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ebuild start here---------------------------------

 inherit kde-functions eutils libtool flag-o-matic

 DESCRIPTION="WYSIWYM frontend for LaTeX"
 HOMEPAGE="http://www.lyx.org/"
 SRC_URI="ftp://ftp.devel.lyx.org/pub/lyx/pre/lyx-1.4.0pre3.tar.bz2
	http://movementarian.org/latex-xft-fonts-0.1.tar.gz
	http://www.math.tau.ac.il/~dekelts/lyx/files/hebrew.bind
	http://www.math.tau.ac.il/~dekelts/lyx/files/preferences"


 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~sparc ~x86"
 IUSE="cjk cups debug nls qt"

 # these dependencies need looking at.
 # does lyx only need qt to compile but not run ?
 # I'll look into it <obz@gentoo.org>
 DEPEND="virtual/x11
	virtual/tetex
	>=dev-lang/perl-5
	nls? ( sys-devel/gettext )
	app-text/aiksaurus
	qt? ( =x11-libs/qt-3* )
	!qt? ( cjk? ( =x11-libs/xforms-1.0-r1 )
		!cjk? ( =x11-libs/xforms-1* ) )"

 RDEPEND="${DEPEND}
	virtual/ghostscript
	virtual/pdfviewer
	virtual/psviewer
	virtual/aspell-dict
	dev-tex/latex2html
	media-gfx/imagemagick
	cups? ( virtual/lpr )
	app-text/sgmltools-lite
	app-text/noweb
	dev-tex/chktex"

 DEPEND="$DEPEND >=sys-devel/autoconf-2.58"

 src_unpack() {
	unpack lyx-1.4.0pre3.tar.bz2
	mv ${WORKDIR}/lyx-1.4.0pre3 ${WORKDIR}/lyx-1.4.0_pre3
	unpack latex-xft-fonts-0.1.tar.gz
	cd ${S}
	# epatch ${FILESDIR}/${P}-gentoo.diff
	# if use cjk && use qt ; then
	# 	epatch ${DISTDIR}/CJK-LyX-qt-${PV}-1.patch
	# elif use cjk && built_with_use '=x11-libs/xforms-1.0-r1' cjk ; then
	# 	epatch ${DISTDIR}/CJK-LyX-xforms-${PV}-1.patch
	# elif use cjk ; then
	#	eerror
	#	eerror 'CJK-LyX requires qt USE flag enabled or x11-libs/xforms-1.0-r1'
	#	eerror 'built with cjk USE flag. You should either'
	#	eerror '1) USE="cjk qt" emerge lyx'
	#	eerror 'or'
	#	eerror '2) USE="cjk" emerge xforms-1.0-r1; USE="cjk -qt" emerge lyx'
	#	eerror 'or'
	#	eerror '3) USE="-cjk" emerge lyx (normal LyX will be built)'
	#	eerror
	#	die "Please remerge xforms-1.0-r1 with cjk USE flag enabled."
	# fi
	elibtoolize || die
 }

 src_compile() {
	local myconf=""
	if use qt ; then
		set-qtdir 3
		myconf="$myconf --with-frontend=qt --with-qt-dir=${QTDIR}"
	else
		export CPPFLAGS="${CPPFLAGS} -I/usr/X11R6/include/X11"
		myconf="$myconf --with-frontend=xforms"
	fi

	export WANT_AUTOCONF=2.5

	local flags="${CXXFLAGS} $(test_flag -fno-stack-protector) $(test_flag -fno-stack-protector-all)"
	unset CFLAGS
	unset CXXFLAGS
	econf 		$(use_enable nls) 		$(use_enable debug) 		${myconf} 		--enable-optimization="${flags/-Os}" 		|| die
	# bug 57479
	emake || die "emake failed"

 }

 src_install() {
	einstall || die
	dodoc README* UPGRADING INSTALL* ChangeLog NEWS COPYING 		ANNOUNCE ABOUT-NLS ${DISTDIR}/preferences
	insinto /usr/share/lyx/bind
	doins ${DISTDIR}/hebrew.bind

	domenu ${FILESDIR}/lyx.desktop

	# install the latex-xft fonts, which should fix
	# the problems outlined in bug #15629
	# <obz@gentoo.org>
	cd ${WORKDIR}/latex-xft-fonts-0.1
	make DESTDIR=${D} install || die "Font installation failed"

	mkfontscale ${D}/usr/share/fonts/latex-xft-fonts
	mkfontdir -e /usr/share/fonts/encodings 		-e /usr/share/fonts/encodings/large 		-e /usr/X11R6/$(get_libdir)/X11/fonts/encodings 		${D}/usr/share/fonts/latex-xft-fonts
	HOME=/root fc-cache -f ${D}/usr/share/fonts/latex-xft-fonts

	# fix for bug 91108
	dodir /usr/share/texmf/tex/latex
	cd ${D}/usr/share/texmf/tex/latex
	ln -s ../../../lyx/tex lyx
 }

 pkg_postinst() {

	# fix for bug 91108
	texhash

	draw_line
	einfo ""
	einfo "How to use Hebrew in LyX:"
	einfo "1. emerge app-text/ivritex."
	einfo "2. unzip /usr/share/doc/${P}/preferences.gz into ~/.lyx/preferences"
	einfo "or, read http://www.math.tau.ac.il/~dekelts/lyx/instructions2.html"
	einfo "for instructions on using lyx's own preferences dialog to equal effect."
	einfo "3. use lyx's qt interface (compile with USE=qt) for maximum effect."
	einfo ""

	if ! useq qt ; then
	draw_line
	einfo ""
	einfo "If you have a multi-head setup not using xinerama you can only use lyx"
	einfo "on the 2nd head if not using qt (maybe due to a xforms bug). See bug #40392."
	einfo ""
	fi
 }

ebuild stops here------------------------------------------------

It's quick and dirty... but it works. To use it inside portage only run following command.

 ebuild lyx-1.4.0_pre3.ebuild digest

User Note: With modular X I had to erase virtual/x11 to make it work.