diff options
Diffstat (limited to 'sci-chemistry/avogadro')
14 files changed, 494 insertions, 0 deletions
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 f5478f34db2d20ae08c26b3db4c9334c7794c5948652c0199e78ea760054932297c00b5ff4c001ed3eed98e050c6970766d8c117748d5dc6a43ed0cc15ab5651 +AUX avogadro-1.1.0-xlibs.patch 680 SHA256 13f01a86b51ab48dab22ea8e547946eaa48b5c4a650ad95fcafc8f9fc21e21dc SHA512 df2727e4aea1549daada56778d7710656f3f6ff9fa31c441c06e82241c8e5b0733c39d575c98f2d1b57b9be0a52d445412ecd6cca7a1f319c6982035e789f21d WHIRLPOOL 2cadc10899f317ce1f90da250486b839604ce6664da568178243538966023591753ec0354f515c22548426f3263540117efd36d401b0f454ae704c48fd37a3ec +AUX avogadro-1.1.1-boost-join-moc.patch 2051 SHA256 133c121ff6ec2a1e0a76727d61edfcac4f76207a0d605b2d745ce114498ae976 SHA512 d4e4ef54d94cccb0f34c4960d302772f9da47e27cb79e1ee0a4e928ef248ac629fd59f1564bedf7c82a2a7ca8b25456878c22569dbcda26478a6c06e5815a084 WHIRLPOOL d5a32e4a7bc51b112fe5c01bb001da752319747d7adc7faf1f7da811acb781e1314ebdd8737fb11cd397ce25412c7e4bd0858926d1be29758d5d3add21d5eb08 +AUX avogadro-1.1.1-eigen3.patch 2230 SHA256 4ff7d5f079376d8e125b6f32a27d6eb1a356eafe5c50c66f0d8b8da75b58bf36 SHA512 df6a53cacebee613739d230fc0c7dc21cb67d553950af82cf83d04750f1d9fa98a3bb052c15fffebacf41d2e53dcd3503bffff2aa8dfbfcb47e2d1ebccd77614 WHIRLPOOL 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9208ddd27d182a799b54480520df6050433aecb7c8e74a4aa5d8492c1a592bd7 SHA512 23f477c9deb4befb87a92eb1edaabdd8e52a25f24a36ec9dbf345b0686442cec229a16fbb118e3336cf28592d8af4fc51d0a3e5e9d7a7d7c11a65080c08a074d WHIRLPOOL 74cdb0c4530c7376456217a91b0fa1e73e7199ca5fdab273d8e208910f79a53ccf1997ef6329c3add54bedf01eb05f699ba80c0abe92b2682e4b82952b285517 +AUX avogadro-1.1.1-pkgconfig_eigen.patch 387 SHA256 57fa3b1bbc22b17feffcaa4f763ef50aa4c125ab6a85aafde21898331020ab94 SHA512 4e1e838f7cd88ef3ef49c26565aecf16a3cfb5c735d67c2525e877aa64671ac787733b0eee7f02ef79c6ada05d7dd7fc3c4a470e6d4549fcd0fea7d49e780e99 WHIRLPOOL 3e01193837f5542c722d92820916a323ce7caf4d254c179c095d1fd007add898a668d0fb94ea064f19d3b5b0329f4f93c6efee02faafb070018c85e280198b43 +DIST avogadro-1.0.3.tar.bz2 4971989 SHA256 efb6fda223da3c027436f0c218a47ce804f7469c58b41134230e9ebad1c98468 SHA512 49e7b8ca43f0f52a65efc7bf9dc45670ae5a5de5d1aa6bf7b58b8368e816be30fe6529c45fa658d7337d4a69327bb0aa8799d8d4b4805860aace28011cc74210 WHIRLPOOL c835ac24b317a1fa310bf3ea75bae4002d01f364d4754e6a7d841594dcce321435c827d60e125d9410f05670a94c887cc250bf49759d02cde34a5839d2324c92 +DIST avogadro-1.1.0.tar.bz2 10741835 SHA256 6b4eaf57ae52bf43df9b103c77e6abae71e067053d5c99f82acbce9855ecceb0 SHA512 d621dd3ea9e9223d3a29c6b0c0eec89a935837d0c587fcaaa549f91274a76f78a8c60c2a68a67d2f3aa2e107826befb6658be601c46c5bc0760c95bf7284540a WHIRLPOOL c81e866e60b3383a58de515317c754e3982e716c27974ce43ca0c1209d24544949361a7f2f93a4a940d73fd7a18b184f68c7a1856fea89ae5eba75db74b1012d +DIST avogadro-1.1.1.tar.bz2 11118046 SHA256 fe6f7bdea17a27a20be25b70d975145999aae9d90ef320217af2bc4d6e7a0a14 SHA512 37e2fc9400f8727b7e69d84c13989aaba6fc88287e106a6ed137e4d0fd8ea181dc4ab49b08148d2077754f014748c8ed6f46881f31a1455029f876b599754827 WHIRLPOOL 6bea2c25675ba29729785b561cbaed33929aeb4638180454b1aed8913160cd6d0315bb09e6ee4033a8d27ce84fd7a4573851fd02c76b64b6aa86e615a19b8c38 +EBUILD avogadro-1.0.3-r2.ebuild 1298 SHA256 af4e3cd17a733b067b991a7457bf974631fb5d3a06d5f18c0bd1a2ff66d2e60e SHA512 54b364267975e585b7fdc510688d92f3aa7e5cf477a0288f6ccfe7d468c496d785b1c9f3d37e7b0ce7df8729565614b63fa3544507c50359d5e67189a4ab6e45 WHIRLPOOL d0053824b722643b3975bbf2c44bd1fda162ae5dbb3cf857aad8f56a1e733e9edb09528d6ee9711d8d6c7479b0bfea6dfc69cd4921ec0b179cc01e3caddd6ffb +EBUILD avogadro-1.1.0.ebuild 1482 SHA256 b924e0bb506bdebbf5d86e8d61e52f137dd2ba19832f6a3d47ba1aae77e74fe0 SHA512 d3f0095e7b1644cb963ad4223a43fcc0201f5c14247b0e0b04c570f47ce2c33f52bb46373d347dedeee662cdfd4924dce27d809bdc9826e785e34e5f73f935d9 WHIRLPOOL d1a94503cc711087d424968b6e0c1103022a7f9021d8ac6559db256d6d45df102f2b6b2429756119cd2082f53ff3ece22f7db179ce77e4263da86a5eaedda57e +EBUILD avogadro-1.1.1.ebuild 1976 SHA256 5abae5f879b0b0fa30baba648102d3a69e618b989cc151cf483453a3226e9171 SHA512 c6a83d047ab126e32ce74adc07f6702da476c19c96483b30753a634a66521f712ca302c71f1ff7bc72e92da0874e419f5a7edaf1a926631baa0e05634bccd909 WHIRLPOOL 7412f68617c56e86ce7e6c242053b38c0bb9e00339368e2c87ed28ede74e8b7d084d8158562b3c1fe830b822b4d0b8fcf4ab06065c4df334d2ccd385a3e6a6a0 +MISC ChangeLog 3988 SHA256 0c2f9a9d7e8b549f4e4e97756463e58d52520625e3a3292ad67e860d1e2ed4f6 SHA512 a518a58d309a39f60762e2fff76a48c891a4785103fb7727939244996c03492ffa92b0a2610320fad08ddff5f92155509b6da1f69c4fc1a60e1fb99193bdce19 WHIRLPOOL 8e3c8306dde4a18b585bfd84a5870290401269bab4519cd20a83ad005b2656472c86c22a967fa4f6d4960059a1fb6b4ee2b8f263f2d690ec4db934a6369dff3d +MISC ChangeLog-2015 8157 SHA256 b764019c5586469b24e84bbef958e4df39ef4019ddb1be25f95bfce96c549c83 SHA512 fc061195a7e791a171759d27ac25fc7cd2cc2c0347a7d353af49c449c1131c50cc7ba0b325d752785c563eb0d5c20a5a3933f37438bc3552f2fb41ffc355edec WHIRLPOOL 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 <gl2ps.h> + + #include <avogadro/pluginmanager.h> + +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 <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-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 @@ +<?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> |