gentoo resync : 19.04.2018

20 files changed, 376 insertions, 378 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index a4a7efbfe97c..6514084e97f4 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/avogadro2/Manifest b/sci-chemistry/avogadro2/Manifest
index 039a585eb04e..6065c99351f1 100644
--- a/sci-chemistry/avogadro2/Manifest
+++ b/sci-chemistry/avogadro2/Manifest
@@ -1,3 +1,4 @@
+AUX avogadro2-1.90.0_p20180211-qt-5.11b3.patch 1134 BLAKE2B ff96a5b19d17768de242490e555679270d568ce41b321e549e88986c66c931e7275c88697ee71600cdab7990f473f6c214f903771754d292ff0766874a82f810 SHA512 5362a64709127b30656f1f7830d902ac00291cdf39160c4639f121568666fe1249f2f92c9378f75b2fc6cf44cecf74e92e207b73c029a9c9d997ac852f02ed86
 DIST avogadro2-1.90.0_p20180211.tar.gz 1099312 BLAKE2B fbf8e2006c46114632587615b48ac130e45a46ce2859a9c34270714091bc8397d9d7a93c3166bf58833f100e3e40afd1962012e479a8f92ba8ff9078200d51c5 SHA512 db9b0983d2161df493138ddf18c5dbda54cf2f8b75ebc944f1f57dab0f1e2048582362e5f46a78b1610aba080aaac8a66d2b2b71db748e031ffde306d3609856
-EBUILD avogadro2-1.90.0_p20180211.ebuild 1225 BLAKE2B 28916f43f2a48e1cb855f70a2ca3df5a03438420841481bc4d33816333c3f54e04979c5d06238ece6c990ca8458862eeba04b7f060b3cb69ae0d5b82c63f96ad SHA512 249c0905f92fd3021da53327945ece37e30d48650b4a47267231f5833a85a1d97d27f3e87e3b41255ae4d9ce67f0169cdbc06c755db99c895cc3e57b8edb2a7c
+EBUILD avogadro2-1.90.0_p20180211.ebuild 1273 BLAKE2B b0f9d795978e059158ae4929cdbe97425f58f84da99f67407b858e0b59672d35dbd83864d0e08d23fd0f3a1cb7d7ef70f9db0475e94e7b6a837f376313b9209e SHA512 d790a4f9c61937bf832c48ee7551ca9e63061732507e771d6ad9cf9b024da318ae83b7879f344360aff60a98473791cb741264c5cc73e4f930a8a3256fb65970
 MISC metadata.xml 513 BLAKE2B f721104691759eb8a87d9cb6dd56bef45ac151e180caa68376406274a57df6c04e3fec6ba6d7e2aabf4355356002d27dd92e5b850c55103b3b23340d9b64d891 SHA512 4209c0681f7055b240f1054a10d58d5c22dca467903096ab1f5eb1b8cf276990f694b2033b4e9b4e4838cce65dd7c7660633079764248f394e32ece0048f09a0
diff --git a/sci-chemistry/avogadro2/avogadro2-1.90.0_p20180211.ebuild b/sci-chemistry/avogadro2/avogadro2-1.90.0_p20180211.ebuild
index 8b017684a578..8345cd9619e5 100644
--- a/sci-chemistry/avogadro2/avogadro2-1.90.0_p20180211.ebuild
+++ b/sci-chemistry/avogadro2/avogadro2-1.90.0_p20180211.ebuild
@@ -33,6 +33,8 @@ RESTRICT="test"
 
 S="${WORKDIR}/${MY_PN}-${COMMIT}"
 
+PATCHES=( "${FILESDIR}/${P}-qt-5.11b3.patch" )
+
 src_prepare() {
 	cmake-utils_src_prepare
 	sed -e "/LICENSE/d" -i CMakeLists.txt || die
diff --git a/sci-chemistry/avogadro2/files/avogadro2-1.90.0_p20180211-qt-5.11b3.patch b/sci-chemistry/avogadro2/files/avogadro2-1.90.0_p20180211-qt-5.11b3.patch
new file mode 100644
index 000000000000..1e7a23f0b54e
--- /dev/null
+++ b/sci-chemistry/avogadro2/files/avogadro2-1.90.0_p20180211-qt-5.11b3.patch
@@ -0,0 +1,34 @@
+From 2c70d9bf7248d8da7691a5830ba6a0972fd9eea7 Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner <asturm@gentoo.org>
+Date: Tue, 17 Apr 2018 11:57:32 +0200
+Subject: [PATCH] Fix build with Qt 5.11_beta3 (dropping qt5_use_modules)
+
+---
+ avogadro/CMakeLists.txt | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/avogadro/CMakeLists.txt b/avogadro/CMakeLists.txt
+index 115b798..f564eb5 100644
+--- a/avogadro/CMakeLists.txt
++++ b/avogadro/CMakeLists.txt
+@@ -16,7 +16,7 @@ if(MSVC)
+ endif()
+ 
+ # Find the Qt components we need.
+-find_package(Qt5 COMPONENTS Widgets Network REQUIRED)
++find_package(Qt5 REQUIRED COMPONENTS Concurrent Widgets Network CONFIG)
+ 
+ configure_file(avogadroappconfig.h.in avogadroappconfig.h)
+ 
+@@ -88,7 +88,7 @@ endif()
+ 
+ add_executable(avogadro WIN32 MACOSX_BUNDLE
+   ${avogadro_srcs} ${ui_srcs} ${rcc_srcs})
+-qt5_use_modules(avogadro Widgets Network Concurrent)
++target_link_libraries(avogadro Qt5::Widgets Qt5::Network Qt5::Concurrent)
+ if(WIN32)
+   set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /NODEFAULTLIB:MSVCRTD")
+   target_link_libraries(avogadro Qt5::WinMain)
+-- 
+2.17.0
+
diff --git a/sci-chemistry/elem/Manifest b/sci-chemistry/elem/Manifest
index 419abe3b4650..db952304a6d8 100644
--- a/sci-chemistry/elem/Manifest
+++ b/sci-chemistry/elem/Manifest
@@ -1,4 +1,5 @@
+AUX elem-1.0.3-fix-build-system.patch 2544 BLAKE2B 174bfc3e2036a17d918534d02b51def6d933e8799c15cc3e6b75a8580155be614b5691b3241e1fcf88ea7e8124c3e65d73101d862c21f7603a9a8b794d640e6a SHA512 2d691f1d0fdc0a786a45706b68243fab17706328e0417cf805f657576c462315551719a7168ad8e58e651c695a0d53da3f776f479dc540b6b01af899e1b97208
+AUX elem-1.0.3-missing-stdlib.patch 133 BLAKE2B 2ab00632e93401db578910b4e44e8f0ad4e899fb3afce5b9d1b6612ba181fd0fc3922c8cc229404164bdef562850337f006cce4047e52b2e459954419bc05529 SHA512 769c5e19928ed64b5595cd37f16d4df893889c3c0ea7e6673e182646bcaca89a6e46e7c6611c586c9213a417c439de043c0beb84a9543e478f78e4d9843a1c3e
 DIST elem-src-1.0.3-Linux.tgz 58364 BLAKE2B bdedb844ca62f928fdae5b01b13b88e5f43f5e37f40b47f7b8b9b1a2cb11053b9aefa7b1b4bb78a8632f3329f37afeadfc34eddee1b9f7cd109bee89aa9cdf32 SHA512 24b163c5cc3019c1beb677ce7b432b21289352f7cdbad686ab9161c628d3aadbb90d8abf9bef49f1c7d077b706bbd4ea6b381f356cc85adf907f3c15a4f4893c
-EBUILD elem-1.0.3-r1.ebuild 668 BLAKE2B 20d89d85a70dca3aadccb29360535f1799b5683e4ade3fec5a56e61d04b5407dc33d63ae875aeedd9a171de6ea28cce451c17a9a66576bf85f1d1850c55f99ea SHA512 b83e43f0cc8198e19276e6b85e3f48c045c9c5f569718507c93bec4215cdd9dbb5e29575f204db23269a6a4e016071fa3e0778e60f9a858424188f3fe4fe3e6c
-EBUILD elem-1.0.3-r2.ebuild 801 BLAKE2B edb28ba6fb92772b9718311a533dc48e0d6721a8f6a95639af1b2a00292946bbbf2ffcb6e2fbb25fb369cdae2ae1e654ddf079df8e59d9ccfaa7d0ecb7a776d4 SHA512 4a13dd36dd4c09ab9a4af15a6d1f0f4b6f07421a2a41e5a5fddce083448635a64ded03011f393b868c720691e184332541628bc7ad62f48e1bd7e9c3e28d1e5b
+EBUILD elem-1.0.3-r2.ebuild 665 BLAKE2B 865ddeecb1c7c9be1d3467d320454bf057359d84cd8cf4566c475d605d9355c83a34c452e5cac1505c362521ea7c720a60d1b9b7aeea25f6f58b43dc29b3f3e1 SHA512 e00037731116bab8060dddf9d461f607299b564e201053101afe2129bfb69d9080831801eb391a21f03365f6ad65b2e2216ea2c0b4597d94c7923862b272b8c3
 MISC metadata.xml 339 BLAKE2B 73c4ef3e56cdf6f1061537c5c3a3932b7c38af40ec483cb4f12c21722a65dbeb0ce2dc162911a96a8f4147150a232eb398e2a4fecf7bde60ba2738994dc7a534 SHA512 daecddff7728e2a0b00d5e16bb4fc1c88bd316783f8921705dc76b41f427a8918ead92e663fa202ff57508242daa454cae2c04057c8bf9cf767b95d59e43c177
diff --git a/sci-chemistry/elem/elem-1.0.3-r1.ebuild b/sci-chemistry/elem/elem-1.0.3-r1.ebuild
deleted file mode 100644
index eafbb9c4c0b7..000000000000
--- a/sci-chemistry/elem/elem-1.0.3-r1.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-inherit toolchain-funcs
-
-DESCRIPTION="periodic table of the elements"
-HOMEPAGE="http://elem.sourceforge.net/"
-SRC_URI="mirror://sourceforge/elem/${PN}-src-${PV}-Linux.tgz"
-LICENSE="GPL-2"
-KEYWORDS="amd64 sparc x86"
-SLOT="0"
-IUSE=""
-
-DEPEND="x11-libs/xforms"
-RDEPEND="${DEPEND}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	sed -e 's:\(^LIBS = .*\):\1 -lXpm:' -i Makefile || die "sed failed"
-}
-
-src_compile () {
-	emake COMPILER="$(tc-getCC)" FLAGS="${CFLAGS}" all || die "Build failed."
-}
-
-src_install () {
-	into /usr
-	dobin elem elem-de elem-en
-	dohtml -r doc/*
-}
diff --git a/sci-chemistry/elem/elem-1.0.3-r2.ebuild b/sci-chemistry/elem/elem-1.0.3-r2.ebuild
index 5a9a8c132cf3..daade3396d36 100644
--- a/sci-chemistry/elem/elem-1.0.3-r2.ebuild
+++ b/sci-chemistry/elem/elem-1.0.3-r2.ebuild
@@ -1,34 +1,39 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
+EAPI=6
+
 inherit toolchain-funcs
 
 DESCRIPTION="periodic table of the elements"
 HOMEPAGE="http://elem.sourceforge.net/"
 SRC_URI="mirror://sourceforge/elem/${PN}-src-${PV}-Linux.tgz"
+
 LICENSE="GPL-2"
-KEYWORDS="~amd64 ~sparc ~x86"
+KEYWORDS="amd64 sparc x86"
 SLOT="0"
 IUSE=""
 
 DEPEND="x11-libs/xforms"
 RDEPEND="${DEPEND}"
 
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	sed -e 's:\(^LIBS = .*\):\1 -lXpm:' \
-		-e "s:\${FLAGS} -o elem:\$(LDFLAGS) &:" \
-		-i Makefile || die #336190
-	sed -e "/string.h/ i #include <stdlib.h>" \
-		-i elem_cb.c || die #implicit exit()
+PATCHES=(
+	"${FILESDIR}"/${P}-fix-build-system.patch
+	"${FILESDIR}"/${P}-missing-stdlib.patch
+)
+
+src_configure() {
+	tc-export CC
 }
 
 src_compile () {
-	emake COMPILER="$(tc-getCC)" FLAGS="${CFLAGS}" all || die "Build failed."
+	emake all
 }
 
 src_install () {
-	dobin elem elem-de elem-en || die
-	dohtml -r doc/* || die
+	dobin elem elem-de elem-en
+
+	rm -rf doc/CVS || die
+	HTML_DOCS=( doc/. )
+	einstalldocs
 }
diff --git a/sci-chemistry/elem/files/elem-1.0.3-fix-build-system.patch b/sci-chemistry/elem/files/elem-1.0.3-fix-build-system.patch
new file mode 100644
index 000000000000..b89f226e46a7
--- /dev/null
+++ b/sci-chemistry/elem/files/elem-1.0.3-fix-build-system.patch
@@ -0,0 +1,65 @@
+--- a/Makefile
++++ b/Makefile
+@@ -1,8 +1,4 @@
+-COMPILER=gcc
+-LIBS = -lm -L./  -lforms -L/usr/X11R6/lib -lX11 -lnsl 
+-INCLUDE=-I/usr/X11R6/include/X11 -I/usr/include -I/usr/X11R6/include -I/usr/local/X11/include/ -I/usr/X/include/
+-FLAGS = -g -O2
+-DESTDIR =
++LIBS = -lm -L./ -lforms
+ 
+ 
+ default:
+@@ -35,7 +31,7 @@
+ 	@echo "erzeuge deutsche Version von elem"
+ 
+ elem-de: elem_main_de.o elem_cb_de.o elem_de.o deutsch.h
+-	${COMPILER} ${FLAGS} -o elem-de elem_main_de.o elem_cb_de.o elem_de.o ${LIBS} -DDEUTSCH
++	$(CC) $(LDFLAGS) $(CFLAGS) -o elem-de elem_main_de.o elem_cb_de.o elem_de.o $(LIBS)
+ 
+ 
+ 
+@@ -43,34 +39,34 @@
+ 	@echo "creating english version of elem"
+ 
+ elem-en: elem_main_en.o elem_cb_en.o elem_en.o english.h
+-	${COMPILER} ${FLAGS} -o elem-en elem_main_en.o elem_cb_en.o elem_en.o ${LIBS} -DENGLISH
++	$(CC) $(LDFLAGS) $(CFLAGS) -o elem-en elem_main_en.o elem_cb_en.o elem_en.o $(LIBS)
+ 
+ static-de : elem_main_de.o elem_cb_de.o elem_de.o
+-	${COMPILER} ${FLAGS} -static -o elem-static-de elem_main_de.o elem_cb_de.o elem_de.o  ${LIBS} -DDEUTSCH
++	$(CC) $(LDFLAGS) $(CFLAGS) -static -o elem-static-de elem_main_de.o elem_cb_de.o elem_de.o $(LIBS)
+ 
+ static-en : elem_main_en.o elem_cb_en.o elem_en.o
+-	${COMPILER} ${FLAGS} -static -o elem-static-en elem_main_en.o elem_cb_en.o elem_en.o  ${LIBS} -DENGLISH
++	$(CC) $(LDFLAGS) $(CFLAGS) -static -o elem-static-en elem_main_en.o elem_cb_en.o elem_en.o $(LIBS)
+ 
+ 
+ 
+ 
+ elem_main_de.o : elem_main.c elem.h deutsch.h
+-	${COMPILER} ${FLAGS} -DDEUTSCH -o elem_main_de.o -c elem_main.c ${INCLUDE}
++	$(CC) $(CFLAGS) $(CPPFLAGS) -DDEUTSCH -o elem_main_de.o -c elem_main.c
+ 
+ elem_main_en.o : elem_main.c elem.h english.h
+-	${COMPILER} ${FLAGS} -DENGLISH -o elem_main_en.o -c elem_main.c ${INCLUDE}
++	$(CC) $(CFLAGS) $(CPPFLAGS) -DENGLISH -o elem_main_en.o -c elem_main.c
+ 
+ 
+ elem_cb_de.o : elem_cb.c elem.h deutsch.h
+-	${COMPILER} ${FLAGS} -DDEUTSCH -o elem_cb_de.o -c elem_cb.c ${INCLUDE}
++	$(CC) $(CFLAGS) $(CPPFLAGS) -DDEUTSCH -o elem_cb_de.o -c elem_cb.c
+ elem_cb_en.o : elem_cb.c elem.h english.h
+-	${COMPILER} ${FLAGS} -DENGLISH -o elem_cb_en.o -c elem_cb.c ${INCLUDE}
++	$(CC) $(CFLAGS) $(CPPFLAGS) -DENGLISH -o elem_cb_en.o -c elem_cb.c
+ 
+ 
+ elem_de.o : elem.c elem.h
+-	${COMPILER} ${FLAGS} -DDEUTSCH  -o elem_de.o -c elem.c ${INCLUDE}
++	$(CC) $(CFLAGS) $(CPPFLAGS) -DDEUTSCH  -o elem_de.o -c elem.c
+ elem_en.o : elem.c elem.h
+-	${COMPILER} ${FLAGS} -DENGLISH  -o elem_en.o -c elem.c ${INCLUDE}
++	$(CC) $(CFLAGS) $(CPPFLAGS) -DENGLISH  -o elem_en.o -c elem.c
+ 
+ 
+ install-de: deutsch
diff --git a/sci-chemistry/elem/files/elem-1.0.3-missing-stdlib.patch b/sci-chemistry/elem/files/elem-1.0.3-missing-stdlib.patch
new file mode 100644
index 000000000000..e1937734a51c
--- /dev/null
+++ b/sci-chemistry/elem/files/elem-1.0.3-missing-stdlib.patch
@@ -0,0 +1,9 @@
+--- a/elem_cb.c
++++ b/elem_cb.c
+@@ -1,5 +1,6 @@
+ #include "forms.h"
+ #include "elem.h"
++#include <stdlib.h>
+ #include <string.h>
+ 
+ 
diff --git a/sci-chemistry/ghemical/Manifest b/sci-chemistry/ghemical/Manifest
index 648c6e80979d..d96c08f98719 100644
--- a/sci-chemistry/ghemical/Manifest
+++ b/sci-chemistry/ghemical/Manifest
@@ -1,4 +1,4 @@
 AUX 2.99.2-docs.patch 785 BLAKE2B c731e7366ad44dde7c8754dc6e450e26436f69f4dda5547c61e73d4aa2da69be66cf46204481b1726a7ca746712f0a35c3e689f9da99d4376bc62097512958ec SHA512 0d8754b31eeec184a0d3becb75d3c69c2e922abbe00c175c8cb23d7ea96838896db2da90de45653a7612a041975975f062d289d7d362f6f1abae1d916dbc4b89
 DIST ghemical-3.0.0.tar.gz 2196716 BLAKE2B 62008667c58cb058beb8eb3946bb96fb03aceff7cc93f64aecc697a7648946936208063b419aca57f740d5760a90d923d81f8cc8d80fb68bdf924b23cd2061b3 SHA512 d4dd0b063a4dea33fa7430e77a2da253c74079fd8b5f21e8c2b5da1383f3689b93305417e1bf0d4908b87c91afb33c3266dd6bd6fbcd768cc98614a3f730ee94
-EBUILD ghemical-3.0.0.ebuild 1348 BLAKE2B 9148486b590ad538b225722fc5cddc51aee51b6243be59b040de628370cf1b3981b0490c9b2a821e0e8a1246a624ecbc82bb4903f42a5509a718b010f901d798 SHA512 a6c018a4b4e49d46eef4b004ebb3c55db9dff66c05390c465a51903af62c03f0bea15a8d33a1d27ca8123207ad8214295bb0dc8888385d200f8268d8aab05fb4
+EBUILD ghemical-3.0.0.ebuild 1353 BLAKE2B 5037472809fb5ff199c6683d4db73bd2c86ebd1764f4c2263bbcb5fb0910c12d768692451f7a8a27dc5307023f5a710b1cac933da16f211705d5744db8129028 SHA512 790b807c3e9e33230a752187cb362336de8f2f953e5bc6cbe834c53a85cd74509449c4e20e1fd0cc22f9e092c44bb4f24c57cf2a96ec38cb7059188a68f5237e
 MISC metadata.xml 775 BLAKE2B c41e23e584e920e6ec68591abedaf69d746279e5c0cf45d65eb3afd150a2c4c747a2bdcc15386e85309300200877d2013fdd6d5aaf8b09bcfa8b45cfa32084c3 SHA512 59e27f59b90d5f7436855509a6de0c0b296cd9ae1ccaec02570a5055482e033c12df040430f466a1ba2c004b555fdd89617ad65b608590a40fe27790888940fe
diff --git a/sci-chemistry/ghemical/ghemical-3.0.0.ebuild b/sci-chemistry/ghemical/ghemical-3.0.0.ebuild
index ed816b7a5491..5704b7df145c 100644
--- a/sci-chemistry/ghemical/ghemical-3.0.0.ebuild
+++ b/sci-chemistry/ghemical/ghemical-3.0.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-inherit autotools eutils
+inherit autotools desktop
 
 DESCRIPTION="Chemical quantum mechanics and molecular mechanics"
 HOMEPAGE="http://bioinformatics.org/ghemical/"
@@ -11,7 +11,7 @@ SRC_URI="http://bioinformatics.org/ghemical/download/current/${P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="amd64 x86"
+KEYWORDS="~amd64 ~x86"
 IUSE="openbabel seamonkey threads"
 
 RDEPEND="
@@ -36,9 +36,9 @@ src_prepare() {
 }
 
 src_configure() {
-# With amd64, if you want gamess I recommend adding gamess and gtk-gamess to package.provided for now.
+	# With amd64, if you want gamess I recommend adding gamess and gtk-gamess to package.provided for now.
 
-# Change the built-in help browser.
+	# Change the built-in help browser.
 	if use seamonkey ; then
 		sed -i -e 's|mozilla|seamonkey|g' src/gtk_app.cpp || die "sed failed for seamonkey!"
 	else
diff --git a/sci-chemistry/molequeue/Manifest b/sci-chemistry/molequeue/Manifest
index 65a52494b05b..5297d5f0b10b 100644
--- a/sci-chemistry/molequeue/Manifest
+++ b/sci-chemistry/molequeue/Manifest
@@ -1,4 +1,7 @@
 AUX molequeue-0.8.0-cmake.patch 4285 BLAKE2B 916f0c248f487b6d7c11dd34e20364b5dfb494d2e27e657bc5a13f9d6c3f71ae2ab6818bace7df04c0a1388f6f85c42e3e0ab96fc5d3d892c0a95612532baf28 SHA512 9031fd3e5efe0a9332db4b1f46d82486fc804cef55c9fab35030bc562d1a40f5f16a02a5eb8c31bf4c50c7a0abcf22c11da5bdd4e2a45a37a8b6f4ff994d3ad6
+AUX molequeue-0.9.0-qt-5.11b3.patch 6380 BLAKE2B 8d4a66dab1b233880269559cff9b566593ec271fc2b0982a92eec1d60a7c2c42e7186c0007be2afc956200d28c250822b36d3146d1a9ff1fb33b574f97969c60 SHA512 09429566422a1490c2621fd895238d4aeba3c324563cab411290a60942c749e9fa967dd6399f4f4efdc635fa77c339d08824def3e6a175aadc1061893df7df9c
 DIST molequeue-0.8.0.tar.gz 643072 BLAKE2B c9ba0a93e4dac3027de1aeb5ae6c62fc3e4229786973d6c3b56af4b70476b0ed54a563837d489912a40c76b9ce0013e13633a327eb314c34305ba17d7f0b4cf7 SHA512 b9539d2ad2c67188ad254f186c1d67c122a15a32047801c632a1613a4f9c887f38baf2da1bb80cb123391948c2a44604fb1082e475ca6de1e683fbe51266ac84
+DIST molequeue-0.9.0.tar.gz 604015 BLAKE2B 37e7f404a0fefb40defb198295659372121fbe770269c2f9fb92e856aceb8222bec5e83939ecea061b76f925c0cbde1be0a854db41f992a92a2b2b9e0651f2e1 SHA512 87ddd8ca59227cab60c0ce2643e5bd435d9ac7e23b929659b95f190478734a5b71d4935f37d03eeadbc39939cbffb3604e0a283d50b0a23a1a000b57c1fce335
 EBUILD molequeue-0.8.0.ebuild 1613 BLAKE2B 21ddbe84fb9ad674cc796330ee2a26f5fdcfc7f6187869d2775e5679bbb2bf2dc147d80c79617867f9b1424bf07eb797315fb5cab3cb59359c39171315cf353c SHA512 6971db16063f3c1dfad7a780adae7aaf438c2957f46698a1739a65ac3d658ccac501f687db18eddc1305a4e6a220cac206d781f5783cdcb0d38b4e952c550ed7
+EBUILD molequeue-0.9.0.ebuild 1471 BLAKE2B ace497ea7a4c5ebaae14755f27ac18348fc7190246f7292318d50d2f1b120152fb626af0efd735f27b9d1aed4d615912261f304b589f4f947f3461d6989f26cb SHA512 05afccaad6d36c69a8838278a9e4d5af3257aff61c99467958fd62074c7e4823100d15e80c86521e626fc3625d1333c5cdaea78a16f51fa3ed9a166f34ea3325
 MISC metadata.xml 1257 BLAKE2B 181f9234f11d0cb14fd6b93b42ef153c089d4df8dcb7cf72bc710dbee11bf4bb573f37ea703d02dbe17fa1f39c0aaf591c6d28ad1429abced5108b9ce39f2030 SHA512 10e3dd48ec1e54bc0d47d4c2f0aca427875cc0ceb59a93ab41ab2734607aa6474e80f3ae622e45fa319753591f16439118dd0b301068cb3e16fd79ff11a4f058
diff --git a/sci-chemistry/molequeue/files/molequeue-0.9.0-qt-5.11b3.patch b/sci-chemistry/molequeue/files/molequeue-0.9.0-qt-5.11b3.patch
new file mode 100644
index 000000000000..0e04e22f7434
--- /dev/null
+++ b/sci-chemistry/molequeue/files/molequeue-0.9.0-qt-5.11b3.patch
@@ -0,0 +1,154 @@
+From 844c6a7ee7f4ad00bc8225549d26c6bde8b683ab Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner <asturm@gentoo.org>
+Date: Tue, 17 Apr 2018 10:50:36 +0200
+Subject: [PATCH] Fix build with Qt 5.11_beta3 (dropping qt5_use_modules)
+
+---
+ molequeue/app/CMakeLists.txt                       | 14 +++++---------
+ molequeue/app/testing/CMakeLists.txt               |  6 ++----
+ molequeue/app/testing/clienttestsrc/CMakeLists.txt |  3 +--
+ molequeue/client/CMakeLists.txt                    |  2 +-
+ molequeue/plugins/localsocketserver/CMakeLists.txt |  3 +--
+ molequeue/servercore/CMakeLists.txt                |  2 +-
+ molequeue/zeromq/CMakeLists.txt                    |  3 +--
+ 7 files changed, 12 insertions(+), 21 deletions(-)
+
+diff --git a/molequeue/app/CMakeLists.txt b/molequeue/app/CMakeLists.txt
+index d40fce5..b6e72f8 100644
+--- a/molequeue/app/CMakeLists.txt
++++ b/molequeue/app/CMakeLists.txt
+@@ -1,11 +1,9 @@
+-set(qt_components Core Widgets Network)
++find_package(Qt5 REQUIRED COMPONENTS Core Widgets Network)
+ 
+ if(MoleQueue_USE_EZHPC_UIT)
+-  list(APPEND qt_components XmlPatterns)
++  find_package(Qt5XmlPatterns REQUIRED)
+ endif()
+ 
+-find_package(Qt5 COMPONENTS ${qt_components} REQUIRED)
+-
+ # Provide some simple API to find the plugins, scripts, etc.
+ if(APPLE)
+   # It is a special case, the app bundle logic breaks the relative pathing.
+@@ -170,12 +168,11 @@ qt5_wrap_ui(ui_srcs ${ui_files})
+ qt5_add_resources(rcc_srcs queuetray.qrc)
+ 
+ add_library(molequeue_static STATIC ${mq_srcs} ${ui_srcs})
+-qt5_use_modules(molequeue_static ${qt_components})
+ set_target_properties(molequeue_static PROPERTIES AUTOMOC TRUE)
+-target_link_libraries(molequeue_static MoleQueueServerCore)
++target_link_libraries(molequeue_static MoleQueueServerCore Qt5::Core Qt5::Widgets Qt5::Network)
+ 
+ if(MoleQueue_USE_EZHPC_UIT)
+-  target_link_libraries(molequeue_static KDSoap::kdsoap)
++  target_link_libraries(molequeue_static KDSoap::kdsoap Qt5::XmlPatterns)
+ endif()
+ 
+ if(MoleQueue_BUILD_CLIENT)
+@@ -195,8 +192,7 @@ elseif(WIN32)
+ endif()
+ 
+ add_executable(molequeue WIN32 MACOSX_BUNDLE ${sources} ${rcc_srcs})
+-qt5_use_modules(molequeue ${qt_components})
+-target_link_libraries(molequeue molequeue_static)
++target_link_libraries(molequeue molequeue_static Qt5::Core Qt5::Widgets Qt5::Network)
+ if(WIN32)
+   target_link_libraries(molequeue Qt5::WinMain)
+ endif()
+diff --git a/molequeue/app/testing/CMakeLists.txt b/molequeue/app/testing/CMakeLists.txt
+index 5b88038..f79a17a 100644
+--- a/molequeue/app/testing/CMakeLists.txt
++++ b/molequeue/app/testing/CMakeLists.txt
+@@ -31,8 +31,7 @@ set(testutils_SRCS
+ 
+ add_library(testutils STATIC ${testutils_SRCS})
+ set_target_properties(testutils PROPERTIES AUTOMOC TRUE)
+-qt5_use_modules(testutils Test)
+-target_link_libraries(testutils molequeue_static)
++target_link_libraries(testutils molequeue_static Qt5::Test)
+ 
+ set(MyTests
+   filespecification
+@@ -71,9 +70,8 @@ endif()
+ 
+ foreach(test ${MyTests})
+   add_executable(${test}test MACOSX_BUNDLE ${test}test.cpp)
+-  qt5_use_modules(${test}test Test)
+   set_target_properties(${test}test PROPERTIES AUTOMOC TRUE)
+-  target_link_libraries(${test}test testutils)
++  target_link_libraries(${test}test testutils Qt5::Test)
+   add_test(NAME molequeue-${test} COMMAND ${test}test)
+ endforeach()
+ 
+diff --git a/molequeue/app/testing/clienttestsrc/CMakeLists.txt b/molequeue/app/testing/clienttestsrc/CMakeLists.txt
+index d506010..7377e3c 100644
+--- a/molequeue/app/testing/clienttestsrc/CMakeLists.txt
++++ b/molequeue/app/testing/clienttestsrc/CMakeLists.txt
+@@ -9,6 +9,5 @@ set(srcs sendRpcKill)
+ foreach(source ${srcs})
+   add_executable(${source} ${source}.cpp)
+   set_target_properties(${source} PROPERTIES AUTOMOC TRUE)
+-  qt5_use_modules(${source} Core)
+-  target_link_libraries(${source} MoleQueueClient)
++  target_link_libraries(${source} MoleQueueClient Qt5::Core)
+ endforeach()
+diff --git a/molequeue/client/CMakeLists.txt b/molequeue/client/CMakeLists.txt
+index 8cb131a..c614aea 100644
+--- a/molequeue/client/CMakeLists.txt
++++ b/molequeue/client/CMakeLists.txt
+@@ -15,7 +15,7 @@ set(headers
+ include_directories(${CMAKE_CURRENT_BINARY_DIR})
+ 
+ add_library(MoleQueueClient ${sources})
+-qt5_use_modules(MoleQueueClient Network)
++target_link_libraries(MoleQueueClient Qt5::Network)
+ set_target_properties(MoleQueueClient PROPERTIES AUTOMOC TRUE)
+ include(GenerateExportHeader)
+ generate_export_header(MoleQueueClient EXPORT_FILE_NAME molequeueclientexport.h)
+diff --git a/molequeue/plugins/localsocketserver/CMakeLists.txt b/molequeue/plugins/localsocketserver/CMakeLists.txt
+index fd030f9..80018c3 100644
+--- a/molequeue/plugins/localsocketserver/CMakeLists.txt
++++ b/molequeue/plugins/localsocketserver/CMakeLists.txt
+@@ -2,9 +2,8 @@ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY
+   ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/../lib/molequeue/plugins)
+ 
+ add_library(LocalSocketServer MODULE localsocketconnectionlistenerfactory.cpp)
+-qt5_use_modules(LocalSocketServer Network)
+ set_target_properties(LocalSocketServer PROPERTIES AUTOMOC TRUE PREFIX "")
+-target_link_libraries(LocalSocketServer MoleQueueServerCore)
++target_link_libraries(LocalSocketServer MoleQueueServerCore Qt5::Network)
+ 
+ set_property(GLOBAL APPEND PROPERTY MoleQueue_PLUGINS LocalSocketServer)
+ 
+diff --git a/molequeue/servercore/CMakeLists.txt b/molequeue/servercore/CMakeLists.txt
+index aab0bec..eee1bfd 100644
+--- a/molequeue/servercore/CMakeLists.txt
++++ b/molequeue/servercore/CMakeLists.txt
+@@ -12,7 +12,7 @@ add_library(MoleQueueServerCore
+   messageidmanager_p.cpp
+ )
+ 
+-qt5_use_modules(MoleQueueServerCore Network)
++target_link_libraries(MoleQueueServerCore Qt5::Network)
+ set_target_properties(MoleQueueServerCore PROPERTIES AUTOMOC TRUE)
+ #target_link_libraries(MoleQueueServerCore)
+ 
+diff --git a/molequeue/zeromq/CMakeLists.txt b/molequeue/zeromq/CMakeLists.txt
+index 188f437..451c0ec 100644
+--- a/molequeue/zeromq/CMakeLists.txt
++++ b/molequeue/zeromq/CMakeLists.txt
+@@ -13,9 +13,8 @@ set(sources
+ )
+ 
+ add_library(MoleQueueZeroMq ${sources})
+-qt5_use_modules(MoleQueueZeroMq Network)
+ set_target_properties(MoleQueueZeroMq PROPERTIES AUTOMOC TRUE)
+-target_link_libraries(MoleQueueZeroMq MoleQueueServerCore ${ZeroMQ_LIBRARIES})
++target_link_libraries(MoleQueueZeroMq MoleQueueServerCore ${ZeroMQ_LIBRARIES} Qt5::Network)
+ 
+ generate_export_header(MoleQueueZeroMq
+   EXPORT_FILE_NAME molequeuezeromqexport.h)
+-- 
+2.17.0
+
diff --git a/sci-chemistry/molequeue/molequeue-0.9.0.ebuild b/sci-chemistry/molequeue/molequeue-0.9.0.ebuild
new file mode 100644
index 000000000000..1f484848233a
--- /dev/null
+++ b/sci-chemistry/molequeue/molequeue-0.9.0.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils python-single-r1 virtualx
+
+DESCRIPTION="Abstract, manage and coordinate execution of tasks"
+HOMEPAGE="https://www.openchemistry.org/projects/molequeue/"
+SRC_URI="https://github.com/OpenChemistry/molequeue/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+client doc server test +zeromq"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}
+	server? ( client )
+	test? ( server )"
+
+RDEPEND="${PYTHON_DEPS}
+	dev-qt/qtcore:5
+	dev-qt/qtgui:5
+	dev-qt/qtnetwork:5
+	dev-qt/qtwidgets:5
+	zeromq? ( net-libs/cppzmq:0= )"
+DEPEND="${RDEPEND}
+	doc? ( app-doc/doxygen )"
+
+PATCHES=( "${FILESDIR}"/${P}-qt-5.11b3.patch )
+
+src_configure() {
+	local mycmakeargs=(
+		-DMoleQueue_USE_EZHPC_UIT=OFF
+		-DBUILD_DOCUMENTATION=$(usex doc)
+		-DMoleQueue_BUILD_CLIENT=$(usex client)
+		-DMoleQueue_BUILD_APPLICATION=$(usex server)
+		-DENABLE_TESTING=$(usex test)
+		-DUSE_ZERO_MQ=$(usex zeromq)
+		-DINSTALL_LIBRARY_DIR=$(get_libdir)
+	)
+	use zeromq && \
+		mycmakeargs+=( -DZeroMQ_ROOT_DIR=\"${EPREFIX}/usr\" )
+
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	cmake-utils_src_compile all $(usex doc documentation "")
+}
+
+src_test() {
+	VIRTUALX_COMMAND=cmake-utils_src_test
+	virtualmake
+}
+
+src_install() {
+	use doc && local HTML_DOCS=( "${BUILD_DIR}"/docs/html/. )
+	cmake-utils_src_install
+}
diff --git a/sci-chemistry/mpqc/Manifest b/sci-chemistry/mpqc/Manifest
index 9109f253ea43..a3e4f501b1c8 100644
--- a/sci-chemistry/mpqc/Manifest
+++ b/sci-chemistry/mpqc/Manifest
@@ -4,8 +4,5 @@ AUX mpqc-2.3.1-respect-ldflags.patch 666 BLAKE2B 63e6f1234b63e3ef44b99e360adfd01
 AUX mpqc-2.3.1-test-failure-hack.patch 543 BLAKE2B 77800cac8c280bd6ffc60153ad703a46d693eba2faa5759b5f5ff8b24f3ed9f516c66f466a15128540eaad778fa447e9a02ea563304deeb9aba1796b9786b29d SHA512 ae626fd6b723f6089b4cf6c2866863ab622aded5636735475cc2d85450b3753bc1cd3168ae1dcb49a579c4a15103cc64256c96eb12b52fcf0599e12bbdacfbc9
 AUX mpqc-2.3.1-wformat-security.patch 2284 BLAKE2B c733b98618e611e93a6ed3939b47476c1c7bdb4275c19f4bbceae5ca28ccd0ee6da2c97fc0ab952d64ea5cb951cfbbfbc13b01b960c8ad7f9cb4973347b38f37 SHA512 22b30cc10f64ff96d027d2727643a3f3bfb08315f33996dfd8b9a28e0dcb9bee2d07cf1d8eead0df22be3117206737a52e350e7dfcfa07d381086610a6b94595
 DIST mpqc-2.3.1.tar.bz2 2521392 BLAKE2B 0c2cd9ac2fe32791ab5f0226972b5f1376e5f0ed368e12f6e89f8ff44cb11e4e2cf150f24b3768eb119e94289aca989a5287fef9b51dbd67e2856e944b61c299 SHA512 34f24f72c6c0024e72d47c7fd17927ca2a88020b30d22a791954fbc933f67ed6dd6741ee8a80ddd4fdb007f1a357b5f5ea7fc284cab85474bf60e9f29aaaa747
-EBUILD mpqc-2.3.1-r1.ebuild 2267 BLAKE2B 8d76ea864b51ad58c571dc95b8453bc9eae5028d810b6fbce669c3bebeec4b782229256c85b39091376c4432b41cc574a05203386654821749c800a3dd8344f8 SHA512 4b191021570bd3f29e58e76fdd63a0c25a6eed87160df189d8fbe202b4fb1f0dc4c63aba0c5500e87ab39c8a018eefda25252560bf6e1acd4ad29fe3a2c504e1
-EBUILD mpqc-2.3.1-r2.ebuild 2471 BLAKE2B 3b7b069e709ad64ee7a4e22d8fa51703a22cf7077a1d36c3d506e9598a3a515fe2775f8a5c74268f571dc329d43ae064fcf78571974fdab15017b2421ee92c01 SHA512 c87973d00b02822c0966151fc61c113430ed51ce4f9c048173163b77928fbc4ca4f664ad46d48455c33c7307835173ce1609197286441d4ff329dcdbacab4f16
-EBUILD mpqc-2.3.1-r3.ebuild 2481 BLAKE2B c1e5c1df4e1fd0d947b0a3384413e4e28c93742897254cb02b2c9f99a5aedcabaa017444196a4af64d995b1cea7a9a55064d5398b3d43521486cbf6a623a1c35 SHA512 e169bc991e917b036ae715d2a08c8ee013c585a4607f16c70edaf8910ff577a3b8325b10d8ae0d59bf653ecee2a1c897364338c7da925683c1b30f8e50b87826
 EBUILD mpqc-2.3.1-r4.ebuild 2418 BLAKE2B 16a077d68bc41da4670cc19fcd404b7f73e3e07213c7e9f2baefacae27cda7fbf5b9bfeda90e256f5cae7648834a2dd15958fd44faa8ff7bf49b1d568691584d SHA512 41e91bcdc68613f53a712cb9235c3b0783f3d841395594c8f7bc90211cb80d30981b9d0c4290906cee52269e3486560576b5f09a836ccf5ccb96cc2bae7db512
 MISC metadata.xml 349 BLAKE2B a0ae0f532958bd0dd101b63a303db066c64197b45cc6b73521073e38c0bf52bef1209575e8232928aed14d541928b9ffa7f537c7723c3b14ed69cf3b09c49f17 SHA512 4cdfca1b779b107326bdc77fd120008a4daa7da9b93ed3f783e95637796545b95c04477786633856f3d3e1656339db042953d3b2644a18cc25a2b1dc91dc80c6
diff --git a/sci-chemistry/mpqc/mpqc-2.3.1-r1.ebuild b/sci-chemistry/mpqc/mpqc-2.3.1-r1.ebuild
deleted file mode 100644
index 794008aa31d9..000000000000
--- a/sci-chemistry/mpqc/mpqc-2.3.1-r1.ebuild
+++ /dev/null
@@ -1,92 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-DESCRIPTION="The Massively Parallel Quantum Chemistry Program"
-HOMEPAGE="http://www.mpqc.org/"
-SRC_URI="mirror://sourceforge/mpqc/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ppc ppc64 x86"
-IUSE="doc threads tk"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	tk? ( dev-lang/tk )"
-DEPEND="${RDEPEND}
-	dev-lang/perl
-	sys-devel/flex
-	sys-apps/sed
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		media-gfx/graphviz )"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	# do not install tkmolrender if not requested
-	if ! use tk; then
-		sed \
-			-e "s:.*/bin/molrender/tkmolrender.*::" \
-			-e "s:.*\$(INSTALLBINOPT) tkmolrender.*::" \
-			-e "s:/bin/rm -f tkmolrender::" \
-			-i "./src/bin/molrender/Makefile" \
-			|| die "failed to disable tkmolrender"
-	fi
-}
-
-src_compile() {
-	# Only shared will work on ppc64 - bug #62124
-	# But we always want shared libraries
-	econf \
-		$(use_enable threads) \
-		--enable-shared \
-		${myconf}
-
-	sed \
-		-e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS}:" \
-		-e "s:^FFLAGS =.*$:FFLAGS=${FFLAGS:- -O2}:" \
-		-e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS}:" \
-		lib/LocalMakefile
-	emake || die "emake failed"
-}
-
-src_test() {
-	cd "${S}"/src/bin/mpqc/validate
-
-	# we'll only run the small test set, since the
-	# medium and large ones take >10h and >24h on my
-	# 1.8Ghz P4M
-	emake -j1 check0 || die "failed in test routines"
-}
-
-src_install() {
-	emake -j1 installroot="${D}" install install_devel install_inc \
-		|| die "install failed"
-
-	dodoc CHANGES CITATION README || die "failed to install docs"
-
-	# make extended docs
-	if use doc; then
-		cd "${S}"/doc
-		emake -j1 all || die "failed to generate documentation"
-		doman man/man1/* man/man3/* || \
-			die "failed to install man pages"
-		dohtml -r html/
-	fi
-}
-
-pkg_postinst() {
-	echo
-	einfo "MPQC can be picky with regard to compilation flags."
-	einfo "If during mpqc runs you have trouble converging or "
-	einfo "experience oscillations during SCF interations, "
-	einfo "consider recompiling with less aggressive CFLAGS/CXXFLAGS."
-	einfo "Particularly, replacing -march=pentium4 by -march=pentium3"
-	einfo "might help if you encounter problems with correlation "
-	einfo "consistent basis sets."
-	echo
-}
diff --git a/sci-chemistry/mpqc/mpqc-2.3.1-r2.ebuild b/sci-chemistry/mpqc/mpqc-2.3.1-r2.ebuild
deleted file mode 100644
index c2776b711a1d..000000000000
--- a/sci-chemistry/mpqc/mpqc-2.3.1-r2.ebuild
+++ /dev/null
@@ -1,102 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=2
-
-inherit autotools eutils toolchain-funcs
-
-DESCRIPTION="The Massively Parallel Quantum Chemistry Program"
-HOMEPAGE="http://www.mpqc.org/"
-SRC_URI="mirror://sourceforge/mpqc/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 x86"
-IUSE="doc mpi threads tk"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	mpi? ( virtual/mpi[cxx] )
-	tk? ( dev-lang/tk )"
-DEPEND="${RDEPEND}
-	dev-lang/perl
-	sys-devel/flex
-	sys-apps/sed
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		media-gfx/graphviz )"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-as-needed.patch \
-		"${FILESDIR}"/${P}-respect-ldflags.patch \
-		"${FILESDIR}"/${P}-test-failure-hack.patch
-	# do not install tkmolrender if not requested
-	if ! use tk; then
-		sed \
-			-e "s:.*/bin/molrender/tkmolrender.*::" \
-			-e "s:.*\$(INSTALLBINOPT) tkmolrender.*::" \
-			-e "s:/bin/rm -f tkmolrender::" \
-			-i "./src/bin/molrender/Makefile" \
-			|| die "failed to disable tkmolrender"
-	fi
-	eautoreconf
-}
-
-src_configure() {
-	tc-export CC CXX
-	if use mpi; then
-		export CC=mpicc
-		export CXX=mpicxx
-	fi
-	econf \
-		$(use_enable threads) \
-		$(use_enable mpi parallel) \
-		--enable-shared \
-		${myconf}
-
-	sed \
-		-e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS}:" \
-		-e "s:^FFLAGS =.*$:FFLAGS=${FFLAGS:- -O2}:" \
-		-e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS}:" \
-		lib/LocalMakefile
-}
-
-src_test() {
-	cd "${S}"/src/bin/mpqc/validate
-
-	# we'll only run the small test set, since the
-	# medium and large ones take >10h and >24h on my
-	# 1.8Ghz P4M
-	emake -j1 check0 || die "failed in test routines"
-}
-
-src_install() {
-	emake installroot="${D}" install install_devel install_inc \
-		|| die "install failed"
-
-	dodoc CHANGES CITATION README || die "failed to install docs"
-
-	# make extended docs
-	if use doc; then
-		cd "${S}"/doc
-		emake -j1 all || die "failed to generate documentation"
-		doman man/man1/* man/man3/* || \
-			die "failed to install man pages"
-		dohtml -r html/
-	fi
-}
-
-pkg_postinst() {
-	echo
-	einfo "MPQC can be picky with regard to compilation flags."
-	einfo "If during mpqc runs you have trouble converging or "
-	einfo "experience oscillations during SCF interations, "
-	einfo "consider recompiling with less aggressive CFLAGS/CXXFLAGS."
-	einfo "Particularly, replacing -march=pentium4 by -march=pentium3"
-	einfo "might help if you encounter problems with correlation "
-	einfo "consistent basis sets."
-	echo
-}
diff --git a/sci-chemistry/mpqc/mpqc-2.3.1-r3.ebuild b/sci-chemistry/mpqc/mpqc-2.3.1-r3.ebuild
deleted file mode 100644
index b53abbdc26cb..000000000000
--- a/sci-chemistry/mpqc/mpqc-2.3.1-r3.ebuild
+++ /dev/null
@@ -1,106 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit autotools-utils toolchain-funcs
-
-DESCRIPTION="The Massively Parallel Quantum Chemistry Program"
-HOMEPAGE="http://www.mpqc.org/"
-SRC_URI="mirror://sourceforge/mpqc/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ppc ppc64 x86"
-IUSE="doc mpi threads static-libs tk"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	mpi? ( virtual/mpi[cxx] )
-	tk? ( dev-lang/tk )"
-DEPEND="${RDEPEND}
-	dev-lang/perl
-	sys-devel/flex
-	sys-apps/sed
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		media-gfx/graphviz )"
-
-PATCHES=(
-		"${FILESDIR}"/${P}-as-needed.patch
-		"${FILESDIR}"/${P}-respect-ldflags.patch
-		"${FILESDIR}"/${P}-test-failure-hack.patch
-		"${FILESDIR}"/${P}-blas.patch
-	)
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-DOCS=(CHANGES CITATION README)
-
-src_prepare() {
-	# do not install tkmolrender if not requested
-	if ! use tk; then
-		sed \
-			-e "s:.*/bin/molrender/tkmolrender.*::" \
-			-e "s:.*\$(INSTALLBINOPT) tkmolrender.*::" \
-			-e "s:/bin/rm -f tkmolrender::" \
-			-i "./src/bin/molrender/Makefile" \
-			|| die "failed to disable tkmolrender"
-	fi
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	tc-export CC CXX
-	if use mpi; then
-		export CC=mpicc
-		export CXX=mpicxx
-	fi
-	local myeconfargs=(
-		$(use_enable threads)
-		$(use_enable mpi parallel) )
-
-	autotools-utils_src_configure
-	sed \
-		-e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS}:" \
-		-e "s:^FFLAGS =.*$:FFLAGS=${FFLAGS:- -O2}:" \
-		-e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS}:" \
-		-i lib/LocalMakefile || die
-}
-
-src_test() {
-	cd "${AUTOTOOLS_BUILD_DIR}"/src/bin/mpqc/validate
-
-	# we'll only run the small test set, since the
-	# medium and large ones take >10h and >24h on my
-	# 1.8Ghz P4M
-	emake -j1 check1
-}
-
-src_install() {
-	autotools-utils_src_install installroot="${D}" install install_devel install_inc
-
-	# make extended docs
-	if use doc; then
-		cd "${AUTOTOOLS_BUILD_DIR}"/doc
-		emake -j1 all
-		doman man/man1/* man/man3/*
-		dohtml -r html
-	fi
-}
-
-pkg_postinst() {
-	echo
-	einfo "MPQC can be picky with regard to compilation flags."
-	einfo "If during mpqc runs you have trouble converging or "
-	einfo "experience oscillations during SCF interations, "
-	einfo "consider recompiling with less aggressive CFLAGS/CXXFLAGS."
-	einfo "Particularly, replacing -march=pentium4 by -march=pentium3"
-	einfo "might help if you encounter problems with correlation "
-	einfo "consistent basis sets."
-	echo
-}
diff --git a/sci-chemistry/prekin/Manifest b/sci-chemistry/prekin/Manifest
index 1d1e0de863e4..8ef0a2f31be5 100644
--- a/sci-chemistry/prekin/Manifest
+++ b/sci-chemistry/prekin/Manifest
@@ -1,5 +1,5 @@
 AUX 6.51.081122-Makefile.patch 1456 BLAKE2B 769c5237659ddc6abcbeea88d620993b7c52f77ee4b12a8bb200e452b0e5dd8fe41ba2c18056439998ba7d2dea90351e2fc7997cc71e5ec447e128e3c1535b62 SHA512 96b8cda8fc71b2e72c0e8e0a70560a7928456fe81aaa40810a8bcbe77835a7242e8e0d39fac3258e5848a4e4ac14bf9d7dfd4dff8385eb983f359a9f85af9838
 AUX 6.51.081122-overflow.patch 1156 BLAKE2B 86c70ec89564972a451d23a41863969e31b2d0b866c0282728625fe200928aaf87bec7751e8df3fefbce6c2d4f0a21aba13b1d117247ab6b2b14c7d1db2e45b8 SHA512 fe0ff6e3432177653d29ef51ef3a767dc3872fc0a5350c786b3623b6b4d63866fbfbaf4369676feb545766cac5620b209bd87e92c0ecf2280bb39470e7dd5f7b
 DIST prekin.6.51.081122.src.tgz 350756 BLAKE2B 657706e83d06be74f2565abb4db1c886c19247b736200cf309cc143f71c7f47e4c85d869b286ec3e250ecb0d714e1454044836001aa6b883513d9149683bb320 SHA512 9a41f30a9de955c78ee5685807482b2b073705643cceb53bf57eaf7c0c4753dc88fa8dc19f09d4c8a07124c3c3c73716f29126860ae37ff4dd6fb6178b829d1f
-EBUILD prekin-6.51.081122-r1.ebuild 1052 BLAKE2B 8738d2f9cf0f55938eacc0c9871431913ef36ad819835cee717f9f021d5600bae001e28abf87ebad60f7205817efa561e0f9f7fcba8ba01056f922ff9cf85939 SHA512 5149cbb41bc53b92c2c6c467d30adb271c32cd7233480ed0d6c2bf01f61d7b1f159c44cb656aafe1c6cfffb918aba2d448723a0700725a70e8369fb90691d776
+EBUILD prekin-6.51.081122-r1.ebuild 934 BLAKE2B c24b0ffb0d9e7ef0fb1a7519cc7eb8d126f0ebb3b4a9754ae7966cc9d6f9415b293f74ebe5617a3e141a34793d1f35dfbe0e980cf4f9b353b3828d4cfd922204 SHA512 1ad9797f5778a892f6e604ab43973f06b18c30acdb9570b0613b1de730dfa2e51ce449426d58ae83613ed5bfb9fb2f05b27913c4e53764b92a34b062f1e5f395
 MISC metadata.xml 261 BLAKE2B 509ce9958149f9cd522a2c68dd0d23ed851d19d02494611456592897093378d180a6006cddf1575fd60106119e72726255c49db2e10fde1b370bdf2f3cf8c94a SHA512 72682d17ec2b918131b551bd1ff41004965d3cf0c00d24222b34741d2eabf601cf36d4266be70ba7fb7bd0ab55d9dcb5b8e4ca41125bc31f176516797459c8c7
diff --git a/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild b/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild
index 8bea9cc52301..db0c34eca49b 100644
--- a/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild
+++ b/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI="2"
+EAPI=6
 
-inherit toolchain-funcs eutils multilib
+inherit toolchain-funcs
 
 MY_P=${PN}.${PV}
 
@@ -16,37 +16,33 @@ SLOT="0"
 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
 IUSE="X"
 
-RDEPEND="x11-libs/libXext
+RDEPEND="
+	x11-libs/libXext
 	x11-libs/libXmu
 	x11-libs/libX11
 	x11-libs/libXt
-	X? ( >=x11-libs/motif-2.3:0 )"
+	X? ( >=x11-libs/motif-2.3:0= )"
 DEPEND="${RDEPEND}"
 
 S=${WORKDIR}/${MY_P}
+PATCHES=(
+	"${FILESDIR}"/${PV}-Makefile.patch
+	"${FILESDIR}"/${PV}-overflow.patch
+)
 
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-Makefile.patch \
-		"${FILESDIR}"/${PV}-overflow.patch
-	sed  \
+src_configure() {
+	tc-export CC
+
+	sed \
 		-e 's:cc:$(CC):g' \
 		-e "s:GENTOOLIBDIR:$(get_libdir):g" \
-		"${S}"/Makefile.linux > Makefile || die
+		Makefile.linux > Makefile || die
 }
 
 src_compile() {
-	local mytarget
-
-	if use X; then
-		mytarget="${PN}"
-	else
-		mytarget="nogui"
-	fi
-
-	emake CC="$(tc-getCC)" ${mytarget} || die
+	emake $(usex X ${PN} nogui)
 }
 
 src_install() {
-	dobin "${S}"/prekin || die
+	dobin prekin
 }