sci-physics/root: Merge changes from sci overlay

(Portage version: 2.2.7/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

3 files changed, 457 insertions, 21 deletions

diff --git a/sci-physics/root/ChangeLog b/sci-physics/root/ChangeLog
index eba237eb7813..553b118b3ee8 100644
--- a/sci-physics/root/ChangeLog
+++ b/sci-physics/root/ChangeLog
@@ -1,6 +1,17 @@
 # ChangeLog for sci-physics/root
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/ChangeLog,v 1.125 2013/12/05 17:34:12 bicatali Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/ChangeLog,v 1.126 2013/12/10 16:41:01 jlec Exp $
+
+*root-5.34.13-r1 (10 Dec 2013)
+
+  10 Dec 2013; Justin Lecher <jlec@gentoo.org> +root-5.34.13-r1.ebuild,
+  metadata.xml:
+  Merge changes from sci overlay
+
+  10 Dec 2013; Andrew Savchenko <bircoph@gmail.com> -root-5.34.10-r2.ebuild,
+  root-5.34.13.ebuild, -files/root-5.28.00b-unuran.patch:
+  Add ROOTPrimer and Spectrum user guides.
+  Remove old versions.
 
 *root-5.34.13 (05 Dec 2013)
 
diff --git a/sci-physics/root/metadata.xml b/sci-physics/root/metadata.xml
index c4e415433298..bdcb7471a9dd 100644
--- a/sci-physics/root/metadata.xml
+++ b/sci-physics/root/metadata.xml
@@ -1,14 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<maintainer>
-  <email>bircoph@gmail.com</email>
-  <name>Andrew Savchenko</name>
-  <description>Maintainer. Assign bugs to him</description>
-</maintainer>
-<herd>sci-physics</herd>
-<herd>proxy-maintainers</herd>
-<longdescription lang="en">
+  <maintainer>
+    <email>bircoph@gmail.com</email>
+    <name>Andrew Savchenko</name>
+    <description>Maintainer. Assign bugs to him</description>
+  </maintainer>
+  <herd>sci-physics</herd>
+  <herd>proxy-maintainers</herd>
+  <longdescription lang="en">
   ROOT Object Oriented Technologies is an object oriented data
   analysis framework written in C++ by the CERN. Widely used in
   high energy physics, but also in other data analysis applications. It
@@ -16,16 +16,16 @@
   statistics, serialization, optimization, linear algebra, graphics,
   GUI toolkit, and a complete visualization framework.
 </longdescription>
-<use>
-  <flag name="c++0x"> Build ROOT using the C++11 standard. Not supported, requires <pkg>sys-devel/gcc</pkg>&gt;=4.7.0</flag>
-  <flag name="clarens"> Build the Clarens and PEAC plug-ins, to use in a GRID enabled analysis</flag>
-  <flag name="fits">Support for images and data from FITS files with <pkg>sci-libs/cfitsio</pkg></flag>
-  <flag name="htmldoc">Generate html documentation</flag>
-  <flag name="math">Build all math related libraries plugins, needs <pkg>sci-libs/gsl</pkg> </flag>
-  <flag name="metric">Default to A4 paper size and metric measurement</flag>
-  <flag name="pythia6">Build the interface for <pkg>sci-physics/pythia</pkg> version 6.x </flag>
-  <flag name="pythia8">Build the interface for <pkg>sci-physics/pythia</pkg> version 8.x </flag>
-  <flag name="reflex">Build the reflection database for the C++ interpreter</flag>
-  <flag name="xrootd">Build the interface for <pkg>net-libs/xrootd</pkg> </flag>
-</use>
+  <use>
+    <flag name="c++0x"> Build ROOT using the C++11 standard. Not supported, requires <pkg>sys-devel/gcc</pkg>&gt;=4.7.0</flag>
+    <flag name="clarens"> Build the Clarens and PEAC plug-ins, to use in a GRID enabled analysis</flag>
+    <flag name="fits">Support for images and data from FITS files with <pkg>sci-libs/cfitsio</pkg></flag>
+    <flag name="htmldoc">Generate html documentation</flag>
+    <flag name="math">Build all math related libraries plugins, needs <pkg>sci-libs/gsl</pkg> </flag>
+    <flag name="metric">Default to A4 paper size and metric measurement</flag>
+    <flag name="pythia6">Build the interface for <pkg>sci-physics/pythia</pkg> version 6.x </flag>
+    <flag name="pythia8">Build the interface for <pkg>sci-physics/pythia</pkg> version 8.x </flag>
+    <flag name="reflex">Build the reflection database for the C++ interpreter</flag>
+    <flag name="xrootd">Build the interface for <pkg>net-libs/xrootd</pkg> </flag>
+  </use>
 </pkgmetadata>
diff --git a/sci-physics/root/root-5.34.13-r1.ebuild b/sci-physics/root/root-5.34.13-r1.ebuild
new file mode 100644
index 000000000000..12a1521a10f6
--- /dev/null
+++ b/sci-physics/root/root-5.34.13-r1.ebuild
@@ -0,0 +1,425 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.34.13-r1.ebuild,v 1.1 2013/12/10 16:41:01 jlec Exp $
+
+EAPI=5
+
+if [[ ${PV} == "9999" ]] ; then
+	_GIT=git-2
+	EGIT_REPO_URI="http://root.cern.ch/git/root.git"
+	SRC_URI=""
+	KEYWORDS=""
+else
+	SRC_URI="ftp://root.cern.ch/${PN}/${PN}_v${PV}.source.tar.gz"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+PYTHON_COMPAT=( python2_{6,7} )
+inherit elisp-common eutils fdo-mime fortran-2 ${_GIT} multilib python-single-r1 toolchain-funcs user versionator
+
+ROOFIT_DOC_PV=2.91-33
+TMVA_DOC_PV=4.03
+PATCH_PV=5.28.00b
+PATCH_PV2=5.32.00
+PATCH_PV3=5.34.05
+PATCH_PV4=5.34.13
+
+DESCRIPTION="C++ data analysis framework and interpreter from CERN"
+HOMEPAGE="http://root.cern.ch/"
+SRC_URI="${SRC_URI}
+	!minimal? ( doc? (
+		math? (
+			ftp://root.cern.ch/${PN}/doc/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf
+			http://tmva.sourceforge.net/docu/TMVAUsersGuide.pdf -> TMVAUsersGuide-v${TMVA_DOC_PV}.pdf
+			metric? ( ftp://root.cern.ch/root/doc/spectrum/Spectrum.pdf -> Spectrum-${PV}.pdf )
+			!metric? ( ftp://root.cern.ch/root/doc/spectrum/SpectrumLetter.pdf -> SpectrumLetter-${PV}.pdf )
+		)
+		metric? (
+			ftp://root.cern.ch/${PN}/doc/ROOTUsersGuideA4.pdf -> ROOTUsersGuideA4-${PV}.pdf
+			ftp://root.cern.ch/root/doc/primer/ROOTPrimer.pdf -> ROOTPrimer-${PV}.pdf )
+		!metric? (
+			ftp://root.cern.ch/${PN}/doc/ROOTUsersGuideLetter.pdf -> ROOTUsersGuideLetter-${PV}.pdf
+			ftp://root.cern.ch/root/doc/primer/ROOTPrimerLetter.pdf -> ROOTPrimerLetter-${PV}.pdf )
+		htmldoc? (
+			http://root.cern.ch/drupal/sites/default/files/rootdrawing-logo.png
+			http://root.cern.ch/drupal/sites/all/themes/newsflash/images/blue/root-banner.png
+			http://root.cern.ch/drupal/sites/all/themes/newsflash/images/info.png )
+	) )"
+
+SLOT="0"
+LICENSE="LGPL-2.1"
+IUSE="+X afs avahi c++0x doc emacs examples fits fftw graphviz htmldoc
+	kerberos ldap +math +metric minimal mpi mysql odbc +opengl openmp oracle postgres
+	prefix pythia6 pythia8 python qt4 +reflex ruby sqlite ssl xinetd xml xrootd"
+
+REQUIRED_USE="
+	!X? ( !opengl !qt4 )
+	htmldoc? ( doc )
+	mpi? ( math !openmp )
+	openmp? ( math !mpi )
+	python? ( ${PYTHON_REQUIRED_USE} )"
+
+CDEPEND="
+	app-arch/xz-utils
+	>=dev-lang/cfortran-4.4-r2
+	dev-libs/libpcre
+	media-fonts/dejavu
+	media-libs/freetype
+	media-libs/giflib
+	media-libs/libpng:0
+	media-libs/tiff:0
+	sys-libs/zlib
+	virtual/jpeg
+	virtual/shadow
+	X? (
+		media-libs/ftgl
+		media-libs/glew
+		x11-libs/libX11
+		x11-libs/libXext
+		x11-libs/libXpm
+		!minimal? (
+			|| (
+				>=media-libs/libafterimage-1.20[gif,jpeg,png,tiff]
+				>=x11-wm/afterstep-2.2.11[gif,jpeg,png,tiff]
+			)
+			opengl? ( virtual/opengl virtual/glu x11-libs/gl2ps )
+			qt4? (
+				dev-qt/qtgui:4
+				dev-qt/qtopengl:4
+				dev-qt/qt3support:4
+				dev-qt/qtsvg:4
+				dev-qt/qtwebkit:4
+				dev-qt/qtxmlpatterns:4
+			)
+			x11-libs/libXft
+		)
+	)
+	!minimal? (
+		afs? ( net-fs/openafs )
+		avahi? ( net-dns/avahi )
+		emacs? ( virtual/emacs )
+		fits? ( sci-libs/cfitsio )
+		fftw? ( sci-libs/fftw:3.0 )
+		graphviz? ( media-gfx/graphviz )
+		kerberos? ( virtual/krb5 )
+		ldap? ( net-nds/openldap )
+		math? ( sci-libs/gsl sci-mathematics/unuran mpi? ( virtual/mpi ) )
+		mysql? ( virtual/mysql )
+		odbc? ( || ( dev-db/libiodbc dev-db/unixODBC ) )
+		oracle? ( dev-db/oracle-instantclient-basic )
+		postgres? ( dev-db/postgresql-base )
+		pythia6? ( sci-physics/pythia:6 )
+		pythia8? ( >=sci-physics/pythia-8.1.80:8 )
+		python? ( ${PYTHON_DEPS} )
+		ruby? (
+				dev-lang/ruby
+				dev-ruby/rubygems )
+		sqlite? ( dev-db/sqlite:3 )
+		ssl? ( dev-libs/openssl )
+		xml? ( dev-libs/libxml2 )
+		xrootd? ( >=net-libs/xrootd-3.2.0 )
+	)"
+
+DEPEND="${CDEPEND}
+	virtual/pkgconfig"
+
+RDEPEND="${CDEPEND}
+	reflex? ( dev-cpp/gccxml )
+	xinetd? ( sys-apps/xinetd )"
+
+PDEPEND="htmldoc? ( ~app-doc/root-docs-${PV} )"
+
+S="${WORKDIR}/${PN}"
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	use python && python-single-r1_pkg_setup
+	echo
+	elog "There are extra options on packages not yet in Gentoo:"
+	elog "Afdsmgrd, AliEn, castor, Chirp, dCache, gfal, Globus, gLite,"
+	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=${EROOT%/}/usr/$(get_libdir)\""
+	echo
+	enewgroup rootd
+	enewuser rootd -1 -1 /var/spool/rootd rootd
+	use minimal && return
+
+	if use math; then
+		if use openmp; then
+			if [[ $(tc-getCXX)$ == *g++* ]] && ! tc-has-openmp; then
+				ewarn "You are using a g++ without OpenMP capabilities"
+				die "Need an OpenMP capable compiler"
+			else
+				export USE_OPENMP=1 USE_PARALLEL_MINUIT2=1
+			fi
+		elif use mpi; then
+			export USE_MPI=1 USE_PARALLEL_MINUIT2=1
+		fi
+	fi
+	if use c++0x && [[ $(tc-getCXX) == *g++* ]] && \
+		! version_is_at_least "4.7" "$(gcc-version)"; then
+		eerror "You are using a g++ without C++0x capabilities"
+		die "Need an C++0x capable compiler"
+	fi
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PN}-${PATCH_PV2}-prop-flags.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV3}-nobyte-compile.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV}-glibc212.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV4}-unuran.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV2}-afs.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV2}-cfitsio.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV2}-chklib64.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV2}-dotfont.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV4}-pythia8.patch \
+		"${FILESDIR}"/${PN}-${PATCH_PV4}-desktop.patch
+
+	# make sure we use system libs and headers
+	rm montecarlo/eg/inc/cfortran.h README/cfortran.doc || die
+	rm -r graf2d/asimage/src/libAfterImage || die
+	rm -r graf3d/ftgl/{inc,src} || die
+	rm -r graf2d/freetype/src || die
+	rm -r graf3d/glew/{inc,src} || die
+	rm -r core/pcre/src || die
+	rm -r math/unuran/src/unuran-*.tar.gz || die
+	LANG=C LC_ALL=C find core/zip -type f -name "[a-z]*" -print0 | xargs -0 rm -f || die
+	rm -r core/lzma/src/*.tar.gz || die
+	rm graf3d/gl/{inc,src}/gl2ps.* || die
+	sed -i -e 's/^GLLIBS *:= .* $(OPENGLLIB)/& -lgl2ps/' graf3d/gl/Module.mk || die
+
+	# In Gentoo, libPythia6 is called libpythia6
+	# libungif is called libgif,
+	# iodbc is in /usr/include/iodbc
+	# pg_config.h is checked instead of libpq-fe.h
+	sed -i \
+		-e 's:libPythia6:libpythia6:g' \
+		-e 's:ungif:gif:g' \
+		-e 's:$ODBCINCDIR:$ODBCINCDIR /usr/include/iodbc:' \
+		-e 's:libpq-fe.h:pg_config.h:' \
+		configure || die "adjusting configure for Gentoo failed"
+
+	# prefixify the configure script
+	sed -i \
+		-e 's:/usr:${EPREFIX}/usr:g' \
+		configure || die "prefixify configure failed"
+
+	# QTDIR only used for qt3 in gentoo, and configure looks for it.
+	unset QTDIR
+
+	# Make html docs self-consistent for offline work (based on Fedora spec)
+	if use htmldoc && ! use minimal; then
+		epatch "${FILESDIR}"/${PN}-${PATCH_PV2}-htmldoc.patch
+		# make images local
+		sed 's!http://root.cern.ch/drupal/sites/all/themes/newsflash/images/blue/!!' \
+			-i etc/html/ROOT.css || die "htmldoc sed failed"
+		sed 's!http://root.cern.ch/drupal/sites/all/themes/newsflash/images/!!' \
+			-i etc/html/ROOT.css || die "htmldoc sed failed"
+		sed 's!http://root.cern.ch/drupal/sites/default/files/!!' \
+			-i etc/html/header.html || die "htmldoc sed failed"
+
+		cp "${DISTDIR}"/{rootdrawing-logo.png,root-banner.png,info.png} etc/html ||
+			die "htmldoc preparation failed"
+	fi
+}
+
+src_configure() {
+	# the configure script is not the standard autotools
+	local mycommonconf="
+		--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-ld=$(tc-getCXX) \
+		--nohowto
+	"
+	if use minimal; then
+		./configure \
+			${mycommonconf} \
+			$(usex X --gminimal --minimal) \
+			|| die "configure failed"
+		return
+	fi
+	# cling is disabled because in requires live llvm and clang
+	./configure \
+		${mycommonconf} \
+		--with-afs-shared=yes \
+		--with-sys-iconpath="${EPREFIX}"/usr/share/pixmaps \
+		--disable-builtin-afterimage \
+		--disable-builtin-ftgl \
+		--disable-builtin-freetype \
+		--disable-builtin-glew \
+		--disable-builtin-pcre \
+		--disable-builtin-zlib \
+		--disable-builtin-lzma \
+		--disable-cling \
+		--enable-astiff \
+		--enable-explicitlink \
+		--enable-gdml \
+		--enable-memstat \
+		--enable-shadowpw \
+		--enable-shared	\
+		--enable-soversion \
+		--enable-table \
+		--fail-on-missing \
+		$(use_enable X x11) \
+		$(use_enable X asimage) \
+		$(use_enable X xft) \
+		$(use_enable afs) \
+		$(use_enable avahi bonjour) \
+		$(use_enable c++0x cxx11) \
+		$(use_enable fits fitsio) \
+		$(use_enable fftw fftw3) \
+		$(use_enable graphviz gviz) \
+		$(use_enable kerberos krb5) \
+		$(use_enable ldap) \
+		$(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 oracle) \
+		$(use_enable postgres pgsql) \
+		$(usex postgres "--with-pgsql-incdir=$(pg_config --includedir)" "") \
+		$(use_enable prefix rpath) \
+		$(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 sqlite) \
+		$(use_enable ssl) \
+		$(use_enable xml) \
+		$(use_enable xrootd) \
+		${EXTRA_ECONF} \
+		|| die "configure failed"
+}
+
+src_compile() {
+	emake OPT="${CXXFLAGS}" F77OPT="${FFLAGS}" ROOTSYS="${S}" LD_LIBRARY_PATH="${S}/lib"
+	if use emacs && ! use minimal; then
+		elisp-compile build/misc/*.el || die "elisp-compile failed"
+	fi
+}
+
+doc_install() {
+	cd "${S}"
+	if use doc && ! use minimal; then
+		einfo "Installing user's guides"
+		if use metric; then
+			dodoc "${DISTDIR}"/ROOTUsersGuideA4-${PV}.pdf
+			dodoc "${DISTDIR}"/ROOTPrimer-${PV}.pdf
+			use math && dodoc "${DISTDIR}"/Spectrum-${PV}.pdf
+		else
+			dodoc "${DISTDIR}"/ROOTUsersGuideLetter-${PV}.pdf
+			dodoc "${DISTDIR}"/ROOTPrimerLetter-${PV}.pdf
+			use math && dodoc "${DISTDIR}"/SpectrumLetter-${PV}.pdf
+		fi
+		use math && dodoc \
+			"${DISTDIR}"/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf \
+			"${DISTDIR}"/TMVAUsersGuide-v${TMVA_DOC_PV}.pdf
+	fi
+
+	if use examples && ! use minimal; then
+		# these should really be taken care of by the root make install
+		insinto /usr/share/doc/${PF}/examples/tutorials/tmva
+		doins -r tmva/test
+	else
+		rm -r "${ED}"/usr/share/doc/${PF}/examples || die
+	fi
+}
+
+daemon_install() {
+	cd "${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}
+
+	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}"
+	echo "Icon=root-system-bin" >> etc/root.desktop
+	domenu etc/root.desktop
+	doicon 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="${D}" install
+
+	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/root" > 99root
+	if ! use minimal; then
+		use pythia8 && echo "PYTHIA8=${EPREFIX}/usr" >> 99root
+		if use python; then
+			echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/root" >> 99root
+			python_optimize "${D}/usr/$(get_libdir)/root"
+		fi
+		use ruby && echo "RUBYLIB=${EPREFIX}/usr/$(get_libdir)/root" >> 99root
+	fi
+	doenvd 99root
+
+	# The build system installs Emacs support unconditionally and in the wrong
+	# directory. Remove it and call elisp-install in case of USE=emacs.
+	rm -r "${ED}"/usr/share/emacs
+	if use emacs && ! use minimal; 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/${PF}/{INSTALL,LICENSE,COPYING.CINT} || die
+	rm "${ED}"usr/share/root/fonts/LICENSE || die
+	pushd "${ED}"usr/$(get_libdir)/root/cint/cint/lib > /dev/null
+	rm posix/mktypes dll_stl/setup \
+		G__* dll_stl/G__* dll_stl/rootcint_* posix/exten.o || die
+	rm "${ED}"usr/$(get_libdir)/root/cint/cint/include/makehpib || die
+	rm "${ED}"/etc/root/proof/*.sample || die
+	rm -r "${ED}"/etc/root/daemons || die
+	popd > /dev/null
+	# these should be in PATH
+	mv "${ED}"etc/root/proof/utils/pq2/pq2* \
+		"${ED}"usr/bin/ || die
+}
+
+pkg_postinst() {
+	fdo-mime_desktop_database_update
+}
+
+pkg_postrm() {
+	fdo-mime_desktop_database_update
+}