gentoo resync : 03.11.2018

12 files changed, 389 insertions, 88 deletions

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index 855abf45ecfa..58f845ed7c2a 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/geos/Manifest b/sci-libs/geos/Manifest
index 4598bef808ef..c0fd449c4079 100644
--- a/sci-libs/geos/Manifest
+++ b/sci-libs/geos/Manifest
@@ -2,5 +2,5 @@ AUX 3.4.2-solaris-isnan.patch 575 BLAKE2B 34e2fddd46e4e503630d0c44c03ee72ceb8bb1
 DIST geos-3.6.2.tar.bz2 2030705 BLAKE2B f23cf1fc080fb7b353fb6292900d84811ace04a5364200bfea19f79d7b09a795d36e30cd6e4dbb7acd8417245bc2ce644298dc1b4140ef70495e4f7d71fc522b SHA512 515d8700b8a28282678e481faee355e3a43d7b70160472a63335b8d7225d9ba10437be782378f18f31a15288118126d411a2d862f01ce35d27c96f6bc0a73016
 DIST geos-3.7.0.tar.bz2 2028814 BLAKE2B 17385d9be831d4812391a30627e13989d3ca099ca9b0a719a92cdb2503dadff3693d4b3d320652764185db05782b33760ca14d155365d87167bb4ef6d6c2463c SHA512 fcca5e503efa32bb388376b2a06b9ca5c74fbcddba750cce6b3b4109eb2eb122058aead12b9462cdd881f425cd75d7241645ab344f25ce022bc0659954560742
 EBUILD geos-3.6.2.ebuild 1342 BLAKE2B 2cdc55473a3c7e2f4cf45b77de88e3e359598e1b9a7f6ee33d221474853ad191c61692ed84b1648204fe71b4e8c3fec70710725a1f30f4c81c89c3607db6e51a SHA512 91f4a1f15927b151e2d7811410dfa3cf4ccee0a667751eb05f6ebdcaa12b2a8c38e0c6ce08018f22da7bb7220ac77846a5975d4dd439c230eb326718a03ea6ba
-EBUILD geos-3.7.0.ebuild 1341 BLAKE2B 63aea3f6575420ac79fff622b78a0163e50c869a834aae6cd1a3c0d4b987ad8cf828c134315c3614ded327cee90fe90ecc53fb8e125613b767de4ace789ed2a9 SHA512 11defd6dcdc8a34580a6c9b1b55a6dd6adf95a44882b13627b12b6e206979f3ade8938a40a4c06f6eb51146bd34fa8574d62323a2c9dc628b6e95c6bcd4b9d2b
+EBUILD geos-3.7.0.ebuild 1340 BLAKE2B 1aabe23b1bea2f7800b909c76c5bab28d94fe580d2df0ee48fb484ef328a92064df1a94c403de778414e64b620cb17f12155f7af74550a4a264d2b08fbd7bbf9 SHA512 2be4b6ab790c8cfddb5559924d9985c31bffdd6ee695433d0bd04ffdb7b854e810529a2a398f4114ef1b71430e1dc4086f2727cd988e7b3d152c58d548f0fcf7
 MISC metadata.xml 941 BLAKE2B 037cfbe59d6e841cfd50acce4eb41b58d1caf2459205cbb9432a1c2187a26196c09785665df2e8fd17498e672a1a66fb3d50f8bb8ced62e54bf963b821b93181 SHA512 cf93ad12e2e2d23ce6b454ae1032e8362beccd952a0f431780467c2985c07fa284edcb10a5d7b61d098a70c097f091a7f771be5a1650c1ed431ba249f73e5b1c
diff --git a/sci-libs/geos/geos-3.7.0.ebuild b/sci-libs/geos/geos-3.7.0.ebuild
index 0fff8e009461..8d66cd012ccd 100644
--- a/sci-libs/geos/geos-3.7.0.ebuild
+++ b/sci-libs/geos/geos-3.7.0.ebuild
@@ -13,7 +13,7 @@ SRC_URI="http://download.osgeo.org/geos/${P}.tar.bz2"
 
 LICENSE="LGPL-2.1"
 SLOT="0"
-KEYWORDS="~amd64 ~arm ~arm64 ia64 ppc ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris ~x64-solaris"
+KEYWORDS="amd64 ~arm ~arm64 ia64 ppc ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris ~x64-solaris"
 IUSE="doc python ruby static-libs"
 REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
 
diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 4c8cfa8cc490..7616be52568a 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,3 +1,5 @@
 DIST htslib-1.5.tar.bz2 1051132 BLAKE2B 90c6aeeaa2a2692228aa1f530d775a6e81f9275d321e8b2d6005b86b9a25e5967acca19dd898311a5bc4f3c17d4e8ea36d18da4602e18fadee47666350122077 SHA512 fd58552ddbd178f9797123fdaf47914ccd0e2aefd055fc6557ac8f479c600775616107cfa871c3acd93079f45974a19f443941a79f2acfd2a8c2983ef35b8917
+DIST htslib-1.9.tar.bz2 1178859 BLAKE2B a0229313d3572717101f4f23d39fa124f3bb38d8b2e65055f4f801dbb5f1549df95115e8beadd8fa024171b3ff8a874d20087bf71819c36700666f168dbe41ab SHA512 ddb0e2d970e4c2c27e203b064898f95cb7c187cd497c02fc7b4312dcea25669d0b6063d537687521e7a065f6daefa1ae897add2df4981037a187b499d08fdef7
 EBUILD htslib-1.5.ebuild 769 BLAKE2B 0a40bc1059beabd9671df35ea8febf7b5a11c8b46aa0f66891879962698789b36326fd91423200312497b2f9691766c1dc8aae5dceab5626a7e8de119881793a SHA512 e5df03c2dfa5088743674af125f7464a6e2add8d9c092060d7ddfc914cac4cff16d65eabb35ca3c199290461b92f7424a4347fded4f76dce763801b2b70f91c2
+EBUILD htslib-1.9.ebuild 945 BLAKE2B c198b14431fb321dd125fc344bdccd328b5d1943f08e5d691ad4343fba78637424f12a75498099ccf99aa46df479499ec528f2de737a7d9af668030593c6e860 SHA512 8d7d48327fea34bcb022b4b9ca28eb90fc019c50a4095ae7fbf4ea4ee5fdf1ae0f1f85996d250fd0f26862f1e18d5ea0377f02cdbb9906fa4d2f623d3f8ef36b
 MISC metadata.xml 349 BLAKE2B 0a67c5034cea0b990b01f90cf319622a73d2c8c23b89d207f013f1ac27fbfd2f267f4d0a8d331b9ab9de792cea9914671cfb2568a56fc09aeec890f69934e943 SHA512 9108691a0c4c68ececa5e93d1719b4a6fc42c423c0b7dca3c037007873a40c86a44610c54139c6868391bb903d509b0202a87640d7114815d07ef62e478ffce7
diff --git a/sci-libs/htslib/htslib-1.9.ebuild b/sci-libs/htslib/htslib-1.9.ebuild
new file mode 100644
index 000000000000..69df48a332f2
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.9.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2018 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
+
+SLOT="0/2"
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+bzip2 curl +lzma static-libs"
+
+RDEPEND="
+	bzip2? ( app-arch/bzip2:= )
+	curl? ( net-misc/curl )
+	lzma? ( app-arch/xz-utils:= )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	default
+
+	# upstream injects LDFLAGS into the .pc file,
+	# which is a big nono for QA
+	sed 's/private_LIBS=$LDFLAGS/private_LIBS=""/g' -i configure || die
+}
+
+src_configure() {
+	econf \
+		--disable-gcs \
+		--disable-plugins \
+		--disable-s3 \
+		$(use_enable bzip2 bz2) \
+		$(use_enable curl libcurl) \
+		$(use_enable lzma)
+}
+
+src_install() {
+	default
+
+	if ! use static-libs; then
+		find "${D}" -name '*.a' -delete || die
+	fi
+}
diff --git a/sci-libs/netcdf-cxx/Manifest b/sci-libs/netcdf-cxx/Manifest
index f220cce7f7c6..70cb298c9a3d 100644
--- a/sci-libs/netcdf-cxx/Manifest
+++ b/sci-libs/netcdf-cxx/Manifest
@@ -2,7 +2,7 @@ AUX netcdf-cxx-4.2-config.patch 829 BLAKE2B cd4285ce14647bc1822ac474b3a632fcacfb
 DIST netcdf-cxx-4.2.1.tar.gz 456547 BLAKE2B e973f064ad40c0d0cb76766f3b1639d16ed7eaae73d8e55db011645fc0d4e6f8949a60aeb9d47a4f8e88b3c5b2d486d42442e417908a2194b8b9a5e720ba2ff5 SHA512 d51ab1cbda74db5f7b074799d2407d0214d1c920af780ae3bb7a47b3708e45f721be7eec61902e035968a9df5019a7b2b5a10f236f6bab4cb47a26e4e7867adb
 DIST netcdf-cxx-4.2.tar.gz 703482 BLAKE2B a6727b7305204d2b53e6ee951c8165b03cd07f14e5d59a306445481272d0e10eb077e4bc62a2586c57652cb8273b9098ed77836f9023817d8a9e6ef51ac2cfe8 SHA512 347ddbc518ac2186868d69417342e5146e285fc3a88f7c55edc33063f5c9a6647af7e512a03b9b6a8f67a448b85a1edcdde5df707b893f6a1527821cfd78e643
 DIST netcdf-cxx-4.3.0.tar.gz 985897 BLAKE2B 89cfd85764ff8fc730c7cb4187df21a4245cd932bcf86df4edf36eb7ae636906eaafc25cfcbb3dd58bc1d346edacd7f80daa3be9a544d5d777d32ad115cfd00f SHA512 8e77333c979513721209e6b3fde31c298e18a45d7ea08123056e8120469eb8c4024d71289fab2b9182ee19ee7b6ad22bd133525bef048a497ede4aa2e9017465
-EBUILD netcdf-cxx-4.2-r300.ebuild 609 BLAKE2B 2a2b8c693ee9768726040db45196e04f50d02a7aa67aaa6ab62613d0ad947dfb2cf58a123bddf21d706e96d883665a36503ce9e3925580ad6417992cfb1815c8 SHA512 36eb7b2e20a8bb802510f7c9f17c4c94d36799c4e42ca449d57e455161c19465a2738897ace70672e1eab3fdc09e29dd21231075152db59148f1d8a378a9ed2d
+EBUILD netcdf-cxx-4.2-r300.ebuild 609 BLAKE2B 9e47eb431106ee5e8dd5401bc367b9208785f0588bd3e5fb7ba674a18b806cf212875ab10a5fd6d91971d73a9147ef113894e58cc9d6015e9bf5e509b0ef5de7 SHA512 0d3e37ec51bceb183f0efd2e7922e36922fb7a6c1a07f915efeb9fd967c57b4061ac7801c59ad5eac0a445125b7ac119a6e1977c469d66421d0f41b438e3b202
 EBUILD netcdf-cxx-4.2.1-r1.ebuild 725 BLAKE2B 894a989b391336811b680c3642a22c9449ea0e059ca5d95ad617985dcf9f9bc44de0d10882dacda16bdf00b67069d85d2e17aa6bc649dcbb34754eff7b024804 SHA512 f17fdf36f7234ad67e1a75787916dfe57ba3e074a96482901d016ac1d0aeb47d6e3d1e383e71b4292158374bb7939eec2b3a1f88e75f8064dd8c8737ea15f143
 EBUILD netcdf-cxx-4.2.1.ebuild 754 BLAKE2B a8defcffabafa13894b9ae70e3fb8d64a4e5eedec56336f9df961872b1b3bf0fea8dae7254adde67204905b547d8973ce978f7bd03b4152eab8f281ebc998b81 SHA512 cd2bade6d82df307186bb3a0bf5cdaee00798d222e843eb3e71943b3f67839543dccb309df7fec5feab37d32b83ba3186d771cf2aa9952a528962bc671c5b910
 EBUILD netcdf-cxx-4.3.0.ebuild 674 BLAKE2B 53ff5dd82a10f7ce78ced0f0e272a16a02ade44c6728107a8ba85892f479dd19987490f1f5672e390b0d257bb44e2b194d553a996de23c3719f3c4fcba6fab6c SHA512 7d7ec27fa8d1c787daec327f6dae8079e9fe704552b1f8d98cb7b31daff2eacacb913e99a4cded280113dec76d6aadad197d327c922f881318bc98745fe49dbd
diff --git a/sci-libs/netcdf-cxx/netcdf-cxx-4.2-r300.ebuild b/sci-libs/netcdf-cxx/netcdf-cxx-4.2-r300.ebuild
index 79fd2e1b0aa7..35eed157f022 100644
--- a/sci-libs/netcdf-cxx/netcdf-cxx-4.2-r300.ebuild
+++ b/sci-libs/netcdf-cxx/netcdf-cxx-4.2-r300.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -14,7 +14,7 @@ SLOT="3"
 KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux"
 IUSE="examples static-libs"
 
-RDEPEND=">=sci-libs/netcdf-4.2"
+RDEPEND=">=sci-libs/netcdf-4.2:0="
 DEPEND="${RDEPEND}"
 
 src_install() {
diff --git a/sci-libs/vtk/Manifest b/sci-libs/vtk/Manifest
index 90c09bb15e97..3177be830de3 100644
--- a/sci-libs/vtk/Manifest
+++ b/sci-libs/vtk/Manifest
@@ -24,5 +24,6 @@ EBUILD vtk-6.1.0-r4.ebuild 10480 BLAKE2B 72dc967f163fed46bcbe7dc0a2b4de89840c951
 EBUILD vtk-7.1.0.ebuild 9296 BLAKE2B 0fd4cb6ff13fe68d9a39bd686a18477fc0f8daad711910135448aacc96e06820251921263dc9517f400454fbdbda26ad5dc9633e98557b2246fe6e8658495537 SHA512 622eabfbb2a4b2c80a6254b09779f05b9354082402f3fead1010767c660b86c0e94413026a27bd06ea8eb7a07bea14d747db3bec51d9b5bf6ccb669d660d937f
 EBUILD vtk-8.1.0-r1.ebuild 9027 BLAKE2B 45d5ef5b8177e418424135b9ee70af8e4d681731584a595bb4108cdff1e8f3fe29f0293bd668fba67967dfcd4e9b7e26ae51e3dea92e72ed0bc7d4589c82597c SHA512 36a149ad672f38d48f767c4381bb04bc4054edd76776430d3157f034f4faf58ddaed43675c712e1d4787ae01f05ed8c2b64988dfb30392a43faeb6c37416d115
 EBUILD vtk-8.1.0-r2.ebuild 9037 BLAKE2B 8f8f89c3d158b826591eb07fe0250c16d0ba9dca9ea11011254152ac37b15bb840a815eb1bcb7b8a7c92524eb12f44d56a5ca16d91ca47b0d2797fa6e43db214 SHA512 5e0285464d4a41370a9e6586f9fb57fa6a1bebc2785f996c9a48d4066022f05103a7f233570cb729a79052a6684c51e682229376afab359b2c56bdbe52ad0a33
+EBUILD vtk-8.1.0-r3.ebuild 9057 BLAKE2B e5329bd6ed31f37152614d1e4773ed62a0eb92e9bfdecd0695dc57ebbf5c6cce9d0e5ab27a793774acabe9a9b9c4170ec579ccdf75fcbdc02e6666eafee2b6b2 SHA512 db6b2eea35c79c1ece9a0ce00dd5e9863eb3b312fd90101da5b7d216dcff2a365445d4f91fccdf49f176dfc626652a05da396c270dd27251db74b1cf69f08238
 EBUILD vtk-8.1.0.ebuild 9214 BLAKE2B 4705a1ba19eee614686234bb3297f70104fd1b050f51bfd3c16f2c01cc33f745d2fdcf70331dc060852923da8f319cbc554c9296e76d6a742215e3c31990b77d SHA512 34a8ab6760d0b3fbb25dbf9d2c4a9eb5507b7de777bcce509b8d80e92131290d31b747921a1cd0905001b4657c6eba68f6497b024f2ff70cecaa7bdacaccb11a
 MISC metadata.xml 1120 BLAKE2B 17456da598e4b7dfddec75a323def586e3b099ddfaa2e5883410afdd9143d317a6db53ead747b097cf8631f738d6a0b38a1e27ea37b445ba667a403053223e02 SHA512 d0d9ccd1922afe496e24d38fee05793fdf3983f798bef817a00c77bb632f2cabe3d2be554d0e979c223fd4005f3186b9ef78d394050539bd21cba5c2b6e56143
diff --git a/sci-libs/vtk/vtk-8.1.0-r3.ebuild b/sci-libs/vtk/vtk-8.1.0-r3.ebuild
new file mode 100644
index 000000000000..bfe60457d8c5
--- /dev/null
+++ b/sci-libs/vtk/vtk-8.1.0-r3.ebuild
@@ -0,0 +1,333 @@
+# Copyright 1999-2018 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python{2_7,3_5,3_6} )
+WEBAPP_OPTIONAL=yes
+WEBAPP_MANUAL_SLOT=yes
+
+inherit flag-o-matic java-pkg-opt-2 python-single-r1 qmake-utils versionator toolchain-funcs cmake-utils virtualx webapp
+
+# Short package version
+SPV="$(get_version_component_range 1-2)"
+
+DESCRIPTION="The Visualization Toolkit"
+HOMEPAGE="https://www.vtk.org/"
+SRC_URI="
+	https://www.vtk.org/files/release/${SPV}/VTK-${PV}.tar.gz
+	doc? ( https://www.vtk.org/files/release/${SPV}/vtkDocHtml-${PV}.tar.gz )
+	examples? (
+		https://www.vtk.org/files/release/${SPV}/VTKData-${PV}.tar.gz
+		https://www.vtk.org/files/release/${SPV}/VTKLargeData-${PV}.tar.gz
+	)"
+
+LICENSE="BSD LGPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+SLOT="0"
+IUSE="
+	all-modules aqua boost doc examples imaging ffmpeg gdal java json kaapi mpi
+	mysql odbc offscreen postgres python qt5 rendering tbb theora tk tcl
+	video_cards_nvidia views web R +X xdmf2"
+
+REQUIRED_USE="
+	all-modules? ( python xdmf2 boost )
+	java? ( qt5 )
+	python? ( ${PYTHON_REQUIRED_USE} )
+	tcl? ( rendering )
+	examples? ( python )
+	tk? ( tcl )
+	web? ( python )
+	^^ ( X aqua offscreen )"
+
+RDEPEND="
+	app-arch/lz4
+	dev-libs/expat
+	dev-libs/jsoncpp:=
+	dev-libs/libxml2:2
+	>=media-libs/freetype-2.5.4
+	>=media-libs/libharu-2.3.0-r2
+	media-libs/libpng:0=
+	media-libs/libtheora
+	media-libs/mesa
+	media-libs/tiff:0
+	sci-libs/exodusii
+	sci-libs/hdf5:=
+	sci-libs/netcdf:0=
+	sci-libs/netcdf-cxx:3
+	sys-libs/zlib
+	virtual/jpeg:0
+	virtual/opengl
+	x11-libs/libX11
+	x11-libs/libXmu
+	x11-libs/libXt
+	boost? ( dev-libs/boost:=[mpi?] )
+	examples? (
+		dev-qt/qtcore:5
+		dev-qt/qtgui:5
+	)
+	ffmpeg? ( virtual/ffmpeg )
+	gdal? ( sci-libs/gdal )
+	java? ( >=virtual/jdk-1.7:* )
+	kaapi? ( <sci-libs/xkaapi-3 )
+	mpi? (
+		virtual/mpi[cxx,romio]
+		python? ( dev-python/mpi4py[${PYTHON_USEDEP}] )
+	)
+	mysql? ( virtual/mysql )
+	odbc? ( dev-db/unixODBC )
+	offscreen? ( media-libs/mesa[osmesa] )
+	postgres? ( dev-db/postgresql:= )
+	python? (
+		${PYTHON_DEPS}
+		dev-python/sip[${PYTHON_USEDEP}]
+	)
+	qt5? (
+		dev-qt/designer:5
+		dev-qt/qtcore:5
+		dev-qt/qtgui:5
+		dev-qt/qtopengl:5
+		dev-qt/qtsql:5
+		dev-qt/qtwebkit:5
+		dev-qt/qtx11extras:5
+		python? ( dev-python/PyQt5[${PYTHON_USEDEP}] )
+	)
+	R? ( dev-lang/R )
+	tbb? ( dev-cpp/tbb )
+	tcl? ( dev-lang/tcl:0= )
+	tk? ( dev-lang/tk:0= )
+	video_cards_nvidia? ( x11-drivers/nvidia-drivers[tools,static-libs] )
+	web? (
+		${WEBAPP_DEPEND}
+		dev-python/autobahn[${PYTHON_USEDEP}]
+		dev-python/constantly[${PYTHON_USEDEP}]
+		dev-python/hyperlink[${PYTHON_USEDEP}]
+		dev-python/incremental[${PYTHON_USEDEP}]
+		dev-python/six[${PYTHON_USEDEP}]
+		dev-python/twisted[${PYTHON_USEDEP}]
+		dev-python/txaio[${PYTHON_USEDEP}]
+		dev-python/zope-interface[${PYTHON_USEDEP}]
+	)
+	xdmf2? ( sci-libs/xdmf2 )"
+DEPEND="${RDEPEND}
+	doc? ( app-doc/doxygen )"
+
+S="${WORKDIR}"/VTK-${PV}
+
+RESTRICT="test"
+
+pkg_setup() {
+	use java && java-pkg-opt-2_pkg_setup
+	use python && python-single-r1_pkg_setup
+	use web && webapp_pkg_setup
+}
+
+src_prepare() {
+	local x
+	# missing: VPIC freerange libproj4 mrmpi sqlite utf8 verdict xmdf2 xmdf3
+	for x in constantly expat freetype hdf5 hyperlink incremental jpeg jsoncpp libharu libxml2 lz4 netcdf oggtheora png tiff Twisted txaio zlib ZopeInterface; do
+		ebegin "Dropping bundled ${x}"
+		rm -r ThirdParty/${x}/vtk${x} || die
+		eend $?
+	done
+	rm -r \
+		ThirdParty/AutobahnPython/vtkAutobahn \
+		|| die
+
+	if use doc; then
+		einfo "Removing .md5 files from documents."
+		rm -f "${WORKDIR}"/html/*.md5 || die "Failed to remove superfluous hashes"
+		sed -e "s|\${VTK_BINARY_DIR}/Utilities/Doxygen/doc|${WORKDIR}|" \
+			-i Utilities/Doxygen/CMakeLists.txt || die
+	fi
+
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	# general configuration
+	local mycmakeargs=(
+		-Wno-dev
+		-DVTK_DIR="${S}"
+		-DVTK_INSTALL_LIBRARY_DIR=$(get_libdir)
+		-DVTK_INSTALL_DOC_DIR="${EPREFIX}/usr/share/doc/${PF}"
+		-DVTK_DATA_ROOT="${EPREFIX}/usr/share/${PN}/data"
+		-DVTK_CUSTOM_LIBRARY_SUFFIX=""
+		-DBUILD_SHARED_LIBS=ON
+		-DVTK_USE_SYSTEM_AUTOBAHN=ON
+		-DVTK_USE_SYSTEM_EXPAT=ON
+		-DVTK_USE_SYSTEM_FREETYPE=ON
+		-DVTK_USE_SYSTEM_FreeType=ON
+		# Use bundled gl2ps (bundled version is a patched version of 1.3.9. Post 1.3.9 versions should be compatible)
+		-DVTK_USE_SYSTEM_GL2PS=OFF
+		-DVTK_USE_SYSTEM_HDF5=ON
+		-DVTK_USE_SYSTEM_JPEG=ON
+		-DVTK_USE_SYSTEM_LIBPROJ4=OFF
+		-DVTK_USE_SYSTEM_LIBXML2=ON
+		-DVTK_USE_SYSTEM_LibXml2=ON
+		-DVTK_USE_SYSTEM_NETCDF=ON
+		-DVTK_USE_SYSTEM_OGGTHEORA=ON
+		-DVTK_USE_SYSTEM_PNG=ON
+		-DVTK_USE_SYSTEM_TIFF=ON
+		-DVTK_USE_SYSTEM_TWISTED=ON
+		-DVTK_USE_SYSTEM_XDMF2=OFF
+		-DVTK_USE_SYSTEM_XDMF3=OFF
+		-DVTK_USE_SYSTEM_ZLIB=ON
+		-DVTK_USE_SYSTEM_ZOPE=ON
+		-DVTK_USE_SYSTEM_LIBRARIES=ON
+		# Use bundled diy2 (no gentoo package / upstream does not provide a Finddiy2.cmake or diy2Config.cmake / diy2-config.cmake)
+		-DVTK_USE_SYSTEM_DIY2=OFF
+		-DVTK_USE_GL2PS=ON
+		-DVTK_USE_LARGE_DATA=ON
+		-DVTK_USE_PARALLEL=ON
+		-DVTK_EXTRA_COMPILER_WARNINGS=ON
+		-DVTK_Group_StandAlone=ON
+		-DBUILD_DOCUMENTATION=$(usex doc)
+		-DBUILD_EXAMPLES=$(usex examples)
+		-DBUILD_VTK_BUILD_ALL_MODULES_FOR_TESTS=off
+		-DVTK_BUILD_ALL_MODULES=$(usex all-modules)
+		-DUSE_DOCUMENTATION_HTML_HELP=$(usex doc)
+		-DVTK_Group_Imaging=$(usex imaging)
+		-DVTK_Group_MPI=$(usex mpi)
+		-DVTK_Group_Rendering=$(usex rendering)
+		-DVTK_Group_Tk=$(usex tk)
+		-DVTK_Group_Views=$(usex views)
+		-DVTK_Group_Web=$(usex web)
+		-DVTK_WWW_DIR="${ED%/}/${MY_HTDOCSDIR}"
+		-DVTK_WRAP_JAVA=$(usex java)
+		-DVTK_WRAP_PYTHON=$(usex python)
+		-DVTK_WRAP_PYTHON_SIP=$(usex python)
+		-DVTK_WRAP_TCL=$(usex tcl)
+		-DVTK_USE_BOOST=$(usex boost)
+		-DUSE_VTK_USE_BOOST=$(usex boost)
+		-DModule_vtkInfovisBoost=$(usex boost)
+		-DModule_vtkInfovisBoostGraphAlgorithms=$(usex boost)
+		-DVTK_USE_ODBC=$(usex odbc)
+		-DModule_vtkIOODBC=$(usex odbc)
+		-DVTK_USE_OFFSCREEN=$(usex offscreen)
+		-DVTK_OPENGL_HAS_OSMESA=$(usex offscreen)
+		-DVTK_USE_OGGTHEORA_ENCODER=$(usex theora)
+		-DVTK_USE_NVCONTROL=$(usex video_cards_nvidia)
+		-DModule_vtkFiltersStatisticsGnuR=$(usex R)
+		-DVTK_USE_X=$(usex X)
+	# IO
+		-DVTK_USE_FFMPEG_ENCODER=$(usex ffmpeg)
+		-DModule_vtkIOGDAL=$(usex gdal)
+		-DModule_vtkIOGeoJSON=$(usex json)
+		-DModule_vtkIOXdmf2=$(usex xdmf2)
+		-DBUILD_TESTING=$(usex examples)
+	# Apple stuff, does it really work?
+		-DVTK_USE_COCOA=$(usex aqua)
+	)
+
+	if use java; then
+		local javacargs=$(java-pkg_javac-args)
+		mycmakeargs+=( -DJAVAC_OPTIONS=${javacargs// /;} )
+	fi
+
+	if use kaapi; then
+		mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="Kaapi" )
+	elif use tbb; then
+		mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="TBB" )
+	else
+		mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="Sequential" )
+	fi
+
+	if use python; then
+		mycmakeargs+=(
+			-DVTK_INSTALL_PYTHON_MODULE_DIR="$(python_get_sitedir)"
+			-DPYTHON_INCLUDE_DIR="$(python_get_includedir)"
+			-DPYTHON_LIBRARY="$(python_get_library_path)"
+			-DSIP_PYQT_DIR="${EPREFIX}/usr/share/sip"
+			-DSIP_INCLUDE_DIR="$(python_get_includedir)"
+			-DVTK_PYTHON_INCLUDE_DIR="$(python_get_includedir)"
+			-DVTK_PYTHON_LIBRARY="$(python_get_library_path)"
+			-DVTK_PYTHON_SETUP_ARGS:STRING="--prefix=${EPREFIX} --root=${D}"
+			-DVTK_USE_SYSTEM_SIX=ON
+		)
+	fi
+
+	if use qt5; then
+		mycmakeargs+=(
+			-DVTK_USE_QVTK=ON
+			-DVTK_USE_QVTK_OPENGL=ON
+			-DVTK_USE_QVTK_QTOPENGL=ON
+			-DQT_WRAP_CPP=ON
+			-DQT_WRAP_UI=ON
+			-DVTK_INSTALL_QT_DIR="$(qt5_get_libdir)/qt5/plugins/designer"
+			-DDESIRED_QT_VERSION=5
+			-DVTK_QT_VERSION=5
+			-DQT_MOC_EXECUTABLE="$(qt5_get_bindir)/moc"
+			-DQT_UIC_EXECUTABLE="$(qt5_get_bindir)/uic"
+			-DQT_INCLUDE_DIR="${EPREFIX}/usr/include/qt5"
+			-DQT_QMAKE_EXECUTABLE="$(qt5_get_bindir)/qmake"
+			-DVTK_Group_Qt:BOOL=ON
+		)
+	fi
+
+	if use R; then
+		mycmakeargs+=(
+			-DR_LIBRARY_BLAS=/usr/$(get_libdir)/R/lib/libR.so
+			-DR_LIBRARY_LAPACK=/usr/$(get_libdir)/R/lib/libR.so
+		)
+	fi
+
+	append-cppflags -D__STDC_CONSTANT_MACROS -D_UNICODE
+
+	use java && export JAVA_HOME="${EPREFIX}/etc/java-config-2/current-system-vm"
+
+	if use mpi; then
+		export CC=mpicc
+		export CXX=mpicxx
+		export FC=mpif90
+		export F90=mpif90
+		export F77=mpif77
+	fi
+
+	cmake-utils_src_configure
+}
+
+src_install() {
+	use web && webapp_src_preinst
+
+	cmake-utils_src_install
+
+	use java && java-pkg_regjar "${ED%/}"/usr/$(get_libdir)/${PN}.jar
+
+	# Stop web page images from being compressed
+	use doc && docompress -x /usr/share/doc/${PF}/doxygen
+
+	if use tcl; then
+		# install Tcl docs
+		docinto vtk_tcl
+		dodoc Wrapping/Tcl/README
+		docinto .
+	fi
+
+	# install examples
+	if use examples; then
+		einfo "Installing examples"
+		mv -v {E,e}xamples || die
+		dodoc -r examples
+		docompress -x /usr/share/doc/${PF}/examples
+	fi
+
+	# environment
+	cat >> "${T}"/40${PN} <<- EOF || die
+		VTK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data
+		VTK_DIR=${EPREFIX}/usr/$(get_libdir)/${PN}-${SPV}
+		VTKHOME=${EPREFIX}/usr
+		EOF
+	doenvd "${T}"/40${PN}
+
+	use web && webapp_src_install
+}
+
+# webapp.eclass exports these but we want it optional #534036
+pkg_postinst() {
+	use web && webapp_pkg_postinst
+}
+
+pkg_prerm() {
+	use web && webapp_pkg_prerm
+}
diff --git a/sci-libs/xdmf2/Manifest b/sci-libs/xdmf2/Manifest
index 4f3898144366..66160288b2ff 100644
--- a/sci-libs/xdmf2/Manifest
+++ b/sci-libs/xdmf2/Manifest
@@ -3,6 +3,5 @@ AUX xdmf2-1.0_p141226-cmake-3.12.patch 422 BLAKE2B 904de870ce6e7cb9aaa4454dbecd4
 AUX xdmf2-1.0_p141226-module.patch 452 BLAKE2B 1611edbdf962ba25b72dab702044b7c7299abe5d92757c333827f08eb643fd17661739a4c0f7c0e759c516d9eeba794733145bdb03ef6779d1a9ef6e315fc5db SHA512 9a9e05001f1d8ea8250a7bb9231a43e8cceeface61fb125330b6255a1ba452650a80cb6592a69fdecc04212752c0d1fa195151b13c88262c40a36ca566a33dcd
 DIST xdmf2-1.0_p141226.tar.xz 267096 BLAKE2B 230ed73cc0521f04ff519c0050559ccf3837b915a196336de4b439cf05cae02220270a81290a6aac70e04095695b853e7de35613fba39cef6a90e93e6c99a3f9 SHA512 031b947ccd942c39cb40504e939f03bc9e3190ae1a7baf8325809decf70a040e860b43d5bc9debfcf2f3838f5f0d7a9c77c92561c89fc0d632306e140b136db9
 EBUILD xdmf2-1.0_p141226-r1.ebuild 1540 BLAKE2B fb84d09a0aa7082f90deb5ec8fffa003a409da6ed0318b33837473d1c61bbb9bce6793eeb92152efe4e5495e0baf255432170866764318218250b92b40052f92 SHA512 4758b233409d8979fe16e6c700528692c61784573613f74d154e99902e09b80bf37463558e96627b4e422bdcc98516aaf10066533465d9a0315c8f917c115115
-EBUILD xdmf2-1.0_p141226-r2.ebuild 1842 BLAKE2B 68a934b26e310b71f731dce6976e6cfed38748772c5901266d78cdfd329499cdab6da4f13643db97320de22c14eb52fe0fc3246caba714c1e2d8ab2b7c95a329 SHA512 2449dc11ade78c5675d468fc76843a4a61a9485bad1bcc07dcbcf56ed0c070d48f2ad0d6c5a5372ffffaf7c5ae626e062c95059f0766901d21e62f0d6aa379ab
-EBUILD xdmf2-1.0_p141226-r3.ebuild 1804 BLAKE2B d28284c7baea14314147481b2ddce3a27c80b0b71355e71f9a6930bac821113010c3d3e41d72e7926a7fa34ee116b971c58af5036509e9a3162580232965d445 SHA512 00a34db9765b2d20faeaf27f6b4c3ca086c5e4eb101c024f4f857aa021ffb4c5fd92ce2f9da4f3b996a60c0b09c4bc9c924f891fb8d5dd96bbb2fe5f02120557
+EBUILD xdmf2-1.0_p141226-r3.ebuild 1800 BLAKE2B 127b5fc924f917e410e0264a613a57fc7b481367ddf382eff184c5e8648f6e17fdd1edf37e57aef2073438d9a02ba24c530ffb08cd80a201592063c8dd672d71 SHA512 86fba3e44c93562df87a4a518cd0c720387d75e3d29a8b05ee483e8174872d6466e597fd6866321014a1825efba4f27e1bd4cd84732ee1dc446fea2b0c740537
 MISC metadata.xml 259 BLAKE2B dfc879984b6adce945d0e0a50f6ede2bca87147b9db99491359cdeccc2e74a20d56e14ae8903dbb80c94854f89bee539f14a4e3ce864204e277accf3f124a748 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706
diff --git a/sci-libs/xdmf2/xdmf2-1.0_p141226-r2.ebuild b/sci-libs/xdmf2/xdmf2-1.0_p141226-r2.ebuild
deleted file mode 100644
index 08550ddf6c16..000000000000
--- a/sci-libs/xdmf2/xdmf2-1.0_p141226-r2.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils flag-o-matic python-single-r1
-
-DESCRIPTION="eXtensible Data Model and Format"
-HOMEPAGE="http://xdmf.org/index.php/Main_Page"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
-
-SLOT="0"
-LICENSE="VTK"
-KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc python test"
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	dev-libs/boost:=
-	sci-libs/hdf5:=
-	dev-libs/libxml2:2
-	python? ( ${PYTHON_DEPS} )
-	"
-
-# TODO: fix builds for cmake 3.12+. See bug #661860
-DEPEND="${RDEPEND}
-	<=dev-util/cmake-3.12
-	doc? ( app-doc/doxygen )
-	python? ( dev-lang/swig:0 )
-"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-module.patch
-	"${FILESDIR}"/${P}-cannot-find-hdf5-bug-591302.patch
-)
-
-pkg_setup() {
-	use python && python-single-r1_pkg_setup && python_export
-}
-
-src_prepare() {
-	if use python; then
-		local _site=$(python_get_sitedir)
-		sed \
-			-e "/DESTINATION/s:python:${_site##${EPREFIX}/usr/$(get_libdir)/}:g" \
-			-i CMakeLists.txt || die
-	fi
-
-	sed \
-		-e "/DESTINATION/s:lib:$(get_libdir):g" \
-		-e "/INSTALL/s:lib:$(get_libdir):g" \
-		-i CMakeLists.txt core/CMakeLists.txt || die
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	# bug 619604
-	append-cxxflags -std=c++14
-
-	local mycmakeargs=(
-		-DBUILD_SHARED_LIBS=1
-		-DXDMF_BUILD_DOCUMENTATION=$(usex doc)
-		-DBUILD_TESTING=$(usex test)
-		-DXDMF_WRAP_PYTHON=$(usex python)
-#		-DXDMF_WRAP_JAVA=$(usex java)
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-	dosym XdmfConfig.cmake /usr/share/cmake/Modules/${PN}Config.cmake
-
-	# need to byte-compile 'XdmfCore.py' and 'Xdmf.py'
-	# as the CMake build system does not compile them itself
-	use python && python_optimize "${D%/}$(python_get_sitedir)"
-}
diff --git a/sci-libs/xdmf2/xdmf2-1.0_p141226-r3.ebuild b/sci-libs/xdmf2/xdmf2-1.0_p141226-r3.ebuild
index 205807de8ada..87f9c1e1fbb2 100644
--- a/sci-libs/xdmf2/xdmf2-1.0_p141226-r3.ebuild
+++ b/sci-libs/xdmf2/xdmf2-1.0_p141226-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -13,7 +13,7 @@ SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
 
 SLOT="0"
 LICENSE="VTK"
-KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~arm x86 ~amd64-linux ~x86-linux"
 IUSE="doc python test"
 REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"