Drop old

(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

4 files changed, 7 insertions, 790 deletions

diff --git a/sci-chemistry/ccp4-apps/ChangeLog b/sci-chemistry/ccp4-apps/ChangeLog
index cd79b931501c..5ffa7d7eb663 100644
--- a/sci-chemistry/ccp4-apps/ChangeLog
+++ b/sci-chemistry/ccp4-apps/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-chemistry/ccp4-apps
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.46 2015/03/25 14:07:43 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.47 2015/05/05 08:53:26 jlec Exp $
+
+  05 May 2015; Justin Lecher <jlec@gentoo.org> -ccp4-apps-6.1.3-r11.ebuild,
+  -ccp4-apps-6.1.3-r12.ebuild, ccp4-apps-6.1.3-r13.ebuild:
+  Drop old
 
   25 Mar 2015; Agostino Sarubbo <ago@gentoo.org> ccp4-apps-6.1.3-r13.ebuild:
   Stable for x86, wrt bug #542694
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r11.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r11.ebuild
deleted file mode 100644
index c2bc7d86b316..000000000000
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r11.ebuild
+++ /dev/null
@@ -1,392 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r11.ebuild,v 1.5 2015/03/09 13:24:16 jlec Exp $
-
-EAPI=3
-
-PYTHON_DEPEND="2"
-
-inherit autotools eutils fortran-2 flag-o-matic gnuconfig python toolchain-funcs
-
-MY_P="${PN/-apps}-${PV}"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-PATCH_TOT="0"
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-SRC_URI="
-	${SRC}/${PV}/${MY_P}-core-src.tar.gz
-	http://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2"
-# patch tarball from upstream
-	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
-# patches created by us
-	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
-
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
-IUSE="examples X"
-
-X11DEPS="
-	x11-libs/libX11
-	x11-libs/libXaw
-	x11-libs/libXt
-	x11-libs/libxdl_view"
-
-TKDEPS="
-	>=dev-lang/tk-8.3
-	>=dev-tcltk/blt-2.4
-	dev-tcltk/iwidgets
-	dev-tcltk/itcl
-	dev-tcltk/itk
-	>=dev-tcltk/tdom-0.8
-	dev-tcltk/tktreectrl"
-
-SCILIBS="
-	~sci-libs/ccp4-libs-${PV}
-	>=sci-libs/ccp4-libs-${PV}-r7
-	sci-libs/clipper
-	sci-libs/fftw:2.1
-	sci-libs/mmdb:0
-	sci-libs/ssm
-	virtual/blas
-	virtual/lapack"
-
-SCIAPPS="
-	sci-chemistry/pdb-extract
-	sci-chemistry/pymol
-	sci-chemistry/rasmol
-	>=sci-chemistry/oasis-4.0-r1"
-
-RDEPEND="
-	${TKDEPS}
-	${SCILIBS}
-	app-shells/tcsh
-	dev-python/pyxml
-	dev-libs/libxml2:2
-	dev-libs/libjwc_c
-	dev-libs/libjwc_f
-	dev-libs/boehm-gc
-	!app-office/sc
-	!<sci-chemistry/ccp4-6.1.3
-	X? ( ${X11DEPS} )"
-DEPEND="${RDEPEND}
-	X? (
-		x11-misc/imake
-		x11-proto/inputproto
-		x11-proto/xextproto
-	)"
-PDEPEND="${SCIAPPS}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python_set_active_version 2
-}
-
-src_prepare() {
-	tc-export PKG_CONFIG
-	einfo "Applying upstream patches ..."
-	for patch in $(seq $PATCH_TOT); do
-		base="PATCH${patch}"
-		dir=$(eval echo \${${base}[0]})
-		p=$(eval echo \${${base}[1]})
-		pushd "${dir}" >& /dev/null
-		ccp_patch "${DISTDIR}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-
-	# it tries to create libdir, bindir etc on live system in configure
-	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# We already have sci-chemistry/rasmol
-	# Also remember to create the bindir.
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch
-
-	# libraries come from sci-libs/ccp4-libs
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
-
-	# We have seperate ebuilds for those
-	for bin in molref xia scala imosflm balbes; do
-		ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch
-	done
-
-	# don't configure what is not build
-	ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-pisa.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch
-
-	# Fix upstreams code
-	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
-
-	# Not renaming, but unbundling libs
-	ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch
-
-	# Use pkg-config to detect BLAS/LAPCK
-	ccp_patch "${FILESDIR}"/${PV}-lapack.patch
-
-	# Update things for oasis 4 usage
-	epatch "${WORKDIR}"/${PV}-oasis4.0.patch
-	sed 's: oasis : :g' -i src/Makefile.in || die
-
-	# unbundle libs
-	ccp_patch "${FILESDIR}"/${PV}-unbundle.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete
-
-	sed \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		-e 's:-Wl,-rpath,$CLIB::g' \
-		-e 's: -rpath $CLIB::g' \
-		-e 's: -I${srcdir}/include/cpp_c_headers::g' \
-		-e 's:sleep 1:sleep .2:g' \
-		-e 's:\\$(XCIF_LIB):-L$srcdir/lib/ccif -lccif:g' \
-		-e 's:\\$(XLAPACK_LIB):${XLAPACK_LIB}:g' \
-		-e 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' \
-		-e 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' \
-		-i configure || die
-
-	sed \
-		-e '/o crunch2/s:$: ${XLAPACK_LIB}:g' \
-		-i src/Makefile* || die
-
-	find "${S}" -name "Makefile.*" \
-		-exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \;
-
-	# Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version
-	sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die
-
-	# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
-	pushd src/rapper 2>/dev/null
-		eautoreconf
-	popd 2>/dev/null
-
-	gnuconfig_update
-
-	python_convert_shebangs $(python_get_version) src/ccp4_pipeline_simple.py ./share/smartie/*.py
-}
-
-src_configure() {
-	# Build system is broken if we set LDFLAGS
-	export GENTOOLDFLAGS="${LDFLAGS}"
-	unset LDFLAGS
-
-	# These are broken with ./src/procheck/ps.f
-	filter-flags "-floop-*"
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "$(tc-getFC)" = "ifort" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure || die
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=$(tc-getFC)
-	export FOPTIM=${FFLAGS:- -O2}
-	export BINSORT_SCR="${T}"
-	export CCP4_MASTER="${WORKDIR}"
-	export CCP4I_TCLTK="${EPREFIX}/usr/bin"
-	export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		$(use_enable X x) \
-		--with-shared-libs \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-warnings \
-		--disable-pdb_extract \
-		--disable-cctbx \
-		--disable-phaser \
-		--disable-diffractionImg \
-		--disable-clipper \
-		--disable-ssm \
-		--disable-mosflm \
-		--disable-mrbump \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "configure failed"
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-	econf \
-		--prefix="${S}" \
-		--bindir="${ED}"/usr/libexec/ccp4/bin \
-		--with-ccp4="${S}" \
-		--with-clipper="${EPREFIX}/usr" \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-mmdb="${EPREFIX}/usr" \
-		CXX=$(tc-getCXX)
-	popd 2>/dev/null
-}
-
-src_compile() {
-	# fsplit is required for the programs
-	pushd lib/src 2>/dev/null
-		emake fsplit -j1 || die
-	popd 2>/dev/null
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-		emake || die
-	popd 2>/dev/null
-
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	# if we don't make this, a ton of programs fail to install
-	mkdir "${S}"/bin || die
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd "${S}"/src/clipper_progs 2>/dev/null
-		emake install || die
-	popd 2>/dev/null
-
-	einstall || die "install failed"
-
-	# Collision with sci-chemistry/mrbump
-	rm -f "${S}"/bin/{mrbump,pydbviewer} || die
-
-	# Bins
-	exeinto /usr/libexec/ccp4/bin/
-	doexe "${S}"/bin/* || die
-
-	# Libs
-	for file in "${S}"/lib/*; do
-		if [[ -d ${file} ]]; then
-			continue
-		elif [[ -x ${file} ]]; then
-			dolib.so ${file} || die
-		else
-			insinto /usr/$(get_libdir)
-			doins ${file} || die
-		fi
-	done
-
-	rm -f "${S}"/include/ccp4.setup*
-
-	# smartie -- log parsing
-	insinto /usr/share/ccp4
-	doins -r "${S}"/share/smartie || die
-
-	# Install docs and examples
-	local _man
-	pushd "${S}"/man/cat1 > /dev/null
-	for _man in *; do
-		newman ${_man} ${_man%??}-ccp4${_man:${#_man}-2:2}
-	done
-	popd > /dev/null
-
-	mv "${S}"/manual/README "${S}"/manual/README-manual
-	dodoc manual/* README CHANGES doc/* examples/README || die
-
-	rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.*
-	rm "${ED}"/usr/share/doc/${PF}/COPYING.*
-
-	dohtml -r "${S}"/html/*
-
-	if use examples; then
-		for i in data rnase toxd; do
-			docinto examples/${i}
-			dodoc "${S}"/examples/${i}/*
-		done
-
-		docinto examples/tutorial
-		dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css
-		for i in data results; do
-			docinto examples/tutorial/${i}
-			dodoc "${S}"/examples/tutorial/${i}/*
-		done
-
-		for i in non-runnable runnable; do
-			docinto examples/unix/${i}
-			dodoc "${S}"/examples/unix/${i}/*
-		done
-	fi
-	# Needed for ccp4i docs to work
-	dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die
-
-	cat >> "${T}"/baubles <<- EOF
-	#!${EPREFIX}/bin/bash
-	exec $(PYTHON) \${CCP4}/share/ccp4/smartie/baubles.py
-	EOF
-
-	exeinto /usr/libexec/ccp4/bin/
-	doexe "${T}"/baubles || die
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r12.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r12.ebuild
deleted file mode 100644
index a3e9a6fe1307..000000000000
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r12.ebuild
+++ /dev/null
@@ -1,395 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r12.ebuild,v 1.4 2015/03/09 13:24:16 jlec Exp $
-
-EAPI=3
-
-PYTHON_DEPEND="2"
-
-inherit autotools eutils fortran-2 flag-o-matic gnuconfig python toolchain-funcs
-
-MY_P="${PN/-apps}-${PV}"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-PATCH_TOT="0"
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-SRC_URI="
-	${SRC}/${PV}/${MY_P}-core-src.tar.gz
-	http://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2"
-# patch tarball from upstream
-	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
-# patches created by us
-	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
-
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples X"
-
-X11DEPS="
-	x11-libs/libX11
-	x11-libs/libXaw
-	x11-libs/libXt
-	x11-libs/libxdl_view"
-
-TKDEPS="
-	>=dev-lang/tk-8.3
-	>=dev-tcltk/blt-2.4
-	dev-tcltk/iwidgets
-	dev-tcltk/itcl
-	dev-tcltk/itk
-	>=dev-tcltk/tdom-0.8
-	dev-tcltk/tktreectrl"
-
-SCILIBS="
-	~sci-libs/ccp4-libs-${PV}
-	>=sci-libs/ccp4-libs-${PV}-r7
-	sci-libs/clipper
-	sci-libs/fftw:2.1
-	sci-libs/mmdb:0
-	sci-libs/ssm
-	virtual/blas
-	virtual/lapack"
-
-SCIAPPS="
-	sci-chemistry/pdb-extract
-	sci-chemistry/pymol
-	sci-chemistry/rasmol
-	>=sci-chemistry/oasis-4.0-r1"
-
-RDEPEND="
-	${TKDEPS}
-	${SCILIBS}
-	app-shells/tcsh
-	dev-python/pyxml
-	dev-libs/libxml2:2
-	dev-libs/libjwc_c
-	dev-libs/libjwc_f
-	dev-libs/boehm-gc
-	!app-office/sc
-	!<sci-chemistry/ccp4-6.1.3
-	X? ( ${X11DEPS} )"
-DEPEND="${RDEPEND}
-	X? (
-		x11-misc/imake
-		x11-proto/inputproto
-		x11-proto/xextproto
-	)"
-PDEPEND="${SCIAPPS}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python_set_active_version 2
-}
-
-src_prepare() {
-	tc-export PKG_CONFIG
-	einfo "Applying upstream patches ..."
-	for patch in $(seq $PATCH_TOT); do
-		base="PATCH${patch}"
-		dir=$(eval echo \${${base}[0]})
-		p=$(eval echo \${${base}[1]})
-		pushd "${dir}" >& /dev/null
-		ccp_patch "${DISTDIR}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-
-	# it tries to create libdir, bindir etc on live system in configure
-	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# We already have sci-chemistry/rasmol
-	# Also remember to create the bindir.
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch
-
-	# libraries come from sci-libs/ccp4-libs
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
-
-	# We have seperate ebuilds for those
-	for bin in molref xia scala imosflm balbes; do
-		ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch
-	done
-
-	# don't configure what is not build
-	ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-pisa.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch
-
-	# Fix upstreams code
-	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
-
-	# Not renaming, but unbundling libs
-	ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch
-
-	# Use pkg-config to detect BLAS/LAPCK
-	ccp_patch "${FILESDIR}"/${PV}-lapack.patch
-
-	# unbundle libs
-	ccp_patch "${FILESDIR}"/${PV}-unbundle.patch
-
-	# tcl-8.6
-	ccp_patch "${FILESDIR}"/${P}-tcl8.6.patch
-
-	# Update things for oasis 4 usage
-	epatch "${WORKDIR}"/${PV}-oasis4.0.patch
-	sed 's: oasis : :g' -i src/Makefile.in || die
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete
-
-	sed \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		-e 's:-Wl,-rpath,$CLIB::g' \
-		-e 's: -rpath $CLIB::g' \
-		-e 's: -I${srcdir}/include/cpp_c_headers::g' \
-		-e 's:sleep 1:sleep .2:g' \
-		-e 's:\\$(XCIF_LIB):-L$srcdir/lib/ccif -lccif:g' \
-		-e 's:\\$(XLAPACK_LIB):${XLAPACK_LIB}:g' \
-		-e 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' \
-		-e 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' \
-		-i configure || die
-
-	sed \
-		-e '/o crunch2/s:$: ${XLAPACK_LIB}:g' \
-		-i src/Makefile* || die
-
-	find "${S}" -name "Makefile.*" \
-		-exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \;
-
-	# Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version
-	sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die
-
-	# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
-	pushd src/rapper 2>/dev/null
-		eautoreconf
-	popd 2>/dev/null
-
-	gnuconfig_update
-
-	python_convert_shebangs $(python_get_version) src/ccp4_pipeline_simple.py ./share/smartie/*.py
-}
-
-src_configure() {
-	# Build system is broken if we set LDFLAGS
-	export GENTOOLDFLAGS="${LDFLAGS}"
-	unset LDFLAGS
-
-	# These are broken with ./src/procheck/ps.f
-	filter-flags "-floop-*"
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "$(tc-getFC)" = "ifort" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure || die
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=$(tc-getFC)
-	export FOPTIM=${FFLAGS:- -O2}
-	export BINSORT_SCR="${T}"
-	export CCP4_MASTER="${WORKDIR}"
-	export CCP4I_TCLTK="${EPREFIX}/usr/bin"
-	export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		$(use_enable X x) \
-		--with-shared-libs \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-warnings \
-		--disable-pdb_extract \
-		--disable-cctbx \
-		--disable-phaser \
-		--disable-diffractionImg \
-		--disable-clipper \
-		--disable-ssm \
-		--disable-mosflm \
-		--disable-mrbump \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "configure failed"
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-	econf \
-		--prefix="${S}" \
-		--bindir="${ED}"/usr/libexec/ccp4/bin \
-		--with-ccp4="${S}" \
-		--with-clipper="${EPREFIX}/usr" \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-mmdb="${EPREFIX}/usr" \
-		CXX=$(tc-getCXX)
-	popd 2>/dev/null
-}
-
-src_compile() {
-	# fsplit is required for the programs
-	pushd lib/src 2>/dev/null
-		emake fsplit -j1 || die
-	popd 2>/dev/null
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-		emake || die
-	popd 2>/dev/null
-
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	# if we don't make this, a ton of programs fail to install
-	mkdir "${S}"/bin || die
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd "${S}"/src/clipper_progs 2>/dev/null
-		emake install || die
-	popd 2>/dev/null
-
-	einstall || die "install failed"
-
-	# Collision with sci-chemistry/mrbump
-	rm -f "${S}"/bin/{mrbump,pydbviewer} || die
-
-	# Bins
-	exeinto /usr/libexec/ccp4/bin/
-	doexe "${S}"/bin/* || die
-
-	# Libs
-	for file in "${S}"/lib/*; do
-		if [[ -d ${file} ]]; then
-			continue
-		elif [[ -x ${file} ]]; then
-			dolib.so ${file} || die
-		else
-			insinto /usr/$(get_libdir)
-			doins ${file} || die
-		fi
-	done
-
-	rm -f "${S}"/include/ccp4.setup*
-
-	# smartie -- log parsing
-	insinto /usr/share/ccp4
-	doins -r "${S}"/share/smartie || die
-
-	# Install docs and examples
-	local _man
-	pushd "${S}"/man/cat1 > /dev/null
-	for _man in *; do
-		newman ${_man} ${_man%??}-ccp4${_man:${#_man}-2:2}
-	done
-	popd > /dev/null
-
-	mv "${S}"/manual/README "${S}"/manual/README-manual
-	dodoc manual/* README CHANGES doc/* examples/README || die
-
-	rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.*
-	rm "${ED}"/usr/share/doc/${PF}/COPYING.*
-
-	dohtml -r "${S}"/html/*
-
-	if use examples; then
-		for i in data rnase toxd; do
-			docinto examples/${i}
-			dodoc "${S}"/examples/${i}/*
-		done
-
-		docinto examples/tutorial
-		dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css
-		for i in data results; do
-			docinto examples/tutorial/${i}
-			dodoc "${S}"/examples/tutorial/${i}/*
-		done
-
-		for i in non-runnable runnable; do
-			docinto examples/unix/${i}
-			dodoc "${S}"/examples/unix/${i}/*
-		done
-	fi
-	# Needed for ccp4i docs to work
-	dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die
-
-	cat >> "${T}"/baubles <<- EOF
-	#!${EPREFIX}/bin/bash
-	exec $(PYTHON) \${CCP4}/share/ccp4/smartie/baubles.py
-	EOF
-
-	exeinto /usr/libexec/ccp4/bin/
-	doexe "${T}"/baubles || die
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild
index 76923ea8a289..3db7c60c81ca 100644
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild
+++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild,v 1.4 2015/03/25 14:07:43 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild,v 1.5 2015/05/05 08:53:26 jlec Exp $
 
 EAPI=5
 
@@ -44,7 +44,7 @@ X11DEPS="
 	x11-libs/libxdl_view"
 
 TKDEPS="
-	>=dev-lang/tk-8.3
+	>=dev-lang/tk-8.3:0=
 	>=dev-tcltk/blt-2.4
 	dev-tcltk/iwidgets
 	dev-tcltk/itcl