6 files changed, 0 insertions, 173 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 5c77a1d62ab3..7e68e2b43d86 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/avogadro/Manifest b/sci-chemistry/avogadro/Manifest
index e1221628478b..83d4da03e654 100644
--- a/sci-chemistry/avogadro/Manifest
+++ b/sci-chemistry/avogadro/Manifest
@@ -1,14 +1,9 @@
-AUX avogadro-1.1.0-xlibs.patch 680 BLAKE2B 381597d8b1444f412ecefdf1de2860f557172b195b400e869ee1404b1614b494015c1815a0cafbdf1b19483aa23d0793f09c68df6e6a3a53e9de19524b431528 SHA512 df2727e4aea1549daada56778d7710656f3f6ff9fa31c441c06e82241c8e5b0733c39d575c98f2d1b57b9be0a52d445412ecd6cca7a1f319c6982035e789f21d
 AUX avogadro-1.1.1-boost-join-moc.patch 2051 BLAKE2B 8711c60f2ad0d63d6b4cb39c8461a70f5ced9d9045e5b9b18cea5577721f15e7c9314c8d86d844f47fca5b769837167268903d91328219c5eda16c72f3007967 SHA512 d4e4ef54d94cccb0f34c4960d302772f9da47e27cb79e1ee0a4e928ef248ac629fd59f1564bedf7c82a2a7ca8b25456878c22569dbcda26478a6c06e5815a084
-AUX avogadro-1.1.1-eigen3.patch 2230 BLAKE2B c22f039d1c91a8fbe06d8e7f272900111bde03635b1120accc73ca47a241c36fffe68ed9766bba088eb3137de1ccd6acb1c70a26f0970cac5a9ab6096b87eeda SHA512 df6a53cacebee613739d230fc0c7dc21cb67d553950af82cf83d04750f1d9fa98a3bb052c15fffebacf41d2e53dcd3503bffff2aa8dfbfcb47e2d1ebccd77614
-AUX avogadro-1.1.1-gcc-version.patch 997 BLAKE2B d04059442cf31f4224c6be12b695b379f580717131b590b43e919e7b4789ccb643f93ec3f89d7a4572ca94a08442ea17b01e430162f7187078fe5688af78fd25 SHA512 1a1d204a7f8a050446d5691fce0b7c46e0a6e619a042e769771f8a3a3596f9ae176c33b070d212c07dc977b20db82e19a9ee1e64963e5cae68c43a9d379818b4
 AUX avogadro-1.1.1-mkspecs-dir.patch 580 BLAKE2B ca9da1dcbf5560fbedd84f12023d921f9cb11f8475aea5094454195eeb37eb21a1a92cbef268b166e26f7477a086a74337b0c262eab729c8012d1067987bee6d SHA512 6c5b67d9f9e1e9fa3c11ae235f467525129fa9d81f34211ed8b97c199690e12cd1457df3aac861615d94efb452af306df6b53218309ff87f6ca1f68edffbf6b2
 AUX avogadro-1.1.1-no-strip.patch 745 BLAKE2B d06400dc0737b7991fe5da6888159b41e7765c851c7ade14619a12571d40c40332363b34da1b0b4af521ee37d2575c28d8cb075bbcf7916b78596af21f395e89 SHA512 921b1333bf37135d5890222193ebdb5b351739d16bf1434c59509e8aab0135ea5cde6812b63d4159fafac29d4eb6297320d03513e474466a7fb857ed16301d6e
 AUX avogadro-1.1.1-openbabel.patch 655 BLAKE2B a0bee7e87a75db2c0881036f977e5a8513ba1f6a66360f8e8cad26eaf269df16140721c4b33d3cf4abde35c0be7f13614e6466b6bc34edcc158cf340b42da20e SHA512 23f477c9deb4befb87a92eb1edaabdd8e52a25f24a36ec9dbf345b0686442cec229a16fbb118e3336cf28592d8af4fc51d0a3e5e9d7a7d7c11a65080c08a074d
 AUX avogadro-1.1.1-pkgconfig_eigen.patch 387 BLAKE2B f842b6f0eacdf351688f2a8c83b248cee0602cf1e96bf180bc0be8181e3cb6c3bbbf8e67572088d763d69d0eadfb7936199d29b5e68076cd6ec89138d5051845 SHA512 4e1e838f7cd88ef3ef49c26565aecf16a3cfb5c735d67c2525e877aa64671ac787733b0eee7f02ef79c6ada05d7dd7fc3c4a470e6d4549fcd0fea7d49e780e99
 AUX avogadro-1.2.0-numpy.patch 448 BLAKE2B 2bbde3ba9e4b8fd5ead2afa3a9cecb458600cf454b50011034ce445ff569212052d04cce9142aab4207da8d84a6b9290d567c4d9262547dcd41c71f7071fa0e3 SHA512 20155043af3ef2f5a01d63dd80cfb3dc7402a2ea43bb3d47dd57e7850671fba62981310280d9361d37ac3359e9dda2daa80f6627836ac53a8dec0f0c2a009905
-DIST avogadro-1.1.1.tar.bz2 11118046 BLAKE2B 358eda508c56247fb34e9cf4b4d790859cc156e000fa10f9e2f2700e9e295557dd5e615ca626227a918fa4f699c089bee23596d186f613f8934a73b8cfeeb358 SHA512 37e2fc9400f8727b7e69d84c13989aaba6fc88287e106a6ed137e4d0fd8ea181dc4ab49b08148d2077754f014748c8ed6f46881f31a1455029f876b599754827
 DIST avogadro-1.2.0_p20170207.tar.gz 16805634 BLAKE2B 012ac0fa6e86bdff1ec117e81faf88ddda2e3264b36c3997ce60814f5a5900dc8722266a52bda70715279e640a3deb04a38bc2bfdfc4ae856182d94e25b7c705 SHA512 c5088ba1e1b48f3202766e38b1c3f2016c3facbf4ea544e24eedb0706328815e7500bcebdedfea2a330e665b97f76c7f86b669339c6f5a765533bfd3a88d7b51
-EBUILD avogadro-1.1.1.ebuild 2014 BLAKE2B fc1c386acd5ee23c6609fdfdf2bfa77571818c4b7f1aad7db978dc4274963e3c28b1840d6e66d05f67931fd8b17006772f4d97e3c30566f18ad9b9aee818a6a3 SHA512 08bb5a96d92ae5f81f266dd141f31ec2a3e7dd3b61b841c275ebc68750ec6b778ae26b4d7c7f76179c889f908ccde9ef89a78561912cce8a5a14309e7dc6a4f0
 EBUILD avogadro-1.2.0_p20170207.ebuild 2107 BLAKE2B 80c56bab7a8c08d9023c8cd187996f05df7f2316353884a139980d2b2794a34ac050922c9e9c58de67d481a01d3c694a9b104bc2d18cde37454bb8fba2d445e3 SHA512 4ef7346cab4937ba189de8439ee78a710d3e398519bbe077b38b2099d412e913baee830d134e770e060f947ce23ab8ffd9d2ddd7930400c1b281f90f36715327
 MISC metadata.xml 703 BLAKE2B 64270fc03ee237b6778aa8b07bef13c3d283cf4b43c341c7e529a8a99cf465a548c8f6b64bba21d68c3f5f298104fd3a6e4e719a6a8f6c9749d71376b1248b0d SHA512 3602707feca1ecb4317f30fd06404b087fb7264929204dd488138c60e82a3d6a11537ba3e29d9f2c491f2be6e06ba874167509905f587ec147b83b773f341c67
diff --git a/sci-chemistry/avogadro/avogadro-1.1.1.ebuild b/sci-chemistry/avogadro/avogadro-1.1.1.ebuild
deleted file mode 100644
index 63150ada5fa9..000000000000
--- a/sci-chemistry/avogadro/avogadro-1.1.1.ebuild
+++ /dev/null
@@ -1,78 +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="Advanced molecular editor that uses Qt4 and OpenGL"
-HOMEPAGE="http://avogadro.openmolecules.net/"
-SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~x86"
-IUSE="+glsl python cpu_flags_x86_sse2 test"
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	>=sci-chemistry/openbabel-2.3.0
-	>=dev-qt/qtgui-4.8.5:4
-	>=dev-qt/qtopengl-4.8.5:4
-	x11-libs/gl2ps
-	glsl? ( >=media-libs/glew-1.5.0:0= )
-	python? (
-		>=dev-libs/boost-1.35.0-r5[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-		dev-python/sip[${PYTHON_USEDEP}]
-		${PYTHON_DEPS}
-	)"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	dev-cpp/eigen"
-
-# https://sourceforge.net/p/avogadro/bugs/653/
-RESTRICT="test"
-
-PATCHES=(
-	#"${FILESDIR}"/${PN}-1.1.0-textrel.patch
-	"${FILESDIR}"/${PN}-1.1.0-xlibs.patch
-	"${FILESDIR}"/${P}-eigen3.patch
-	"${FILESDIR}"/${P}-mkspecs-dir.patch
-	"${FILESDIR}"/${P}-no-strip.patch
-	"${FILESDIR}"/${P}-pkgconfig_eigen.patch
-	"${FILESDIR}"/${P}-openbabel.patch
-	"${FILESDIR}"/${P}-boost-join-moc.patch
-	"${FILESDIR}"/${P}-gcc-version.patch
-)
-
-pkg_setup() {
-	use python && python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	sed \
-		-e 's:_BSD_SOURCE:_DEFAULT_SOURCE:g' \
-		-i CMakeLists.txt || die
-	# warning: "Eigen2 support is deprecated in Eigen 3.2.x and it will be removed in Eigen 3.3."
-	append-cppflags -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DENABLE_THREADEDGL=OFF
-		-DENABLE_RPATH=OFF
-		-DENABLE_UPDATE_CHECKER=OFF
-		-DQT_MKSPECS_DIR="${EPREFIX}/usr/share/qt4/mkspecs"
-		-DQT_MKSPECS_RELATIVE=share/qt4/mkspecs
-		-DENABLE_glsl="$(usex glsl)"
-		-DENABLE_TESTS="$(usex test)"
-		-DWITH_SSE2="$(usex cpu_flags_x86_sse2)"
-		-DENABLE_python="$(usex python)"
-	)
-
-	cmake-utils_src_configure
-}
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch b/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch
deleted file mode 100644
index 74a5889ec8ae..000000000000
--- a/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- * Info: Using [gentoo] (https://bugs.gentoo.org/xmlrpc.cgi)
- * Info: Getting attachment 403034
- * Info: Viewing attachment: "X11.patch"
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 60ec98f..03443a7 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -225,6 +225,7 @@ set(I18N_LANGUAGE "" CACHE STRING "Build i18n only for selected language")
- 
- find_package(Qt4 4.6.0 REQUIRED) # find and setup Qt4 for this project
- find_package(OpenGL REQUIRED) # find and setup OpenGL
-+find_package(X11 REQUIRED)
- find_package(Linguist) # find and setup Linguist
- if(NOT Linguist_FOUND)
-   message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations")
-
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch
deleted file mode 100644
index dc07d6974e12..000000000000
--- a/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch
+++ /dev/null
@@ -1,51 +0,0 @@
---- avogadro-1.1.1/CMakeLists.txt.omv~	2014-01-30 13:58:22.999443609 +0100
-+++ avogadro-1.1.1/CMakeLists.txt	2014-01-30 13:59:31.086106925 +0100
-@@ -230,13 +230,15 @@ if(NOT Linguist_FOUND)
-   message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations")
- endif()
- 
--find_package(Eigen3) # find and setup Eigen3 if available
-+find_package(Eigen3 REQUIRED) # find and setup Eigen3 if available
- if(NOT EIGEN3_FOUND)
-    message(STATUS "Cannot find Eigen3, trying Eigen2")
--   find_package(Eigen2 REQUIRED) # Some version is required
-+   find_package(Eigen2) # Some version is required
- else()
- # Use Stage10 Eigen3 support
-    set (EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API TRUE)
-+   add_definitions (-DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API)
-+   set (EIGEN2_INCLUDE_DIR ${EIGEN3_INCLUDE_DIR})
- endif()
- 
- find_package(ZLIB REQUIRED)
---- avogadro-1.1.1/libavogadro/src/extensions/qtaim/CMakeLists.txt.omv~	2014-01-30 14:12:33.859401753 +0100
-+++ avogadro-1.1.1/libavogadro/src/extensions/qtaim/CMakeLists.txt	2014-01-30 14:15:07.652727522 +0100
-@@ -4,6 +4,8 @@ set(LINK_LIBS avogadro)
- set(PLUGIN_LABEL extensions)
- set(PLUGIN_TARGET extensions)
- 
-+add_definitions(-DEIGEN2_SUPPORT_STAGE20_RESOLVE_API_CONFLICTS -std=gnu++11)
-+
- set(qtaimextension_SRCS
-     qtaimextension.cpp
- #    qtaimdialog.cpp
---- avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt.omv~	2014-01-30 13:59:05.889441500 +0100
-+++ avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt	2014-01-30 13:59:08.832774688 +0100
-@@ -1,5 +1,5 @@
- find_package(Qt4 4.6 REQUIRED)
--find_package(Eigen2 REQUIRED)
-+find_package(Eigen3 REQUIRED)
- 
- include_directories(${QT_INCLUDE_DIR} ${EIGEN2_INCLUDE_DIR})
- 
---- avogadro-1.1.1/cmake/modules/AvogadroUse.cmake.orig	2014-10-13 20:13:59.909828034 +0100
-+++ avogadro-1.1.1/cmake/modules/AvogadroUse.cmake	2014-10-13 20:15:09.492822908 +0100
-@@ -12,7 +12,7 @@
- 
- # Add the Avogadro modules directory to the CMake module path
- set(CMAKE_MODULE_PATH ${Avogadro_PLUGIN_DIR}/cmake ${CMAKE_MODULE_PATH})
--find_package(Eigen2 REQUIRED)
-+find_package(Eigen3 REQUIRED)
- include_directories(${EIGEN2_INCLUDE_DIR})
- if(Avogadro_ENABLE_GLSL)
-   find_package(GLEW)
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-gcc-version.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-gcc-version.patch
deleted file mode 100644
index 48840204a8a0..000000000000
--- a/sci-chemistry/avogadro/files/avogadro-1.1.1-gcc-version.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-From a8bf7bcd7881147c3bcec97d247a2fa4160019d9 Mon Sep 17 00:00:00 2001
-From: Heiko Becker <heirecka@exherbo.org>
-Date: Tue, 5 Jul 2016 00:10:26 +0200
-Subject: [PATCH] Fix detection of gcc6's version number
-
-...and be safe for further new versions.
----
- CMakeLists.txt | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 1cbeb8f10..8d2958739 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -69,7 +69,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
-   # Now check if we can use visibility to selectively export symbols
-   # Get the GCC version - from KDE4 cmake files
-   exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE	_gcc_version_info)
--  string (REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
-+  string (REGEX MATCH "[3-9]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
-   # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
-   # patch level, handle this here:
-   if (NOT _gcc_version)