gentoo resync : 10.04.2018

18 files changed, 379 insertions, 115 deletions

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index 92111c824b6a..38511ace4c93 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/avogadrolibs/Manifest b/sci-libs/avogadrolibs/Manifest
index fd0ff3c18502..c73b0ab3e9f9 100644
--- a/sci-libs/avogadrolibs/Manifest
+++ b/sci-libs/avogadrolibs/Manifest
@@ -1,5 +1,8 @@
 AUX avogadrolibs-0.7.2-6464.patch 902 BLAKE2B 29a06e0d5e814aee4c1aff30af3642e374d32813e4e9837706ef652f89ffde173ff043fc3589fc08b22592e3ded2c0d8ef9c544e54a561ac658ae43651403633 SHA512 3851a3c5f7c599e439b4faa491ea080264e60bf2a7c4d35e01a10726f901a5797026bf32535107b46ca44335c5723d9ec7f0b6a46e9eebf7ffd9f90c7f2103d3
-AUX avogadrolibs-0.8.0-underlinking.patch 1170 BLAKE2B 4edc41c544ca71fea851ac0248903234129fabe8fed1c1dff09f788702cebee28619736941f8c88363c987a6b0cf1fa7376e3ccdef1e0ae413dec31d93b6d4c9 SHA512 2520af361e250dc2459beec78d073686f44b41166cf81fd7c2a98e2ed30c5f20b5c910fb3808a56202420068043044900e7a504657506a12d16bd0acac87a466
-DIST avogadrolibs-0.9.0.tar.gz 742370 BLAKE2B cd104cea48b82a1ac86fdb9e93717e2647f57a0d713673d8b340d259f73d6d9985decf0c4e4d83f13d54d12ae2aefee8e75b5d04861f8ab67b9b42690c3c74f7 SHA512 7cb000cd6399f33483c38b4f8a9c4a4688f5054cba35e101bed0f2371cea614ace6b3fc65c3ed1418976afef4462a09be868500435a5ae9c98a7ac496c10c36f
-EBUILD avogadrolibs-0.9.0.ebuild 1399 BLAKE2B 912eda5882b0e2caa12d1684684c9d3d74579e51f645673ae99482438d6a57b8fdb847ceceed5709e56a742cdf4061fbff55627131d8a4666865129ed173a9b2 SHA512 321dff768e0ec9984630900adb06eea78f2d30f78da5f6ca53f1405d1aae6f24c4c7a2d0c4dc6d2abe9615e19221abd119baeb8bb8dbfa093ce684082a1b2cba
-MISC metadata.xml 561 BLAKE2B 92ca6dca915abd65a8b8a3b9a00bdc2314590839d4bf61e3991477f5e53abfb9c6075d4dbfb31b8c8bb3ae4bd822ab7fc4d68cd0cf612582e77a56efd4278a9b SHA512 20bee27014f13bcb3d1ca6addad61f4553fb77197c6113d65e71f97cbd6bda4a69e5db7f3ca12db41dc5d4afb09882bb89312a8e4babf5110957d6e86c1cbc81
+AUX avogadrolibs-1.91.0_pre20180406-bundled-genxrdpattern.patch 1644 BLAKE2B 3b25bc2648b323b803b5d0b6e10be2689ef9e4c988d0c55abe172bf4312da8f5f9b527262a2f8e48d0b2391b01a03a976bc36cc22c467ac9a44fb85cc43c7a6d SHA512 515c7029e6f99c5e88a37f43387e656b2873b99e14e8d8e9b1b20bf82604f70be8f669d8b97383e80969b0f80d43439647fdfd17566bbf6fbd32cb75ce2fb4e3
+AUX avogadrolibs-1.91.0_pre20180406-unbundle-jsoncpp.patch 5377 BLAKE2B 5de00cdcd90d7642ddb82aa8ae0e6685ad17c2a6332a4ef9ba28be66f48a6eabf51d557173a6129b588b9eafb394db74d332fc178b2a323d29777e88e37174a7 SHA512 b4445aa7377370fd1336b7fdf0aa3dfa93b6d538efa70ca383cdcf85d9f54e64a6bd0c2af5e0f5c80ed731d4babd4c2a1f7a4e909fb5cf2a30bf72224737870a
+AUX avogadrolibs-1.91.0_pre20180406-underlinking.patch 549 BLAKE2B e773e8994677a4cc0880013455efbe153ecdf92061599b787e3486638a6a2a0b5ebe731387a6f79357ff8f049c74b2a5efdeec0ed886b89e02f5160268dda4a2 SHA512 05d7ef99d1d5d395962def8896fb0c61ae437aeb0199ea8ce26a6076abba0559973aff5a4a4620f5c7dbe6413c80237490ad6b80f8a7503a8b2d3ae92f81fbf4
+DIST avogadrolibs-1.91.0_pre20180406.tar.gz 857345 BLAKE2B 8e5c6b0a838a2a6b7dc925c1b544ab4d4de8b7769b1fe8d787127a1014b1243da89a2a6f6cfc871181f81a443c3ee63d758369f003afaf591c9373c9d5122ee3 SHA512 1814b2105615aabc1df78b14c581e78fea20a1e4ace8979bb2ad123ab0994d90c3935e37f0cc58b60d3307ffe682599a93d8cadddc22b4ba524caaec1a2c5319
+DIST linux64-genXrdPattern 7480152 BLAKE2B dca8285c41aadfaa20c72f337e0f02db8ee07ce30c11ae84bf3aa7bd0b2220273d33f484d63f761d41a8946c6a0b77a0fb27906c480bcae01ae49b1531ae5cbb SHA512 538bde12e1e52600a21640d5907f43fcc853c6f3c111880f39eb238093e3d1358ccdfa1f45e944ec8b8e5ee3c2dff269cefe5334db5d73300e6ca327c95520b8
+EBUILD avogadrolibs-1.91.0_pre20180406.ebuild 2027 BLAKE2B 92fe377bed2c30b2eea8b4e67c9695fa19d61c6a8dceda0479f41fa9df10e077988b3c9249812d69221ed269df258f9a3bd864fb8a1e92126d63b6f6c9b8b6db SHA512 8e96e1b50e5c35346d6827d261ddb6f2483acba94b21d33c3638594442cf04582b9ed9c52f4e04e1f33ade1f4bdce3dc7651f3c5451edbac639ba7a813ceb128
+MISC metadata.xml 670 BLAKE2B 39737e6ffacaf9284506e41dfa1154f233a6bf37dd514c0eafe6bdf7bd7129a43d81cf4c3e510759b7888277bb403ad933e21abf0ba4dbedd43fda2aa2b55edd SHA512 781b3e67a291253d83d6c2e11124b07dbae652267de2702a1a2b10680f7db19cf35bda8964b320658d849091bd9ead07eeb5fc682a8817101dd1e7a1e9e20757
diff --git a/sci-libs/avogadrolibs/avogadrolibs-0.9.0.ebuild b/sci-libs/avogadrolibs/avogadrolibs-0.9.0.ebuild
deleted file mode 100644
index ea71fa95ce6e..000000000000
--- a/sci-libs/avogadrolibs/avogadrolibs-0.9.0.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Advanced molecule editor and visualizer 2 - libraries"
-HOMEPAGE="http://www.openchemistry.org/"
-SRC_URI="https://github.com/OpenChemistry/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD GPL-2+"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc hdf5 opengl qt5 static-plugins test vtk"
-
-REQUIRED_USE="qt5? ( opengl )"
-
-RDEPEND="
-	>=sci-chemistry/molequeue-0.7
-	sci-libs/chemkit
-	hdf5? ( sci-libs/hdf5:= )
-	opengl? (
-		dev-qt/qtopengl:5
-		media-libs/glew
-	)
-	qt5? (
-		dev-qt/qtconcurrent:5
-		dev-qt/qtcore:5
-		dev-qt/qtgui:5
-		dev-qt/qtnetwork:5
-		dev-qt/qtwidgets:5
-	)
-	vtk? ( sci-libs/vtk )
-"
-DEPEND="${DEPEND}
-	dev-cpp/eigen:3
-	test? ( dev-cpp/gtest )"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-0.7.2-6464.patch
-	"${FILESDIR}/"${PN}-0.8.0-underlinking.patch
-)
-
-src_configure() {
-	local mycmakeargs=(
-		-DUSE_PROTOCALL=OFF
-		-DBUILD_GPL_PLUGINS=ON
-		-DUSE_MOLEQUEUE=ON
-		-DUSE_HDF5=$(usex hdf5)
-		-DBUILD_DOCUMENTATION=$(usex doc)
-		-DUSE_OPENGL=$(usex opengl)
-		-DUSE_QT=$(usex qt5)
-		-DBUILD_STATIC_PLUGINS=$(usex static-plugins)
-		-DENABLE_TESTING=$(usex test)
-		-DUSE_VTK=$(usex vtk)
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	# TODO: bundles jsoncpp
-	rm "${ED%/}"/usr/lib64/libjsoncpp.a || die
-}
diff --git a/sci-libs/avogadrolibs/avogadrolibs-1.91.0_pre20180406.ebuild b/sci-libs/avogadrolibs/avogadrolibs-1.91.0_pre20180406.ebuild
new file mode 100644
index 000000000000..f7417ab49bf5
--- /dev/null
+++ b/sci-libs/avogadrolibs/avogadrolibs-1.91.0_pre20180406.ebuild
@@ -0,0 +1,82 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+COMMIT=f414794a168712f72884cdcfba818def5f42e721
+inherit cmake-utils
+
+DESCRIPTION="Advanced molecule editor and visualizer 2 - libraries"
+HOMEPAGE="https://www.openchemistry.org/"
+SRC_URI="https://github.com/OpenChemistry/${PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz
+	vtk? ( https://github.com/psavery/genXrdPattern/releases/download/1.0-static/linux64-genXrdPattern )"
+
+SLOT="0"
+LICENSE="BSD GPL-2+"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="archive doc hdf5 qt5 static-plugins test vtk"
+
+REQUIRED_USE="vtk? ( qt5 )"
+
+# TODO: Not yet packaged:
+# sci-libs/libmsym (https://github.com/mcodev31/libmsym)
+# sci-libs/spglib (https://atztogo.github.io/spglib/)
+RDEPEND="
+	dev-libs/jsoncpp:=
+	>=sci-chemistry/molequeue-0.7
+	archive? ( app-arch/libarchive )
+	hdf5? ( sci-libs/hdf5:= )
+	qt5? (
+		dev-qt/qtconcurrent:5
+		dev-qt/qtcore:5
+		dev-qt/qtgui:5
+		dev-qt/qtnetwork:5
+		dev-qt/qtwidgets:5
+		media-libs/glew:0=
+		virtual/opengl
+	)
+	vtk? ( sci-libs/vtk[qt5] )
+"
+DEPEND="${RDEPEND}
+	dev-cpp/eigen:3
+	test? ( dev-cpp/gtest )"
+
+S="${WORKDIR}/${PN}-${COMMIT}"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-0.7.2-6464.patch
+	"${FILESDIR}/"${P}-underlinking.patch
+	"${FILESDIR}/"${P}-unbundle-jsoncpp.patch
+	"${FILESDIR}/"${P}-bundled-genxrdpattern.patch
+)
+
+src_unpack() {
+	unpack ${P}.tar.gz
+	if use vtk; then
+		cp "${DISTDIR}"/linux64-genXrdPattern "${WORKDIR}/genXrdPattern" || die
+	fi
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_PROTOCALL=OFF
+		-DBUILD_GPL_PLUGINS=ON
+		-DUSE_MOLEQUEUE=ON
+		-DUSE_LIBMSYM=OFF
+		-DUSE_LIBSPG=OFF
+		-DUSE_PYTHON=OFF
+		-DUSE_LIBARCHIVE=$(usex archive)
+		-DBUILD_DOCUMENTATION=$(usex doc)
+		-DUSE_HDF5=$(usex hdf5)
+		-DUSE_OPENGL=$(usex qt5)
+		-DUSE_QT=$(usex qt5)
+		-DBUILD_STATIC_PLUGINS=$(usex static-plugins)
+		-DENABLE_TESTING=$(usex test)
+		-DUSE_VTK=$(usex vtk)
+	)
+	use vtk && mycmakeargs+=(
+		-DBUNDLED_GENXRDPATTERN="${WORKDIR}/genXrdPattern"
+	)
+
+	cmake-utils_src_configure
+}
diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-0.8.0-underlinking.patch b/sci-libs/avogadrolibs/files/avogadrolibs-0.8.0-underlinking.patch
deleted file mode 100644
index b29f3afe7613..000000000000
--- a/sci-libs/avogadrolibs/files/avogadrolibs-0.8.0-underlinking.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-Fix underlinking problems in shared libraries.
-
---- avogadrolibs-0.8.0/avogadro/qtplugins/apbs/CMakeLists.txt
-+++ avogadrolibs-0.8.0/avogadro/qtplugins/apbs/CMakeLists.txt
-@@ -23,4 +23,4 @@
-   "${apbs_uis}"
- )
- 
--target_link_libraries(apbs LINK_PRIVATE AvogadroIO MoleQueueClient)
-+target_link_libraries(apbs LINK_PRIVATE AvogadroIO MoleQueueClient AvogadroMoleQueue)
---- avogadrolibs-0.8.0/avogadro/qtplugins/playertool/CMakeLists.txt
-+++ avogadrolibs-0.8.0/avogadro/qtplugins/playertool/CMakeLists.txt
-@@ -7,3 +7,5 @@
-   ""
-   playertool.qrc
- )
-+
-+target_link_libraries(PlayerTool LINK_PRIVATE Qt5OpenGL)
---- avogadrolibs-0.8.0/avogadro/qtplugins/povray/CMakeLists.txt
-+++ avogadrolibs-0.8.0/avogadro/qtplugins/povray/CMakeLists.txt
-@@ -8,3 +8,5 @@
-   "povray.cpp"
-   ""
- )
-+
-+target_link_libraries(POVRay LINK_PRIVATE AvogadroRendering)
---- avogadrolibs-0.8.0/avogadro/qtplugins/qtaim/CMakeLists.txt
-+++ avogadrolibs-0.8.0/avogadro/qtplugins/qtaim/CMakeLists.txt
-@@ -34,3 +34,5 @@
- 
- target_link_libraries(QTAIMScenePlugin
-   LINK_PRIVATE AvogadroRendering ${Qt5Concurrent_LIBRARIES})
-+target_link_libraries(QTAIMExtension
-+  LINK_PRIVATE ${Qt5Concurrent_LIBRARIES})
diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-bundled-genxrdpattern.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-bundled-genxrdpattern.patch
new file mode 100644
index 000000000000..2072b8fa9b66
--- /dev/null
+++ b/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-bundled-genxrdpattern.patch
@@ -0,0 +1,44 @@
+From 0287e83eb8706f5237d66873cb6a1b3730891c07 Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner <andreas.sturmlechner@gmail.com>
+Date: Sun, 8 Apr 2018 11:21:17 +0200
+Subject: [PATCH] Provide overrideable BUNDLED_GENXRDPATTERN location
+
+---
+ cmake/DownloadGenXrdPattern.cmake | 10 +++++++---
+ 1 file changed, 7 insertions(+), 3 deletions(-)
+
+diff --git a/cmake/DownloadGenXrdPattern.cmake b/cmake/DownloadGenXrdPattern.cmake
+index ab5c5f0..7d4ecb4 100644
+--- a/cmake/DownloadGenXrdPattern.cmake
++++ b/cmake/DownloadGenXrdPattern.cmake
+@@ -10,8 +10,12 @@ macro(DownloadGenXrdPattern)
+     set(GENXRDPATTERN_NAME "genXrdPattern")
+   endif(WIN32)
+ 
++  if(NOT BUNDLED_GENXRDPATTERN)
++    set(BUNDLED_GENXRDPATTERN "${CMAKE_CURRENT_BINARY_DIR}/bin/${GENXRDPATTERN_NAME}")
++  endif()
++
+   # If it already exists, don't download it again
+-  if(NOT EXISTS "${CMAKE_CURRENT_BINARY_DIR}/bin/${GENXRDPATTERN_NAME}")
++  if(NOT EXISTS "${BUNDLED_GENXRDPATTERN}")
+     set(GENXRDPATTERN_V "1.0-static")
+     # Linux
+     if(UNIX AND NOT APPLE)
+@@ -52,11 +56,11 @@ macro(DownloadGenXrdPattern)
+     # Now remove the temporary directory
+     file(REMOVE_RECURSE "${CMAKE_CURRENT_BINARY_DIR}/tmp")
+ 
+-  endif(NOT EXISTS "${CMAKE_CURRENT_BINARY_DIR}/bin/${GENXRDPATTERN_NAME}")
++  endif(NOT EXISTS "${BUNDLED_GENXRDPATTERN}")
+ 
+   set(GENXRDPATTERN_DESTINATION "bin")
+ 
+-  install(FILES "${CMAKE_CURRENT_BINARY_DIR}/bin/${GENXRDPATTERN_NAME}"
++  install(FILES "${BUNDLED_GENXRDPATTERN}"
+           DESTINATION "${GENXRDPATTERN_DESTINATION}"
+           PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE
+                       GROUP_READ GROUP_EXECUTE
+-- 
+2.17.0
+
diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-unbundle-jsoncpp.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-unbundle-jsoncpp.patch
new file mode 100644
index 000000000000..3b5280cdc47e
--- /dev/null
+++ b/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-unbundle-jsoncpp.patch
@@ -0,0 +1,143 @@
+From 7e01a11dde25af75b21090fdaa2ca574ef703e53 Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner <andreas.sturmlechner@gmail.com>
+Date: Sun, 8 Apr 2018 01:48:27 +0200
+Subject: [PATCH 1/2] Drop bogus jsoncpp.cpp include from spectra.cpp
+
+---
+ avogadro/qtplugins/spectra/spectra.cpp | 2 --
+ 1 file changed, 2 deletions(-)
+
+diff --git a/avogadro/qtplugins/spectra/spectra.cpp b/avogadro/qtplugins/spectra/spectra.cpp
+index 043b52e..aa9c641 100644
+--- a/avogadro/qtplugins/spectra/spectra.cpp
++++ b/avogadro/qtplugins/spectra/spectra.cpp
+@@ -26,8 +26,6 @@
+ #include <QtWidgets/QFileDialog>
+ #include <avogadro/qtgui/molecule.h>
+ 
+-#include <jsoncpp.cpp>
+-
+ namespace Avogadro {
+ namespace QtPlugins {
+ 
+-- 
+2.17.0
+
+
+From 52cd35662aa2094db77ab4002b7c44f3dab2802d Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner <andreas.sturmlechner@gmail.com>
+Date: Sun, 8 Apr 2018 02:00:30 +0200
+Subject: [PATCH 2/2] Use pkgconfig to find system-jsoncpp
+
+---
+ CMakeLists.txt                                     | 5 ++++-
+ avogadro/io/CMakeLists.txt                         | 4 ++--
+ avogadro/qtplugins/importpqr/CMakeLists.txt        | 4 ++--
+ avogadro/qtplugins/plugindownloader/CMakeLists.txt | 4 ++--
+ avogadro/qtplugins/spectra/CMakeLists.txt          | 2 +-
+ avogadro/quantumio/CMakeLists.txt                  | 4 ++--
+ 6 files changed, 13 insertions(+), 10 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 7574fa0..7ce80b0 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -52,8 +52,11 @@ option(USE_PROTOCALL "Enable libraries that use ProtoCall" OFF)
+ option(USE_MOLEQUEUE "Enable the MoleQueue dependent functionality" ON)
+ option(USE_PYTHON "Use Python to wrap some of our API" OFF)
+ 
++find_package(PkgConfig REQUIRED)
++pkg_check_modules(JSONCPP jsoncpp)
++
+ add_subdirectory(utilities)
+-add_subdirectory(thirdparty)
++# add_subdirectory(thirdparty)
+ add_subdirectory(avogadro)
+ 
+ if(ENABLE_TESTING)
+diff --git a/avogadro/io/CMakeLists.txt b/avogadro/io/CMakeLists.txt
+index 1dd7967..10ddbb6 100644
+--- a/avogadro/io/CMakeLists.txt
++++ b/avogadro/io/CMakeLists.txt
+@@ -15,7 +15,7 @@ endif()
+ # compilers that support that notion.
+ include_directories(SYSTEM "${EIGEN3_INCLUDE_DIR}"
+   "${AvogadroLibs_SOURCE_DIR}/thirdparty/pugixml"
+-  "${AvogadroLibs_SOURCE_DIR}/thirdparty/jsoncpp")
++  "${JSONCPP_INCLUDE_DIRS}")
+ 
+ if(DEFINED AvogadroLibs_MEMORY_INCLUDE_DIRS)
+   # The smart pointer classes just require headers.
+@@ -51,7 +51,7 @@ endif()
+ 
+ avogadro_add_library(AvogadroIO ${HEADERS} ${SOURCES})
+ 
+-target_link_libraries(AvogadroIO LINK_PUBLIC AvogadroCore LINK_PRIVATE jsoncpp)
++target_link_libraries(AvogadroIO LINK_PUBLIC AvogadroCore LINK_PRIVATE ${JSONCPP_LIBRARIES})
+ if(USE_HDF5)
+   target_link_libraries(AvogadroIO LINK_PRIVATE ${HDF5_LIBRARIES})
+ endif()
+diff --git a/avogadro/qtplugins/importpqr/CMakeLists.txt b/avogadro/qtplugins/importpqr/CMakeLists.txt
+index ee27da9..365c51a 100644
+--- a/avogadro/qtplugins/importpqr/CMakeLists.txt
++++ b/avogadro/qtplugins/importpqr/CMakeLists.txt
+@@ -1,4 +1,4 @@
+-include_directories(SYSTEM "${AvogadroLibs_SOURCE_DIR}/thirdparty/jsoncpp")
++include_directories(SYSTEM ${JSONCPP_INCLUDE_DIRS})
+ 
+ # Extension
+ set(importpqr_srcs
+@@ -17,4 +17,4 @@ avogadro_plugin(ImportPQR
+   ""
+ )
+ 
+-target_link_libraries(ImportPQR LINK_PRIVATE ${Qt5Network_LIBRARIES} jsoncpp)
++target_link_libraries(ImportPQR LINK_PRIVATE ${Qt5Network_LIBRARIES} ${JSONCPP_LIBRARIES})
+diff --git a/avogadro/qtplugins/plugindownloader/CMakeLists.txt b/avogadro/qtplugins/plugindownloader/CMakeLists.txt
+index 4b07a53..ab4c661 100644
+--- a/avogadro/qtplugins/plugindownloader/CMakeLists.txt
++++ b/avogadro/qtplugins/plugindownloader/CMakeLists.txt
+@@ -1,4 +1,4 @@
+-include_directories(SYSTEM "${AvogadroLibs_SOURCE_DIR}/thirdparty/jsoncpp")
++include_directories(SYSTEM ${JSONCPP_INCLUDE_DIRS})
+ 
+ find_package(LibArchive REQUIRED)
+ include_directories(SYSTEM ${LIBARCHIVE_INCLUDE_DIRS})
+@@ -20,4 +20,4 @@ avogadro_plugin(PluginDownloader
+ )
+ 
+ target_link_libraries(PluginDownloader LINK_PRIVATE ${Qt5Network_LIBRARIES}
+-  ${LIBARCHIVE_LIBRARIES} jsoncpp)
++  ${LIBARCHIVE_LIBRARIES} ${JSONCPP_LIBRARIES})
+diff --git a/avogadro/qtplugins/spectra/CMakeLists.txt b/avogadro/qtplugins/spectra/CMakeLists.txt
+index a2216b8..09d8fc9 100644
+--- a/avogadro/qtplugins/spectra/CMakeLists.txt
++++ b/avogadro/qtplugins/spectra/CMakeLists.txt
+@@ -1,4 +1,4 @@
+-include_directories(SYSTEM "${AvogadroLibs_SOURCE_DIR}/thirdparty/jsoncpp")
++include_directories(SYSTEM ${JSONCPP_INCLUDE_DIRS})
+ 
+ set(plugin_srcs
+   vibrationdialog.cpp
+diff --git a/avogadro/quantumio/CMakeLists.txt b/avogadro/quantumio/CMakeLists.txt
+index 15073e8..35fc766 100644
+--- a/avogadro/quantumio/CMakeLists.txt
++++ b/avogadro/quantumio/CMakeLists.txt
+@@ -2,7 +2,7 @@ find_package(Eigen3 REQUIRED)
+ # Add as "system headers" to avoid warnings generated by them with
+ # compilers that support that notion.
+ include_directories(SYSTEM "${EIGEN3_INCLUDE_DIR}"
+-  "${AvogadroLibs_SOURCE_DIR}/thirdparty/jsoncpp")
++  ${JSONCPP_INCLUDE_DIRS})
+ 
+ include_directories(${CMAKE_CURRENT_BINARY_DIR})
+ 
+@@ -30,4 +30,4 @@ set(SOURCES
+ )
+ 
+ avogadro_add_library(AvogadroQuantumIO ${HEADERS} ${SOURCES})
+-target_link_libraries(AvogadroQuantumIO LINK_PUBLIC AvogadroIO LINK_PRIVATE jsoncpp)
++target_link_libraries(AvogadroQuantumIO LINK_PUBLIC AvogadroIO LINK_PRIVATE ${JSONCPP_LIBRARIES})
+-- 
+2.17.0
+
diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-underlinking.patch b/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-underlinking.patch
new file mode 100644
index 000000000000..f6f39c9e6b7b
--- /dev/null
+++ b/sci-libs/avogadrolibs/files/avogadrolibs-1.91.0_pre20180406-underlinking.patch
@@ -0,0 +1,18 @@
+Fix underlinking problems in shared libraries.
+
+--- a/avogadro/qtplugins/playertool/CMakeLists.txt
++++ b/avogadro/qtplugins/playertool/CMakeLists.txt
+@@ -7,3 +7,5 @@
+   ""
+   playertool.qrc
+ )
++
++target_link_libraries(PlayerTool LINK_PRIVATE Qt5OpenGL)
+--- a/avogadro/qtplugins/qtaim/CMakeLists.txt
++++ b/avogadro/qtplugins/qtaim/CMakeLists.txt
+@@ -34,3 +34,5 @@
+ 
+ target_link_libraries(QTAIMScenePlugin
+   LINK_PRIVATE AvogadroRendering ${Qt5Concurrent_LIBRARIES})
++target_link_libraries(QTAIMExtension
++  LINK_PRIVATE ${Qt5Concurrent_LIBRARIES})
diff --git a/sci-libs/avogadrolibs/metadata.xml b/sci-libs/avogadrolibs/metadata.xml
index ea8e4fdee064..ff1789dfa774 100644
--- a/sci-libs/avogadrolibs/metadata.xml
+++ b/sci-libs/avogadrolibs/metadata.xml
@@ -6,8 +6,9 @@
 		<name>Gentoo Chemistry Project</name>
 	</maintainer>
 	<use>
+		<flag name="archive">Enable archive support using <pkg>app-arch/libarchive</pkg></flag>
 		<flag name="static-plugins">Build all plugins statically into main plugin modules</flag>
-		<flag name="vtk">include vtk support</flag>
+		<flag name="vtk">Enable <pkg>sci-libs/vtk</pkg> support</flag>
 	</use>
 	<upstream>
 		<remote-id type="github">OpenChemistry/avogadrolibs</remote-id>
diff --git a/sci-libs/chemkit/Manifest b/sci-libs/chemkit/Manifest
index cf36a345298e..8639b6d20b90 100644
--- a/sci-libs/chemkit/Manifest
+++ b/sci-libs/chemkit/Manifest
@@ -1,5 +1,5 @@
 AUX chemkit-0.1-multilib.patch 4694 BLAKE2B f52836ec887b9673c8eabac6ca4fb008aa23def355419f02704605438de44457f2a017a56a7fdd3ce387df08e5b57a0352052d2b88ff0e051a6cf47a192ffd1e SHA512 dedde9e5db14f088e5a70ebfcd9f46b6fbb2d60b1800a61ece1f7afef24caac502f129573823807caec050ba1515ad402a3615953b903a239c5287a5b96aa8b8
 AUX chemkit-0.1-unbundle.patch 6103 BLAKE2B 9ee0f121fec938a528abb837ab386fec62a8576b5c7d123538ce95604953f4f30d0b285b27a153ef98629f053954324f7c384329fe3ca6873f2d18700e914ff8 SHA512 9edd39008763b56eb7697562536c4c4d476880a414ae1a305d1af64cee04e4ccb82585cfd15d2f7608b5200e39863a9a97c2a152110b28e501fbd055737ce015
 DIST chemkit-0.1.tar.gz 5842235 BLAKE2B 9cf28dc6d2c067403172c4f54a057bf38ea9aeaebc96b9be819f4861d1559c1db440dd33baf15f739b2b0e6dc6ba3e73010e0b5aa1b46309435e7bbffb889259 SHA512 0273f8735333000b04007ccd7adc58f0c4809a570fa5a72e4161652d72e8953bf89cad0893c20ecbb3484d6c13a8828c92f12366dddeedaf591815c35f6ef011
-EBUILD chemkit-0.1-r2.ebuild 1901 BLAKE2B 2ffeacbbe0d24820327b0f19b3e876da35c654ab029ccafd0aaba9cea23c4c2489c5c584643f4383de7fa298299dc9d19ecdf2f9b90d19b130e2c78aed808891 SHA512 261ec048b4e31e7f73a82277bf3cac0721e92f83a849973dad0f74a6fd388adcaaa29dbbb5bd3f9ea45070d00cd7e3d47a87647ec09186f54e94e7a57b7ab4ef
+EBUILD chemkit-0.1-r2.ebuild 1904 BLAKE2B 8e047c10ed8fb80fb35bbd6176e508ba13c52e97e458783c42e0d978b001c7367e9427dd1198e86143fc6211d310fe3bb18b5bc091df0ed918f2449e1649f4f4 SHA512 1078f0af1f8b32d324e25e8bd790559f0ce8cd86170ebb52c15318b058ca490e9b85416e9ce1d11abdc607af76ca02093a4f9f356cd7ac80ba75e7be3d257ed2
 MISC metadata.xml 352 BLAKE2B fbab9c9aa637ace5d90660942c8a34550c45bdf692b98ef583a77e5ed8d666877c09076314f6ec4081f91d12803fd1d8f50b7a715991e8e0ed0541e8473563b3 SHA512 b197aa62c04a5f668822db2e277407e7e871505f7adf5cfceaab36b5bc808f0b7582f17f9a00c7d4013eb4728b7a6ef61a52325deb182d6cd4a344e5d1e98cb1
diff --git a/sci-libs/chemkit/chemkit-0.1-r2.ebuild b/sci-libs/chemkit/chemkit-0.1-r2.ebuild
index 987c32161c18..c687d55922e1 100644
--- a/sci-libs/chemkit/chemkit-0.1-r2.ebuild
+++ b/sci-libs/chemkit/chemkit-0.1-r2.ebuild
@@ -5,10 +5,10 @@ EAPI=6
 
 PYTHON_COMPAT=( python2_7 )
 
-inherit cmake-utils multilib python-single-r1 virtualx
+inherit cmake-utils python-single-r1 virtualx
 
 DESCRIPTION="Library for chemistry applications"
-HOMEPAGE="http://www.chemkit.org/"
+HOMEPAGE="https://github.com/kylelutz/chemkit"
 SRC_URI="mirror://sourceforge/project/${PN}/${P}.tar.gz"
 
 SLOT="0"
diff --git a/sci-libs/libnova/Manifest b/sci-libs/libnova/Manifest
index 476ca6814fe4..bcd9bb58abf9 100644
--- a/sci-libs/libnova/Manifest
+++ b/sci-libs/libnova/Manifest
@@ -4,5 +4,5 @@ DIST libnova-0.14.0.tar.gz 1547373 BLAKE2B 75078d77868419e3cc6d6a7b5c513ebbf3206
 DIST libnova-0.15.0.tar.gz 1533794 BLAKE2B e87ffd3b8a895ca7ac9913ad3aacff526718442546df5687f2156718f721665ffff27e69af4bcb65bac5df1fda89fc6fc8fe9876a4b74392986771cf157dc48c SHA512 77ab0ccbfe462c03a21e88656cb4d6389994ea1da0ee8da997f19a83d24ad8fd9e505e70e1580b75332e826e5b7859b5f2af4417f65eb811440493ba586f2574
 EBUILD libnova-0.12.3.ebuild 1127 BLAKE2B 6203f62ea6219ab024501af2f5e641f922b129076f1d60fc8e6a62fc1d679ff27c4b635f644bcfa24669a088aa03a10aa2174cec0315155363646ddd014fbf36 SHA512 d6490764d1558afb0fc4eec5d473e198924e6f983d4439931475f9348427b742fb30a12d9d2a082902a28b042e416acf52c8ec711323f76df42d63e505446a35
 EBUILD libnova-0.14.0.ebuild 823 BLAKE2B a96161abf24de6ef882ed02d0103140b6272cbe31de519f071ffd0e753f4ebacbd4adcfeb7cadcd86014ae70e0242b5baeec127ff74fd1e821e28e02476e18af SHA512 b8867669b87e048a909ed22f1d0d1bc017bc99645e8e5cbfcca3601e78d9385d8c73f929ee7b983d84dbe684a3ee1d8e0b0d147f85428153ad807968c4278ff5
-EBUILD libnova-0.15.0.ebuild 884 BLAKE2B 39d68994d14d37a1531826a624d71c01eedcd70eed0f24eaaec93baf1cdfcec250d1b86d949199d686bf06318fe005cf1a3bb33a812ee6ce39cb21da764bbf17 SHA512 ce77f9c2ed41d5a287447c50736e85eb963063a2c176b6f6a94a468ed5f6a975d434ff0e33e126642aee032a0df6be8e13fee89bf3d8aa0cc961b53ab25ae389
+EBUILD libnova-0.15.0.ebuild 883 BLAKE2B f8f05303c582298a9fb7c0d9862c3c85e10ff7a2797d1c81b14831b1e14074627a35a924dbd793f3a7921e2f75d4f4537ed4ca70a963f9a94bec1e73cb89fd45 SHA512 7eacc54f8b2dd3ef3b25e76b7a8650578ff56748636d73c7e13e25ca9a1fa587a1aff9b86d452a06d8cef52b323e591b027b9c6d589e512ef768ff188910f154
 MISC metadata.xml 637 BLAKE2B dff43562550feffed3b305c3aa5473a1ea4256c10f1db163b8e7af9f751611525d0720d18eff17a64dd3cd0de1a441a912b79e86e43e307d50b439cb95ccc480 SHA512 f94be1667b076464ade40edbc7fdc3e73ee743c518e862df1277914826e91d9adc075d1a756e6a48a309bc32da384dfc17d5973f1e2b9e116d48cda697c5ece8
diff --git a/sci-libs/libnova/libnova-0.15.0.ebuild b/sci-libs/libnova/libnova-0.15.0.ebuild
index 8e4aa22c43d4..5f190893d757 100644
--- a/sci-libs/libnova/libnova-0.15.0.ebuild
+++ b/sci-libs/libnova/libnova-0.15.0.ebuild
@@ -12,7 +12,7 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
 
 LICENSE="LGPL-2"
 SLOT="0"
-KEYWORDS="amd64 ~hppa ~ppc ~ppc64 x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 ~hppa ~ppc ppc64 x86 ~amd64-linux ~x86-linux"
 IUSE="doc examples static-libs"
 
 DEPEND="doc? ( app-doc/doxygen )"
diff --git a/sci-libs/orocos_kdl/Manifest b/sci-libs/orocos_kdl/Manifest
index 632abe856e78..a2b0375e922d 100644
--- a/sci-libs/orocos_kdl/Manifest
+++ b/sci-libs/orocos_kdl/Manifest
@@ -1,4 +1,6 @@
 DIST orocos_kinematics_dynamics-1.3.1.tar.gz 202471 BLAKE2B 46b7bdb62c09e9077b84d914b4d780995f27d486d9c734ef2ee1f8b8c2219265cdba5e63830225e2435b5760b79f00d478670e95b71666959afa773f8bcfe5ce SHA512 93abd9dd5aef3710f784f9db8eea4738458bffa5295923993e2d77656c18f7354559412fb7eb5f1e9da7112de19aa36d3f0f68f149852f955bce960fd3b719e7
+DIST orocos_kinematics_dynamics-1.4.0.tar.gz 215004 BLAKE2B 02ca44195af2ae2bd5c2293869893c56846501e2055ca1cacef602ffdd44824fc618ed528d351ee2212b7c087ff5e69438ab87e9fb8813d8a4eb4c143fdbfd27 SHA512 7156465e2aff02f472933617512069355836a03a02d4587cfe03c1b1d667a9762a4e3ed6e055b2a44f1fce1b6746179203c7204389626a7b458dcab1b28930d8
 EBUILD orocos_kdl-1.3.1-r1.ebuild 1621 BLAKE2B 1bb89339ce08a5b8c90eaeac83daeafc934ec870d231512d28ce092176aa9fab1126bdb7f8ac1c60d1b5755a2819693115e23cbf88a436d1c3dcbee78e46d416 SHA512 10f3ae388edcbbea0495f742c053a2caa6711e6ba6283896cb032a84cf099b4c700484c2237bea3662a187d357acefa9293dfc00f6ad8c32a6c08bea511c9909
-EBUILD orocos_kdl-9999.ebuild 1621 BLAKE2B 1bb89339ce08a5b8c90eaeac83daeafc934ec870d231512d28ce092176aa9fab1126bdb7f8ac1c60d1b5755a2819693115e23cbf88a436d1c3dcbee78e46d416 SHA512 10f3ae388edcbbea0495f742c053a2caa6711e6ba6283896cb032a84cf099b4c700484c2237bea3662a187d357acefa9293dfc00f6ad8c32a6c08bea511c9909
+EBUILD orocos_kdl-1.4.0.ebuild 1624 BLAKE2B 9d9f1541bb0c0c96b31320b52d7d76a79d56765fb73879781dac262240a23af4c7345f0e6cbad3e106cf30339d8a7efbcc727c5d52e90d65baaea8af9d3d953b SHA512 a6505a22cd092dfb4eec38a07e047d06d0f15213d8178eed4198f07f8344dd30a32ff78f17ecfef7bd83cb915ffeacb6e008068bb9bb819bba95608710f581bc
+EBUILD orocos_kdl-9999.ebuild 1624 BLAKE2B 9d9f1541bb0c0c96b31320b52d7d76a79d56765fb73879781dac262240a23af4c7345f0e6cbad3e106cf30339d8a7efbcc727c5d52e90d65baaea8af9d3d953b SHA512 a6505a22cd092dfb4eec38a07e047d06d0f15213d8178eed4198f07f8344dd30a32ff78f17ecfef7bd83cb915ffeacb6e008068bb9bb819bba95608710f581bc
 MISC metadata.xml 934 BLAKE2B d82ddb6554a65a4221e67f46cfc6ff218c8caff71662090cd22332bc8f77c88b54c0ed8a7ccde53f00c6ef9c7faa386a82ca4654652ed7876c84105cd4426451 SHA512 09dc8b8c362da950ea685ee6cb2d7eb3ee400f34fca286fa0bf064f3cc4338a5ad2ca8917c951211e9407122a3bd7a1f23e5d394bfed901d6f69e9caefe5eaed
diff --git a/sci-libs/orocos_kdl/orocos_kdl-1.4.0.ebuild b/sci-libs/orocos_kdl/orocos_kdl-1.4.0.ebuild
new file mode 100644
index 000000000000..aa74627a9e43
--- /dev/null
+++ b/sci-libs/orocos_kdl/orocos_kdl-1.4.0.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+SCM=""
+if [ "${PV#9999}" != "${PV}" ] ; then
+	SCM="git-r3"
+	EGIT_REPO_URI="https://github.com/orocos/orocos_kinematics_dynamics"
+fi
+
+inherit ${SCM} cmake-utils
+
+if [ "${PV#9999}" != "${PV}" ] ; then
+	KEYWORDS=""
+	SRC_URI=""
+else
+	KEYWORDS="~amd64 ~arm ~x86"
+	SRC_URI="https://github.com/orocos/orocos_kinematics_dynamics/archive/v${PV}.tar.gz -> orocos_kinematics_dynamics-${PV}.tar.gz"
+fi
+
+DESCRIPTION="Kinematics and Dynamics Library (KDL)"
+HOMEPAGE="http://www.orocos.org/kdl"
+LICENSE="LGPL-2.1"
+SLOT="0/14"
+IUSE="doc test examples models"
+
+RDEPEND="dev-cpp/eigen:3"
+DEPEND="${RDEPEND}
+	test? ( dev-util/cppunit )
+	doc? ( app-doc/doxygen )"
+REQUIRED_USE="examples? ( models )"
+
+DOCS=( README )
+
+if [ "${PV#9999}" != "${PV}" ] ; then
+	S=${WORKDIR}/${P}/orocos_kdl
+else
+	S=${WORKDIR}/orocos_kinematics_dynamics-${PV}/orocos_kdl
+fi
+
+src_configure() {
+	local mycmakeargs=(
+		"$(cmake-utils_use_enable test TESTS)"
+		"$(cmake-utils_use_enable examples EXAMPLES)"
+		"-DBUILD_MODELS=$(usex models ON OFF)"
+	)
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	cmake-utils_src_compile
+	cd "${BUILD_DIR}"
+	use doc && emake docs
+}
+
+src_test() {
+	cd "${BUILD_DIR}"
+	emake check
+}
+
+src_install() {
+	cmake-utils_src_install
+	cd "${BUILD_DIR}"
+	use doc && dohtml -r doc/api/html/*
+	use examples && dobin "${BUILD_DIR}/examples/"{geometry,trajectory_example,chainiksolverpos_lma_demo}
+
+	# Need to have package.xml in our custom gentoo path
+	insinto /usr/share/ros_packages/${PN}
+	doins "${ED}/usr/share/${PN}/package.xml"
+}
diff --git a/sci-libs/orocos_kdl/orocos_kdl-9999.ebuild b/sci-libs/orocos_kdl/orocos_kdl-9999.ebuild
index e2fe4f9b4756..aa74627a9e43 100644
--- a/sci-libs/orocos_kdl/orocos_kdl-9999.ebuild
+++ b/sci-libs/orocos_kdl/orocos_kdl-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -22,7 +22,7 @@ fi
 DESCRIPTION="Kinematics and Dynamics Library (KDL)"
 HOMEPAGE="http://www.orocos.org/kdl"
 LICENSE="LGPL-2.1"
-SLOT="0"
+SLOT="0/14"
 IUSE="doc test examples models"
 
 RDEPEND="dev-cpp/eigen:3"
diff --git a/sci-libs/szip/Manifest b/sci-libs/szip/Manifest
index 12aabc4b9cac..10f1b36fa37a 100644
--- a/sci-libs/szip/Manifest
+++ b/sci-libs/szip/Manifest
@@ -1,4 +1,4 @@
 DIST szip-2.1.tar.gz 383219 BLAKE2B 84e10763bcec885a423d64c2c3cff0632d7a6a39c8cd177cf607f549cb4cd02a4ca03362464c2c4ec4539c80149493329427f529f5d6daea4a35b91af6fa1538 SHA512 bb7e0af6dfaaaaa85013ef52e6901d5b7b6159795338d285c2e843bd2879230a6397fb072662fdfeda5690981db4e9af94782c057bf993f92516d92a8934cb75
-EBUILD szip-2.1-r2.ebuild 714 BLAKE2B dcdd543f2c706c5f7976608c91570cac16838c448e28b878ee0c7b9019b7e2818924aeb0f6d2f234427dbdc257dc542f88f691b0d65620691e187f51a0ac8d0d SHA512 e4018879eb35a30d0465e5823d889037ab00b97ce93179b882fb228285aff96680cbaef836f20f1a73e9f77042024ab2f2bb035fbd099bed697bdfcc731fdd1f
+EBUILD szip-2.1-r2.ebuild 713 BLAKE2B ac72a826e233d8e816e2e37b8ea2af7ec6687414cfc189cece4d53541e1c67bbdf891706276f85d8833dcac333da318c3653300d206622496c7c5ff1c9c90651 SHA512 83f1adfd72ed84a2d7cc446ca6c40d4e68cf62fe8d2688d35d310678c0a04d525d4062e356e1532282ef4e5c21bac9706f0ca0be63d5d6e0517e25e4cdcf822d
 EBUILD szip-2.1.ebuild 649 BLAKE2B 93a9fd8bf30d89079ac58ae79658b9b84896bbdcadae530e84da7c62845a887f4f581034a3d333f2e727a3f5dbb9a52307222d6374998254328c07a63badc887 SHA512 fbcaffb62c0827464c812a577e9b828f54f7cab5de9bce1d189a4deb5eab0980142b3d48b20ff263cd40a0c07dc0baaa89d608fa331e2bc71a89532618140890
 MISC metadata.xml 765 BLAKE2B a720dfb9f71c9f9adc5e539b2a791b8edcd2fce2b1540b17066c09e1d3895d40e147ddd2ef86499c6a9db3c2c68c3bb9aae3357f13d86370d7fba8069f968368 SHA512 c56edc42adeff2e523e9a312b0393f45647b2a902334221d2b9842afa1ecd885a17f108041cad69a0797bdc1eb58c75672226a0c3a2f4c8f561ab8a70eb28b27
diff --git a/sci-libs/szip/szip-2.1-r2.ebuild b/sci-libs/szip/szip-2.1-r2.ebuild
index fca656b73b0f..3f07f2a9542e 100644
--- a/sci-libs/szip/szip-2.1-r2.ebuild
+++ b/sci-libs/szip/szip-2.1-r2.ebuild
@@ -11,7 +11,7 @@ SRC_URI="ftp://ftp.hdfgroup.org/lib-external/${PN}/${PV}/src/${P}.tar.gz"
 LICENSE="szip"
 
 SLOT="0/2"
-KEYWORDS="alpha amd64 ~arm ~arm64 ~hppa ia64 ~ppc ~ppc64 sparc x86 ~x86-fbsd ~amd64-linux ~x86-linux"
+KEYWORDS="alpha amd64 ~arm ~arm64 ~hppa ia64 ~ppc ppc64 sparc x86 ~x86-fbsd ~amd64-linux ~x86-linux"
 
 IUSE="static-libs"
 RDEPEND="!sci-libs/libaec[szip]"