Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  [sci-libs/amdlibm] version bump wrt #405803 by Matthias Dahl <ua_gentoo_bugzilla@binary-island.eu>
  fix manifest
  Bump intel compiler suite
  New package, ebuild written by me
  sci-libs/bigdft-1.6.0 corrected, sci-physics/abinit-6.12.1 added and moved to autotools-utils, sci-libs/bigdft-1.6_pre1 it depends on added. Old versions of bigdft needed by old versions of abinit ressurected.
  version bump
  sci-physics/root: updave live ebuild
  sci-physics/root: bug fix for #406817

* github.com:gentoo-science/sci:
  [sci-libs/amdlibm] version bump wrt #405803 by Matthias Dahl <ua_gentoo_bugzilla@binary-island.eu>
  fix manifest
  Bump intel compiler suite
  New package, ebuild written by me
  sci-libs/bigdft-1.6.0 corrected, sci-physics/abinit-6.12.1 added and moved to autotools-utils, sci-libs/bigdft-1.6_pre1 it depends on added. Old versions of bigdft needed by old versions of abinit ressurected.
  version bump
  sci-physics/root: updave live ebuild
  sci-physics/root: bug fix for #406817

40 files changed, 2000 insertions, 274 deletions

diff --git a/dev-lang/icc/Manifest b/dev-lang/icc/Manifest
index 8560ec37a..3e61adb25 100644
--- a/dev-lang/icc/Manifest
+++ b/dev-lang/icc/Manifest
@@ -4,3 +4,6 @@ DIST parallel_studio_xe_2011_sp1_intel64.tgz 980466846 RMD160 961d2bc618681dcadb
 DIST parallel_studio_xe_2011_sp1_update1.tgz 1608904361 SHA256 b2d66360aba8b26736ec6ed819a0b4f79fa989eab99bf343217c95554a116ef9 SHA512 6df28624891b94ff0ecabae1c59fb1c360703194ba14ddef382cfd7f789123da055882040642d656b9f9c9ca2c448ff17ef517b1983cecc85b24a1ede8332c00 WHIRLPOOL 4b21fc9224c93323b50fad80a20cd4620e978cd119bf4d5a97c67e2473900f0a74818fa3e8da97ed337b5716d41f1df83f9a17ecaf9ad75acb7def20db7835dd
 DIST parallel_studio_xe_2011_sp1_update1_ia32.tgz 881192408 SHA256 58b2241b38fce637d90223816959a1e3ad8d4285be8475a5255d50051ca99625 SHA512 07d8ae1a3477e3b1d31f7f4a5f4e27e59917a2a23e8e5af79c5c09c36c3e4d7d08f3a93a7d834ef001ee3b32acf1dfed4220bb3880a66a1355a8a576aead471d WHIRLPOOL 2fe5399fe4caae04acaa0cc332e73cfdc880208cbde31a360e0965ad91214eafee1b7c3b011a47de1ae54dd4cc12432d92a226f5e51c6bff3d8d60504942c710
 DIST parallel_studio_xe_2011_sp1_update1_intel64.tgz 1039713499 SHA256 0a95872af59df087d1c9d024a88929ba70279b4d68a1ac18f157eec2decced2d SHA512 3f7d51b66fd45688819d24d955c035d8edb88f3e7d380db4a631415359973b1e1f65299858285679cd7c68b8d8a2bc2b4d992837375bc818bd5e82ec0f4f691e WHIRLPOOL cd9619a38d77a12ac312d338921c135e8dda7a7599f96010df3df81b83094c2c20fb96ad30656c424cb59feb1c1d00231ba108fc05f76ab82cec89130b20890a
+DIST parallel_studio_xe_2011_sp1_update2.tgz 1647876132 SHA256 111783571f42c7e88fe3ebcd8d4a1d30349257e5eed6abc1d0f85fe9a3d0e503 SHA512 46d59c06f44f472126be0843a8f0d5c35d7fd4823707b3b23af2ba55f76b212f05f63074858cdb1c7bc3253d151428d31e3e86c413071c207d1f5e858eb9dacc WHIRLPOOL 1a04fa7326e6b3c99539933afe3b3e4063b930d95e6e5dcc8082848d683328ce5c3e4fa6b189039c93378a8dbfdc8e8ce4d45f12bd3a0c7d58d0e0d00b7959fb
+DIST parallel_studio_xe_2011_sp1_update2_ia32.tgz 903838934 SHA256 3f056a5f4c01aac865f3363851bce43f8dc96b8734f08eeb2e1a32f007bd7869 SHA512 8dc0c4daff07fd850d5e3cb0288add598cd397c79bd4454f77609eb03a846630208de403e8527376bddb3a06c78f6535f33449a5a0f3ccb3c770b610be7814dc WHIRLPOOL d1590be5accc26d21582e831fd525d9856df8bad58a86838fffac3bf711edb0c54c3f0291b67c019dc4e0fdba869725b8b1b2649034ca611ebd67d2839a0e92e
+DIST parallel_studio_xe_2011_sp1_update2_intel64.tgz 1065783483 SHA256 3b8bfdf80c0c30ddf449465e1bd7942b7f78b6f00eae2fd6073a1c7c7c504c1b SHA512 55a1e0779d125dcd30099e750506597ba499891efd14bbc005d19fbbfe2c51878109892625e2198a3f948fd2853214b41bcc48be13292eebe0bb2593431aa70e WHIRLPOOL 16ec120d981f1bfadaf146dbb2d043347ae7e859cf4e6dc84785136c135fdb4ef61606115454abeea683a7644e03a604c96263be442fbbfa357f02ca7b1563d2
diff --git a/dev-lang/icc/icc-12.1.9.293.ebuild b/dev-lang/icc/icc-12.1.9.293.ebuild
new file mode 100644
index 000000000..afaa5967c
--- /dev/null
+++ b/dev-lang/icc/icc-12.1.9.293.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+INTEL_DPN=parallel_studio_xe
+INTEL_DID=2504
+INTEL_DPV=2011_sp1_update2
+INTEL_SUBDIR=composerxe
+
+inherit intel-sdp
+
+DESCRIPTION="Intel C/C++ Compiler"
+HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
+
+IUSE="eclipse"
+
+DEPEND="~dev-libs/intel-common-${PV}[compiler]"
+RDEPEND="${DEPEND}
+	eclipse? ( dev-util/eclipse-sdk )"
+
+QA_PREBUILT="
+	${INTEL_SDP_DIR}/bin/*/*
+	${INTEL_SDP_DIR}/compiler/lib/*/*
+	${INTEL_SDP_DIR}/mpirt/bin/*/*
+	${INTEL_SDP_DIR}/mpirt/lib/*/*"
+QA_PRESTRIPPED="${INTEL_SDP_DIR}/compiler/lib/*/.*libFNP.so"
+
+INTEL_BIN_RPMS="compilerproc compilerproc-devel"
+INTEL_DAT_RPMS="compilerproc-common"
+
+src_install() {
+	intel-sdp_src_install
+	local i
+	local idir=/opt/intel/composerxe-2011.$(get_version_component_range 3-4)/compiler/lib
+	for i in ${idir}/{ia32,intel64}/locale/ja_JP/{diagspt,flexnet,helpxi}.cat; do
+		if [[ -e "${EPREFIX}${i}" ]]; then
+			rm -rf "${ED}${i}" || die
+		fi
+	done
+}
diff --git a/dev-lang/ifc/Manifest b/dev-lang/ifc/Manifest
index 2a6677b52..e414737ed 100644
--- a/dev-lang/ifc/Manifest
+++ b/dev-lang/ifc/Manifest
@@ -4,3 +4,6 @@ DIST parallel_studio_xe_2011_sp1_intel64.tgz 980466846 SHA256 f91c44b168057df311
 DIST parallel_studio_xe_2011_sp1_update1.tgz 1608904361 SHA256 b2d66360aba8b26736ec6ed819a0b4f79fa989eab99bf343217c95554a116ef9 SHA512 6df28624891b94ff0ecabae1c59fb1c360703194ba14ddef382cfd7f789123da055882040642d656b9f9c9ca2c448ff17ef517b1983cecc85b24a1ede8332c00 WHIRLPOOL 4b21fc9224c93323b50fad80a20cd4620e978cd119bf4d5a97c67e2473900f0a74818fa3e8da97ed337b5716d41f1df83f9a17ecaf9ad75acb7def20db7835dd
 DIST parallel_studio_xe_2011_sp1_update1_ia32.tgz 881192408 SHA256 58b2241b38fce637d90223816959a1e3ad8d4285be8475a5255d50051ca99625 SHA512 07d8ae1a3477e3b1d31f7f4a5f4e27e59917a2a23e8e5af79c5c09c36c3e4d7d08f3a93a7d834ef001ee3b32acf1dfed4220bb3880a66a1355a8a576aead471d WHIRLPOOL 2fe5399fe4caae04acaa0cc332e73cfdc880208cbde31a360e0965ad91214eafee1b7c3b011a47de1ae54dd4cc12432d92a226f5e51c6bff3d8d60504942c710
 DIST parallel_studio_xe_2011_sp1_update1_intel64.tgz 1039713499 SHA256 0a95872af59df087d1c9d024a88929ba70279b4d68a1ac18f157eec2decced2d SHA512 3f7d51b66fd45688819d24d955c035d8edb88f3e7d380db4a631415359973b1e1f65299858285679cd7c68b8d8a2bc2b4d992837375bc818bd5e82ec0f4f691e WHIRLPOOL cd9619a38d77a12ac312d338921c135e8dda7a7599f96010df3df81b83094c2c20fb96ad30656c424cb59feb1c1d00231ba108fc05f76ab82cec89130b20890a
+DIST parallel_studio_xe_2011_sp1_update2.tgz 1647876132 SHA256 111783571f42c7e88fe3ebcd8d4a1d30349257e5eed6abc1d0f85fe9a3d0e503 SHA512 46d59c06f44f472126be0843a8f0d5c35d7fd4823707b3b23af2ba55f76b212f05f63074858cdb1c7bc3253d151428d31e3e86c413071c207d1f5e858eb9dacc WHIRLPOOL 1a04fa7326e6b3c99539933afe3b3e4063b930d95e6e5dcc8082848d683328ce5c3e4fa6b189039c93378a8dbfdc8e8ce4d45f12bd3a0c7d58d0e0d00b7959fb
+DIST parallel_studio_xe_2011_sp1_update2_ia32.tgz 903838934 SHA256 3f056a5f4c01aac865f3363851bce43f8dc96b8734f08eeb2e1a32f007bd7869 SHA512 8dc0c4daff07fd850d5e3cb0288add598cd397c79bd4454f77609eb03a846630208de403e8527376bddb3a06c78f6535f33449a5a0f3ccb3c770b610be7814dc WHIRLPOOL d1590be5accc26d21582e831fd525d9856df8bad58a86838fffac3bf711edb0c54c3f0291b67c019dc4e0fdba869725b8b1b2649034ca611ebd67d2839a0e92e
+DIST parallel_studio_xe_2011_sp1_update2_intel64.tgz 1065783483 SHA256 3b8bfdf80c0c30ddf449465e1bd7942b7f78b6f00eae2fd6073a1c7c7c504c1b SHA512 55a1e0779d125dcd30099e750506597ba499891efd14bbc005d19fbbfe2c51878109892625e2198a3f948fd2853214b41bcc48be13292eebe0bb2593431aa70e WHIRLPOOL 16ec120d981f1bfadaf146dbb2d043347ae7e859cf4e6dc84785136c135fdb4ef61606115454abeea683a7644e03a604c96263be442fbbfa357f02ca7b1563d2
diff --git a/dev-lang/ifc/ifc-12.1.9.293.ebuild b/dev-lang/ifc/ifc-12.1.9.293.ebuild
new file mode 100644
index 000000000..99186b35c
--- /dev/null
+++ b/dev-lang/ifc/ifc-12.1.9.293.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+INTEL_DPN=parallel_studio_xe
+INTEL_DID=2504
+INTEL_DPV=2011_sp1_update2
+INTEL_SUBDIR=composerxe
+
+inherit intel-sdp versionator
+
+DESCRIPTION="Intel FORTRAN Compiler"
+HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/"
+
+IUSE=""
+
+RDEPEND="~dev-libs/intel-common-${PV}[compiler]"
+DEPEND="${RDEPEND}"
+
+QA_PREBUILT="
+	${INTEL_SDP_DIR}/bin/*/*
+	${INTEL_SDP_DIR}/compiler/lib/*/*
+	${INTEL_SDP_DIR}/mpirt/bin/*/*
+	${INTEL_SDP_DIR}/mpirt/lib/*/*"
+QA_PRESTRIPPED="${INTEL_SDP_DIR}/compiler/lib/*/.*libFNP.so"
+
+INTEL_BIN_RPMS="compilerprof compilerprof-devel"
+INTEL_DAT_RPMS="compilerprof-common"
+
+src_install() {
+	intel-sdp_src_install
+	local i
+	local idir=/opt/intel/composerxe-2011.$(get_version_component_range 3-4)/compiler/lib
+	for i in ${idir}/{ia32,intel64}/locale/ja_JP/{diagspt,flexnet,helpxi}.cat; do
+		if [[ -e "${EPREFIX}${i}" ]]; then
+			rm -rf "${ED}${i}" || die
+		fi
+	done
+}
diff --git a/dev-libs/intel-common/Manifest b/dev-libs/intel-common/Manifest
index 9c546ef32..b3e439631 100644
--- a/dev-libs/intel-common/Manifest
+++ b/dev-libs/intel-common/Manifest
@@ -4,3 +4,6 @@ DIST parallel_studio_xe_2011_sp1_intel64.tgz 980466846 RMD160 961d2bc618681dcadb
 DIST parallel_studio_xe_2011_sp1_update1.tgz 1608904361 SHA256 b2d66360aba8b26736ec6ed819a0b4f79fa989eab99bf343217c95554a116ef9 SHA512 6df28624891b94ff0ecabae1c59fb1c360703194ba14ddef382cfd7f789123da055882040642d656b9f9c9ca2c448ff17ef517b1983cecc85b24a1ede8332c00 WHIRLPOOL 4b21fc9224c93323b50fad80a20cd4620e978cd119bf4d5a97c67e2473900f0a74818fa3e8da97ed337b5716d41f1df83f9a17ecaf9ad75acb7def20db7835dd
 DIST parallel_studio_xe_2011_sp1_update1_ia32.tgz 881192408 SHA256 58b2241b38fce637d90223816959a1e3ad8d4285be8475a5255d50051ca99625 SHA512 07d8ae1a3477e3b1d31f7f4a5f4e27e59917a2a23e8e5af79c5c09c36c3e4d7d08f3a93a7d834ef001ee3b32acf1dfed4220bb3880a66a1355a8a576aead471d WHIRLPOOL 2fe5399fe4caae04acaa0cc332e73cfdc880208cbde31a360e0965ad91214eafee1b7c3b011a47de1ae54dd4cc12432d92a226f5e51c6bff3d8d60504942c710
 DIST parallel_studio_xe_2011_sp1_update1_intel64.tgz 1039713499 SHA256 0a95872af59df087d1c9d024a88929ba70279b4d68a1ac18f157eec2decced2d SHA512 3f7d51b66fd45688819d24d955c035d8edb88f3e7d380db4a631415359973b1e1f65299858285679cd7c68b8d8a2bc2b4d992837375bc818bd5e82ec0f4f691e WHIRLPOOL cd9619a38d77a12ac312d338921c135e8dda7a7599f96010df3df81b83094c2c20fb96ad30656c424cb59feb1c1d00231ba108fc05f76ab82cec89130b20890a
+DIST parallel_studio_xe_2011_sp1_update2.tgz 1647876132 SHA256 111783571f42c7e88fe3ebcd8d4a1d30349257e5eed6abc1d0f85fe9a3d0e503 SHA512 46d59c06f44f472126be0843a8f0d5c35d7fd4823707b3b23af2ba55f76b212f05f63074858cdb1c7bc3253d151428d31e3e86c413071c207d1f5e858eb9dacc WHIRLPOOL 1a04fa7326e6b3c99539933afe3b3e4063b930d95e6e5dcc8082848d683328ce5c3e4fa6b189039c93378a8dbfdc8e8ce4d45f12bd3a0c7d58d0e0d00b7959fb
+DIST parallel_studio_xe_2011_sp1_update2_ia32.tgz 903838934 SHA256 3f056a5f4c01aac865f3363851bce43f8dc96b8734f08eeb2e1a32f007bd7869 SHA512 8dc0c4daff07fd850d5e3cb0288add598cd397c79bd4454f77609eb03a846630208de403e8527376bddb3a06c78f6535f33449a5a0f3ccb3c770b610be7814dc WHIRLPOOL d1590be5accc26d21582e831fd525d9856df8bad58a86838fffac3bf711edb0c54c3f0291b67c019dc4e0fdba869725b8b1b2649034ca611ebd67d2839a0e92e
+DIST parallel_studio_xe_2011_sp1_update2_intel64.tgz 1065783483 SHA256 3b8bfdf80c0c30ddf449465e1bd7942b7f78b6f00eae2fd6073a1c7c7c504c1b SHA512 55a1e0779d125dcd30099e750506597ba499891efd14bbc005d19fbbfe2c51878109892625e2198a3f948fd2853214b41bcc48be13292eebe0bb2593431aa70e WHIRLPOOL 16ec120d981f1bfadaf146dbb2d043347ae7e859cf4e6dc84785136c135fdb4ef61606115454abeea683a7644e03a604c96263be442fbbfa357f02ca7b1563d2
diff --git a/dev-libs/intel-common/intel-common-12.1.9.293.ebuild b/dev-libs/intel-common/intel-common-12.1.9.293.ebuild
new file mode 100644
index 000000000..a5906d2b2
--- /dev/null
+++ b/dev-libs/intel-common/intel-common-12.1.9.293.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+INTEL_DPN=parallel_studio_xe
+INTEL_DID=2504
+INTEL_DPV=2011_sp1_update2
+INTEL_SUBDIR=composerxe
+
+inherit intel-sdp
+
+DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries"
+HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/"
+
+IUSE="+compiler"
+
+QA_PREBUILT="
+	${INTEL_SDP_DIR}/compiler/lib/*/*
+	${INTEL_SDP_DIR}/bin/sourcechecker/*/*/*
+	${INTEL_SDP_DIR}/bin/*/*"
+
+QA_PRESTRIPPED="
+	${INTEL_SDP_DIR}/compiler/lib/*/.*libFNP.so
+	${INTEL_SDP_DIR}/bin/sourcechecker/lib/*/pinruntime/.*
+	${INTEL_SDP_DIR}/bin/sourcechecker/*/*/.*"
+
+pkg_setup() {
+	einfo ${INTEL_SDP_DIR}
+	INTEL_BIN_RPMS="openmp openmp-devel"
+	INTEL_DAT_RPMS="compilerpro-common"
+	if use compiler; then
+		INTEL_BIN_RPMS="${INTEL_BIN_RPMS} compilerpro-devel sourcechecker-devel"
+		INTEL_DAT_RPMS="${INTEL_DAT_RPMS} compilerpro-vars sourcechecker-common"
+	fi
+	intel-sdp_pkg_setup
+}
+
+src_install() {
+	intel-sdp_src_install
+	local path rootpath ldpath arch fenv=35intelsdp
+	cat > ${fenv} <<-EOF
+		NLSPATH=${INTEL_SDP_EDIR}/lib/locale/en_US/%N
+		MANPATH=${INTEL_SDP_EDIR}/man/en_US
+		INTEL_LICENSE_FILE=${INTEL_SDP_EDIR}/licenses
+	EOF
+	for arch in ${INTEL_ARCH}; do
+			path=${path}:${INTEL_SDP_EDIR}/bin/${arch}:${INTEL_SDP_EDIR}/mpirt/bin/${arch}
+			rootpath=${rootpath}:${INTEL_SDP_EDIR}/bin/${arch}:${INTEL_SDP_EDIR}/mpirt/bin/${arch}
+			ldpath=${ldpath}:${INTEL_SDP_EDIR}/compiler/lib/${arch}:${INTEL_SDP_EDIR}/mpirt/lib/${arch}
+	done
+	cat >> ${fenv} <<-EOF
+		PATH=${path#:}
+		ROOTPATH=${rootpath#:}
+		LDPATH=${ldpath#:}
+	EOF
+
+	doenvd ${fenv}
+	dodir ${INTEL_SDP_DIR}/licenses
+}
diff --git a/sci-biology/blasr/ChangeLog b/sci-biology/blasr/ChangeLog
new file mode 100644
index 000000000..f10ba2293
--- /dev/null
+++ b/sci-biology/blasr/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/blasr
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*blasr-9999 (22 Mar 2012)
+
+  22 Mar 2012; Andrey Kislyuk <weaver@gentoo.org> +blasr-9999.ebuild,
+  +metadata.xml:
+  New package, ebuild written by me
+
diff --git a/sci-biology/blasr/Manifest b/sci-biology/blasr/Manifest
new file mode 100644
index 000000000..f0cffa05b
--- /dev/null
+++ b/sci-biology/blasr/Manifest
@@ -0,0 +1,3 @@
+EBUILD blasr-9999.ebuild 754 RMD160 ada0b6b464ddccfe5dc9e785814812321a747580 SHA1 45f6852797f5b4b7bc3119a833da677cfb49a36c SHA256 276896a1e64d5940abd3b500a34a4b26e88be72974e7b3733c2d21e9725ce38c
+MISC ChangeLog 269 RMD160 d21a6fc5e4aad19cb2c7f551588aabfe06ee36cb SHA1 ea4a5afd80d0c4bc409e52ba14d4cd73c60004bc SHA256 0941218f7fd828b2662b2bbae81f1baead5cb6702dacd48ae2e77603a79079a1
+MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/blasr/blasr-9999.ebuild b/sci-biology/blasr/blasr-9999.ebuild
new file mode 100644
index 000000000..94e874fa1
--- /dev/null
+++ b/sci-biology/blasr/blasr-9999.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/gatk-9999.ebuild,v 1.1 2011/10/31 21:18:17 weaver Exp $
+
+EAPI=4
+
+MY_HASH=885c33a
+
+EGIT_REPO_URI="https://github.com/PacificBiosciences/blasr.git"
+
+inherit git
+
+DESCRIPTION="The PacBio long read aligner"
+HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR"
+#SRC_URI="https://github.com/PacificBiosciences/blasr/tarball/${PV} -> ${P}.tar.gz"
+SRC_URI=""
+
+LICENSE="as-is"
+SLOT="0"
+IUSE=""
+KEYWORDS=""
+
+DEPEND="sci-libs/hdf5[cxx]"
+RDEPEND=""
+
+S="${WORKDIR}/blasr-${MY_HASH}"
+
+ASSEMBLY_HOME="${D}/usr"
+
+src_install() {
+	dodir /usr/bin
+	make install ASSEMBLY_HOME="${D}/usr" || die
+}
diff --git a/sci-biology/blasr/metadata.xml b/sci-biology/blasr/metadata.xml
new file mode 100644
index 000000000..3302123e5
--- /dev/null
+++ b/sci-biology/blasr/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-libs/amdlibm/amdlibm-3.0.2.ebuild b/sci-libs/amdlibm/amdlibm-3.0.2.ebuild
new file mode 100644
index 000000000..43e6a4479
--- /dev/null
+++ b/sci-libs/amdlibm/amdlibm-3.0.2.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/acml/acml-4.1.0-r1.ebuild,v 1.4 2008/12/07 18:28:37 vapier Exp $
+
+EAPI=4
+
+inherit multilib versionator
+
+MYP=${PN}-$(replace_all_version_separators '-')
+
+DESCRIPTION="Optimized libm replacement from AMD for x86_64 architectures"
+HOMEPAGE="http://developer.amd.com/cpu/Libraries/LibM/Pages/default.aspx"
+SRC_URI="${PN}${PV}lin64.tar.gz"
+LICENSE="AMD"
+SLOT="0"
+KEYWORDS="-* ~amd64"
+IUSE="examples"
+RESTRICT="fetch strip"
+
+S=${WORKDIR}/${MYP}
+
+QA_PREBUILT="/opt/${PN}/lib64/lib${PN}.so"
+
+pkg_nofetch() {
+	einfo "The package's license prohibits redistribution."
+	einfo "Please download ${A} from"
+	einfo "   ${HOMEPAGE}"
+	einfo "and place it into ${DISTDIR}."
+}
+
+src_prepare() {
+	cat <<- EOF > "${T}/99${PN}"
+		LDPATH="/opt/${PN}/$(get_libdir)"
+	EOF
+
+	cat <<- EOF > "${T}/${PN}.pc"
+		prefix=/opt/${PN}
+		exec_prefix=\${prefix}
+		libdir=\${prefix}/$(get_libdir)
+		includedir=\${prefix}/include
+
+		Name: amdlibm
+		Description: ${DESCRIPTION}
+		Version: ${PV}
+		Libs: -L\${libdir} -l${PN}
+		Cflags: -I\${includedir}
+	EOF
+}
+
+src_test() {
+	cd examples
+	sh build_and_run.sh || die
+}
+
+src_install() {
+	dodoc ReleaseNotes.txt
+	
+	into /opt/${PN}
+	dolib.so lib/dynamic/lib${PN}.so
+	dolib.a lib/static/lib${PN}.a
+	
+	insinto /opt/${PN}
+	doins -r include
+
+	if use examples; then
+		insinto /usr/share/doc/${PF}
+		doins -r examples
+	fi
+
+	insinto /usr/$(get_libdir)/pkgconfig
+	doins "${T}/${PN}.pc"
+	doenvd "${T}/99${PN}"
+}
diff --git a/sci-libs/bigdft/ChangeLog b/sci-libs/bigdft/ChangeLog
index ec29389bf..60bf2cd54 100644
--- a/sci-libs/bigdft/ChangeLog
+++ b/sci-libs/bigdft/ChangeLog
@@ -2,6 +2,21 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*bigdft-1.6_pre1 (22 Mar 2012)
+*bigdft-1.6_pre0 (22 Mar 2012)
+
+  22 Mar 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
+  +bigdft-1.2.0.2.ebuild, +bigdft-1.2.0.5.ebuild, +bigdft-1.6_pre0.ebuild,
+  +bigdft-1.6_pre1.ebuild, bigdft-1.6.0.ebuild,
+  +files/bigdft-1.6.0-libxc_dir_include.patch,
+  +files/bigdft-1.6-tuto.1-bigdft.pc.patch,
+  +files/bigdft-1.6-tuto.1-libxc_dir_include.patch,
+  +files/bigdft-1.6-tuto-bigdft.pc.patch,
+  +files/bigdft-1.6-tuto-libxc_dir_include.patch:
+  Old versions used by old versions of abinit ressurected. May be removed
+  forever if nobody complains about the latest abinit. 1.6.0 corrected,
+  1.6_pre0 and 1.6_pre1 added; 1.6_pre1 is used by sci-physics/abinit-6.12.1.
+
 *bigdft-1.6.0 (18 Feb 2012)
 
   18 Feb 2012; Justin Lecher <jlec@gentoo.org> -bigdft-1.2.0.2.ebuild,
diff --git a/sci-libs/bigdft/Manifest b/sci-libs/bigdft/Manifest
index 639578a8a..e94f02430 100644
--- a/sci-libs/bigdft/Manifest
+++ b/sci-libs/bigdft/Manifest
@@ -1,2 +1,6 @@
+DIST bigdft-1.2.0.2.tar.gz 944219 SHA256 3143e203879a2f8b1f05789336ceed91250960ef0681c1530868011fc16f56df SHA512 4af0077b00e0f28da1ee5a766a8d58d6942bd191ed37b218d2e5ed5c46867e50946bfd1a5b8e2ea7421d476512092c692330fe5bdff8c65213b44637149a5fd4 WHIRLPOOL 4f4bad4d81ddebc20ae0c96ae8d907f2bcce54311b718232d55475ed53a2a252ffedc1d61bec0eb05446fa4074fc5c3799078edbae2a7832cc0321cc443d1c6e
+DIST bigdft-1.2.0.5.tar.gz 959834 SHA256 e0e6e905b21d784265f812619bfe081388e16eb385a8a502404e39a559a32a92 SHA512 52b647c33d2250488d5fbd61e12a833a7565743dd343023c0c07e68543680ca2882de1433c7c49a6a4d61be3c8e5bf509a4c417585f598253883396b496c5782 WHIRLPOOL bb23bbf5c70582446f0faf580b2f40ea8cd6b1a363717338c1b181a3ce40b7c058a2bc9a6996ab6d9c5e7ad0a2f53cd6b47c52ab67ffd20988b1a629226f9dd2
 DIST bigdft-1.3.2.tar.gz 1370869 SHA256 b18234c321bee98450ea0b6a3c249480ecec66d18dadcc32a7ba0d2d019c820d SHA512 8af2830a9fcf3ef9fa2d51eb05c3339b263ceec4cd0af4dd8a3fdd1901a130fa88867820faf4122d158e2f479fe0e82984244d921b38e1393d7263a0c9a5fd69 WHIRLPOOL 5c52ebd2a45446e774040ef0395057d7c7785141dbbc43897f018242bc5767265d900d5381f8cb3e21aaa319dd302d42f336da86fd9cf2f66e9300209757d31c
+DIST bigdft-1.6-tuto.1.tar.gz 7510733 SHA256 32020c7e58b36fe1f58a47ef02af99bd0da81c6da7d6f15e89b8075494d39d87 SHA512 48684413b0807b5dcee4b97b5b83d9a839c44043801b923c5f0ce7c8a92024cfee64c1065d4d2ffc67cb249cfcd485680b5526aaaedba06e6a88ccc52ba290f2 WHIRLPOOL d6efcc6f9ded331c42e8e3b13a9260e2acd922c4fa0bf303455e33924a930df6aa01abec897c1d190d5016a5bb3781c491e8a17d500e5485717989bddd4f579d
+DIST bigdft-1.6-tuto.tar.gz 7504186 SHA256 265dab2f5d12dd26e5932af5c09b28cbc2e473d87e05679b9bd888ec4ccfeaf3 SHA512 9a3d9695c0a27520711dd65887710099f02ddb89b9ff2457265f49a958212e524a0cfa258f9616bd21add292183a1a358611a66efe267a5ff6a26df40486a602 WHIRLPOOL fa0f509f9b94fed792133700a79c94e8e0e76b6630d03a6747e00cac021bc29e36871ae40f4a7d7aca7c88183f778c2334382280c6c25639132dd2c3dc2769f5
 DIST bigdft-1.6.0.tar.gz 8876759 SHA256 2d3212ef5f1ebc10fe7c627397ac6282ad41e1433ec6e66905f9d39a302913c0 SHA512 facbb78d126885dd04fed6451aa9cd1f5c755055e146cda1d2d4e90e3310fc3066b661635477db96d5b143ffaaa3ebb01107681437fd9965f3c764cf1b034361 WHIRLPOOL 97bc6c28296a92b09139e3a65266daa583011620fad5aed208e0e48627ab1d9c0ef9993d6c4c3cce5696d5c707bcdfb4b8ca7e64379909b3cf073206e32f9572
diff --git a/sci-libs/bigdft/bigdft-1.2.0.2.ebuild b/sci-libs/bigdft/bigdft-1.2.0.2.ebuild
new file mode 100644
index 000000000..208b45dbd
--- /dev/null
+++ b/sci-libs/bigdft/bigdft-1.2.0.2.ebuild
@@ -0,0 +1,89 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils fortran-2 toolchain-funcs
+
+DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
+HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
+SRC_URI="
+	http://inac.cea.fr/L_Sim/BigDFT/${P}.tar.gz
+	http://inac.cea.fr/L_Sim/BigDFT/${PN}-1.3.2.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cuda doc mpi test"
+
+RDEPEND="
+	=sci-libs/libxc-1*[fortran]
+	virtual/blas
+	virtual/fortran
+	virtual/lapack
+	mpi? ( virtual/mpi )
+	cuda? ( dev-util/nvidia-cuda-sdk )"
+DEPEND="${RDEPEND}
+	dev-util/pkgconfig
+	>=sys-devel/autoconf-2.59
+	doc? ( virtual/latex-base )"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-0001.patch \
+		"${FILESDIR}"/${P}-0002.patch \
+		"${FILESDIR}"/${P}-0003.patch \
+		"${FILESDIR}"/${P}-0004.patch \
+		"${FILESDIR}"/${P}-testH.patch
+
+	rm -r src/PSolver/ABINIT-common
+	mv ../${PN}-1.3.2/src/PSolver/ABINIT-common src/PSolver/
+	sed -i -e's%@LIBXC_INCLUDE@%-I/usr/lib/finclude%g' \
+		src/PSolver/ABINIT-common/Makefile.*
+	sed -i -e's%config\.inc%config.h%g' \
+		src/PSolver/ABINIT-common/*.F90
+}
+
+src_configure() {
+	# fortran-2.eclass does not handle mpi wrappers
+	if use mpi; then
+		export FC="mpif90"
+		export CC="mpicc"
+	else
+		tc-export FC CC
+	fi
+
+	econf \
+		$(use_enable mpi) \
+		--enable-libpoissonsolver \
+		--enable-libbigdft \
+		--enable-binaries \
+		--with-moduledir=/usr/$(get_libdir)/finclude \
+		--with-ext-linalg="`pkg-config --libs-only-l lapack`" \
+		--with-ext-linalg-path="`pkg-config --libs-only-L lapack`" \
+		--with-xc-module-path="/usr/lib/finclude" \
+		$(use_enable cuda cuda-gpu) \
+		$(use_with cuda cuda-path /opt/cuda) \
+		$(use_with cuda lib-cutils /opt/cuda/lib) \
+		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}" \
+		LD="$(tc-getLD)"
+}
+
+src_compile() {
+	emake -j1 HAVE_LIBXC=1 || die "make failed"
+	if use doc; then
+		emake HAVE_LIBXC=1 doc || die "make doc failed"
+	fi
+}
+
+src_test() {
+	if use test; then
+		emake check
+	fi
+}
+
+src_install() {
+	emake HAVE_LIBXC=1 DESTDIR="${D}" install || die "install failed"
+	dodoc README INSTALL ChangeLog AUTHORS NEWS || die "dodoc failed"
+}
diff --git a/sci-libs/bigdft/bigdft-1.2.0.5.ebuild b/sci-libs/bigdft/bigdft-1.2.0.5.ebuild
new file mode 100644
index 000000000..161d7def0
--- /dev/null
+++ b/sci-libs/bigdft/bigdft-1.2.0.5.ebuild
@@ -0,0 +1,86 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils fortran-2 toolchain-funcs
+
+DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
+HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
+SRC_URI="
+	http://inac.cea.fr/L_Sim/BigDFT/${P}.tar.gz
+	http://inac.cea.fr/L_Sim/BigDFT/${PN}-1.3.2.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cuda doc mpi test"
+
+RDEPEND="
+	=sci-libs/libxc-1*[fortran]
+	virtual/blas
+	virtual/fortran
+	virtual/lapack
+	mpi? ( virtual/mpi )
+	cuda? ( dev-util/nvidia-cuda-sdk )"
+DEPEND="${RDEPEND}
+	dev-util/pkgconfig
+	>=sys-devel/autoconf-2.59
+	doc? ( virtual/latex-base )"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-0001.patch \
+		"${FILESDIR}"/${PN}-1.2.0.2-testH.patch
+
+	rm -r src/PSolver/ABINIT-common
+	mv ../${PN}-1.3.2/src/PSolver/ABINIT-common src/PSolver/
+	sed -i -e's%@LIBXC_INCLUDE@%-I/usr/lib/finclude%g' \
+		src/PSolver/ABINIT-common/Makefile.*
+	sed -i -e's%config\.inc%config.h%g' \
+		src/PSolver/ABINIT-common/*.F90
+}
+
+src_configure() {
+	# fortran-2.eclass does not handle mpi wrappers
+	if use mpi; then
+		export FC="mpif90"
+		export CC="mpicc"
+	else
+		tc-export FC CC
+	fi
+
+	econf \
+		$(use_enable mpi) \
+		--enable-libpoissonsolver \
+		--enable-libbigdft \
+		--enable-binaries \
+		--with-moduledir=/usr/$(get_libdir)/finclude \
+		--with-ext-linalg="`pkg-config --libs-only-l lapack`" \
+		--with-ext-linalg-path="`pkg-config --libs-only-L lapack`" \
+		--with-xc-module-path="/usr/lib/finclude" \
+		$(use_enable cuda cuda-gpu) \
+		$(use_with cuda cuda-path /opt/cuda) \
+		$(use_with cuda lib-cutils /opt/cuda/lib) \
+		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}" \
+		LD="$(tc-getLD)"
+}
+
+src_compile() {
+	emake -j1 HAVE_ETSF_XC=1 || die "make failed"
+	if use doc; then
+		emake HAVE_ETSF_XC=1 doc || die "make doc failed"
+	fi
+}
+
+src_test() {
+	if use test; then
+		emake check
+	fi
+}
+
+src_install() {
+	emake HAVE_ETSF_XC=1 DESTDIR="${D}" install || die "install failed"
+	dodoc README INSTALL ChangeLog AUTHORS NEWS || die "dodoc failed"
+}
diff --git a/sci-libs/bigdft/bigdft-1.6.0.ebuild b/sci-libs/bigdft/bigdft-1.6.0.ebuild
index 2def6c600..66ea41fb5 100644
--- a/sci-libs/bigdft/bigdft-1.6.0.ebuild
+++ b/sci-libs/bigdft/bigdft-1.6.0.ebuild
@@ -2,82 +2,122 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI="4"
 
-FORTRAN_STANDARD=90
-
-inherit autotools-utils eutils fortran-2 toolchain-funcs
+inherit autotools-utils flag-o-matic fortran-2 toolchain-funcs
 
 DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
 HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
+
+REAL_P="${P/_pre0/-tuto}"
+S="${WORKDIR}/${REAL_P}"
+
 SRC_URI="
-	http://inac.cea.fr/L_Sim/BigDFT/${P}.tar.gz
-	http://inac.cea.fr/L_Sim/BigDFT/${PN}-1.3.2.tar.gz"
+	http://inac.cea.fr/L_Sim/BigDFT/${REAL_P}.tar.gz
+	"
 
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="cuda doc mpi static-libs test"
+IUSE="cuda doc etsf_io mpi netcdf opencl test"
 
 RDEPEND="
-	sci-libs/libxc[fortran]
+	=sci-libs/libxc-1*[fortran]
 	virtual/blas
 	virtual/fortran
 	virtual/lapack
-	virtual/opencl
 	mpi? ( virtual/mpi )
-	cuda? ( dev-util/nvidia-cuda-sdk )"
+	cuda? ( dev-util/nvidia-cuda-sdk )
+	opencl? (
+		|| (
+			dev-util/nvidia-cuda-sdk
+			dev-util/amdstream
+			)
+		)
+	etsf_io? ( sci-libs/etsf_io )
+	netcdf? (
+		sci-libs/netcdf[fortran]
+		)
+	"
 DEPEND="${RDEPEND}
 	dev-util/pkgconfig
 	>=sys-devel/autoconf-2.59
 	doc? ( virtual/latex-base )"
 
+DOCS=( README INSTALL ChangeLog AUTHORS NEWS )
+
+FORTRAN_STANDARD=90
+
 pkg_setup() {
 	# fortran-2.eclass does not handle mpi wrappers
 	if use mpi; then
 		export FC="mpif90"
+		export F77="mpif77"
 		export CC="mpicc"
 	else
-		tc-export FC CC
+		tc-export FC F77 CC
 	fi
+
 	fortran-2_pkg_setup
 }
 
 src_prepare() {
-	mv ../${PN}-1.3.2/src/PSolver/ABINIT-common src/PSolver/ || die
-	sed -i -e's%@LIBXC_INCLUDE@%-I/usr/lib/finclude%g' \
-		src/PSolver/ABINIT-common/Makefile.* || die
-	sed -i -e's%config\.inc%config.h%g' \
-		src/PSolver/ABINIT-common/*.F90 || die
-	autotools-utils_src_prepare
+	epatch "${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch
+	eautoreconf
 }
 
 src_configure() {
-
+	local modules="/usr/$(get_libdir)/finclude"
+	local netcdff_libs="-lnetcdff"
+	filter-flags '-m*' '-O*' "-pipe"
+	local nvcflags="${CFLAGS}"
+#	_filter-var nvcflags '-m*' '-O*' "-pipe"
 	local myeconfargs=(
-		--enable-libpoissonsolver
+		$(use_enable mpi)
+		--enable-optimised-convolution
+		--enable-pseudo
 		--enable-libbigdft
 		--enable-binaries
-		--with-moduledir=/usr/$(get_libdir)/finclude
-		--with-ext-linalg="$(pkg-config --libs-only-l lapack)"
-		--with-ext-linalg-path="$(pkg-config --libs-only-L lapack)"
-		--with-xc-module-path="/usr/lib/finclude"
-		$(use_enable mpi)
+		--disable-minima-hopping
+		--with-moduledir="${modules}"
+		--with-ext-linalg="$(pkg-config --libs-only-l lapack) \
+			$(pkg-config --libs-only-l blas)"
+		--with-ext-linalg-path="$(pkg-config --libs-only-L lapack) \
+			$(pkg-config --libs-only-L blas)"
+		--disable-internal-libxc
+		--with-libxc-path="/usr"
+		--with-libxc-include="${modules}"
 		$(use_enable cuda cuda-gpu)
 		$(use_with cuda cuda-path /opt/cuda)
-		$(use_with cuda lib-cutils /opt/cuda/lib)
-		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}}"
+		$(use_with cuda nvcc-flags "${nvcflags}")
+		$(use_enable opencl)
+		$(use_with opencl ocl-path /usr)
+		$(use_with etsf_io etsf-io)
+		$(use_with etsf_io etsf-io-path "/usr")
+		$(use_with etsf_io netcdf-path "$(pkg-config --libs-only-L netcdf)")
+		"$(use etsf_io && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")"
+		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} -I${modules}"
 		LD="$(tc-getLD)"
+		CPP="$(tc-getCPP)"
 		)
 	autotools-utils_src_configure
 }
 
 src_compile() {
-	autotools-utils_src_compile HAVE_ETSF_XC=1
-	use doc && autotools-utils_src_compile HAVE_ETSF_XC=1 doc
+	#autotools-utils_src_compile() expanded
+	_check_build_dir
+	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+	emake -j1 || die 'emake failed'
+	sed -i -e's%\$(top_builddir)/src/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
+	popd > /dev/null
+
+	use doc && autotools-utils_src_compile doc
+}
+
+src_test() {
+	use test && autotools-utils_src_test
 }
 
 src_install() {
-	emake HAVE_ETSF_XC=1 DESTDIR="${D}" install || die "install failed"
-	dodoc README INSTALL ChangeLog AUTHORS NEWS || die "dodoc failed"
+	autotools-utils_src_install HAVE_LIBXC=1
 }
diff --git a/sci-libs/bigdft/bigdft-1.6_pre0.ebuild b/sci-libs/bigdft/bigdft-1.6_pre0.ebuild
new file mode 100644
index 000000000..f15fa237a
--- /dev/null
+++ b/sci-libs/bigdft/bigdft-1.6_pre0.ebuild
@@ -0,0 +1,125 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="4"
+
+inherit autotools-utils flag-o-matic fortran-2 toolchain-funcs
+
+DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
+HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
+
+REAL_P="${P/_pre/-tuto.}"
+REAL_P="${REAL_P/-tuto.0/-tuto}"
+S="${WORKDIR}/${REAL_P}"
+
+SRC_URI="
+	http://inac.cea.fr/L_Sim/BigDFT/${REAL_P}.tar.gz
+	"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cuda doc etsf_io mpi netcdf opencl test"
+
+RDEPEND="
+	=sci-libs/libxc-1*[fortran]
+	virtual/blas
+	virtual/fortran
+	virtual/lapack
+	mpi? ( virtual/mpi )
+	cuda? ( dev-util/nvidia-cuda-sdk )
+	opencl? (
+		|| (
+			dev-util/nvidia-cuda-sdk
+			dev-util/amdstream
+			)
+		)
+	etsf_io? ( sci-libs/etsf_io )
+	netcdf? (
+		sci-libs/netcdf[fortran]
+		)
+	"
+DEPEND="${RDEPEND}
+	dev-util/pkgconfig
+	>=sys-devel/autoconf-2.59
+	doc? ( virtual/latex-base )"
+
+DOCS=( README INSTALL ChangeLog AUTHORS NEWS )
+
+FORTRAN_STANDARD=90
+
+pkg_setup() {
+	# fortran-2.eclass does not handle mpi wrappers
+	if use mpi; then
+		export FC="mpif90"
+		export F77="mpif77"
+		export CC="mpicc"
+	else
+		tc-export FC F77 CC
+	fi
+
+	fortran-2_pkg_setup
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch
+	epatch "${FILESDIR}"/"${REAL_P}"-bigdft.pc.patch
+	eautoreconf
+}
+
+src_configure() {
+	local modules="/usr/$(get_libdir)/finclude"
+	local netcdff_libs="-lnetcdff"
+	filter-flags '-m*' '-O*' "-pipe"
+	local nvcflags="${CFLAGS}"
+#	_filter-var nvcflags '-m*' '-O*' "-pipe"
+	local myeconfargs=(
+		$(use_enable mpi)
+		--enable-optimised-convolution
+		--enable-pseudo
+		--enable-libbigdft
+		--enable-binaries
+		--disable-minima-hopping
+		--with-moduledir="${modules}"
+		--with-ext-linalg="$(pkg-config --libs-only-l lapack) \
+			$(pkg-config --libs-only-l blas)"
+		--with-ext-linalg-path="$(pkg-config --libs-only-L lapack) \
+			$(pkg-config --libs-only-L blas)"
+		--disable-internal-libxc
+		--with-libxc-path="/usr"
+		--with-libxc-include="${modules}"
+		$(use_enable cuda cuda-gpu)
+		$(use_with cuda cuda-path /opt/cuda)
+		$(use_with cuda nvcc-flags "${nvcflags}")
+		$(use_enable opencl)
+		$(use_with opencl ocl-path /usr)
+		$(use_with etsf_io etsf-io)
+		$(use_with etsf_io etsf-io-path "/usr")
+		$(use_with etsf_io netcdf-path "$(pkg-config --libs-only-L netcdf)")
+		"$(use etsf_io && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")"
+		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} -I${modules}"
+		LD="$(tc-getLD)"
+		CPP="$(tc-getCPP)"
+		)
+	autotools-utils_src_configure
+}
+
+src_compile() {
+	#autotools-utils_src_compile() expanded
+	_check_build_dir
+	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+	emake -j1 || die 'emake failed'
+	sed -i -e's%\$(top_builddir)/src/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
+	popd > /dev/null
+
+	use doc && autotools-utils_src_compile doc
+}
+
+src_test() {
+	use test && autotools-utils_src_test
+}
+
+src_install() {
+	autotools-utils_src_install HAVE_LIBXC=1
+}
diff --git a/sci-libs/bigdft/bigdft-1.6_pre1.ebuild b/sci-libs/bigdft/bigdft-1.6_pre1.ebuild
new file mode 100644
index 000000000..21cff15a1
--- /dev/null
+++ b/sci-libs/bigdft/bigdft-1.6_pre1.ebuild
@@ -0,0 +1,128 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="4"
+
+inherit autotools-utils flag-o-matic fortran-2 toolchain-funcs
+
+DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
+HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/"
+
+REAL_P="${P/_pre/-tuto.}"
+REAL_P="${REAL_P/-tuto.0/-tuto}"
+S="${WORKDIR}/${REAL_P}"
+
+SRC_URI="
+	http://inac.cea.fr/L_Sim/BigDFT/${REAL_P}.tar.gz
+	"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cuda doc etsf_io mpi netcdf opencl test"
+
+RDEPEND="
+	=sci-libs/libxc-1*[fortran]
+	virtual/blas
+	virtual/fortran
+	virtual/lapack
+	mpi? ( virtual/mpi )
+	cuda? ( dev-util/nvidia-cuda-sdk )
+	opencl? (
+		|| (
+			dev-util/nvidia-cuda-sdk
+			dev-util/amdstream
+			)
+		)
+	etsf_io? ( sci-libs/etsf_io )
+	netcdf? (
+		sci-libs/netcdf[fortran]
+		)
+	"
+DEPEND="${RDEPEND}
+	dev-util/pkgconfig
+	>=sys-devel/autoconf-2.59
+	doc? ( virtual/latex-base )"
+
+DOCS=( README INSTALL ChangeLog AUTHORS NEWS )
+
+FORTRAN_STANDARD=90
+
+pkg_setup() {
+	# fortran-2.eclass does not handle mpi wrappers
+	if use mpi; then
+		export FC="mpif90"
+		export F77="mpif77"
+		export CC="mpicc"
+	else
+		tc-export FC F77 CC
+	fi
+
+	fortran-2_pkg_setup
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch
+	epatch "${FILESDIR}"/"${REAL_P}"-bigdft.pc.patch
+	sed -i -e's/capitalize_module_ext/ax_fc_mod_ext/g' "${S}"/configure
+	sed -i -e's/capitalize_module_ext/ax_fc_mod_ext/g' "${S}"/configure.ac
+	eautoreconf
+}
+
+src_configure() {
+	local modules="/usr/$(get_libdir)/finclude"
+	local netcdff_libs="-lnetcdff"
+	filter-flags '-m*' '-O*' "-pipe"
+	local nvcflags="${CFLAGS}"
+#	_filter-var nvcflags '-m*' '-O*' "-pipe"
+	local myeconfargs=(
+		$(use_enable mpi)
+		--enable-optimised-convolution
+		--enable-pseudo
+		--enable-libbigdft
+		--enable-binaries
+		--disable-minima-hopping
+		--with-moduledir="${modules}"
+		--with-ext-linalg="$(pkg-config --libs-only-l lapack) \
+			$(pkg-config --libs-only-l blas)"
+		--with-ext-linalg-path="$(pkg-config --libs-only-L lapack) \
+			$(pkg-config --libs-only-L blas)"
+		--enable-libxc
+		--disable-internal-libxc
+		--with-libxc-path="/usr"
+		--with-libxc-include="${modules}"
+		$(use_enable cuda cuda-gpu)
+		$(use_with cuda cuda-path /opt/cuda)
+		$(use_with cuda nvcc-flags "${nvcflags}")
+		$(use_enable opencl)
+		$(use_with opencl ocl-path /usr)
+		$(use_with etsf_io etsf-io)
+		$(use_with etsf_io etsf-io-path "/usr")
+		$(use_with etsf_io netcdf-path "$(pkg-config --libs-only-L netcdf)")
+		"$(use etsf_io && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")"
+		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} -I${modules}"
+		LD="$(tc-getLD)"
+		CPP="$(tc-getCPP)"
+		)
+	autotools-utils_src_configure
+}
+
+src_compile() {
+	#autotools-utils_src_compile() expanded
+	_check_build_dir
+	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+	emake -j1 || die 'emake failed'
+	sed -i -e's%\$(top_builddir)/src/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
+	popd > /dev/null
+
+	use doc && autotools-utils_src_compile doc
+}
+
+src_test() {
+	use test && autotools-utils_src_test
+}
+
+src_install() {
+	autotools-utils_src_install HAVE_LIBXC=1
+}
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch
new file mode 100644
index 000000000..3ddde7014
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.6-tuto-bigdft.pc.patch
@@ -0,0 +1,203 @@
+diff -Naur bigdft-1.6-tuto_orig/Makefile.am bigdft-1.6-tuto/Makefile.am
+--- Makefile.am	2011-10-18 07:39:52.000000000 +0000
++++ Makefile.am	2012-03-21 10:08:44.000000000 +0000
+@@ -4,7 +4,10 @@
+ 
+ ACLOCAL_AMFLAGS = -I config/m4
+ 
+-DISTCLEANFILES = config.inc
++DISTCLEANFILES = config.inc bigdft.pc
++
++pkgconfigdir = $(libdir)/pkgconfig
++pkgconfig_DATA = bigdft.pc
+ 
+ if BUILD_LIBABINIT
+ libABINIT_dir = libABINIT/src
+diff -Naur bigdft-1.6-tuto_orig/Makefile.in bigdft-1.6-tuto/Makefile.in
+--- Makefile.in	2012-03-21 10:03:28.000000000 +0000
++++ Makefile.in	2012-03-21 10:20:48.000000000 +0000
+@@ -33,7 +33,7 @@
+ POST_UNINSTALL = :
+ subdir = .
+ DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
+-	$(srcdir)/Makefile.in $(srcdir)/config.h.in \
++	$(srcdir)/Makefile.in $(srcdir)/bigdft.pc.in $(srcdir)/config.h.in \
+ 	$(top_srcdir)/config/Doxyfile.in $(top_srcdir)/configure \
+ 	AUTHORS COPYING ChangeLog INSTALL NEWS config/depcomp \
+ 	config/install-sh config/missing
+@@ -48,7 +48,7 @@
+  configure.lineno config.status.lineno
+ mkinstalldirs = $(install_sh) -d
+ CONFIG_HEADER = config.h
+-CONFIG_CLEAN_FILES = config/Doxyfile
++CONFIG_CLEAN_FILES = bigdft.pc config/Doxyfile
+ CONFIG_CLEAN_VPATH_FILES =
+ SOURCES =
+ DIST_SOURCES =
+@@ -59,6 +59,35 @@
+ 	install-pdf-recursive install-ps-recursive install-recursive \
+ 	installcheck-recursive installdirs-recursive pdf-recursive \
+ 	ps-recursive uninstall-recursive
++am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
++am__vpath_adj = case $$p in \
++    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
++    *) f=$$p;; \
++  esac;
++am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
++am__install_max = 40
++am__nobase_strip_setup = \
++  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
++am__nobase_strip = \
++  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
++am__nobase_list = $(am__nobase_strip_setup); \
++  for p in $$list; do echo "$$p $$p"; done | \
++  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
++  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
++    if (++n[$$2] == $(am__install_max)) \
++      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
++    END { for (dir in files) print dir, files[dir] }'
++am__base_list = \
++  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
++  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
++am__uninstall_files_from_dir = { \
++  test -z "$$files" \
++    || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
++    || { echo " ( cd '$$dir' && rm -f" $$files ")"; \
++         $(am__cd) "$$dir" && rm -f $$files; }; \
++  }
++am__installdirs = "$(DESTDIR)$(pkgconfigdir)"
++DATA = $(pkgconfig_DATA)
+ RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
+   distclean-recursive maintainer-clean-recursive
+ AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
+@@ -232,7 +261,9 @@
+ 	config/m4
+ 
+ ACLOCAL_AMFLAGS = -I config/m4
+-DISTCLEANFILES = config.inc
++DISTCLEANFILES = config.inc bigdft.pc
++pkgconfigdir = $(libdir)/pkgconfig
++pkgconfig_DATA = bigdft.pc
+ @BUILD_LIBABINIT_FALSE@libABINIT_dir = 
+ @BUILD_LIBABINIT_TRUE@libABINIT_dir = libABINIT/src
+ @BUILD_LIBXC_FALSE@libXC_dir = 
+@@ -307,8 +338,28 @@
+ 
+ distclean-hdr:
+ 	-rm -f config.h stamp-h1
++bigdft.pc: $(top_builddir)/config.status $(srcdir)/bigdft.pc.in
++	cd $(top_builddir) && $(SHELL) ./config.status $@
+ config/Doxyfile: $(top_builddir)/config.status $(top_srcdir)/config/Doxyfile.in
+ 	cd $(top_builddir) && $(SHELL) ./config.status $@
++install-pkgconfigDATA: $(pkgconfig_DATA)
++	@$(NORMAL_INSTALL)
++	test -z "$(pkgconfigdir)" || $(MKDIR_P) "$(DESTDIR)$(pkgconfigdir)"
++	@list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
++	for p in $$list; do \
++	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
++	  echo "$$d$$p"; \
++	done | $(am__base_list) | \
++	while read files; do \
++	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(pkgconfigdir)'"; \
++	  $(INSTALL_DATA) $$files "$(DESTDIR)$(pkgconfigdir)" || exit $$?; \
++	done
++
++uninstall-pkgconfigDATA:
++	@$(NORMAL_UNINSTALL)
++	@list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
++	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
++	dir='$(DESTDIR)$(pkgconfigdir)'; $(am__uninstall_files_from_dir)
+ 
+ # This directory's subdirectories are mostly independent; you can cd
+ # into them and run `make' without going through this Makefile.
+@@ -622,9 +673,12 @@
+ 	       exit 1; } >&2
+ check-am: all-am
+ check: check-recursive
+-all-am: Makefile config.h
++all-am: Makefile $(DATA) config.h
+ installdirs: installdirs-recursive
+ installdirs-am:
++	for dir in "$(DESTDIR)$(pkgconfigdir)"; do \
++	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
++	done
+ install: install-recursive
+ install-exec: install-exec-recursive
+ install-data: install-data-recursive
+@@ -672,7 +726,7 @@
+ 
+ info-am:
+ 
+-install-data-am:
++install-data-am: install-pkgconfigDATA
+ 
+ install-dvi: install-dvi-recursive
+ 
+@@ -718,7 +772,7 @@
+ 
+ ps-am:
+ 
+-uninstall-am:
++uninstall-am: uninstall-pkgconfigDATA
+ 
+ .MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \
+ 	ctags-recursive install-am install-strip tags-recursive
+@@ -733,10 +787,10 @@
+ 	install-data-am install-dvi install-dvi-am install-exec \
+ 	install-exec-am install-html install-html-am install-info \
+ 	install-info-am install-man install-pdf install-pdf-am \
+-	install-ps install-ps-am install-strip installcheck \
++	install-pkgconfigDATA install-ps install-ps-am install-strip installcheck \
+ 	installcheck-am installdirs installdirs-am maintainer-clean \
+ 	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
+-	pdf-am ps ps-am tags tags-recursive uninstall uninstall-am
++	pdf-am ps ps-am tags tags-recursive uninstall uninstall-am uninstall-pkgconfigDATA
+ 
+ 	configure
+ 
+diff -Naur bigdft-1.6-tuto_orig/bigdft.pc.in bigdft-1.6-tuto/bigdft.pc.in
+--- bigdft.pc.in	1970-01-01 00:00:00.000000000 +0000
++++ bigdft.pc.in	2012-02-01 09:43:59.000000000 +0000
+@@ -0,0 +1,11 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: libbigdft
++Description: Library for DFT calculation over wavelets.
++Requires: 
++Version: @VERSION@
++Libs: -L${libdir} -lbigdft -lpoissonsolver @LIBS@ @FCLIBS@
++Cflags: -I${includedir}
+diff -Naur bigdft-1.6-tuto_orig/configure bigdft-1.6-tuto/configure
+--- configure	2012-03-21 10:03:26.000000000 +0000
++++ configure	2012-03-21 11:04:52.000000000 +0000
+@@ -8512,7 +8512,7 @@
+ docdir="${docdir}"
+ 
+ 
+-ac_config_files="$ac_config_files Makefile libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile"
++ac_config_files="$ac_config_files Makefile bigdft.pc libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile"
+ 
+ 
+ # Call libXC ./configure script recursively.
+@@ -9349,6 +9349,7 @@
+     "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
+     "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+     "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
++    "bigdft.pc") CONFIG_FILES="$CONFIG_FILES bigdft.pc" ;;
+     "libABINIT/src/Makefile") CONFIG_FILES="$CONFIG_FILES libABINIT/src/Makefile" ;;
+     "config/Doxyfile") CONFIG_FILES="$CONFIG_FILES config/Doxyfile" ;;
+     "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
+diff -Naur bigdft-1.6-tuto_orig/configure.ac bigdft-1.6-tuto/configure.ac
+--- configure.ac	2012-03-21 10:03:02.000000000 +0000
++++ configure.ac	2012-03-21 10:48:53.000000000 +0000
+@@ -715,6 +715,7 @@
+ dnl Give the name of file.in to transform to file
+ AC_CONFIG_FILES([
+ Makefile
++bigdft.pc
+ libABINIT/src/Makefile
+ config/Doxyfile
+ src/Makefile
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patch
new file mode 100644
index 000000000..16aca5ef4
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.6-tuto-libxc_dir_include.patch
@@ -0,0 +1,50 @@
+--- configure.ac.orig	2011-11-23 14:02:15.000000000 +0000
++++ configure.ac	2011-11-23 14:09:19.000000000 +0000
+@@ -564,14 +564,17 @@
+ dnl Test the libXC library
+ ac_internal_libxc="yes"
+ AC_ARG_ENABLE(internal-libxc, AS_HELP_STRING([--disable-internal-libxc], [Do not build and link with internal libXC library (default = yes).]), ac_internal_libxc=$enableval, ac_internal_libxc="yes")
+-AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib and module files (default = None).]),
++AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib files (default = None).]),
+             ac_libxc_dir=$withval, ac_libxc_dir=)
++AC_ARG_WITH(libxc-include, AS_HELP_STRING([--with-libxc-include], [Give the path for an external libXC library module files (default = None).]),
++            ac_libxc_dir_include=$withval, ac_libxc_dir_include=)
+ ac_use_libxc="no"
+ ac_build_libxc=$ac_internal_libxc
+ if test "$ac_internal_libxc" = "yes" ; then
+   ac_build_libxc="yes"
+   ac_use_libxc="yes"
+   ac_libxc_dir="$top_builddir"/libxc-1.1.0/src
++  ac_libxc_dir_include="$ac_libxc_dir"/include
+   AC_SUBST(LIBXC_DIR, "\$(top_builddir)"/libxc-1.1.0/src)
+   AC_SUBST(LIBXC_INCLUDE, "-I\$(top_builddir)"/libxc-1.1.0/src)
+   LDFLAGS="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs"
+@@ -579,6 +582,9 @@
+ else
+   if test -n "$ac_libxc_dir" ; then
+     LDFLAGS="$LDFLAGS -L$ac_libxc_dir/lib"
++    if test x"$ac_libxc_dir_include" = x ; then
++      ac_libxc_dir_include="$ac_libxc_dir"/include
++    fi
+     
+     dnl Test the given implementation of libXC.
+     ac_libxc_libname="xc"
+@@ -587,13 +593,13 @@
+       ac_libxc_libname="dft_xc"
+       AC_CHECK_LIB($ac_libxc_libname, xc_f90_lda_vxc, withlibxc=yes, withlibxc=no)
+     fi
+-    AC_CHECK_FILE($ac_libxc_dir/include/libxc_funcs_m.$capitalize_module_ext, funcs="yes", funcs="no")
+-    AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no")
+-    AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no")
++    AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$capitalize_module_ext, funcs="yes", funcs="no")
++    AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no")
++    AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no")
+     if test "$withlibxc" = "yes" -a "$funcs" = "yes" -a "$lib" = "yes" -a "$types" = "yes"; then
+       ac_use_libxc="yes"
+-      AC_SUBST(LIBXC_DIR, $ac_libxc_dir/include)
+-      AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir/include)
++      AC_SUBST(LIBXC_DIR, $ac_libxc_dir_include)
++      AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir_include)
+       LIBXC_LIBS="-l"$ac_libxc_libname
+     fi
+   else
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc.patch
new file mode 100644
index 000000000..3ddde7014
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc.patch
@@ -0,0 +1,203 @@
+diff -Naur bigdft-1.6-tuto_orig/Makefile.am bigdft-1.6-tuto/Makefile.am
+--- Makefile.am	2011-10-18 07:39:52.000000000 +0000
++++ Makefile.am	2012-03-21 10:08:44.000000000 +0000
+@@ -4,7 +4,10 @@
+ 
+ ACLOCAL_AMFLAGS = -I config/m4
+ 
+-DISTCLEANFILES = config.inc
++DISTCLEANFILES = config.inc bigdft.pc
++
++pkgconfigdir = $(libdir)/pkgconfig
++pkgconfig_DATA = bigdft.pc
+ 
+ if BUILD_LIBABINIT
+ libABINIT_dir = libABINIT/src
+diff -Naur bigdft-1.6-tuto_orig/Makefile.in bigdft-1.6-tuto/Makefile.in
+--- Makefile.in	2012-03-21 10:03:28.000000000 +0000
++++ Makefile.in	2012-03-21 10:20:48.000000000 +0000
+@@ -33,7 +33,7 @@
+ POST_UNINSTALL = :
+ subdir = .
+ DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
+-	$(srcdir)/Makefile.in $(srcdir)/config.h.in \
++	$(srcdir)/Makefile.in $(srcdir)/bigdft.pc.in $(srcdir)/config.h.in \
+ 	$(top_srcdir)/config/Doxyfile.in $(top_srcdir)/configure \
+ 	AUTHORS COPYING ChangeLog INSTALL NEWS config/depcomp \
+ 	config/install-sh config/missing
+@@ -48,7 +48,7 @@
+  configure.lineno config.status.lineno
+ mkinstalldirs = $(install_sh) -d
+ CONFIG_HEADER = config.h
+-CONFIG_CLEAN_FILES = config/Doxyfile
++CONFIG_CLEAN_FILES = bigdft.pc config/Doxyfile
+ CONFIG_CLEAN_VPATH_FILES =
+ SOURCES =
+ DIST_SOURCES =
+@@ -59,6 +59,35 @@
+ 	install-pdf-recursive install-ps-recursive install-recursive \
+ 	installcheck-recursive installdirs-recursive pdf-recursive \
+ 	ps-recursive uninstall-recursive
++am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
++am__vpath_adj = case $$p in \
++    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
++    *) f=$$p;; \
++  esac;
++am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
++am__install_max = 40
++am__nobase_strip_setup = \
++  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
++am__nobase_strip = \
++  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
++am__nobase_list = $(am__nobase_strip_setup); \
++  for p in $$list; do echo "$$p $$p"; done | \
++  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
++  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
++    if (++n[$$2] == $(am__install_max)) \
++      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
++    END { for (dir in files) print dir, files[dir] }'
++am__base_list = \
++  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
++  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
++am__uninstall_files_from_dir = { \
++  test -z "$$files" \
++    || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
++    || { echo " ( cd '$$dir' && rm -f" $$files ")"; \
++         $(am__cd) "$$dir" && rm -f $$files; }; \
++  }
++am__installdirs = "$(DESTDIR)$(pkgconfigdir)"
++DATA = $(pkgconfig_DATA)
+ RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
+   distclean-recursive maintainer-clean-recursive
+ AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
+@@ -232,7 +261,9 @@
+ 	config/m4
+ 
+ ACLOCAL_AMFLAGS = -I config/m4
+-DISTCLEANFILES = config.inc
++DISTCLEANFILES = config.inc bigdft.pc
++pkgconfigdir = $(libdir)/pkgconfig
++pkgconfig_DATA = bigdft.pc
+ @BUILD_LIBABINIT_FALSE@libABINIT_dir = 
+ @BUILD_LIBABINIT_TRUE@libABINIT_dir = libABINIT/src
+ @BUILD_LIBXC_FALSE@libXC_dir = 
+@@ -307,8 +338,28 @@
+ 
+ distclean-hdr:
+ 	-rm -f config.h stamp-h1
++bigdft.pc: $(top_builddir)/config.status $(srcdir)/bigdft.pc.in
++	cd $(top_builddir) && $(SHELL) ./config.status $@
+ config/Doxyfile: $(top_builddir)/config.status $(top_srcdir)/config/Doxyfile.in
+ 	cd $(top_builddir) && $(SHELL) ./config.status $@
++install-pkgconfigDATA: $(pkgconfig_DATA)
++	@$(NORMAL_INSTALL)
++	test -z "$(pkgconfigdir)" || $(MKDIR_P) "$(DESTDIR)$(pkgconfigdir)"
++	@list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
++	for p in $$list; do \
++	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
++	  echo "$$d$$p"; \
++	done | $(am__base_list) | \
++	while read files; do \
++	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(pkgconfigdir)'"; \
++	  $(INSTALL_DATA) $$files "$(DESTDIR)$(pkgconfigdir)" || exit $$?; \
++	done
++
++uninstall-pkgconfigDATA:
++	@$(NORMAL_UNINSTALL)
++	@list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \
++	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
++	dir='$(DESTDIR)$(pkgconfigdir)'; $(am__uninstall_files_from_dir)
+ 
+ # This directory's subdirectories are mostly independent; you can cd
+ # into them and run `make' without going through this Makefile.
+@@ -622,9 +673,12 @@
+ 	       exit 1; } >&2
+ check-am: all-am
+ check: check-recursive
+-all-am: Makefile config.h
++all-am: Makefile $(DATA) config.h
+ installdirs: installdirs-recursive
+ installdirs-am:
++	for dir in "$(DESTDIR)$(pkgconfigdir)"; do \
++	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
++	done
+ install: install-recursive
+ install-exec: install-exec-recursive
+ install-data: install-data-recursive
+@@ -672,7 +726,7 @@
+ 
+ info-am:
+ 
+-install-data-am:
++install-data-am: install-pkgconfigDATA
+ 
+ install-dvi: install-dvi-recursive
+ 
+@@ -718,7 +772,7 @@
+ 
+ ps-am:
+ 
+-uninstall-am:
++uninstall-am: uninstall-pkgconfigDATA
+ 
+ .MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \
+ 	ctags-recursive install-am install-strip tags-recursive
+@@ -733,10 +787,10 @@
+ 	install-data-am install-dvi install-dvi-am install-exec \
+ 	install-exec-am install-html install-html-am install-info \
+ 	install-info-am install-man install-pdf install-pdf-am \
+-	install-ps install-ps-am install-strip installcheck \
++	install-pkgconfigDATA install-ps install-ps-am install-strip installcheck \
+ 	installcheck-am installdirs installdirs-am maintainer-clean \
+ 	maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
+-	pdf-am ps ps-am tags tags-recursive uninstall uninstall-am
++	pdf-am ps ps-am tags tags-recursive uninstall uninstall-am uninstall-pkgconfigDATA
+ 
+ 	configure
+ 
+diff -Naur bigdft-1.6-tuto_orig/bigdft.pc.in bigdft-1.6-tuto/bigdft.pc.in
+--- bigdft.pc.in	1970-01-01 00:00:00.000000000 +0000
++++ bigdft.pc.in	2012-02-01 09:43:59.000000000 +0000
+@@ -0,0 +1,11 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: libbigdft
++Description: Library for DFT calculation over wavelets.
++Requires: 
++Version: @VERSION@
++Libs: -L${libdir} -lbigdft -lpoissonsolver @LIBS@ @FCLIBS@
++Cflags: -I${includedir}
+diff -Naur bigdft-1.6-tuto_orig/configure bigdft-1.6-tuto/configure
+--- configure	2012-03-21 10:03:26.000000000 +0000
++++ configure	2012-03-21 11:04:52.000000000 +0000
+@@ -8512,7 +8512,7 @@
+ docdir="${docdir}"
+ 
+ 
+-ac_config_files="$ac_config_files Makefile libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile"
++ac_config_files="$ac_config_files Makefile bigdft.pc libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile"
+ 
+ 
+ # Call libXC ./configure script recursively.
+@@ -9349,6 +9349,7 @@
+     "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
+     "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+     "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
++    "bigdft.pc") CONFIG_FILES="$CONFIG_FILES bigdft.pc" ;;
+     "libABINIT/src/Makefile") CONFIG_FILES="$CONFIG_FILES libABINIT/src/Makefile" ;;
+     "config/Doxyfile") CONFIG_FILES="$CONFIG_FILES config/Doxyfile" ;;
+     "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
+diff -Naur bigdft-1.6-tuto_orig/configure.ac bigdft-1.6-tuto/configure.ac
+--- configure.ac	2012-03-21 10:03:02.000000000 +0000
++++ configure.ac	2012-03-21 10:48:53.000000000 +0000
+@@ -715,6 +715,7 @@
+ dnl Give the name of file.in to transform to file
+ AC_CONFIG_FILES([
+ Makefile
++bigdft.pc
+ libABINIT/src/Makefile
+ config/Doxyfile
+ src/Makefile
diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-libxc_dir_include.patch
new file mode 100644
index 000000000..6d0f6046a
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-libxc_dir_include.patch
@@ -0,0 +1,50 @@
+--- configure.ac.orig	2011-11-23 14:02:15.000000000 +0000
++++ configure.ac	2011-11-23 14:09:19.000000000 +0000
+@@ -551,14 +551,17 @@
+ ac_build_libxc="no"
+ AC_ARG_ENABLE(libxc, AS_HELP_STRING([--disable-libxc], [Do not link with libXC library (default = yes).]), ac_use_libxc=$enableval, ac_use_libxc="yes")
+ AC_ARG_ENABLE(internal-libxc, AS_HELP_STRING([--disable-internal-libxc], [Do not build and link with internal libXC library (default = yes).]), ac_internal_libxc=$enableval, ac_internal_libxc="yes")
+-AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib and module files (default = None).]),
++AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib files (default = None).]),
+             ac_libxc_dir=$withval, ac_libxc_dir=)
++AC_ARG_WITH(libxc-include, AS_HELP_STRING([--with-libxc-include], [Give the path for an external libXC library module files (default = None).]),
++            ac_libxc_dir_include=$withval, ac_libxc_dir_include=)
+ if test x"$ac_use_libxc" = x"yes" ; then
+   ac_build_libxc=$ac_internal_libxc
+   if test "$ac_internal_libxc" = "yes" ; then
+     ac_build_libxc="yes"
+     ac_use_libxc="yes"
+     ac_libxc_dir="$top_builddir"/libxc-1.1.0/src
++    ac_libxc_dir_include="$ac_libxc_dir"/include
+     AC_SUBST(LIBXC_DIR, "\$(top_builddir)"/libxc-1.1.0/src)
+     AC_SUBST(LIBXC_INCLUDE, "-I\$(top_builddir)"/libxc-1.1.0/src)
+     LDFLAGS="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs"
+@@ -566,6 +569,9 @@
+   else
+     if test -n "$ac_libxc_dir" ; then
+       LDFLAGS="$LDFLAGS -L$ac_libxc_dir/lib"
++      if test x"$ac_libxc_dir_include" = x ; then
++        ac_libxc_dir_include="$ac_libxc_dir"/include
++      fi
+       
+       dnl Test the given implementation of libXC.
+       ac_libxc_libname="xc"
+@@ -574,13 +580,13 @@
+         ac_libxc_libname="dft_xc"
+         AC_CHECK_LIB($ac_libxc_libname, xc_f90_lda_vxc, withlibxc=yes, withlibxc=no)
+       fi
+-      AC_CHECK_FILE($ac_libxc_dir/include/libxc_funcs_m.$capitalize_module_ext, funcs="yes", funcs="no")
+-      AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no")
+-      AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no")
++      AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$capitalize_module_ext, funcs="yes", funcs="no")
++      AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no")
++      AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no")
+       if test "$withlibxc" = "yes" -a "$funcs" = "yes" -a "$lib" = "yes" -a "$types" = "yes"; then
+         ac_use_libxc="yes"
+-        AC_SUBST(LIBXC_DIR, $ac_libxc_dir/include)
+-        AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir/include)
++        AC_SUBST(LIBXC_DIR, $ac_libxc_dir_include)
++        AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir_include)
+         LIBXC_LIBS="-l"$ac_libxc_libname
+       fi
+     else
diff --git a/sci-libs/bigdft/files/bigdft-1.6.0-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.6.0-libxc_dir_include.patch
new file mode 100644
index 000000000..7179fcb0f
--- /dev/null
+++ b/sci-libs/bigdft/files/bigdft-1.6.0-libxc_dir_include.patch
@@ -0,0 +1,50 @@
+--- configure.ac.orig	2011-11-23 14:02:15.000000000 +0000
++++ configure.ac	2011-11-23 14:09:19.000000000 +0000
+@@ -604,14 +604,17 @@
+ ac_build_libxc="no"
+ AC_ARG_WITH(libxc, AS_HELP_STRING([--without-libxc], [Do not link with libXC library (default = yes).]), ac_use_libxc=$enableval, ac_use_libxc="yes")
+ AC_ARG_ENABLE(internal-libxc, AS_HELP_STRING([--disable-internal-libxc], [Do not build and link with internal libXC library (default = yes).]), ac_internal_libxc=$enableval, ac_internal_libxc="yes")
+-AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib and module files (default = None).]),
++AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib files (default = None).]),
+             ac_libxc_dir=$withval, ac_libxc_dir=)
++AC_ARG_WITH(libxc-include, AS_HELP_STRING([--with-libxc-include], [Give the path for an external libXC library module files (default = None).]),
++            ac_libxc_dir_include=$withval, ac_libxc_dir_include=)
+ if test x"$ac_use_libxc" = x"yes" ; then
+   ac_build_libxc=$ac_internal_libxc
+   if test "$ac_internal_libxc" = "yes" ; then
+     ac_build_libxc="yes"
+     ac_use_libxc="yes"
+     ac_libxc_dir="$top_builddir"/libxc-1.1.0/src
++    ac_libxc_dir_include="$ac_libxc_dir"/include
+     AC_SUBST(LIBXC_DIR, "\$(top_builddir)"/libxc-1.1.0/src)
+     AC_SUBST(LIBXC_INCLUDE, "-I\$(top_builddir)"/libxc-1.1.0/src)
+     LDFLAGS="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs"
+@@ -619,6 +622,9 @@
+   else
+     if test -n "$ac_libxc_dir" ; then
+       LDFLAGS="$LDFLAGS -L$ac_libxc_dir/lib"
++      if test x"$ac_libxc_dir_include" = x ; then
++        ac_libxc_dir_include="$ac_libxc_dir"/include
++      fi
+       
+       dnl Test the given implementation of libXC.
+       ac_libxc_libname="xc"
+@@ -587,13 +593,13 @@
+         ac_libxc_libname="dft_xc"
+         AC_CHECK_LIB($ac_libxc_libname, xc_f90_lda_vxc, withlibxc=yes, withlibxc=no)
+       fi
+-      AC_CHECK_FILE($ac_libxc_dir/include/libxc_funcs_m.$ax_fc_mod_ext, funcs="yes", funcs="no")
+-      AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$ax_fc_mod_ext, lib="yes", lib="no")
+-      AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$ax_fc_mod_ext, types="yes", types="no")
++      AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$ax_fc_mod_ext, funcs="yes", funcs="no")
++      AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$ax_fc_mod_ext, lib="yes", lib="no")
++      AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$ax_fc_mod_ext, types="yes", types="no")
+       if test "$withlibxc" = "yes" -a "$funcs" = "yes" -a "$lib" = "yes" -a "$types" = "yes"; then
+         ac_use_libxc="yes"
+-        AC_SUBST(LIBXC_DIR, $ac_libxc_dir/include)
+-        AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir/include)
++        AC_SUBST(LIBXC_DIR, $ac_libxc_dir_include)
++        AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir_include)
+         LIBXC_LIBS="-l"$ac_libxc_libname
+       fi
+     else
diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index b6b882218..2a5c1ee69 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -1,7 +1,20 @@
 # ChangeLog for sci-physics/abinit
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*abinit-6.12.1 (22 Mar 2012)
+
+  22 Mar 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
+  +files/6.12.1-autoconf.patch, -abinit-6.10.1.ebuild,
+  +files/6.12.1-gui-conf.patch, +abinit-6.12.1.ebuild,
+  +files/6.12.1-libabinit_options.patch, +files/6.12.1-xmalloc.patch,
+  +files/6.12.1-bigDFT-1.6.0.patch, metadata.xml:
+  6.12.1 added, moved towards autotools-utils. Uses sci-libs/bigdft-1.6_pre1,
+  patching to use the latest 1.6.0 still not done. Libraries installed,
+  pkg-config file corrected; libabinit made an option, but for now would
+  conflict with sci-libs/bigdft. TO DO: Make sci-libs/bigdft compile against
+  libabinit of sci-physics/abinit, solve the resulting circular dependency.
+
 *abinit-6.10.3 (14 Dec 2011)
 
   14 Dec 2011; Honza Macháček <Hloupy.Honza@centrum.cz> -abinit-6.8.1.ebuild,
diff --git a/sci-physics/abinit/Manifest b/sci-physics/abinit/Manifest
index 412fab010..e35fffeac 100644
--- a/sci-physics/abinit/Manifest
+++ b/sci-physics/abinit/Manifest
@@ -1,4 +1,4 @@
-DIST abinit-6.10.1.tar.gz 44363678 RMD160 44d4aaeb58fdbc81f376025dbf4c13af91e6aa4d SHA1 2fb55ab80b1a90756dd664086c3263636716ef82 SHA256 a28c76829d4230937c3a4e670cebeaf3b8e3989a532c189dddabdafe26da8c8a
-DIST abinit-6.10.3.tar.gz 69158203 RMD160 5b9c9fea3d488aa5f819037e8ae0acc0a19512ef SHA1 d47b72e226d722eed3eadb30890ad534617328e3 SHA256 185c45c7c9caf5f735d841fa85b2dfc612eee81b76f905a9988b5f0994be6fb5
-DIST abinit-6.6.3.tar.gz 41161321 RMD160 f9169812cfb2dc30f752bf0ab0ffc41250ea0bbb SHA1 02c9fd6abe1b73164b804b6e0b1f829ec9fd286e SHA256 fad84d3e774e3b4ba16f2a2924e60b8ba42ab21fefd89d8ce4848f9a9e03f774
-DIST abinit-6.8.2.tar.gz 43565001 RMD160 151fcd3fa3c8aad204aa01a0877b101b7faf0550 SHA1 2b96bb175e1946c48ee3a72064b08ccc1b8dbdea SHA256 7a0e8ebfce50ae18e5c4f25f9bfd534623a41985082efead918a3878464a181c
+DIST abinit-6.10.3.tar.gz 69158203 SHA256 185c45c7c9caf5f735d841fa85b2dfc612eee81b76f905a9988b5f0994be6fb5 SHA512 010fee8f0740cc05208f1abe52f5aae25077d5792331a98466ecc13f27605776e19a17bdeab2c7cf09eb233109ae7f14d55afecd89113a91a0d67494f2c5abb2 WHIRLPOOL be7f127116a6f59ea4cbd84f01e3371b5959275bae0957e654eea9dadeef278ad0081f8600476e716865ef32b5aea536ccb09f12f5934f95aaf8eeccb06bc5d6
+DIST abinit-6.12.1.tar.gz 58474634 SHA256 1b0f0fe5a6f8ce97b3da7ea7640f16c36902c7a5bc08651abd139eb7e13222b6 SHA512 59d757400539d0eb385fd37c9a6e2824bd3a2a6378a6c8f39a2f336cf3f842120538a014633561a5c16b9debf4ec054d51beaec2952629e0a88ab283dc2db431 WHIRLPOOL 9c02b1184fabe96405fe05ecd9c40d48f104d92d55ed2900dc3755758aca12cb4dd64e6fea3e3f949bcbb8a615ecd359a76bc9752969e585189865cd75c14c1d
+DIST abinit-6.6.3.tar.gz 41161321 SHA256 fad84d3e774e3b4ba16f2a2924e60b8ba42ab21fefd89d8ce4848f9a9e03f774 SHA512 834bd017a81444a75335d13579c37efe1d58b571a0b2a673f8dfb60342cd10fb849e6a2e92042be59445835e1ad3a484149faa260280e4e6db9b284ed03c208a WHIRLPOOL 302cf85a65e4c07ee716379844d1435503ee042fb987f3c43e5fc4e60ffe32ec0498f8d31dcc7a61043bfcedf56b87eadca11657156fb6d912f6c4627aa60bbf
+DIST abinit-6.8.2.tar.gz 43565001 SHA256 7a0e8ebfce50ae18e5c4f25f9bfd534623a41985082efead918a3878464a181c SHA512 97287a7527f1088435c95697b90a27eaf6cb5b8921e2d4e702279552f9d8669735242d5bfa62b944a7da418286a317131c352952ac0fac58540de4e8ded56385 WHIRLPOOL 27b11310695179e2a8794dbb7b0a3e041477cf9bec1ddc3468f6c54e3549806cef66c348dbb34839d3dfb0633191b5a9531f4e415d2c0a1d776ddf9dddff3756
diff --git a/sci-physics/abinit/abinit-6.10.1.ebuild b/sci-physics/abinit/abinit-6.10.1.ebuild
deleted file mode 100644
index cdd495fd1..000000000
--- a/sci-physics/abinit/abinit-6.10.1.ebuild
+++ /dev/null
@@ -1,211 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="3"
-
-inherit autotools eutils fortran-2 multilib toolchain-funcs
-
-DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory"
-HOMEPAGE="http://www.abinit.org/"
-SRC_URI="http://ftp.abinit.org/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cuda -debug +fftw +fftw-threads +fox gsl +hdf5 mpi +netcdf python -test +threads -vdwxc"
-
-RDEPEND=">=sci-libs/bigdft-1.2.0.2
-	sci-libs/etsf_io
-	=sci-libs/libxc-1.0[fortran]
-	sci-physics/atompaw[libxc]
-	fox? ( sci-libs/fox[dom,sax,wcml,wxml] )
-	netcdf? (
-		sci-libs/netcdf[fortran]
-		hdf5? (
-		      sci-libs/netcdf[fortran,hdf5]
-		      )
-		)
-	hdf5? ( sci-libs/hdf5[fortran] )
-	sci-libs/wannier90
-	virtual/blas
-	virtual/lapack
-	gsl? ( sci-libs/gsl )
-	fftw? (
-		sci-libs/fftw:3.0
-		fftw-threads? ( sci-libs/fftw:3.0[threads] )
-		)
-	mpi? ( virtual/mpi )
-	python? ( dev-python/numpy )
-	cuda? ( dev-util/nvidia-cuda-sdk )"
-DEPEND="${RDEPEND}
-	dev-util/pkgconfig
-	dev-perl/Text-Markdown"
-
-S=${WORKDIR}/${P%[a-z]}
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	# Doesn't compile with gcc-4.0, only >=4.1
-	if [[ $(tc-getFC) == *gfortran ]]; then
-		if [[ $(gcc-major-version) -eq 4 ]] \
-			&& [[ $(gcc-minor-version) -lt 1  ]]; then
-				die "Requires gcc-4.1 or newer"
-		fi
-	fi
-	if use fftw-threads && ! use fftw; then
-		ewarn "fftw-threads set but fftw not used, ignored"
-	fi
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/6.2.2-change-default-directories.patch
-	epatch "${FILESDIR}"/6.0.3-fftw.patch
-	eautoreconf
-}
-
-src_configure() {
-	local libs="-L/usr/$(get_libdir)"
-	local modules="-I/usr/$(get_libdir)/finclude"
-	local FoX_libs="${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys"
-	local trio_flavor="etsf_io"
-	use fox && trio_flavor="${trio_flavor}+fox"
-	use netcdf && trio_flavor="${trio_flavor}+netcdf"
-	local netcdff_libs="-lnetcdff"
-	use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran"
-	local fft_flavor="fftw3"
-	local fft_libs="-L/usr/lib"
-	# The fftw threads support is protected by black magick.
-	# Anybody removes it, dies.
-	# New USE flag "fftw-threads" was added to control usage
-	# of the threaded fftw variant. Since fftw-3.3 has expanded
-	# the paralel options by MPI and OpenMP support, analogical
-	# USE flags should be added to select them in future;
-	# unusable with previous FFTW versions, they are postponed
-	# for now.
-	if use fftw-threads; then
-		fft_flavor="fftw3-threads"
-		if has_version '>=sci-libs/fftw-3.3'; then
-			# pkg-config files for fftw-3.3 are broken
-			# All the parallel stuff is separated
-			# from the main body of common routines,
-			# and -lfftw3 must be always included alongside.
-			# Until version 3.3 this used to be masked by
-			# .la files.
-			# Bug 384645
-			fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads) $(pkg-config --libs fftw3)"
-		else
-			fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads)"
-		fi
-	else
-		fft_libs="${fft_libs} $(pkg-config --libs fftw3)"
-	fi
-	if use mpi; then
-		MY_FC="mpif90"
-		MY_CC="mpicc"
-		MY_CXX="mpic++"
-	else
-		MY_FC="$(tc-getFC)"
-		MY_CC="$(tc-getCC)"
-		MY_CXX="$(tc-getCXX)"
-	fi
-	MARKDOWN=Markdown.pl econf \
-		$(use_enable debug debug enhanced) \
-		$(use_enable mpi) \
-		$(use_enable mpi mpi-io) \
-		--disable-smp \
-		$(use_enable vdwxc) \
-		$(use_enable cuda gpu) \
-		"$(use cuda && echo "--with-gpu-flavor=cuda-single")" \
-		"$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")" \
-		"$(use gsl && echo "--with-math-flavor=gsl")" \
-		"$(use gsl && echo "--with-math-incs=$(pkg-config --cflags gsl)")" \
-		"$(use gsl && echo "--with-math-libs=$(pkg-config --libs gsl)")" \
-		--with-linalg-flavor="atlas" \
-		--with-linalg-libs="$(pkg-config --libs lapack)" \
-		--with-trio-flavor="${trio_flavor}" \
-		"$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")" \
-		"$(use netcdf && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")" \
-		"$(use fox && echo "--with-fox-incs=${modules}")" \
-		"$(use fox && echo "--with-fox-libs=${FoX_libs}")" \
-		--with-etsf-io-incs="${modules}" \
-		--with-etsf-io-libs="${libs} -letsf_io -letsf_io_utils -letsf_io_low_level" \
-		--with-dft-flavor="libxc+bigdft+atompaw+wannier90" \
-		--with-libxc-incs="${modules}" \
-		--with-libxc-libs="${libs} -lxc" \
-		--with-bigdft-incs="${modules}" \
-		--with-bigdft-libs="${libs} -lpoissonsolver -lbigdft" \
-		--with-atompaw-incs="${modules}" \
-		--with-atompaw-libs="${libs} -latompaw" \
-		--with-wannier90-bins="/usr/bin" \
-		--with-wannier90-incs="${modules}" \
-		--with-wannier90-libs="${libs} -lwannier $(pkg-config --libs lapack)" \
-		"$(use fftw && echo "--with-fft-flavor=${fft_flavor}")" \
-		"$(use fftw && echo "--with-fft-incs=-I/usr/include")" \
-		"$(use fftw && echo "--with-fft-libs=${fft_libs}")" \
-		--with-timer-flavor="abinit" \
-		FC="${MY_FC}" \
-		CC="${MY_CC}" \
-		CXX="${MY_CXX}" \
-		LD="$(tc-getLD)" \
-		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include"
-}
-
-src_compile() {
-	emake || die
-}
-
-src_test() {
-	einfo "The tests take quite a while, on the order of 1-2 hours"
-	einfo "on an Intel Penryn (2.5 GHz)."
-	cd "${S}"/tests
-	emake tests_min || ewarn "Minimal tests failed"
-	emake tests_paw || ewarn "PAW tests failed"
-	emake tests_gw || ewarn "GW tests failed"
-	emake tests_gw_paw || ewarn "GW-PAW tests failed"
-	emake tests tdft || ewarn "TDFT tests failed"
-	emake tests_bench || ewarn "Benchmarks failed"
-
-	local REPORT
-	for REPORT in $(find . -name report); do
-		REPORT=${REPORT#*/}
-		elog "Parameters and unusual results for ${REPORT%%/*} tests"
-		echo "Parameters and unusual results for ${REPORT%%/*} tests" >>tests_summary.txt
-		while read line; do
-			elog "${line}"
-			echo "${line}" >>tests_summary.txt
-		done \
-			< <(grep -v -e succeeded -e passed ${REPORT})
-	done
-
-	local testdir
-	find . -name "tmp-test*" -print | \
-		while read testdir; do
-			if [ -e summary_of_tests.tar ]; then
-				tar rvf summary_of_tests.tar ${testdir}
-			else tar cvf summary_of_tests.tar ${testdir}
-			fi
-		done
-
-	elog "The full test results will be installed as summary_of_tests.tar.bz2."
-	elog "Also a concise report tests_summary.txt is installed."
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die "make install failed"
-
-	if use test; then
-		dodoc tests/tests_summary.txt || ewarn "Copying tests summary failed"
-		dodoc tests/summary_tests.tar || ewarn "Copying tests results failed"
-		dodoc tests/summary_of_tests.tar || ewarn "Copying tests results failed"
-	fi
-
-	dodoc KNOWN_PROBLEMS README || die "Copying doc files failed"
-}
-
-pkg_postinst() {
-	if use test; then
-		elog "The full test results will be installed as summary_tests.tar.bz2."
-		elog "Also a concise report tests_summary.txt is installed."
-	fi
-}
diff --git a/sci-physics/abinit/abinit-6.12.1.ebuild b/sci-physics/abinit/abinit-6.12.1.ebuild
new file mode 100644
index 000000000..00e1fa2fb
--- /dev/null
+++ b/sci-physics/abinit/abinit-6.12.1.ebuild
@@ -0,0 +1,334 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="4"
+
+inherit autotools-utils fortran-2 multilib toolchain-funcs
+
+DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory"
+HOMEPAGE="http://www.abinit.org/"
+SRC_URI="http://ftp.abinit.org/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl gui +hdf5 libabinit mpi +netcdf python -test +threads -vdwxc"
+
+RDEPEND="=sci-libs/bigdft-1.6_pre1
+	sci-libs/etsf_io
+	=sci-libs/libxc-1*[fortran]
+	sci-physics/atompaw[libxc]
+	etsf_io? ( sci-libs/etsf_io )
+	fox? ( sci-libs/fox[dom,sax,wcml,wxml] )
+	netcdf? (
+		sci-libs/netcdf[fortran]
+		hdf5? (
+			  sci-libs/netcdf[fortran,hdf5]
+			  )
+		)
+	hdf5? ( sci-libs/hdf5[fortran] )
+	sci-libs/wannier90
+	virtual/blas
+	virtual/lapack
+	gsl? ( sci-libs/gsl )
+	fftw? (
+		sci-libs/fftw:3.0
+		fftw-threads? ( sci-libs/fftw:3.0[threads] )
+		)
+	mpi? ( virtual/mpi )
+	python? ( dev-python/numpy )
+	cuda? ( dev-util/nvidia-cuda-sdk )"
+DEPEND="${RDEPEND}
+	dev-util/pkgconfig
+	gui? ( >=virtual/jdk-1.6.0
+		app-arch/sharutils
+		sys-apps/gawk )
+	dev-perl/Text-Markdown"
+
+S=${WORKDIR}/${P%[a-z]}
+
+lat1loc=""
+
+DOCS=( AUTHORS ChangeLog COPYING INSTALL KNOWN_PROBLEMS NEWS PACKAGING
+	README README.ChangeLog README.GPU README.xlf RELNOTES THANKS )
+
+FORTRAN_STANDARD=90
+
+pkg_setup() {
+	# fortran-2.eclass does not handle mpi wrappers
+	if use mpi; then
+		export FC="mpif90"
+		export F77="mpif77"
+		export CC="mpicc"
+		export CXX="mpic++"
+	else
+		tc-export FC F77 CC CXX
+	fi
+	fortran-2_pkg_setup
+
+	# Doesn't compile with gcc-4.0, only >=4.1
+	if [[ $(tc-getFC) == *gfortran ]]; then
+		if [[ $(gcc-major-version) -eq 4 ]] \
+			&& [[ $(gcc-minor-version) -lt 1  ]]; then
+				die "Requires gcc-4.1 or newer"
+		fi
+	fi
+
+	# Sort out some USE options
+	if use fftw-threads && ! use fftw; then
+		ewarn "fftw-threads set but fftw not used, ignored"
+	fi
+	if use cuda-double && ! use cuda; then
+		ewarn "cuda-double set but cuda not used, ignored"
+	fi
+	if use gui; then
+		lat1loc="$(locale |awk '/LC_CTYPE="(.*)"/{sub("LC_CTYPE=\"",""); sub("\" *$", ""); print}')"
+		if locale charmap |grep -i "\<iso885915\?\>"; then
+			einfo "Good, locale compatible with the GUI build"
+		else
+			ewarn "The locale ${lat1loc} incompatible with the GUI build"
+			if latloc=`locale -a| grep -i "\<iso885915\?\>"`; then
+				if echo "${latloc}" |grep -q "^fr"; then
+					lat1loc="$(echo "${latloc}" | grep -im1 "^fr")"
+				else
+					lat1loc="$(echo "${latloc}" | grep -im1 "iso88591")"
+				fi
+				einfo "Will use ${lat1loc} to build the GUI"
+			else
+				ewarn "No ISO-8859-1 nor ISO-8859-15 locale available, the GUI build may crash"
+			fi
+		fi
+	fi
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/6.2.2-change-default-directories.patch
+	epatch "${FILESDIR}"/6.0.3-fftw.patch
+	epatch "${FILESDIR}"/6.12.1-autoconf.patch
+	epatch "${FILESDIR}"/6.12.1-xmalloc.patch
+	epatch "${FILESDIR}"/6.12.1-libabinit_options.patch
+	eautoreconf
+
+	if use gui; then
+		epatch "${FILESDIR}"/6.12.1-gui-conf.patch
+#		pushd "${S}"/gui
+		pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+		"${S}"/gui/autogen.sh
+		popd
+	fi
+}
+
+src_configure() {
+	local libs="-L/usr/$(get_libdir)"
+	local modules="-I/usr/$(get_libdir)/finclude"
+	local FoX_libs="${libs} -lFoX_dom -lFoX_sax -lFoX_wcml -lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys"
+	local trio_flavor=""
+	use etsf_io && trio_flavor="${trio_flavor}+etsf_io"
+	use fox && trio_flavor="${trio_flavor}+fox"
+	use netcdf && trio_flavor="${trio_flavor}+netcdf"
+	test "no${trio_flavor}" = "no" && trio_flavor="none"
+	local netcdff_libs="-lnetcdff"
+	use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran"
+	local fft_flavor="fftw3"
+	local fft_libs="-L/usr/lib"
+	# The fftw threads support is protected by black magick.
+	# Anybody removes it, dies.
+	# New USE flag "fftw-threads" was added to control usage
+	# of the threaded fftw variant. Since fftw-3.3 has expanded
+	# the paralel options by MPI and OpenMP support, analogical
+	# USE flags should be added to select them in future;
+	# unusable with previous FFTW versions, they are postponed
+	# for now.
+	if use fftw-threads; then
+		fft_flavor="fftw3-threads"
+		if has_version '>=sci-libs/fftw-3.3'; then
+			# pkg-config files for fftw-3.3 are broken
+			# All the parallel stuff is separated
+			# from the main body of common routines,
+			# and -lfftw3 must be always included alongside.
+			# Until version 3.3 this used to be masked by
+			# .la files.
+			# Bug 384645
+			fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads) $(pkg-config --libs fftw3)"
+		else
+			fft_libs="${fft_libs} $(pkg-config --libs fftw3_threads)"
+		fi
+	else
+		fft_libs="${fft_libs} $(pkg-config --libs fftw3)"
+	fi
+	local gpu_flavor="none"
+	if use cuda; then
+		gpu_flavor="cuda-single"
+		if use cuda-double; then
+			gpu_flavor="cuda-double"
+		fi
+	fi
+
+	local myeconfargs=(
+		--enable-clib
+		--enable-exports
+		$(use_enable gui)
+		$(use_enable debug debug enhanced)
+		$(use_enable mpi)
+		$(use_enable mpi mpi-io)
+		--disable-smp
+		$(use_enable vdwxc)
+		$(use_enable cuda gpu)
+		"$(use cuda && echo "--with-gpu-flavor=${gpu_flavor}")"
+		"$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")"
+		"$(use gsl && echo "--with-math-flavor=gsl")"
+		"$(use gsl && echo "--with-math-incs=$(pkg-config --cflags gsl)")"
+		"$(use gsl && echo "--with-math-libs=$(pkg-config --libs gsl)")"
+		--with-linalg-flavor="atlas"
+		--with-linalg-libs="$(pkg-config --libs lapack)"
+		--with-trio-flavor="${trio_flavor}"
+		"$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")"
+		"$(use netcdf && echo "--with-netcdf-libs=$(pkg-config --libs netcdf) ${netcdff_libs}")"
+		"$(use fox && echo "--with-fox-incs=${modules}")"
+		"$(use fox && echo "--with-fox-libs=${FoX_libs}")"
+		"$(use etsf_io && echo "--with-etsf-io-incs=${modules}")"
+		"$(use etsf_io && echo "--with-etsf-io-libs=${libs} -letsf_io -letsf_io_utils -letsf_io_low_level")"
+		--with-dft-flavor="libxc+bigdft+atompaw+wannier90"
+		--with-libxc-incs="${modules}"
+		--with-libxc-libs="${libs} -lxc"
+		--with-bigdft-incs="${modules}"
+		--with-bigdft-libs="$(pkg-config --libs bigdft)"
+		--with-atompaw-incs="${modules}"
+		--with-atompaw-libs="${libs} -latompaw"
+		--with-wannier90-bins="/usr/bin"
+		--with-wannier90-incs="${modules}"
+		--with-wannier90-libs="${libs} -lwannier $(pkg-config --libs lapack)"
+		"$(use fftw && echo "--with-fft-flavor=${fft_flavor}")"
+		"$(use fftw && echo "--with-fft-incs=-I/usr/include")"
+		"$(use fftw && echo "--with-fft-libs=${fft_libs}")"
+		--with-timer-flavor="abinit"
+		LD="$(tc-getLD)"
+		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include"
+		)
+
+	MARKDOWN=Markdown.pl autotools-utils_src_configure
+
+	if use gui; then
+		# autotools-utils_src_configure() part expanded
+		_check_build_dir
+		pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+		mkdir -p gui
+		cd gui
+		ECONF_SOURCE="${S}"/gui econf
+	fi
+}
+
+src_compile() {
+	autotools-utils_src_compile
+
+	# Apparently libabinit.a is not built by default
+	# Used by BigDFT. Should probably be built separately,
+	# as a package of its own: BigDFT used by Abinit.
+	# Does libabinit.a depend on BigDFT, if used?
+	# Can Abinit use external libabinit.a?
+	use libabinit && autotools-utils_src_compile libabinit.a
+
+	if use gui; then
+		#autotools-utils_src_compile() expanded
+		# _check_build_dir has already been called
+		pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+		# now what the function cannot be called to do
+		cd gui
+		LC_CTYPE="${lat1loc}" emake || die "Making GUI failed"
+		popd > /dev/null
+	fi
+
+	sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc
+}
+
+src_test() {
+	einfo "The tests take quite a while, easily several hours"
+	# autotools-utils_src_test() expanded
+	_check_build_dir
+	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+	# again something the autotools-utils function cannot be called to do
+	# now quite a lot of work actually
+	cd tests
+	emake tests_min || ewarn "Minimal tests failed"
+	emake tests_paw || ewarn "PAW tests failed"
+	emake tests_gw || ewarn "GW tests failed"
+	emake tests_gw_paw || ewarn "GW-PAW tests failed"
+	emake tests tdft || ewarn "TDFT tests failed"
+	emake tests_bench || ewarn "Benchmarks failed"
+
+	local REPORT
+	for REPORT in $(find . -name report); do
+		REPORT=${REPORT#*/}
+		elog "Parameters and unusual results for ${REPORT%%/*} tests"
+		echo "Parameters and unusual results for ${REPORT%%/*} tests" >>tests_summary.txt
+		while read line; do
+			elog "${line}"
+			echo "${line}" >>tests_summary.txt
+		done \
+			< <(grep -v -e succeeded -e passed ${REPORT})
+	done
+
+	local testdir
+	find . -name "tmp-test*" -print | \
+		while read testdir; do
+			if [ -e summary_of_tests.tar ]; then
+				tar rvf summary_of_tests.tar ${testdir}
+			else tar cvf summary_of_tests.tar ${testdir}
+			fi
+		done
+	popd > /dev/null
+
+	elog "The full test results will be installed as summary_of_tests.tar.bz2."
+	elog "Also a concise report tests_summary.txt is installed."
+}
+
+src_install() {
+	#autotools-utils_src_install() expanded
+	_check_build_dir
+	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+	emake DESTDIR="${D}" install || die "make install failed"
+
+	use libabinit && dolib libabinit.a
+
+	if use gui; then
+		pushd gui
+		emake DESTDIR="${D}" install || die "The GUI install failed"
+		popd
+	fi
+
+	if use test; then
+		for dc in tests_summary.txt summary_tests.tar summary_of_tests.tar; do
+			test -e tests/"${dc}" && dodoc tests/"${dc}" || ewarn "Copying tests results failed"
+		done
+	fi
+
+	popd > /dev/null
+
+	# XXX: support installing them from builddir as well!!!
+	if [[ ${DOCS} ]]; then
+		dodoc "${DOCS[@]}" || die "dodoc failed"
+	else
+		local f
+		# same list as in PMS
+		for f in README* ChangeLog AUTHORS NEWS TODO CHANGES \
+				THANKS BUGS FAQ CREDITS CHANGELOG; do
+			if [[ -s ${f} ]]; then
+				dodoc "${f}" || die "(default) dodoc ${f} failed"
+			fi
+		done
+	fi
+	if [[ ${HTML_DOCS} ]]; then
+		dohtml -r "${HTML_DOCS[@]}" || die "dohtml failed"
+	fi
+
+	# Remove libtool files and unnecessary static libs
+	remove_libtool_files
+}
+
+pkg_postinst() {
+	if use test; then
+		elog "The full test results will be installed as summary_tests.tar.bz2."
+		elog "Also a concise report tests_summary.txt is installed."
+	fi
+}
diff --git a/sci-physics/abinit/files/6.12.1-autoconf.patch b/sci-physics/abinit/files/6.12.1-autoconf.patch
new file mode 100644
index 000000000..7e0169f63
--- /dev/null
+++ b/sci-physics/abinit/files/6.12.1-autoconf.patch
@@ -0,0 +1,21 @@
+diff -Naur old/fallbacks/configure.ac new/fallbacks/configure.ac
+--- old/fallbacks/configure.ac	2012-01-30 19:40:41.000000000 +0000
++++ new/fallbacks/configure.ac	2012-02-13 08:16:08.000000000 +0000
+@@ -114,6 +114,17 @@
+ 
+ # ---------------------------------------------------------------------------- #
+ 
++AM_CONDITIONAL([DO_BUILD_FOX],[test "${enable_fox}" = "yes"])
++AM_CONDITIONAL([DO_BUILD_LIBXC],[test "${enable_libxc}" = "yes"])
++AM_CONDITIONAL([DO_BUILD_LINALG],[test "${enable_linalg}" = "yes"])
++AM_CONDITIONAL([DO_BUILD_NETCDF],[test "${enable_netcdf}" = "yes"])
++AM_CONDITIONAL([DO_BUILD_ETSF_IO],[test "${enable_etsf_io}" = "yes"])
++AM_CONDITIONAL([DO_BUILD_ATOMPAW],[test "${enable_atompaw}" = "yes"])
++AM_CONDITIONAL([DO_BUILD_WANNIER90],[test "${enable_wannier90}" = "yes"])
++AM_CONDITIONAL([DO_BUILD_BIGDFT],[test "${enable_bigdft}" = "yes"])
++
++# ---------------------------------------------------------------------------- #
++
+ #
+ # Downloading support
+ #
diff --git a/sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch b/sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch
new file mode 100644
index 000000000..857a27abc
--- /dev/null
+++ b/sci-physics/abinit/files/6.12.1-bigDFT-1.6.0.patch
@@ -0,0 +1,61 @@
+diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_descr_psp_set.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_descr_psp_set.F90
+--- src/42_wvl_wrappers/wvl_descr_psp_set.F90	2012-01-30 20:43:51.000000000 +0000
++++ src/42_wvl_wrappers/wvl_descr_psp_set.F90	2012-03-19 13:06:59.000000000 +0000
+@@ -105,7 +105,7 @@
+  ! Missing currently read radii_cf.
+  wvl%atoms%donlcc = .false.
+  ! TODO: add symmetry support
+- wvl%atoms%symObj = -1
++ wvl%atoms%sym%symObj = -1
+ #endif  
+ end subroutine wvl_descr_psp_set
+ !!***
+diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_projectors_set.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_projectors_set.F90
+--- src/42_wvl_wrappers/wvl_projectors_set.F90	2012-01-30 20:43:50.000000000 +0000
++++ src/42_wvl_wrappers/wvl_projectors_set.F90	2012-03-19 13:17:37.000000000 +0000
+@@ -122,7 +122,7 @@
+  ABI_ALLOCATE(xcart,(3, natom))
+  call xredxcart(natom, 1, rprimd, xcart, xred)
+ 
+- call createProjectorsArrays(me, wfs%Glr%d%n1, wfs%Glr%d%n2, wfs%Glr%d%n3, &
++ call createProjectorsArrays(me, wfs%Glr, &
+       & xcart, wvl%atoms, wfs%orbs, psps%gth_params%radii_cf, &
+       & wvl_frmult, wvl_frmult, wvl%h(1), wvl%h(2), wvl%h(3), proj%keys, proj%proj)
+  write(message, '(a,a,a,a,I0)' ) ch10,&
+diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_wfs_free.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_wfs_free.F90
+--- src/42_wvl_wrappers/wvl_wfs_free.F90	2012-01-30 20:43:50.000000000 +0000
++++ src/42_wvl_wrappers/wvl_wfs_free.F90	2012-03-19 13:01:03.000000000 +0000
+@@ -68,7 +68,7 @@
+ #if defined HAVE_DFT_BIGDFT
+   call deallocate_lr(wfs%Glr, sub)
+   call deallocate_orbs(wfs%orbs, sub)
+-  call deallocate_diis_objects(wfs%diis, sub)
++  ! call deallocate_diis_objects(wfs%diis, sub)
+   call deallocate_comms(wfs%comms, sub)
+   if (associated(wfs%orbs%eval))  then
+     ABI_DEALLOCATE(wfs%orbs%eval)
+diff -Naur abinit-6.12.1_orig/src/42_wvl_wrappers/wvl_wfs_set.F90 abinit-6.12.1/src/42_wvl_wrappers/wvl_wfs_set.F90
+--- src/42_wvl_wrappers/wvl_wfs_set.F90	2012-01-30 20:43:55.000000000 +0000
++++ src/42_wvl_wrappers/wvl_wfs_set.F90	2012-03-19 12:58:54.000000000 +0000
+@@ -59,7 +59,7 @@
+  use defs_wvltypes
+ #if defined HAVE_DFT_BIGDFT
+   use BigDFT_API, only: createWavefunctionsDescriptors, orbitals_descriptors, &
+-       & orbitals_communicators, allocate_diis_objects, wvl_timing => timing
++       & orbitals_communicators, wvl_timing => timing
+ #endif
+ 
+ !This section has been created automatically by the script Abilint (TD).
+@@ -179,9 +179,9 @@
+  call wvl_timing(me,'CrtDescriptors','OF')
+ 
+  ! allocate arrays necessary for DIIS convergence acceleration
+- call allocate_diis_objects(nwfshist,1._dp,&
+-      & sum(wfs%comms%ncntt(0:nproc-1)), wfs%orbs%nkptsp, wfs%orbs%nspinor, &
+-      & wfs%orbs%norbd, wfs%diis, "wvl_init_wfs_type")
++ ! call allocate_diis_objects(nwfshist,1._dp,&
++ !      & sum(wfs%comms%ncntt(0:nproc-1)), wfs%orbs%nkptsp, wfs%orbs%nspinor, &
++ !      & wfs%orbs%norbd, wfs%diis, "wvl_init_wfs_type")
+ 
+ #else
+  write(message, '(a,a,a,a)' ) ch10,&
diff --git a/sci-physics/abinit/files/6.12.1-gui-conf.patch b/sci-physics/abinit/files/6.12.1-gui-conf.patch
new file mode 100644
index 000000000..95c12b354
--- /dev/null
+++ b/sci-physics/abinit/files/6.12.1-gui-conf.patch
@@ -0,0 +1,12 @@
+diff -Naur abinit-6.12.1_orig/gui/configure abinit-6.12.1/gui/configure
+--- gui/configure	2012-01-30 19:42:26.000000000 +0000
++++ gui/configure	2012-03-16 13:38:54.000000000 +0000
+@@ -3143,7 +3143,7 @@
+   test -z "$as_dir" && as_dir=.
+     for ac_exec_ext in '' $ac_executable_extensions; do
+   if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+-    ac_cv_prog_UUDECODE="no"
++    ac_cv_prog_UUDECODE="$as_dir/$ac_word$ac_exec_ext"
+     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+     break 2
+   fi
diff --git a/sci-physics/abinit/files/6.12.1-libabinit_options.patch b/sci-physics/abinit/files/6.12.1-libabinit_options.patch
new file mode 100644
index 000000000..ad28a8183
--- /dev/null
+++ b/sci-physics/abinit/files/6.12.1-libabinit_options.patch
@@ -0,0 +1,57 @@
+diff -Naur abinit-6.12.1_orig/Makefile.am abinit-6.12.1/Makefile.am
+--- Makefile.am	2012-01-30 19:42:26.000000000 +0000
++++ Makefile.am	2012-03-22 10:32:50.000000000 +0000
+@@ -1279,12 +1279,16 @@
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/13_memory_mpi/lib13_memory_mpi.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a
++if DO_BUILD_15_GPU_TOOLBOX
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a
++endif
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/18_timing/lib18_timing.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/27_toolbox_oop/lib27_toolbox_oop.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/28_numeric_noabirule/lib28_numeric_noabirule.a
++if DO_BUILD_32_CONTRACT
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_contract/lib32_contract.a
++endif
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_util/lib32_util.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/42_geometry/lib42_geometry.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/42_nlstrain/lib42_nlstrain.a
+@@ -1298,7 +1302,9 @@
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a
++if DO_BUILD_52_MANAGE_CUDA
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a
++endif
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_abiutil/lib53_abiutil.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_ffts/lib53_ffts.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a
+diff -Naur abinit-6.12.1_orig/Makefile.in abinit-6.12.1/Makefile.in
+--- Makefile.in	2012-03-22 09:23:51.000000000 +0000
++++ Makefile.in	2012-03-22 10:33:22.000000000 +0000
+@@ -2638,12 +2638,12 @@
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/13_memory_mpi/lib13_memory_mpi.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a
+-	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a
++@DO_BUILD_15_GPU_TOOLBOX_TRUE@	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/18_timing/lib18_timing.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/27_toolbox_oop/lib27_toolbox_oop.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/28_numeric_noabirule/lib28_numeric_noabirule.a
+-	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_contract/lib32_contract.a
++@DO_BUILD_32_CONTRACT_TRUE@	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_contract/lib32_contract.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_util/lib32_util.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/42_geometry/lib42_geometry.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/42_nlstrain/lib42_nlstrain.a
+@@ -2657,7 +2657,7 @@
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a
+-	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a
++@DO_BUILD_52_MANAGE_CUDA_TRUE@	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_abiutil/lib53_abiutil.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_ffts/lib53_ffts.a
+ 	cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a
diff --git a/sci-physics/abinit/files/6.12.1-xmalloc.patch b/sci-physics/abinit/files/6.12.1-xmalloc.patch
new file mode 100644
index 000000000..0c8d98eea
--- /dev/null
+++ b/sci-physics/abinit/files/6.12.1-xmalloc.patch
@@ -0,0 +1,48 @@
+diff -Naur abinit-6.12.1_orig/src/02_clib/fsi_posix.c abinit-6.12.1/src/02_clib/fsi_posix.c
+--- src/02_clib/fsi_posix.c	2012-01-30 19:40:41.000000000 +0000
++++ src/02_clib/fsi_posix.c	2012-03-22 08:21:46.000000000 +0000
+@@ -19,7 +19,7 @@
+ */
+ 
+ #include "abi_clib.h"
+-#include "xmalloc.h"
++/* #include "xmalloc.h" */
+ #include "string_f.h"
+ 
+ /* Create a directory */
+diff -Naur abinit-6.12.1_orig/src/02_clib/intrinsics.c abinit-6.12.1/src/02_clib/intrinsics.c
+--- src/02_clib/intrinsics.c	2012-01-30 19:40:41.000000000 +0000
++++ src/02_clib/intrinsics.c	2012-03-22 08:20:26.000000000 +0000
+@@ -18,7 +18,7 @@
+  */
+ 
+ #include "abi_clib.h"
+-#include "xmalloc.h"
++/* #include "xmalloc.h" */
+ #include "string_f.h"
+ 
+ /* 
+diff -Naur abinit-6.12.1_orig/src/02_clib/progress_bar.c abinit-6.12.1/src/02_clib/progress_bar.c
+--- src/02_clib/progress_bar.c	2012-01-30 19:40:41.000000000 +0000
++++ src/02_clib/progress_bar.c	2012-03-22 08:21:06.000000000 +0000
+@@ -20,7 +20,7 @@
+ */
+ 
+ #include "abi_clib.h"
+-#include "xmalloc.h"
++/* #include "xmalloc.h" */
+ 
+ #include <sys/time.h>
+ #include <sys/ioctl.h>
+diff -Naur abinit-6.12.1_orig/src/02_clib/xmalloc.c abinit-6.12.1/src/02_clib/xmalloc.c
+--- src/02_clib/xmalloc.c	2012-01-30 19:40:41.000000000 +0000
++++ src/02_clib/xmalloc.c	2012-03-22 08:22:09.000000000 +0000
+@@ -19,7 +19,7 @@
+  */
+ 
+ #include "abi_clib.h"
+-#include "xmalloc.h"
++/* #include "xmalloc.h" */
+ 
+ static void
+ memory_error_and_abort (const char *fname)
diff --git a/sci-physics/abinit/metadata.xml b/sci-physics/abinit/metadata.xml
index c14bc6829..0a34647b9 100644
--- a/sci-physics/abinit/metadata.xml
+++ b/sci-physics/abinit/metadata.xml
@@ -11,6 +11,11 @@ ABINIT is a package whose main program allows one to find the total energy, char
   </flag>
 </use>
 <use>
+  <flag name="cuda-double">
+   Enable support for double precision nVidia CUDA
+  </flag>
+</use>
+<use>
   <flag name="fftw-threads">
    Use the threaded version of sci-libs/fftw
   </flag>
diff --git a/sci-physics/espresso/ChangeLog b/sci-physics/espresso/ChangeLog
index e5ea3c74d..cbb451433 100644
--- a/sci-physics/espresso/ChangeLog
+++ b/sci-physics/espresso/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-physics/espresso
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  22 Mar 2012; Christoph Junghans <ottxor@gentoo.org> espresso-9999.ebuild:
+  version bump
+
   25 Jun 2011; Christoph Junghans <ottxor@gentoo.org> espresso-9999.ebuild:
   migrate to git-2
 
diff --git a/sci-physics/espresso/espresso-9999.ebuild b/sci-physics/espresso/espresso-9999.ebuild
index 6522b9004..c8ba5bd9a 100644
--- a/sci-physics/espresso/espresso-9999.ebuild
+++ b/sci-physics/espresso/espresso-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-physics/espresso/espresso-3.0.0.ebuild,v 1.1 2011/04/20 13:03:00 ottxor Exp $
 
@@ -9,7 +9,7 @@ inherit autotools-utils savedconfig
 DESCRIPTION="Extensible Simulation Package for Research on Soft matter"
 HOMEPAGE="http://www.espressomd.org"
 
-if [ "${PV%9999}" != "${PV}" ]; then
+if [[ ${PV} = 9999 ]]; then
 	EGIT_REPO_URI="git://git.savannah.nongnu.org/espressomd.git"
 	EGIT_BRANCH="master"
 	inherit git-2
@@ -33,6 +33,7 @@ RDEPEND="
 	X? ( x11-libs/libX11 )"
 
 DEPEND="${RDEPEND}
+	dev-lang/python
 	doc? (
 		app-doc/doxygen[-nodot]
 		virtual/latex-base )"
@@ -41,9 +42,6 @@ DOCS=( AUTHORS NEWS README ChangeLog )
 
 src_prepare() {
 	autotools-utils_src_prepare
-	sed -i -e '/^[^S]/s/tutorials/tutorial/g' \
-		-e 's/cd tutorial/&s/' doc/Makefile.am \
-		|| die "sed of Makefile.am failed"
 	eautoreconf
 	restore_config myconfig.h
 }
@@ -60,7 +58,8 @@ src_configure() {
 
 src_compile() {
 	autotools-utils_src_compile
-	use doc && autotools-utils_src_compile doc
+	use doc && autotools-utils_src_compile ug doxygen tutorials
+	[[ ${PV} = 9999 ]] && use doc && autotools-utils_src_compile dg
 }
 
 src_install() {
@@ -74,12 +73,11 @@ src_install() {
 	save_config ${AUTOTOOLS_BUILD_DIR}/src/myconfig-final.h
 
 	if use doc; then
-		local where="."
-		[ "${PV%9999}" != "${PV}" ] && where="${AUTOTOOLS_BUILD_DIR}"
-		newdoc ${where}/doc/ug/ug.pdf user_guide.pdf
-		newdoc ${where}/doc/dg/dg.pdf developer_guide.pdf
+		[[ ${PV} = 9999 ]] && \
+			newdoc ${AUTOTOOLS_BUILD_DIR}/doc/dg/dg.pdf developer_guide.pdf
+		newdoc ${AUTOTOOLS_BUILD_DIR}/doc/ug/ug.pdf user_guide.pdf
 		dohtml -r ${AUTOTOOLS_BUILD_DIR}/doc/doxygen/html/*
-		for i in ${where}/doc/tutorials/*/[0-9]*.pdf; do
+		for i in ${AUTOTOOLS_BUILD_DIR}/doc/tutorials/*/[0-9]*.pdf; do
 			newdoc ${i} tutorial_${i##*/}
 		done
 	fi
diff --git a/sci-physics/root/ChangeLog b/sci-physics/root/ChangeLog
index 8478ce818..322c79e10 100644
--- a/sci-physics/root/ChangeLog
+++ b/sci-physics/root/ChangeLog
@@ -2,6 +2,20 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-physics/root/ChangeLog,v 1.93 2012/03/02 05:34:01 bicatali Exp $
 
+  22 Mar 2012; Andrew Savchenko <bircoph@gmail.com> root-5.32.01-r2.ebuild,
+  root-9999.ebuild:
+  Apply chklib64 fix to the live ebuild as well.
+  Remove deprecated ncurses support and editline option: they are
+  deprecated and do nothing actually.
+
+  21 Mar 2012; Andrew Savchenko <bircoph@gmail.com>
+  +files/root-5.32.00-chklib64.patch, root-5.32.01-r2.ebuild:
+  Fix library architecture check (32/64 bit) for libraries having .so
+  file installed as an ld script instead of normal binary file.
+  See bug 406817 for details.
+  Thanks to Jean-Francois Ostiguy and Jauhien Piatlicki for their
+  major work on this bug.
+
 *root-9999 (09 Mar 2012)
 *root-5.32.01-r2 (09 Mar 2012)
 
diff --git a/sci-physics/root/Manifest b/sci-physics/root/Manifest
index 6b79e4eaf..a5db27450 100644
--- a/sci-physics/root/Manifest
+++ b/sci-physics/root/Manifest
@@ -1,9 +1,36 @@
-DIST RooFit_Users_Manual_2.91-33.pdf 1330062 SHA256 101c4e4c41962238fcabf1caa86cafc51241a1800594491b2e62ef8b565a5646 SHA512 732d7dea3541b51e5f0b9b5b70dae57e1bdbb2504c4222d5e5095ec0f9b67307011c1f31c2c95be419b53dd8426f52f62f6c9370084208176a2ed3d7f25d783b WHIRLPOOL 033897bef4bdb13246a81ea6749f7895e6c4d639752e932130234ad9153bb399a4e5d416237850da27f139d3cccc53d9adb7a077abf20d257ce057157d6c3696
-DIST TMVAUsersGuide-v4.03.pdf 3913533 SHA256 0cdbb4a2d19eb7a86e2911cfa73a905932e862d6c94be10b7662a9355b0241af SHA512 d8bb2ce35ef32c4877059898f56513db0b1057924e21935a3d3a6f114748e167984c43fd2ec7e54197fccff875540543968fea9a8e75bf63f5f13521724a7ddb WHIRLPOOL 0a3e2e61e8e32f3a22757178adf033f9fbb89014aecd4df7f8bd49677d772bb3ad2c0f5526259611879f6bb20df647c01e23f53ade483d7a3e2242f8aee6c6aa
-DIST TMVAUsersGuide-v4.pdf 2355827 SHA256 bbc6563fd14a6a4a88efca55fa75e74d9b5c2a9f5d3044239f3f83dc2967ad62 SHA512 93010625ea21239acdecfca421ccd7556b6f10d44ebb2a8416462229628cafb85c21d0fa23aa674878245d1f7e78aab73e3b10e6123253d83b88839aaa2ba0c3 WHIRLPOOL a9ea70e5f4fd150eba3d27cb8755e59d3a7658c7629f2c340a105439a60b5dc881e340fd90baddb42cc16bd854db3e27fc33360a7a9102bbf51aa8bd8a4b5b6c
-DIST Users_Guide_5_26.pdf 9914765 SHA256 d0887800de7ffe7d6c0957891d44a4b34bf9d0eeb3da7e34b735ef998770bf39 SHA512 c2d428c9bb301af68626ffdd404acfde792b3c9539f1c85a5c467651074c67da861688c8ab61a0045cb5b947a7173633c64125c3a722360cc649f877bec888be WHIRLPOOL 59d9b07250dddd6d71912d24808711635b3b3845413b0f1f91e98b86843d0d295c097485f6e9258bb591195b4f077cb928686658f45337a9f72c5071ccc0003b
-DIST root-5.26.00e-patches.tar.bz2 7102 SHA256 f29bf8251b8c7e1809993c4f5ae0f990d5c6e6721e77eb62107d27fa55b9bf47 SHA512 674e73f404277e0a25801fb1093a7e9bee22d93ac073f247958b481b9f89ac86e9c440ae6cb43826ff460d9f328409a457fab37eb01ff45f368dc7f3f3bafdcc WHIRLPOOL 4a00ca8b07770e5c750ea337774b67541b51647359b15370e34392ca53b648dc7397951de5c25fe4afecc3ec688775bc785d8e25bb3d6fb73358ba6112f90f87
-DIST root-5.28.00b-xrootd-prop-flags.patch.bz2 3894 SHA256 093b1acd8336f5bb723802455296d8db884a2909a4e483cce637b8191039b4cd SHA512 e4544dd548a1599745bd75a9a069418c7eb8b09520d681e13d1e36140e29024b97da812f8fa6d8bf647c6b715a9ce14550165f2cd7cdec293e496c6808d8e6a3 WHIRLPOOL ddf5c736b6aab2cf1d6d0f5d850ec6ebdefb7dd91fcac3e6b5eef272ed684c0556d00c1161a8059c9a964604b13a2d875a24fcf14e7ab8225f56801a4664ae47
-DIST root_v5.26.00g.source.tar.gz 29356003 SHA256 d8ae10f492239d58e49b09a6269b1fe9657d50afe3827246991df66a79e67c74 SHA512 8d0c9d0eaed10490d8bb50b485f8e874dd8f2fb3f60633119ec5d6946222ab229fbea2e0a45a9d09bb8e1b82944c5235cfaf9099ad8856acd32349c21942334c WHIRLPOOL 94f1440605750f0b0dd24b288d95c3551e5caaca1fae534c9d4ca857feb888af7eca1916828823c34acd30aa336f850034b7a9345fdd1925ff53f9a1df362625
-DIST root_v5.28.00h.source.tar.gz 31654844 SHA256 2adc46c70a01761215b5f685fb0ca4c62e03a3b53165a459ed72190627242651 SHA512 e3c69333a6c1cc5392b2ef8da0730e1c8b9bbc0afa56b06f4336f1fdf49aaebd7b485cf06222e5afb8d2184ede140945f7f14000837bace7b87801288af9ef01 WHIRLPOOL eaa0bc5ef8a540ab66e6a1c82d5ecf6631ef9fafd56420d7edd5b4735a0fb074c8c01d2ac0f9588b018dba75e2af0ff6bb177b2c13de97a040a19a7b7789cc2e
-DIST root_v5.32.01.source.tar.gz 55509057 SHA256 0cd3147f3d127386f63bb65a1ea16f8712dde730f55a7a48d847032bc48f2ca4 SHA512 ede055311cf18151f2b0f3546eb3e6902b93ed3857f80920b0ed586372e7d2c09379654f43f10cf85d3af2c97457cb55eeb617ed2df65e4f7f9838bcda0505bc WHIRLPOOL d39af0f267e25720e0a428622a1567eeb97c29b2c40404cc8d9c983ac37bd946409d28baca99d8335ee48a9b32bbd4ba4e3a2768a3a5fa908f7d56a6e674935a
+AUX olbd.confd 197 RMD160 798de1808502f3e4ecfc5f024b56a419d9824057 SHA1 f2a4385fdf9849eafb1d5457727f6fbe80af1da3 SHA256 5a34da76bbe56cd3b8128f05c0d9900f9d7f7ffdcffc5deeb816c78ea46679ba
+AUX olbd.initd 714 RMD160 19a09e2264b984245f6a6b55c302a218bc41e452 SHA1 75e5d0764f00d5f9ef52966b597fa66c67bf7058 SHA256 a12efc3a4af4116558a6efd0964646b677d06879bb2114fc508324d9162bf815
+AUX proofd.confd 415 RMD160 3814aacb63d82b9d060086f9bef304d431a15b4e SHA1 31eb7af239a0042f887b5089a7c6c7ec5d6662e9 SHA256 261738817b4ba50fb07007741305d0a88e9067a45e3cbfd1d3fc8bebe70ece38
+AUX proofd.initd 717 RMD160 09157e82a659255d802a02466dca833135c7839a SHA1 47d139d8cb08e055674018b6b7f68522bf65b5ca SHA256 f60fa92173370e237e3e2cf5be7add5aa63752e3b7496cf3a0a5acc1dc927ebc
+AUX root-5.26.00e-libpng15.patch 1261 RMD160 6fa4b2a6c20f0a0eb7cca381045074c5f2d27ed7 SHA1 598abe303d20b1d3029080af8c60498211840b1c SHA256 94fd93a4e9081ef8070e2bcaeb09f169ae4475689fe4987c3a9acfec879a45f2
+AUX root-5.26.00g-explicit-functions.patch 410 RMD160 f3fb8458bb671f7f68cc74ca92363f708a083e4f SHA1 d1bbef441ed3f6fbd3e41ffaaf831f73e80abede SHA256 e1799d5c8ad4e8af3161c4b3ed8e457eee48fe94e092ef8f3fb73b13d72e0c92
+AUX root-5.28.00b-asneeded.patch 712 RMD160 0b3a3d41e309f13310fda607955ad88cc6bc176e SHA1 4fa704d2790e19933155da2587a9c6998d3c4e4f SHA256 17d1d41d8c7f78abbb7cd284af0a6aca544820db72fa72956b473c7c1817a96b
+AUX root-5.28.00b-glibc212.patch 276 RMD160 02901df4c8e5e3c7d50a78916f843fde83faf1f0 SHA1 842129d6247255b5fa72778a12f08e1383247cd8 SHA256 e51e127a80e2bf1afad41c2b7ca5233c362bce017057ca489bedb2a9442efb62
+AUX root-5.28.00b-nobyte-compile.patch 5483 RMD160 490801842ba9ca6c980e498224d48dc676fcf0fa SHA1 538ac62083b8b12c558b97d72235dd047a64b632 SHA256 81b015dd6c122176fbc3103c75f62b7b1c3db569ad6d461ca544248f4e017b5c
+AUX root-5.28.00b-prop-ldflags.patch 433 RMD160 fd1717af9210471d7de0f06a47011e03d3f76d9a SHA1 b5dac8b013219dcfe577f2972fcc1d548f153cc3 SHA256 04f4b65a91e28386c7a857fe361f091943f4bb6fc82a9473ac7605412c199191
+AUX root-5.28.00b-unuran.patch 1531 RMD160 8083784cc831fc304f2e94fdf3b8aa8379d0bd9a SHA1 5c4537ba1922775fb63d65340a18a3c2b1d2311b SHA256 09458c60c9d38af2d204939f752ec25364d04cf66810b7cae5e88368f84c31c8
+AUX root-5.28.00h-explicit-functions.patch 427 RMD160 3d62d982a35523249bc1ffbf9fee50056f007a36 SHA1 49479965e8116480d17efdb557a3c2844decbed6 SHA256 ef1a3bb5c89ebbd6baba2a27e6504822cca1b65893c910709974119a7e650ff8
+AUX root-5.32.00-afs.patch 1322 RMD160 208adb0105edbad04f74206363f582c0a4dbcf73 SHA1 e713c26f5481755ded620d50a6dffc63eb0cba9d SHA256 a8f8d551668299516e2e091fd29ae15ceb1ba034d9df95b76f99b1dabc94a8dc
+AUX root-5.32.00-cfitsio.patch 593 RMD160 c9fb2e0e57ad6c08bc26eb626772bc3ec901ac46 SHA1 9d07035b5ab27bede96033a777e3d21a26b3ae27 SHA256 9f4f244f272d75e115d8f139670fdcc0cdbcb68972689edbc78e467c3fad3e40
+AUX root-5.32.00-chklib64.patch 866 RMD160 9fada23b979e80dec76184e22895e47e689b55b4 SHA1 fde081f24090a3bb10473170a611384593072134 SHA256 5260cb5e7ab62bb19f6586cf4d9033597bcfd0132f178192be69ce515b2c7c35
+AUX root-5.32.00-explicit-functions.patch 610 RMD160 b8eb20aa9b6864fe138674c5991fe13aaa68981c SHA1 9f4faf15cf43cfa1e3ff4a394db5a4807bed713e SHA256 1afa92168b1f25ed457c08db85c85173613b82050b558765ba25e056f6f60abc
+AUX root-5.32.00-nobyte-compile.patch 5527 RMD160 61c3dfdd4b8f71f64772e20901f6ee11b8f53e12 SHA1 f914ccb7f7d88dd8d9ba4c1f4d940b14134f2c3b SHA256 82152c92efd5002f9c2b230f141cae6c8111b03bd18370030d62f0f7d7127420
+AUX rootd.confd 199 RMD160 9ca9864292e7301d3feb6c36d88ba16002b7d7fa SHA1 822983a24e219bd860124f363a1e4250a17026dd SHA256 7b69f646ce0b2546ce797ec4a05949b02302dc5f4e41d2e8896ed0bc6575ac8d
+AUX rootd.initd 732 RMD160 9cce585e528e27c0fbd791be1f90fa6a1bb3164b SHA1 c15e805b0397bc8513e1c7e5631f2337c3564bbc SHA256 42b9fe01aa41965359c16d4b23f874cea65806d8c7ec11215dbba95ab80e90f3
+AUX xrootd.confd 200 RMD160 2344c73ca3c27adeb70b092850cfd292af7d58bd SHA1 f2b895f43d3537e8614a907c7c94642f01c084e4 SHA256 03c1191168ddea3bc6621e26eb56e509e6c9a4d58756ffbbd07ff6657200e57d
+AUX xrootd.initd 720 RMD160 fb03f7410061e5340cb1f03c1659c553b62cb81f SHA1 a52eebc9bda2a92d0c5f3bbd20d7ea27cecc8cca SHA256 08c85596b8489fec0cea64e1fa9a092094fb05ea0f1151fd26775e4d5a024a8e
+DIST RooFit_Users_Manual_2.91-33.pdf 1330062 RMD160 650b616018a5493d5fd7da1dc06c6e54eaa419fb SHA1 f176782746542b00ff60320b4a41e1218db3d006 SHA256 101c4e4c41962238fcabf1caa86cafc51241a1800594491b2e62ef8b565a5646
+DIST TMVAUsersGuide-v4.03.pdf 3913533 RMD160 fbd62b90e7ad47ad69ec62d584417463ec13bf9c SHA1 84a63140cc3e01267d2cc7ffa374a7c24fbed37e SHA256 0cdbb4a2d19eb7a86e2911cfa73a905932e862d6c94be10b7662a9355b0241af
+DIST TMVAUsersGuide-v4.pdf 2355827 RMD160 0624a6ed7e006581eacdaa69e82bbdca91aa42a9 SHA1 98016f0ccfa6c54234e22b46032bb0b2f5d7ac20 SHA256 bbc6563fd14a6a4a88efca55fa75e74d9b5c2a9f5d3044239f3f83dc2967ad62
+DIST Users_Guide_5_26.pdf 9914765 RMD160 9e67a407d5a4d4f7019ab7b9b29bc696b7974987 SHA1 c2ecb87226e2fa38e6214aaf76dd789663d260dd SHA256 d0887800de7ffe7d6c0957891d44a4b34bf9d0eeb3da7e34b735ef998770bf39
+DIST root-5.26.00e-patches.tar.bz2 7102 RMD160 d513c643ec8acdbe293e7ca159f59c765c52a2ad SHA1 ca8a958186fc8a77c04348f61c97e2d836493026 SHA256 f29bf8251b8c7e1809993c4f5ae0f990d5c6e6721e77eb62107d27fa55b9bf47
+DIST root-5.28.00b-xrootd-prop-flags.patch.bz2 3894 RMD160 ef6b06d4783320ee7d6189dbe122ac49605bc6f4 SHA1 8026dda3cb74da40359ccc6d4ee787c01eee958b SHA256 093b1acd8336f5bb723802455296d8db884a2909a4e483cce637b8191039b4cd
+DIST root_v5.26.00g.source.tar.gz 29356003 RMD160 92d967cfa1859441da896bdaf58badb269b1747d SHA1 ce354c11d58beac567062c0f2036a0cfaf8936f3 SHA256 d8ae10f492239d58e49b09a6269b1fe9657d50afe3827246991df66a79e67c74
+DIST root_v5.28.00h.source.tar.gz 31654844 RMD160 b4ad8b71b833a1a1b7826b7b29c186504fb9a18c SHA1 5cd8c02ba2a1e84f11295c91b95a0f455ec016d8 SHA256 2adc46c70a01761215b5f685fb0ca4c62e03a3b53165a459ed72190627242651
+DIST root_v5.32.01.source.tar.gz 55509057 RMD160 d218c89a98ba1350b801912da0766afd07de6677 SHA1 c108db0c20ea964b6d9027ed6173dbc29ca48564 SHA256 0cd3147f3d127386f63bb65a1ea16f8712dde730f55a7a48d847032bc48f2ca4
+EBUILD root-5.26.00g.ebuild 9479 RMD160 6bb77fa39b293822c21c9869aecc662e7b82bbaa SHA1 17f7002a10177dca15d0fd26107415da5ad63b3d SHA256 c65aebebec8276549e9e2d18c798b79851a73b14c4b83744d3b9d203e123515c
+EBUILD root-5.28.00h.ebuild 9935 RMD160 b3bb8fa9c561e95cc07e04f2e2d6422cbfcf8747 SHA1 ea4511a0c03d92ec10c5dcfd8a8a5565d61ae4b9 SHA256 6c5079518bcae55c44bc49cc4d6302710c180a4c8f9c86ddadde27cc261cf68c
+EBUILD root-5.32.01-r2.ebuild 10026 RMD160 da961d1b5a0e9f62d9e50fa16aca4db43b1f1c51 SHA1 8858e2b94236c699e0d6d27cc08e7f3fe4e384fd SHA256 8169f2246a06c21ad552af78c742c0004be1a980720df008831dda5ff483a0a3
+EBUILD root-9999.ebuild 10304 RMD160 61b1ce2b42935d749226c0bd668e4a94bb60afb2 SHA1 e73440f509416f1288078165fa0031645ce7f02f SHA256 96ccf03de5650e3e4d1b6dfbbd4b29185a6c1bbcdf574ce54d4875b6f89663ae
+MISC ChangeLog 27157 RMD160 ee52116a97ddf5b2c2a211e58e6969d9b04b0118 SHA1 343e0735654fdcc9d642db8479d204bf8bd65149 SHA256 121c5cc860244f4227b60e2756a06d52552b04d766f8c389163e310491209ba5
+MISC metadata.xml 1627 RMD160 5478d04d172076f583e1d9f541d62e880e5be1fa SHA1 707468734b4d2db052f5d9a2f50cd487aafc0288 SHA256 09e5bb09c9bb3a412303b03fb3b3aa09e958e980874e26b0577e20b86164c5e5
diff --git a/sci-physics/root/files/root-5.32.00-chklib64.patch b/sci-physics/root/files/root-5.32.00-chklib64.patch
new file mode 100644
index 000000000..a5c052cdd
--- /dev/null
+++ b/sci-physics/root/files/root-5.32.00-chklib64.patch
@@ -0,0 +1,23 @@
+--- configure.orig	2012-02-29 19:46:41.000000000 +0400
++++ configure	2012-03-22 03:28:43.458968696 +0400
+@@ -441,14 +441,13 @@
+         fi
+     else
+         if file $filearg $chklib64 | grep 'ASCII' > /dev/null 2>& 1 ; then
+-            check_link $chklib64
+-            ret=$link_result
+-        else
+-            logmsg " file $filearg $chklib64 | grep '64-bit'"
+-            if file $filearg $chklib64 | grep '64-bit' > /dev/null 2>& 1 ; then
+-                ret=1
+-            fi
++            # get real binary .so name from .so ld script
++            chklib64=$(gawk '($1 == "GROUP") { print $3 }' $chklib64)
+         fi
++        logmsg " file $filearg $chklib64 | grep '64-bit'"
++        if file $filearg $chklib64 | grep '64-bit' > /dev/null 2>& 1 ; then
++            ret=1
++            fi
+     fi
+     logmsg " result: $ret"
+     if test $ret -eq 1 ; then
diff --git a/sci-physics/root/root-5.32.01-r2.ebuild b/sci-physics/root/root-5.32.01-r2.ebuild
index c0a794425..244b397e5 100644
--- a/sci-physics/root/root-5.32.01-r2.ebuild
+++ b/sci-physics/root/root-5.32.01-r2.ebuild
@@ -24,7 +24,7 @@ SLOT="0"
 LICENSE="LGPL-2.1"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="+X afs avahi clarens doc emacs examples fits fftw graphviz kerberos ldap
-	+math mpi mysql ncurses odbc +opengl openmp oracle postgres prefix
+	+math mpi mysql odbc +opengl openmp oracle postgres prefix
 	pythia6	pythia8	python qt4 +reflex ruby ssl xft xinetd xml xrootd"
 
 CDEPEND="
@@ -66,7 +66,6 @@ CDEPEND="
 	ldap? ( net-nds/openldap )
 	math? ( sci-libs/gsl sci-mathematics/unuran mpi? ( virtual/mpi ) )
 	mysql? ( virtual/mysql )
-	ncurses? ( sys-libs/ncurses )
 	odbc? ( || ( dev-db/libiodbc dev-db/unixODBC ) )
 	oracle? ( dev-db/oracle-instantclient-basic )
 	postgres? ( dev-db/postgresql-base )
@@ -128,6 +127,7 @@ src_prepare() {
 		"${FILESDIR}"/${PN}-${PATCH_PV}-unuran.patch \
 		"${FILESDIR}"/${PN}-${PATCH_PV2}-afs.patch \
 		"${FILESDIR}"/${PN}-${PATCH_PV2}-cfitsio.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV2}-chklib64.patch \
 		"${FILESDIR}"/${PN}-${PATCH_PV2}-explicit-functions.patch
 
 	# make sure we use system libs and headers
@@ -201,7 +201,6 @@ src_configure() {
 		$(use_enable avahi bonjour) \
 		$(use_enable clarens) \
 		$(use_enable clarens peac) \
-		$(use_enable ncurses editline) \
 		$(use_enable fits fitsio) \
 		$(use_enable fftw fftw3) \
 		$(use_enable graphviz gviz) \
diff --git a/sci-physics/root/root-9999.ebuild b/sci-physics/root/root-9999.ebuild
index bdf6caa66..51f5afccf 100644
--- a/sci-physics/root/root-9999.ebuild
+++ b/sci-physics/root/root-9999.ebuild
@@ -34,7 +34,7 @@ SRC_URI="${SRC_URI}
 SLOT="0"
 LICENSE="LGPL-2.1"
 IUSE="+X afs avahi clarens doc emacs examples fits fftw graphviz kerberos ldap
-	llvm +math mpi mysql ncurses odbc +opengl openmp oracle postgres prefix
+	llvm +math mpi mysql odbc +opengl openmp oracle postgres prefix
 	pythia6	pythia8	python qt4 +reflex ruby ssl xft xinetd xml xrootd"
 
 CDEPEND="
@@ -77,7 +77,6 @@ CDEPEND="
 	llvm? ( =sys-devel/clang-9999 =sys-devel/llvm-9999 )
 	math? ( sci-libs/gsl sci-mathematics/unuran mpi? ( virtual/mpi ) )
 	mysql? ( virtual/mysql )
-	ncurses? ( sys-libs/ncurses )
 	odbc? ( || ( dev-db/libiodbc dev-db/unixODBC ) )
 	oracle? ( dev-db/oracle-instantclient-basic )
 	postgres? ( dev-db/postgresql-base )
@@ -138,7 +137,8 @@ src_prepare() {
 		"${FILESDIR}"/${PN}-${PATCH_PV}-glibc212.patch \
 		"${FILESDIR}"/${PN}-${PATCH_PV}-unuran.patch \
 		"${FILESDIR}"/${PN}-${PATCH_PV2}-afs.patch \
-		"${FILESDIR}"/${PN}-${PATCH_PV2}-cfitsio.patch
+		"${FILESDIR}"/${PN}-${PATCH_PV2}-cfitsio.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV2}-chklib64.patch
 
 	# make sure we use system libs and headers
 	rm montecarlo/eg/inc/cfortran.h README/cfortran.doc
@@ -211,7 +211,6 @@ src_configure() {
 		$(use_enable avahi bonjour) \
 		$(use_enable clarens) \
 		$(use_enable clarens peac) \
-		$(use_enable ncurses editline) \
 		$(use_enable fits fitsio) \
 		$(use_enable fftw fftw3) \
 		$(use_enable graphviz gviz) \