29 files changed, 37 insertions, 969 deletions

diff --git a/dev-libs/boost-compute/boost-compute-0.4-r1.ebuild b/dev-libs/boost-compute/boost-compute-0.4-r1.ebuild
index 9d7d8f1da..abbc7457d 100644
--- a/dev-libs/boost-compute/boost-compute-0.4-r1.ebuild
+++ b/dev-libs/boost-compute/boost-compute-0.4-r1.ebuild
@@ -9,19 +9,18 @@ inherit eutils cmake-utils
 DESCRIPTION="A header-only C++ Computing Library for OpenCL"
 HOMEPAGE="https://github.com/boostorg/compute"
 SRC_URI="https://github.com/boostorg/compute/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-KEYWORDS="~amd64"
-S="${WORKDIR}/compute-${PV}"
 
 LICENSE="Boost-1.0"
 SLOT="0"
-
-PATCHES=(
-	"${FILESDIR}/${P}"-CMakeLists.patch
-)
-
+KEYWORDS="~amd64"
+IUSE=""
 
 RDEPEND="
 	dev-libs/boost
 	virtual/opencl
 "
 DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/compute-${PV}"
+
+PATCHES=( "${FILESDIR}/${P}"-CMakeLists.patch )
diff --git a/dev-libs/boost-compute/boost-compute-9999.ebuild b/dev-libs/boost-compute/boost-compute-9999.ebuild
index c79ed92ca..d73cf9573 100644
--- a/dev-libs/boost-compute/boost-compute-9999.ebuild
+++ b/dev-libs/boost-compute/boost-compute-9999.ebuild
@@ -8,11 +8,14 @@ inherit eutils cmake-utils git-r3
 
 DESCRIPTION="A header-only C++ Computing Library for OpenCL"
 HOMEPAGE="https://github.com/boostorg/compute"
-EGIT_REPO_URI="https://github.com/boostorg/compute.git git://github.com/boostorg/compute.git"
-KEYWORDS=""
+EGIT_REPO_URI="
+	https://github.com/boostorg/compute.git
+	git://github.com/boostorg/compute.git"
 
 LICENSE="Boost-1.0"
 SLOT="0"
+KEYWORDS=""
+IUSE=""
 
 RDEPEND="
 	dev-libs/boost
diff --git a/dev-libs/boost/ChangeLog b/dev-libs/boost/ChangeLog
deleted file mode 100644
index 3aeda1cb1..000000000
--- a/dev-libs/boost/ChangeLog
+++ /dev/null
@@ -1,27 +0,0 @@
-# ChangeLog for dev-libs/boost
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Id$
-
-  08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
-  dev-libs/boost: Updating remote-id in metadata.xml
-
-  02 Apr 2015; Justin Lecher <jlec@gentoo.org> boost-1.56.0-r2.ebuild,
-  metadata.xml:
-  dev-libs/boost: Move to new CAT
-
-  19 Feb 2015; Christoph Junghans <ottxor@gentoo.org> boost-1.56.0-r2.ebuild:
-  dropped sparc
-
-*boost-1.56.0-r2 (17 Feb 2015)
-
-  17 Feb 2015; Christoph Junghans <ottxor@gentoo.org> +boost-1.56.0-r2.ebuild,
-  +files/boost-1.48.0-disable_icu_rpath.patch,
-  +files/boost-1.48.0-disable_libboost_python3.patch,
-  +files/boost-1.48.0-no_strict_aliasing_python2.patch,
-  +files/boost-1.48.0-python_linking.patch,
-  +files/boost-1.51.0-respect_python-buildid.patch,
-  +files/boost-1.51.0-support_dots_in_python-buildid.patch,
-  +files/boost-1.52.0-threads.patch, +files/boost-1.55.0-context-x32.patch,
-  +files/boost-1.55.0-tools-c98-compat.patch,
-  +files/boost-1.56.0-build-auto_index-tool.patch, +metadata.xml:
-  added full multilib version
diff --git a/dev-libs/boost/Manifest b/dev-libs/boost/Manifest
deleted file mode 100644
index 0f7f203dd..000000000
--- a/dev-libs/boost/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST boost_1_56_0.tar.bz2 94777674 SHA256 134732acaf3a6e7eba85988118d943f0fa6b7f0850f65131fff89823ad30ff1d SHA512 1ce9871c3a2519682538a5f1331938b948123432d99aea0ce026958cbebd25d84019a3a28c452724b9693df98a8d1264bb2d93d2fee508453f8b42836e67481e WHIRLPOOL e9e9bb965816b687141d55bc026e378a56ed577a2bf0bdad61a1736e7f11d1797e0cac0185a1fa25b6c4b9fe1f75cbb0bb73a5ea05e84d59385bb3b17a90fd12
diff --git a/dev-libs/boost/boost-1.56.0-r2.ebuild b/dev-libs/boost/boost-1.56.0-r2.ebuild
deleted file mode 100644
index c023e7c35..000000000
--- a/dev-libs/boost/boost-1.56.0-r2.ebuild
+++ /dev/null
@@ -1,398 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="5"
-PYTHON_COMPAT=( python{2_7,3_3,3_4} )
-
-inherit eutils flag-o-matic multilib multiprocessing python-r1 toolchain-funcs versionator multilib-minimal
-
-MY_P="${PN}_$(replace_all_version_separators _)"
-MAJOR_V="$(get_version_component_range 1-2)"
-
-DESCRIPTION="Boost Libraries for C++"
-HOMEPAGE="http://www.boost.org/"
-SRC_URI="mirror://sourceforge/boost/${MY_P}.tar.bz2"
-
-LICENSE="Boost-1.0"
-SLOT="0/${PV}" # ${PV} instead ${MAJOR_V} due to bug 486122
-KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~x86 ~ppc-aix ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris ~x86-solaris ~x86-winnt"
-
-IUSE="context debug doc icu +nls mpi python static-libs +threads tools"
-
-RDEPEND="abi_x86_32? ( !app-emulation/emul-linux-x86-cpplibs[-abi_x86_32(-)] )
-	icu? ( >=dev-libs/icu-3.6:=[${MULTILIB_USEDEP}] )
-	!icu? ( virtual/libiconv[${MULTILIB_USEDEP}] )
-	mpi? ( >=virtual/mpi-2.0-r4[${MULTILIB_USEDEP},cxx,threads] )
-	python? ( ${PYTHON_DEPS} )
-	app-arch/bzip2[${MULTILIB_USEDEP}]
-	sys-libs/zlib[${MULTILIB_USEDEP}]
-	!app-eselect/eselect-boost"
-DEPEND="${RDEPEND}
-	=dev-util/boost-build-${MAJOR_V}*"
-REQUIRED_USE="
-	mpi? ( threads )
-	python? ( ${PYTHON_REQUIRED_USE} )"
-
-S="${WORKDIR}/${MY_P}"
-
-# the tests will never fail because these are not intended as sanity
-# tests at all. They are more a way for upstream to check their own code
-# on new compilers. Since they would either be completely unreliable
-# (failing for no good reason) or completely useless (never failing)
-# there is no point in having them in the ebuild to begin with.
-RESTRICT="test"
-
-python_bindings_needed() {
-	multilib_is_native_abi && use python
-}
-
-tools_needed() {
-	multilib_is_native_abi && use tools
-}
-
-create_user-config.jam() {
-	local compiler compiler_version compiler_executable
-
-	if [[ ${CHOST} == *-darwin* ]]; then
-		compiler="darwin"
-		compiler_version="$(gcc-fullversion)"
-		compiler_executable="$(tc-getCXX)"
-	else
-		compiler="gcc"
-		compiler_version="$(gcc-version)"
-		compiler_executable="$(tc-getCXX)"
-	fi
-	local mpi_configuration python_configuration
-
-	if use mpi; then
-		mpi_configuration="using mpi ;"
-	fi
-
-	if python_bindings_needed; then
-		if tc-is-cross-compiler; then
-			python_configuration="using python : ${EPYTHON#python} : : ${SYSROOT:-${EROOT}}/usr/include/${EPYTHON} : ${SYSROOT:-${EROOT}}/usr/$(get_libdir) ;"
-		else
-			python_configuration="using python : : ${PYTHON} ;"
-		fi
-	fi
-
-	cat > "${BOOST_ROOT}/user-config.jam" << __EOF__
-using ${compiler} : ${compiler_version} : ${compiler_executable} : <cflags>"${CFLAGS}" <cxxflags>"${CXXFLAGS}" <linkflags>"${LDFLAGS}" ;
-${mpi_configuration}
-${python_configuration}
-__EOF__
-}
-
-pkg_setup() {
-	# Bail out on unsupported build configuration, bug #456792
-	if [[ -f "${EROOT}etc/site-config.jam" ]]; then
-		grep -q gentoorelease "${EROOT}etc/site-config.jam" && grep -q gentoodebug "${EROOT}etc/site-config.jam" ||
-		(
-			eerror "You are using custom ${EROOT}etc/site-config.jam without defined gentoorelease/gentoodebug targets."
-			eerror "Boost can not be built in such configuration."
-			eerror "Please, either remove this file or add targets from ${EROOT}usr/share/boost-build/site-config.jam to it."
-			die
-		)
-	fi
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}/${PN}-1.51.0-respect_python-buildid.patch" \
-		"${FILESDIR}/${PN}-1.51.0-support_dots_in_python-buildid.patch" \
-		"${FILESDIR}/${PN}-1.48.0-no_strict_aliasing_python2.patch" \
-		"${FILESDIR}/${PN}-1.48.0-disable_libboost_python3.patch" \
-		"${FILESDIR}/${PN}-1.48.0-python_linking.patch" \
-		"${FILESDIR}/${PN}-1.48.0-disable_icu_rpath.patch" \
-		"${FILESDIR}/${PN}-1.55.0-context-x32.patch" \
-		"${FILESDIR}/${PN}-1.55.0-tools-c98-compat.patch" \
-		"${FILESDIR}/${PN}-1.52.0-threads.patch" \
-		"${FILESDIR}/${PN}-1.56.0-build-auto_index-tool.patch"
-
-	# Do not try to build missing 'wave' tool, bug #522682
-	# Upstream bugreport - https://svn.boost.org/trac/boost/ticket/10507
-	sed -i -e 's:wave/build//wave::' tools/Jamfile.v2 || die
-
-	epatch_user
-
-	multilib_copy_sources
-}
-
-ejam() {
-	local b2_opts="--user-config=${BOOST_ROOT}/user-config.jam $@"
-	echo b2 ${b2_opts}
-	b2 ${b2_opts}
-}
-
-src_configure() {
-	# Workaround for too many parallel processes requested, bug #506064
-	[ "$(makeopts_jobs)" -gt 64 ] && MAKEOPTS="${MAKEOPTS} -j64"
-
-	OPTIONS="$(usex debug gentoodebug gentoorelease) -j$(makeopts_jobs) -q -d+2"
-
-	if [[ ${CHOST} == *-darwin* ]]; then
-		# We need to add the prefix, and in two cases this exceeds, so prepare
-		# for the largest possible space allocation.
-		append-ldflags -Wl,-headerpad_max_install_names
-	elif [[ ${CHOST} == *-winnt* ]]; then
-		compiler=parity
-		if [[ $($(tc-getCXX) -v) == *trunk* ]]; then
-			compilerVersion=trunk
-		else
-			compilerVersion=$($(tc-getCXX) -v | sed '1q' \
-				| sed -e 's,\([a-z]*\) \([0-9]\.[0-9]\.[0-9][^ \t]*\) .*,\2,')
-		fi
-		compilerExecutable=$(tc-getCXX)
-	fi
-
-	# bug 298489
-	if use ppc || use ppc64; then
-		[[ $(gcc-version) > 4.3 ]] && append-flags -mno-altivec
-	fi
-
-	# Do _not_ use C++11 yet, make sure to force GNU C++ 98 standard.
-	append-cxxflags -std=gnu++98
-
-	use icu && OPTIONS+=" -sICU_PATH=${EPREFIX}/usr"
-	use icu || OPTIONS+=" --disable-icu boost.locale.icu=off"
-	use mpi || OPTIONS+=" --without-mpi"
-	use nls || OPTIONS+=" --without-locale"
-	use context || OPTIONS+=" --without-context --without-coroutine"
-
-	OPTIONS+=" pch=off"
-	OPTIONS+=" --boost-build=${EPREFIX}/usr/share/boost-build --prefix=\"${ED}usr\""
-	OPTIONS+=" --layout=system"
-	OPTIONS+=" threading=$(usex threads multi single) link=$(usex static-libs shared,static shared)"
-
-	[[ ${CHOST} == *-winnt* ]] && OPTIONS+=" -sNO_BZIP2=1"
-}
-
-multilib_src_compile() {
-	local -x BOOST_ROOT="${BUILD_DIR}"
-	PYTHON_DIRS=""
-	MPI_PYTHON_MODULE=""
-
-	building() {
-		create_user-config.jam
-
-		local PYTHON_OPTIONS
-		if python_bindings_needed; then
-			PYTHON_OPTIONS=" --python-buildid=${EPYTHON#python}"
-		else
-			PYTHON_OPTIONS=" --without-python"
-		fi
-
-		ejam \
-			${OPTIONS} \
-			${PYTHON_OPTIONS} \
-			|| die "Building of Boost libraries failed"
-
-		if python_bindings_needed; then
-			if [[ -z "${PYTHON_DIRS}" ]]; then
-				PYTHON_DIRS="$(find bin.v2/libs -name python | sort)"
-			else
-				if [[ "${PYTHON_DIRS}" != "$(find bin.v2/libs -name python | sort)" ]]; then
-					die "Inconsistent structure of build directories"
-				fi
-			fi
-
-			local dir
-			for dir in ${PYTHON_DIRS}; do
-				mv ${dir} ${dir}-${EPYTHON} \
-					|| die "Renaming of '${dir}' to '${dir}-${EPYTHON}' failed"
-			done
-
-			if use mpi; then
-				if [[ -z "${MPI_PYTHON_MODULE}" ]]; then
-					MPI_PYTHON_MODULE="$(find bin.v2/libs/mpi/build/*/gentoo* -name mpi.so)"
-					if [[ "$(echo "${MPI_PYTHON_MODULE}" | wc -l)" -ne 1 ]]; then
-						die "Multiple mpi.so files found"
-					fi
-				else
-					if [[ "${MPI_PYTHON_MODULE}" != "$(find bin.v2/libs/mpi/build/*/gentoo* -name mpi.so)" ]]; then
-						die "Inconsistent structure of build directories"
-					fi
-				fi
-
-				mv stage/lib/mpi.so stage/lib/mpi.so-${EPYTHON} \
-					|| die "Renaming of 'stage/lib/mpi.so' to 'stage/lib/mpi.so-${EPYTHON}' failed"
-			fi
-		fi
-	}
-	if python_bindings_needed; then
-		python_foreach_impl building
-	else
-		building
-	fi
-
-	if tools_needed; then
-		pushd tools > /dev/null || die
-
-		ejam \
-			${OPTIONS} \
-			${PYTHON_OPTIONS} \
-			|| die "Building of Boost tools failed"
-		popd > /dev/null || die
-	fi
-}
-
-multilib_src_install_all() {
-	if ! use python; then
-		rm -r "${ED}"/usr/include/boost/python* || die
-	fi
-
-	if ! use nls; then
-		rm -r "${ED}"/usr/include/boost/locale || die
-	fi
-
-	if ! use context; then
-		rm -r "${ED}"/usr/include/boost/context || die
-		rm -r "${ED}"/usr/include/boost/coroutine || die
-	fi
-
-	if use doc; then
-		find libs/*/* -iname "test" -or -iname "src" | xargs rm -rf
-		dohtml \
-			-A pdf,txt,cpp,hpp \
-			*.{htm,html,png,css} \
-			-r doc
-		dohtml -A pdf,txt -r tools
-		insinto /usr/share/doc/${PF}/html
-		doins -r libs
-		doins -r more
-
-		# To avoid broken links
-		insinto /usr/share/doc/${PF}/html
-		doins LICENSE_1_0.txt
-
-		dosym /usr/include/boost /usr/share/doc/${PF}/html/boost
-	fi
-}
-
-multilib_src_install() {
-	local -x BOOST_ROOT="${BUILD_DIR}"
-	installation() {
-		create_user-config.jam
-
-		local PYTHON_OPTIONS
-		if python_bindings_needed; then
-			local dir
-			for dir in ${PYTHON_DIRS}; do
-				cp -pr ${dir}-${EPYTHON} ${dir} \
-					|| die "Copying of '${dir}-${EPYTHON}' to '${dir}' failed"
-			done
-
-			if use mpi; then
-				cp -p stage/lib/mpi.so-${EPYTHON} "${MPI_PYTHON_MODULE}" \
-					|| die "Copying of 'stage/lib/mpi.so-${EPYTHON}' to '${MPI_PYTHON_MODULE}' failed"
-				cp -p stage/lib/mpi.so-${EPYTHON} stage/lib/mpi.so \
-					|| die "Copying of 'stage/lib/mpi.so-${EPYTHON}' to 'stage/lib/mpi.so' failed"
-			fi
-			PYTHON_OPTIONS=" --python-buildid=${EPYTHON#python}"
-		else
-			PYTHON_OPTIONS=" --without-python"
-		fi
-
-		ejam \
-			${OPTIONS} \
-			${PYTHON_OPTIONS} \
-			--includedir="${ED}usr/include" \
-			--libdir="${ED}usr/$(get_libdir)" \
-			install || die "Installation of Boost libraries failed"
-
-		if python_bindings_needed; then
-			rm -r ${PYTHON_DIRS} || die
-
-			# Move mpi.so Python module to Python site-packages directory.
-			# https://svn.boost.org/trac/boost/ticket/2838
-			if use mpi; then
-				local moddir=$(python_get_sitedir)/boost
-				# moddir already includes eprefix
-				mkdir -p "${D}${moddir}" || die
-				mv "${ED}usr/$(get_libdir)/mpi.so" "${D}${moddir}" || die
-				cat << EOF > "${D}${moddir}/__init__.py" || die
-import sys
-if sys.platform.startswith('linux'):
-	import DLFCN
-	flags = sys.getdlopenflags()
-	sys.setdlopenflags(DLFCN.RTLD_NOW | DLFCN.RTLD_GLOBAL)
-	from . import mpi
-	sys.setdlopenflags(flags)
-	del DLFCN, flags
-else:
-	from . import mpi
-del sys
-EOF
-			fi
-
-			python_optimize
-		fi
-	}
-	if python_bindings_needed; then
-		python_foreach_impl installation
-	else
-		installation
-	fi
-
-	pushd "${ED}usr/$(get_libdir)" > /dev/null || die
-
-	local ext=$(get_libname)
-	if use threads; then
-		local f
-		for f in *${ext}; do
-			dosym ${f} /usr/$(get_libdir)/${f/${ext}/-mt${ext}}
-		done
-	fi
-
-	popd > /dev/null || die
-
-	if tools_needed; then
-		dobin dist/bin/*
-
-		insinto /usr/share
-		doins -r dist/share/boostbook
-	fi
-
-	# boost's build system truely sucks for not having a destdir.  Because for
-	# this reason we are forced to build with a prefix that includes the
-	# DESTROOT, dynamic libraries on Darwin end messed up, referencing the
-	# DESTROOT instread of the actual EPREFIX.  There is no way out of here
-	# but to do it the dirty way of manually setting the right install_names.
-	if [[ ${CHOST} == *-darwin* ]]; then
-		einfo "Working around completely broken build-system(tm)"
-		local d
-		for d in "${ED}"usr/lib/*.dylib; do
-			if [[ -f ${d} ]]; then
-				# fix the "soname"
-				ebegin "  correcting install_name of ${d#${ED}}"
-				install_name_tool -id "/${d#${D}}" "${d}"
-				eend $?
-				# fix references to other libs
-				refs=$(otool -XL "${d}" | \
-					sed -e '1d' -e 's/^\t//' | \
-					grep "^libboost_" | \
-					cut -f1 -d' ')
-				local r
-				for r in ${refs}; do
-					ebegin "    correcting reference to ${r}"
-					install_name_tool -change \
-						"${r}" \
-						"${EPREFIX}/usr/lib/${r}" \
-						"${d}"
-					eend $?
-				done
-			fi
-		done
-	fi
-}
-
-pkg_preinst() {
-	# Yai for having symlinks that are nigh-impossible to remove without
-	# resorting to dirty hacks like these. Removes lingering symlinks
-	# from the slotted versions.
-	local symlink
-	for symlink in "${EROOT}usr/include/boost" "${EROOT}usr/share/boostbook"; do
-		[[ -L ${symlink} ]] && rm -f "${symlink}"
-	done
-}
diff --git a/dev-libs/boost/files/boost-1.48.0-disable_icu_rpath.patch b/dev-libs/boost/files/boost-1.48.0-disable_icu_rpath.patch
deleted file mode 100644
index a902d61bb..000000000
--- a/dev-libs/boost/files/boost-1.48.0-disable_icu_rpath.patch
+++ /dev/null
@@ -1,29 +0,0 @@
---- libs/locale/build/Jamfile.v2
-+++ libs/locale/build/Jamfile.v2
-@@ -58,8 +58,8 @@
- 
- if $(ICU_LINK)
- {
--    ICU_OPTS = <include>$(ICU_PATH)/include <linkflags>$(ICU_LINK) <dll-path>$(ICU_PATH)/bin <runtime-link>shared ;
--    ICU64_OPTS = <include>$(ICU_PATH)/include <linkflags>$(ICU_LINK) <dll-path>$(ICU_PATH)/bin64 <runtime-link>shared ;
-+    ICU_OPTS = <include>$(ICU_PATH)/include <linkflags>$(ICU_LINK) <runtime-link>shared ;
-+    ICU64_OPTS = <include>$(ICU_PATH)/include <linkflags>$(ICU_LINK) <runtime-link>shared ;
- }
- else
- {
-@@ -117,7 +117,6 @@
-       <library>icuuc/<link>shared/<runtime-link>shared 
-       <library>icudt/<link>shared/<runtime-link>shared 
-       <library>icuin/<link>shared/<runtime-link>shared
--      <dll-path>$(ICU_PATH)/bin
-         <runtime-link>shared ;
- 
- 
-@@ -176,7 +175,6 @@
-       <library>icuuc_64/<link>shared/<runtime-link>shared 
-       <library>icudt_64/<link>shared/<runtime-link>shared 
-       <library>icuin_64/<link>shared/<runtime-link>shared
--      <dll-path>$(ICU_PATH)/bin64
-         <runtime-link>shared ;
-  
-     
diff --git a/dev-libs/boost/files/boost-1.48.0-disable_libboost_python3.patch b/dev-libs/boost/files/boost-1.48.0-disable_libboost_python3.patch
deleted file mode 100644
index c24a56c6b..000000000
--- a/dev-libs/boost/files/boost-1.48.0-disable_libboost_python3.patch
+++ /dev/null
@@ -1,62 +0,0 @@
---- libs/python/build/Jamfile.v2
-+++ libs/python/build/Jamfile.v2
-@@ -39,23 +39,6 @@
-     PYTHON_ID = [ regex.replace $(python-id) "[*\\/:\"\']" "_" ] ;
- }
- 
--
--rule find-py3-version
--{
--    local versions = [ feature.values python ] ;
--    local py3ver ;
--    for local v in $(versions)
--    {
--        if $(v) >= 3.0
--        {
--            py3ver = $(v) ;
--        }
--    }
--    return $(py3ver) ;
--}
--
--py3-version = [ find-py3-version ] ;
--
- project boost/python
-   : source-location ../src
-   : requirements
-@@ -82,7 +65,7 @@
- rule cond ( test ? : yes * : no * ) { if $(test) { return $(yes) ; } else { return $(no) ; } }
- rule unless ( test ? : yes * : no * ) { if ! $(test) { return $(yes) ; } else { return $(no) ; } }
- 
--rule lib_boost_python ( is-py3 ? )
-+rule lib_boost_python
- {
- 
-     local python_major_version = [ MATCH "^([^.]+)" : [ feature.values python ] ] ;
-@@ -91,7 +74,7 @@
-     {
-         python2 = true ;
-     }
--    lib [ cond $(is-py3) : boost_python3 : boost_python ]
-+    lib boost_python
-         : # sources
-         numeric.cpp
-         list.cpp
-@@ -148,7 +131,6 @@
-             <dependency>config-warning
- 
-             <python-debugging>on:<define>BOOST_DEBUG_PYTHON
--            [ cond $(is-py3) : <python>$(py3-version) ]
-         :   # default build
-             <link>shared
-         :   # usage requirements
-@@ -160,9 +142,3 @@
- 
- lib_boost_python ;
- boost-install boost_python ;
--
--if $(py3-version)
--{
--    lib_boost_python yes ;
--    boost-install boost_python3 ;
--}
diff --git a/dev-libs/boost/files/boost-1.48.0-no_strict_aliasing_python2.patch b/dev-libs/boost/files/boost-1.48.0-no_strict_aliasing_python2.patch
deleted file mode 100644
index 89f8109a4..000000000
--- a/dev-libs/boost/files/boost-1.48.0-no_strict_aliasing_python2.patch
+++ /dev/null
@@ -1,23 +0,0 @@
---- libs/python/build/Jamfile.v2
-+++ libs/python/build/Jamfile.v2
-@@ -85,6 +85,12 @@
- rule lib_boost_python ( is-py3 ? )
- {
- 
-+    local python_major_version = [ MATCH "^([^.]+)" : [ feature.values python ] ] ;
-+    local python2 ;
-+    if $(python_major_version) = 2
-+    {
-+        python2 = true ;
-+    }
-     lib [ cond $(is-py3) : boost_python3 : boost_python ]
-         : # sources
-         numeric.cpp
-@@ -119,6 +125,7 @@
-         :   # requirements
-             <link>static:<define>BOOST_PYTHON_STATIC_LIB 
-             <define>BOOST_PYTHON_SOURCE
-+            [ cond $(python2) : <cxxflags>-fno-strict-aliasing ]
-           
-             # On Windows, all code using Python has to link to the Python
-             # import library.
diff --git a/dev-libs/boost/files/boost-1.48.0-python_linking.patch b/dev-libs/boost/files/boost-1.48.0-python_linking.patch
deleted file mode 100644
index e7f4e7c99..000000000
--- a/dev-libs/boost/files/boost-1.48.0-python_linking.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- libs/python/build/Jamfile.v2
-+++ libs/python/build/Jamfile.v2
-@@ -109,20 +109,7 @@
-             <link>static:<define>BOOST_PYTHON_STATIC_LIB 
-             <define>BOOST_PYTHON_SOURCE
-             [ cond $(python2) : <cxxflags>-fno-strict-aliasing ]
--          
--            # On Windows, all code using Python has to link to the Python
--            # import library.
--            #
--            # On *nix we never link libboost_python to libpython.  When
--            # extending Python, all Python symbols are provided by the
--            # Python interpreter executable.  When embedding Python, the
--            # client executable is expected to explicitly link to
--            # /python//python (the target representing libpython) itself.
--            #
--            # python_for_extensions is a target defined by Boost.Build to
--            # provide the Python include paths, and on Windows, the Python
--            # import library, as usage requirements.
--            [ cond [ python.configured ] : <library>/python//python_for_extensions ]
-+            [ cond [ python.configured ] : <library>/python//python ]
-             
-             # we prevent building when there is no python available
-             # as it's not possible anyway, and to cause dependents to
diff --git a/dev-libs/boost/files/boost-1.51.0-respect_python-buildid.patch b/dev-libs/boost/files/boost-1.51.0-respect_python-buildid.patch
deleted file mode 100644
index 327429e2c..000000000
--- a/dev-libs/boost/files/boost-1.51.0-respect_python-buildid.patch
+++ /dev/null
@@ -1,69 +0,0 @@
-https://svn.boost.org/trac/boost/ticket/6286
-
---- boostcpp.jam
-+++ boostcpp.jam
-@@ -99,13 +99,6 @@
-     BUILD_ID = [ regex.replace $(build-id) "[*\\/:.\"\' ]" _ ] ;
- }
- 
--# Python build id (for Python libraries only).
--python-id = [ option.get "python-buildid" ] ;
--if $(python-id)
--{
--    PYTHON_ID = [ regex.replace $(python-id) [*\\/:.\"\'] _ ] ;
--}
--
- 
- ################################################################################
- #
---- libs/mpi/build/Jamfile.v2
-+++ libs/mpi/build/Jamfile.v2
-@@ -8,6 +8,8 @@
- #  Authors: Douglas Gregor
- #           Andrew Lumsdaine
- 
-+import option ;
-+import regex ;
- import mpi ;
- import indirect ;
- import python ;
-@@ -24,6 +26,13 @@
-     <tag>@$(__name__).tag
-   ;
- 
-+# Python build id (for Python libraries only).
-+python-id = [ option.get "python-buildid" ] ;
-+if $(python-id)
-+{
-+    PYTHON_ID = [ regex.replace $(python-id) [*\\/:.\"\'] _ ] ;
-+}
-+
- rule tag ( name : type ? : property-set )
- {
-     local result = $(name) ;
---- libs/python/build/Jamfile.v2
-+++ libs/python/build/Jamfile.v2
-@@ -2,6 +2,8 @@
- # Software License, Version 1.0. (See accompanying
- # file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
- 
-+import option ;
-+import regex ;
- import os ;
- import indirect ;
- import modules ;
-@@ -30,6 +32,14 @@
-         ;
- }
- 
-+# Python build id (for Python libraries only).
-+python-id = [ option.get "python-buildid" ] ;
-+if $(python-id)
-+{
-+    PYTHON_ID = [ regex.replace $(python-id) [*\\/:.\"\'] _ ] ;
-+}
-+
-+
- rule find-py3-version
- {
-     local versions = [ feature.values python ] ;
diff --git a/dev-libs/boost/files/boost-1.51.0-support_dots_in_python-buildid.patch b/dev-libs/boost/files/boost-1.51.0-support_dots_in_python-buildid.patch
deleted file mode 100644
index c8dc6e1b7..000000000
--- a/dev-libs/boost/files/boost-1.51.0-support_dots_in_python-buildid.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- libs/mpi/build/Jamfile.v2
-+++ libs/mpi/build/Jamfile.v2
-@@ -30,7 +30,7 @@
- python-id = [ option.get "python-buildid" ] ;
- if $(python-id)
- {
--    PYTHON_ID = [ regex.replace $(python-id) [*\\/:.\"\'] _ ] ;
-+    PYTHON_ID = [ regex.replace $(python-id) [*\\/:\"\'] _ ] ;
- }
- 
- rule tag ( name : type ? : property-set )
---- libs/python/build/Jamfile.v2
-+++ libs/python/build/Jamfile.v2
-@@ -36,7 +36,7 @@
- python-id = [ option.get "python-buildid" ] ;
- if $(python-id)
- {
--    PYTHON_ID = [ regex.replace $(python-id) [*\\/:.\"\'] _ ] ;
-+    PYTHON_ID = [ regex.replace $(python-id) [*\\/:\"\'] _ ] ;
- }
- 
- 
diff --git a/dev-libs/boost/files/boost-1.52.0-threads.patch b/dev-libs/boost/files/boost-1.52.0-threads.patch
deleted file mode 100644
index e078fc2e1..000000000
--- a/dev-libs/boost/files/boost-1.52.0-threads.patch
+++ /dev/null
@@ -1,63 +0,0 @@
-Index: /trunk/boostcpp.jam

-===================================================================

---- /trunk/boostcpp.jam	(revision 79301)

-+++ /trunk/boostcpp.jam	(revision 81000)

-@@ -210,6 +210,44 @@

- }

- 

-+rule filtered-target ( name : message + : sources + : requirements * )

-+{

-+    message $(name)-message : warning: $(message) ;

-+    alias $(name) : $(sources) : $(requirements) ;

-+    alias $(name) : $(name)-message ;

-+

-+    local p = [ project.current ] ;

-+    $(p).mark-target-as-explicit $(name) ;

-+    $(p).mark-target-as-explicit $(name)-message ;

-+}

-+

- rule declare_install_and_stage_proper_targets ( libraries * : headers * )

- {

-+    for local l in $(libraries)

-+    {

-+        if $(l) = locale

-+        {

-+            filtered-target $(l)-for-install :

-+                Skipping Boost.Locale library with threading=single. :

-+                libs/$(l)/build : <threading>multi ;

-+        }

-+        else if $(l) = wave

-+        {

-+            filtered-target $(l)-for-install :

-+                Skipping Boost.Wave library with threading=single. :

-+                libs/$(l)/build : <threading>multi ;

-+        }

-+        else if $(l) = thread

-+        {

-+            filtered-target $(l)-for-install :

-+                Skipping Boost.Thread library with threading=single. :

-+                libs/$(l)/build : <threading>multi ;

-+        }

-+        else

-+        {

-+            alias $(l)-for-install : libs/$(l)/build ; 

-+        }

-+    }

-+    local library-targets = $(libraries)-for-install ;

-+

-     install-requirements = <install-source-root>$(BOOST_ROOT)/boost ;

- 

-@@ -239,5 +277,5 @@

-         : $(install-requirements) <install-no-version-symlinks>on

-         :

--        : libs/$(libraries)/build

-+        : $(libraries)-for-install

-         : $(headers)

-         ;

-@@ -246,5 +284,5 @@

-     # Install just library.

-     install stage-proper

--        : libs/$(libraries)/build

-+        : $(libraries)-for-install

-         : <location>$(stage-locate)/lib

-           <install-dependencies>on <install-type>LIB

diff --git a/dev-libs/boost/files/boost-1.55.0-context-x32.patch b/dev-libs/boost/files/boost-1.55.0-context-x32.patch
deleted file mode 100644
index 5bf740625..000000000
--- a/dev-libs/boost/files/boost-1.55.0-context-x32.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-https://svn.boost.org/trac/boost/ticket/9445
-
-hack to fix x32 builds
-
---- a/libs/context/src/asm/jump_i386_sysv_elf_gas.S
-+++ b/libs/context/src/asm/jump_i386_sysv_elf_gas.S
-@@ -31,6 +31,10 @@
-  *                                                                  *
-  * *****************************************************************/
- 
-+#ifdef __x86_64__
-+#include "jump_x86_64_sysv_elf_gas.S"
-+#else
-+
- .text
- .globl jump_fcontext
- .align 2
-@@ -73,3 +77,5 @@ jump_fcontext:
- 
- /* Mark that we don't need executable stack.  */
- .section .note.GNU-stack,"",%progbits
-+
-+#endif
---- a/libs/context/src/asm/make_i386_sysv_elf_gas.S
-+++ b/libs/context/src/asm/make_i386_sysv_elf_gas.S
-@@ -31,6 +31,10 @@
-  *                                                                  *
-  * *****************************************************************/
- 
-+#ifdef __x86_64__
-+#include "make_x86_64_sysv_elf_gas.S"
-+#else
-+
- .text
- .globl make_fcontext
- .align 2
-@@ -78,3 +82,5 @@ finish:
- 
- /* Mark that we don't need executable stack.  */
- .section .note.GNU-stack,"",%progbits
-+
-+#endif
diff --git a/dev-libs/boost/files/boost-1.55.0-tools-c98-compat.patch b/dev-libs/boost/files/boost-1.55.0-tools-c98-compat.patch
deleted file mode 100644
index df2a14a34..000000000
--- a/dev-libs/boost/files/boost-1.55.0-tools-c98-compat.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Make tools compiled successfully with forced C++98
-
-Gentoo bugreport: https://bugs.gentoo.org/show_bug.cgi?id=503468
-
-diff --git a/tools/regression/src/compiler_status.cpp b/tools/regression/src/compiler_status.cpp
-index 63f8134..3f3374a 100644
---- a/tools/regression/src/compiler_status.cpp
-+++ b/tools/regression/src/compiler_status.cpp
-@@ -128,7 +128,7 @@ namespace
-         string ln(line);
-         if (ln.find("Revision: ") != string::npos)
-         {
--          for(auto itr = ln.begin()+10; itr != ln.end() && isdigit(*itr); ++itr)
-+          for(string::iterator itr = ln.begin()+10; itr != ln.end() && isdigit(*itr); ++itr)
-             rev += *itr;
-         }
-       }
diff --git a/dev-libs/boost/files/boost-1.56.0-build-auto_index-tool.patch b/dev-libs/boost/files/boost-1.56.0-build-auto_index-tool.patch
deleted file mode 100644
index 5175800e3..000000000
--- a/dev-libs/boost/files/boost-1.56.0-build-auto_index-tool.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Build auto_index tool with USE="tools"
-Gentoo bug report: https://bugs.gentoo.org/show_bug.cgi?id=529066
-
---- tools/Jamfile.v2.orig	2014-12-24 12:57:32.290880067 +0300
-+++ tools/Jamfile.v2	2014-12-24 12:58:38.403883250 +0300
-@@ -20,6 +20,7 @@
- use-project /boost/regression : regression/build ;
- 
- TOOLS =
-+    auto_index/build//auto_index
-     bcp//bcp
-     inspect/build//inspect
-     quickbook//quickbook
diff --git a/dev-libs/boost/metadata.xml b/dev-libs/boost/metadata.xml
deleted file mode 100644
index 3fc1693b8..000000000
--- a/dev-libs/boost/metadata.xml
+++ /dev/null
@@ -1,41 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>cpp</herd>
-  <use>
-    <flag name="context">
-      Build and install the Boost.Context library and all other 
-      Boostlibraries that depends on it
-    </flag>
-    <flag name="tools">
-      Build and install the boost tools (bcp, quickbook, inspect,
-      wave)
-    </flag>
-    <flag name="debug" restrict="&lt;dev-libs/boost-1.50.0-r3">
-      Build and install debug versions of the Boost libraries. These
-      libraries are not used by default, and should not be used unless
-      you're developing against Boost.
-    </flag>
-    <flag name="debug" restrict="&gt;dev-libs/boost-1.52.0-r2">
-      Build and install only the debug version of the Boost
-      libraries. Only enable this flag if you're developing against
-      boost.
-    </flag>
-    <flag name="threads">
-      Build multi-thread-compatible libraries instead of
-      single-threaded only.
-    </flag>
-    <flag name="nls">
-      Build libboost_locale. This library requires compatible C
-      library interfaces, which might not be provided by uClibc or
-      other embedded libraries.
-    </flag>
-    <flag name="doc">
-      Install the full API documentation documentation. This takes
-      over 200MB of extra disk space.
-    </flag>
-  </use>
-  <upstream>
-    <remote-id type="sourceforge">boost</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/dev-python/notebook/notebook-9999.ebuild b/dev-python/notebook/notebook-9999.ebuild
index 155fbac1c..f6efc4551 100644
--- a/dev-python/notebook/notebook-9999.ebuild
+++ b/dev-python/notebook/notebook-9999.ebuild
@@ -43,7 +43,7 @@ DEPEND="${RDEPEND}
 		dev-python/coverage[${PYTHON_USEDEP}]
 	)
 	doc? (
-        app-text/pandoc
+		app-text/pandoc
 		>=dev-python/ipython-4.0.0[${PYTHON_USEDEP}]
 		>=dev-python/sphinx-1.1[${PYTHON_USEDEP}]
 	)
diff --git a/sci-biology/polyphen/polyphen-2.2.2.ebuild b/sci-biology/polyphen/polyphen-2.2.2.ebuild
index 5ffb60d0c..6038eee3e 100644
--- a/sci-biology/polyphen/polyphen-2.2.2.ebuild
+++ b/sci-biology/polyphen/polyphen-2.2.2.ebuild
@@ -13,9 +13,6 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}"
-
 # 3.7GB
 # ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-databases-2011_12.tar.bz2
 
@@ -24,4 +21,3 @@ RDEPEND="${DEPEND}"
 
 # 895MB
 # ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2
-
diff --git a/sci-biology/weblogo/weblogo-2.8.2.ebuild b/sci-biology/weblogo/weblogo-2.8.2.ebuild
index 759952ba6..0ecdf1f7a 100644
--- a/sci-biology/weblogo/weblogo-2.8.2.ebuild
+++ b/sci-biology/weblogo/weblogo-2.8.2.ebuild
@@ -1,13 +1,13 @@
 # Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: $
+# $Id$
 
 EAPI=5
 
 PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module
+inherit eutils perl-module
 
-DESCRIPTION="seqlogo: generate consensus sequence logo figures"
+DESCRIPTION="generate consensus sequence logo figures"
 HOMEPAGE="http://weblogo.berkeley.edu/"
 SRC_URI="http://weblogo.berkeley.edu/release/weblogo.2.8.2.tar.gz"
 
@@ -31,5 +31,7 @@ src_install(){
 	doins -r img
 	insinto ${VENDOR_LIB}
 	doins *.pm
-	dodoc examples.html Crooks-2004-GR-WebLogo.pdf
+	HTML_DOCS=( examples.html )
+	DOCS=( Crooks-2004-GR-WebLogo.pdf )
+	einstalldocs
 }
diff --git a/sci-libs/clfft/Manifest b/sci-libs/clfft/Manifest
index 0684d9118..9105d4dab 100644
--- a/sci-libs/clfft/Manifest
+++ b/sci-libs/clfft/Manifest
@@ -1,2 +1 @@
-DIST clfft-2.4.tar.gz 678262 SHA256 d77506af774bbe8ccf4226a58e623c8a29587edcf02984e72851099be0efe04b SHA512 3450f3ee962e1722c765e962178c57df0bf298508603ac5b4ec12bd6396dc10279136d5b91383b9da56d95cebd0e552bf78e2c01ccaeb8cd43ed947b7d536209 WHIRLPOOL 6ec21e182deac2a8c0a102a96c974289e56cf3f9908fbf067d7105f50646270bee2e17cf98fdf6cecf8ce28c8714c710ce46f514f7cfc1de205d5ef48bb5a0ed
 DIST clfft-2.6.1.tar.gz 893794 SHA256 2b5b15b903baeef4dcea6bb8efbe6aba284510148c04d20f9b151a94ae71c050 SHA512 6022ba6a2f09ae3139c3869464fb7807b0a76f26ef9b9cc856f65abc3e6278004242ebbe3d259406bc8a619684f5ccf24b2019bdbe4dfaf6c745572e0a0ae4b0 WHIRLPOOL 9a61d7c84bccf4744983a851e97cfd4d5b8cd0d7d868d8adc6a022a535b681f13d6ab687d42e5e2ca2773f560ef93403d705ee4f9caa970fa17d45ea525956dc
diff --git a/sci-libs/clfft/clfft-0.9999.ebuild b/sci-libs/clfft/clfft-0.9999.ebuild
deleted file mode 100644
index fa91bc59c..000000000
--- a/sci-libs/clfft/clfft-0.9999.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit cmake-utils git-r3
-
-MY_PN="clFFT"
-
-DESCRIPTION="A software library containing FFT functions written in OpenCL"
-HOMEPAGE="https://github.com/clMathLibraries/clFFT"
-EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git git://github.com/clMathLibraries/${MY_PN}.git"
-S="${WORKDIR}/${P}/src"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-IUSE="test"
-
-RDEPEND="
-	>=sys-devel/gcc-4.6:*
-	virtual/opencl
-	dev-libs/boost"
-DEPEND="${RDEPEND}"
-#	test? (
-#		dev-cpp/gtest
-#		sci-libs/fftw:3.0
-#	)"
-
-# The tests only get compiled to an executable named Test, which is not recogniozed by cmake.
-# Therefore src_test() won't execute any test.
-RESTRICT="test"
-
-PATCHES=(
-	"${FILESDIR}"/clfft-2.4-fix-cmake-config-install.patch
-)
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then
-			die "Compilation with gcc older than 4.6 is not supported."
-		fi
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-	   $(cmake-utils_use_build test TEST)
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/clfft/clfft-2.4-r1.ebuild b/sci-libs/clfft/clfft-2.4-r1.ebuild
deleted file mode 100644
index 00f177e40..000000000
--- a/sci-libs/clfft/clfft-2.4-r1.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit cmake-utils
-
-MY_PN="clFFT"
-
-DESCRIPTION="A software library containing FFT functions written in OpenCL"
-HOMEPAGE="https://github.com/clMathLibraries/clFFT"
-SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-KEYWORDS="~amd64"
-S="${WORKDIR}/${MY_PN}-${PV}/src"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-IUSE="test"
-
-RDEPEND="
-	>=sys-devel/gcc-4.6:*
-	virtual/opencl
-	dev-libs/boost"
-DEPEND="${RDEPEND}"
-#	test? (
-#		dev-cpp/gtest
-#		sci-libs/fftw:3.0
-#	)"
-
-# The tests only get compiled to an executable named Test, which is not recogniozed by cmake.
-# Therefore src_test() won't execute any test.
-RESTRICT="test"
-
-PATCHES=(
-	"${FILESDIR}/${P}"-client_CMakeLists.patch
-	"${FILESDIR}/${P}"-scripts_perf_CMakeLists.patch
-	"${FILESDIR}/${P}"-fix-cmake-config-install.patch
-)
-
-pkg_pretend() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then
-			die "Compilation with gcc older than 4.6 is not supported."
-		fi
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-	   $(cmake-utils_use_build test TEST)
-	)
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/clfft/clfft-2.6.1.ebuild b/sci-libs/clfft/clfft-2.6.1.ebuild
index 0e7011600..bbb7f4e05 100644
--- a/sci-libs/clfft/clfft-2.6.1.ebuild
+++ b/sci-libs/clfft/clfft-2.6.1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: $
+# $Id$
 
 EAPI=5
 
@@ -8,14 +8,13 @@ inherit cmake-utils
 
 MY_PN="clFFT"
 
-DESCRIPTION="A software library containing FFT functions written in OpenCL"
+DESCRIPTION="Library containing FFT functions written in OpenCL"
 HOMEPAGE="https://github.com/clMathLibraries/clFFT"
 SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-KEYWORDS="~amd64"
-S="${WORKDIR}/${MY_PN}-${PV}/src"
 
 LICENSE="Apache-2.0"
 SLOT="0"
+KEYWORDS="~amd64"
 IUSE="+client examples test"
 
 RDEPEND="
@@ -32,6 +31,8 @@ DEPEND="${RDEPEND}"
 # Therefore src_test() won't execute any test.
 RESTRICT="test"
 
+S="${WORKDIR}/${MY_PN}-${PV}/src"
+
 PATCHES=(
 	"${FILESDIR}/${P}"-Install-cmake-configuration-to-lib-cmake-clFFT.patch
 	"${FILESDIR}/${P}"-Install-examples-to-share-clFFT-examples.patch
diff --git a/sci-libs/clfft/clfft-9999.ebuild b/sci-libs/clfft/clfft-9999.ebuild
index 3edc6c948..7c62a2c41 100644
--- a/sci-libs/clfft/clfft-9999.ebuild
+++ b/sci-libs/clfft/clfft-9999.ebuild
@@ -8,14 +8,17 @@ inherit cmake-utils git-r3
 
 MY_PN="clFFT"
 
-DESCRIPTION="A software library containing FFT functions written in OpenCL"
+DESCRIPTION="Library containing FFT functions written in OpenCL"
 HOMEPAGE="https://github.com/clMathLibraries/clFFT"
-EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git git://github.com/clMathLibraries/${MY_PN}.git"
+EGIT_REPO_URI="
+	https://github.com/clMathLibraries/${MY_PN}.git
+	git://github.com/clMathLibraries/${MY_PN}.git
+	"
 EGIT_BRANCH="develop"
-S="${WORKDIR}/${P}/src"
 
 LICENSE="Apache-2.0"
 SLOT="0"
+KEYWORDS=""
 IUSE="+client examples test"
 
 RDEPEND="
@@ -32,6 +35,8 @@ DEPEND="${RDEPEND}"
 # Therefore src_test() won't execute any test.
 RESTRICT="test"
 
+S="${WORKDIR}/${P}/src"
+
 pkg_pretend() {
 	if [[ ${MERGE_TYPE} != binary ]]; then
 		if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then
@@ -42,9 +47,9 @@ pkg_pretend() {
 
 src_configure() {
 	local mycmakeargs=(
-        $(cmake-utils_use_build client CLIENT)
-        $(cmake-utils_use_build examples EXAMPLES)
-        $(cmake-utils_use_build test TEST)
+		$(cmake-utils_use_build client CLIENT)
+		$(cmake-utils_use_build examples EXAMPLES)
+		$(cmake-utils_use_build test TEST)
 	)
 	cmake-utils_src_configure
 }
diff --git a/sci-libs/nipype/nipype-9999.ebuild b/sci-libs/nipype/nipype-9999.ebuild
index 414e447be..4ece8a80e 100644
--- a/sci-libs/nipype/nipype-9999.ebuild
+++ b/sci-libs/nipype/nipype-9999.ebuild
@@ -31,7 +31,6 @@ RDEPEND="
 	dev-python/networkx[${PYTHON_USEDEP}]
 	dev-python/pygraphviz[${PYTHON_USEDEP}]"
 
-
 python_test() {
 	nosetests -v || die
 }
diff --git a/sci-mathematics/gap/Manifest b/sci-mathematics/gap/Manifest
new file mode 100644
index 000000000..3f9f17633
--- /dev/null
+++ b/sci-mathematics/gap/Manifest
@@ -0,0 +1,2 @@
+DIST gap4r4p12.tar.bz2 47715810 SHA256 5ff56c5eb89b1fd0da9f216dbe1dce8fe44674858b6ad06cb277d36b7960be4d SHA512 2b97e8678a34ba4e90b47d90cefe426dbb68f9c0fbb984b6552a069481bfe370fdc0e0646b58d18ee414055980e25391d92bc3cab8de962a38ae9e66c7314034 WHIRLPOOL 38758754d05ce39d25faca24804025c5a3f083255b5973001d1cecd006caa4ccaf33f121c0f6c45e28de8967949ca8e1e6f0eb3a4af07dbb6180c63ef9a55514
+DIST xtom1r1p4.tar.bz2 11480845 SHA256 5591dfa222d2fb6c4596c3e5c5347db339e08f209798e4a332a0d902035d4f66 SHA512 58fb39676691fffc835badbebb448369f15aef542c6ac0f2c3a5d08790e5a833d416227d4864826803aaeb86ce753e7bcedac594657206d0c3930dbb9917fd76 WHIRLPOOL 445e8db1484126af09d392872434fa25a1c6af5381290a74d7b628e356c61cbbdf73ca7e45a3fe082fcad4d965a5ddc1e4ccab7c3fbed0df225a02effe385137
diff --git a/sci-visualization/forge/forge-3.1.ebuild b/sci-visualization/forge/forge-3.1.ebuild
index a1e79ed53..9dfe85f77 100644
--- a/sci-visualization/forge/forge-3.1.ebuild
+++ b/sci-visualization/forge/forge-3.1.ebuild
@@ -45,4 +45,3 @@ src_configure() {
 	)
 	cmake-utils_src_configure
 }
-
diff --git a/sci-visualization/forge/forge-9999.ebuild b/sci-visualization/forge/forge-9999.ebuild
index a3358e31f..d325d899b 100644
--- a/sci-visualization/forge/forge-9999.ebuild
+++ b/sci-visualization/forge/forge-9999.ebuild
@@ -41,4 +41,3 @@ src_configure() {
 	)
 	cmake-utils_src_configure
 }
-
diff --git a/sci-visualization/forge/metadata.xml b/sci-visualization/forge/metadata.xml
index 58cc3cac3..e01edcd11 100644
--- a/sci-visualization/forge/metadata.xml
+++ b/sci-visualization/forge/metadata.xml
@@ -10,7 +10,7 @@
     A prototype of the OpenGL interop library that can be used with
     ArrayFire. The goal of Forge is to provide high performance OpenGL
     visualizations for C/C++ applications that use CUDA/OpenCL. Forge
-    uses OpenGL >=3.3 forward compatible contexts, so please make sure
+    uses OpenGL &gt;=3.3 forward compatible contexts, so please make sure
     you have capable hardware before trying it out.
   </longdescription>
 </pkgmetadata>