16 files changed, 64 insertions, 200 deletions
diff --git a/sci-libs/avogadro-libs/ChangeLog b/sci-libs/avogadro-libs/ChangeLog
deleted file mode 100644
index ef0eee144..000000000
--- a/sci-libs/avogadro-libs/ChangeLog
+++ /dev/null
@@ -1,18 +0,0 @@
-# ChangeLog for sci-libs/avogadro-libs
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  12 Aug 2013; Justin Lecher <jlec@gentoo.org> avogadro-libs-0.6.0.ebuild,
-  +files/avogadro-libs-0.6.0-underlinking.patch, metadata.xml:
-  Fix underlinking reported by ercpe, allow monolithic plugin module
-
-  12 Aug 2013; Justin Lecher <jlec@gentoo.org> avogadro-libs-0.6.0.ebuild,
-  +files/avogadro-libs-0.6.0-underlinking.patch, metadata.xml:
-  Fix underlinking reported by ercpe, allow monolithic plugin module
-
-*avogadro-libs-0.6.0 (23 Jul 2013)
-
-  23 Jul 2013; Justin Lecher <jlec@gentoo.org> +avogadro-libs-0.6.0.ebuild,
-  +metadata.xml:
-  New addition written by me
-
diff --git a/sci-libs/avogadro-libs/Manifest b/sci-libs/avogadro-libs/Manifest
deleted file mode 100644
index bd4c7ba99..000000000
--- a/sci-libs/avogadro-libs/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST avogadrolibs-0.6.0.tar.gz 459937 SHA256 9a524eb122358231cc76a0f4efd0fb9313608598af6a105c92c045ec026fbde1 SHA512 fbcf8f07de32ca7f6f0fab32b96a288e7e6a19e7a00b3ed08290b6d9b4efb4284d8f60d18bf26334a4266afd15aefbf9faf1740e6f752b4cea4c183e89e7bc29 WHIRLPOOL ffb04d0e04891bee4eb9deda5dd6da5973fc7dbd222e9acb2acc52ec04610f4953bc83623a456e8f4a7e6b7f9b51e95295af6a8fe989c5cc2dde5bbd5e59573f
diff --git a/sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild b/sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild
deleted file mode 100644
index 46e1a2789..000000000
--- a/sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-inherit cmake-utils versionator
-
-MY_PN="${PN/-/}"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="Advanced molecule editor and visualizer 2"
-HOMEPAGE="http://www.openchemistry.org/"
-SRC_URI="http://openchemistry.org/files/v$(get_version_component_range 1-2)/${MY_P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc opengl qt4 static-plugins test vtk"
-
-REQUIRED_USE="qt4? ( opengl )"
-
-RDEPEND="
-	sci-chemistry/molequeue
-	sci-libs/chemkit"
-DEPEND="${DEPEND}
-	test? ( dev-cpp/gtest )"
-
-S="${WORKDIR}"/${MY_P}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-underlinking.patch
-)
-
-src_configure() {
-	local mycmakeargs=(
-		-DUSE_PROTOCALL=OFF
-		$(cmake-utils_use_build doc DOCUMENTATION)
-		$(cmake-utils_use_use opengl OPENGL)
-		$(cmake-utils_use_use qt4 QT)
-		$(cmake-utils_use_build static-plugins STATIC_PLUGINS)
-		$(cmake-utils_use_enable test TESTING)
-		$(cmake-utils_use_use vtk VTK)
-		)
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/avogadro-libs/files/avogadro-libs-0.6.0-underlinking.patch b/sci-libs/avogadro-libs/files/avogadro-libs-0.6.0-underlinking.patch
deleted file mode 100644
index ef9793939..000000000
--- a/sci-libs/avogadro-libs/files/avogadro-libs-0.6.0-underlinking.patch
+++ /dev/null
@@ -1,14 +0,0 @@
- avogadro/qtplugins/vanderwaalsao/CMakeLists.txt | 3 +++
- 1 file changed, 3 insertions(+)
-
-diff --git a/avogadro/qtplugins/vanderwaalsao/CMakeLists.txt b/avogadro/qtplugins/vanderwaalsao/CMakeLists.txt
-index 291dc9e..8547406 100644
---- a/avogadro/qtplugins/vanderwaalsao/CMakeLists.txt
-+++ b/avogadro/qtplugins/vanderwaalsao/CMakeLists.txt
-@@ -5,3 +5,6 @@ avogadro_plugin(VanDerWaalsAO
-   VanDerWaalsAO
-   vanderwaalsao.cpp
-   "")
-+
-+target_link_libraries(VanDerWaalsAO AvogadroRendering)
-+
diff --git a/sci-libs/avogadro-libs/metadata.xml b/sci-libs/avogadro-libs/metadata.xml
deleted file mode 100644
index 7bbb97f1b..000000000
--- a/sci-libs/avogadro-libs/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-  <maintainer>
-    <email>jlec@gentoo.org</email>
-  </maintainer>
-  <use>
-    <flag name="static-plugins">
-		build all plugins statically into main plugin modules
-	</flag>
-    <flag name="vtk">include vtk support</flag>
-  </use>
-</pkgmetadata>
diff --git a/sci-libs/chemkit/ChangeLog b/sci-libs/chemkit/ChangeLog
deleted file mode 100644
index 62d386007..000000000
--- a/sci-libs/chemkit/ChangeLog
+++ /dev/null
@@ -1,10 +0,0 @@
-# ChangeLog for sci-libs/chemkit
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*chemkit-0.1 (22 Jul 2013)
-
-  22 Jul 2013; Justin Lecher <jlec@gentoo.org> +chemkit-0.1.ebuild,
-  +metadata.xml:
-  New addition written by me
-
diff --git a/sci-libs/chemkit/Manifest b/sci-libs/chemkit/Manifest
deleted file mode 100644
index 13f90d9ca..000000000
--- a/sci-libs/chemkit/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST chemkit-0.1.tar.gz 5842235 SHA256 bec718ce4ae2fcb4cda63004d05a6e6bf65c1887179f665fcee118cbe7bec11b SHA512 0273f8735333000b04007ccd7adc58f0c4809a570fa5a72e4161652d72e8953bf89cad0893c20ecbb3484d6c13a8828c92f12366dddeedaf591815c35f6ef011 WHIRLPOOL 30c73d5d2bb7e946204d3dcdd87b82fa3e5278e799b06df523557f46ca4c71ae7d5b9c37d82af8dcdee48bb83f8840c5f2900b4331c3cf643c323ef20abc1883
diff --git a/sci-libs/chemkit/chemkit-0.1.ebuild b/sci-libs/chemkit/chemkit-0.1.ebuild
deleted file mode 100644
index 8f17cdd6c..000000000
--- a/sci-libs/chemkit/chemkit-0.1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_6,2_7} )
-
-inherit cmake-utils multilib
-
-DESCRIPTION="Library for chemistry applications"
-HOMEPAGE="http://www.chemkit.org/"
-SRC_URI="mirror://sourceforge/project/${PN}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="applications examples python test"
-
-RDEPEND="${PYTHON_DEPS}
-	dev-libs/boost
-	dev-cpp/eigen:3
-	examples? (
-		x11-libs/libX11
-		x11-libs/libXext
-	)"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/${PN}
-
-src_prepare() {
-	sed \
-		-e "/install/s:lib:$(get_libdir):g" \
-		-i CMakeLists.txt src/CMakeLists.txt src/plugins/CMakeLists.txt || die
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DCHEMKIT_BUILD_PLUGIN_BABEL=on
-		$(cmake-utils_use applications CHEMKIT_BUILD_APPS)
-		$(cmake-utils_use applications CHEMKIT_BUILD_QT_DESIGNER_PLUGINS)
-		$(cmake-utils_use examples CHEMKIT_BUILD_EXAMPLES)
-		$(cmake-utils_use examples CHEMKIT_BUILD_DEMOS)
-		$(cmake-utils_use python CHEMKIT_BUILD_BINDINGS_PYTHON)
-		$(cmake-utils_use test CHEMKIT_BUILD_TESTS)
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	use examples && dobin demos/*-viewer/*-viewer examples/uff-energy/uff-energy
-
-	cmake-utils_src_install
-}
diff --git a/sci-libs/chemkit/metadata.xml b/sci-libs/chemkit/metadata.xml
deleted file mode 100644
index 200ba799f..000000000
--- a/sci-libs/chemkit/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-  <maintainer>
-    <email>jlec@gentoo.org</email>
-  </maintainer>
-  <use>
-    <flag name="applications">Build also applications not only the libraries</flag>
-  </use>
-</pkgmetadata>
diff --git a/sci-libs/lemon/ChangeLog b/sci-libs/lemon/ChangeLog
index f565264cf..da26d24b9 100644
--- a/sci-libs/lemon/ChangeLog
+++ b/sci-libs/lemon/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  14 Jan 2014; Justin Lecher <jlec@gentoo.org> -lemon-1.3.ebuild,
+  +lemon-1.3-r1.ebuild, +files/lemon-1.3-underlinking.patch:
+  Import latest tree changes
+
   13 Jan 2014; Justin Lecher <jlec@gentoo.org> lemon-1.3.ebuild,
   +files/lemon-1.3-multilib.patch, metadata.xml:
   Fix for multilib-strict
diff --git a/sci-libs/lemon/files/lemon-1.3-underlinking.patch b/sci-libs/lemon/files/lemon-1.3-underlinking.patch
new file mode 100644
index 000000000..94aa1960a
--- /dev/null
+++ b/sci-libs/lemon/files/lemon-1.3-underlinking.patch
@@ -0,0 +1,47 @@
+ CMakeLists.txt       | 4 ++++
+ lemon/CMakeLists.txt | 2 ++
+ 2 files changed, 6 insertions(+)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index b06e5c7..fa68aa8 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -84,21 +84,25 @@ IF(GLPK_FOUND)
+   SET(LEMON_HAVE_LP TRUE)
+   SET(LEMON_HAVE_MIP TRUE)
+   SET(LEMON_HAVE_GLPK TRUE)
++  SET(LEMON_LP_LIBRARY ${GLPK_LIBRARY})
+ ENDIF(GLPK_FOUND)
+ IF(ILOG_FOUND)
+   SET(LEMON_HAVE_LP TRUE)
+   SET(LEMON_HAVE_MIP TRUE)
+   SET(LEMON_HAVE_CPLEX TRUE)
++  SET(LEMON_LP_LIBRARY ${ILOG_LIBRARY})
+ ENDIF(ILOG_FOUND)
+ IF(COIN_FOUND)
+   SET(LEMON_HAVE_LP TRUE)
+   SET(LEMON_HAVE_MIP TRUE)
+   SET(LEMON_HAVE_CLP TRUE)
+   SET(LEMON_HAVE_CBC TRUE)
++  SET(LEMON_LP_LIBRARY ${COIN_LIBRARY})
+ ENDIF(COIN_FOUND)
+ IF(SOPLEX_FOUND)
+   SET(LEMON_HAVE_LP TRUE)
+   SET(LEMON_HAVE_SOPLEX TRUE)
++  SET(LEMON_LP_LIBRARY ${COIN_LIBRARY})
+ ENDIF(SOPLEX_FOUND)
+ 
+ IF(ILOG_FOUND)
+diff --git a/lemon/CMakeLists.txt b/lemon/CMakeLists.txt
+index 8011833..2487345 100644
+--- a/lemon/CMakeLists.txt
++++ b/lemon/CMakeLists.txt
+@@ -59,6 +59,8 @@ IF(UNIX)
+   SET_TARGET_PROPERTIES(lemon PROPERTIES OUTPUT_NAME emon)
+ ENDIF()
+ 
++TARGET_LINK_LIBRARIES(lemon ${LEMON_LP_LIBRARY})
++
+ INSTALL(
+   TARGETS lemon
+   ARCHIVE DESTINATION lib
diff --git a/sci-libs/lemon/lemon-1.3.ebuild b/sci-libs/lemon/lemon-1.3-r1.ebuild
index de536b186..076e37f0b 100644
--- a/sci-libs/lemon/lemon-1.3.ebuild
+++ b/sci-libs/lemon/lemon-1.3-r1.ebuild
@@ -26,7 +26,10 @@ DEPEND="${RDEPEND}
 
 REQUIRED_USE="|| ( coin glpk )"
 
-PATCHES=( "${FILESDIR}"/${P}-multilib.patch )
+PATCHES=(
+	"${FILESDIR}"/${P}-multilib.patch
+	"${FILESDIR}"/${P}-underlinking.patch
+	)
 
 src_prepare() {
 	sed -i \
@@ -69,6 +72,8 @@ src_configure() {
 		$(cmake-utils_use doc LEMON_DOC_USE_MATHJAX)
 		$(cmake-utils_use coin LEMON_ENABLE_COIN)
 		$(cmake-utils_use glpk LEMON_ENABLE_GLPK)
+		-DLEMON_ENABLE_ILOG=NO
+		-DLEMON_ENABLE_SOPLEX=NO
 	)
 	cmake-utils_src_configure
 }
diff --git a/sci-libs/openlibm/ChangeLog b/sci-libs/openlibm/ChangeLog
index 72d966302..6807d384e 100644
--- a/sci-libs/openlibm/ChangeLog
+++ b/sci-libs/openlibm/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  14 Jan 2014;  <xhochy@gentoo.org> -files/openlibm-extras-soname.patch,
+  -files/openlibm-soname.patch, openlibm-9999.ebuild:
+  [sci-libs/openlibm] Remove extras and soname patch
+
   06 Jan 2014; Justin Lecher <jlec@gentoo.org> openlibm-9999.ebuild,
   metadata.xml:
   Switch from git-2 to git-r3
diff --git a/sci-libs/openlibm/files/openlibm-extras-soname.patch b/sci-libs/openlibm/files/openlibm-extras-soname.patch
deleted file mode 100644
index 7ee69a2ba..000000000
--- a/sci-libs/openlibm/files/openlibm-extras-soname.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- Makefile.extras.orig	2013-07-02 22:35:31.150277524 -0400
-+++ Makefile.extras	2013-07-02 22:35:56.993276767 -0400
-@@ -25,7 +25,7 @@
- libopenlibm-extras.a: $(OBJS)  
- 	$(AR) -rcs libopenlibm-extras.a $(OBJS)
- libopenlibm-extras.$(SHLIB_EXT): $(OBJS)
--	$(FC) -shared $(OBJS) $(LDFLAGS) -o libopenlibm-extras.$(SHLIB_EXT)
-+	$(FC) -shared $(OBJS) $(LDFLAGS) -Wl,--soname=libopenlibm-extras.$(SHLIB_EXT) -o libopenlibm-extras.$(SHLIB_EXT)
- 
- distclean:
- 	rm -f $(OBJS) *.a *.$(SHLIB_EXT)
diff --git a/sci-libs/openlibm/files/openlibm-soname.patch b/sci-libs/openlibm/files/openlibm-soname.patch
deleted file mode 100644
index 8852e0aef..000000000
--- a/sci-libs/openlibm/files/openlibm-soname.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- Makefile.orig	2013-07-16 15:55:33.481244590 -0700
-+++ Makefile	2013-07-16 15:56:15.535491859 -0700
-@@ -26,7 +26,7 @@
- libopenlibm.a: $(OBJS)  
- 	$(AR) -rcs libopenlibm.a $(OBJS)
- libopenlibm.$(SHLIB_EXT): $(OBJS)
--	$(FC) -shared $(OBJS) $(LDFLAGS) -o libopenlibm.$(SHLIB_EXT)
-+	$(FC) -shared $(OBJS) $(LDFLAGS) -Wl,--soname=libopenlibm.$(SHLIB_EXT) -o libopenlibm.$(SHLIB_EXT)
- 
- distclean:
- 	rm -f $(OBJS) *.a *.$(SHLIB_EXT)
diff --git a/sci-libs/openlibm/openlibm-9999.ebuild b/sci-libs/openlibm/openlibm-9999.ebuild
index 3d58a7205..a2b5442b2 100644
--- a/sci-libs/openlibm/openlibm-9999.ebuild
+++ b/sci-libs/openlibm/openlibm-9999.ebuild
@@ -18,16 +18,12 @@ IUSE="static-libs"
 
 src_prepare() {
 	epatch \
-		"${FILESDIR}"/${PN}-respect-toolchain.patch \
-		"${FILESDIR}"/${PN}-soname.patch \
-		"${FILESDIR}"/${PN}-extras-soname.patch
+		"${FILESDIR}"/${PN}-respect-toolchain.patch
 }
 
 src_compile() {
 	emake libopenlibm.so
 	use static-libs && emake libopenlibm.a
-	emake -f Makefile.extras libopenlibm-extras.so
-	use static-libs && emake -f Makefile.extras libopenlibm-extras.a
 }
 
 src_test() {
@@ -35,8 +31,8 @@ src_test() {
 }
 
 src_install() {
-	dolib.so libopenlibm.so libopenlibm-extras.so
-	use static-libs && dolib.a libopenlibm.a liboenlibm-extras.a
+	dolib.so libopenlibm.so*
+	use static-libs && dolib.a libopenlibm.a
 	doheader include/{cdefs,types}-compat.h src/openlibm.h
 	dodoc README.md
 }