sci-chemistry/ccp4: Drop old

(Portage version: 2.2.0_alpha101/cvs/Linux x86_64)

5 files changed, 5 insertions, 1383 deletions

diff --git a/sci-chemistry/ccp4/ChangeLog b/sci-chemistry/ccp4/ChangeLog
index 6bf443a3a523..861302dcb905 100644
--- a/sci-chemistry/ccp4/ChangeLog
+++ b/sci-chemistry/ccp4/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-chemistry/ccp4
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ChangeLog,v 1.33 2012/04/14 09:59:34 nativemad Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ChangeLog,v 1.34 2012/04/26 15:51:26 jlec Exp $
+
+  26 Apr 2012; Justin Lecher <jlec@gentoo.org> -ccp4-6.0.1-r1.ebuild,
+  -ccp4-6.0.2.ebuild, -ccp4-6.0.2-r1.ebuild, -ccp4-6.1.3.ebuild:
+  Drop old
 
   14 Apr 2012; Andreas Schuerch <nativemad@gentoo.org> ccp4-6.1.3-r1.ebuild:
   x86 stable, see bug 376463
diff --git a/sci-chemistry/ccp4/ccp4-6.0.1-r1.ebuild b/sci-chemistry/ccp4/ccp4-6.0.1-r1.ebuild
deleted file mode 100644
index 7b6aa7dd02cb..000000000000
--- a/sci-chemistry/ccp4/ccp4-6.0.1-r1.ebuild
+++ /dev/null
@@ -1,453 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ccp4-6.0.1-r1.ebuild,v 1.13 2011/06/21 16:05:14 jlec Exp $
-
-inherit eutils fortran-2 gnuconfig toolchain-funcs
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-PATCH_TOT="12"
-PATCH1=( src/mmdb_app_
-	chainsaw.cpp-11May2006.diff )
-PATCH2=( src
-	anisoanl.f-r1.22-r1.24.diff )
-PATCH3=( src/sc_
-	sc.f-r1.9-r1.9.2.1.diff )
-PATCH4=( src/sc_
-	setup.fh-r1.5-r1.5.2.1.diff )
-PATCH5=( src
-	contact.f-12June2006.diff )
-PATCH6=( ccp4i/tasks
-	refmac5.tcl-r1.39.2.3-r1.42.diff )
-PATCH7=( src
-	act.f-6July2006.diff )
-PATCH8=( src
-	rotmat.f-17July2006.diff )
-PATCH9=( src/molrep_
-	molrep.f-r1.28-r1.28.2.1.diff )
-PATCH10=( src
-	cad.f-r1.70-r1.72.diff )
-PATCH11=( src
-	mtztona4.f-r1.23-r1.24.diff )
-PATCH12=( src
-	omit.f-r1.12-r1.13.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-SRC_URI="${SRC}/${PV}/packed/${P}-core-src.tar.gz"
-
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="ppc x86"
-IUSE="X"
-
-# app-office/sc overlaps sc binary and man page
-# We can't rename ours since the automated ccp4i interface expects it there,
-# as do many scripts. app-office/sc can't rename its because that's the name
-# of the package.
-RDEPEND="
-	virtual/fortran
-
-		>=dev-lang/tcl-8.3
-		>=dev-lang/tk-8.3
-		>=dev-tcltk/blt-2.4
-		virtual/lapack
-		virtual/blas
-		=sci-libs/fftw-2*
-		sci-chemistry/pdb-extract
-		sci-chemistry/rasmol
-		sci-libs/mccp4
-		app-shells/tcsh
-		!app-office/sc
-		X? (
-			x11-libs/libX11
-			x11-libs/libXt
-			x11-libs/libXaw
-		)"
-DEPEND="${RDEPEND}
-		X? (
-			x11-misc/imake
-			x11-proto/inputproto
-			x11-proto/xextproto
-		)"
-
-S="${WORKDIR}/${PN}-${PV}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	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}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	einfo "Applying Gentoo patches ..."
-	# These two only needed when attempting to install outside build dir via
-	# --bindir and --libdir instead of straight copying after build
-
-	# it attempts to install some libraries during the build
-	#ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
-	# hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
-	# without this patch when --libdir is set
-	# Rotgen still needs more patching to find it
-	#ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
-
-	# 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
-	ccp_patch "${FILESDIR}"/dont-build-rasmol.patch
-
-	# We already have sci-chemistry/pdb-extract
-# Use configure option instead
-#	ccp_patch "${FILESDIR}"/dont-build-pdb-extract.patch
-
-	ccp_patch "${FILESDIR}"/create-mosflm-bindir.patch
-	ccp_patch "${FILESDIR}"/make-mosflm-libdir.patch
-	ccp_patch "${FILESDIR}"/make-mosflm-index-libdir.patch
-	ccp_patch "${FILESDIR}"/make-mosflm-cbf-libdir.patch
-	ccp_patch "${FILESDIR}"/make-ipmosflm-dir.patch
-
-# Don't use these when we aren't building phaser
-#	ccp_patch "${FILESDIR}"/make-phaser-bindir.patch
-#	ccp_patch "${FILESDIR}"/no-phaser-ld-assume-kernel.patch
-#	# scons config.py tries to chmod python on live system
-#	ccp_patch "${FILESDIR}"/dont-chmod-python-binary.patch
-
-	# Don't use this when we aren't building clipper
-	# For some reason clipper check for $enableval even when --enable is passed
-	ccp_patch "${FILESDIR}"/pass-clipper-enablevals.patch
-	ccp_patch "${FILESDIR}"/clipper-find-mccp4-includes.patch
-
-	# Default to firefox browser, not 'netscape'
-	ccp_patch "${FILESDIR}"/ccp4i-default-to-firefox.patch
-
-	# Also use -lpthread when linking blas and lapack
-	# We may need more fixing to use libcblas for the C files
-	ccp_patch "${FILESDIR}"/check-blas-lapack-pthread.patch
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch "${FILESDIR}"/${PV}-ppc-double-define-gerror.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "$(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
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
-		"${S}"/include/ccp4.setup*
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-	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}
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		$(use_enable X x) \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-pdb_extract \
-		--disable-cctbx \
-		--disable-phaser \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-# Only needed when using --bindir and --libdir
-	# Needed to avoid errors. Originally tried to make lib and bin
-	# in configure script, now patched out by dont-make-dirs-in-configure.patch
-#	dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-#	make install || die "install failed"
-	einstall || die "install failed"
-
-	# Fix env
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \
-		-e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
-		-e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
-		-e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
-		-e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \
-		-e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \
-		-e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \
-		-e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \
-		"${S}"/include/ccp4.setup*
-
-	# Get rid of S instances
-	# Also the main clipper library is built as libclipper-core, not libclipper
-	sed -i \
-		-e "s:${S}:usr:g" \
-		-e "s:lclipper :lclipper-core :g" \
-		"${S}"/bin/clipper-config
-#	sed -i \
-#		-e "s:${S}:usr:g" \
-#		"${S}"/$(get_libdir)/cctbx/cctbx_build/setpaths*
-
-	# Bins
-	dobin "${S}"/bin/* || die
-
-	# Libs
-	for file in "${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
-
-	# Fix libdir in all *.la files
-	sed -i \
-		-e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
-		"${D}"/usr/$(get_libdir)/*.la
-
-	# Library symlinks
-	local LIBNAMES="libclipper-ccp4.so.0.0.0
-		libclipper-cif.so.0.0.0
-		libclipper-contrib.so.0.0.0
-		libclipper-core.so.0.0.0
-		libclipper-minimol.so.0.0.0
-		libclipper-mmdbold.so.0.0.0
-		libclipper-mmdb.so.0.0.0
-		libclipper-mtz.so.1.0.0
-		libclipper-phs.so.0.0.0
-		libjwc_c.so.0.1.1
-		libjwc_f.so.0.1.1
-		libssm.so.0.0.0
-		libxdl_viewextra.so.0.0.0
-		libxdl_view.so.2.0.0"
-
-	for LIBNAME in ${LIBNAMES}; do
-		library_dosym ${LIBNAME}
-	done
-
-#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so
-#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0
-#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0.0
-#
-#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so
-#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0
-#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0.0
-#
-#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so
-#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0
-#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0.0
-#
-#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so
-#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0
-#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0.0
-#
-#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so
-#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0
-#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0.0
-#
-#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so
-#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0
-#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0.0
-#
-#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so
-#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0
-#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0.0
-#
-#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so
-#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1
-#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1.0
-#
-#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so
-#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0
-#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0.0
-#
-#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so
-#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0
-#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0.1
-#
-#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so
-#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0
-#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0.1
-#
-#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so
-#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0
-#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0.0
-#
-#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so
-#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0
-#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0.0
-#
-#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so
-#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2
-#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2.0
-
-	# Environment files, setup scripts, etc.
-	insinto /usr/share/ccp4/include
-	doins "${S}"/include/* || die
-
-	# CCP4Interface - GUI
-	insinto /usr/$(get_libdir)/ccp4
-	doins -r "${S}"/ccp4i || die
-	exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin
-	doexe "${S}"/ccp4i/bin/* || die
-
-	# Data
-	insinto /usr/share/ccp4
-	doins -r "${S}"/lib/data || die
-
-	# Include files
-	insinto /usr/include
-	for i in ccp4 clipper mmdb ssm; do
-		doins -r "${S}"/include/${i} || die
-	done
-
-	# Install docs and examples
-
-	doman "${S}"/man/cat1/*
-
-	mv "${S}"/manual/README "${S}"/manual/README-manual
-	dodoc "${S}"/manual/*
-
-	dodoc "${S}"/README "${S}"/CHANGES
-
-	dodoc "${S}"/doc/*
-	rm "${D}"/usr/share/doc/${PF}/GNUmakefile.gz
-	rm "${D}"/usr/share/doc/${PF}/COPYING.gz
-
-	dohtml -r "${S}"/html/*
-	dodoc "${S}"/examples/README
-
-	# Fix wrongly installed HTML pages from clipper
-	dohtml "${D}"/usr/html/*
-	rm -rf "${D}"/usr/html
-
-	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
-
-	# Needed for ccp4i docs to work
-	dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html
-
-	# Fix overlaps with other packages
-	rm "${D}"/usr/share/man/man1/rasmol.1*
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in /usr/share/ccp4/include/ccp4.setup* to modify this."
-
-	ewarn "Set your .bashrc or other shell login file to source"
-	ewarn "one of the ccp4.setup* files in ${ROOT}usr/share/ccp4/include."
-	ewarn "CCP4 will not work without this."
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
-
-# Links libname.so, libname.so.major and libname.so.major.minor
-# to libname.so.major.minor.micro
-library_dosym() {
-	local LIBNAME LIBDIR SUFFIX CORE_LIBNAME LIB_MAJOR LIB_MINOR LIB_VERSIONS
-
-	LIBNAME=${1}
-	LIBDIR=${2:-/usr/$(get_libdir)}
-
-	# Tag / on the end of libdir if needed
-	if [[ ${LIBDIR:$((${#LIBDIR}-1)):1} != "/" ]]; then
-		LIBDIR="${LIBDIR}/"
-	fi
-
-	if [[ "${LIBNAME}" != *.so.* ]]; then
-		msg="library_dosym() requires a shared, versioned library as an argument"
-		eerror "$msg"
-		die "$msg"
-	fi
-
-	SUFFIX=${LIBNAME##*so.}
-	CORE_LIBNAME=${LIBNAME%.so.*}
-	CORE_LIBNAME="${CORE_LIBNAME}.so"
-	LIB_MAJOR=${SUFFIX%%.*}
-	LIB_MINOR=${SUFFIX#*.}
-	LIB_MINOR=${SUFFIX%%.*}
-	LIB_VERSIONS="${LIB_MAJOR} ${LIB_MAJOR}.${LIB_MINOR}"
-	for LIB_SUFFIX in .${LIB_MAJOR} .${LIB_MAJOR}.${LIB_MINOR} ""; do
-		einfo "Calling dosym ${LIBNAME} ${LIBDIR} ${CORE_LIBNAME} ${LIB_SUFFIX}"
-		dosym ${LIBNAME} ${LIBDIR}${CORE_LIBNAME}${LIB_SUFFIX}
-	done
-}
diff --git a/sci-chemistry/ccp4/ccp4-6.0.2-r1.ebuild b/sci-chemistry/ccp4/ccp4-6.0.2-r1.ebuild
deleted file mode 100644
index 7b336edb3cdf..000000000000
--- a/sci-chemistry/ccp4/ccp4-6.0.2-r1.ebuild
+++ /dev/null
@@ -1,460 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ccp4-6.0.2-r1.ebuild,v 1.11 2011/06/21 16:05:14 jlec Exp $
-
-inherit eutils fortran-2 gnuconfig toolchain-funcs
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-PATCH_TOT="10"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-PATCH1=( src/topp_
-topp.f-r1.16.2.5-r1.16.2.6.diff )
-PATCH2=( .
-configure-r1.372.2.18-r1.372.2.19.diff )
-PATCH3=( src/scala_
-scala.f-r1.101.2.3-r1.101.2.4.diff )
-PATCH4=( ccp4i/src
-util_windows.tcl-r1.27-r1.27.2.1.diff )
-PATCH5=( src
-amore.f-r1.115-r1.116.diff )
-PATCH6=( src/bp3_
-crystal.C-r1.5-r1.6.diff )
-PATCH7=( src
-mtz2various.f-r1.124.2.3-r1.124.2.4.diff )
-PATCH8=( src
-rstats.f-r1.39-r1.40.diff )
-PATCH9=( src/refmac5_
-rharvest.fh-r1.13-r1.14.diff )
-PATCH10=( ccp4i/utils
-amore_utils.tcl-r1.14-r1.15.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-SRC_URI="${SRC}/${PV}/source/${P}-core-src.tar.gz"
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE="X"
-
-# app-office/sc overlaps sc binary and man page
-# We can't rename ours since the automated ccp4i interface expects it there,
-# as do many scripts. app-office/sc can't rename its because that's the name
-# of the package.
-RDEPEND="
-	virtual/fortran
-
-		>=dev-lang/tcl-8.3
-		>=dev-lang/tk-8.3
-		>=dev-tcltk/blt-2.4
-		virtual/lapack
-		virtual/blas
-		=sci-libs/fftw-2*
-		sci-chemistry/pdb-extract
-		sci-chemistry/rasmol
-		sci-libs/mccp4
-		app-shells/tcsh
-		!app-office/sc
-		X? (
-			x11-libs/libX11
-			x11-libs/libXt
-			x11-libs/libXaw
-		)"
-DEPEND="${RDEPEND}
-		X? (
-			x11-misc/imake
-			x11-proto/inputproto
-			x11-proto/xextproto
-		)"
-
-S="${WORKDIR}/${PN}-${PV}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	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}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	einfo "Applying Gentoo patches ..."
-	# These two only needed when attempting to install outside build dir via
-	# --bindir and --libdir instead of straight copying after build
-
-	# it attempts to install some libraries during the build
-	#ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
-	# hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
-	# without this patch when --libdir is set
-	# Rotgen still needs more patching to find it
-	#ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
-
-	# 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
-	ccp_patch "${FILESDIR}"/dont-build-rasmol.patch
-
-	# We already have sci-chemistry/pdb-extract
-# Use configure option instead
-#	ccp_patch "${FILESDIR}"/dont-build-pdb-extract.patch
-
-	ccp_patch "${FILESDIR}"/create-mosflm-bindir.patch
-	ccp_patch "${FILESDIR}"/make-mosflm-libdir.patch
-	ccp_patch "${FILESDIR}"/make-mosflm-index-libdir.patch
-	ccp_patch "${FILESDIR}"/make-mosflm-cbf-libdir.patch
-	ccp_patch "${FILESDIR}"/make-ipmosflm-dir.patch
-
-# Don't use these when we aren't building phaser
-#	ccp_patch "${FILESDIR}"/make-phaser-bindir.patch
-#	ccp_patch "${FILESDIR}"/no-phaser-ld-assume-kernel.patch
-#	# scons config.py tries to chmod python on live system
-#	ccp_patch "${FILESDIR}"/dont-chmod-python-binary.patch
-
-	# Don't use this when we aren't building clipper
-	# For some reason clipper check for $enableval even when --enable is passed
-	ccp_patch "${FILESDIR}"/pass-clipper-enablevals.patch
-	ccp_patch "${FILESDIR}"/clipper-find-mccp4-includes.patch
-
-	# Default to firefox browser, not 'netscape'
-	ccp_patch "${FILESDIR}"/ccp4i-default-to-firefox.patch
-
-	# Also use -lpthread when linking blas and lapack
-	# We may need more fixing to use libcblas for the C files
-	ccp_patch "${FILESDIR}"/check-blas-lapack-pthread.patch
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch "${FILESDIR}"/${PV}-ppc-double-define-gerror.patch
-
-	# Replace IDATE with UIDATE for compat with gcc 4.1.2
-	ccp_patch "${FILESDIR}"/${PV}-gcc-4.1.2-idate-fix.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "$(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
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
-		"${S}"/include/ccp4.setup*
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-	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}
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		$(use_enable X x) \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-pdb_extract \
-		--disable-cctbx \
-		--disable-phaser \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-# Only needed when using --bindir and --libdir
-	# Needed to avoid errors. Originally tried to make lib and bin
-	# in configure script, now patched out by dont-make-dirs-in-configure.patch
-#	dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-#	make install || die "install failed"
-	einstall || die "install failed"
-
-	# Fix env
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \
-		-e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
-		-e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
-		-e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1\$CCP4/share/ccp4/include~g" \
-		-e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1\$CCP4/share/ccp4/data~g" \
-		-e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1/share/ccp4/data/monomers/~g" \
-		-e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1/share/ccp4/data/monomers/~g" \
-		-e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \
-		"${S}"/include/ccp4.setup*
-
-	# Get rid of S instances
-	# Also the main clipper library is built as libclipper-core, not libclipper
-	sed -i \
-		-e "s:${S}:$usr:g" \
-		-e "s:lclipper :lclipper-core :g" \
-		"${S}"/bin/clipper-config
-#	sed -i \
-#		-e "s:${S}:usr:g" \
-#		"${S}"/$(get_libdir)/cctbx/cctbx_build/setpaths*
-
-	# Bins
-	dobin "${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
-
-	# Fix libdir in all *.la files
-	sed -i \
-		-e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
-		"${D}"/usr/$(get_libdir)/*.la
-
-	# Library symlinks
-	local LIBNAMES="libclipper-ccp4.so.0.0.0
-		libclipper-cif.so.0.0.0
-		libclipper-contrib.so.0.0.0
-		libclipper-core.so.0.0.0
-		libclipper-minimol.so.0.0.0
-		libclipper-mmdbold.so.0.0.0
-		libclipper-mmdb.so.0.0.0
-		libclipper-mtz.so.1.0.0
-		libclipper-phs.so.0.0.0
-		libjwc_c.so.0.1.1
-		libjwc_f.so.0.1.1
-		libssm.so.0.0.0
-		libxdl_viewextra.so.0.0.0
-		libxdl_view.so.2.0.0"
-
-	for LIBNAME in ${LIBNAMES}; do
-		library_dosym ${LIBNAME}
-	done
-
-#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so
-#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0
-#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0.0
-#
-#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so
-#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0
-#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0.0
-#
-#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so
-#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0
-#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0.0
-#
-#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so
-#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0
-#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0.0
-#
-#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so
-#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0
-#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0.0
-#
-#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so
-#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0
-#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0.0
-#
-#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so
-#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0
-#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0.0
-#
-#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so
-#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1
-#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1.0
-#
-#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so
-#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0
-#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0.0
-#
-#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so
-#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0
-#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0.1
-#
-#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so
-#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0
-#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0.1
-#
-#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so
-#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0
-#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0.0
-#
-#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so
-#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0
-#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0.0
-#
-#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so
-#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2
-#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2.0
-
-	# Setup scripts
-	insinto /etc/profile.d
-	newins "${S}"/include/ccp4.setup-bash ccp4.setup.sh
-	newins "${S}"/include/ccp4.setup-dist ccp4.setup.csh
-	rm -f "${S}"/include/ccp4.setup-bash
-	rm -f "${S}"/include/ccp4.setup-dist
-
-	# Environment files, setup scripts, etc.
-	insinto /usr/share/ccp4/include
-	doins "${S}"/include/* || die
-
-	# CCP4Interface - GUI
-	insinto /usr/$(get_libdir)/ccp4
-	doins -r "${S}"/ccp4i || die
-	exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin
-	doexe "${S}"/ccp4i/bin/* || die
-
-	# Data
-	insinto /usr/share/ccp4
-	doins -r "${S}"/lib/data || die
-
-	# Include files
-	insinto /usr/include
-	for i in ccp4 mmdb; do
-		doins -r "${S}"/include/${i} || die
-	done
-
-	# Install docs and examples
-
-	doman "${S}"/man/cat1/*
-
-	mv "${S}"/manual/README "${S}"/manual/README-manual
-	dodoc "${S}"/manual/*
-
-	dodoc "${S}"/README "${S}"/CHANGES
-
-	dodoc "${S}"/doc/*
-	rm "${D}"/usr/share/doc/${PF}/GNUmakefile.*
-	rm "${D}"/usr/share/doc/${PF}/COPYING.*
-
-	dohtml -r "${S}"/html/*
-	dodoc "${S}"/examples/README
-
-	# Fix wrongly installed HTML pages from clipper
-	dohtml "${D}"/usr/html/*
-	rm -rf "${D}"/usr/html
-
-	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
-
-	# Needed for ccp4i docs to work
-	dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html
-
-	# Fix overlaps with other packages
-	rm -f "${D}"/usr/share/man/man1/rasmol.1*
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in /usr/share/ccp4/include/ccp4.setup* to modify this."
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
-
-# Links libname.so, libname.so.major and libname.so.major.minor
-# to libname.so.major.minor.micro
-library_dosym() {
-	local LIBNAME LIBDIR SUFFIX CORE_LIBNAME LIB_MAJOR LIB_MINOR LIB_VERSIONS
-
-	LIBNAME=${1}
-	LIBDIR=${2:-/usr/$(get_libdir)}
-
-	# Tag / on the end of libdir if needed
-	if [[ ${LIBDIR:$((${#LIBDIR}-1)):1} != "/" ]]; then
-		LIBDIR="${LIBDIR}/"
-	fi
-
-	if [[ "${LIBNAME}" != *.so.* ]]; then
-		msg="library_dosym() requires a shared, versioned library as an argument"
-		eerror "$msg"
-		die "$msg"
-	fi
-
-	SUFFIX=${LIBNAME##*so.}
-	CORE_LIBNAME=${LIBNAME%.so.*}
-	CORE_LIBNAME="${CORE_LIBNAME}.so"
-	LIB_MAJOR=${SUFFIX%%.*}
-	LIB_MINOR=${SUFFIX#*.}
-	LIB_MINOR=${SUFFIX%%.*}
-	LIB_VERSIONS="${LIB_MAJOR} ${LIB_MAJOR}.${LIB_MINOR}"
-	for LIB_SUFFIX in .${LIB_MAJOR} .${LIB_MAJOR}.${LIB_MINOR} ""; do
-		einfo "Calling dosym ${LIBNAME} ${LIBDIR} ${CORE_LIBNAME} ${LIB_SUFFIX}"
-		dosym ${LIBNAME} ${LIBDIR}${CORE_LIBNAME}${LIB_SUFFIX}
-	done
-}
diff --git a/sci-chemistry/ccp4/ccp4-6.0.2.ebuild b/sci-chemistry/ccp4/ccp4-6.0.2.ebuild
deleted file mode 100644
index 0bf4b0cd9fec..000000000000
--- a/sci-chemistry/ccp4/ccp4-6.0.2.ebuild
+++ /dev/null
@@ -1,432 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ccp4-6.0.2.ebuild,v 1.11 2011/06/21 16:05:14 jlec Exp $
-
-inherit eutils fortran-2 gnuconfig toolchain-funcs
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-PATCH_TOT="0"
-#PATCH1=( src/mmdb_app_
-#	chainsaw.cpp-11May2006.diff )
-#PATCH2=( src
-#	anisoanl.f-r1.22-r1.24.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-SRC_URI="${SRC}/${PV}/source/${P}-core-src.tar.gz"
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~ppc ~x86"
-IUSE="X"
-
-# app-office/sc overlaps sc binary and man page
-# We can't rename ours since the automated ccp4i interface expects it there,
-# as do many scripts. app-office/sc can't rename its because that's the name
-# of the package.
-RDEPEND="
-	virtual/fortran
-
-		>=dev-lang/tcl-8.3
-		>=dev-lang/tk-8.3
-		>=dev-tcltk/blt-2.4
-		virtual/lapack
-		virtual/blas
-		=sci-libs/fftw-2*
-		sci-chemistry/pdb-extract
-		sci-chemistry/rasmol
-		sci-libs/mccp4
-		app-shells/tcsh
-		!app-office/sc
-		X? (
-			x11-libs/libX11
-			x11-libs/libXt
-			x11-libs/libXaw
-		)"
-DEPEND="${RDEPEND}
-		X? (
-			x11-misc/imake
-			x11-proto/inputproto
-			x11-proto/xextproto
-		)"
-
-S="${WORKDIR}/${PN}-${PV}"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	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}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	einfo "Applying Gentoo patches ..."
-	# These two only needed when attempting to install outside build dir via
-	# --bindir and --libdir instead of straight copying after build
-
-	# it attempts to install some libraries during the build
-	#ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
-	# hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
-	# without this patch when --libdir is set
-	# Rotgen still needs more patching to find it
-	#ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
-
-	# 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
-	ccp_patch "${FILESDIR}"/dont-build-rasmol.patch
-
-	# We already have sci-chemistry/pdb-extract
-# Use configure option instead
-#	ccp_patch "${FILESDIR}"/dont-build-pdb-extract.patch
-
-	ccp_patch "${FILESDIR}"/create-mosflm-bindir.patch
-	ccp_patch "${FILESDIR}"/make-mosflm-libdir.patch
-	ccp_patch "${FILESDIR}"/make-mosflm-index-libdir.patch
-	ccp_patch "${FILESDIR}"/make-mosflm-cbf-libdir.patch
-	ccp_patch "${FILESDIR}"/make-ipmosflm-dir.patch
-
-# Don't use these when we aren't building phaser
-#	ccp_patch "${FILESDIR}"/make-phaser-bindir.patch
-#	ccp_patch "${FILESDIR}"/no-phaser-ld-assume-kernel.patch
-#	# scons config.py tries to chmod python on live system
-#	ccp_patch "${FILESDIR}"/dont-chmod-python-binary.patch
-
-	# Don't use this when we aren't building clipper
-	# For some reason clipper check for $enableval even when --enable is passed
-	ccp_patch "${FILESDIR}"/pass-clipper-enablevals.patch
-	ccp_patch "${FILESDIR}"/clipper-find-mccp4-includes.patch
-
-	# Default to firefox browser, not 'netscape'
-	ccp_patch "${FILESDIR}"/ccp4i-default-to-firefox.patch
-
-	# Also use -lpthread when linking blas and lapack
-	# We may need more fixing to use libcblas for the C files
-	ccp_patch "${FILESDIR}"/check-blas-lapack-pthread.patch
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch "${FILESDIR}"/${PV}-ppc-double-define-gerror.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "$(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
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
-		"${S}"/include/ccp4.setup*
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-	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}
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		$(use_enable X x) \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-pdb_extract \
-		--disable-cctbx \
-		--disable-phaser \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-# Only needed when using --bindir and --libdir
-	# Needed to avoid errors. Originally tried to make lib and bin
-	# in configure script, now patched out by dont-make-dirs-in-configure.patch
-#	dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-#	make install || die "install failed"
-	einstall || die "install failed"
-
-	# Fix env
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \
-		-e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
-		-e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
-		-e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
-		-e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \
-		-e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \
-		-e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \
-		-e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \
-		"${S}"/include/ccp4.setup*
-
-	# Get rid of S instances
-	# Also the main clipper library is built as libclipper-core, not libclipper
-	sed -i \
-		-e "s:${S}:$usr:g" \
-		-e "s:lclipper :lclipper-core :g" \
-		"${S}"/bin/clipper-config
-#	sed -i \
-#		-e "s:${S}:usr:g" \
-#		"${S}"/$(get_libdir)/cctbx/cctbx_build/setpaths*
-
-	# Bins
-	dobin "${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
-
-	# Fix libdir in all *.la files
-	sed -i \
-		-e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
-		"${D}"/usr/$(get_libdir)/*.la
-
-	# Library symlinks
-	local LIBNAMES="libclipper-ccp4.so.0.0.0
-		libclipper-cif.so.0.0.0
-		libclipper-contrib.so.0.0.0
-		libclipper-core.so.0.0.0
-		libclipper-minimol.so.0.0.0
-		libclipper-mmdbold.so.0.0.0
-		libclipper-mmdb.so.0.0.0
-		libclipper-mtz.so.1.0.0
-		libclipper-phs.so.0.0.0
-		libjwc_c.so.0.1.1
-		libjwc_f.so.0.1.1
-		libssm.so.0.0.0
-		libxdl_viewextra.so.0.0.0
-		libxdl_view.so.2.0.0"
-
-	for LIBNAME in ${LIBNAMES}; do
-		library_dosym ${LIBNAME}
-	done
-
-#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so
-#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0
-#	dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0.0
-#
-#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so
-#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0
-#	dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0.0
-#
-#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so
-#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0
-#	dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0.0
-#
-#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so
-#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0
-#	dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0.0
-#
-#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so
-#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0
-#	dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0.0
-#
-#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so
-#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0
-#	dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0.0
-#
-#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so
-#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0
-#	dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0.0
-#
-#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so
-#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1
-#	dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1.0
-#
-#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so
-#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0
-#	dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0.0
-#
-#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so
-#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0
-#	dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0.1
-#
-#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so
-#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0
-#	dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0.1
-#
-#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so
-#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0
-#	dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0.0
-#
-#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so
-#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0
-#	dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0.0
-#
-#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so
-#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2
-#	dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2.0
-
-	# Environment files, setup scripts, etc.
-	insinto /usr/share/ccp4/include
-	doins "${S}"/include/* || die
-
-	# CCP4Interface - GUI
-	insinto /usr/$(get_libdir)/ccp4
-	doins -r "${S}"/ccp4i || die
-	exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin
-	doexe "${S}"/ccp4i/bin/* || die
-
-	# Data
-	insinto /usr/share/ccp4
-	doins -r "${S}"/lib/data || die
-
-	# Include files
-	insinto /usr/include
-	for i in ccp4 clipper mmdb ssm; do
-		doins -r "${S}"/include/${i} || die
-	done
-
-	# Install docs and examples
-
-	doman "${S}"/man/cat1/*
-
-	mv "${S}"/manual/README "${S}"/manual/README-manual
-	dodoc "${S}"/manual/*
-
-	dodoc "${S}"/README "${S}"/CHANGES
-
-	dodoc "${S}"/doc/*
-	rm "${D}"/usr/share/doc/${PF}/GNUmakefile.gz
-	rm "${D}"/usr/share/doc/${PF}/COPYING.gz
-
-	dohtml -r "${S}"/html/*
-	dodoc "${S}"/examples/README
-
-	# Fix wrongly installed HTML pages from clipper
-	dohtml "${D}"/usr/html/*
-	rm -rf "${D}"/usr/html
-
-	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
-
-	# Needed for ccp4i docs to work
-	dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html
-
-	# Fix overlaps with other packages
-	rm "${D}"/usr/share/man/man1/rasmol.1*
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in /usr/share/ccp4/include/ccp4.setup* to modify this."
-
-	ewarn "Set your .bashrc or other shell login file to source"
-	ewarn "one of the ccp4.setup* files in ${ROOT}usr/share/ccp4/include."
-	ewarn "CCP4 will not work without this."
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
-
-# Links libname.so, libname.so.major and libname.so.major.minor
-# to libname.so.major.minor.micro
-library_dosym() {
-	local LIBNAME LIBDIR SUFFIX CORE_LIBNAME LIB_MAJOR LIB_MINOR LIB_VERSIONS
-
-	LIBNAME=${1}
-	LIBDIR=${2:-/usr/$(get_libdir)}
-
-	# Tag / on the end of libdir if needed
-	if [[ ${LIBDIR:$((${#LIBDIR}-1)):1} != "/" ]]; then
-		LIBDIR="${LIBDIR}/"
-	fi
-
-	if [[ "${LIBNAME}" != *.so.* ]]; then
-		msg="library_dosym() requires a shared, versioned library as an argument"
-		eerror "$msg"
-		die "$msg"
-	fi
-
-	SUFFIX=${LIBNAME##*so.}
-	CORE_LIBNAME=${LIBNAME%.so.*}
-	CORE_LIBNAME="${CORE_LIBNAME}.so"
-	LIB_MAJOR=${SUFFIX%%.*}
-	LIB_MINOR=${SUFFIX#*.}
-	LIB_MINOR=${SUFFIX%%.*}
-	LIB_VERSIONS="${LIB_MAJOR} ${LIB_MAJOR}.${LIB_MINOR}"
-	for LIB_SUFFIX in .${LIB_MAJOR} .${LIB_MAJOR}.${LIB_MINOR} ""; do
-		einfo "Calling dosym ${LIBNAME} ${LIBDIR} ${CORE_LIBNAME} ${LIB_SUFFIX}"
-		dosym ${LIBNAME} ${LIBDIR}${CORE_LIBNAME}${LIB_SUFFIX}
-	done
-}
diff --git a/sci-chemistry/ccp4/ccp4-6.1.3.ebuild b/sci-chemistry/ccp4/ccp4-6.1.3.ebuild
deleted file mode 100644
index e3bfa57a803b..000000000000
--- a/sci-chemistry/ccp4/ccp4-6.1.3.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ccp4-6.1.3.ebuild,v 1.3 2011/06/21 16:05:14 jlec Exp $
-
-EAPI="2"
-
-DESCRIPTION="Protein X-ray crystallography toolkit -- meta package"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI=""
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="X arpwarp +balbes"
-
-RDEPEND="
-	virtual/fortran
-
-	~sci-chemistry/ccp4-apps-${PV}[X?]
-	sci-chemistry/molrep
-	sci-chemistry/mosflm
-	sci-chemistry/mrbump[X?]
-	sci-chemistry/oasis
-	sci-chemistry/pdb-extract
-	sci-chemistry/refmac
-	sci-chemistry/scala
-	sci-chemistry/sfcheck
-	sci-chemistry/xia2
-	arpwarp? ( sci-chemistry/arp-warp-bin )
-	balbes? ( sci-chemistry/balbes )
-	X? (
-		~sci-chemistry/ccp4i-${PV}
-		sci-chemistry/imosflm
-		sci-chemistry/pymol
-		sci-chemistry/rasmol
-		)"
-DEPEND=""