www.paraview.org"
-SRC_URI="http://www.paraview.org/files/v${MAJOR_PV}/${MY_P}.tar.gz"
-RESTRICT="mirror"
-
-LICENSE="paraview GPL-2"
-KEYWORDS="~x86 ~amd64"
-SLOT="0"
-IUSE="boost cg -coprocessing doc examples +gui mpi mysql gl2ps nvcontrol +plugins +python ffmpeg theora"
-
-RDEPEND="
-	~sci-libs/netcdf-4.1.3[cxx,hdf5]
-	sci-libs/hdf5[mpi=]
-	mpi? ( virtual/mpi[cxx,romio] )
-	gui? (
-		dev-qt/qtgui:4
-		dev-qt/qt3support:4
-		dev-qt/qtopengl:4
-		|| ( >=dev-qt/qthelp-4.7.0:4[compat] <dev-qt/qthelp-4.7.0:4 )
-		dev-qt/qtsql:4
-		dev-qt/qtwebkit:4 )
-	mysql? ( virtual/mysql )
-	coprocessing? ( plugins? (
-			dev-qt/qtgui:4
-			dev-python/PyQt4 ) )
-	python? (
-		dev-python/sip
-		gui? ( dev-python/PyQt4[opengl,webkit] )
-		dev-python/numpy
-		mpi? ( dev-python/mpi4py )
-	)
-	ffmpeg? ( virtual/ffmpeg )
-	theora? ( media-libs/libtheora )
-	gl2ps? ( x11-libs/gl2ps )
-	dev-libs/libxml2:2
-	dev-db/sqlite:3
-	media-libs/libpng
-	virtual/jpeg
-	media-libs/tiff
-	dev-libs/expat
-	sys-libs/zlib
-	media-libs/freetype
-	>=app-admin/eselect-opengl-1.0.6-r1
-	virtual/opengl
-	sci-libs/netcdf
-	x11-libs/libXmu"
-DEPEND="${RDEPEND}
-		doc? ( app-doc/doxygen )
-		boost? ( >=dev-libs/boost-1.40.0[mpi?] )
-		dev-libs/protobuf
-		>=dev-util/cmake-2.6.4"
-
-PVLIBDIR=$(get_libdir)/${PN}-${MAJOR_PV}
-S=${WORKDIR}/${MY_P}
-
-pkg_setup() {
-	use python && python_set_active_version 2
-}
-
-src_prepare() {
-	# gcc header fix
-	epatch "${FILESDIR}"/${PN}-3.8.0-xdmf-cstring.patch
-	# disable automatic byte compiling that act directly on the live system
-	epatch "${FILESDIR}"/${PN}-3.8.0-xdmf-bc.patch
-	# Do not install ffmpeg libraries if used
-	epatch "${FILESDIR}"/${PN}-3.14.1-ffmpeg-noinstall.patch
-	# patch from debian for some underlinking in xdmf
-	epatch "${FILESDIR}"/${PN}-3.14.1-xdmf-linking.patch
-	# upstream http://paraview.org/Bug/view.php?id=13222 and 
-	# commit https://github.com/Kitware/ParaView/commit/559af72e540f418310b6425055348336a48ad557
-	epatch "${FILESDIR}"/${PN}-3.14.1-python-exit.patch
-	# disable internal mpi4py copy
-	epatch "${FILESDIR}"/${PN}-3.14.1-mpi4py.patch
-	# remove the internal copy of sqlite (vtksqlite)
-	# http://patch-tracker.debian.org/patch/series/view/paraview/3.14.1-7/removesqlite.patch
-	epatch "${FILESDIR}"/${PN}-3.14.1-removesqlite.patch
-	# gcc 4.7 fix
-	# http://patch-tracker.debian.org/patch/series/view/paraview/3.14.1-7/fix_FTBFS_gcc-4.7.patch
-	epatch "${FILESDIR}"/${PN}-3.14.1-gcc-4.7.patch
-	# adapted from debian patch need to be applied after paraview-3.14.1-removesqlite.patch
-	epatch "${FILESDIR}"/${PN}-3.14.1-vtknetcd.patch
-
-	# lib64 fixes
-	sed -i "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \
-		Utilities/Xdmf2/libsrc/CMakeLists.txt || die
-	sed -i "s:\/lib\/python:\/$(get_libdir)\/python:g" \
-		Utilities/Xdmf2/CMake/setup_install_paths.py || die
-
-	# Install internal vtk binaries to PV_INSTALL_LIB_DIR as noted in the comment in the cmake file.
-	# upstream doesn't even do what they say they do.
-	sed -e 's:VTK_INSTALL_BIN_DIR \"/${PV_INSTALL_BIN_DIR}\":VTK_INSTALL_BIN_DIR \"/${PV_INSTALL_LIB_DIR}\":' \
-		-i CMake/ParaViewCommon.cmake || die "failed to patch vtk install location"
-
-	cd VTK
-	epatch "${FILESDIR}"/vtk-5.6.0-cg-path.patch
-	epatch "${FILESDIR}"/vtk-5.6.0-odbc.patch
-	epatch "${FILESDIR}"/vtk-5.6.1-ffmpeg.patch
-	epatch "${FILESDIR}"/vtk-5.6.1-libav-0.8.patch
-	# debian patch for recent boost should work with 1.48 too
-	epatch "${FILESDIR}"/vtk-boost1.49.patch
-}
-
-src_configure() {
-	mycmakeargs=(
-		-DPV_INSTALL_LIB_DIR="${PVLIBDIR}"
-		-DCMAKE_INSTALL_PREFIX="${EPREFIX}"/usr
-		-DPV_INSTALL_DOC_DIR="${EPREFIX}/usr/share/doc/${PF}"
-		-DEXPAT_INCLUDE_DIR="${EPREFIX}"/usr/include
-		-DEXPAT_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libexpat.so
-		-DOPENGL_gl_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libGL.so
-		-DOPENGL_glu_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libGLU.so
-		-DCMAKE_SKIP_RPATH=YES
-		-DVTK_USE_RPATH=OFF
-		-DBUILD_SHARED_LIBS=ON
-		-DVTK_USE_SYSTEM_FREETYPE=ON
-		-DVTK_USE_SYSTEM_JPEG=ON
-		-DVTK_USE_SYSTEM_PNG=ON
-		-DVTK_USE_SYSTEM_TIFF=ON
-		-DVTK_USE_SYSTEM_ZLIB=ON
-		-DVTK_USE_SYSTEM_EXPAT=ON
-		-DPARAVIEW_USE_SYSTEM_HDF5=ON
-		-DVTK_USE_SYSTEM_HDF5=ON
-		-DCMAKE_VERBOSE_MAKEFILE=ON
-		-DCMAKE_COLOR_MAKEFILE=TRUE
-		-DVTK_USE_SYSTEM_LIBXML2=ON
-		-DVTK_USE_OFFSCREEN=TRUE
-		-DCMAKE_USE_PTHREADS=ON
-		-DVTK_USE_FFMPEG_ENCODER=OFF
-		-DPARAVIEW_INSTALL_THIRD_PARTY_LIBRARIES=OFF
-		-DPROTOC_LOCATION=$(which protoc))
-
-	# use flag triggered options
-	mycmakeargs+=(
-		$(cmake-utils_use gui PARAVIEW_BUILD_QT_GUI)
-		$(cmake-utils_use gui VTK_USE_QVTK)
-		$(cmake-utils_use gui VTK_USE_QVTK_QTOPENGL)
-		$(cmake-utils_use boost VTK_USE_BOOST)
-		$(cmake-utils_use boost VTK_USE_TEXT_ANALYSIS)
-		$(cmake-utils_use mpi PARAVIEW_USE_MPI)
-		$(cmake-utils_use mpi PARAVIEW_USE_MPI_SSEND)
-		$(cmake-utils_use python PARAVIEW_ENABLE_PYTHON)
-		$(cmake-utils_use python VTK_WRAP_PYTHON_SIP)
-		$(cmake-utils_use python XDMF_WRAP_PYTHON)
-		$(cmake-utils_use doc BUILD_DOCUMENTATION)
-		$(cmake-utils_use examples BUILD_EXAMPLES)
-		$(cmake-utils_use cg VTK_USE_CG_SHADERS)
-		$(cmake-utils_use nvcontrol VTK_USE_NVCONTROL)
-		$(cmake-utils_use mysql XDMF_USE_MYSQL)
-		$(cmake-utils_use mysql VTK_USE_MYSQL)
-		$(cmake-utils_use gl2ps VTK_USE_GL2PS)
-		$(cmake-utils_use gl2ps VTK_USE_SYSTEM_GL2PS)
-		$(cmake-utils_use coprocessing PARAVIEW_ENABLE_COPROCESSING)
-		$(cmake-utils_use ffmpeg VTK_USE_FFMPEG_ENCODER)
-		$(cmake-utils_use theora VTK_USE_THEORA_ENCODER)
-		$(cmake-utils_use theora VTK_USE_SYSTEM_OGGTHEORA))
-
-	# testing, disabling vtk testing as vtkpython is tested and will fail.
-	mycmakeargs+=(
-		$(cmake-utils_use test BUILD_TESTING)
-		$(cmake-utils_use test PARAVIEW_DISABLE_VTK_TESTING))
-
-	if ( use gui ); then
-		mycmakeargs+=(
-			-DVTK_INSTALL_QT_DIR=/${PVLIBDIR}/plugins/designer
-			-DVTK_QT_USE_WEBKIT=ON )
-		if use python ; then
-			# paraview cannot guess sip directory right probably because a path is not propagated properly
-			mycmakeargs+=(
-				-DSIP_PYQT_DIR="${EPREFIX}/usr/share/sip"
-				-DSIP_INCLUDE_DIR="${EPREFIX}$(python_get_includedir)")
-		fi
-	fi
-
-	# the rest of the plugins
-	mycmakeargs+=(
-		$(cmake-utils_use plugins PARAVIEW_INSTALL_DEVELOPMENT)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_ClientChartView)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_CosmoFilters)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_H5PartReader)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_Moments)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_PointSprite)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_Prism)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_SLACTools)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_AnalyzeNIfTIReaderWriter)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_SurfaceLIC)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_EyeDomeLighting)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_ForceTime)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_SierraPlotTools)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_StreamingView)
-		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_VisTrailPlugin))
-
-	if use python; then
-		mycmakeargs+=(
-			$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_pvblot))
-	fi
-
-	if use coprocessing; then
-		mycmakeargs+=($(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_CoProcessingScriptGenerator))
-	fi
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	# set up the environment
-	echo "LDPATH=${EPREFIX}/usr/${PVLIBDIR}" >> "${T}"/40${PN}
-	echo "PYTHONPATH="${EPREFIX}"/usr/${PVLIBDIR}:/usr/${PVLIBDIR}/site-packages" >> "${T}"/40${PN}
-	doenvd "${T}"/40${PN}
-
-	# last but not least lets make a desktop entry
-	newicon "${S}"/Applications/ParaView/pvIcon.png paraview.png \
-		|| die "Failed to create paraview icon."
-	make_desktop_entry paraview "Paraview" paraview \
-		|| die "Failed to install Paraview desktop entry"
-
-}
-
-pkg_postinst() {
-	# with Qt4.5 there seem to be issues reading data files
-	# under certain locales. Setting LC_ALL=C should fix these.
-	echo
-	elog "If you experience data corruption during parsing of"
-	elog "data files with paraview please try setting your"
-	elog "locale to LC_ALL=C."
-	elog "If you plan to use paraview component from an existing shell"
-	elog "you should run env-update and . /etc/profile first"
-	echo
-}
-
-pkg_postrm() {
-	if use python ; then
-		python_mod_cleanup "${EPREFIX}"/usr/$(get_libdir)/"${PN}-${MAJOR_PV}"/site-packages
-	fi
-}
diff --git a/virtual/cblas/ChangeLog b/virtual/cblas/ChangeLog
index 742eb39eb..92dfa12b2 100644
--- a/virtual/cblas/ChangeLog
+++ b/virtual/cblas/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for virtual/cblas
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/virtual/cblas/ChangeLog,v 1.6 2010/01/11 10:56:05 ulm Exp $
 
+  25 Jul 2013; Sébastien Fabbro <bicatali@gentoo.org> cblas-2.0.ebuild:
+  virtual/cblas: Adapted for new openblas
+
   19 Dec 2012; Denis Dupeyron <calchan@gentoo.org> cblas-2.0.ebuild:
   Only consider sci-libs/gsl as a valid cblas implementation if the
   cblas-external USE flag is not set. Update sci-libs/gsl version to 1.15-r3.
@@ -33,4 +36,3 @@
   10 Oct 2007; Sébastien Fabbro <bicatali@gentoo.org> +metadata.xml,
   +cblas-1.0.ebuild:
   New style virtual for cblas. Version number is abitrary.
-
diff --git a/virtual/cblas/cblas-2.0.ebuild b/virtual/cblas/cblas-2.0.ebuild
index 3e0f93f3e..8845eda9e 100644
--- a/virtual/cblas/cblas-2.0.ebuild
+++ b/virtual/cblas/cblas-2.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -10,15 +10,15 @@ SRC_URI=""
 
 LICENSE=""
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
 RDEPEND="|| (
 		>=sci-libs/cblas-reference-20110218
+		sci-libs/openblas
 		>=sci-libs/gsl-1.15-r3[-cblas-external]
 		>=sci-libs/gotoblas2-1.13[incblas]
 		>=sci-libs/atlas-3.9.34
 		>=sci-libs/mkl-10.3
-		sci-libs/openblas[incblas]
 	)"
 DEPEND=""