gentoo resync : 25.08.2018

17 files changed, 418 insertions, 399 deletions

diff --git a/sci-physics/Manifest.gz b/sci-physics/Manifest.gz
index f189f3cebe4f..fd7a7449a688 100644
--- a/sci-physics/Manifest.gz
+++ b/sci-physics/Manifest.gz
diff --git a/sci-physics/geant-vmc/Manifest b/sci-physics/geant-vmc/Manifest
new file mode 100644
index 000000000000..850a112f232c
--- /dev/null
+++ b/sci-physics/geant-vmc/Manifest
@@ -0,0 +1,4 @@
+DIST geant4_vmc.3.6.tar.gz 1017407 BLAKE2B f386ea49843abedbed16ba1d12a10ae4165123fb0f7842482c416becf4141bc15360be1038626ce40f96a9dbb15d27116cd2fbd46d74b856d5a9391d073784a5 SHA512 eaf8626a3702149a1c5be4adff7843ef828da8024aafb8de489dd6b55b4ee05850581318d01032a4008767ad4e2fc0fde23e1aa5c751693e902d51ce9ad3d1df
+EBUILD geant-vmc-4.3.6.ebuild 2100 BLAKE2B 50f6b40d3f35d0835c4d9872055930cabe73ba2bdd03a0ee35e9b85697dc82f304659a55caf0fd5b5ecd6a2db3be13b512b6d1d08be86ef4a7ab8cca86c28460 SHA512 88de1fd5ff56a131daafb174968a93d67d89590e64fc709a8ecb7dd29b312f28a6984592df4451dfc900cc084715845e93f79745dc745d28b5b95a42e9b2d03a
+EBUILD geant-vmc-9999.ebuild 2100 BLAKE2B 50f6b40d3f35d0835c4d9872055930cabe73ba2bdd03a0ee35e9b85697dc82f304659a55caf0fd5b5ecd6a2db3be13b512b6d1d08be86ef4a7ab8cca86c28460 SHA512 88de1fd5ff56a131daafb174968a93d67d89590e64fc709a8ecb7dd29b312f28a6984592df4451dfc900cc084715845e93f79745dc745d28b5b95a42e9b2d03a
+MISC metadata.xml 859 BLAKE2B 4bec2c6236dfc1bdb9ba9f1caff6c9b545861c6e51c58d90bfa652d2d5aaa323437473173912f1840ba3c690f92798929980e5bcb3cacb5fe4cdd8a0edb014d9 SHA512 15a0f421563051a8553e2bdf9a8f82dc5077e336513cc18ef7e9bea49e084ea4dc1aa32800fbc928743d8c09036d136518a5a6a74c2f57c61215da2f44dc9727
diff --git a/sci-physics/geant-vmc/geant-vmc-4.3.6.ebuild b/sci-physics/geant-vmc/geant-vmc-4.3.6.ebuild
new file mode 100644
index 000000000000..2156a04588fa
--- /dev/null
+++ b/sci-physics/geant-vmc/geant-vmc-4.3.6.ebuild
@@ -0,0 +1,88 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit cmake-utils eapi7-ver
+
+if [[ ${PV} == *9999* ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/vmc-project/geant4_vmc.git"
+else
+	DOWN_PV=$(ver_cut 2-)
+	SRC_URI="http://root.cern.ch/download/vmc/geant4_vmc.${DOWN_PV}.tar.gz"
+	SOURCE_PV=$(ver_rs 1- - ${DOWN_PV})
+	S="${WORKDIR}/geant4_vmc-${SOURCE_PV}"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+DESCRIPTION="Virtual Monte Carlo Geant4 implementation"
+HOMEPAGE="http://root.cern.ch/root/vmc/VirtualMC.html"
+
+LICENSE="GPL-2"
+SLOT="4"
+IUSE="doc examples geant3 +g4root +mtroot vgm test"
+
+# sci-physics/root[root7] flag activates std=c++14, which we could only support if also Geant is built with it.
+# Disable for now.
+RDEPEND="
+	>=sci-physics/geant-4.10.03:=[opengl,geant3?]
+	sci-physics/root:=[-root7]
+	vgm? ( >=sci-physics/vgm-4.4:= )"
+DEPEND="${RDEPEND}
+	doc? ( app-doc/doxygen )"
+RESTRICT="
+	!geant3? ( test )
+	!g4root? ( test )
+	!mtroot? ( test )
+	!vgm? ( test )"
+
+DOCS=(
+	history
+	README.md
+)
+
+src_configure() {
+	local mycmakeargs=(
+		-DGeant4VMC_USE_VGM="$(usex vgm)"
+		-DGeant4VMC_USE_GEANT4_G3TOG4="$(usex geant3)"
+		-DGeant4VMC_USE_G4Root="$(usex g4root)"
+		-DGeant4VMC_BUILD_MTRoot="$(usex mtroot)"
+		-DGeant4VMC_BUILD_EXAMPLES="$(usex test)"
+		-DGeant4VMC_INSTALL_EXAMPLES="$(usex examples)"
+	)
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	cmake-utils_src_compile
+	if use doc ; then
+		local dirs=(
+			source
+			$(usev g4root)
+			$(usev mtroot)
+			$(usev examples)
+		)
+		local d
+		for d in "${dirs[@]}"; do
+			pushd "${d}" > /dev/null || die
+			doxygen || die
+			popd > /dev/null || die
+		done
+	fi
+}
+
+src_test() {
+	# Required by sci-physics/root for pointer validity checking,
+	# see e.g. https://sft.its.cern.ch/jira/browse/ROOT-8146 .
+	addwrite /dev/random
+	cd examples || die
+	./test_suite.sh --g3=off --builddir="${BUILD_DIR}" || die
+	./test_suite_exe.sh --g3=off --builddir="${BUILD_DIR}" || die
+}
+
+src_install() {
+	cmake-utils_src_install
+	use doc && local HTML_DOCS=(doc/.)
+	einstalldocs
+}
diff --git a/sci-physics/geant-vmc/geant-vmc-9999.ebuild b/sci-physics/geant-vmc/geant-vmc-9999.ebuild
new file mode 100644
index 000000000000..2156a04588fa
--- /dev/null
+++ b/sci-physics/geant-vmc/geant-vmc-9999.ebuild
@@ -0,0 +1,88 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit cmake-utils eapi7-ver
+
+if [[ ${PV} == *9999* ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/vmc-project/geant4_vmc.git"
+else
+	DOWN_PV=$(ver_cut 2-)
+	SRC_URI="http://root.cern.ch/download/vmc/geant4_vmc.${DOWN_PV}.tar.gz"
+	SOURCE_PV=$(ver_rs 1- - ${DOWN_PV})
+	S="${WORKDIR}/geant4_vmc-${SOURCE_PV}"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+DESCRIPTION="Virtual Monte Carlo Geant4 implementation"
+HOMEPAGE="http://root.cern.ch/root/vmc/VirtualMC.html"
+
+LICENSE="GPL-2"
+SLOT="4"
+IUSE="doc examples geant3 +g4root +mtroot vgm test"
+
+# sci-physics/root[root7] flag activates std=c++14, which we could only support if also Geant is built with it.
+# Disable for now.
+RDEPEND="
+	>=sci-physics/geant-4.10.03:=[opengl,geant3?]
+	sci-physics/root:=[-root7]
+	vgm? ( >=sci-physics/vgm-4.4:= )"
+DEPEND="${RDEPEND}
+	doc? ( app-doc/doxygen )"
+RESTRICT="
+	!geant3? ( test )
+	!g4root? ( test )
+	!mtroot? ( test )
+	!vgm? ( test )"
+
+DOCS=(
+	history
+	README.md
+)
+
+src_configure() {
+	local mycmakeargs=(
+		-DGeant4VMC_USE_VGM="$(usex vgm)"
+		-DGeant4VMC_USE_GEANT4_G3TOG4="$(usex geant3)"
+		-DGeant4VMC_USE_G4Root="$(usex g4root)"
+		-DGeant4VMC_BUILD_MTRoot="$(usex mtroot)"
+		-DGeant4VMC_BUILD_EXAMPLES="$(usex test)"
+		-DGeant4VMC_INSTALL_EXAMPLES="$(usex examples)"
+	)
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	cmake-utils_src_compile
+	if use doc ; then
+		local dirs=(
+			source
+			$(usev g4root)
+			$(usev mtroot)
+			$(usev examples)
+		)
+		local d
+		for d in "${dirs[@]}"; do
+			pushd "${d}" > /dev/null || die
+			doxygen || die
+			popd > /dev/null || die
+		done
+	fi
+}
+
+src_test() {
+	# Required by sci-physics/root for pointer validity checking,
+	# see e.g. https://sft.its.cern.ch/jira/browse/ROOT-8146 .
+	addwrite /dev/random
+	cd examples || die
+	./test_suite.sh --g3=off --builddir="${BUILD_DIR}" || die
+	./test_suite_exe.sh --g3=off --builddir="${BUILD_DIR}" || die
+}
+
+src_install() {
+	cmake-utils_src_install
+	use doc && local HTML_DOCS=(doc/.)
+	einstalldocs
+}
diff --git a/sci-physics/geant-vmc/metadata.xml b/sci-physics/geant-vmc/metadata.xml
new file mode 100644
index 000000000000..ef4bdfb269e8
--- /dev/null
+++ b/sci-physics/geant-vmc/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>o.freyermuth@googlemail.com</email>
+    <name>Oliver Freyermuth</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>proxy-maint@gentoo.org</email>
+    <name>Proxy Maintainers</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="github">vmc-project/geant4_vmc</remote-id>
+  </upstream>
+  <use>
+    <flag name="vgm">Enable the Virtual Geometry Model (<pkg>sci-physics/vgm</pkg>)</flag>
+    <flag name="g4root">Build G4Root (interface for GEANT4 simulation with a ROOT geometry)</flag>
+    <flag name="geant3">Build with Geant4 G3toG4 library</flag>
+    <flag name="mtroot">Build MTRoot (provides ROOT IO manager classes with multi-threading support)</flag>
+  </use>
+</pkgmetadata>
diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest
index e7c2f930b8d4..98e454a1ac8a 100644
--- a/sci-physics/lammps/Manifest
+++ b/sci-physics/lammps/Manifest
@@ -1,3 +1,4 @@
+AUX 1080.patch 922 BLAKE2B 59325abb5d2f9d9e501c34b539a98efea521ee38872f1e2d3850442aac82adaea3a3c32e644f3d2982aa9aa86dbdfb5bd1373175a89acffac63d87ac542919a7 SHA512 a94bba2ad992f85db0f7d7d04cef235a79e4600e353897032d78ffc3e1f899bc340a5ad8aa1d8da41f9783b67d912dab8c3cd2f83a605a9e0c0ef51bdb909279
 AUX fm_exp.patch 347 BLAKE2B 230da9c04160d445a3da1c813453a788ad04b1d174c494ab9dd1de628ba3c1bf7f9aeb5070b165ec545a280208f07254afaa4d9120fffff5ee98975233d9fc9e SHA512 d0c8303bfe623fe766a545e1614f7576709381597e56f7c7634e90768376bccb9fbe37d4c0eeb6491c9b45d911a913a37386e0280ec3f05a90388aad7bb23c3e
 AUX gcc-6.patch 397 BLAKE2B 7ef1bf4e884763d84ea661ad09dc1e373db10a177e1bf09f617edfc6bcefef5d494def037ba62a8ea76d83cb2eba172dc0188ba4f0ad1877b7cadd3a91d1f583 SHA512 eebb9041347dbe260be6028d9462183188ce95f3114873b2a776990aa77c71dd4b0ba37d2fe3fbf0b8bff64f85dfafaec93ad7234502791a1048ab6bfd1d06ed
 AUX lammps-python3-r1.patch 544 BLAKE2B dcde498a0d886f941aefef6818429efe2a9d253285239a122b983a5bc6ab7b7c053f3fa78b24b995b21891c190f3c82d7032d07015f9baf3c525320e7421a3c4 SHA512 833ec755ba4dadf072ced646220a7a68147023548da9eeebdd1d4a6c198ee48fed1e60a7fc26de7093b5d9b77a906e162a7ef4f5f929918196943564f69037d5
@@ -27,6 +28,7 @@ DIST lammps-9Jan17.tar.gz 109694893 BLAKE2B dc3af18d4a7db43d22bc4d2ed79366f7f1b7
 DIST lammps-patch_16Mar2018.tar.gz 91908414 BLAKE2B 0d2363ba507765d439988be9f17390889539ecf22132145f5f5f5411c6c3bf097b278b24b005374e4b176efcfbd01edb48b55076bfa41403718ad14d3905e062 SHA512 2847f9ffa368b966cba4792ebe86ea38dfc1e147647e2b738753121a09689901cea7197d3d95fa69cd065cd1d30aa37cbeffcb78b62ec85d88cd9f3ab25e25c2
 DIST lammps-patch_17Jan2018.tar.gz 91721592 BLAKE2B d606a5fd699f3e7aaa777065532f778e96a5b21b88de3fcce69e79c4931fea233ed1ad68f56120865061623c6e33282b9f23f927a7a9820f8f824a241e5cd823 SHA512 533ada073882e9bfc6431db62c4899005983d9efbbb043bcb50b2b0a7af2b11c411bbcc6523b2ffbd5d46531b24573f4b98a07dc757bacbc2f27bb056d7956ff
 DIST lammps-patch_1Sep2017.tar.gz 88751184 BLAKE2B 013ba612c67767c0e11b64f0b726a81c534ceb763ac9eba9a94ef9e02166278c28cb5937162b83f783b80fef6471b0e265e45245cc5594eaa2b27ec2d5f972cf SHA512 01b56484d6e9d03c0cdc2f8100f571d6e0a354b08bda7f22176744f2724e566443514e7d8abb0571d4207709155441644d4c6dbcf17ee2a8dc4f10cb6c3e8ac1
+DIST lammps-patch_22Aug2018.tar.gz 108761265 BLAKE2B fc509ccd8f5fda9fea9cf7f54b888df235b5d499a0aa3eee24bba81d35c95355cfc72ebb60f32a4adb879c0ab176659ebe634f9bbaeefd54ffc0d02329054f9f SHA512 bb1c11ef9c287b101b9f3483d6b90e55dc69a048529e5076f6f7d46e54802d0d75efc899865d462f9dd76937089e1080a126c1dc4bbb2648eda91cb38ba142b0
 DIST lammps-patch_22Feb2018.tar.gz 91869050 BLAKE2B 09d364b489d4402145b879ca40b290a4e33f39b6e5e4183bcccb09001002cb742917c8792f942a8b64bd992cde5c0f8dcd8b76506048f1392d33d1192aa4551d SHA512 8d4ac0f9cdcf4caa10bfb48129eec21cf31f7ce881b4cbd803c20fb638f7e55a1e645d314e172fe70eab473a4976c7f482e8c059e0c4e82527eb9438437ae146
 DIST lammps-patch_8Mar2018.tar.gz 91878683 BLAKE2B a4cf307769b1ac27c9cbe781a70f307d5275d2ccd4f6f77a2a21f00413ffa0af499577207afd23afd95ef6126071e8b779f6c52d50ff7117afb63161613c9f5b SHA512 57885d12e9e0ea9a6735cc2f7a2a8a9314dacbe9eaf5a46cb6d20fd7e2d0e8b0ebb3e24731eb750861973efe4d3cf0cf5a739cc9d51407f26bf3d556243c186f
 EBUILD lammps-20150210.ebuild 4832 BLAKE2B f857d2e0e82c2e5b05fe89c62fda44b917d8be0a184171235eadee85c97699de5d4f22a1ea20c12a5523702ab376df9c80d486a7751cd3fbc9527a6954e59026 SHA512 fbbfd6768d9ee99f49aea6abb030486a7f80c4aad95412407031499681a2a36997c31cb4873e0ab867425678b952a44284129accde9abe60c1bfb891c38d2dfa
@@ -56,4 +58,5 @@ EBUILD lammps-20180117.ebuild 3040 BLAKE2B 74b48a09ab862dc1fb0d7b1fc927b16250926
 EBUILD lammps-20180222.ebuild 3040 BLAKE2B 74b48a09ab862dc1fb0d7b1fc927b16250926d7b528d1d36a8cbe1fb3ce1fd58522355bb7559f7a4ae999b5748d0b66e2982c218a8acd40435243825d6a07cc2 SHA512 6965f3a6102e86b375482a35061ffbd6d1b3ee2bd7e8023f66c639af9630e29face9be627196cb0658e28b9b09a19f55b5bd62688370a8f01cc78152b5952b80
 EBUILD lammps-20180308.ebuild 3040 BLAKE2B 74b48a09ab862dc1fb0d7b1fc927b16250926d7b528d1d36a8cbe1fb3ce1fd58522355bb7559f7a4ae999b5748d0b66e2982c218a8acd40435243825d6a07cc2 SHA512 6965f3a6102e86b375482a35061ffbd6d1b3ee2bd7e8023f66c639af9630e29face9be627196cb0658e28b9b09a19f55b5bd62688370a8f01cc78152b5952b80
 EBUILD lammps-20180316.ebuild 3038 BLAKE2B a212f0fa069fb7e116ce13b44dc9351dbd59fbc9da4fb70994b5bf182c3eb2456029fa75e0640d5225ae87e7fa77185962a6feb19a26222dfe736b582feb651a SHA512 860d93f1837193c778d14b3d77c5b64aace3161501159d364002037b92e3179c2fcac408bbb1f3aa1ffcc52106530c326f14551762e25eb38c5c8713a226b906
+EBUILD lammps-20180822.ebuild 2808 BLAKE2B c627112df16849842409b56a6be66ea52b79a848b5279bcc321e770ad854365d51863464e3f0cf2454a61caac809c80353114829b1fa4985ad4e311d38a48beb SHA512 ca505928c1c73438f89b1ddf2d80fd0277ce5745bb92b76343a82891f4efff9702cede0a469b1897cccd4d12c733db19e4c2a4b878449b0026e6a4b06e1cea39
 MISC metadata.xml 1338 BLAKE2B 553629a0b3221db88a37cd6b0bfa806da9265caf2df038736211351a87ac34af5a98f0e7f3e34246d814a378cd64b1ed82d69f4c26e18c3a7700441f8be6fa2d SHA512 b3556e8444b4cb42d1fa80cc8735e11e07cd2928af67104d4518b874e167d5755840c3585e3ffefa88057f84d711cafe0a60405323b4ad6a9546c19d4a5d94bd
diff --git a/sci-physics/lammps/files/1080.patch b/sci-physics/lammps/files/1080.patch
new file mode 100644
index 000000000000..85538b2a638c
--- /dev/null
+++ b/sci-physics/lammps/files/1080.patch
@@ -0,0 +1,29 @@
+From a10bb4b96f40f3b5574b0fade2cfece8bf4c6fc9 Mon Sep 17 00:00:00 2001
+From: Christoph Junghans <junghans@lanl.gov>
+Date: Thu, 23 Aug 2018 15:02:36 -0600
+Subject: [PATCH] cmake: fix link issue with --as-needed
+
+---
+ cmake/CMakeLists.txt | 5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
+index 460d177c92..51997593db 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -276,11 +276,14 @@ endif()
+ 
+ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
+   find_package(LAPACK)
+-  if(NOT LAPACK_FOUND)
++  find_package(BLAS)
++  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
+     enable_language(Fortran)
+     file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
+     add_library(linalg STATIC ${LAPACK_SOURCES})
+     set(LAPACK_LIBRARIES linalg)
++  else()
++    list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
+   endif()
+ endif()
+ 
diff --git a/sci-physics/lammps/lammps-20180822.ebuild b/sci-physics/lammps/lammps-20180822.ebuild
new file mode 100644
index 000000000000..dfa18f8327bf
--- /dev/null
+++ b/sci-physics/lammps/lammps-20180822.ebuild
@@ -0,0 +1,129 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
+
+inherit cmake-utils fortran-2 python-r1
+
+convert_month() {
+	local months=( "" Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec )
+	echo ${months[${1#0}]}
+}
+
+MY_PV="patch_$((10#${PV:6:2}))$(convert_month ${PV:4:2})${PV:0:4}"
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="Large-scale Atomic/Molecular Massively Parallel Simulator"
+HOMEPAGE="http://lammps.sandia.gov/"
+SRC_URI="https://github.com/lammps/lammps/archive/${MY_PV}.tar.gz -> ${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cuda examples gzip lammps-memalign mpi netcdf python test"
+
+DEPEND="
+	app-arch/gzip
+	media-libs/libpng:0
+	sys-libs/zlib
+	mpi? (
+		virtual/mpi
+		sci-libs/hdf5[mpi]
+	)
+	python? ( ${PYTHON_DEPS} )
+	sci-libs/voro++
+	virtual/blas
+	virtual/lapack
+	sci-libs/fftw:3.0
+	netcdf? ( sci-libs/netcdf )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+	dev-cpp/eigen:3
+	"
+RDEPEND="${DEPEND}"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+# https://github.com/lammps/lammps/pull/1080
+PATCHES=( "${FILESDIR}/1080.patch" )
+
+S="${WORKDIR}/${MY_P}/cmake"
+
+src_configure() {
+	local mycmakeargs=(
+	    -DCMAKE_INSTALL_SYSCONFDIR="${EPREFIX}/etc"
+	    -DBUILD_SHARED_LIBS=ON
+		-DBUILD_MPI=$(usex mpi)
+		-DPKG_GPU=$(usex cuda)
+		-DGPU_API=CUDA
+		-DENABLE_TESTING=$(usex test)
+		-DPKG_ASPHERE=ON
+		-DPKG_BODY=ON
+		-DPKG_CLASS2=ON
+		-DPKG_COLLOID=ON
+		-DPKG_COMPRESS=ON
+		-DPKG_CORESHELL=ON
+		-DPKG_DIPOLE=ON
+		-DPKG_GRANULAR=ON
+		-DPKG_KSPACE=ON
+		-DFFT=FFTW3
+		-DPKG_MANYBODY=ON
+		-DPKG_MC=ON
+		-DPKG_MEAM=ON
+		-DPKG_MISC=ON
+		-DPKG_MOLECULE=ON
+		-DPKG_PERI=ON
+		-DPKG_QEQ=ON
+		-DPKG_REAX=ON
+		-DPKG_REPLICA=ON
+		-DPKG_RIGID=ON
+		-DPKG_SHOCK=ON
+		-DPKG_SNAP=ON
+		-DPKG_SRD=ON
+		-DPKG_PYTHON=ON
+		-DPKG_MPIIO=$(usex mpi)
+		-DPKG_VORONOI=ON
+		-DPKG_USER-ATC=ON
+		-DPKG_USER-AWPMD=ON
+		-DPKG_USER-CGDNA=ON
+		-DPKG_USER-CGSDK=ON
+		-DPKG_USER-COLVARS=ON
+		-DPKG_USER-DIFFRACTION=ON
+		-DPKG_USER-DPD=ON
+		-DPKG_USER-DRUDE=ON
+		-DPKG_USER-EFF=ON
+		-DPKG_USER-FEP=ON
+		-DPKG_USER-H5MD=$(usex mpi)
+		-DPKG_USER-LB=$(usex mpi)
+		-DPKG_USER-MANIFOLD=ON
+		-DPKG_USER-MEAMC=ON
+		-DPKG_USER-MGPT=ON
+		-DPKG_USER-MISC=ON
+		-DPKG_USER-MOLFILE=ON
+		-DPKG_USER-NETCDF=$(usex netcdf)
+		-DPKG_USER-PHONON=ON
+		-DPKG_USER-QTB=ON
+		-DPKG_USER-REAXC=ON
+		-DPKG_USER-SMD=ON
+		-DPKG_USER-SMTBQ=ON
+		-DPKG_USER-SPH=ON
+		-DPKG_USER-TALLY=ON
+	)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	cmake-utils_src_install
+
+	# Install python script.
+	use python && python_foreach_impl python_domodule "${S}"/../python/lammps.py
+
+	if use examples; then
+		for d in examples bench; do
+			local LAMMPS_EXAMPLES="/usr/share/${PN}/${d}"
+			insinto "${LAMMPS_EXAMPLES}"
+			doins -r "${S}"/../${d}/*
+		done
+	fi
+}
diff --git a/sci-physics/root/Manifest b/sci-physics/root/Manifest
index d7c16532e085..fa355d54caff 100644
--- a/sci-physics/root/Manifest
+++ b/sci-physics/root/Manifest
@@ -10,9 +10,8 @@ AUX root-6.14.00-http.patch 1130 BLAKE2B b2967a7e2a56d3989ebbcc84d82aa0395708ff8
 AUX rootd.confd 199 BLAKE2B d7638f5ee8ccb4fcb428d07c59d776a9ab8773fa8a8911281e8f76b32fab5902e3f6f6086ad210af39480df514c947719cc5e76d29c7dbf2a8715ae58ef49880 SHA512 2ce6753d37a7f22cc3656f110f802b8e07c1469bfe4524606c1472369352f8c584c01c716760252fab40369470b72d8c77cdbb2d52126c39371faaf597bf58d8
 AUX rootd.initd 622 BLAKE2B 7edeaf3cf550303642a89eb69edb65e6625215ac2daae5766904bcc14f1b30f6277c6eac6b895f46fbda01656df80cb71fdad6294a19bf581badceaa29278fdf SHA512 fde858a37b52540285d228e52845c963b18065a250aef0753f469753d541f577ac401f01438297c030e47176350bb23c3c0280c9b4ccbc1feda3313ab7c9be2e
 DIST root_v6.12.06.source.tar.gz 162284452 BLAKE2B 944b5e899677bab40842d7ec969ff08cfa470e63be9a02b948a49ae088e8da72ce433a5071d9196bfd98f71e6861b1bda285354012620eee6c61cffcee71a0c8 SHA512 3d44749ccfc3d40a2f516ae53ef40fb244ed785eee0dbc18ff822bbb811a15b943039d30282ef5358a283d485e62531880c877ec77a86089503b06d6f37e42e1
-DIST root_v6.14.02.source.tar.gz 162458882 BLAKE2B 70778819c6348f3fda9d7a224639da41f2a1522baec669e0cb88680f978fc64e98f87790d96b177e42ca5639e47f2646b94e65c112dd3b237bdd3dcfa9f6aeac SHA512 7117a74c622cc2d7d8b616abf8571444f6178c911dd768274af6def95e7cd7d1e39506a3b57f694fd4a687ad3bd1f6c68e64ff3eccdcd3236b0b59b08db6b934
-EBUILD root-6.12.06-r1.ebuild 9188 BLAKE2B 3a23869ac2344c4949eb1cdaec9fd4763ad84641defbe928b2c940f2a3db4bf7f00d16f60abf2284b647f169fdb234ee9155215346f878fcc12a2bf073f1e8ad SHA512 ed545ac2493b7ebddaf71d438d71b2b6f58cb562ec3017311d185084a7e0838aa8c253a320392cab1a3ca7b46655f95a786c55fd3b3ab18c06dfcc7edc02f543
-EBUILD root-6.12.06-r4.ebuild 7914 BLAKE2B fbe59c55e9ff7f257c5f9861eeabb5b76d2c1fd1236057879c108da63bf65fe1aeb0f3eff846e6f57175cce019a1aee786420d7fc7549bd8cf1d0dc8c043ba81 SHA512 5c094fd843a68ac5591a4fbf45ae4ef6073d10ed4f3b10613fab39e5017ed3c28c99bfc5a3841151a6aae228e2477a820ec5edba4b7225d361f00d960cc81aad
-EBUILD root-6.14.02.ebuild 7904 BLAKE2B 09e0636a2911e52005cb464732cb75112ab2bbba0faa9e805334323b695443cee43076acbc2d001a03646c6da67fd421891b4f42c67012914caf526ac31020ba SHA512 acf4ef7a89cf0df8dda63e233e00ba8400d916e5c4f14d01410a4cbb3fa2487f863784bdf560e5c3d7ce243bc0ce676e4969de2cf3eec0d9e32d3ca9fdebfcf8
-EBUILD root-9999.ebuild 8103 BLAKE2B c23d1d152ce67fbdc52b1eb9163b40b827471198eb6456f96ce38c36e463a4138e0db377c4a316e5c028cf3971cf73fa849b71c12542809efdc3d37b769f5444 SHA512 f0acc7909028c63f49ff0507199e89acdfe207d3c121ee110aa7ccd1beee0fe618b3741763f893da4621c8cb82e733534a363ae1bcdcceb421908241c66884bd
-MISC metadata.xml 3019 BLAKE2B 2d09d1b38ea45967ac74fd23265070df4393b66757dd3fee20541115b564dbbd017152b7f28d3e73ce19e44eeacd7be491c6b6d1d920216942586c5169a6695f SHA512 a51afe372f4aa84e622ff58bf89cee5665c0daf900c7ed7647a25167c58bbe3c45ebb0df342c30dea446b4c171d787b445136dec8eeaa32a2a5e0aecc04d737f
+DIST root_v6.14.04.source.tar.gz 162451369 BLAKE2B c7af9cf18736c900f71c35b7f9df91784058406c738ac49cf93aa6d1caee13b79e1f68be53ea600fc7311a5af76207f9de71f8438bf6eb43681c93f1815b39a7 SHA512 eb8f3fe89f70b222962ecec7bb7a1ff107dd600bc7ad63cbefc5d4e00561cc80b6430da90d1e59f70dbff69158929eec54614bb5df9894d342482b41c051353f
+EBUILD root-6.12.06-r5.ebuild 7853 BLAKE2B bf54b63a0a3bba4ed71312225797b305f50469df2336ab3b472c520316e96ace4dce9e435d82817cb8026deb5a19fcf58efde705736032179edf43cdb054e971 SHA512 a92fbc57da54858a1ebf86a9ba6b7dd0d0550a09a4981fc0bec11e57a32be7fe1d0dfccf78537b820057c97dc7b5d964038cfc3460c7923d55d6c0c2fa5da1be
+EBUILD root-6.14.04.ebuild 7918 BLAKE2B 6da1afa289996aaeed93335ae67a7e604d34e0f1ea61c538012b2a5548b8f003e1600e6c015262e6552b1d4b80944b3334196320baa3a30098f43db9bf71da62 SHA512 1f32b5b71687b5b88dd836954a9bf8d8ad2031351093cde00ba5111941b3bfeed68e6bbf3bfb56cc517204140c61845b35912fd9e990dbd06d29bddb84bd68f6
+EBUILD root-9999.ebuild 8129 BLAKE2B 7807440d9e8844a5e8bbcfce247e254b27492345aa34f984826038e817ccc2850b42afc0cb850958ef4da59e12b0f2124d7bb09eb90b8a3d27ebdb27add66ecb SHA512 61a92228cc1a584f1956efc244f39c53f48795561a2addc35c6e563fff0538e8e6e07705b9732ea58bd991c05ed36d8e83ed508e51a339d75e39805c420df165
+MISC metadata.xml 2977 BLAKE2B f0c2cd6f71ff44c2e3f767ec08ee7051c3501f6e57998dc0ad744f609862c0ac686d85fa65f85cf562edfbc51d4f62048a3beaa31e6c66aa965d8a182d438a42 SHA512 f9d4a99776394f7c273b7eb2c69060e5580bbc4f546b6f2001690c1dbcfc5f56e090c259beadc18d54aae4a0fcb3ba517143e6fad268caa8e60adac453f1b689
diff --git a/sci-physics/root/metadata.xml b/sci-physics/root/metadata.xml
index da893cfc0e6c..baf90a1a37bc 100644
--- a/sci-physics/root/metadata.xml
+++ b/sci-physics/root/metadata.xml
@@ -21,6 +21,7 @@
   </longdescription>
   <use>
     <flag name="asimage">Enable support for <pkg>media-libs/libafterimage</pkg></flag>
+    <flag name="cuda">Enable support for nVidia CUDA</flag>
     <flag name="davix">Enable support for DAVIX Data Management Client (https://cern.ch/davix)</flag>
     <flag name="fits">Enable support for images and data from FITS files with <pkg>sci-libs/cfitsio</pkg></flag>
     <flag name="fortran">Compile included Fortran programs</flag>
@@ -28,7 +29,6 @@
     <flag name="http">Enable http server support including but not limited to fastcgi support</flag>
     <flag name="jemalloc">Enable support for <pkg>dev-libs/jemalloc</pkg></flag>
     <flag name="libcxx">Build ROOT against <pkg>sys-libs/libcxx</pkg></flag>
-    <flag name="math">Build all math related libraries plugins, needs <pkg>sci-libs/gsl</pkg> </flag>
     <flag name="memstat">Build memory statistics library, helps to detect memory leaks</flag>
     <flag name="minuit">Build ROOT's internal versions of minuit (fortran) and minuit2 (C++)</flag>
     <flag name="pythia6">Build the interface for <pkg>sci-physics/pythia</pkg> version 6.x </flag>
diff --git a/sci-physics/root/root-6.12.06-r1.ebuild b/sci-physics/root/root-6.12.06-r1.ebuild
deleted file mode 100644
index f3b7aeca416d..000000000000
--- a/sci-physics/root/root-6.12.06-r1.ebuild
+++ /dev/null
@@ -1,349 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-CMAKE_BUILD_TYPE=Release
-# ninja does not work due to fortran
-CMAKE_MAKEFILE_GENERATOR=emake
-FORTRAN_NEEDED="fortran"
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
-
-inherit cmake-utils elisp-common eutils fortran-2 gnome2-utils prefix \
-	python-single-r1 toolchain-funcs user versionator xdg-utils
-
-DESCRIPTION="C++ data analysis framework and interpreter from CERN"
-HOMEPAGE="https://root.cern"
-SRC_URI="https://root.cern/download/${PN}_v${PV}.source.tar.gz"
-
-IUSE="+X avahi aqua +asimage +davix emacs +examples fits fftw fortran +gdml
-	graphviz +gsl http jemalloc kerberos ldap libcxx +math memstat +minuit
-	mysql odbc +opengl oracle postgres prefix pythia6 pythia8 +python qt4
-	R +roofit root7 shadow sqlite ssl table +tbb test +threads +tiff +tmva
-	+unuran vc xinetd +xml xrootd"
-
-MY_PV="$(get_version_component_range 1-2 ${PV})"
-MY_P="${PN}/$(get_version_component_range 1-2 ${PV})"
-MY_PREFIX=opt/${MY_P}
-
-SLOT="${MY_PV}/$(get_version_component_range 3 ${PV})"
-LICENSE="LGPL-2.1 freedist MSttfEULA LGPL-3 libpng UoI-NCSA"
-KEYWORDS="~amd64 ~x86"
-
-REQUIRED_USE="
-	!X? ( !asimage !opengl !qt4 !tiff )
-	python? ( ${PYTHON_REQUIRED_USE} )
-	tmva? ( math gsl )
-	davix? ( ssl )
-"
-
-CDEPEND="
-	app-arch/lz4
-	app-arch/xz-utils
-	fortran? ( dev-lang/cfortran )
-	dev-libs/libpcre:3=
-	dev-libs/xxhash
-	media-fonts/dejavu
-	media-libs/freetype:2=
-	media-libs/libpng:0=
-	sys-libs/ncurses:=
-	sys-libs/zlib:0=
-	X? (
-		x11-libs/libX11:0=
-		x11-libs/libXext:0=
-		x11-libs/libXft:0=
-		x11-libs/libXpm:0=
-		opengl? (
-			media-libs/ftgl:0=
-			media-libs/glew:0=
-			virtual/opengl
-			virtual/glu
-			x11-libs/gl2ps:0=
-		)
-		qt4? (
-			dev-qt/qtcore:4=
-			dev-qt/qtgui:4=
-			opengl? ( dev-qt/qtopengl:4= )
-		)
-	)
-	asimage? ( || (
-		media-libs/libafterimage[gif,jpeg,png,tiff?]
-		>=x11-wm/afterstep-2.2.11[gif,jpeg,png,tiff?]
-	) )
-	avahi? ( net-dns/avahi[mdnsresponder-compat] )
-	davix? ( net-libs/davix )
-	fftw? ( sci-libs/fftw:3.0= )
-	fits? ( sci-libs/cfitsio:0= )
-	graphviz? ( media-gfx/graphviz:0= )
-	gsl? ( sci-libs/gsl )
-	http? ( dev-libs/fcgi:0= )
-	jemalloc? ( dev-libs/jemalloc )
-	kerberos? ( virtual/krb5 )
-	ldap? ( net-nds/openldap:0= )
-	libcxx? ( sys-libs/libcxx )
-	unuran? ( sci-mathematics/unuran:0= )
-	minuit? ( !sci-libs/minuit )
-	mysql? ( virtual/mysql )
-	odbc? ( || ( dev-db/libiodbc dev-db/unixODBC ) )
-	oracle? ( dev-db/oracle-instantclient-basic )
-	postgres? ( dev-db/postgresql:= )
-	pythia6? ( sci-physics/pythia:6= )
-	pythia8? ( sci-physics/pythia:8= )
-	python? ( ${PYTHON_DEPS} )
-	R? ( dev-lang/R )
-	shadow? ( virtual/shadow )
-	sqlite? ( dev-db/sqlite:3= )
-	ssl? ( dev-libs/openssl:0= )
-	tbb? ( dev-cpp/tbb )
-	vc? ( dev-libs/vc )
-	xml? ( dev-libs/libxml2:2= )
-	xrootd? ( net-libs/xrootd:0= )
-"
-
-DEPEND="${CDEPEND}
-	virtual/pkgconfig"
-
-RDEPEND="${CDEPEND}
-	xinetd? ( sys-apps/xinetd )"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-6.11.02-hsimple.patch
-	"${FILESDIR}"/${PN}-6.12.04-no-ocaml.patch
-	"${FILESDIR}"/${PN}-6.12.04-no-opengl.patch
-	"${FILESDIR}"/${PN}-6.12.04-z3.patch
-)
-
-pkg_setup() {
-	use fortran && fortran-2_pkg_setup
-	use python && python-single-r1_pkg_setup
-
-	echo
-	elog "There are extra options on packages not yet in Gentoo:"
-	elog "Afdsmgrd, AliEn, castor, Chirp, dCache, gfal, Globus, gLite,"
-	elog "HDFS, Monalisa, MaxDB/SapDB, SRP, VecCore."
-	elog "You can use the env variable EXTRA_ECONF variable for this."
-	elog "For example, for Chirp, you would set: "
-	elog "EXTRA_ECONF=\"-Dchirp=ON\""
-	echo
-
-	enewgroup rootd
-	enewuser rootd -1 -1 /var/spool/rootd rootd
-}
-
-src_prepare() {
-	cmake-utils_src_prepare
-
-	hprefixify build/CMakeLists.txt core/clingutils/CMakeLists.txt
-	eapply "${FILESDIR}"/${PN}-6.12.06_cling-runtime-sysroot.patch
-
-	# CSS should use local images
-	sed -i -e 's,http://.*/,,' etc/html/ROOT.css || die "html sed failed"
-}
-
-# Note: ROOT uses bundled LLVM, because it is patched and API-incompatible with system LLVM.
-# Note: ROOT will install many compiler headers and other files into suboptimal places, so
-#       we install it into /opt due to QA concerns over the files installed into <prefix>/etc
-
-src_configure() {
-	local mycmakeargs=(
-		-DCMAKE_C_FLAGS="${CFLAGS}"
-		-DCMAKE_CXX_FLAGS="${CXXFLAGS}"
-		-DCMAKE_INSTALL_PREFIX="${EPREFIX}/${MY_PREFIX}"
-		-DDEFAULT_SYSROOT="${EPREFIX}"
-		-Dexplicitlink=ON
-		-Dexceptions=ON
-		-Dfail-on-missing=ON
-		-Dshared=ON
-		-Dsoversion=ON
-		-Dbuiltin_llvm=ON
-		-Dbuiltin_afterimage=OFF
-		-Dbuiltin_cfitsio=OFF
-		-Dbuiltin_davix=OFF
-		-Dbuiltin_fftw3=OFF
-		-Dbuiltin_freetype=OFF
-		-Dbuiltin_ftgl=OFF
-		-Dbuiltin_gl2ps=OFF
-		-Dbuiltin_glew=OFF
-		-Dbuiltin_gsl=OFF
-		-Dbuiltin_lz4=OFF
-		-Dbuiltin_lzma=OFF
-		-Dbuiltin_openssl=OFF
-		-Dbuiltin_pcre=OFF
-		-Dbuiltin_tbb=OFF
-		-Dbuiltin_unuran=OFF
-		-Dbuiltin_vc=OFF
-		-Dbuiltin_vdt=OFF
-		-Dbuiltin_veccore=OFF
-		-Dbuiltin_xrootd=OFF
-		-Dbuiltin_xxhash=OFF
-		-Dbuiltin_zlib=OFF
-		-Dx11=$(usex X)
-		-Dxft=$(usex X)
-		-Dafdsmgrd=OFF
-		-Dafs=OFF # option not implemented
-		-Dalien=OFF
-		-Dasimage=$(usex asimage)
-		-Dastiff=$(usex tiff)
-		-Dbonjour=$(usex avahi)
-		-Dccache=OFF # use ccache via portage
-		-Dcastor=OFF
-		-Dchirp=OFF
-		# -Dcling=ON # cling=OFF is broken
-		-Dcocoa=$(usex aqua)
-		-Dcxx14=$(usex root7)
-		# -Dcxxmodules=OFF # use clang C++ modules
-		-Ddavix=$(usex davix)
-		-Ddcache=OFF # not in Gentoo
-		-Dfftw3=$(usex fftw)
-		-Dfitsio=$(usex fits)
-		-Dfortran=$(usex fortran)
-		-Dftgl=$(usex opengl)
-		-Dgdml=$(usex gdml)
-		-Dgl2ps=$(usex opengl)
-		-Dgeocad=OFF # default OFF
-		-Dgenvector=$(usex math) # default ON
-		-Dgfal=OFF # not in Gentoo
-		-Dglite=OFF # option not implemented
-		-Dglobus=OFF
-		-Dgminimal=OFF
-		-Dgnuinstall=OFF
-		-Dgsl_shared=$(usex gsl)
-		-Dgviz=$(usex graphviz)
-		-Dhdfs=OFF # deps not in Gentoo
-		-Dhttp=$(usex http)
-		-Dimt=$(usex tbb)
-		-Djemalloc=$(usex jemalloc)
-		-Dkrb5=$(usex kerberos)
-		-Dldap=$(usex ldap)
-		-Dlibcxx=$(usex libcxx)
-		-Dmathmore=$(usex math)
-		-Dmemstat=$(usex memstat)
-		#-Dminimal=$(usex minimal) # default OFF
-		-Dminuit=$(usex minuit)
-		-Dminuit2=$(usex minuit)
-		-Dmonalisa=OFF # not in Gentoo
-		-Dmysql=$(usex mysql)
-		-Dodbc=$(usex odbc)
-		-Dopengl=$(usex opengl)
-		-Doracle=$(usex oracle)
-		# -Dpch=$(usex pch) # needs cling
-		-Dpgsql=$(usex postgres)
-		-Dpythia6=$(usex pythia6)
-		-Dpythia8=$(usex pythia8)
-		-Dpython=$(usex python)
-		-Dqt=$(usex qt4)
-		-Dqtgsi=$(usex qt4)
-		-Dr=$(usex R) # requires Rcpp and RInside
-		-Drfio=OFF
-		-Droofit=$(usex roofit)
-		-Droot7=$(usex root7) # requires C++14
-		-Droottest=OFF # requires network
-		-Drpath=$(usex prefix)
-		-Druby=OFF # unmantained upstream
-		# -Druntime_cxxmodules=OFF # use clang C++ modules
-		-Dsapdb=OFF # option not implemented
-		-Dshadowpw=$(usex shadow)
-		-Dsqlite=$(usex sqlite)
-		-Dsrp=OFF # option not implemented
-		-Dssl=$(usex ssl)
-		-Dtable=$(usex table)
-		-Dtbb=$(usex tbb)
-		-Dtcmalloc=OFF
-		-Dtesting=$(usex test)
-		-Dthread=$(usex threads)
-		-Dtmva=$(usex tmva)
-		-Dunuran=$(usex unuran)
-		-Dvc=$(usex vc)
-		-Dvdt=OFF # not in Gentoo
-		# -Dveccore=OFF # not in Gentoo
-		-Dxml=$(usex xml) # default ON
-		-Dxrootd=$(usex xrootd) # default ON
-		${EXTRA_ECONF}
-	)
-
-	cmake-utils_src_configure
-}
-
-daemon_install() {
-	local daemons="rootd proofd"
-	dodir /var/spool/rootd
-	fowners rootd:rootd /var/spool/rootd
-	dodir /var/spool/rootd/{pub,tmp}
-	fperms 1777 /var/spool/rootd/{pub,tmp}
-	keepdir /var/spool/rootd/{pub,tmp}
-
-	local i
-	for i in ${daemons}; do
-		newinitd "${FILESDIR}"/${i}.initd ${i}
-		newconfd "${FILESDIR}"/${i}.confd ${i}
-	done
-	if use xinetd; then
-		insinto /etc/xinetd
-		doins "${BUILD_DIR}"/etc/daemons/{rootd,proofd}.xinetd
-	fi
-}
-
-desktop_install() {
-	pushd "${S}" > /dev/null
-	echo "Icon=root-system-bin" >> etc/root.desktop
-	domenu etc/root.desktop
-	doicon build/package/debian/root-system-bin.png
-
-	insinto /usr/share/icons/hicolor/48x48/mimetypes
-	doins build/package/debian/application-x-root.png
-
-	insinto /usr/share/icons/hicolor/48x48/apps
-	doicon build/package/debian/root-system-bin.xpm
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	# root fails without this symlink, because it looks only into lib
-	[[ -d lib ]] || dosym $(get_libdir) /${MY_PREFIX}/lib
-
-	use emacs && elisp-install ${PN} "${BUILD_DIR}"/root-help.el
-
-	echo "PATH=${EPREFIX}/${MY_PREFIX}/bin" > 99root || die
-	echo "ROOTPATH=${EPREFIX}/${MY_PREFIX}/bin" >> 99root || die
-	echo "LDPATH=${EPREFIX}/${MY_PREFIX}/$(get_libdir)" >> 99root || die
-
-	if use pythia8; then
-		echo "PYTHIA8=${EPREFIX}/usr" >> 99root || die
-	fi
-
-	if use python; then
-		echo "PYTHONPATH=${EPREFIX}/${MY_PREFIX}/lib" >> 99root
-		python_optimize "${ED}/${MY_PREFIX}/lib"
-	fi
-
-	doenvd 99root
-
-	daemon_install
-	desktop_install
-
-	pushd "${ED}" > /dev/null
-	rm -r ${MY_PREFIX}/{config,emacs,etc/vmc,fonts} || die
-
-	if ! use examples; then
-		rm -r ${MY_PREFIX}/{test,tutorials} || die
-	fi
-
-	if use tmva; then
-		rm -r ${MY_PREFIX}/tmva || die
-	fi
-
-	# do not copress files used by ROOT's CLI (.credit, .demo, .license)
-	docompress -x "${MY_PREFIX}/README/CREDITS"
-	use examples && docompress -x "${MY_PREFIX}/tutorials"
-}
-
-pkg_postinst() {
-	xdg_desktop_database_update
-	gnome2_icon_cache_update
-}
-
-pkg_postrm() {
-	xdg_desktop_database_update
-	gnome2_icon_cache_update
-}
diff --git a/sci-physics/root/root-6.12.06-r4.ebuild b/sci-physics/root/root-6.12.06-r5.ebuild
index 151a9f60739f..3d0a62781de4 100644
--- a/sci-physics/root/root-6.12.06-r4.ebuild
+++ b/sci-physics/root/root-6.12.06-r5.ebuild
@@ -19,7 +19,7 @@ SRC_URI="https://root.cern/download/${PN}_v${PV}.source.tar.gz"
 IUSE="+X avahi aqua +asimage +davix emacs +examples fits fftw fortran
 	+gdml graphviz +gsl http jemalloc kerberos ldap libcxx memstat
 	+minuit mysql odbc +opengl oracle postgres prefix pythia6 pythia8
-	+python qt4 qt5 R +roofit root7 shadow sqlite +ssl table +tbb test
+	+python qt5 R +roofit root7 shadow sqlite +ssl table +tbb test
 	+threads +tiff +tmva +unuran vc xinetd +xml xrootd"
 
 SLOT="$(ver_cut 1-2)/$(ver_cut 3)"
@@ -27,10 +27,11 @@ LICENSE="LGPL-2.1 freedist MSttfEULA LGPL-3 libpng UoI-NCSA"
 KEYWORDS="~amd64 ~x86"
 
 REQUIRED_USE="
-	!X? ( !asimage !opengl !qt4 !qt5 !tiff )
+	!X? ( !asimage !opengl !qt5 !tiff )
+	davix? ( ssl xml )
 	python? ( ${PYTHON_REQUIRED_USE} )
+	qt5? ( root7 )
 	tmva? ( gsl )
-	davix? ( ssl xml )
 "
 
 CDEPEND="
@@ -56,10 +57,6 @@ CDEPEND="
 			virtual/glu
 			x11-libs/gl2ps:0=
 		)
-		qt4? (
-			dev-qt/qtcore:4=
-			dev-qt/qtgui:4=
-		)
 		qt5? (
 			dev-qt/qtcore:5=
 			dev-qt/qtgui:5=
@@ -233,8 +230,8 @@ src_configure() {
 		-Dpythia8=$(usex pythia8)
 		-Dpython=$(usex python)
 		-Dqt5web=$(usex qt5)
-		-Dqtgsi=$(usex qt4)
-		-Dqt=$(usex qt4)
+		-Dqtgsi=OFF
+		-Dqt=OFF
 		-Drfio=OFF
 		-Droofit=$(usex roofit)
 		-Droot7=$(usex root7)
diff --git a/sci-physics/root/root-6.14.02.ebuild b/sci-physics/root/root-6.14.04.ebuild
index 4d725bd70a50..e34bbf30b94e 100644
--- a/sci-physics/root/root-6.14.02.ebuild
+++ b/sci-physics/root/root-6.14.04.ebuild
@@ -9,17 +9,17 @@ CMAKE_MAKEFILE_GENERATOR=emake
 FORTRAN_NEEDED="fortran"
 PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
 
-inherit cmake-utils eapi7-ver elisp-common eutils fortran-2 \
+inherit cmake-utils cuda eapi7-ver elisp-common eutils fortran-2 \
 	prefix python-single-r1 toolchain-funcs
 
 DESCRIPTION="C++ data analysis framework and interpreter from CERN"
 HOMEPAGE="https://root.cern"
 SRC_URI="https://root.cern/download/${PN}_v${PV}.source.tar.gz"
 
-IUSE="+X avahi aqua +asimage +davix emacs +examples fits fftw fortran
+IUSE="+X avahi aqua +asimage cuda +davix emacs +examples fits fftw fortran
 	+gdml graphviz +gsl http jemalloc kerberos ldap libcxx memstat
 	+minuit mysql odbc +opengl oracle postgres prefix pythia6 pythia8
-	+python qt4 qt5 R +roofit root7 shadow sqlite +ssl table +tbb test
+	+python qt5 R +roofit root7 shadow sqlite +ssl table +tbb test
 	+threads +tiff +tmva +unuran vc xinetd +xml xrootd"
 
 SLOT="$(ver_cut 1-2)/$(ver_cut 3)"
@@ -27,10 +27,11 @@ LICENSE="LGPL-2.1 freedist MSttfEULA LGPL-3 libpng UoI-NCSA"
 KEYWORDS="~amd64 ~x86"
 
 REQUIRED_USE="
-	!X? ( !asimage !opengl !qt4 !qt5 !tiff )
+	!X? ( !asimage !opengl !qt5 !tiff )
+	davix? ( ssl xml )
 	python? ( ${PYTHON_REQUIRED_USE} )
+	qt5? ( root7 )
 	tmva? ( gsl )
-	davix? ( ssl xml )
 "
 
 CDEPEND="
@@ -56,10 +57,6 @@ CDEPEND="
 			virtual/glu
 			x11-libs/gl2ps:0=
 		)
-		qt4? (
-			dev-qt/qtcore:4=
-			dev-qt/qtgui:4=
-		)
 		qt5? (
 			dev-qt/qtcore:5=
 			dev-qt/qtgui:5=
@@ -71,6 +68,7 @@ CDEPEND="
 		>=x11-wm/afterstep-2.2.11[gif,jpeg,png,tiff?]
 	) )
 	avahi? ( net-dns/avahi[mdnsresponder-compat] )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-9.0 )
 	davix? ( net-libs/davix )
 	emacs? ( virtual/emacs )
 	fftw? ( sci-libs/fftw:3.0= )
@@ -157,6 +155,7 @@ src_configure() {
 		-Dshared=ON
 		-Dsoversion=ON
 		-Dbuiltin_llvm=ON
+		-Dbuiltin_clang=ON
 		-Dbuiltin_afterimage=OFF
 		-Dbuiltin_cfitsio=OFF
 		-Dbuiltin_davix=OFF
@@ -192,6 +191,7 @@ src_configure() {
 		-Dchirp=OFF
 		-Dcling=ON # cling=OFF is broken
 		-Dcocoa=$(usex aqua)
+		-Dcuda=$(usex cuda)
 		-Dcxx14=$(usex root7)
 		-Dcxxmodules=OFF # requires clang, unstable
 		-Ddavix=$(usex davix)
@@ -232,14 +232,14 @@ src_configure() {
 		-Dpythia8=$(usex pythia8)
 		-Dpython=$(usex python)
 		-Dqt5web=$(usex qt5)
-		-Dqtgsi=$(usex qt4)
-		-Dqt=$(usex qt4)
+		-Dqtgsi=OFF
+		-Dqt=OFF
 		-Drfio=OFF
 		-Droofit=$(usex roofit)
 		-Droot7=$(usex root7)
 		-Drootbench=OFF
 		-Droottest=$(usex test)
-		# -Drpath=ON # needed for multi-slot to work
+		-Drpath=OFF
 		-Druby=OFF # deprecated and broken
 		-Druntime_cxxmodules=OFF # does not work yet
 		-Dr=$(usex R)
@@ -253,9 +253,9 @@ src_configure() {
 		-Dtcmalloc=OFF
 		-Dtesting=$(usex test)
 		-Dthread=$(usex threads)
-		-Dtmva-cpu=$(usex tmva)
-		-Dtmva-gpu=OFF
 		-Dtmva=$(usex tmva)
+		-Dtmva-cpu=$(usex tmva)
+		-Dtmva-gpu=$(usex cuda)
 		-Dunuran=$(usex unuran)
 		-Dvc=$(usex vc)
 		-Dvdt=OFF
diff --git a/sci-physics/root/root-9999.ebuild b/sci-physics/root/root-9999.ebuild
index 9231a3e5261a..b9e470282f89 100644
--- a/sci-physics/root/root-9999.ebuild
+++ b/sci-physics/root/root-9999.ebuild
@@ -9,7 +9,7 @@ CMAKE_MAKEFILE_GENERATOR=emake
 FORTRAN_NEEDED="fortran"
 PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
 
-inherit cmake-utils eapi7-ver elisp-common eutils fortran-2 \
+inherit cmake-utils cuda eapi7-ver elisp-common eutils fortran-2 \
 	prefix python-single-r1 toolchain-funcs
 
 if [[ ${PV} == "9999" ]] ; then
@@ -26,19 +26,20 @@ fi
 DESCRIPTION="C++ data analysis framework and interpreter from CERN"
 HOMEPAGE="https://root.cern"
 
-IUSE="+X avahi aqua +asimage +davix emacs +examples fits fftw fortran
+IUSE="+X avahi aqua +asimage cuda +davix emacs +examples fits fftw fortran
 	+gdml graphviz +gsl http jemalloc kerberos ldap libcxx memstat
 	+minuit mysql odbc +opengl oracle postgres prefix pythia6 pythia8
-	+python qt4 qt5 R +roofit root7 shadow sqlite +ssl table +tbb test
+	+python qt5 R +roofit root7 shadow sqlite +ssl table +tbb test
 	+threads +tiff +tmva +unuran vc xinetd +xml xrootd"
 
 LICENSE="LGPL-2.1 freedist MSttfEULA LGPL-3 libpng UoI-NCSA"
 
 REQUIRED_USE="
-	!X? ( !asimage !opengl !qt4 !qt5 !tiff )
+	!X? ( !asimage !opengl !qt5 !tiff )
+	davix? ( ssl xml )
 	python? ( ${PYTHON_REQUIRED_USE} )
+	qt5? ( root7 )
 	tmva? ( gsl )
-	davix? ( ssl xml )
 "
 
 CDEPEND="
@@ -65,10 +66,6 @@ CDEPEND="
 			virtual/glu
 			x11-libs/gl2ps:0=
 		)
-		qt4? (
-			dev-qt/qtcore:4=
-			dev-qt/qtgui:4=
-		)
 		qt5? (
 			dev-qt/qtcore:5=
 			dev-qt/qtgui:5=
@@ -80,6 +77,7 @@ CDEPEND="
 		>=x11-wm/afterstep-2.2.11[gif,jpeg,png,tiff?]
 	) )
 	avahi? ( net-dns/avahi[mdnsresponder-compat] )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-9.0 )
 	davix? ( net-libs/davix )
 	emacs? ( virtual/emacs )
 	fftw? ( sci-libs/fftw:3.0= )
@@ -201,6 +199,7 @@ src_configure() {
 		-Dchirp=OFF
 		-Dcling=ON # cling=OFF is broken
 		-Dcocoa=$(usex aqua)
+		-Dcuda=$(usex cuda)
 		-Dcxx14=$(usex root7)
 		-Dcxxmodules=OFF # requires clang, unstable
 		-Ddavix=$(usex davix)
@@ -242,8 +241,8 @@ src_configure() {
 		-Dpythia8=$(usex pythia8)
 		-Dpython=$(usex python)
 		-Dqt5web=$(usex qt5)
-		-Dqtgsi=$(usex qt4)
-		-Dqt=$(usex qt4)
+		-Dqtgsi=OFF
+		-Dqt=OFF
 		-Drfio=OFF
 		-Droofit=$(usex roofit)
 		-Droot7=$(usex root7)
@@ -263,9 +262,9 @@ src_configure() {
 		-Dtcmalloc=OFF
 		-Dtesting=$(usex test)
 		-Dthread=$(usex threads)
-		-Dtmva-cpu=$(usex tmva)
-		-Dtmva-gpu=OFF
 		-Dtmva=$(usex tmva)
+		-Dtmva-cpu=$(usex tmva)
+		-Dtmva-gpu=$(usex cuda)
 		-Dunuran=$(usex unuran)
 		-Dvc=$(usex vc)
 		-Dvdt=OFF
diff --git a/sci-physics/vgm/Manifest b/sci-physics/vgm/Manifest
index a1980489fcb8..da08439a03d2 100644
--- a/sci-physics/vgm/Manifest
+++ b/sci-physics/vgm/Manifest
@@ -1,4 +1,4 @@
 DIST vgm.4.4.tar.gz 3064087 BLAKE2B 845d04fa3ebaaa07f90ef7f216cac10e5ca4129ebbd6161e3fecce39663379b2575026186fe2b88ae8bf08f71bed6d8afcbbd5d7aa9922d37b3f9ed900d35a33 SHA512 500ae0e2ac66b580bbc26b6cd1a8bd6d6e3127c99e6fe6babe5825406e576d72da5cd76d22d0d1b82d7df9eb74ddddf084ee9a96b544c97af5b12cbf948d3406
-EBUILD vgm-4.4.ebuild 1503 BLAKE2B 6764a9390ab89da0acf288d84faa3d81a6e5625b297aa33a24672a8a485b16ab3c3520d1c01ce0f39234a4d9b6e594c8fd79db59639a2ee0a2aadf592d209f1d SHA512 c3303252cba3c9aa77d8cac84515cbed4cbe7e51e35f15af76c5093213727deff9c1efe09cb6511d7d8bcae2e16380b328bef916324ff4ab5e7a660de91f3609
-EBUILD vgm-9999.ebuild 1503 BLAKE2B 6764a9390ab89da0acf288d84faa3d81a6e5625b297aa33a24672a8a485b16ab3c3520d1c01ce0f39234a4d9b6e594c8fd79db59639a2ee0a2aadf592d209f1d SHA512 c3303252cba3c9aa77d8cac84515cbed4cbe7e51e35f15af76c5093213727deff9c1efe09cb6511d7d8bcae2e16380b328bef916324ff4ab5e7a660de91f3609
+EBUILD vgm-4.4.ebuild 1687 BLAKE2B 465f91a5943a39258201724d093dc5cefdf20fe5179c3215945f97bd8fea6b5b4c059daf9a8b652c604463bf3cdfce47c575814ad0db0112dc0e7588b1e807c6 SHA512 01dadc26e284d521c00cbeaa46ab1a3de612435c5e667e57d21f82b87bb9bb099a238c07a9b67bfb368edaa27447c265e666fd2330ebab867a8c15f496567be7
+EBUILD vgm-9999.ebuild 1597 BLAKE2B 52ec50d53da0b17a8e2a038dbe478a8a3ca283472209daf489e08228dc9778e4ae9a2ba6a9e270e63644c16177bdb4729ac29433a90e4b85c17c19a193f9771a SHA512 4df20b7c0874135222b0025e025c119d9cc5e556a49a7f3e8ba05c5455f2329c577b959dd8c229b54936a430962eecd3daec5e6af405d846fd17b05dfc76bbf4
 MISC metadata.xml 887 BLAKE2B 2bed4c9deeb9bbda28704462bf45eaf31d810b115608bd66ccdd8f5e8494556b87962301395d0f0cbf229aaf8d497b1f07b9821600d6c101aad34c5ef49cf643 SHA512 5e52d57dc9cc78020a147c4984aa037b3441f910f6288e75a3919398a0b22d16f312fd910bf0a692bfb039c3540f2854e4f2c660f7d3c4a4c23cbc63f9885dbf
diff --git a/sci-physics/vgm/vgm-4.4.ebuild b/sci-physics/vgm/vgm-4.4.ebuild
index c7202c3244e6..831f0cc0c4a2 100644
--- a/sci-physics/vgm/vgm-4.4.ebuild
+++ b/sci-physics/vgm/vgm-4.4.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=6
 
-inherit cmake-utils versionator
+inherit cmake-utils
 
 if [[ ${PV} == *9999* ]]; then
 	inherit git-r3
@@ -21,12 +21,18 @@ LICENSE="GPL-2"
 SLOT="0"
 IUSE="doc examples +geant4 +root test"
 
+# sci-physics/root[root7] flag activates std=c++14, only supported from VGM >4.4.
 RDEPEND="
 	sci-physics/clhep:=
-	root? ( sci-physics/root:= )
+	root? ( sci-physics/root:=[-root7] )
 	geant4? ( >=sci-physics/geant-4.10.03 )"
 DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen[dot] )"
+	doc? ( app-doc/doxygen[dot] )
+	test? ( sci-physics/geant-vmc[g4root] )"
+RESTRICT="
+	!geant4? ( test )
+	!root? ( test )
+	!test? ( test )"
 
 DOCS=(
 	doc/README
diff --git a/sci-physics/vgm/vgm-9999.ebuild b/sci-physics/vgm/vgm-9999.ebuild
index c7202c3244e6..b303e23a06c6 100644
--- a/sci-physics/vgm/vgm-9999.ebuild
+++ b/sci-physics/vgm/vgm-9999.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=6
 
-inherit cmake-utils versionator
+inherit cmake-utils
 
 if [[ ${PV} == *9999* ]]; then
 	inherit git-r3
@@ -26,7 +26,12 @@ RDEPEND="
 	root? ( sci-physics/root:= )
 	geant4? ( >=sci-physics/geant-4.10.03 )"
 DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen[dot] )"
+	doc? ( app-doc/doxygen[dot] )
+	test? ( sci-physics/geant-vmc[g4root] )"
+RESTRICT="
+	!geant4? ( test )
+	!root? ( test )
+	!test? ( test )"
 
 DOCS=(
 	doc/README