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

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  media-gfx/librecad: Cleaned up old versions
  In main tree
  sci-physics/root: 5.28.00g update
  [dev-cpp/eigen] Version bump

14 files changed, 586 insertions, 141 deletions

diff --git a/dev-cpp/eigen/ChangeLog b/dev-cpp/eigen/ChangeLog
index 87125c3db..cbe1086a6 100644
--- a/dev-cpp/eigen/ChangeLog
+++ b/dev-cpp/eigen/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/dev-cpp/eigen/ChangeLog,v 1.44 2011/03/25 16:01:28 jlec Exp $
 
+* eigen-3.0.3 (7 Oct 2011)
+
+  7 Oct 2011; Andrea Arteaga <andyspiros@gmail.com> eigen-3.0.3.ebuild
+  Version bump.
+
 *eigen-3.0.2 (29 Aug 2011)
 
   29 Aug 2011; Justin Lecher <jlec@gentoo.org> +eigen-3.0.2.ebuild:
@@ -32,13 +37,13 @@
 
 *eigen-3.0.1-r1 (15 Jun 2011)
 
-  15 Jun 2011; Sébastien Fabbro <bicatali@gentoo.org> -eigen-3.0.0-r1.ebuild,
+  15 Jun 2011; Sébastien Fabbro <bicatali@gentoo.org> -eigen-3.0.0-r1.ebuild,
   +eigen-3.0.1-r1.ebuild:
   Bump
 
 *eigen-3.0.0-r1 (31 Mar 2011)
 
-  31 Mar 2011; Sébastien Fabbro <bicatali@gentoo.org> +eigen-3.0.0-r1.ebuild,
+  31 Mar 2011; Sébastien Fabbro <bicatali@gentoo.org> +eigen-3.0.0-r1.ebuild,
   +metadata.xml:
   Added a few extras flags to pull dependencies for unsupported eigen features.
   Also now build a blas implementation
@@ -49,7 +54,7 @@
   eigen-2.0.15.ebuild, +eigen-3.0.0.ebuild:
   Version Bump, Adapted to new tarball, #358761
 
-  13 Feb 2011; Tomáš Chvátal <scarabeus@gentoo.org> -eigen-2.0.5.ebuild,
+  13 Feb 2011; Tomáš Chvátal <scarabeus@gentoo.org> -eigen-2.0.5.ebuild,
   -eigen-2.0.14.ebuild:
   old
 
@@ -62,7 +67,7 @@
   eigen-2.0.14.ebuild, +eigen-2.0.15.ebuild:
   Version Bump, 339258
 
-  27 Aug 2010; Raúl Porcel <armin76@gentoo.org> eigen-2.0.13.ebuild:
+  27 Aug 2010; Raúl Porcel <armin76@gentoo.org> eigen-2.0.13.ebuild:
   alpha/ia64/sparc stable wrt #327581
 
   23 Jul 2010; Markus Meier <maekke@gentoo.org> eigen-2.0.13.ebuild:
@@ -95,15 +100,15 @@
   14 Jan 2010; Jeroen Roovers <jer@gentoo.org> eigen-2.0.5.ebuild:
   Stable for HPPA (bug #295884).
 
-  28 Dec 2009; Tomáš Chvátal <scarabeus@gentoo.org> eigen-2.0.5.ebuild,
+  28 Dec 2009; Tomáš Chvátal <scarabeus@gentoo.org> eigen-2.0.5.ebuild,
   eigen-2.0.10.ebuild:
   Reorder the deps to not rdepend on doxygen.
 
-  28 Dec 2009; Tomáš Chvátal <scarabeus@gentoo.org> eigen-2.0.5.ebuild,
+  28 Dec 2009; Tomáš Chvátal <scarabeus@gentoo.org> eigen-2.0.5.ebuild,
   eigen-2.0.10.ebuild:
   Doc useflag require doxygen. Per bug #298074.
 
-  27 Dec 2009; Raúl Porcel <armin76@gentoo.org> eigen-2.0.5.ebuild:
+  27 Dec 2009; Raúl Porcel <armin76@gentoo.org> eigen-2.0.5.ebuild:
   alpha/ia64/sparc stable
 
 *eigen-2.0.10 (10 Dec 2009)
@@ -124,7 +129,7 @@
   30 Nov 2009; Joseph Jezak <josejx@gentoo.org> Manifest:
   Marked ppc/ppc64 stable.
 
-  29 Nov 2009; Raúl Porcel <armin76@gentoo.org> eigen-2.0.9.ebuild:
+  29 Nov 2009; Raúl Porcel <armin76@gentoo.org> eigen-2.0.9.ebuild:
   Add ~sparc
 
 *eigen-2.0.9 (01 Nov 2009)
@@ -171,7 +176,7 @@
 
 *eigen-2.0.3 (30 Jul 2009)
 
-  30 Jul 2009; Tomáš Chvátal <scarabeus@gentoo.org> +eigen-2.0.3.ebuild,
+  30 Jul 2009; Tomáš Chvátal <scarabeus@gentoo.org> +eigen-2.0.3.ebuild,
   +files/eigen-ppc-define.patch:
   Version bump.
 
@@ -192,7 +197,7 @@
   14 Apr 2009; Tomas Chvatal <scarabeus@gentoo.org> +eigen-2.0.1.ebuild:
   Version bump.
 
-  11 Apr 2009; Raúl Porcel <armin76@gentoo.org> eigen-2.0.0.ebuild:
+  11 Apr 2009; Raúl Porcel <armin76@gentoo.org> eigen-2.0.0.ebuild:
   Add ~alpha/~ia64 wrt #260777
 
   09 Mar 2009; Brent Baude <ranger@gentoo.org> eigen-2.0.0.ebuild:
diff --git a/dev-cpp/eigen/Manifest b/dev-cpp/eigen/Manifest
index 9f00bd8f5..cdf4b9b32 100644
--- a/dev-cpp/eigen/Manifest
+++ b/dev-cpp/eigen/Manifest
@@ -1,37 +1,9 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
-
-- -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
-
-- - -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
-
 DIST eigen-3.0.1.tar.bz2 903484 RMD160 ac3343dddc208cada82d316b78b1b34d7031eafe SHA1 6fe629cd1eaef1a44430a068ff7202fc27209ee4 SHA256 d4d10aabe3fb92b2eadf71a0f15f0129864c6f80def31bdbd2a8d8ead132e5a6
 DIST eigen-3.0.2.tar.bz2 955760 RMD160 7686dc72ac8ee96cb055d4bca8cd6da526d5780c SHA1 2bcc7a6b415f5c75b5e061a399c3f9ab9aadb708 SHA256 cd76169b426f89b667db24beaaaf2d982b48664d9615ad781bdf9e83f0be5e5f
+DIST eigen-3.0.3.tar.bz2 955653 RMD160 ffce3636bf740094a3600317e06ad8ccc6660c2d SHA1 eff65146d6d6d4c99ca11191fb08de07858fa1ea SHA256 1397d4153baffae2d7a3fe80a620e21bcd4ee5a8f4ac5de47157763206253d75
 EBUILD eigen-3.0.1-r2.ebuild 2038 RMD160 ba6b7960f7e73cf8389a4efbcc932a622dcf84c9 SHA1 52082b7904a0a703e79d939c0568ee509dad2803 SHA256 446e2f58e41b8285c24774e83a58a941adfd786310ff7ead28c1a099d1d703b4
 EBUILD eigen-3.0.2.ebuild 2106 RMD160 6c1dbc11ebdf4863eec35197c9f43093a4c592a6 SHA1 2375bc3c4d7909baccd2328c3a5452209d1b68c2 SHA256 ea53c2ae7f23d78dc9cee892eff8f258f81c609da9851f7259faa90345f95bc9
+EBUILD eigen-3.0.3.ebuild 2106 RMD160 6c1dbc11ebdf4863eec35197c9f43093a4c592a6 SHA1 2375bc3c4d7909baccd2328c3a5452209d1b68c2 SHA256 ea53c2ae7f23d78dc9cee892eff8f258f81c609da9851f7259faa90345f95bc9
 EBUILD eigen-9999.ebuild 1965 RMD160 09b9d492e0f8d51545f58c77c914a96aa9fe3f13 SHA1 1407975ba4b73388d740824817e0f9954f730dc7 SHA256 7383a573d2a00ad8ee49ddffde8da0676499241e2e35a61de96ca42fdc2c2642
-MISC ChangeLog 7160 RMD160 1b592a23619fc1c3582711a8cf74fa17db264b33 SHA1 94ff55a08c02413f2f569ea6315f031835d31c88 SHA256 0af3a8db785fd761aee523a54e91233d9e0b437f225cbad4c1fb2150ad24eb9f
+MISC ChangeLog 7312 RMD160 04d7df3f5ab8600010c6bbf5bf310cfabc2846a1 SHA1 b7ccff4ce809fadfa547e9e60765b2273bfed364 SHA256 debe6d5846b40daa6a1ec6025818804a416fd00d7c5748c36aa21fd443a51828
 MISC metadata.xml 867 RMD160 aa9dd92c298151ecc8c6f7bbb4d18f85be82bfac SHA1 06d4827b1fd0f87cf7aa23ca28b389a2c0dcc785 SHA256 6d74c99087833e44098a46949815591563c8df4a3812444472f1330d64155548
-- - -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.18 (GNU/Linux)
-
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-jwgAn2ME0gnmkzMQyu7Kq8QIHFbIMafV
-=RbMg
-- - -----END PGP SIGNATURE-----
-- -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.18 (GNU/Linux)
-
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-7zoAnj8tmfZywJcZvo4Egr7qjNmsd023
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-Version: GnuPG v2.0.18 (GNU/Linux)
-
-iEYEAREKAAYFAk5bpsEACgkQgAnW8HDreRYUzQCgnjfBSL5ewtIe+aa5Y8Sk2+Hc
-8f8AoKUdU0+PH7iDWW47Da2/jDIPnpya
-=+N9e
------END PGP SIGNATURE-----
diff --git a/dev-cpp/eigen/eigen-3.0.3.ebuild b/dev-cpp/eigen/eigen-3.0.3.ebuild
new file mode 100644
index 000000000..57a955794
--- /dev/null
+++ b/dev-cpp/eigen/eigen-3.0.3.ebuild
@@ -0,0 +1,82 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+inherit cmake-utils alternatives-2
+
+DESCRIPTION="C++ template library for linear algebra"
+HOMEPAGE="http://eigen.tuxfamily.org/"
+SRC_URI="http://bitbucket.org/eigen/eigen/get/${PV}.tar.bz2 -> ${P}.tar.bz2"
+
+LICENSE="|| ( LGPL-3 GPL-2 )"
+KEYWORDS="~amd64 ~x86"
+SLOT="3"
+IUSE="adolc fortran fftw doc gmp sparse static-libs test"
+
+CDEPEND="adolc? ( sci-libs/adolc[sparse?] )
+	fftw? ( >=sci-libs/fftw-3 )
+	gmp? ( dev-libs/gmp dev-libs/mpfr )
+	sparse? ( dev-cpp/sparsehash
+			sci-libs/cholmod
+			sci-libs/superlu
+			sci-libs/umfpack )"
+
+DEPEND="doc? ( app-doc/doxygen )
+	test? ( ${CDEPEND} )"
+
+RDEPEND="!dev-cpp/eigen:0
+	${CDEPEND}"
+
+src_unpack() {
+	unpack ${A} && mv ${PN}* ${P}
+}
+
+src_configure() {
+	#TOFIX: static-libs for blas are always built with PIC
+	#TOFIX: BTL benchmarks
+	#TOFIX: is it worth fixing all the automagic given no library is built?
+	mycmakeargs=(
+		-DEIGEN_BUILD_BTL=OFF
+	)
+	CMAKE_BUILD_TYPE="release" cmake-utils_src_configure
+	use fortran && FORTRAN_LIBS="blas" # lapack not ready yet
+}
+
+src_compile() {
+	cmake-utils_src_compile
+	pushd "${S}_build" > /dev/null
+	use doc && emake doc
+	use fortran && emake ${FORTRAN_LIBS}
+	use test && emake buildtests
+	popd > /dev/null
+}
+
+src_install() {
+	cmake-utils_src_install
+	use doc && dohtml -r "${CMAKE_BUILD_DIR}"/doc/html/*
+	local x
+	for x in ${FORTRAN_LIBS}; do
+		local libname="eigen_${x}"
+		cd "${CMAKE_BUILD_DIR}"/${x}
+		dolib.so lib${libname}.so
+		use static-libs && newlib.a lib${libname}_static.a lib${libname}.a
+		#TOFIX: lapack implementation needs a Requires: field in pc file.
+		cat <<-EOF > ${libname}.pc
+			prefix="${EPREFIX}"/usr
+			libdir=\${prefix}/$(get_libdir)
+			includedir=\${prefix}/include
+			Name: ${PN}
+			Description: ${DESCRIPTION}
+			Version: ${PV}
+			URL: ${HOMEPAGE}
+			Libs: -L\${libdir} -l${libname}
+			Libs.private: -lm
+		EOF
+		alternatives_for ${x} eigen 0 \
+			/usr/$(get_libdir)/pkgconfig/${x}.pc ${libname}.pc
+		insinto /usr/$(get_libdir)/pkgconfig
+		doins ${libname}.pc
+	done
+}
diff --git a/media-gfx/librecad/ChangeLog b/media-gfx/librecad/ChangeLog
index f4dda6198..b657da323 100644
--- a/media-gfx/librecad/ChangeLog
+++ b/media-gfx/librecad/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header$
 
+  10 Oct 2011; Dongxu Li <dongxuli2011@gmail.com> -librecad-1.0.0_rc2.ebuild:
+  Cleaned up old versions
+
   06 Oct 2011; Dongxu Li <dongxuli2011@gmail.com> librecad-9999.ebuild:
   Added boost dependency
 
diff --git a/media-gfx/librecad/Manifest b/media-gfx/librecad/Manifest
index dd0032693..41b5efd9b 100644
--- a/media-gfx/librecad/Manifest
+++ b/media-gfx/librecad/Manifest
@@ -1,9 +1,7 @@
 AUX 1.0.0_rc2-gcc4.6.patch 1404 RMD160 a2e72683beb7bb3fb5e27118dc0819b00cc5a328 SHA1 f38fe80a5eeaab8f942ca84cd061f7593b22161b SHA256 3e6cd17cdb896d0da670e4731154600e3a7cfcc536982a802027a3c175721572
 AUX librecad-1.0.0_rc2-version.patch 532 RMD160 ef600cab3da265fa5b9b336e61386037eb0bdb28 SHA1 88c3605f71f3cef2cd44f810604716acdea03a0d SHA256 e43d1f3c5e10583ffbc2b6c6d7ff1b70c2dbef54593c510c05d443fb842b2d81
-DIST librecad-1.0.0_rc2.tar.gz 6317712 RMD160 619c8b7cc3247325526810ae866ffebc4410e299 SHA1 2d093576d75488cb4c750fef8a2a6126705ee435 SHA256 b6866e82e5f9d2a72c71ab2c9064f46c2685e083cb3f190c9612cc020c1f9003
-DIST librecad-1.0.0_rc3.tar.gz 6318228 RMD160 bcf363c23e8f34fae1d8101160404c58bfd955ff SHA1 b3bd301302d4cd0a6a5413e337bfd86f532e4124 SHA256 a30ebd450cb17213fb095dd51a66f838e8b29229c0a19a314a33729a80bf49f3
-EBUILD librecad-1.0.0_rc2.ebuild 875 RMD160 d237bf7f8ab09661292670f63b2a133e02599d54 SHA1 4ca5f399e33b0e9cf42bdab70eedbff3200c9780 SHA256 dbca38aeb92657d5f7592943eec8d95c72ec9800a89e8d267912538bf0b7969a
+DIST librecad-1.0.0_rc3.tar.gz 3533857 RMD160 f552989eb70d33c5a4b92984fa2276731056ea07 SHA1 6ff6b05aab915d62fea9605f1a6203dc849a45dd SHA256 1584d7b7ca6cdbc1e323cd508c1e00a388eb0991e81e7f2c7a7f11d58fbd9565
 EBUILD librecad-1.0.0_rc3.ebuild 864 RMD160 c0dfb19e4663859fdba9054069e8d06d3489fe33 SHA1 8857889076961ecf8334ae0bdff658cc9d6af5ab SHA256 7d596c19e42e04dde6750afd1cd0e19d3b78967ed6c409956ba770f42d8b7c32
 EBUILD librecad-9999.ebuild 992 RMD160 a7954a695b9ce2d1304d60e9c5422475205c4d15 SHA1 d787e83ea6da10c2cc815ffb034e935b3f686dcc SHA256 fd07782a763602b414446460bf91269e22ccf5ae1465b6b1daaac6321b83fd64
-MISC ChangeLog 1552 RMD160 b26708abb8e72299c2ac816777a4ab16f8d4a340 SHA1 1969544782ecc57750675f8b006e558abc830f1c SHA256 451d70ec63f74ee67476a0ac23f45d95bf675ca4aca390826e4f575e6d182990
+MISC ChangeLog 1657 RMD160 0a2ee08e15be765de57e24072d67ab85e70dde73 SHA1 f3d0ac5b0dda8e431a9e87c3f504dc88aea4ce12 SHA256 2313b4520e3854a963fdfb744d4695bdc98b534ef9397bb11ead7f19072b54b0
 MISC metadata.xml 532 RMD160 65faefb44be12c802b877c564528a7d947b7df90 SHA1 177502bff5b6a28d28d77fea9289e07653254e51 SHA256 4503c12d4f7786303e7bfdf5ed0840870d6767c04290d24acf33128f18634c01
diff --git a/media-gfx/librecad/librecad-1.0.0_rc2.ebuild b/media-gfx/librecad/librecad-1.0.0_rc2.ebuild
deleted file mode 100644
index 792915a42..000000000
--- a/media-gfx/librecad/librecad-1.0.0_rc2.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit qt4-r2
-
-DESCRIPTION="An generic 2D CAD program"
-HOMEPAGE="http://www.librecad.org/"
-SRC_URI="https://nodeload.github.com/LibreCAD/LibreCAD/tarball/1.0.0rc2 -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug doc"
-
-RDEPEND="
-	x11-libs/qt-gui[qt3support]
-	x11-libs/qt-assistant:4
-	x11-libs/qt-qt3support:4"
-DEPEND="${RDEPEND}"
-
-src_unpack() {
-	unpack ${A}
-	mv * ${P}
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-gcc4.6.patch \
-		"${FILESDIR}"/${P}-version.patch
-}
-
-src_install() {
-	dobin unix/librecad || die
-	insinto /usr/share/"${PN}"
-	doins -r unix/resources/* || die
-	if use doc ; then
-		dohtml -r support/doc/*
-	fi
-	doicon res/main/"${PN}".png
-	make_desktop_entry "${PN}" LibreCAD "${PN}.png" Graphics
-}
diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog
deleted file mode 100644
index 3fd80712f..000000000
--- a/sci-biology/bedtools/ChangeLog
+++ /dev/null
@@ -1,7 +0,0 @@
-# ChangeLog for sci-biology/bedtools
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  24 Jun 2011; Justin Lecher <jlec@gentoo.org> bedtools-2.10.1.ebuild:
-  SOme ebuild cleaning
-
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
deleted file mode 100644
index e3af7c57a..000000000
--- a/sci-biology/bedtools/Manifest
+++ /dev/null
@@ -1,14 +0,0 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-DIST BEDTools.v2.10.1.tar.gz 904396 RMD160 db6b9f103bff28a04479d243b05de7c8cb38c208 SHA1 67ece0f2747b6886de8ab9642365fa071d0fe32c SHA256 b128ee474827aad2a3bd8808aeaeca484120fc202ac5f1f7b805c21d0be76458
-EBUILD bedtools-2.10.1.ebuild 485 RMD160 039c6cbbceb4154a022fe95635bb00fac8e443fc SHA1 bacae16709812d7687b14a9f07fe6a4f680f38fa SHA256 efb1a05b1f80ac6a04747572380b6fe53827423cfa7c0a4e63f0f1228d4238ad
-MISC ChangeLog 216 RMD160 6779ba4504285979c47f966da1e0141322da629f SHA1 4fc8043870c49461873e220c9768396ea90376a3 SHA256 ebf9a0ba64734c49cad21cadb00c7c5633fc9680211dbf60975b5eb06a3a4907
-MISC metadata.xml 373 RMD160 492d63a640c8667cd2c3e48f9f79916348eaa425 SHA1 57afd5cc95b7a6fd4ed4ecdc8a2dd40f3036d6ba SHA256 9cd28401c75e322432ebbf23f9e9ba4c32154e951171de78c83668a33147e042
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-=sZl+
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diff --git a/sci-biology/bedtools/bedtools-2.10.1.ebuild b/sci-biology/bedtools/bedtools-2.10.1.ebuild
deleted file mode 100644
index 541b05647..000000000
--- a/sci-biology/bedtools/bedtools-2.10.1.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
-HOMEPAGE="http://code.google.com/p/bedtools/"
-SRC_URI="http://bedtools.googlecode.com/files/BEDTools.v${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-S="${WORKDIR}"BEDTools-Version-${PV}
-
-src_install(){
-	newbin bin/overlap bt_ovelap
-}
diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml
deleted file mode 100644
index 7789d7d4f..000000000
--- a/sci-biology/bedtools/metadata.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>no-herd</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<longdescription>BEDTools: a flexible suite of utilities for comparing genomic features.</longdescription>
-</pkgmetadata>
diff --git a/sci-physics/root/ChangeLog b/sci-physics/root/ChangeLog
index 77b72ad07..e5d0e093d 100644
--- a/sci-physics/root/ChangeLog
+++ b/sci-physics/root/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*root-5.28.00g (07 Oct 2011)
+
+  07 Oct 2011; Andrew Savchenko <bircoph@gmail.com>
+  +files/root-5.28.00b-nobyte-compile.patch, +root-5.28.00g.ebuild:
+  Version bump for 5.28 branch as requester per bug 384729.
+
 *root-5.30.02 (03 Oct 2011)
 
   03 Oct 2011; Andrew Savchenko <bircoph@gmail.com> +root-5.30.02.ebuild:
diff --git a/sci-physics/root/Manifest b/sci-physics/root/Manifest
index a5d230dd7..d22fa6348 100644
--- a/sci-physics/root/Manifest
+++ b/sci-physics/root/Manifest
@@ -4,6 +4,7 @@ AUX proofd.confd 415 RMD160 3814aacb63d82b9d060086f9bef304d431a15b4e SHA1 31eb7a
 AUX proofd.initd 717 RMD160 a1818375ca1e698f39823d2cdd829e84e6642284 SHA1 0eec6610e5619f2ef9ea614fa1c369d3f2018d3c SHA256 0e8c30f73d7086f71f3d44e6556060af7b62de9ca8262efc932f437246c9a843
 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-5.30.00-lzma.patch 533 RMD160 6ae18ea2b9562473466dd55bc305e3fe7f947904 SHA1 213f906f083a76428a36a46fdd33a07d1999c637 SHA256 eb8ff6193e40f855d4bd6cb7457260f9bf60d0518734aaa5ca6ed0253ded051c
@@ -16,11 +17,14 @@ AUX xrootd.initd 720 RMD160 8465440c1d60d1e713b05f91398300f32a90df0b SHA1 094134
 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 Users_Guide_5_26.pdf 9914765 RMD160 9e67a407d5a4d4f7019ab7b9b29bc696b7974987 SHA1 c2ecb87226e2fa38e6214aaf76dd789663d260dd SHA256 d0887800de7ffe7d6c0957891d44a4b34bf9d0eeb3da7e34b735ef998770bf39
+DIST root-5.28.00b-xrootd-prop-flags.patch.bz2 3894 RMD160 ef6b06d4783320ee7d6189dbe122ac49605bc6f4 SHA1 8026dda3cb74da40359ccc6d4ee787c01eee958b SHA256 093b1acd8336f5bb723802455296d8db884a2909a4e483cce637b8191039b4cd
+DIST root_v5.28.00g.source.tar.gz 31180580 RMD160 8fb03599a5aa44e0c601e4b74906a259d3c0afbb SHA1 4847369593015ff75dd5d5b7015f6771b619a77b SHA256 40fe67445eaea8ccfe539cd22eaf7383d9413fd3aad9d5e3cafb2ccebcacd49c
 DIST root_v5.30.00.source.tar.gz 40828616 RMD160 027558ac9b0d294fd26437ff31cb4e149f4dd7e7 SHA1 9549bd357e85bb3855abd78c7183c26dbd247fbb SHA256 9be4a4f01dde85d69d4746d5ee750f31abd6e73eff8738e67b4c50f7b52ec647
 DIST root_v5.30.01.source.tar.gz 40838436 RMD160 bc68936ac58dedd3138921d7d6fdab8097b4edb5 SHA1 d5297bbdcdb1df5a00520b82eda59577b25c53c8 SHA256 3cc27b8887d15b107fbc00d3da99f2fbb4d6c0e44835e44a160f3faf33815ee6
 DIST root_v5.30.02.source.tar.gz 40842401 RMD160 7a4f54935c986cf2335bd20ef380c3edb6266bce SHA1 0617b9a1dc7e040cb15c7133ad9399cf1b707d93 SHA256 e5d5874770ac0128606f7d20c560ce29498ec6b4ef45325d6206677f244d3b4e
+EBUILD root-5.28.00g.ebuild 10025 RMD160 65ff9bdba7257ccfd6734a3bbcb58b3f18777194 SHA1 363e8e381f757f5719c1ca41c322e0416b07b6d9 SHA256 7081183857331522101f13346c6ca8e211e4799b0c5a262f56afb571eb0f838a
 EBUILD root-5.30.00.ebuild 10162 RMD160 edb830c2b607211a310b576bab4525a6457f994d SHA1 9bba32d10a6c6f53cc64336a05efe770fdff2df2 SHA256 7e3e78e4d2ee6693890676411fa17a90ba229cfaa9054faafaf133ad0ac0688d
 EBUILD root-5.30.01.ebuild 10174 RMD160 7d2e97523f9b4a8531074744224ff730150934a3 SHA1 ece7a93d9cf5bba0b1286c647db6a04c0e2f5048 SHA256 39e63ed14b4a373a95e437b41479afb8fc1ab590daf1d3636e0145c5e078c9df
 EBUILD root-5.30.02.ebuild 10174 RMD160 7d2e97523f9b4a8531074744224ff730150934a3 SHA1 ece7a93d9cf5bba0b1286c647db6a04c0e2f5048 SHA256 39e63ed14b4a373a95e437b41479afb8fc1ab590daf1d3636e0145c5e078c9df
-MISC ChangeLog 1531 RMD160 1b76279409cc0b4ed6e2786528b4f3911a0f03ad SHA1 c635793382ef4177dea13269283b7a29d89e4311 SHA256 842cf62316b9fec62f4283cccee535f4f2d88c492ac2ee028e36228569d7ccb6
+MISC ChangeLog 1742 RMD160 407bba31059b45ff9ae9f6cfba8f700cbafe55f2 SHA1 96fd16428b20ad1582ee5b535b9fa6f5135e5bd5 SHA256 ffdaadc2a26ff51a903ddb7425637c5cd4203db6715fc06e551fa5daed9ce0e2
 MISC metadata.xml 1491 RMD160 65724809b563fa497bc739148758b89f4a14d52b SHA1 8c8078d0383141d06ca0467aad45d461fa3229ba SHA256 3ae2d0f5bd3c567a41c98be907e8ecdcd58175d64202d17623ffdf34371051f8
diff --git a/sci-physics/root/files/root-5.28.00b-nobyte-compile.patch b/sci-physics/root/files/root-5.28.00b-nobyte-compile.patch
new file mode 100644
index 000000000..7029bf169
--- /dev/null
+++ b/sci-physics/root/files/root-5.28.00b-nobyte-compile.patch
@@ -0,0 +1,138 @@
+diff -Naur root.orig/Makefile root/Makefile
+--- root.orig/Makefile	2010-12-17 22:48:40.577775091 +0300
++++ root/Makefile	2010-12-17 22:49:27.902497903 +0300
+@@ -1148,10 +1148,7 @@
+ 	   if test "x$(RFLX_GRFLXPY)" != "x"; then \
+ 	      rm -f $(DESTDIR)$(LIBDIR)/$(RFLX_GRFLXPY); \
+ 	   fi; \
+-	   if test "x$(RFLX_GRFLXPYC)" != "x"; then \
+-	      rm -f $(DESTDIR)$(LIBDIR)/$(RFLX_GRFLXPYC); \
+-	   fi; \
+-	   if test "x$(RFLX_GRFLXPY)$(RFLX_GRFLXPYC)" != "x"; then \
++	   if test "x$(RFLX_GRFLXPY)" != "x"; then \
+ 	      dir=$(RFLX_GRFLXDD:lib/=); \
+ 	      while test "x$${dir}" != "x" && \
+ 	         test -d $(DESTDIR)$(LIBDIR)/$${dir} && \
+diff -Naur root.orig/bindings/pyroot/Module.mk root/bindings/pyroot/Module.mk
+--- root.orig/bindings/pyroot/Module.mk	2010-12-17 22:48:39.941179413 +0300
++++ root/bindings/pyroot/Module.mk	2010-12-17 22:49:27.899164943 +0300
+@@ -48,8 +48,6 @@
+ ROOTPY       := $(subst $(MODDIR),$(LPATH),$(ROOTPYS))
+ $(LPATH)/%.py: $(MODDIR)/%.py; cp $< $@
+ endif
+-ROOTPYC      := $(ROOTPY:.py=.pyc)
+-ROOTPYO      := $(ROOTPY:.py=.pyo)
+ 
+ # used in the main Makefile
+ ALLHDRS      += $(patsubst $(MODDIRI)/%.h,include/%.h,$(PYROOTH))
+@@ -68,10 +66,8 @@
+ include/%.h:    $(PYROOTDIRI)/%.h
+ 		cp $< $@
+ 
+-%.pyc: %.py;    python -c 'import py_compile; py_compile.compile( "$<" )'
+-%.pyo: %.py;    python -O -c 'import py_compile; py_compile.compile( "$<" )'
+ 
+-$(PYROOTLIB):   $(PYROOTO) $(PYROOTDO) $(ROOTPY) $(ROOTPYC) $(ROOTPYO) \
++$(PYROOTLIB):   $(PYROOTO) $(PYROOTDO) $(ROOTPY) \
+                 $(ROOTLIBSDEP) $(PYTHONLIBDEP)
+ 		@$(MAKELIB) $(PLATFORM) $(LD) "$(LDFLAGS)" \
+ 		  "$(SOFLAGS)" libPyROOT.$(SOEXT) $@ \
+@@ -113,7 +109,7 @@
+ 
+ distclean-$(MODNAME): clean-$(MODNAME)
+ 		@rm -f $(PYROOTDEP) $(PYROOTDS) $(PYROOTDH) $(PYROOTLIB) \
+-		   $(ROOTPY) $(ROOTPYC) $(ROOTPYO) $(PYROOTMAP) \
++		   $(ROOTPY) $(PYROOTMAP) \
+ 		   $(PYROOTPYD) $(PYTHON64DEP) $(PYTHON64)
+ 
+ distclean::     distclean-$(MODNAME)
+diff -Naur root.orig/build/package/debian/rules root/build/package/debian/rules
+--- root.orig/build/package/debian/rules	2010-12-17 22:48:40.197817461 +0300
++++ root/build/package/debian/rules	2010-12-17 22:49:27.902497903 +0300
+@@ -623,10 +623,6 @@
+ 		-X$(SYSCONFDIR)/root/system.rootauthrc			\
+ 		-X$(SYSCONFDIR)/root/system.rootdaemonrc		\
+ 		-X$(PREFIX)/lib/root/$(SOVERS)/libAfterImage.a		\
+-		-X$(PREFIX)/lib/root/$(SOVERS)/PyCintex.pyc		\
+-		-X$(PREFIX)/lib/root/$(SOVERS)/PyCintex.pyo		\
+-		-X$(PREFIX)/lib/root/$(SOVERS)/ROOT.pyc			\
+-		-X$(PREFIX)/lib/root/$(SOVERS)/ROOT.pyo			
+ #		$(foreach i, \
+ #		   $(wildcard $(DTMP)/$(PREFIX)/lib/root/lib*.so.$(SOVERS)), \
+ #		    -X$(i:$(DTMP)/%=%) )
+diff -Naur root.orig/cint/cintex/Module.mk root/cint/cintex/Module.mk
+--- root.orig/cint/cintex/Module.mk	2010-12-17 22:48:40.057833071 +0300
++++ root/cint/cintex/Module.mk	2010-12-17 22:49:27.902497903 +0300
+@@ -31,10 +31,6 @@
+ CINTEXPY     := $(subst $(MODDIR)/python,$(LPATH),$(CINTEXPYS))
+ $(LPATH)/%.py: $(MODDIR)/python/%.py; cp $< $@
+ endif
+-ifneq ($(BUILDPYTHON),no)
+-CINTEXPYC    := $(CINTEXPY:.py=.pyc)
+-CINTEXPYO    := $(CINTEXPY:.py=.pyo)
+-endif
+ 
+ # used in the main Makefile
+ ALLHDRS      += $(patsubst $(MODDIRI)/Cintex/%.h,include/Cintex/%.h,$(CINTEXH))
+@@ -86,8 +82,6 @@
+ 		fi)
+ 		cp $< $@
+ 
+-%.pyc: %.py;    python -c 'import py_compile; py_compile.compile( "$<" )'
+-%.pyo: %.py;    python -O -c 'import py_compile; py_compile.compile( "$<" )'
+ 
+ $(CINTEXLIB):   $(CINTEXO) $(CINTEXPY) $(CINTEXPYC) $(CINTEXPYO) \
+                 $(ORDER_) $(subst $(CINTEXLIB),,$(MAINLIBS)) $(CINTEXLIBDEP)
+diff -Naur root.orig/cint/reflex/Module.mk root/cint/reflex/Module.mk
+--- root.orig/cint/reflex/Module.mk	2010-12-17 22:48:40.037835301 +0300
++++ root/cint/reflex/Module.mk	2010-12-17 22:51:36.871451359 +0300
+@@ -48,9 +48,6 @@
+ RFLX_GRFLXS   := $(wildcard $(RFLX_GRFLXSD)/*.py)
+ RFLX_GRFLXPY  := $(patsubst $(RFLX_GRFLXSD)/%.py,$(RFLX_GRFLXDD)/%.py,$(RFLX_GRFLXS))
+ RFLX_GRFLXPY  += $(RFLX_GCCXMLPATHPY)
+-ifneq ($(BUILDPYTHON),no)
+-RFLX_GRFLXPYC := $(subst .py,.pyc,$(RFLX_GRFLXPY))
+-endif
+ 
+ RFLX_LIBDIR = $(LIBDIR)
+ 
+@@ -92,7 +89,7 @@
+ 
+ ALLEXECS += $(RFLX_GENMAPX)
+ 
+-POSTBIN  += $(RFLX_GRFLXPYC) $(RFLX_GRFLXPY)
++POSTBIN  += $(RFLX_GRFLXPY)
+ 
+ ##### local rules #####
+ .PHONY:         all-$(MODNAME) clean-$(MODNAME) distclean-$(MODNAME) \
+@@ -122,8 +119,6 @@
+ 		  mkdir -p lib/python/genreflex; fi )
+ 		cp $< $@
+ 
+-$(RFLX_GRFLXDD)/%.pyc: $(RFLX_GRFLXDD)/%.py
+-		@python -c 'import py_compile; py_compile.compile( "$<" )'
+ 
+ $(RFLX_GENMAPO) : CXXFLAGS += -I$(REFLEXDIRS)/genmap
+ 
+@@ -149,7 +144,7 @@
+ 		$(RLIBMAP) -o $@ -l $(REFLEXDICTLIB) \
+ 		   -d $(REFLEXDICTLIBDEPM) -c $(REFLEXL)
+ 
+-all-$(MODNAME): $(REFLEXLIB) $(REFLEXDICTLIB) $(REFLEXDICTMAP) $(RFLX_GRFLXPYC) $(RFLX_GRFLXPY)
++all-$(MODNAME): $(REFLEXLIB) $(REFLEXDICTLIB) $(REFLEXDICTMAP) $(RFLX_GRFLXPY)
+ 
+ clean-genreflex:
+ 		@rm -rf lib/python/genreflex
+diff -Naur root.orig/cint/reflex/python/CMakeLists.txt root/cint/reflex/python/CMakeLists.txt
+--- root.orig/cint/reflex/python/CMakeLists.txt	2010-12-17 22:48:40.037835301 +0300
++++ root/cint/reflex/python/CMakeLists.txt	2010-12-17 22:49:27.902497903 +0300
+@@ -15,7 +15,7 @@
+ #####################   sources   ####################
+ 
+ FILE(GLOB_RECURSE GENREFLEX_SRCS RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} genreflex/*.py)
+-SET(GENREFLEX_SCRIPT ${CMAKE_CURRENT_BINARY_DIR}/genreflex/genreflex.pyc PARENT_SCOPE)
++SET(GENREFLEX_SCRIPT PARENT_SCOPE)
+ 
+ #####################  gccxmlpath ####################
+ 
+
diff --git a/sci-physics/root/root-5.28.00g.ebuild b/sci-physics/root/root-5.28.00g.ebuild
new file mode 100644
index 000000000..89904116d
--- /dev/null
+++ b/sci-physics/root/root-5.28.00g.ebuild
@@ -0,0 +1,332 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.28.00d.ebuild,v 1.3 2011/06/21 14:31:50 jlec Exp $
+
+EAPI=3
+PYTHON_DEPEND="python? 2"
+inherit versionator eutils fortran-2 elisp-common fdo-mime python toolchain-funcs flag-o-matic
+
+#DOC_PV=$(get_major_version)_$(get_version_component_range 2)
+DOC_PV=5_26
+ROOFIT_DOC_PV=2.91-33
+TMVA_DOC_PV=4.03
+PATCH_PV=5.28.00b
+
+DESCRIPTION="C++ data analysis framework and interpreter from CERN"
+HOMEPAGE="http://root.cern.ch/"
+SRC_URI="ftp://root.cern.ch/${PN}/${PN}_v${PV}.source.tar.gz
+	http://dev.gentoo.org/~bicatali/${PN}-${PATCH_PV}-xrootd-prop-flags.patch.bz2
+	doc? ( ftp://root.cern.ch/${PN}/doc/Users_Guide_${DOC_PV}.pdf
+	math? (
+		ftp://root.cern.ch/${PN}/doc/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf
+		http://tmva.sourceforge.net/docu/TMVAUsersGuide.pdf -> TMVAUsersGuide-v${TMVA_DOC_PV}.pdf ) )"
+
+SLOT="0"
+LICENSE="LGPL-2.1"
+KEYWORDS="~amd64 ~x86"
+IUSE="afs avahi clarens doc emacs examples fits fftw graphviz kerberos ldap
+	llvm +math mpi mysql ncurses odbc +opengl openmp oracle postgres pythia6
+	pythia8	python +reflex ruby qt4 ssl xft xml xinetd xrootd"
+
+CDEPEND=">=dev-lang/cfortran-4.4-r2
+	dev-libs/libpcre
+	media-libs/ftgl
+	media-libs/giflib
+	media-libs/glew
+	media-libs/libpng
+	media-libs/tiff
+	sys-apps/shadow
+	virtual/jpeg
+	x11-libs/libX11
+	x11-libs/libXext
+	x11-libs/libXft
+	x11-libs/libXpm
+	|| ( >=media-libs/libafterimage-1.20 >=x11-wm/afterstep-2.2.11 )
+	afs? ( net-fs/openafs )
+	avahi? ( net-dns/avahi )
+	clarens? ( dev-libs/xmlrpc-c )
+	emacs? ( virtual/emacs )
+	fits? ( sci-libs/cfitsio )
+	fftw? ( sci-libs/fftw:3.0 )
+	graphviz? ( media-gfx/graphviz )
+	kerberos? ( virtual/krb5 )
+	ldap? ( net-nds/openldap )
+	llvm? ( sys-devel/llvm )
+	math? ( sci-libs/gsl sci-mathematics/unuran mpi? ( virtual/mpi ) )
+	mysql? ( virtual/mysql )
+	ncurses? ( sys-libs/ncurses )
+	odbc? ( || ( dev-db/libiodbc dev-db/unixODBC ) )
+	opengl? ( virtual/opengl virtual/glu x11-libs/gl2ps )
+	oracle? ( dev-db/oracle-instantclient-basic )
+	postgres? ( dev-db/postgresql-base )
+	pythia6? ( sci-physics/pythia:6 )
+	pythia8? ( sci-physics/pythia:8 )
+	qt4? ( x11-libs/qt-gui:4
+		x11-libs/qt-opengl:4
+		x11-libs/qt-qt3support:4
+		x11-libs/qt-svg:4
+		x11-libs/qt-webkit:4
+		x11-libs/qt-xmlpatterns:4 )
+	ruby? ( dev-lang/ruby
+			dev-ruby/rubygems )
+	ssl? ( dev-libs/openssl )
+	xml? ( dev-libs/libxml2 )"
+
+DEPEND="${CDEPEND}
+	dev-util/pkgconfig"
+
+RDEPEND="
+	virtual/fortran
+${CDEPEND}
+	reflex? ( dev-cpp/gccxml )
+	xinetd? ( sys-apps/xinetd )"
+
+S="${WORKDIR}/${PN}"
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	elog
+	elog "There are extra options on packages not yet in Gentoo:"
+	elog "AliEn, castor, Chirp, dCache, gfal, gLite, Globus,"
+	elog "HDFS, Monalisa, MaxDB/SapDB, SRP."
+	elog "You can use the env variable EXTRA_ECONF variable for this."
+	elog "For example, for SRP, you would set: "
+	elog "EXTRA_ECONF=\"--enable-srp --with-srp-libdir=/usr/$(get_libdir)\""
+	elog
+	enewgroup rootd
+	enewuser rootd -1 -1 /var/spool/rootd rootd
+
+	if use math; then
+		if use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then
+			ewarn "You are using gcc and OpenMP is available with gcc >= 4.2"
+			ewarn "If you want to build this package with OpenMP, abort now,"
+			ewarn "and set CC to an OpenMP capable compiler"
+		elif use openmp; then
+			export USE_OPENMP=1 USE_PARALLEL_MINUIT2=1
+		elif use mpi; then
+			export USE_MPI=1 USE_PARALLEL_MINUIT2=1
+		fi
+	fi
+}
+
+src_prepare() {
+	epatch \
+		"${WORKDIR}"/${PN}-${PATCH_PV}-xrootd-prop-flags.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV}-prop-ldflags.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV}-asneeded.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV}-nobyte-compile.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV}-glibc212.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV}-unuran.patch
+
+	# make sure we use system libs and headers
+	rm montecarlo/eg/inc/cfortran.h README/cfortran.doc
+	rm -rf graf2d/asimage/src/libAfterImage
+	rm -rf graf3d/ftgl/{inc,src}
+	rm -rf graf2d/freetype/src
+	rm -rf graf3d/glew/{inc,src}
+	rm -rf core/pcre/src
+	rm -rf math/unuran/src/unuran-*.tar.gz
+	find core/zip -type f -name "[a-z]*" | xargs rm
+	rm graf3d/gl/{inc,src}/gl2ps.*
+	sed -i -e 's/^GLLIBS *:= .* $(OPENGLLIB)/& -lgl2ps/' graf3d/gl/Module.mk
+
+	# TODO: unbundle xrootd as a new package
+	#rm -rf net/xrootd/src
+	#sed -i \
+	#	-e 's:-lXrdOuc:-lXrd &:' \
+	#	-e 's:$(XROOTDDIRL)/lib\(Xrd\w*\).a:-l\1:g' \
+	#	proof/proofd/Module.mk || die
+
+	# In Gentoo, libPythia6 is called libpythia6
+	# libungif is called libgif,
+	# iodbc is in /usr/include/iodbc
+	# pg_config.h is checked instead of libpq-fe.h
+	sed -i \
+		-e 's:libPythia6:libpythia6:g' \
+		-e 's:ungif:gif:g' \
+		-e 's:$ODBCINC:$ODBCINC /usr/include/iodbc:' \
+		-e 's:libpq-fe.h:pg_config.h:' \
+		configure || die "adjusting configure for Gentoo failed"
+
+	# prefixify the configure script
+	sed -i \
+		-e 's:/usr:${EPREFIX}/usr:g' \
+		configure || die "prefixify configure failed"
+
+	# QTDIR only used for qt3 in gentoo, and configure looks for it.
+	unset QTDIR
+}
+
+src_configure() {
+	# the configure script is not the standard autotools
+	./configure \
+		--prefix="${EPREFIX}"/usr \
+		--etcdir="${EPREFIX}"/etc/root \
+		--libdir="${EPREFIX}"/usr/$(get_libdir)/${PN} \
+		--docdir="${EPREFIX}"/usr/share/doc/${PF} \
+		--tutdir="${EPREFIX}"/usr/share/doc/${PF}/examples/tutorials \
+		--testdir="${EPREFIX}"/usr/share/doc/${PF}/examples/tests \
+		--with-cc=$(tc-getCC) \
+		--with-cxx=$(tc-getCXX) \
+		--with-f77=$(tc-getFC) \
+		--with-sys-iconpath="${EPREFIX}"/usr/share/pixmaps \
+		--disable-builtin-afterimage \
+		--disable-builtin-freetype \
+		--disable-builtin-ftgl \
+		--disable-builtin-glew \
+		--disable-builtin-pcre \
+		--disable-builtin-zlib \
+		--disable-rpath \
+		--enable-asimage \
+		--enable-astiff \
+		--enable-exceptions	\
+		--enable-explicitlink \
+		--enable-gdml \
+		--enable-memstat \
+		--enable-shadowpw \
+		--enable-shared	\
+		--enable-soversion \
+		--enable-table \
+		--fail-on-missing \
+		--with-afs-shared=yes \
+		$(use_enable afs) \
+		$(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) \
+		$(use_enable kerberos krb5) \
+		$(use_enable ldap) \
+		$(use_enable llvm cling) \
+		$(use_enable math gsl-shared) \
+		$(use_enable math genvector) \
+		$(use_enable math mathmore) \
+		$(use_enable math minuit2) \
+		$(use_enable math roofit) \
+		$(use_enable math tmva) \
+		$(use_enable math unuran) \
+		$(use_enable mysql) \
+		$(use_enable odbc) \
+		$(use_enable opengl) \
+		$(use_enable postgres pgsql) \
+		$(use_enable pythia6) \
+		$(use_enable pythia8) \
+		$(use_enable python) \
+		$(use_enable qt4 qt) \
+		$(use_enable qt4 qtgsi) \
+		$(use_enable reflex cintex) \
+		$(use_enable reflex) \
+		$(use_enable ruby) \
+		$(use_enable ssl) \
+		$(use_enable xft) \
+		$(use_enable xml) \
+		$(use_enable xrootd) \
+		${EXTRA_ECONF} \
+		|| die "configure failed"
+}
+
+src_compile() {
+	emake OPT="${CFLAGS}" F77OPT="${FFLAGS}" || die "emake failed"
+	if use emacs; then
+		elisp-compile build/misc/*.el || die "elisp-compile failed"
+	fi
+}
+
+doc_install() {
+	cd "${S}"
+	if use doc; then
+		einfo "Installing user's guides"
+		dodoc "${DISTDIR}"/Users_Guide_${DOC_PV}.pdf \
+		use math && dodoc \
+			"${DISTDIR}"/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf \
+			"${DISTDIR}"/TMVAUsersGuide-v${TMVA_DOC_PV}.pdf
+	fi
+
+	if use examples; then
+		# these should really be taken care of by the root make install
+		insinto /usr/share/doc/${PF}/examples/tutorials/tmva
+		doins -r tmva/test
+	else
+		rm -rf "${ED}"/usr/share/doc/${PF}/examples
+	fi
+}
+
+daemon_install() {
+	cd "${S}"
+	local daemons="rootd proofd"
+	dodir /var/spool/rootd
+	fowners rootd:rootd /var/spool/rootd
+	dodir /var/spool/rootd/{pub,tmp}
+	fperms 1777 /var/spool/rootd/{pub,tmp}
+
+	use xrootd && daemons="${daemons} xrootd olbd"
+	for i in ${daemons}; do
+		newinitd "${FILESDIR}"/${i}.initd ${i}
+		newconfd "${FILESDIR}"/${i}.confd ${i}
+	done
+	if use xinetd; then
+		insinto /etc/xinetd
+		doins etc/daemons/{rootd,proofd}.xinetd
+	fi
+}
+
+desktop_install() {
+	cd "${S}"
+	sed -e 's,@prefix@,/usr,' \
+		build/package/debian/root-system-bin.desktop.in > root.desktop
+	domenu root.desktop
+	doicon "${S}"/build/package/debian/root-system-bin.png
+
+	insinto /usr/share/icons/hicolor/48x48/mimetypes
+	doins build/package/debian/application-x-root.png
+
+	insinto /usr/share/icons/hicolor/48x48/apps
+	doicon build/package/debian/root-system-bin.xpm
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die "emake install failed"
+
+	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/root" > 99root
+	use pythia8 && echo "PYTHIA8=${EPREFIX}/usr" >> 99root
+	use python && echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/root" >> 99root
+	use ruby && echo "RUBYLIB=${EPREFIX}/usr/$(get_libdir)/root" >> 99root
+	doenvd 99root || die "doenvd failed"
+
+	# The build system installs Emacs support unconditionally and in the wrong
+	# directory. Remove it and call elisp-install in case of USE=emacs.
+	rm -rf "${ED}"/usr/share/emacs
+	if use emacs; then
+		elisp-install ${PN} build/misc/*.{el,elc} || die "elisp-install failed"
+	fi
+
+	doc_install
+	daemon_install
+	desktop_install
+
+	# Cleanup of files either already distributed or unused on Gentoo
+	rm "${ED}"usr/share/doc/${PF}/{INSTALL,LICENSE,COPYING.CINT}
+	rm "${ED}"usr/share/root/fonts/LICENSE
+	pushd "${ED}"usr/$(get_libdir)/root/cint/cint/lib > /dev/null
+	rm -f posix/mktypes dll_stl/setup \
+		G__* dll_stl/G__* dll_stl/rootcint_* posix/exten.o
+	rm -f "${ED}"usr/$(get_libdir)/root/cint/cint/include/makehpib
+	rm -f "${ED}"/etc/root/proof/*.sample
+	rm -rf "${ED}"/etc/root/daemons
+	popd > /dev/null
+	# these should be in PATH
+	mv "${ED}"usr/share/root/proof/utils/pq2/pq2* \
+		"${ED}"usr/bin
+}
+
+pkg_postinst() {
+	fdo-mime_desktop_database_update
+	use python && python_mod_optimize /usr/$(get_libdir)/root
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+	use python && python_mod_cleanup /usr/$(get_libdir)/root
+}