gentoo resync : 08.05.2018

9 files changed, 0 insertions, 258 deletions

diff --git a/sci-chemistry/avogadro/Manifest b/sci-chemistry/avogadro/Manifest
deleted file mode 100644
index 83d4da03e654..000000000000
--- a/sci-chemistry/avogadro/Manifest
+++ /dev/null
@@ -1,9 +0,0 @@
-AUX avogadro-1.1.1-boost-join-moc.patch 2051 BLAKE2B 8711c60f2ad0d63d6b4cb39c8461a70f5ced9d9045e5b9b18cea5577721f15e7c9314c8d86d844f47fca5b769837167268903d91328219c5eda16c72f3007967 SHA512 d4e4ef54d94cccb0f34c4960d302772f9da47e27cb79e1ee0a4e928ef248ac629fd59f1564bedf7c82a2a7ca8b25456878c22569dbcda26478a6c06e5815a084
-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-1.2.0_p20170207.tar.gz 16805634 BLAKE2B 012ac0fa6e86bdff1ec117e81faf88ddda2e3264b36c3997ce60814f5a5900dc8722266a52bda70715279e640a3deb04a38bc2bfdfc4ae856182d94e25b7c705 SHA512 c5088ba1e1b48f3202766e38b1c3f2016c3facbf4ea544e24eedb0706328815e7500bcebdedfea2a330e665b97f76c7f86b669339c6f5a765533bfd3a88d7b51
-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-1.2.0_p20170207.ebuild b/sci-chemistry/avogadro/avogadro-1.2.0_p20170207.ebuild
deleted file mode 100644
index 28d5724b0e50..000000000000
--- a/sci-chemistry/avogadro/avogadro-1.2.0_p20170207.ebuild
+++ /dev/null
@@ -1,90 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-COMMIT=258105b4d8957e0245a341cdf1dc12c72234c833
-PYTHON_COMPAT=( python2_7 )
-inherit cmake-utils flag-o-matic python-single-r1 vcs-snapshot xdg-utils
-
-DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL"
-HOMEPAGE="http://avogadro.openmolecules.net/"
-SRC_URI="https://github.com/cryos/${PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~arm ~x86"
-IUSE="cpu_flags_x86_sse2 +glsl python test"
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	dev-qt/qtcore:4
-	dev-qt/qtgui:4
-	dev-qt/qtopengl:4
-	media-libs/glew:=
-	sci-chemistry/openbabel:=
-	virtual/glu
-	x11-libs/gl2ps
-	glsl? ( >=media-libs/glew-1.5.0:0= )
-	python? (
-		${PYTHON_DEPS}
-		dev-libs/boost:=[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-		dev-python/sip[${PYTHON_USEDEP}]
-	)
-"
-DEPEND="${RDEPEND}
-	dev-cpp/eigen:3
-	virtual/pkgconfig
-"
-
-# https://sourceforge.net/p/avogadro/bugs/653/
-RESTRICT="test"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.1.1-mkspecs-dir.patch
-	"${FILESDIR}"/${PN}-1.1.1-no-strip.patch
-	"${FILESDIR}"/${PN}-1.1.1-pkgconfig_eigen.patch
-	"${FILESDIR}"/${PN}-1.1.1-openbabel.patch
-	"${FILESDIR}"/${PN}-1.1.1-boost-join-moc.patch
-	"${FILESDIR}"/${PN}-1.2.0-numpy.patch
-)
-
-pkg_setup() {
-	use python && python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	sed -e "s:_BSD_SOURCE:_DEFAULT_SOURCE:g" \
-		-i CMakeLists.txt || die
-
-	sed -e "/Version/s/1\.2/1\.0/" \
-		-i avogadro/src/avogadro.desktop || die
-
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DENABLE_THREADEDGL=OFF
-		-DENABLE_RPATH=OFF
-		-DENABLE_UPDATE_CHECKER=OFF
-		-DQT_MKSPECS_DIR="${EPREFIX}/usr/share/qt4/mkspecs"
-		-DWITH_SSE2=$(usex cpu_flags_x86_sse2)
-		-DENABLE_GLSL=$(usex glsl)
-		-DENABLE_PYTHON=$(usex python)
-		-DENABLE_TESTS=$(usex test)
-	)
-
-	QT_MKSPECS_RELATIVE=share/qt4/mkspecs cmake-utils_src_configure
-}
-
-pkg_postinst() {
-	xdg_mimeinfo_database_update
-	xdg_desktop_database_update
-}
-
-pkg_postrm() {
-	xdg_mimeinfo_database_update
-	xdg_desktop_database_update
-}
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-boost-join-moc.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-boost-join-moc.patch
deleted file mode 100644
index a464fdac42ca..000000000000
--- a/sci-chemistry/avogadro/files/avogadro-1.1.1-boost-join-moc.patch
+++ /dev/null
@@ -1,78 +0,0 @@
-Add include guards to all boost includes, as qt's moc trips
-over nested BOOST_JOIN macros:
-* usr/include/boost/type_traits/detail/has_binary_operator.hp:50: Parse error at "BOOST_JOIN"
-* libavogadro/src/CMakeFiles/avogadro.dir/build.make:217: recipe for target 'libavogadro/src/moc_pythonengine_p.cxx' failed
-See also: https://bugs.gentoo.org/show_bug.cgi?id=578896
-
---- avogadro-1.1.1/libavogadro/src/pythonengine_p.h
-+++ avogadro-1.1.1/libavogadro/src/pythonengine_p.h
-@@ -27,7 +27,9 @@
- 
- #include <avogadro/global.h>
- #include <avogadro/engine.h>
-+#ifndef Q_MOC_RUN
- #include <boost/python.hpp>
-+#endif
- 
- namespace Avogadro {
- 
---- avogadro-1.1.1/libavogadro/src/pythonextension_p.h
-+++ avogadro-1.1.1/libavogadro/src/pythonextension_p.h
-@@ -29,7 +29,9 @@
- #include <avogadro/extension.h>
- #include <avogadro/primitive.h>
- #include <avogadro/glwidget.h>
-+#ifndef Q_MOC_RUN
- #include <boost/python.hpp>
-+#endif
- 
- #include <QWidget>
- #include <QList>
---- avogadro-1.1.1/libavogadro/src/pythoninterpreter.h
-+++ avogadro-1.1.1/libavogadro/src/pythoninterpreter.h
-@@ -26,7 +26,9 @@
- #define PYTHONINTERPRETER_H
- 
- #include <avogadro/global.h>
-+#ifndef Q_MOC_RUN
- #include <boost/python.hpp>
-+#endif
- #include <avogadro/primitive.h>
- #include <QString>
- 
---- avogadro-1.1.1/libavogadro/src/pythonscript.h
-+++ avogadro-1.1.1/libavogadro/src/pythonscript.h
-@@ -27,7 +27,9 @@
- #define PYTHONSCRIPT_H
- 
- #include <avogadro/global.h>
-+#ifndef Q_MOC_RUN
- #include <boost/python.hpp>
-+#endif
- 
- #include "pythonerror.h"
- 
---- avogadro-1.1.1/libavogadro/src/pythonthread_p.h
-+++ avogadro-1.1.1/libavogadro/src/pythonthread_p.h
-@@ -26,7 +26,9 @@
- #define PYTHONTHREAD_H
- 
- #include <avogadro/global.h>
-+#ifndef Q_MOC_RUN
- #include <boost/python.hpp>
-+#endif
- 
- namespace Avogadro {
- 
---- avogadro-1.1.1/libavogadro/src/pythontool_p.h
-+++ avogadro-1.1.1/libavogadro/src/pythontool_p.h
-@@ -27,7 +27,9 @@
- 
- #include <avogadro/global.h>
- #include <avogadro/tool.h>
-+#ifndef Q_MOC_RUN
- #include <boost/python.hpp>
-+#endif
- 
- #include <QObject>
- #include <QAction>
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch
deleted file mode 100644
index 45c616422efe..000000000000
--- a/sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -up avogadro-1.1.1/CMakeLists.txt.mkspecs-dir avogadro-1.1.1/CMakeLists.txt
---- avogadro-1.1.1/CMakeLists.txt.mkspecs-dir	2014-01-24 23:43:01.618510517 -0600
-+++ avogadro-1.1.1/CMakeLists.txt	2014-01-24 23:44:03.236844746 -0600
-@@ -547,7 +547,7 @@ if(QT_MKSPECS_DIR AND INSTALL_QMAKE_PRF)
- #    )
-     install(FILES
-       "${CMAKE_CURRENT_BINARY_DIR}/avogadro.prf"
--      DESTINATION "${CMAKE_INSTALL_PREFIX}/${QT_MKSPECS_RELATIVE}/features"
-+      DESTINATION "${QT_MKSPECS_DIR}/features"
-     )
- #  endif ("${QT_MKSPECS_DIR}" MATCHES ^$"${CMAKE_INSTALL_PREFIX}/")
- else()
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch
deleted file mode 100644
index 490dd58907df..000000000000
--- a/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -up avogadro-1.1.1/CMakeLists.txt.no-strip avogadro-1.1.1/CMakeLists.txt
---- avogadro-1.1.1/CMakeLists.txt.no-strip	2014-01-24 23:14:44.473840038 -0600
-+++ avogadro-1.1.1/CMakeLists.txt	2014-01-24 23:15:46.869166459 -0600
-@@ -114,7 +114,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
-   endif()
-   # Set up additional build flags for particular build types. These will be added to CMAKE_CXX_FLAGS,
-   # they will not replace them.
--  set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
-+  set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG -DQT_NO_DEBUG_OUTPUT")
-   set(CMAKE_CXX_FLAGS_RELWITHDEBINFO
-     "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} ${CMAKE_CXX_FLAGS_WARN}")
-   set(CMAKE_CXX_FLAGS_DEBUG   "-g3 -fno-inline ${CMAKE_CXX_FLAGS_WARN}")
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch
deleted file mode 100644
index 4bdc6b2e780e..000000000000
--- a/sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- libavogadro/src/python/CMakeLists.txt | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/libavogadro/src/python/CMakeLists.txt b/libavogadro/src/python/CMakeLists.txt
-index efb518a..1a3d91a 100644
---- a/libavogadro/src/python/CMakeLists.txt
-+++ b/libavogadro/src/python/CMakeLists.txt
-@@ -21,7 +21,7 @@ if (WIN32)
-   target_link_libraries(python-module avogadro ${PYTHON_LIBRARIES})
- else()
-   target_link_libraries(python-module stdc++ avogadro
--    ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${Boost_LIBRARIES})
-+    ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${Boost_LIBRARIES} ${OPENBABEL2_LIBRARIES})
- endif()
- 
- # Let's try to use this instead:
diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch
deleted file mode 100644
index 93dbe2ff4ecc..000000000000
--- a/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch
+++ /dev/null
@@ -1,8 +0,0 @@
-diff -up avogadro-1.1.1/avogadro.pc.in.eigen avogadro-1.1.1/avogadro.pc.in
---- avogadro-1.1.1/avogadro.pc.in.eigen	2013-12-06 09:50:04.000000000 -0600
-+++ avogadro-1.1.1/avogadro.pc.in	2014-01-25 00:37:45.732007852 -0600
-@@ -9,3 +9,4 @@ Description: Avogadro libraries
- Version: @Avogadro_VERSION_FULL@
- Libs: -L${libdir} -lavogadro
- Cflags: -I${pkgincludedir}
-+Requires.private: eigen3
diff --git a/sci-chemistry/avogadro/files/avogadro-1.2.0-numpy.patch b/sci-chemistry/avogadro/files/avogadro-1.2.0-numpy.patch
deleted file mode 100644
index 4869fa4ea79d..000000000000
--- a/sci-chemistry/avogadro/files/avogadro-1.2.0-numpy.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/cmake/modules/FindNumpy.cmake b/cmake/modules/FindNumpy.cmake
-index b348418..49ba206 100644
---- a/cmake/modules/FindNumpy.cmake
-+++ b/cmake/modules/FindNumpy.cmake
-@@ -10,7 +10,7 @@
- #endif (NUMPY_INCLUDE_DIR)
- 
- EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} -c 
--    "import numpy; print numpy.get_include()"
-+	"import numpy; print (numpy.get_include())"
-     OUTPUT_VARIABLE NUMPY_INCLUDE_DIR
-     OUTPUT_STRIP_TRAILING_WHITESPACE)
- 
diff --git a/sci-chemistry/avogadro/metadata.xml b/sci-chemistry/avogadro/metadata.xml
deleted file mode 100644
index 693df91c051a..000000000000
--- a/sci-chemistry/avogadro/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-		Avogadro is an advanced molecular editor designed for cross-platform use in
-		computational chemistry, molecular modeling, bioinformatics, materials
-		science, and related areas. It offers flexible rendering and a powerful
-		plugin architecture.
-	</longdescription>
-	<use>
-		<flag name="glsl">Enable glsl features via GLEW.</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">avogadro</remote-id>
-	</upstream>
-</pkgmetadata>