version bump

(Portage version: 2.2.1/cvs/Linux x86_64, signed Manifest commit with key C2000586)

21 files changed, 266 insertions, 837 deletions

diff --git a/sys-cluster/charm/ChangeLog b/sys-cluster/charm/ChangeLog
index 74848845d058..9aed01762612 100644
--- a/sys-cluster/charm/ChangeLog
+++ b/sys-cluster/charm/ChangeLog
@@ -1,6 +1,23 @@
 # ChangeLog for sys-cluster/charm
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sys-cluster/charm/ChangeLog,v 1.35 2013/06/27 00:01:50 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sys-cluster/charm/ChangeLog,v 1.36 2013/10/09 14:35:27 ottxor Exp $
+
+*charm-6.5.1-r1 (09 Oct 2013)
+
+  09 Oct 2013; Christoph Junghans <ottxor@gentoo.org> +charm-6.5.1-r1.ebuild,
+  +files/charm-6.5.1-CkReductionMgr.patch,
+  +files/charm-6.5.1-charmc-gentoo.patch,
+  +files/charm-6.5.1-cleanup-config.patch,
+  +files/charm-6.5.1-fix-navmenuGenerator.patch,
+  +files/charm-6.5.1-fix-string-parsing.patch, -charm-5.9.ebuild,
+  -charm-6.1.2-r2.ebuild, -charm-6.2.0.ebuild, -charm-6.5.0.ebuild,
+  -files/charm-5.9-gcc-4.2.patch, -files/charm-5.9-gcc4.patch,
+  -files/charm-6.1.2-charmc-gentoo.patch, -files/charm-6.1.2-charmrun.patch,
+  -files/charm-6.2.0-gcc-4.7.patch, -files/charm-6.5.0-charmc-gentoo.patch,
+  -files/charm-charmc-gentoo.patch, -files/charm-doc-makefile-gentoo.patch,
+  -files/charm-examples-gentoo.patch, -files/charm-fpic-gentoo.patch,
+  -files/charm-python-configure-gentoo.patch, metadata.xml:
+  version bump
 
   27 Jun 2013; Christoph Junghans <ottxor@gentoo.org>
   +files/charm-6.5.0-charmc-gentoo.patch:
diff --git a/sys-cluster/charm/charm-5.9.ebuild b/sys-cluster/charm/charm-5.9.ebuild
deleted file mode 100644
index 1ed13c30d987..000000000000
--- a/sys-cluster/charm/charm-5.9.ebuild
+++ /dev/null
@@ -1,156 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sys-cluster/charm/charm-5.9.ebuild,v 1.19 2011/10/05 18:40:35 aballier Exp $
-
-inherit eutils toolchain-funcs flag-o-matic
-
-DESCRIPTION="Charm++ is a message-passing parallel language and runtime system."
-LICENSE="charm"
-HOMEPAGE="http://charm.cs.uiuc.edu/"
-SRC_URI="${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~x86"
-IUSE="cmkopt tcp smp doc"
-
-RESTRICT="fetch"
-
-DEPEND="
-	doc? (
-		app-text/poppler
-		dev-tex/latex2html
-		virtual/latex-base
-		dev-texlive/texlive-genericrecommended
-		dev-texlive/texlive-latexextra
-	)"
-
-RDEPEND="${DEPEND}"
-
-CHARM_ARCH="net-linux"
-CHARM_DOWNLOAD="http://charm.cs.uiuc.edu/download/"
-
-pkg_nofetch() {
-	echo
-	einfo "Please download ${P}.tar.gz from"
-	einfo "${CHARM_DOWNLOAD}"
-	einfo "and then move it to ${DISTDIR}"
-	echo
-}
-
-src_unpack() {
-	unpack ${A}
-
-	epatch "${FILESDIR}"/${P}-gcc-4.2.patch
-
-	# add -fPIC to generate PIC code for charm so's
-	epatch "${FILESDIR}"/${PN}-fpic-gentoo.patch
-
-	# for pdf/html docs we need to patch the makefiles
-	if use doc; then
-		epatch "${FILESDIR}"/${PN}-doc-makefile-gentoo.patch
-	fi
-
-	# patch the example Makefiles so they run out of
-	# the box
-	epatch "${FILESDIR}"/${PN}-examples-gentoo.patch
-
-	# enable proper detection of python in configure
-	epatch "${FILESDIR}"/${PN}-python-configure-gentoo.patch
-
-	# gcc-4.1 fixes
-	epatch "${FILESDIR}"/${P}-gcc4.patch
-
-	# TCP instead of default UDP for socket comunication
-	# protocol
-	if use tcp; then
-		CHARM_OPTS="${CHARM_OPTS} tcp"
-	fi
-
-	# enable direct SMP support using shared memory
-	if use smp; then
-		CHARM_OPTS="${CHARM_OPTS} smp"
-	fi
-
-	# compile with icc if requested (icc or icpc)
-	if [ $(tc-getCC) = icc ] || [ $(tc-getCXX) = ic* ]; then
-		CHARM_OPTS="${CHARM_OPTS} icc"
-	fi
-
-	# CMK optimization
-	if use cmkopt; then
-		append-flags -DCMK_OPTIMIZE=1
-	fi
-}
-
-src_compile() {
-	# build charmm++ first
-	./build charm++ net-linux ${CHARM_OPTS} ${CFLAGS} || \
-		die "Failed to build charm++"
-
-	# make pdf/html docs
-	if use doc; then
-		cd "${S}"/doc
-		make doc || die "failed to create pdf/html docs"
-	fi
-}
-
-src_install() {
-	# make charmc play well with gentoo before
-	# we move it into /usr/bin
-	einfo "Fixing paths in charmc wrapper"
-	epatch "${FILESDIR}"/${PN}-charmc-gentoo.patch
-
-	sed -e "s/gentoo-include/${P}/" -i ./src/scripts/charmc || \
-		die "failed patching charmc script"
-
-	# install binaries
-	cd "${S}"/bin
-	dobin ./charmd ./charmd_faceless ./charmr* ./charmc ./charmxi \
-		./conv-cpm ./dep.pl || die "Failed to install binaries"
-
-	# install headers
-	cd "${S}"/include
-	insinto /usr/include/${P}
-	doins * || die "failed to install header files"
-
-	# install static libs
-	cd "${S}"/lib
-	dolib.a * || die "failed to install static libs"
-
-	# install shared libs
-	cd "${S}"/lib_so
-	dolib.so * || die "failed to install shared libs"
-
-	# basic docs
-	cd "${S}"
-	dodoc CHANGES README  || die "Failed to install docs"
-
-	# install examples after fixing path to charmc
-	find examples/ -name 'Makefile' | xargs sed \
-		-r "s:(../)+bin/charmc:/usr/bin/charmc:" -i || \
-		die "Failed to fix examples"
-	find examples/ -name 'Makefile' | xargs sed \
-		-r "s:./charmrun:./charmrun ++local:" -i || \
-		die "Failed to fix examples"
-	insinto /usr/share/doc/${PF}/examples
-	doins -r examples/charm++/*
-
-	# pdf/html docs
-	if use doc; then
-		cd "${S}"/doc
-		# install pdfs
-		insinto /usr/share/doc/${PF}/pdf
-		doins  doc/pdf/* || die "failed to install pdf docs"
-		# install html
-		docinto html
-		dohtml -r doc/html/* || die "failed to install html docs"
-	fi
-}
-
-pkg_postinst() {
-	echo
-	einfo "Please test your charm installation by copying the"
-	einfo "content of /usr/share/doc/${PF}/examples to a"
-	einfo "temporary location and run 'make test'."
-	echo
-}
diff --git a/sys-cluster/charm/charm-6.1.2-r2.ebuild b/sys-cluster/charm/charm-6.1.2-r2.ebuild
deleted file mode 100644
index 8527ef32af96..000000000000
--- a/sys-cluster/charm/charm-6.1.2-r2.ebuild
+++ /dev/null
@@ -1,130 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sys-cluster/charm/charm-6.1.2-r2.ebuild,v 1.6 2012/02/15 19:10:26 jlec Exp $
-
-EAPI=2
-inherit eutils toolchain-funcs flag-o-matic multilib
-
-DESCRIPTION="Message-passing parallel language and runtime system"
-HOMEPAGE="http://charm.cs.uiuc.edu/"
-SRC_URI="http://charm.cs.uiuc.edu/distrib/${P}_src.tar.gz"
-
-LICENSE="charm"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cmkopt tcp smp doc"
-
-DEPEND="
-	doc? (
-		>=app-text/poppler-0.12.3-r3[utils]
-		dev-tex/latex2html
-		virtual/tex-base )"
-RDEPEND=""
-
-case ${ARCH} in
-	x86)
-		CHARM_ARCH="net-linux" ;;
-
-	amd64)
-		CHARM_ARCH="net-linux-amd64" ;;
-esac
-
-src_prepare() {
-	epatch "${FILESDIR}/${P}-charmrun.patch"
-
-	sed -i \
-		-e "s:bigism_ooc.h:bigsim_ooc.h:" \
-		src/scripts/Makefile || die
-
-	# TCP instead of default UDP for socket comunication
-	# protocol
-	if use tcp; then
-		CHARM_OPTS="${CHARM_OPTS} tcp"
-	fi
-
-	# enable direct SMP support using shared memory
-	if use smp; then
-		CHARM_OPTS="${CHARM_OPTS} smp"
-	fi
-
-	# CMK optimization
-	if use cmkopt; then
-		append-flags -DCMK_OPTIMIZE=1
-	fi
-
-	echo "charm opts: ${CHARM_OPTS}"
-}
-
-src_compile() {
-	# build charmm++ first
-	./build charm++ ${CHARM_ARCH} ${CHARM_OPTS} ${CFLAGS} || \
-		die "Failed to build charm++"
-
-	# make pdf/html docs
-	if use doc; then
-		cd "${S}"/doc
-		make doc || die "failed to create pdf/html docs"
-	fi
-}
-
-src_install() {
-	# make charmc play well with gentoo before
-	# we move it into /usr/bin
-	epatch "${FILESDIR}/${P}-charmc-gentoo.patch"
-
-	sed -e "s|gentoo-include|${P}|" \
-		-e "s|gentoo-libdir|$(get_libdir)|g" \
-		-e "s|VERSION|${P}/VERSION|" \
-		-i ./src/scripts/charmc || die "failed patching charmc script"
-
-	# install binaries
-	cd "${S}"/bin
-	dobin ./charmd ./charmd_faceless ./charmr* ./charmc ./charmxi \
-		./conv-cpm ./dep.pl || die "Failed to install binaries"
-
-	# install headers
-	cd "${S}"/include
-	insinto /usr/include/${P}
-	doins * || die "failed to install header files"
-
-	# install static libs
-	cd "${S}"/lib
-	dolib.a *.a || die "failed to install static libs"
-
-	# install shared libs
-	cd "${S}"/lib_so
-	dolib.so *.so* || die "failed to install shared libs"
-
-	# basic docs
-	cd "${S}"
-	dodoc CHANGES README  || die "Failed to install docs"
-
-	# install examples
-	find examples/ -name 'Makefile' | xargs sed \
-		-r "s:(../)+bin/charmc:/usr/bin/charmc:" -i || \
-		die "Failed to fix examples"
-	find examples/ -name 'Makefile' | xargs sed \
-		-r "s:./charmrun:./charmrun ++local:" -i || \
-		die "Failed to fix examples"
-	insinto /usr/share/doc/${PF}/examples
-	doins -r examples/charm++/*
-
-	# pdf/html docs
-	if use doc; then
-		cd "${S}"/doc
-		# install pdfs
-		insinto /usr/share/doc/${PF}/pdf
-		doins  doc/pdf/* || die "failed to install pdf docs"
-		# install html
-		docinto html
-		dohtml -r doc/html/* || die "failed to install html docs"
-	fi
-}
-
-pkg_postinst() {
-	echo
-	einfo "Please test your charm installation by copying the"
-	einfo "content of /usr/share/doc/${PF}/examples to a"
-	einfo "temporary location and run 'make test'."
-	echo
-}
diff --git a/sys-cluster/charm/charm-6.2.0.ebuild b/sys-cluster/charm/charm-6.2.0.ebuild
deleted file mode 100644
index e2b7f86f05a4..000000000000
--- a/sys-cluster/charm/charm-6.2.0.ebuild
+++ /dev/null
@@ -1,152 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sys-cluster/charm/charm-6.2.0.ebuild,v 1.3 2012/07/01 14:12:34 jlec Exp $
-
-EAPI=4
-
-inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="Message-passing parallel language and runtime system"
-HOMEPAGE="http://charm.cs.uiuc.edu/"
-SRC_URI="http://charm.cs.uiuc.edu/distrib/${P}_src.tar.gz"
-
-LICENSE="charm"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cmkopt tcp smp doc"
-
-DEPEND="
-	doc? (
-	>=app-text/poppler-0.12.3-r3[utils]
-	dev-tex/latex2html
-	virtual/tex-base )"
-RDEPEND=""
-
-case ${ARCH} in
-	x86)
-		CHARM_ARCH="net-linux" ;;
-
-	amd64)
-		CHARM_ARCH="net-linux-amd64" ;;
-esac
-
-FORTRAN_STANDARD="90"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-gcc-4.7.patch
-
-	# TCP instead of default UDP for socket comunication
-	# protocol
-	if use tcp; then
-		CHARM_OPTS="${CHARM_OPTS} tcp"
-	fi
-
-	# enable direct SMP support using shared memory
-	if use smp; then
-		CHARM_OPTS="${CHARM_OPTS} smp"
-	fi
-
-	# CMK optimization
-	if use cmkopt; then
-		append-flags -DCMK_OPTIMIZE=1
-	fi
-
-	sed \
-		-e "/CMK_CF90/s:f90:${FC}:g" \
-		-e "/CMK_CXX/s:g++:$(tc-getCXX):g" \
-		-e "/CMK_CC/s:gcc:$(tc-getCC):g" \
-		-e '/CMK_F90_MODINC/s:-p:-I:g' \
-		-e "/CMK_LD/s:\"$: ${LDFLAGS} \":g" \
-		-i src/arch/net-linux*/*sh || die
-
-	sed \
-		-e "s:\(-o conv-cpm\):${LDFLAGS} \1:g" \
-		-e "s:\(-o charmxi\):${LDFLAGS} \1:g" \
-		-e "s:\(-o charmrun-silent\):${LDFLAGS} \1:g" \
-		-e "s:\(-o charmrun-notify\):${LDFLAGS} \1:g" \
-		-e "s:\(-o charmrun\):${LDFLAGS} \1:g" \
-		-e "s:\(-o charmd_faceless\):${LDFLAGS} \1:g" \
-		-e "s:\(-o charmd\):${LDFLAGS} \1:g" \
-		-i \
-			src/scripts/Makefile \
-			src/arch/net/charmrun/Makefile
-
-	append-cflags -DALLOCA_H
-
-	echo "charm opts: ${CHARM_OPTS}"
-}
-
-src_compile() {
-	# build charmm++ first
-	./build charm++ ${CHARM_ARCH} ${CHARM_OPTS} ${CFLAGS} || \
-		die "Failed to build charm++"
-
-	# make pdf/html docs
-	if use doc; then
-		cd "${S}"/doc
-		make doc || die "failed to create pdf/html docs"
-	fi
-}
-
-src_install() {
-	# make charmc play well with gentoo before
-	# we move it into /usr/bin
-	epatch "${FILESDIR}/charm-6.1.2-charmc-gentoo.patch"
-
-	sed -e "s|gentoo-include|${P}|" \
-		-e "s|gentoo-libdir|$(get_libdir)|g" \
-		-e "s|VERSION|${P}/VERSION|" \
-		-i ./src/scripts/charmc || die "failed patching charmc script"
-
-	# install binaries
-	cd "${S}"/bin
-	dobin ./charmd ./charmd_faceless ./charmr* ./charmc ./charmxi \
-		./conv-cpm ./dep.pl || die "Failed to install binaries"
-
-	# install headers
-	cd "${S}"/include
-	insinto /usr/include/${P}
-	doins * || die "failed to install header files"
-
-	# install static libs
-	# charm has a lot of .o "libs" that it requires at runtime
-	cd "${S}"/lib
-	dolib.a *.{a,o} || die "failed to install static libs"
-
-	# install shared libs
-	cd "${S}"/lib_so
-	dolib.so *.so* || die "failed to install shared libs"
-
-	# basic docs
-	cd "${S}"
-	dodoc CHANGES README  || die "Failed to install docs"
-
-	# install examples
-	find examples/ -name 'Makefile' | xargs sed \
-		-r "s:(../)+bin/charmc:/usr/bin/charmc:" -i || \
-		die "Failed to fix examples"
-	find examples/ -name 'Makefile' | xargs sed \
-		-r "s:./charmrun:./charmrun ++local:" -i || \
-		die "Failed to fix examples"
-	insinto /usr/share/doc/${PF}/examples
-	doins -r examples/charm++/*
-
-	# pdf/html docs
-	if use doc; then
-		cd "${S}"/doc
-		# install pdfs
-		insinto /usr/share/doc/${PF}/pdf
-		doins  doc/pdf/* || die "failed to install pdf docs"
-		# install html
-		docinto html
-		dohtml -r doc/html/* || die "failed to install html docs"
-	fi
-}
-
-pkg_postinst() {
-	echo
-	einfo "Please test your charm installation by copying the"
-	einfo "content of /usr/share/doc/${PF}/examples to a"
-	einfo "temporary location and run 'make test'."
-	echo
-}
diff --git a/sys-cluster/charm/charm-6.5.0.ebuild b/sys-cluster/charm/charm-6.5.1-r1.ebuild
index 25982f85a5d4..9e4d199a8be3 100644
--- a/sys-cluster/charm/charm-6.5.0.ebuild
+++ b/sys-cluster/charm/charm-6.5.1-r1.ebuild
@@ -1,10 +1,12 @@
 # Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sys-cluster/charm/charm-6.5.0.ebuild,v 1.1 2013/06/26 23:58:38 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sys-cluster/charm/charm-6.5.1-r1.ebuild,v 1.1 2013/10/09 14:35:27 ottxor Exp $
 
 EAPI=5
 
-inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs python-single-r1
 
 DESCRIPTION="Message-passing parallel language and runtime system"
 HOMEPAGE="http://charm.cs.uiuc.edu/"
@@ -13,7 +15,7 @@ SRC_URI="http://charm.cs.uiuc.edu/distrib/${P}.tar.gz"
 LICENSE="charm"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="charmdebug charmtracing charmproduction cmkopt doc examples mpi smp static-libs tcp"
+IUSE="charmdebug charmtracing charmproduction cmkopt doc examples mlogft mpi numa smp static-libs syncft tcp"
 
 RDEPEND="mpi? ( virtual/mpi )"
 DEPEND="
@@ -22,39 +24,52 @@ DEPEND="
 		>=app-text/poppler-0.12.3-r3[utils]
 		dev-tex/latex2html
 		virtual/tex-base
+		>=dev-python/beautifulsoup-4[${PYTHON_USEDEP}]
+		dev-python/lxml[${PYTHON_USEDEP}]
+		media-libs/netpbm
+		${PYTHON_DEPS}
 	)"
 
 REQUIRED_USE="
+	doc? ( ${PYTHON_REQUIRED_USE} )
 	cmkopt? ( !charmdebug !charmtracing )
 	charmproduction? ( !charmdebug !charmtracing )"
 
 FORTRAN_STANDARD="90"
 
-src_prepare() {
+get_opts() {
+	local CHARM_OPTS
+
+	# TCP instead of default UDP for socket comunication
+	# protocol
+	CHARM_OPTS+="$(usex tcp ' tcp' '')"
+
+	# enable direct SMP support using shared memory
+	CHARM_OPTS+="$(usex smp ' smp' '')"
+
+	CHARM_OPTS+="$(usex mlogft ' mlogft' '')"
+	CHARM_OPTS+="$(usex syncft ' syncft' '')"
+
 	# Build shared libraries by default.
-	CHARM_OPTS="--build-shared"
+	CHARM_OPTS+=" --build-shared"
+
 	if use charmproduction; then
 		CHARM_OPTS+=" --with-production"
 	else
 		if use charmdebug; then
-			CHARM_OPTS+=" --with-charmdebug"
+			CHARM_OPTS+=" --enable-charmdebug"
 		fi
 
 		if use charmtracing; then
-			CHARM_OPTS+=" --with-tracing --with-tracing-commthread"
+			CHARM_OPTS+=" --enable-tracing --enable-tracing-commthread"
 		fi
 	fi
 
-	# TCP instead of default UDP for socket comunication
-	# protocol
-	CHARM_OPTS+="$(usex tcp ' tcp' '')"
-
-	# enable direct SMP support using shared memory
-	CHARM_OPTS+="$(usex smp ' smp' '')"
-
-	# CMK optimization
-	use cmkopt && append-cppflags -DCMK_OPTIMIZE=1
+	CHARM_OPTS+="$(usex numa ' --with-numa' '')"
+	echo $CHARM_OPTS
+}
 
+src_prepare() {
 	sed \
 		-e "/CMK_CF90/s:f90:$(usex mpi "mpif90" "$(tc-getFC)"):g" \
 		-e "/CMK_CXX/s:g++:$(usex mpi "mpic++" "$(tc-getCXX)"):g" \
@@ -75,18 +90,31 @@ src_prepare() {
 		src/scripts/Makefile \
 		src/arch/net/charmrun/Makefile || die
 
-	einfo "charm opts: ${CHARM_OPTS}"
+	# CMK optimization
+	use cmkopt && append-cppflags -DCMK_OPTIMIZE=1
+
+	# Fix QA notice. Filed report with upstream.
+	append-cflags -DALLOCA_H
+
+	epatch "${FILESDIR}/charm-6.5.1-cleanup-config.patch"
+	epatch "${FILESDIR}/charm-6.5.1-CkReductionMgr.patch"
+	epatch "${FILESDIR}/charm-6.5.1-fix-string-parsing.patch"
+	epatch "${FILESDIR}/charm-6.5.1-fix-navmenuGenerator.patch"
 }
 
 src_compile() {
+	local mybuildoptions="$(usex mpi "mpi" "net")-linux$(usex amd64 "-amd64" '') $(get_opts) ${MAKEOPTS} ${CFLAGS}"
+
 	# Build charmm++ first.
-	./build charm++ $(usex mpi "mpi" "net")-linux$(usex amd64 "-amd64" '') \
-		${CHARM_OPTS} ${MAKEOPTS} ${CFLAGS} || die "Failed to build charm++"
+	einfo "running ./build charm++ ${mybuildoptions}"
+	./build charm++ ${mybuildoptions} || die "Failed to build charm++"
 
 	# make pdf/html docs
 	if use doc; then
-		cd "${S}"/doc
-		make doc || die "failed to create pdf/html docs"
+		python-single-r1_pkg_setup
+		python_fix_shebang "${S}/doc"
+		einfo "forcing ${EPYTHON}"
+		emake -j1 -C doc/charm++
 	fi
 }
 
@@ -95,8 +123,10 @@ src_test() {
 }
 
 src_install() {
-	# Make charmc play well with gentoo before we move it into /usr/bin.
-	epatch "${FILESDIR}/charm-6.5.0-charmc-gentoo.patch"
+	# Make charmc play well with gentoo before we move it into /usr/bin. This
+	# patch cannot be applied during src_prepare() because the charmc wrapper
+	# is used during building.
+	epatch "${FILESDIR}/charm-6.5.1-charmc-gentoo.patch"
 
 	sed -e "s|gentoo-include|${P}|" \
 		-e "s|gentoo-libdir|$(get_libdir)|g" \
@@ -161,13 +191,13 @@ src_install() {
 
 	# Install pdf/html docs
 	if use doc; then
-		cd "${S}"/doc
+		cd "${S}/doc/charm++"
 		# Install pdfs.
 		insinto /usr/share/doc/${PF}/pdf
-		doins  doc/pdf/*
+		doins  *.pdf
 		# Install html.
 		docinto html
-		dohtml -r doc/html/*
+		dohtml -r manual/*
 	fi
 }
 
diff --git a/sys-cluster/charm/files/charm-5.9-gcc-4.2.patch b/sys-cluster/charm/files/charm-5.9-gcc-4.2.patch
deleted file mode 100644
index cc7fb257a5d4..000000000000
--- a/sys-cluster/charm/files/charm-5.9-gcc-4.2.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff -Naur charm-5.9/src/conv-perf/traceCore.h charm-5.9-new/src/conv-perf/traceCore.h
---- charm-5.9/src/conv-perf/traceCore.h	2003-07-18 02:35:09.000000000 -0400
-+++ charm-5.9-new/src/conv-perf/traceCore.h	2007-09-22 08:52:09.000000000 -0400
-@@ -17,7 +17,13 @@
- class TraceLogger;
- class TraceEntry;
- 
-+#ifdef __cplusplus
-+extern "C" {
-+#endif
- CpvCExtern(int, _traceCoreOn);
-+#ifdef __cplusplus
-+}
-+#endif
- /*** structure of events ***/
- 
- struct TraceCoreEvent {
diff --git a/sys-cluster/charm/files/charm-5.9-gcc4.patch b/sys-cluster/charm/files/charm-5.9-gcc4.patch
deleted file mode 100644
index 9a1cb9f1d1d9..000000000000
--- a/sys-cluster/charm/files/charm-5.9-gcc4.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-diff -Naur charm-5.9/src/ck-com/MsgPacker.h charm-5.9-new/src/ck-com/MsgPacker.h
---- charm-5.9/src/ck-com/MsgPacker.h	2005-03-20 23:21:51.000000000 -0600
-+++ charm-5.9-new/src/ck-com/MsgPacker.h	2006-04-19 17:16:05.000000000 -0500
-@@ -83,7 +83,7 @@
-     
-     //Takes a queue of envelopes as char* ptrs and not charm message holders
-     //Used by mesh streaming strategy
--    MsgPacker::MsgPacker(CkQ<char *> &msgq, int n_msgs);
-+    MsgPacker(CkQ<char *> &msgq, int n_msgs);
-     
-     void getMessage(CombinedMessage *&msg, int &size);
-     static void deliver(CombinedMessage *cmb_msg);
-diff -Naur charm-5.9/src/ck-core/charisma.h charm-5.9-new/src/ck-core/charisma.h
---- charm-5.9/src/ck-core/charisma.h	2003-03-20 18:30:50.000000000 -0600
-+++ charm-5.9-new/src/ck-core/charisma.h	2006-04-19 17:19:34.000000000 -0500
-@@ -295,6 +295,7 @@
- class CharismaInPort
- {
-   public:
-+    virtual ~CharismaInPort() {}
-     virtual void send(void *msg, int len) = 0;
-     void _create(const char *name)
-     {
-@@ -307,6 +308,7 @@
-   protected:
-     CharismaInPort *inport;
-   public:
-+    virtual ~CharismaOutPort() {}
-     virtual void emitData(void *data, int len)
-     {
-       inport->send(data, len);
-diff -Naur charm-5.9/src/ck-core/cklocation.h charm-5.9-new/src/ck-core/cklocation.h
---- charm-5.9/src/ck-core/cklocation.h	2004-10-30 11:35:25.000000000 -0500
-+++ charm-5.9-new/src/ck-core/cklocation.h	2006-04-19 17:21:24.000000000 -0500
-@@ -431,6 +431,7 @@
- /// Abstract superclass of all array manager objects 
- class CkArrMgr {
- public:
-+	virtual ~CkArrMgr() {}
- 	/// Insert this initial element on this processor
- 	virtual void insertInitial(const CkArrayIndex &idx,void *ctorMsg, int local=1)=0;
diff --git a/sys-cluster/charm/files/charm-6.1.2-charmrun.patch b/sys-cluster/charm/files/charm-6.1.2-charmrun.patch
deleted file mode 100644
index d677051c8e9d..000000000000
--- a/sys-cluster/charm/files/charm-6.1.2-charmrun.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/arch/net/charmrun/charmrun.c.orig	2009-05-30 10:37:32.676819167 -0500
-+++ src/arch/net/charmrun/charmrun.c	2009-05-30 10:38:08.835027500 -0500
-@@ -1291,7 +1291,7 @@
-     char *tmp=tmpnam(NULL);/*This was once /tmp/fnord*/
- #endif
-     unlink(tmp);
--    fd = open(tmp,O_RDWR | O_CREAT | O_TRUNC);
-+    fd = open(tmp,O_RDWR | O_CREAT | O_TRUNC, 0666);
-     if (fd<0) { 
-       fprintf(stderr,"cannot open temp file /tmp/fnord");
-       exit(1);
diff --git a/sys-cluster/charm/files/charm-6.2.0-gcc-4.7.patch b/sys-cluster/charm/files/charm-6.2.0-gcc-4.7.patch
deleted file mode 100644
index b6ad30e22892..000000000000
--- a/sys-cluster/charm/files/charm-6.2.0-gcc-4.7.patch
+++ /dev/null
@@ -1,45 +0,0 @@
- src/util/cklists.h |   10 +++++-----
- 1 files changed, 5 insertions(+), 5 deletions(-)
-
-diff --git a/src/util/cklists.h b/src/util/cklists.h
-index 2fc6938..df29138 100644
---- a/src/util/cklists.h
-+++ b/src/util/cklists.h
-@@ -47,8 +47,8 @@ class CkQ : private CkSTLHelper<T>, private CkNoncopyable {
- 	mask = 0x0f;
-       }
-       T *newblk = new T[newlen];
--      elementCopy(newblk,block+first,blklen-first);
--      elementCopy(newblk+blklen-first,block,first);
-+      this->elementCopy(newblk,block+first,blklen-first);
-+      this->elementCopy(newblk+blklen-first,block,first);
-       delete[] block; block = newblk;
-       blklen = newlen; first = 0;
-     }
-@@ -197,7 +197,7 @@ class CkVec : private CkSTLHelper<T> {
-     }
-     void copyFrom(const this_type &src) {
-        makeBlock(src.blklen, src.len);
--       elementCopy(block,src.block,blklen);
-+       this->elementCopy(block,src.block,blklen);
-     }
-   public:
-     CkVec(): block(NULL), blklen(0), len(0) {}
-@@ -233,7 +233,7 @@ class CkVec : private CkSTLHelper<T> {
-       T *oldBlock=block; 
-       makeBlock(newcapacity,len);
-       if (newcapacity != blklen) return 0;
--      elementCopy(block,oldBlock,len);
-+      this->elementCopy(block,oldBlock,len);
-       delete[] oldBlock; //WARNING: leaks if element copy throws exception
-       return 1;
-     }
-@@ -504,7 +504,7 @@ class CkPupAblePtrVec : public CkVec< CkZeroPtr<T, CkPupAblePtr<T> > > {
- 	}
- 	void copy_from(const this_type &t) {
- 		for (size_t i=0;i<t.length();i++)
--			push_back((T *)t[i]->clone());
-+			this->push_back((T *)t[i]->clone());
- 	}
- 	void destroy(void) {
- 		for (size_t i=0;i<this->length();i++)
diff --git a/sys-cluster/charm/files/charm-6.5.0-charmc-gentoo.patch b/sys-cluster/charm/files/charm-6.5.0-charmc-gentoo.patch
deleted file mode 100644
index 34923e3f78d3..000000000000
--- a/sys-cluster/charm/files/charm-6.5.0-charmc-gentoo.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- src/scripts/charmc.old	2013-05-30 10:18:02.261819771 -0600
-+++ src/scripts/charmc	2013-05-30 10:19:50.839661634 -0600
-@@ -361,19 +361,9 @@
- 	PROG_EXT=".exe"
- fi
- 
--CHARMLIB="$CHARMBIN/../lib"
--CHARMINC="$CHARMBIN/../include"
--CHARMLIBSO=
--if test -d "$CHARMBIN/../lib_so" 
--then
--  CHARMLIBSO=`cd $CHARMBIN/../lib_so 2>/dev/null && pwd`
--  #getting absolute path is harder than thought because of symbolic links and ..
--  #ksh needs cd -P to resolve werid symbolic links, however -P is not portable
--  #csh is ok too if it exists 
--  test -z "$CHARMLIBSO" && CHARMLIBSO=`cd -P $CHARMBIN/../lib_so 2>/dev/null && pwd`
--  test -z "$CHARMLIBSO" && CHARMLIBSO=`csh -c "cd $CHARMBIN/../lib_so >& /dev/null && pwd"`
--  test -z "$CHARMLIBSO" && echo "$CHARMBIN/../lib_so: not found" && exit 1
--fi
-+CHARMLIB="/usr/gentoo-libdir"
-+CHARMINC="/usr/include/gentoo-include"
-+CHARMLIBSO="/usr/gentoo-libdir"
- 
- ##############################################################################
- #
diff --git a/sys-cluster/charm/files/charm-6.5.1-CkReductionMgr.patch b/sys-cluster/charm/files/charm-6.5.1-CkReductionMgr.patch
new file mode 100644
index 000000000000..ad07fc3aa3bc
--- /dev/null
+++ b/sys-cluster/charm/files/charm-6.5.1-CkReductionMgr.patch
@@ -0,0 +1,34 @@
+From 6b537784e9c345dee7f7cfd108c6abc779a969ae Mon Sep 17 00:00:00 2001
+From: Nicolas Bock <nicolasbock@gmail.com>
+Date: Fri, 27 Sep 2013 10:50:45 -0600
+Subject: [PATCH 2/4] Fixed bug in CkReductionMgr::reduceMessages().
+
+The first contribution of a child node is a single message. In this case
+CkReductionMgr::reduceMessages() simply returns the message without calling
+the reducer. However, when using the CkReduction::set reducer this behavior is
+incorrect, and instead the reducer should be called even for one single
+message so that the message is wrapped into a setElement struct. In the
+current implementation, the reduction becomes corrupted because the
+CkReduction::set() method one tier up in the reduction sizes the remote
+contribution incorrectly assuming a setElement struct and not a simple
+message.
+---
+ src/ck-core/ckreduction.C | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/ck-core/ckreduction.C b/src/ck-core/ckreduction.C
+index 07853a2..ef3e906 100644
+--- a/src/ck-core/ckreduction.C
++++ b/src/ck-core/ckreduction.C
+@@ -850,7 +850,7 @@ CkReductionMsg *CkReductionMgr::reduceMessages(void)
+   else
+   {//Use the reducer to reduce the messages
+ 		//if there is only one msg to be reduced just return that message
+-    if(nMsgs == 1){
++    if(nMsgs == 1 && msgArr[0]->reducer != CkReduction::set) {
+ 	ret = msgArr[0];	
+     }else{
+       if (msgArr[0]->reducer == CkReduction::random) {
+-- 
+1.8.1.5
+
diff --git a/sys-cluster/charm/files/charm-6.1.2-charmc-gentoo.patch b/sys-cluster/charm/files/charm-6.5.1-charmc-gentoo.patch
index e381a7e1db8f..f1502ced7d94 100644
--- a/sys-cluster/charm/files/charm-6.1.2-charmc-gentoo.patch
+++ b/sys-cluster/charm/files/charm-6.5.1-charmc-gentoo.patch
@@ -1,6 +1,17 @@
---- src/scripts/charmc	2009-11-27 02:24:30.648381166 -0600
-+++ src/scripts/charmc.new	2009-11-27 02:31:06.150618002 -0600
-@@ -343,19 +343,9 @@
+From 664eb097d1c5d1a158b1f41badc79d369a06aab6 Mon Sep 17 00:00:00 2001
+From: Nicolas Bock <nicolasbock@gmail.com>
+Date: Fri, 27 Sep 2013 10:53:31 -0600
+Subject: [PATCH 4/4] Fix paths for gentoo.
+
+---
+ src/scripts/charmc | 16 +++-------------
+ 1 file changed, 3 insertions(+), 13 deletions(-)
+
+diff --git a/src/scripts/charmc b/src/scripts/charmc
+index 4d37a6b..8ec2f70 100755
+--- a/src/scripts/charmc
++++ b/src/scripts/charmc
+@@ -361,19 +361,9 @@ then
  	PROG_EXT=".exe"
  fi
  
@@ -23,3 +34,6 @@
  
  ##############################################################################
  #
+-- 
+1.8.1.5
+
diff --git a/sys-cluster/charm/files/charm-6.5.1-cleanup-config.patch b/sys-cluster/charm/files/charm-6.5.1-cleanup-config.patch
new file mode 100644
index 000000000000..ec71eb27d469
--- /dev/null
+++ b/sys-cluster/charm/files/charm-6.5.1-cleanup-config.patch
@@ -0,0 +1,58 @@
+From b0af812652269a59457ad1bbf57165c0543bcd07 Mon Sep 17 00:00:00 2001
+From: Nicolas Bock <nicolasbock@gmail.com>
+Date: Fri, 27 Sep 2013 10:49:52 -0600
+Subject: [PATCH 1/4] Commented out colliding defines in conv-autoconfig.h
+
+The colliding defines (bug #252) are commented out in configure.
+---
+ src/scripts/configure    | 5 +++++
+ src/scripts/configure.in | 3 +++
+ 2 files changed, 8 insertions(+)
+
+diff --git a/src/scripts/configure b/src/scripts/configure
+index acd582c..faf268f 100755
+--- a/src/scripts/configure
++++ b/src/scripts/configure
+@@ -1703,6 +1703,9 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ ac_config_headers="$ac_config_headers conv-autoconfig.h"
+ 
+ 
++ac_config_commands="$ac_config_commands config-cleanup"
++
++
+ CHARMINC="."
+ test -r ./conv-config.sh && . ./conv-config.sh
+ 
+@@ -5259,6 +5262,7 @@ for ac_config_target in $ac_config_targets
+ do
+   case $ac_config_target in
+     "conv-autoconfig.h") CONFIG_HEADERS="$CONFIG_HEADERS conv-autoconfig.h" ;;
++    "config-cleanup") CONFIG_COMMANDS="$CONFIG_COMMANDS config-cleanup" ;;
+     "libs/ck-libs/ampi/ampiCC") CONFIG_FILES="$CONFIG_FILES libs/ck-libs/ampi/ampiCC" ;;
+     "libs/ck-libs/ampi/ampirun") CONFIG_FILES="$CONFIG_FILES libs/ck-libs/ampi/ampirun" ;;
+     "default") CONFIG_COMMANDS="$CONFIG_COMMANDS default" ;;
+@@ -5812,6 +5816,7 @@ $as_echo "$as_me: executing $ac_file commands" >&6;}
+ 
+ 
+   case $ac_file$ac_mode in
++    "config-cleanup":C) sed -i -e 's:^#define\s\+PACKAGE://&:' conv-autoconfig.h ;;
+     "default":C) chmod +x libs/ck-libs/ampi/ampiCC libs/ck-libs/ampi/ampirun
+  ;;
+ 
+diff --git a/src/scripts/configure.in b/src/scripts/configure.in
+index d1285ed..cad9a42 100644
+--- a/src/scripts/configure.in
++++ b/src/scripts/configure.in
+@@ -3,6 +3,9 @@ AC_INIT(./Makefile)
+ 
+ AC_CONFIG_HEADER(conv-autoconfig.h)
+ 
++AC_CONFIG_COMMANDS([config-cleanup],
++  [sed -i -e 's:^#define\s\+PACKAGE://&:' conv-autoconfig.h])
++
+ CHARMINC="."
+ test -r ./conv-config.sh && . ./conv-config.sh
+ 
+-- 
+1.8.1.5
+
diff --git a/sys-cluster/charm/files/charm-6.5.1-fix-navmenuGenerator.patch b/sys-cluster/charm/files/charm-6.5.1-fix-navmenuGenerator.patch
new file mode 100644
index 000000000000..a19a8dba1ff7
--- /dev/null
+++ b/sys-cluster/charm/files/charm-6.5.1-fix-navmenuGenerator.patch
@@ -0,0 +1,30 @@
+From 8b699f6c49df26b979da397b47c7dc7a099ed6b6 Mon Sep 17 00:00:00 2001
+From: Nicolas Bock <nicolasbock@gmail.com>
+Date: Sat, 28 Sep 2013 07:47:36 -0600
+Subject: [PATCH] Properly test for None return value in navmenuGenerator.py
+
+---
+ doc/navmenuGenerator.py | 7 ++++++-
+ 1 file changed, 6 insertions(+), 1 deletion(-)
+
+diff --git a/doc/navmenuGenerator.py b/doc/navmenuGenerator.py
+index c10afb5..5e5b97c 100755
+--- a/doc/navmenuGenerator.py
++++ b/doc/navmenuGenerator.py
+@@ -13,7 +13,12 @@ fileName = sys.argv[1];
+ soup = BeautifulSoup(open(fileName), "lxml")
+ 
+ # Get just the table of contents from the index page
+-toc = soup.find("ul","ChildLinks").extract()
++toc = soup.find("ul","ChildLinks")
++
++if toc == None:
++  sys.exit(0)
++
++toc = toc.extract()
+ 
+ # Retain only part and chapter titles
+ for sctn in toc.select("li > ul > li > ul"):
+-- 
+1.8.1.5
+
diff --git a/sys-cluster/charm/files/charm-6.5.1-fix-string-parsing.patch b/sys-cluster/charm/files/charm-6.5.1-fix-string-parsing.patch
new file mode 100644
index 000000000000..1cc6b432c3d4
--- /dev/null
+++ b/sys-cluster/charm/files/charm-6.5.1-fix-string-parsing.patch
@@ -0,0 +1,50 @@
+From 14f407a5d183cdac7029cc54a9d8ae6b0cb5cbcd Mon Sep 17 00:00:00 2001
+From: Nicolas Bock <nicolasbock@gmail.com>
+Date: Fri, 27 Sep 2013 10:52:18 -0600
+Subject: [PATCH 3/4] charmrun.c: parsing of strings now parses "\n" into '\n'
+
+Since gdb lacks anything like ';' to separate several commands in one line,
+the commands need to be separated by a newline character. I have added some
+parsing logic so that the string "\n" will now be translated into the
+character '\n'.
+---
+ src/arch/net/charmrun/charmrun.c | 23 +++++++++++++++++++++--
+ 1 file changed, 21 insertions(+), 2 deletions(-)
+
+diff --git a/src/arch/net/charmrun/charmrun.c b/src/arch/net/charmrun/charmrun.c
+index 6837712..8818cf8 100644
+--- a/src/arch/net/charmrun/charmrun.c
++++ b/src/arch/net/charmrun/charmrun.c
+@@ -454,8 +454,27 @@ static int pparam_setdef(def, value)
+       if (*p) return -1;
+       return 0;
+     case 's' :
+-      *def->where.s = strdup(value);
+-      return 0;
++      {
++        /* Parse input string and convert a literal "\n" into '\n'. */
++        *def->where.s = (char*) calloc(strlen(value)+1, sizeof(char));
++        char* parsed_value = (char*) *def->where.s;
++        int i;
++        int j = 0;
++        for(i = 0; i < strlen(value); i++)
++        {
++          if(i+1 < strlen(value))
++          {
++            if(value[i] == '\\' && value[i+1] == 'n')
++            {
++              parsed_value[j++] = '\n';
++              i++;
++              continue;
++            }
++          }
++          parsed_value[j++] = value[i];
++        }
++        return 0;
++      }
+     case 'f' :
+       *def->where.f = strtol(value, &p, 10);
+       if (*p) return -1;
+-- 
+1.8.1.5
+
diff --git a/sys-cluster/charm/files/charm-charmc-gentoo.patch b/sys-cluster/charm/files/charm-charmc-gentoo.patch
deleted file mode 100644
index e5be49a1d068..000000000000
--- a/sys-cluster/charm/files/charm-charmc-gentoo.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-# adjust paths in charmc wrapper to point to the proper include
-# and libary directories
-
---- charm-5.9/src/scripts/charmc	2005-01-25 23:13:30.000000000 +0000
-+++ charm-5.9-patched/src/scripts/charmc	2005-09-26 00:52:57.000000000 +0000
-@@ -656,20 +656,9 @@
- 	PROG_EXT=".exe"
- fi
- 
--CHARMLIB="$CHARMBIN/../lib"
--CHARMINC="$CHARMBIN/../include"
--CHARMLIBSO=
--if test -d "$CHARMBIN/../lib_so" 
--then
--  CHARMLIBSO=`cd $CHARMBIN/../lib_so 2>/dev/null && pwd`
--  #getting absolute path is harder than thought because of symbolic links and ..
--  #ksh needs cd -P to resolve werid symbolic links, however -P is not portable
--  #csh is ok too if it exists 
--  test -z "$CHARMLIBSO" && CHARMLIBSO=`cd -P $CHARMBIN/../lib_so 2>/dev/null && pwd`
--  test -z "$CHARMLIBSO" && CHARMLIBSO=`csh -c "cd $CHARMBIN/../lib_so >& /dev/null && pwd"`
--  test -z "$CHARMLIBSO" && echo "$CHARMBIN/../lib_so: not found" && exit 1
--fi
--
-+CHARMLIB="/usr/lib"
-+CHARMINC="/usr/include/gentoo-include"
-+CHARMLIBSO="/usr/lib"
- 
- 
- ##############################################################################
diff --git a/sys-cluster/charm/files/charm-doc-makefile-gentoo.patch b/sys-cluster/charm/files/charm-doc-makefile-gentoo.patch
deleted file mode 100644
index f18497ab30cd..000000000000
--- a/sys-cluster/charm/files/charm-doc-makefile-gentoo.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-# patch to properly build the docs as pdf and html
-
---- charm-5.9/doc/Makefile	2004-10-14 06:12:10.000000000 +0000
-+++ charm-5.9-patched/doc/Makefile	2005-09-24 22:55:53.000000000 +0000
-@@ -1,4 +1,4 @@
--IDIR=../../doc
-+IDIR=./doc
- LNCMD=test ! -f pplmanual.sty && ln -f -s ../pplmanual.sty .
- RMCMD=rm -f ./pplmanual.sty
- DIRS=install converse convext charm++ libraries f90charm pose \
---- charm-5.9/doc/Makefile.common	2005-04-19 17:21:52.000000000 +0000
-+++ charm-5.9-patched/doc/Makefile.common	2005-09-24 22:56:30.000000000 +0000
-@@ -10,7 +10,7 @@
- # (optional) PROJECT_LINK: HTML to include at bottom of page
- 
- # Destination directory for local copy of files (e.g., on user machine)
--DOCDIR=..
-+DOCDIR=../doc
- 
- # Destination directory for web-accessible copy of files (e.g., on PPL machines)
- WEBDIR=/www/ppl_manuals
-@@ -71,12 +71,10 @@
- 	-rm -fr index.tex $(FIG_CLEAN)
- 
- # Build local copy of documentation:
--doc: all
-+doc: pdf html
- 	if [ ! -d $(DOCDIR) ] ; then mkdir $(DOCDIR) ; fi
--	if [ ! -d $(DOCDIR)/ps ] ; then mkdir $(DOCDIR)/ps ; fi
- 	if [ ! -d $(DOCDIR)/pdf ] ; then mkdir $(DOCDIR)/pdf ; fi
- 	if [ ! -d $(DOCDIR)/html ] ; then mkdir $(DOCDIR)/html ; fi
--	/bin/cp $(FILE).ps $(DOCDIR)/ps/$(DEST).ps
- 	/bin/cp $(FILE).pdf $(DOCDIR)/pdf/$(DEST).pdf
- 	/bin/rm -rf $(DOCDIR)/html/$(DEST)
- 	/bin/cp -R $(FILE) $(DOCDIR)/html/$(DEST)
diff --git a/sys-cluster/charm/files/charm-examples-gentoo.patch b/sys-cluster/charm/files/charm-examples-gentoo.patch
deleted file mode 100644
index ef8089f161fe..000000000000
--- a/sys-cluster/charm/files/charm-examples-gentoo.patch
+++ /dev/null
@@ -1,105 +0,0 @@
-diff -Naur charm-5.9/examples/pose/ASIM/Makefile charm-5.9-backup/examples/pose/ASIM/Makefile
---- charm-5.9/examples/pose/ASIM/Makefile	2004-10-22 04:38:26.000000000 +0000
-+++ charm-5.9-backup/examples/pose/ASIM/Makefile	2005-09-27 03:27:08.000000000 +0000
-@@ -12,8 +12,8 @@
- OPTS=-O#-DCMK_OPTIMIZE=1 -DCMK_MEMCHECKS_OFF=1
- 
- CHARMBASE=../../..
--CHARMBIN=$(CHARMBASE)/bin
--CHARMINC=$(CHARMBASE)/include
-+CHARMBIN=/usr/bin
-+CHARMINC=/usr/include/charm-5.9
- 
- CHARMC=$(CHARMBIN)/charmc -I$(CHARMINC)/pose $(OPTS)
- 
-diff -Naur charm-5.9/examples/pose/BigNetSim/Makefile charm-5.9-backup/examples/pose/BigNetSim/Makefile
---- charm-5.9/examples/pose/BigNetSim/Makefile	2004-10-17 22:48:10.000000000 +0000
-+++ charm-5.9-backup/examples/pose/BigNetSim/Makefile	2005-09-27 03:27:08.000000000 +0000
-@@ -16,8 +16,8 @@
- 
- CHARMBASE=../../../
- #CHARMBASE=/expand8/home/gzheng/old/charm-6-8/net-linux/
--CHARMBIN=$(CHARMBASE)/bin
--CHARMINC=$(CHARMBASE)/include
-+CHARMBIN=/usr/bin
-+CHARMINC=/usr/include/charm-5.9
- 
- ifeq ($(SEQUENTIAL),1)
- CHARMC=$(CHARMBIN)/charmc -I$(CHARMINC)/pose $(OPTS) -DSEQUENTIAL_POSE=1
-diff -Naur charm-5.9/examples/pose/ChunkSim/Makefile charm-5.9-backup/examples/pose/ChunkSim/Makefile
---- charm-5.9/examples/pose/ChunkSim/Makefile	2004-10-12 17:12:26.000000000 +0000
-+++ charm-5.9-backup/examples/pose/ChunkSim/Makefile	2005-09-27 03:27:08.000000000 +0000
-@@ -12,8 +12,8 @@
- OPTS=-O#-DCMK_OPTIMIZE=1 -DCMK_MEMCHECKS_OFF=1
- 
- CHARMBASE=../../../
--CHARMBIN=$(CHARMBASE)/bin
--CHARMINC=$(CHARMBASE)/include
-+CHARMBIN=/usr/bin
-+CHARMINC=/usr/include/charm-5.9
- 
- CHARMC=$(CHARMBIN)/charmc -I$(CHARMINC)/pose $(OPTS)
- 
-@@ -109,4 +109,4 @@
- 	$(CHARMBIN)/etrans.pl Worker
- 
- test:
--	./pgm 1000 10 1 RANDOM SPARSE 50 -gf 344
-\ No newline at end of file
-+	./pgm 1000 10 1 RANDOM SPARSE 50 -gf 344
-diff -Naur charm-5.9/examples/pose/HiSim/Makefile.common charm-5.9-backup/examples/pose/HiSim/Makefile.common
---- charm-5.9/examples/pose/HiSim/Makefile.common	2004-11-02 07:29:40.000000000 +0000
-+++ charm-5.9-backup/examples/pose/HiSim/Makefile.common	2005-09-27 03:27:08.000000000 +0000
-@@ -1,8 +1,8 @@
- 
- CHARMBASE=../../../../
- #CHARMBASE=/expand8/home/gzheng/tmp/pose/charm/net-linux
--CHARMBIN=$(CHARMBASE)/bin
--CHARMINC=$(CHARMBASE)/include
-+CHARMBIN=/usr/bin
-+CHARMINC=/usr/include/charm-5.9
- ETRANS=$(CHARMBIN)/etrans.pl
- OPTS=-g
- 
-diff -Naur charm-5.9/examples/pose/LBSim/Makefile charm-5.9-backup/examples/pose/LBSim/Makefile
---- charm-5.9/examples/pose/LBSim/Makefile	2004-11-04 04:30:45.000000000 +0000
-+++ charm-5.9-backup/examples/pose/LBSim/Makefile	2005-09-27 03:27:08.000000000 +0000
-@@ -12,8 +12,8 @@
- OPTS=-O#-DCMK_OPTIMIZE=1 -DCMK_MEMCHECKS_OFF=1
- 
- CHARMBASE=../../../
--CHARMBIN=$(CHARMBASE)/bin
--CHARMINC=$(CHARMBASE)/include
-+CHARMBIN=/usr/bin
-+CHARMINC=/usr/include/charm-5.9
- 
- CHARMC=$(CHARMBIN)/charmc -I$(CHARMINC)/pose $(OPTS)
- 
-diff -Naur charm-5.9/examples/pose/Ring/Makefile charm-5.9-backup/examples/pose/Ring/Makefile
---- charm-5.9/examples/pose/Ring/Makefile	2005-02-08 18:58:05.000000000 +0000
-+++ charm-5.9-backup/examples/pose/Ring/Makefile	2005-09-27 03:27:08.000000000 +0000
-@@ -12,8 +12,8 @@
- OPTS=-O#-DCMK_OPTIMIZE=1 -DCMK_MEMCHECKS_OFF=1
- 
- CHARMBASE=../../..
--CHARMBIN=$(CHARMBASE)/bin
--CHARMINC=$(CHARMBASE)/include
-+CHARMBIN=/usr/bin/
-+CHARMINC=/usr/include/charm-5.9
- 
- CHARMC=$(CHARMBIN)/charmc -I$(CHARMINC)/pose $(OPTS)
- 
-diff -Naur charm-5.9/examples/pose/SimBenchmark/Makefile charm-5.9-backup/examples/pose/SimBenchmark/Makefile
---- charm-5.9/examples/pose/SimBenchmark/Makefile	2005-03-17 22:31:41.000000000 +0000
-+++ charm-5.9-backup/examples/pose/SimBenchmark/Makefile	2005-09-27 03:27:08.000000000 +0000
-@@ -12,8 +12,8 @@
- OPTS=-O#-DCMK_OPTIMIZE=1 -DCMK_MEMCHECKS_OFF=1
- 
- CHARMBASE=../../..
--CHARMBIN=$(CHARMBASE)/bin
--CHARMINC=$(CHARMBASE)/include
-+CHARMBIN=/usr/bin
-+CHARMINC=/usr/include/charm-5.9
- 
- CHARMC=$(CHARMBIN)/charmc -I$(CHARMINC)/pose $(OPTS)
- 
diff --git a/sys-cluster/charm/files/charm-fpic-gentoo.patch b/sys-cluster/charm/files/charm-fpic-gentoo.patch
deleted file mode 100644
index e70874de9daa..000000000000
--- a/sys-cluster/charm/files/charm-fpic-gentoo.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-# compile with -fPIC to avoid TEXTRELs
-
---- charm-5.9/src/arch/net-linux/conv-mach.sh	2005-04-22 01:14:55.000000000 +0000
-+++ charm-5.9-backup/src/arch/net-linux/conv-mach.sh	2005-09-27 18:07:10.000000000 +0000
-@@ -1,8 +1,8 @@
- CMK_CPP_CHARM="/lib/cpp -P"
- CMK_CPP_C="gcc -E"
--CMK_CC="gcc "
--CMK_CXX="g++ "
--CMK_CXXPP="$CMK_CXX -x c++ -E "
-+CMK_CC="gcc -fPIC"
-+CMK_CXX="g++ -fPIC -Wno-deprecated"
-+CMK_CXXPP="$CMK_CXX -E "
- CMK_CF77="g77 "
- CMK_CF90="f90 "
- CMK_CF90_FIXED="$CMK_CF90 -W132 "
-@@ -10,12 +10,12 @@
- CMK_LIBS="-lckqt"
- #CMK_LD="$CMK_CC -Wl,--allow-multiple-definition "
- #CMK_LDXX="$CMK_CXX -Wl,--allow-multiple-definition "
--CMK_LD="$CMK_CC "
--CMK_LDXX="$CMK_CXX "
-+CMK_LD="gcc "
-+CMK_LDXX="g++ "
- CMK_LD_SHARED="-shared"
- CMK_LD_LIBRARY_PATH="-Wl,-rpath,$CHARMLIBSO/"
- CMK_XIOPTS=""
--CMK_F90LIBS="-L/usr/absoft/lib -L/opt/absoft/lib -lf90math -lfio -lU77 -lf77math "
-+CMK_F90LIBS=""
- CMK_F77LIBS="-lg2c "
- CMK_MOD_NAME_ALLCAPS=1
- CMK_MOD_EXT="mod"
diff --git a/sys-cluster/charm/files/charm-python-configure-gentoo.patch b/sys-cluster/charm/files/charm-python-configure-gentoo.patch
deleted file mode 100644
index 6e98642aafe1..000000000000
--- a/sys-cluster/charm/files/charm-python-configure-gentoo.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-# include proper python headers 
-
---- charm-5.9/src/scripts/configure	2005-06-01 03:46:06.000000000 +0000
-+++ charm-5.9-backup/src/scripts/configure	2005-09-27 14:28:48.000000000 +0000
-@@ -1970,11 +1970,12 @@
- fi
- 
- #### test if Python headers are installed ####
-+PYTHON_VERSION=`python -V 2>&1 | awk {'print $2'} | awk -F. {'print $1"."$2'}`
- cat > $t <<EOT
--#include "python/Python.h"
--#include "python/compile.h"
--#include "python/eval.h"
--#include "python/node.h"
-+#include "python${PYTHON_VERSION}/Python.h"
-+#include "python${PYTHON_VERSION}/compile.h"
-+#include "python${PYTHON_VERSION}/eval.h"
-+#include "python${PYTHON_VERSION}/node.h"
- 
- int main() {
-     Py_Initialize();
-@@ -1983,7 +1984,6 @@
-     PyCodeObject *program = PyNode_Compile(programNode, "");
- }
- EOT
--PYTHON_VERSION=`python -V 2>&1 | awk {'print $2'} | awk -F. {'print $1"."$2'}`
- test_link "whether Python is installed" "yes" "no" "-lpython$PYTHON_VERSION -lpthread -lutil -ldl"
- 
- cat >>confdefs.h <<_ACEOF
diff --git a/sys-cluster/charm/metadata.xml b/sys-cluster/charm/metadata.xml
index ea5896e21a07..8ec82bbec5e7 100644
--- a/sys-cluster/charm/metadata.xml
+++ b/sys-cluster/charm/metadata.xml
@@ -10,6 +10,9 @@
 		<flag name="charmproduction">Optimize performance of Charm++ runtime</flag>
 		<flag name="charmtracing">Enable tracing support in Charm++</flag>
 		<flag name="cmkopt">Enable CMK optimisation</flag>
+		<flag name="mlogft">Compile with Charm++ message logging fault tolerance support</flag>
+		<flag name="numa">Support memory affinity with NUMA</flag>
+		<flag name="syncft">Compile with Charm++ fault tolerance support</flag>
 		<flag name="tcp">Use TCP (instead of UPD) for socket communication</flag>
 	</use>
 </pkgmetadata>