Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci

32 files changed, 216 insertions, 310 deletions

diff --git a/dev-java/jgraphx/ChangeLog b/dev-java/jgraphx/ChangeLog
index 1e6b6660e..93b782e99 100644
--- a/dev-java/jgraphx/ChangeLog
+++ b/dev-java/jgraphx/ChangeLog
@@ -1,7 +1,12 @@
 # ChangeLog for dev-java/jgraphx
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  12 Jun 2013; Justin Lecher <jlec@gentoo.org> -jgraphx-1.2.0.7.ebuild,
+  -jgraphx-1.3.0.2.ebuild, jgraphx-1.4.1.0.ebuild, -jgraphx-1.4.1.2.ebuild,
+  jgraphx-1.8.0.6.ebuild, metadata.xml:
+  Drop old; bump EAPI; fix license; QA -> layout
+
 *jgraphx-1.8.0.6 (28 Jul 2012)
 
   28 Jul 2012; Guillaume Horel <guillaume.horel@gmail.com>
diff --git a/dev-java/jgraphx/Manifest b/dev-java/jgraphx/Manifest
index 126a5a322..9e3a58174 100644
--- a/dev-java/jgraphx/Manifest
+++ b/dev-java/jgraphx/Manifest
@@ -1,5 +1,2 @@
-DIST jgraphx-1.2.0.7.zip 3034071 SHA256 9dfc39de448d9ba28ab6b27fe3c8e920033779feb38dbe45cf96145c6d506b08
-DIST jgraphx-1.3.0.2.zip 3055762 SHA256 c58aa9e3b1f334f54633017f1f9b35204e19d18524c41df3a5e68c2aa50d2c2d
 DIST jgraphx-1.4.1.0.zip 4052749 SHA256 086cd3de7d2b381a61f5a7d5eea19e80d3f1f1aaff9642d2b9e582d86a312f59
-DIST jgraphx-1.4.1.2.zip 4148011 SHA256 cb0216df6fe3e9351afae7f02585e6f5c50e28e764d9504dd8aa558a87d3fe95
 DIST jgraphx-1.8.0.6.zip 4216848 SHA256 237035982616769f0c15b805b4ce12616915498a5995fbdae814b97f434c860d SHA512 07985168625f094a8de9ab0e5c6050dd1a5d537b21eb6c73e468ad21db2758ac78a272dfedf22b94585eff4f77288ad99f8f1b70b18462754f0f3048ad06e40f WHIRLPOOL 403b784bdf934fc4a6aae643badb4380279bd15ea87520d6df0ed3d3ed58b020d3f0f979e9d2a2de338256bbdb5793e1e9d50634c60e83d104ceb88b96fcefba
diff --git a/dev-java/jgraphx/jgraphx-1.2.0.7.ebuild b/dev-java/jgraphx/jgraphx-1.2.0.7.ebuild
deleted file mode 100644
index e10480ed7..000000000
--- a/dev-java/jgraphx/jgraphx-1.2.0.7.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=2
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2 versionator
-
-MY_PV=$(replace_all_version_separators '_')
-
-DESCRIPTION="Open-source graph component for Java"
-SRC_URI="http://www.jgraph.com/downloads/jgraphx/archive/${PN}-${MY_PV}.zip -> ${P}.zip"
-HOMEPAGE="http://www.jgraph.com/"
-IUSE="doc examples source"
-DEPEND=">=virtual/jdk-1.5
-	app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5"
-LICENSE="as-is"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	# don't do javadoc always
-	sed -i -e 's/depends="doc"/depends="compile"/' build.xml || \
-		die "sed failed"
-
-	rm -rf doc/api || die
-	rm lib/jgraphx.jar || die
-}
-
-EANT_BUILD_TARGET="build"
-EANT_DOC_TARGET="doc"
-
-src_install() {
-	java-pkg_dojar lib/${PN}.jar
-
-	use doc && java-pkg_dojavadoc docs/api
-	use source && java-pkg_dosrc src/org
-	use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jgraphx/jgraphx-1.3.0.2.ebuild b/dev-java/jgraphx/jgraphx-1.3.0.2.ebuild
deleted file mode 100644
index a04453dd0..000000000
--- a/dev-java/jgraphx/jgraphx-1.3.0.2.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/dev-java/jgraph/jgraph-5.12.0.4.ebuild,v 1.5 2008/05/13 21:09:16 ken69267 Exp $
-
-EAPI=2
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2 versionator
-
-MY_PV=$(replace_all_version_separators '_')
-
-DESCRIPTION="Open-source graph component for Java"
-SRC_URI="http://www.jgraph.com/downloads/jgraphx/archive/${PN}-${MY_PV}.zip\
-		-> ${P}.zip"
-HOMEPAGE="http://www.jgraph.com"
-IUSE="doc examples source"
-DEPEND=">=virtual/jdk-1.5
-	app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5"
-LICENSE="as-is"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	# don't do javadoc always
-	sed -i \
-		-e 's/depends="doc"/depends="compile"/' \
-		build.xml || die "sed failed"
-	rm -rf doc/api lib/jgraphx.jar || die
-}
-
-EANT_BUILD_TARGET="build"
-EANT_DOC_TARGET="doc"
-
-src_install() {
-	java-pkg_dojar lib/${PN}.jar
-
-	use doc && java-pkg_dojavadoc docs/api
-	use source && java-pkg_dosrc src/org
-	use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jgraphx/jgraphx-1.4.1.0.ebuild b/dev-java/jgraphx/jgraphx-1.4.1.0.ebuild
index a0f83e766..1940bda80 100644
--- a/dev-java/jgraphx/jgraphx-1.4.1.0.ebuild
+++ b/dev-java/jgraphx/jgraphx-1.4.1.0.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=2
+EAPI=5
 
 JAVA_PKG_IUSE="doc source"
 
@@ -11,16 +11,18 @@ inherit java-pkg-2 java-ant-2 versionator
 MY_PV=$(replace_all_version_separators '_')
 
 DESCRIPTION="Open-source graph component for Java"
-SRC_URI="http://www.jgraph.com/downloads/jgraphx/archive/${PN}-${MY_PV}.zip\
-		-> ${P}.zip"
 HOMEPAGE="http://www.jgraph.com"
+SRC_URI="http://www.jgraph.com/downloads/jgraphx/archive/${PN}-${MY_PV}.zip -> ${P}.zip"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
 IUSE="doc examples source"
-DEPEND=">=virtual/jdk-1.5
+
+DEPEND="
+	>=virtual/jdk-1.5
 	app-arch/unzip"
 RDEPEND=">=virtual/jre-1.5"
-LICENSE="as-is"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
 
 S="${WORKDIR}/${PN}"
 
diff --git a/dev-java/jgraphx/jgraphx-1.4.1.2.ebuild b/dev-java/jgraphx/jgraphx-1.4.1.2.ebuild
deleted file mode 100644
index a0f83e766..000000000
--- a/dev-java/jgraphx/jgraphx-1.4.1.2.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=2
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2 versionator
-
-MY_PV=$(replace_all_version_separators '_')
-
-DESCRIPTION="Open-source graph component for Java"
-SRC_URI="http://www.jgraph.com/downloads/jgraphx/archive/${PN}-${MY_PV}.zip\
-		-> ${P}.zip"
-HOMEPAGE="http://www.jgraph.com"
-IUSE="doc examples source"
-DEPEND=">=virtual/jdk-1.5
-	app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5"
-LICENSE="as-is"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	# don't do javadoc always
-	sed -i \
-		-e 's/depends="doc"/depends="compile"/' \
-		build.xml || die "sed failed"
-	rm -rf doc/api lib/jgraphx.jar || die
-}
-
-EANT_BUILD_TARGET="build"
-EANT_DOC_TARGET="doc"
-
-src_install() {
-	java-pkg_dojar lib/${PN}.jar
-
-	use doc && java-pkg_dojavadoc docs/api
-	use source && java-pkg_dosrc src/org
-	use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jgraphx/jgraphx-1.8.0.6.ebuild b/dev-java/jgraphx/jgraphx-1.8.0.6.ebuild
index 895650d27..b6d4e2724 100644
--- a/dev-java/jgraphx/jgraphx-1.8.0.6.ebuild
+++ b/dev-java/jgraphx/jgraphx-1.8.0.6.ebuild
@@ -1,24 +1,28 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=4
+EAPI=5
+
 JAVA_PKG_IUSE="doc source"
+
 inherit java-pkg-2 java-ant-2 versionator
 
 MY_PV=$(replace_all_version_separators '_')
 
 DESCRIPTION="Open-source graph component for Java"
-SRC_URI="http://www.jgraph.com/downloads/jgraphx/archive/${PN}-${MY_PV}.zip\
-		-> ${P}.zip"
 HOMEPAGE="http://www.jgraph.com"
+SRC_URI="http://www.jgraph.com/downloads/jgraphx/archive/${PN}-${MY_PV}.zip -> ${P}.zip"
+
+SLOT="1.8"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
 IUSE="doc examples source"
-DEPEND=">=virtual/jdk-1.5
+
+DEPEND="
+	>=virtual/jdk-1.5
 	app-arch/unzip"
 RDEPEND=">=virtual/jre-1.5"
-LICENSE="as-is"
-SLOT="1.8"
-KEYWORDS="~amd64 ~x86"
 
 S="${WORKDIR}/${PN}"
 
diff --git a/dev-java/jgraphx/metadata.xml b/dev-java/jgraphx/metadata.xml
index 8cdee3b70..57850f4e3 100644
--- a/dev-java/jgraphx/metadata.xml
+++ b/dev-java/jgraphx/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
-<longdescription lang="en">
+  <herd>sci</herd>
+  <longdescription lang="en">
   JGraph X is based on the mxGraph architecture, a re-designed core
   based on JGraph experience.
   Overall, JGraph X provides more features that JGraph, with a far
diff --git a/dev-libs/asmjit/ChangeLog b/dev-libs/asmjit/ChangeLog
index 2713d1762..eda4f8cba 100644
--- a/dev-libs/asmjit/ChangeLog
+++ b/dev-libs/asmjit/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for dev-libs/asmjit
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*asmjit-1.0_beta4 (12 Jun 2013)
+
+  12 Jun 2013; Justin Lecher <jlec@gentoo.org> +asmjit-1.0_beta4.ebuild,
+  -asmjit-1.0_beta_p2.ebuild, metadata.xml:
+  Version BUmp, Fix license, bump EAPI
+
 *asmjit-1.0_beta_p2 (12 Nov 2010)
 
   12 Nov 2010; Kacper Kowalik <xarthisius@gentoo.org>
diff --git a/dev-libs/asmjit/Manifest b/dev-libs/asmjit/Manifest
index 891291adb..329d22f72 100644
--- a/dev-libs/asmjit/Manifest
+++ b/dev-libs/asmjit/Manifest
@@ -1 +1 @@
-DIST AsmJit-1.0-beta2.zip 292614 RMD160 bf67c422249af396d4e94f101660671fd1f216de SHA1 5d5963e2ebced73cd0e33f4a472b12c48567b573 SHA256 cc9f1b1935c4d0d3bf5305fc38d39c0d84494205c50a276ac9e529ab81b5cf07
+DIST AsmJit-1.0-beta4.zip 267674 SHA256 f30d76dc01db8d771eda14e7ac194af0a676f905857421e8147ed710e80f5f85 SHA512 dd24f4f9851c546531c0ae9f74c12f8797261e7d064ffa7b0449500ae39b349321e7616356e6e69c1ac89cef73c7862668daf10f357cdcd8afda7fab0bb89ebf WHIRLPOOL c5777d2f76d54a8961b6191a8c1db84bcbb32d97c3d05db1d0a05a82c4d82b6476429df627010ae4bbd2f5728114d6c624ed2f53e9f162948ef0f84f698795b6
diff --git a/dev-libs/asmjit/asmjit-1.0_beta_p2.ebuild b/dev-libs/asmjit/asmjit-1.0_beta4.ebuild
index fdd01fcc1..b3e1be973 100644
--- a/dev-libs/asmjit/asmjit-1.0_beta_p2.ebuild
+++ b/dev-libs/asmjit/asmjit-1.0_beta4.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=5
 
 inherit cmake-utils versionator
 
@@ -15,8 +15,8 @@ DESCRIPTION="complete x86/x64 JIT-Assembler for C++ language"
 HOMEPAGE="http://code.google.com/p/asmjit/"
 SRC_URI="http://${PN}.googlecode.com/files/${MY_P}.zip"
 
-LICENSE="as-is"
 SLOT="0"
+LICENSE="BSD"
 KEYWORDS="~amd64 ~x86"
 IUSE="test"
 
diff --git a/dev-libs/asmjit/metadata.xml b/dev-libs/asmjit/metadata.xml
index a33aea347..c532e117a 100644
--- a/dev-libs/asmjit/metadata.xml
+++ b/dev-libs/asmjit/metadata.xml
@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci</herd>
-	<maintainer>
-		<email>xarthisius@gentoo.org</email>
-		<name>Kacper Kowalik</name>
-	</maintainer>
-	<longdescription lang="en">
+  <herd>sci</herd>
+  <maintainer>
+    <email>xarthisius@gentoo.org</email>
+    <name>Kacper Kowalik</name>
+  </maintainer>
+  <longdescription lang="en">
 		AsmJit is complete x86/x64 JIT-Assembler for C++ language. It supports
 		32/64-bit x86 processors including all usable extensions (FPU, MMX,
 		3dNow, SSE, SSE2, SSE3 and SSE4) through type-safe API that mimics Intel
diff --git a/media-gfx/librecad/ChangeLog b/media-gfx/librecad/ChangeLog
index c157115fb..f180d50a7 100644
--- a/media-gfx/librecad/ChangeLog
+++ b/media-gfx/librecad/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header$
 
+  11 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> librecad-9999.ebuild:
+  media-gfx/librecad: Fixed bug #472472 and ebuild cleaning
+
   8 Jun 2013; Dongxu Li <dongxuli2011@gmail.com> +librecad-2.0.0_rc1.ebuild:
   Versions bumped to 2.0.0_rc1
   
diff --git a/media-gfx/librecad/librecad-9999.ebuild b/media-gfx/librecad/librecad-9999.ebuild
index d3db6f76e..ab66f2424 100644
--- a/media-gfx/librecad/librecad-9999.ebuild
+++ b/media-gfx/librecad/librecad-9999.ebuild
@@ -2,10 +2,10 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="4"
-inherit qt4-r2 eutils git-2 flag-o-matic
+EAPI=5
+inherit qt4-r2 eutils git-2
 
-DESCRIPTION="An generic 2D CAD program"
+DESCRIPTION="Generic 2D CAD program"
 HOMEPAGE="http://www.librecad.org/"
 LICENSE="GPL-2"
 SLOT="0"
@@ -26,17 +26,14 @@ DEPEND="${RDEPEND}
 src_prepare() {
 	#sed -i -e "s:\\\$\+system(git describe --tags):9999:" src/src.pro
 	#enable C++11 by default
-	sed -i -e '/RS_VECTOR2D/ s/^#//' librecad/src/src.pro
+	sed -i -e '/RS_VECTOR2D/ s/^#//' librecad/src/src.pro || die
 }
 
-src_install()
-{
+src_install() {
 	dobin unix/librecad
-	insinto /usr/share/"${PN}"
+	insinto /usr/share/${PN}
 	doins -r unix/resources/*
-	if use doc ; then
-	dohtml -r support/doc/*
-	fi
-	doicon librecad/res/main/"${PN}".png
-	make_desktop_entry "${PN}" LibreCAD "${PN}" Graphics
+	use doc && dohtml -r librecad/support/doc/*
+	doicon librecad/res/main/${PN}.png
+	make_desktop_entry ${PN} LibreCAD ${PN} Graphics
 }
diff --git a/profiles/arch/amd64/no-multilib/package.mask b/profiles/arch/amd64/no-multilib/package.mask
deleted file mode 100644
index 885811b75..000000000
--- a/profiles/arch/amd64/no-multilib/package.mask
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-# When you add an entry to the top of this file, add your name, the date, and
-# an explanation of why something is getting masked. Please be extremely
-# careful not to commit atoms that are not valid, as it can cause large-scale
-# breakage, especially if it ends up in the daily snapshot.
-#
-## Example:
-##
-## # Dev E. Loper <developer@gentoo.org> (28 Jun 2012)
-## # Masking foo USE flag until we can get the
-## # foo stuff to work properly again (bug 12345)
-## =media-video/mplayer-0.90_pre5 foo
-## =media-video/mplayer-0.90_pre5-r1 foo
-#
-
-#--- END OF EXAMPLES ---
-
-# Christoph Junghans <ottxor@gentoo.org> (24 Dec 2012)
-# Needs multilib
-dev-util/ccache-icc
-
-# Justin Lecher <jlec@gentoo.org> (11 Nov 2011)
-# Needs multilib
-sci-chemistry/nmrpipe
diff --git a/profiles/arch/amd64/package.use.mask b/profiles/arch/amd64/package.use.mask
deleted file mode 100644
index c8eef20a6..000000000
--- a/profiles/arch/amd64/package.use.mask
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-# When you add an entry to the top of this file, add your name, the date, and
-# an explanation of why something is getting masked. Please be extremely
-# careful not to commit atoms that are not valid, as it can cause large-scale
-# breakage, especially if it ends up in the daily snapshot.
-#
-## Example:
-##
-## # Dev E. Loper <developer@gentoo.org> (28 Jun 2012)
-## # Masking foo USE flag until we can get the
-## # foo stuff to work properly again (bug 12345)
-## =media-video/mplayer-0.90_pre5 foo
-## =media-video/mplayer-0.90_pre5-r1 foo
-#
-
-#--- END OF EXAMPLES ---
-
-# Justin Lecher <jlec@gentoo.org> (27 Jan 2010)
-# Code only works on 32bit
-sci-chemistry/almost sse
diff --git a/sci-biology/lastz/ChangeLog b/sci-biology/lastz/ChangeLog
index 8c73100f2..97e871bc3 100644
--- a/sci-biology/lastz/ChangeLog
+++ b/sci-biology/lastz/ChangeLog
@@ -1,7 +1,17 @@
 # ChangeLog for sci-biology/lastz
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  12 Jun 2013; Justin Lecher <jlec@gentoo.org> -lastz-1.02.00.ebuild,
+  +lastz-1.03.34.ebuild, +files/lastz-1.03.34-build.patch, metadata.xml:
+  Version BUmp; fix license; bump to EAPI=5; fix buildsystem
+
+*lastz-1.03.34 (12 Jun 2013)
+
+  12 Jun 2013; Justin Lecher <jlec@gentoo.org> -lastz-1.02.00.ebuild,
+  +lastz-1.03.34.ebuild, +files/lastz-1.03.34-build.patch, metadata.xml:
+  Version BUmp; fix license; bump to EAPI=5; fix buildsystem
+
 *lastz-1.02.00 (16 Jan 2012)
 
   16 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/lastz/Manifest b/sci-biology/lastz/Manifest
index d9ecafa01..68cf4df31 100644
--- a/sci-biology/lastz/Manifest
+++ b/sci-biology/lastz/Manifest
@@ -1,2 +1 @@
-DIST lastz-1.02.00.tar.gz 1827527 SHA256 054515f27fdf9392f3d2e84ca421103b5e5575ba7a1979addf3c277212114a21 SHA512 5507f511b98ee3d90af08120c6a41b6606c1c71f458c043f4ee85e2ff8108fb2d02b31c347fd6f211b49fb97aeac0ff1ed5f96895644c7cd94918ac57073ee0c WHIRLPOOL 242a9fecaf57b71b2c3a50033a01e9f12083bc56e3c9945102d8a789f0d4476d0c66ea2b78ce870e914f095409bb1c3b7ac3a5fbee94c7a59a05e351786a22d5
-DIST lav_format.html 11901 SHA256 81949a94b4864481cd1c48c4fac413765ada74b6f5b8a9577684399af8472408 SHA512 93fc8d7b45f893beebb23ff2be10d4352691c6bd93b9ecc5750fdd37f10038f91a644f57e95653b9138e14a2344e124d3ca543e0beeabc5fa922194374659b96 WHIRLPOOL 403110222223787abaa0034a1496f63b5cf115a3abeb9609e77130545ff4d1fbf6193909a820b25e78e011bd5f0340171b82a11e928bc7a8900377674c49b3e2
+DIST lastz-1.03.34.tar.gz 716550 SHA256 b831cfb7dabf85e2f9bf33a76641481ede0d18a941c3a72d57d373b018232fbf SHA512 a29d27cd718c99762397f985ad9320e9cec9b288f94b766224f904abaa6793d4557cc253e82f568223c6a256c35e357c51d29ba89a0af3c915a82f27fadaaf1f WHIRLPOOL 4f3939005aaad44042ca219138355c02b95c6e7f182d4f11ad810a27625044a29075815efefb419aa8476be6cd9cf553d0e07f8a59a0a0fc74dd2bba77f1e9bd
diff --git a/sci-biology/lastz/files/lastz-1.03.34-build.patch b/sci-biology/lastz/files/lastz-1.03.34-build.patch
new file mode 100644
index 000000000..bc3a8c033
--- /dev/null
+++ b/sci-biology/lastz/files/lastz-1.03.34-build.patch
@@ -0,0 +1,43 @@
+ src/Makefile | 11 ++++++-----
+ 1 file changed, 6 insertions(+), 5 deletions(-)
+
+diff --git a/src/Makefile b/src/Makefile
+index f628f3c..5bb11bf 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,7 +1,7 @@
+ include ../make-include.mak
+ include version.mak
+ 
+-CC=gcc
++CC?=gcc
+ 
+ # default targets
+ 
+@@ -48,7 +48,8 @@ VERSION_FLAGS= \
+ 	-DSUBVERSION_REV="\"${SUBVERSION_REV}"\"
+ 
+ 
+-CFLAGS = -O3 ${definedForAll} ${VERSION_FLAGS}
++CFLAGS ?= -O3 ${definedForAll}
++CFLAGS += ${VERSION_FLAGS}
+ 
+ 
+ srcFiles = lastz infer_scores \
+@@ -78,13 +79,13 @@ incFiles = lastz.h infer_scores.h \
+ 
+ 
+ lastz: $(foreach part,${srcFiles},${part}.o)
+-	$(CC) $(foreach part,${srcFiles},${part}.o) -lm -o $@
++	$(CC) $(LDFLAGS) $(foreach part,${srcFiles},${part}.o) -lm -o $@
+ 
+ lastz_D: $(foreach part,${srcFiles},${part}_D.o)
+-	$(CC) $(foreach part,${srcFiles},${part}_D.o) -lm -o $@
++	$(CC) $(LDFLAGS) $(foreach part,${srcFiles},${part}_D.o) -lm -o $@
+ 
+ lastz_32: $(foreach part,${srcFiles},${part}_32.o)
+-	$(CC) $(foreach part,${srcFiles},${part}_32.o) -lm -o $@
++	$(CC) $(LDFLAGS) $(foreach part,${srcFiles},${part}_32.o) -lm -o $@
+ 
+ # cleanup
+ 
diff --git a/sci-biology/lastz/lastz-1.02.00.ebuild b/sci-biology/lastz/lastz-1.03.34.ebuild
index 233691f6d..7fd8e4ed2 100644
--- a/sci-biology/lastz/lastz-1.02.00.ebuild
+++ b/sci-biology/lastz/lastz-1.03.34.ebuild
@@ -1,27 +1,33 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
 
 DESCRIPTION="A pairwise DNA sequence aligner (also chromosome to chromosome), a BLASTZ replacement"
 HOMEPAGE="http://www.bx.psu.edu/~rsharris/lastz/"
-SRC_URI="http://www.bx.psu.edu/miller_lab/dist/lastz-"${PV}".tar.gz
-		http://www.bx.psu.edu/miller_lab/dist/lav_format.html"
+SRC_URI="http://www.bx.psu.edu/~rsharris/lastz/newer/${P}.tar.gz"
 
-LICENSE=""
 SLOT="0"
-#KEYWORDS="~amd64 ~x86"
-KEYWORDS=""
+LICENSE="all-rights-reserved"
+KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}"
-
 S="${WORKDIR}"/lastz-distrib-"${PV}"
 
+RESTRICT="mirror"
+
+src_prepare() {
+	append-lfs-flags
+	epatch "${FILESDIR}"/${P}-build.patch
+
+	tc-export CC
+}
+
 src_install(){
 	dobin src/lastz src/lastz_D
 	dodoc README.lastz.html
-	dodoc "${DISTDIR}"/lav_format.html
+	dohtml lav_format.html
 }
diff --git a/sci-biology/lastz/metadata.xml b/sci-biology/lastz/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/lastz/metadata.xml
+++ b/sci-biology/lastz/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-biology/phylobayes/ChangeLog b/sci-biology/phylobayes/ChangeLog
deleted file mode 100644
index ebd3362c5..000000000
--- a/sci-biology/phylobayes/ChangeLog
+++ /dev/null
@@ -1,10 +0,0 @@
-# ChangeLog for sci-biology/phylobayes
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*phylobayes-3.3b (02 Mar 2012)
-
-  02 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-  +phylobayes-3.3b.ebuild:
-  initial ebuild
-
diff --git a/sci-biology/phylobayes/Manifest b/sci-biology/phylobayes/Manifest
deleted file mode 100644
index a688e0ba6..000000000
--- a/sci-biology/phylobayes/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST phylobayes3.3.pdf 396814 SHA256 6cc295e378ea69dfb04af60e59531b4e924b08f059de809341d463a07e7d5331 SHA512 b87571d17f1020dee8fd0886b904280b57776a6fc69376831e84d99ba0196f86a5cda8ba9f8fd143125c7cdc18772a51d4b6d65b9eee1c7bd942a5a95a5a96af WHIRLPOOL e3e63f47e3c309bd563c22908e7cbf89d2935dfd3f5121145f47b7d99e7a89cf3412da28236dbb9beb9a620aa09adb7ed5db39c5f15fc75b18aecdab14280e40
-DIST phylobayes3.3b.tar.gz 45527386 SHA256 49d7b65b4298ae2a619dc3556bdb5804675217fbbf15eb0cbf25b46abb076e9e SHA512 8155c8023c3ef194871f8192f88080b76d08e829fa6e41b71be4c095a97b39124bb4db9f4a4dd9274d5e686efbeb783eca975023174752b41d92b94dfee0b95a WHIRLPOOL 62eed97b3b966ce30886b112ea5bbb781f9e7295a0d06f77e2bfb2e907402aa0c1e032322d96262f34c8b6a89514c76e9975c0539f7718b4fcd26c3da998271d
diff --git a/sci-biology/phylobayes/metadata.xml b/sci-biology/phylobayes/metadata.xml
deleted file mode 100644
index 07b525505..000000000
--- a/sci-biology/phylobayes/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/phylobayes/phylobayes-3.3b.ebuild b/sci-biology/phylobayes/phylobayes-3.3b.ebuild
deleted file mode 100644
index b456964f2..000000000
--- a/sci-biology/phylobayes/phylobayes-3.3b.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-DESCRIPTION="Phylogenetic Bayesian analysis program"
-HOMEPAGE="http://megasun.bch.umontreal.ca/People/lartillot/www/download.html"
-SRC_URI="http://megasun.bch.umontreal.ca/People/lartillot/www/phylobayes3.3b.tar.gz
-	http://megasun.bch.umontreal.ca/People/lartillot/www/phylobayes3.3.pdf"
-
-LICENSE=""
-SLOT="0"
-#KEYWORDS="~amd64 ~x86"
-KEYWORDS=""
-IUSE="gsl latex"
-
-DEPEND="gsl? ( sci-libs/gsl )"
-RDEPEND="${DEPEND}
-	latex? ( dev-texlive/texlive-latex
-			app-text/dvipsk )"
-
-S="${WORKDIR}"/phylobayes3.3b
-
-src_prepare(){
-	if use gsl; then
-		sed -i 's/#USE_GSL/USE_GSL/' sources/Makefile
-	sed -i 's/CC/CXX/g' sources/Makefile
-	fi
-}
-
-src_install(){
-	dobin exe_lin64/*
-	insinto /usr/share/"${P}"/aux_ps
-	doins aux_ps/header.tex
-	dodoc "${DISTDIR}"/phylobayes3.3.pdf
-}
diff --git a/sci-chemistry/rosetta/ChangeLog b/sci-chemistry/rosetta/ChangeLog
index 02eb37984..89adc6eec 100644
--- a/sci-chemistry/rosetta/ChangeLog
+++ b/sci-chemistry/rosetta/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  11 Jun 2013; Justin Lecher <jlec@gentoo.org> rosetta-3.4.ebuild:
+  Fix: Ebuild calls die in a subshell
+
+  11 Jun 2013; Justin Lecher <jlec@gentoo.org> rosetta-3.4.ebuild,
+  metadata.xml:
+  Add patches from www.csrosetta.org
+
   21 Mar 2013; Justin Lecher <jlec@gentoo.org> rosetta-3.4.ebuild:
   Fix for mpi
 
diff --git a/sci-chemistry/rosetta/Manifest b/sci-chemistry/rosetta/Manifest
index 9cc6fbf0a..cf6a0a086 100644
--- a/sci-chemistry/rosetta/Manifest
+++ b/sci-chemistry/rosetta/Manifest
@@ -1 +1,2 @@
+DIST patch_rosetta3.4_to_CSROSETTA3_ver1.3.txt 1187168 SHA256 071b11f6934ed308fa1f4594ee5500353d72b951c5d795fcbf4792d96e3f53c3 SHA512 7f59e0c41ad3f0a044d23bd3a4e877910aaec8a70478e1ffdf8474d77b0f4a7a5b39ca217180f888d69d1fbd5879dba80ff23b9dba4bc2fb7017a00a344916bf WHIRLPOOL 4bf39a527476e670f7459b4a03394ac800d204e45ddd7eca6d52cb36f04217b5e0ba3374a5166a55c6142939c82bd3b42055b40a320274c73bcead6e0ec120f0
 DIST rosetta3.4_source.tgz 89734375 SHA256 5ad2d06f7e4e08ef7e87c91bfe7c6d5687601f609892203c75b1abe465954e19 SHA512 d887e3660a8baecc91609463e5d64a86a48c76c72394b211cc388bf6eb49d5696a531eb1cfe19342c3bf9d399b49f1b0fb0a9682a0e166ab6594acc050a5f31e WHIRLPOOL f28706d46335da74934a4339c24c71b084fc8b2a2a2177f16a959ee2b9ea23710598b41c136ba4e18699ae7ddacb327f02a58620782554777651d50281e97fd2
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch
new file mode 100644
index 000000000..882534bfd
--- /dev/null
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch
@@ -0,0 +1,32 @@
+ tools/build/options.settings | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/tools/build/options.settings b/tools/build/options.settings
+index 30fb65e..f79ef5b 100644
+--- a/tools/build/options.settings
++++ b/tools/build/options.settings
+@@ -9,7 +9,7 @@
+ options = {
+ 
+     "cxx" : {
+-        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "*" ],
++        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "4.7", "4.8", "*" ],
+         "icc"     : [ "8.0", "8.1", "9.0", "9.1", "10.0", "10.1", "11.1", "*" ], #PBHACK
+         "msvc"    : [ "7.0", "7.1", "8.0", "8.1", "*" ],
+         "xlc"     : [ "7.0", "8.0", "9.0", "XL", "*" ],
+ src/protocols/jd2/SingleFileBuffer.cc | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/protocols/jd2/SingleFileBuffer.cc b/src/protocols/jd2/SingleFileBuffer.cc
+index aa78d91..61ca823 100644
+--- a/src/protocols/jd2/SingleFileBuffer.cc
++++ b/src/protocols/jd2/SingleFileBuffer.cc
+@@ -28,6 +28,8 @@
+ #include <ctime>      // for clock()
+ #endif
+ 
++#include <unistd.h>
++
+ namespace protocols {
+ namespace jd2 {
+ using namespace core;
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch b/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch
new file mode 100644
index 000000000..17e85f882
--- /dev/null
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch
@@ -0,0 +1,22 @@
+ tools/build/setup.py | 8 +++++++-
+ 1 file changed, 7 insertions(+), 1 deletion(-)
+
+diff --git a/tools/build/setup.py b/tools/build/setup.py
+index 4e57ff6..d8a2a08 100644
+--- a/tools/build/setup.py
++++ b/tools/build/setup.py
+@@ -354,7 +354,13 @@ what SCons will use to build the system.
+             symbols = setting.appends.symbols()
+             if symbols.has_key("ENV"):
+                 for key, value in symbols["ENV"].items():
+-                    env["ENV"][key] += value
++                    if key == "PATH":
++                        env["ENV"][key] = value
++                    else:
++                        try:
++                            env["ENV"][key] += value
++                        except:
++                            print key, value
+                 del symbols["ENV"]
+             env.Append(**symbols)
+         if setting.prepends:
diff --git a/sci-chemistry/rosetta/metadata.xml b/sci-chemistry/rosetta/metadata.xml
index 96d9d6378..b8a46614c 100644
--- a/sci-chemistry/rosetta/metadata.xml
+++ b/sci-chemistry/rosetta/metadata.xml
@@ -9,6 +9,7 @@
     <flag name="boinc">compile rosetta as a rosetta@home client</flag>
     <flag name="boost">compile rosetta with boost supported code</flag>
     <flag name="float">Build with floats rather than doubles</flag>
+    <flag name="lange">Apply patches from www.csrosetta.org</flag>
   </use>
   <upstream>
     <bugs-to>general-support@mail.rosettacommons.org</bugs-to>
diff --git a/sci-chemistry/rosetta/rosetta-3.4.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild
index 6ffe8dfb0..7a9ceada5 100644
--- a/sci-chemistry/rosetta/rosetta-3.4.ebuild
+++ b/sci-chemistry/rosetta/rosetta-3.4.ebuild
@@ -13,12 +13,12 @@ MY_P="${PN}${PV}_source"
 
 DESCRIPTION="Prediction and design of protein structures, folding mechanisms, and protein-protein interactions"
 HOMEPAGE="http://www.rosettacommons.org/"
-SRC_URI="${MY_P}.tgz"
+SRC_URI="${MY_P}.tgz patch_rosetta3.4_to_CSROSETTA3_ver1.3.txt"
 
 LICENSE="|| ( rosetta-academic rosetta-commercial )"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="boinc +boost custom-cflags debug doc float mpi +openmp X"
+IUSE="boinc +boost custom-cflags debug doc float +lange mpi +openmp X"
 
 REQUIRED_USE="?? ( mpi boinc )"
 
@@ -51,13 +51,19 @@ src_prepare() {
 	use custom-cflags || \
 		export CXXFLAGS="-O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -pipe"
 
+	export LD_LIBRARY_PATH=""
+	use lange && \
+		epatch \
+			"${DISTDIR}"/patch_${PN}${PV}_to_CSROSETTA3_ver1.3.txt \
+			"${FILESDIR}"/${P}-lange-fix.patch
+
 	epatch \
 		"${FILESDIR}"/${P}-platform.patch \
 		"${FILESDIR}"/${P}-user-settings.patch \
 		"${FILESDIR}"/${P}-fix-valgrind.patch \
 		"${FILESDIR}"/${P}-boinc.patch \
 		"${FILESDIR}"/${P}-boost.patch \
-		"${FILESDIR}"/${P}-gcc4.7.patch
+		"${FILESDIR}"/${P}-gcc4.78.patch
 
 	eprefixify tools/build/*
 
@@ -139,8 +145,13 @@ src_install() {
 		newbin ${BIN} ${BIN%%.*} || die "could not install rosetta program files"
 	done
 
-	mv "${ED}"/usr/bin/cluster{,-${PN}} || die
-	mv "${ED}"/usr/bin/benchmark{,-${PN}} || die
+	if [[ -e "${ED}"/usr/bin/cluster ]]; then
+		mv "${ED}"/usr/bin/cluster{,-${PN}} || die
+	fi
+
+	if [[ -e "${ED}"/usr/bin/benchmark ]]; then
+		mv "${ED}"/usr/bin/benchmark{,-${PN}} || die
+	fi
 }
 
 my_filter_option() {
diff --git a/sys-cluster/modules/modules-3.2.9c-r1.ebuild b/sys-cluster/modules/modules-3.2.9c-r1.ebuild
index f161cb98a..b063785aa 100644
--- a/sys-cluster/modules/modules-3.2.9c-r1.ebuild
+++ b/sys-cluster/modules/modules-3.2.9c-r1.ebuild
@@ -27,7 +27,7 @@ S="${WORKDIR}/${P%[a-z]}"
 DOCS=(ChangeLog README NEWS TODO)
 
 src_prepare() {
-	epatch "${FILESDIR}/${P}-errorline.patch"
+	has_version ">=dev-lang/tcl-8.6.0" && epatch "${FILESDIR}/${P}-errorline.patch"
 }
 
 src_configure() {