gentoo resync : 10.04.2018

8 files changed, 296 insertions, 105 deletions

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>