From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-chemistry/avogadro/Manifest | 18 +++++ sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild | 56 ++++++++++++++++ sci-chemistry/avogadro/avogadro-1.1.0.ebuild | 62 +++++++++++++++++ sci-chemistry/avogadro/avogadro-1.1.1.ebuild | 77 +++++++++++++++++++++ sci-chemistry/avogadro/files/1.0.1-gl2ps.patch | 39 +++++++++++ .../avogadro/files/avogadro-1.1.0-textrel.patch | 29 ++++++++ .../avogadro/files/avogadro-1.1.0-xlibs.patch | 16 +++++ .../files/avogadro-1.1.1-boost-join-moc.patch | 78 ++++++++++++++++++++++ .../avogadro/files/avogadro-1.1.1-eigen3.patch | 51 ++++++++++++++ .../files/avogadro-1.1.1-mkspecs-dir.patch | 12 ++++ .../avogadro/files/avogadro-1.1.1-no-strip.patch | 12 ++++ .../avogadro/files/avogadro-1.1.1-openbabel.patch | 16 +++++ .../files/avogadro-1.1.1-pkgconfig_eigen.patch | 8 +++ sci-chemistry/avogadro/metadata.xml | 20 ++++++ 14 files changed, 494 insertions(+) create mode 100644 sci-chemistry/avogadro/Manifest create mode 100644 sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild create mode 100644 sci-chemistry/avogadro/avogadro-1.1.0.ebuild create mode 100644 sci-chemistry/avogadro/avogadro-1.1.1.ebuild create mode 100644 sci-chemistry/avogadro/files/1.0.1-gl2ps.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.1-boost-join-moc.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch create mode 100644 sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch create mode 100644 sci-chemistry/avogadro/metadata.xml (limited to 'sci-chemistry/avogadro') diff --git a/sci-chemistry/avogadro/Manifest b/sci-chemistry/avogadro/Manifest new file mode 100644 index 000000000000..e517a85fbcf7 --- /dev/null +++ b/sci-chemistry/avogadro/Manifest @@ -0,0 +1,18 @@ +AUX 1.0.1-gl2ps.patch 1511 SHA256 0aae5556233c8e413739fdd890b5d8453d9a1e39dd3251a5a7a7705227a13e7b SHA512 b4a8d0138bffa7c018e2125e16a47cefefba01f19ce3d460488f36e44f55b212cea9c9875429e7c0c596388366adea045b50ace579b6352d2b7e0b073420c67f WHIRLPOOL 015420a79e56b5f3da238d73d12e28573636161e4edcdc94db80149aa84621de05b84f08332d701b5ed89dadb414a30e33badc686788698dd539603d2eeb5a05 +AUX avogadro-1.1.0-textrel.patch 1535 SHA256 55a58d29f47d441a5877e32acf9f9a8ad1e408a75a6629ccdc23ebec8f4d40f8 SHA512 5872a773668cb38b27ab0dbaf14d947eff4cb3d4ae99410c8968cafe576a9df5d3b0937d028b9ffd076c212c5f9b8e213cda74a63afff6caa713346ee338be77 WHIRLPOOL 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10b2d933a605479bc4389e93eeba6351d48cc7695675e298cb0aeeca62d41ba22aa952bb26a01aaf4e5a28adb6f78c12124d66dfb58c4aff76a8ac0be7331fcc +MISC metadata.xml 718 SHA256 3f6c835242302a435220bf9ef9fbe4033578b9ff4040d59e49b14bb8705c8a38 SHA512 c462030593317c5ad343161cc387df47249a728e96eacf736569f9fb8762c22343f4b8b9ba07ee1c728f296951940f690b5c8676908bc50e71d517c542ac15c1 WHIRLPOOL 05477e56231f70a777009a2a4bdc024be4ceec0691de1b36eadf746dadc26755c52215b743c16071ffb0614336443b114c1972c58246568eb41460f635607981 diff --git a/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild b/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild new file mode 100644 index 000000000000..ce624e4ae71f --- /dev/null +++ b/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils eutils python-single-r1 + +DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL" +HOMEPAGE="http://avogadro.openmolecules.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~x86" +IUSE="+glsl python cpu_flags_x86_sse2" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + >=sci-chemistry/openbabel-2.2.3 + >=dev-qt/qtgui-4.5.3:4 + >=dev-qt/qtopengl-4.5.3:4 + x11-libs/gl2ps + glsl? ( >=media-libs/glew-1.5.0:0= ) + python? ( + >=dev-libs/boost-1.35.0-r5[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/sip[${PYTHON_USEDEP}] + ${PYTHON_DEPS} + )" +DEPEND="${RDEPEND} + dev-cpp/eigen:2" + +PATCHES=( + "${FILESDIR}"/1.0.1-gl2ps.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_configure() { + local mycmakeargs=( + -DENABLE_THREADGL=OFF + -DENABLE_RPATH=OFF + -DENABLE_UPDATE_CHECKER=OFF + -DQT_MKSPECS_DIR="${EPREFIX}/usr/share/qt4/mkspecs" + -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs + $(cmake-utils_use_enable glsl) + $(cmake-utils_use_with cpu_flags_x86_sse2 SSE2) + $(cmake-utils_use_enable python) + ) + + cmake-utils_src_configure +} diff --git a/sci-chemistry/avogadro/avogadro-1.1.0.ebuild b/sci-chemistry/avogadro/avogadro-1.1.0.ebuild new file mode 100644 index 000000000000..ff3a9036301b --- /dev/null +++ b/sci-chemistry/avogadro/avogadro-1.1.0.ebuild @@ -0,0 +1,62 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils eutils python-single-r1 + +DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL" +HOMEPAGE="http://avogadro.openmolecules.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~x86" +IUSE="+glsl python cpu_flags_x86_sse2 test" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + >=sci-chemistry/openbabel-2.3.0 + >=dev-qt/qtgui-4.5.3:4 + >=dev-qt/qtopengl-4.5.3:4 + x11-libs/gl2ps + glsl? ( >=media-libs/glew-1.5.0:0= ) + python? ( + >=dev-libs/boost-1.35.0-r5[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/sip[${PYTHON_USEDEP}] + ${PYTHON_DEPS} + )" +DEPEND="${RDEPEND} + dev-cpp/eigen:2" + +# https://sourceforge.net/p/avogadro/bugs/653/ +RESTRICT="test" + +PATCHES=( + "${FILESDIR}"/${P}-textrel.patch + "${FILESDIR}"/${P}-xlibs.patch + "${FILESDIR}"/${PN}-1.1.1-openbabel.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_configure() { + local mycmakeargs=( + -DENABLE_THREADGL=OFF + -DENABLE_RPATH=OFF + -DENABLE_UPDATE_CHECKER=OFF + -DQT_MKSPECS_DIR="${EPREFIX}/usr/share/qt4/mkspecs" + -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs + $(cmake-utils_use_enable glsl) + $(cmake-utils_use_enable test TESTS) + $(cmake-utils_use_with cpu_flags_x86_sse2 SSE2) + $(cmake-utils_use_enable python) + ) + + cmake-utils_src_configure +} diff --git a/sci-chemistry/avogadro/avogadro-1.1.1.ebuild b/sci-chemistry/avogadro/avogadro-1.1.1.ebuild new file mode 100644 index 000000000000..5e9225721e1d --- /dev/null +++ b/sci-chemistry/avogadro/avogadro-1.1.1.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils flag-o-matic python-single-r1 + +DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL" +HOMEPAGE="http://avogadro.openmolecules.net/" +SRC_URI="mirror://sourceforge/project/${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 +) + +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/1.0.1-gl2ps.patch b/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch new file mode 100644 index 000000000000..d8a0c0f758e1 --- /dev/null +++ b/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch @@ -0,0 +1,39 @@ +diff --git a/avogadro/src/CMakeLists.txt b/avogadro/src/CMakeLists.txt +index 75b6dfb..d87ac2c 100644 +--- a/avogadro/src/CMakeLists.txt ++++ b/avogadro/src/CMakeLists.txt +@@ -45,7 +45,7 @@ endif(ENABLE_UPDATE_CHECKER) + FILE(GLOB projectDelegates_SRCS "projectdelegates/*.cpp") + set(avogadro_SRCS ${avogadro_SRCS} ${projectDelegates_SRCS}) + # Add GL2PS to the executable +-set(avogadro_SRCS ${avogadro_SRCS} "../gl2ps/gl2ps.c") ++#set(avogadro_SRCS ${avogadro_SRCS} "../gl2ps/gl2ps.c") + + if( WIN32 ) + set(avogadro_SRCS ${avogadro_SRCS} windows/avogadro.rc) +diff --git a/avogadro/src/mainwindow.cpp b/avogadro/src/mainwindow.cpp +index 66785fd..2933953 100644 +--- a/avogadro/src/mainwindow.cpp ++++ b/avogadro/src/mainwindow.cpp +@@ -51,7 +51,7 @@ + //#endif + + // Include the GL2PS header +-#include "../gl2ps/gl2ps.h" ++#include + + #include + +diff --git a/libavogadro/src/CMakeLists.txt b/libavogadro/src/CMakeLists.txt +index cce8ece..cc084fb 100644 +--- a/libavogadro/src/CMakeLists.txt ++++ b/libavogadro/src/CMakeLists.txt +@@ -152,7 +152,7 @@ endforeach(headerFile ${libavogadro_HDRS}) + add_library(avogadro SHARED ${libavogadro_SRCS} ${libavogadro_QM} ${pythontool_RC_SRCS}) + set_target_properties(avogadro + PROPERTIES VERSION ${Avogadro_VERSION_FULL} SOVERSION 1 ) +-target_link_libraries(avogadro ${AVO_LINK_LIBRARIES}) ++target_link_libraries(avogadro ${AVO_LINK_LIBRARIES} gl2ps) + + install(TARGETS avogadro DESTINATION ${LIB_INSTALL_DIR}) + install(FILES ${libavogadro_HDRS} diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch b/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch new file mode 100644 index 000000000000..6d4536ef7c9b --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch @@ -0,0 +1,29 @@ + libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt | 2 +- + libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt b/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt +index fb88316..2ddcfdf 100644 +--- a/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt ++++ b/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt +@@ -20,6 +20,6 @@ add_library(spglib STATIC ${spglib_SRCS}) + set_target_properties(spglib PROPERTIES COMPILE_FLAGS "-w") + + # Set -fPIC on x86_64 +-if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64") ++if("${CMAKE_SYSTEM_PROCESSOR}" MATCHES "^(i.86|x86|x86_64|ppc|ppc64)$") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC" ) + endif() +diff --git a/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt b/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt +index 0cd0c3e..9e89daf 100644 +--- a/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt ++++ b/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt +@@ -19,7 +19,7 @@ add_library(tubegen STATIC ${tubegen_SRCS}) + set_target_properties(tubegen PROPERTIES COMPILE_FLAGS "-w") + + # Set -fPIC on x86_64 +-if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64") ++if("${CMAKE_SYSTEM_PROCESSOR}" MATCHES "^(i.86|x86|x86_64|ppc|ppc64)$") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC" ) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC" ) + endif() diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch b/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch new file mode 100644 index 000000000000..74a5889ec8ae --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch @@ -0,0 +1,16 @@ + * 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-boost-join-moc.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-boost-join-moc.patch new file mode 100644 index 000000000000..a464fdac42ca --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-boost-join-moc.patch @@ -0,0 +1,78 @@ +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 + #include ++#ifndef Q_MOC_RUN + #include ++#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 + #include + #include ++#ifndef Q_MOC_RUN + #include ++#endif + + #include + #include +--- avogadro-1.1.1/libavogadro/src/pythoninterpreter.h ++++ avogadro-1.1.1/libavogadro/src/pythoninterpreter.h +@@ -26,7 +26,9 @@ + #define PYTHONINTERPRETER_H + + #include ++#ifndef Q_MOC_RUN + #include ++#endif + #include + #include + +--- avogadro-1.1.1/libavogadro/src/pythonscript.h ++++ avogadro-1.1.1/libavogadro/src/pythonscript.h +@@ -27,7 +27,9 @@ + #define PYTHONSCRIPT_H + + #include ++#ifndef Q_MOC_RUN + #include ++#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 ++#ifndef Q_MOC_RUN + #include ++#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 + #include ++#ifndef Q_MOC_RUN + #include ++#endif + + #include + #include diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch new file mode 100644 index 000000000000..dc07d6974e12 --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch @@ -0,0 +1,51 @@ +--- 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-mkspecs-dir.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch new file mode 100644 index 000000000000..45c616422efe --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch @@ -0,0 +1,12 @@ +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 ("${QT_MKSPECS_DIR}" MATCHES ^$"${CMAKE_INSTALL_PREFIX}/") + else() diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch new file mode 100644 index 000000000000..490dd58907df --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch @@ -0,0 +1,12 @@ +diff -up avogadro-1.1.1/CMakeLists.txt.no-strip avogadro-1.1.1/CMakeLists.txt +--- avogadro-1.1.1/CMakeLists.txt.no-strip 2014-01-24 23:14:44.473840038 -0600 ++++ avogadro-1.1.1/CMakeLists.txt 2014-01-24 23:15:46.869166459 -0600 +@@ -114,7 +114,7 @@ if (CMAKE_COMPILER_IS_GNUCXX) + endif() + # Set up additional build flags for particular build types. These will be added to CMAKE_CXX_FLAGS, + # they will not replace them. +- set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s") ++ set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG -DQT_NO_DEBUG_OUTPUT") + set(CMAKE_CXX_FLAGS_RELWITHDEBINFO + "${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 new file mode 100644 index 000000000000..4bdc6b2e780e --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch @@ -0,0 +1,16 @@ + 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} ${OPENBABEL2_LIBRARIES}) + endif() + + # Let's try to use this instead: diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch new file mode 100644 index 000000000000..93dbe2ff4ecc --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch @@ -0,0 +1,8 @@ +diff -up avogadro-1.1.1/avogadro.pc.in.eigen avogadro-1.1.1/avogadro.pc.in +--- avogadro-1.1.1/avogadro.pc.in.eigen 2013-12-06 09:50:04.000000000 -0600 ++++ avogadro-1.1.1/avogadro.pc.in 2014-01-25 00:37:45.732007852 -0600 +@@ -9,3 +9,4 @@ Description: Avogadro libraries + Version: @Avogadro_VERSION_FULL@ + Libs: -L${libdir} -lavogadro + Cflags: -I${pkgincludedir} ++Requires.private: eigen3 diff --git a/sci-chemistry/avogadro/metadata.xml b/sci-chemistry/avogadro/metadata.xml new file mode 100644 index 000000000000..152f2bd72abd --- /dev/null +++ b/sci-chemistry/avogadro/metadata.xml @@ -0,0 +1,20 @@ + + + + + sci-chemistry@gentoo.org + Gentoo Chemistry Project + + + 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. + + + Enable glsl features via GLEW. + + + avogadro + + -- cgit v1.2.3