Drop old

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

4 files changed, 23 insertions, 707 deletions

diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
index 29a64a6f94b2..a493a2794ee3 100644
--- a/sci-libs/ccp4-libs/ChangeLog
+++ b/sci-libs/ccp4-libs/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-libs/ccp4-libs
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.67 2015/03/28 21:30:27 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.68 2015/03/29 09:28:17 jlec Exp $
+
+  29 Mar 2015; Justin Lecher <jlec@gentoo.org> -ccp4-libs-6.1.3-r11.ebuild,
+  -ccp4-libs-6.1.3-r15.ebuild:
+  Drop old
 
   28 Mar 2015; Agostino Sarubbo <ago@gentoo.org> ccp4-libs-6.1.3-r16.ebuild:
   Stable for ppc, wrt bug #542696
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
index ff495eba53f8..e7c58c0a92a5 100644
--- a/sci-libs/ccp4-libs/Manifest
+++ b/sci-libs/ccp4-libs/Manifest
@@ -1,5 +1,5 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX 6.0.2-ppc-double-define-gerror.patch 424 SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61 SHA512 3080aa9ce3fad2d972b5f2622b2f0119ad8c4306f84de6dfcb24c8ef17ebd9a163bf8e807d34508d999b8e205abec9d18daddeb3e5f8fdef075d888301ba4ed9 WHIRLPOOL 55dc0176c7aa84b5b4ab1e6ad397d358f794d0f42737efef2e4048a67cd2060c90652ecb356e3a2847091e0e5d5429c80fd1ce7c5a5348a6693d6065d18969fd
 AUX 6.1.3-cbf.patch 773 SHA256 767a2286956471c6dbf0feee9a5726f5170af21cb2dd85c7f45190cab5cce7a0 SHA512 ecf950cf82fc0c16e4e3f64b06f92a03c283dd04c2fc68932546ad863240fef49d44906a739d49d6913ceac5c8e0672ec3a7dfd2bb973f3c8ed5481c33464823 WHIRLPOOL 1307e0df9243f6cf867cefd18c7b22d4d880711f45ddf56729bedc2703584f7a42328fe87c00be7cf8d418bbd74db957128f3b527e283a384ed956bc0e5691b7
@@ -19,25 +19,25 @@ AUX 6.1.3-unbundle-libs.patch 9063 SHA256 7e5fc919b5204e2d9141f7715afdd8a8b4e3e2
 AUX ccp4-libs-6.1.3-force.patch 448 SHA256 36e31119c685097ed2ba98220e7813dc5d8265cd6fd36d2c202cc87e6a1fc2de SHA512 1045f711ce04f60ae53018c424673eb0b759daef18888b584ff3db106f1fb883f2a902f93a76427ba860e0ded8204db62e36ced23f05f03967e4eefa72a3561c WHIRLPOOL 72b63f206825e7d2cb4aa0a7c1ac783df71b0b695be0eb16a300c88c01080593da61e83f12003cd2c3d10b71b5c12f6a4b3b0d9867ae53a1bc7fe0fa7a88a98c
 AUX ccp4-libs-6.1.3-format-security.patch 626 SHA256 19085719bf567a1f81cbc014773d1185dc3d1698eab463aa5048ad8e78d68eae SHA512 5ae84afa6f3af77abb4bb85ca92a548d61279ec816cef3e1972a268bfe0fd4f3e1d36fa437cb291b45922efd902c87b9a0575bc72e99b437e23d0d5d4c7d44b7 WHIRLPOOL f24b17170bbbde9660881cf348e5f284a38e77c0b7a27eeec9e42c68af5d7f8f5faf8ff590e94959f3c2a7cda93e65d57ebe57449bea1082e975186e41f5aeaf
 DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
-EBUILD ccp4-libs-6.1.3-r11.ebuild 10944 SHA256 1653343f174134586f67f870b747567bf053216581777abf5aee8a6e2715ac3b SHA512 00b2127a5d84f0124752b13184b2fb548bb6be5427c29d85bac4a5140f42f134b304ed6ed7fdfce9c6392651ad08e8f7f73c2a867cc254b5b9128a79d2098a89 WHIRLPOOL bdc0ba45eb16076c010f77edaf9959c4a8b64c30bd2d652dbf59bfdaa7f7e3e08e22b6fdb6f52f244e03acd643da65a050f7670f46102f8824203cc9453a3450
-EBUILD ccp4-libs-6.1.3-r15.ebuild 11178 SHA256 eb005b0dcb478210375d632a0762bb03dfef2e9e32dbe53ed3266faf66324dfe SHA512 a00c92ae5e4217c67d146ac2581c37aaca40093397462af1e2a53383b63813c08714feafacd8ca8f19dc2128ab528cb73aacfa7e5108b4f7fbeec9fec16b1efa WHIRLPOOL 0c41b7678a37e103757ba09736821eb151493b7fd5cbccecddc07b43829cab63c4195fa1779052f0939ff61de80898adf6319b8f14ebf32eabb2b7c238f803a0
 EBUILD ccp4-libs-6.1.3-r16.ebuild 11320 SHA256 43110c8b75ffe36073eb897999889e66028c803a57ed07a4d5f49bfb0b0eb5fb SHA512 45366ed16a8d48a9dfb787dc06f738f41e5500377263db53b159a865671d2822322ec6762657cd77a62507a7e3f8db8b10057cb8ce55de4878ae2e01b417302e WHIRLPOOL 6c63861f357bd63b0c266f979627bb64e46d3e20692ad58dcce870997dd6c65596dfb5c03fc70bfe2b5f3ff7ee42bb0af3cb02916731ed7a26e3d3f39aea606f
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diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild
deleted file mode 100644
index f4ac848c96da..000000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild
+++ /dev/null
@@ -1,337 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild,v 1.13 2015/03/20 15:21:36 jlec Exp $
-
-EAPI=3
-
-PYTHON_DEPEND="2"
-
-inherit autotools eutils fortran-2 gnuconfig multilib python toolchain-funcs
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-
-DESCRIPTION="Protein X-ray crystallography toolkit - Libraries"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
-# 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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	!<sci-chemistry/ccp4-6.1.3
-	!<sci-chemistry/ccp4-apps-${PV}-r10
-	app-shells/tcsh
-	dev-lang/tcl:0
-	>=sci-libs/cbflib-0.9.2.2
-	sci-libs/fftw:2.1
-	sci-libs/mmdb:0
-	sci-libs/monomer-db
-	sci-libs/ssm
-	virtual/jpeg
-	virtual/lapack
-	virtual/blas"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${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 ..."
-	# fix buffer overflows wrt bug 339706
-	ccp_patch "${FILESDIR}"/${PV}-overflows.patch
-
-	# it tries to create libdir, bindir etc on live system in configure
-	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
-	# make creation of libccif.so smooth
-	ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
-
-	# lets try to build libmmdb seperatly
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
-
-	# unbundle libjpeg and cbflib
-	ccp_patch "${FILESDIR}"/${PV}-unbundle-libs-ng2.patch
-
-	# Fix missing DESTIDR
-	# not installing during build
-	ccp_patch "${FILESDIR}"/${PV}-noinstall.patch
-	sed \
-		-e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \
-		-i configure || die
-
-	# Fix upstreams code
-	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
-
-	# use pkg-config to detect BLAS/LAPACK
-	ccp_patch "${FILESDIR}"/${PV}-lapack.patch
-
-	# proto type changing in version 0.9.2.2
-	ccp_patch "${FILESDIR}"/${PV}-cbf.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# not needed, we have it extra
-	rm -rf src/rapper/{libxml2,gc7.0} || die
-
-	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' \
-		-i configure || die
-
-	gnuconfig_update
-
-	for i in lib/DiffractionImage src/rapper src/pisa; do
-		pushd ${i} > /dev/null
-			sed 's:-g::g' -i configure* || die
-			eautoreconf
-		popd > /dev/null
-	done
-
-	## unbundle libssm
-	sed '/libdir/s:ssm::g' -i Makefile.in
-	find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete
-}
-
-src_configure() {
-	rm -rf lib/DiffractionImage/{jpg,CBFlib} || die
-
-	# Build system is broken if we set LDFLAGS
-	userldflags="${LDFLAGS}"
-	export SHARED_LIB_FLAGS="${LDFLAGS}"
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "$(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~^\(export CCP4_MASTER.*\)/.*~\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*
-
-	# 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 SHARE_LIB="\
-		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
-		$(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb) $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		--onlylibs \
-		--with-shared-libs \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-warnings \
-		--disable-cctbx \
-		--disable-clipper \
-		--disable-ssm \
-		--tmpdir="${TMPDIR}" \
-		--bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \
-		--libdir="${EPREFIX}/usr/$(get_libdir)" \
-		${GENTOO_OSNAME} || die "configure failed"
-}
-
-src_compile() {
-	emake -j1 \
-		DESTDIR="${D}" onlylib || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	emake -j1 \
-		DESTDIR="${D}" \
-		includedir="${EPREFIX}/usr/include" \
-		library_includedir="${EPREFIX}/usr/include" \
-		install || die
-
-	sed \
-		-e "330,1000d" \
-		-i "${S}"/include/ccp4.setup-sh || die
-
-	sed \
-		-e "378,1000d" \
-		-i "${S}"/include/ccp4.setup-csh || die
-
-	sed \
-		-e "s:-${PV/-r*/}::g" \
-		-e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \
-		-e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \
-		-e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \
-		-e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \
-		-e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
-		-e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
-		-e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \
-		-e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \
-		-e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
-		-e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
-		-e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
-		-e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
-		-e "s:^\(.*export CLIBS=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*setenv CLIBS \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*export CLIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*setenv CLIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \
-		-e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \
-		-e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \
-		-e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \
-		-e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
-		-e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
-		-e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \
-		-e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \
-		-e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \
-		-e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \
-		-e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
-		-e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
-		-e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \
-		-e "/CCP4_HELPDIR/d" \
-		-e "/IMOSFLM_VERSION/d" \
-		-i "${S}"/include/ccp4.setup* || die
-
-	# Don't check for updates on every sourcing of /etc/profile
-	sed -i \
-		-e "s:\(eval python.*\):#\1:g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Libs
-	for file in "${S}"/lib/*; do
-		if [[ -d ${file} ]]; then
-			continue
-		elif [[ -x ${file} ]]; then
-			dolib.so ${file} || die
-		else
-			insinto /usr/$(get_libdir)
-			doins ${file} || die
-		fi
-	done
-
-	rm -f "${ED}"/usr/$(get_libdir)/*.la || die
-
-	sed \
-		-e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \
-		-i "${S}"/include/ccp4.setup-sh || die
-
-	# Setup scripts
-	insinto /etc/profile.d
-	newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh || die
-	newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh || die
-	rm -f "${S}"/include/ccp4.setup*
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
-
-	# Environment files, setup scripts, etc.
-	rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die
-	insinto /usr/share/ccp4/
-	doins -r "${S}"/include || die
-
-	dodoc "${S}"/lib/data/*.doc || die
-	newdoc "${S}"/lib/data/README DATA-README || die
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this."
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild
deleted file mode 100644
index 0435740bfbe3..000000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild
+++ /dev/null
@@ -1,351 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild,v 1.5 2015/03/20 15:21:36 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools eutils fortran-2 gnuconfig multilib python-single-r1 toolchain-funcs
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-
-DESCRIPTION="Protein X-ray crystallography toolkit - Libraries"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
-# 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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	!<sci-chemistry/ccp4-6.1.3
-	!<sci-chemistry/ccp4-apps-${PV}-r10
-	app-shells/tcsh
-	dev-lang/tcl:0
-	>=sci-libs/cbflib-0.9.2.2
-	sci-libs/fftw:2.1
-	sci-libs/mmdb:0
-	sci-libs/monomer-db
-	sci-libs/ssm
-	virtual/jpeg:0=
-	virtual/lapack
-	virtual/blas"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${MY_P}"
-
-MAKEOPTS+=" -j1"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	tc-export PKG_CONFIG RANLIB AR
-
-	sed \
-		-e "/^AR/s:ar:$(tc-getAR):g" \
-		-i lib/src/Makefile.in src/Makefile.in src/ccp4mapwish_/Makefile.in lib/ccif/Makefile.in || die
-
-	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 ..."
-	# fix buffer overflows wrt bug 339706
-	ccp_patch "${FILESDIR}"/${PV}-overflows.patch
-
-	# it tries to create libdir, bindir etc on live system in configure
-	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
-	# make creation of libccif.so smooth
-	ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
-
-	# lets try to build libmmdb seperatly
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
-
-	# unbundle libjpeg and cbflib
-	ccp_patch "${FILESDIR}"/${PV}-unbundle-libs-ng2.patch
-
-	# Fix missing DESTIDR
-	# not installing during build
-	ccp_patch "${FILESDIR}"/${PV}-noinstall.patch
-	sed \
-		-e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \
-		-i configure || die
-
-	# Fix upstreams code
-	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
-
-	# use pkg-config to detect BLAS/LAPACK
-	ccp_patch "${FILESDIR}"/${PV}-lapack.patch
-
-	# proto type changing in version 0.9.2.2
-	ccp_patch "${FILESDIR}"/${PV}-cbf.patch
-
-	# proto type changing in version 0.9.2.2
-	ccp_patch "${FILESDIR}"/${PV}-no-pypath.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# not needed, we have it extra
-	rm -rf src/rapper/{libxml2,gc7.0} || die
-
-	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' \
-		-i configure || die
-
-	gnuconfig_update
-
-	for i in lib/DiffractionImage src/rapper src/pisa; do
-		pushd ${i} > /dev/null
-			sed 's:-g::g' -i configure* || die
-			eautoreconf
-		popd > /dev/null
-	done
-
-	## unbundle libssm
-	sed -e '/libdir/s:ssm::g' -i Makefile.in || die
-	find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete || die
-}
-
-src_configure() {
-	rm -rf lib/DiffractionImage/{jpg,CBFlib} || die
-
-	# Build system is broken if we set LDFLAGS
-	userldflags="${LDFLAGS}"
-	export SHARED_LIB_FLAGS="${LDFLAGS}"
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "$(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 || die
-
-	# 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 SHARE_LIB="\
-		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
-		$(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb) $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		--onlylibs \
-		--with-shared-libs \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-warnings \
-		--disable-cctbx \
-		--disable-clipper \
-		--disable-ssm \
-		--tmpdir="${TMPDIR}" \
-		--bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \
-		--libdir="${EPREFIX}/usr/$(get_libdir)" \
-		${GENTOO_OSNAME} || die "configure failed"
-}
-
-src_compile() {
-	emake DESTDIR="${D}" onlylib
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	emake \
-		DESTDIR="${D}" \
-		includedir="${EPREFIX}/usr/include" \
-		library_includedir="${EPREFIX}/usr/include" \
-		install
-
-	sed \
-		-e "330,1000d" \
-		-i "${S}"/include/ccp4.setup-sh || die
-
-	sed \
-		-e "378,1000d" \
-		-i "${S}"/include/ccp4.setup-csh || die
-
-	sed \
-		-e "s:-${PV/-r*/}::g" \
-		-e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \
-		-e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \
-		-e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \
-		-e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \
-		-e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
-		-e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
-		-e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \
-		-e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \
-		-e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
-		-e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
-		-e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
-		-e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
-		-e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \
-		-e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \
-		-e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \
-		-e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \
-		-e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
-		-e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
-		-e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \
-		-e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \
-		-e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \
-		-e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \
-		-e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
-		-e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
-		-e "s:\$CLIB/font84.dat:\"${EPREFIX}/usr/$(get_libdir)/font84.dat\":g" \
-		-e "s:\$CLIB/cif_mmdic.lib:\"${EPREFIX}/usr/$(get_libdir)/cif_mmdic.lib\":g" \
-		-e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \
-		-e '/CLIB=/d' \
-		-e '/CLIB /d' \
-		-e '/CLIBS=/d' \
-		-e '/CLIBS /d' \
-		-e "/alias/d" \
-		-e "/CCP4_HELPDIR/d" \
-		-e "/IMOSFLM_VERSION/d" \
-		-i "${S}"/include/ccp4.setup* || die
-
-	# Don't check for updates on every sourcing of /etc/profile
-	sed -i \
-		-e "s:\(eval python.*\):#\1:g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Libs
-	for file in "${S}"/lib/*; do
-		if [[ -d ${file} ]]; then
-			continue
-		elif [[ -x ${file} ]]; then
-			dolib.so ${file}
-		else
-			insinto /usr/$(get_libdir)
-			doins ${file}
-		fi
-	done
-
-	prune_libtool_files
-
-	sed \
-		-e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \
-		-i "${S}"/include/ccp4.setup-sh || die
-
-	# Setup scripts
-	insinto /etc/profile.d
-	newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh
-	newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh
-	rm -f "${S}"/include/ccp4.setup*
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures}
-
-	# Environment files, setup scripts, etc.
-	rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die
-	insinto /usr/share/ccp4/
-	doins -r "${S}"/include
-
-	dodoc "${S}"/lib/data/*.doc
-	newdoc "${S}"/lib/data/README DATA-README
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this."
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}