reinit the tree, so we can have metadata

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 0675c74c759cf67b703add1b9483895ecba83d40bf943e011b0e6edc2eafe2c0f91d78472e6f554bd340236330c3cf1f3fbd0da65fe2158cca7feed727127463
+AUX avogadro-1.1.1-mkspecs-dir.patch 580 SHA256 ffa4e6b05884feabe688dd856efab0f00c9df8358bd17846e74291606b40465a SHA512 6c5b67d9f9e1e9fa3c11ae235f467525129fa9d81f34211ed8b97c199690e12cd1457df3aac861615d94efb452af306df6b53218309ff87f6ca1f68edffbf6b2 WHIRLPOOL e2f2c3521519cfcfe390fe8f1758576741f62ebca7f4ac3dae9e72390b25ef4595f270ae37c4fdc0217ff5265259f2dfaf529ec48e7422debf0bb65b15e8e40e
+AUX avogadro-1.1.1-no-strip.patch 745 SHA256 90cbae3e12a7f64e7f2ec61086b66e229e75bb1aafc5a3d987acf392b7ddc971 SHA512 921b1333bf37135d5890222193ebdb5b351739d16bf1434c59509e8aab0135ea5cde6812b63d4159fafac29d4eb6297320d03513e474466a7fb857ed16301d6e WHIRLPOOL ea1a6006fbb911974d30c65c72def85ce3265818186aa88a21eb7df511f16939a7bb381bc0390e996f138636db9d6350972896c60b45a687c1467e12f8ab7c9f
+AUX avogadro-1.1.1-openbabel.patch 655 SHA256 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>