Drop old

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

5 files changed, 26 insertions, 809 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/Manifest b/sci-chemistry/ccp4-apps/Manifest
index c5524b44bc71..f238720cf802 100644
--- a/sci-chemistry/ccp4-apps/Manifest
+++ b/sci-chemistry/ccp4-apps/Manifest
@@ -1,5 +1,5 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX 6.1.3-clipper-template.patch 2619 SHA256 a185a93f76c23ce06256866cfaf0e9854a5702b95a1e49e4d3a5f732e0d1e2a3 SHA512 27d2e1eeace0ba7e690ac218ba4272e668e693b20292d2824831c6472627fcbf7013409a9255bd514918921cdc9ac98d86709ecda73b255230ccadc8d66e45a9 WHIRLPOOL f1e0694ec4a582cf1b547d845e8c8a86791aa3f109429f6a4aadfb30142719a07fee92d01f3e3a8f0703cc55833aae8fb6c3c2e8503efe741ac94276feb1b3b4
 AUX 6.1.3-dont-build-balbes.patch 489 SHA256 dfe1b810fb07bf536528b9c955e3162dc470a803513ae6fa69848ed6d64503c4 SHA512 db5dba9eca411489baca16408e61bf3652087c238247a8128a39633b8e4a5dcf03931a55c07fa3887a9ee347ed9f7786a350468745258b65553a0e68d7cfb300 WHIRLPOOL 7b523121703f2ae87502dd411b48aa9bdba7e386d4365aa4c9b7de163ce134250c41a71e7fad9457601fea27a024a0d84588d1f937105c9384110ede8bcf25dc
@@ -20,25 +20,25 @@ AUX 6.1.3-unbundle.patch 5736 SHA256 1d50917bdd3733d099cf64df651c8743ab40ce1ea19
 AUX ccp4-apps-6.1.3-tcl8.6.patch 6027 SHA256 665d21a30b78e55480c8eddd83ef2c7e77573b0bffe3cef7e48c065d2601b8b6 SHA512 6bab6305bd3f902309ef0427e510a8000883fb115e5ca302dcad110d3687b71778cd0da31f619b50b477d83a330aba7db608556ccda2efd6087ee99d7dea1648 WHIRLPOOL 865b870abc4d53697d41ce30057cd6716eb032ca38c786c11e6e28bfaf25ecd70cb05ac401bed66faeded62a433b919005da3e9012f1c9dc7d1459b68b78f505
 DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820
 DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
-EBUILD ccp4-apps-6.1.3-r11.ebuild 9982 SHA256 1b2fb8ca855c4a14f82e4900ce6ac435d7c9723524d809a48a2b2a490edd7b6d SHA512 221dec5026f3301c1ea73c94988a5e7403193c1260f678f5412c882f357911d33e20cabdf8a539f88c71a2ceeb81be04b8695898dcbffd75df73225490e6c44c WHIRLPOOL 20c758f55c1229fdd96f9eeafc540bbf6bc0d0c7e3190c71bb5b742c72da6374b77b1c558a38c628cd24f9491a2ad3bb322c20ea6b21e34cfd5d6fd40779a0a6
-EBUILD ccp4-apps-6.1.3-r12.ebuild 10039 SHA256 c7ac13c3079fdc72780bc3ef9dee873898d22dd9f78854a5c90f7e6731de9bc8 SHA512 73002a5691ffd2ca7508dda1d4fb3d871486f61481cfaaead71bdfa7c106b00bdb310b40b124d2ee224b4d3e6e25977eafe1fb25e19b11d895bdcdcda5f8d916 WHIRLPOOL 18ea6ef38b0f76496f466c4a81ad0b46f7fa04c7cea8a26d3adcdf5f80708ddac24a40791cb723c722a06f3fd9eca31287021be9eb5dbd80ce902dbe3414245e
-EBUILD ccp4-apps-6.1.3-r13.ebuild 9989 SHA256 23b39dfbf073a231937a8e9ab3a9db125d84490e88d6a4dca3837fe129730974 SHA512 cc747f1261d16c040219ff7cc77dc3f6a922d797cc9cda051c58cce405d9e69932c80e682f09546a4310159875b6acd45925c61f7d7b4148a3d1964a32a4aea7 WHIRLPOOL 424bbf1f606e8f30ddb536370f5b260fede16ee53ff9590196b7d05f7c969418fbf510ae93e586de72e6278adc999d3af96476ef29a6eb49d572669c6fab0b94
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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