Removed old

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

5 files changed, 9 insertions, 658 deletions

diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
index a95a6f55bbbd..ad17e3ca623e 100644
--- a/sci-libs/ccp4-libs/ChangeLog
+++ b/sci-libs/ccp4-libs/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-libs/ccp4-libs
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.11 2010/07/16 09:41:03 fauli Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.12 2010/07/16 10:14:47 jlec Exp $
+
+  16 Jul 2010; Justin Lecher <jlec@gentoo.org> -ccp4-libs-6.1.3.ebuild,
+  -ccp4-libs-6.1.3-r1.ebuild, -ccp4-libs-6.1.3-r2.ebuild:
+  Removed old
 
   16 Jul 2010; Christian Faulhammer <fauli@gentoo.org>
   ccp4-libs-6.1.3-r3.ebuild:
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
index a6467f1223b3..28c6c61b84ec 100644
--- a/sci-libs/ccp4-libs/Manifest
+++ b/sci-libs/ccp4-libs/Manifest
@@ -10,16 +10,13 @@ AUX 6.1.3-link-proberly.patch 8282 RMD160 c45d3d1931e6a083c0c96b819aff3f67873659
 AUX 6.1.3-noinstall.patch 5188 RMD160 d3b22f11d7c27b37243b003f03615af377c8e632 SHA1 d75402e7b23d3aa15e67cda6cec8c93864d509c2 SHA256 22d96aea9d3d5e6e090713e610b35bdb34eaff9157c41687b47294f0d62ccff7
 AUX 6.1.3-unbundle-libs.patch 9063 RMD160 326af0e6990134546fb2607dae707b94d4588149 SHA1 ef929532e45c12fb168e5fca4eb7fa8c857c376a SHA256 7e5fc919b5204e2d9141f7715afdd8a8b4e3e2a96e2bf95aa00fbd56046f1aa4
 DIST ccp4-6.1.3-core-src.tar.gz 242134076 RMD160 e9b7deb0766fb95d5e8946881f20e086f0896fe9 SHA1 ee5ada892694db5dc9b2d7d2330b4ac694f56580 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324
-EBUILD ccp4-libs-6.1.3-r1.ebuild 6141 RMD160 7b49aedef260644eb31dc5581bffa58f2b452479 SHA1 70c015dc857ee9afc19bdfb8189bcae3c1f57e61 SHA256 54c6997a9ef747c29ae6e1497e83c1f2465ecb9c75cdb73b578caeb89b17dabf
-EBUILD ccp4-libs-6.1.3-r2.ebuild 6141 RMD160 3b629dbda585d8391e64701fab362df0edaf4ebd SHA1 e367891a27dd68f6cc6f70f34516d80795e3623b SHA256 356863aa6ef2ed260fc57d00e95929442a816da11c93f8d1477907ba90ac73c6
 EBUILD ccp4-libs-6.1.3-r3.ebuild 6485 RMD160 5ab8a0698a199249f37ab9fb611126c21be49d88 SHA1 80d50bcc94effe3669c14798bd4925edc0911c1e SHA256 141cb4b230b18d8e0ecb583a3620fc0d678a3a40f3ba666fd2e265e7171270b1
-EBUILD ccp4-libs-6.1.3.ebuild 5892 RMD160 2fb6d639e3201775ba15ed8a27586b69be7707c7 SHA1 c7240c3c925042c04fd112402ac09607ae6448cf SHA256 9fe3acab2d6f59161772fcac0cf45e2150372d3cbb38f7edfafe2d6f47ab5fb8
-MISC ChangeLog 1944 RMD160 054a3c86d51ad704970153d791a3c91b44e4e87a SHA1 ff8473fab3b58b0f6b9b4ec54dbd9af76e70b4e7 SHA256 96e9940ff49c6aeeeb684084b97723759593ff9dc7fb600a365037a7c26fb887
+MISC ChangeLog 2088 RMD160 f6c71b2a0e8ad9ea1df28739c5301e5b57fc1313 SHA1 d346a19788cb6c4bfac4680776fe4c3c9ffd9a28 SHA256 31f0818403b70d669741b2916edfab0999c739a90984d74184473e1ff0c79e88
 MISC metadata.xml 306 RMD160 57ba72f54388a666851bda87e52d313d618084e3 SHA1 7d2f57cb3f35eb6d4567b211e01251b5945d4eb2 SHA256 af351be5ead71b377b6fa2fa118fb9aee74129afdc19f736b41596d3033106aa
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.15 (GNU/Linux)
 
-iEYEARECAAYFAkxAKaYACgkQNQqtfCuFneMTFQCffIbRw6CLPUm0V2+/PF0hYRNX
-WykAniv4pnlhOyv5t0WclfRTV2PUzgg1
-=cDLw
+iEYEARECAAYFAkxAMRwACgkQgAnW8HDreRYItQCeIax3BYNY/ElSQ0p2ooh6rE9A
+/tkAn2Zbx1FUXAL4E7Lsq6SnwJct012z
+=2fA7
 -----END PGP SIGNATURE-----
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r1.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r1.ebuild
deleted file mode 100644
index 1c7f69791124..000000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r1.ebuild
+++ /dev/null
@@ -1,220 +0,0 @@
-# Copyright 1999-2010 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-r1.ebuild,v 1.2 2010/03/28 20:22:02 jlec Exp $
-
-EAPI="3"
-
-inherit fortran eutils gnuconfig toolchain-funcs
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-# 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 )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-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.gentooexperimental.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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	media-libs/jpeg:0
-	app-shells/tcsh
-	!<sci-chemistry/ccp4-6.1.3
-	sci-libs/cbflib
-	=sci-libs/fftw-2*
-	sci-libs/mmdb
-	sci-libs/monomer-db
-	virtual/lapack
-	virtual/blas"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	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
-
-	# 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}"/${PV}-unbundle-libs.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	sed "s:/usr:${EPREFIX}/usr:g" -i configure || die
-
-	gnuconfig_update
-}
-
-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 [[ "${FORTRANC}" = "ifc" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${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${EPREFIX}/usr/bin~g" \
-		"${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=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=${FORTRANC}
-	export FOPTIM=${FFLAGS:- -O2}
-#	export CCP4_SCR="${T}"
-
-	# Fix linking
-#	$(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm -lstdc++ && \
-	export SHARE_LIB="\
-		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L.. -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
-		${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L.. -lccif -L. -lccp4c -lmmdb $(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 \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-}
-
-src_compile() {
-	emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-	einstall || die "install failed"
-
-	# 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
-
-	# Bins
-	dobin bin/{automask,diff2jpeg,diffdump,printpeaks} || die
-	newbin bin/superpose superpose-ccp4 || die
-
-	# Fix libdir in all *.la files
-	sed -i \
-		-e "s:^\(libdir=\).*:\1\'${EPREFIX}/usr/$(get_libdir)\':g" \
-		"${ED}"/usr/$(get_libdir)/*.la || die
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
-	dodoc "${S}"/lib/data/*.doc
-	newdoc "${S}"/lib/data/README DATA-README
-
-	# Include files
-	insinto /usr/include
-	for i in ccp4; do
-		doins -r "${S}"/include/${i} || die
-	done
-}
-
-# 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-r2.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r2.ebuild
deleted file mode 100644
index 642627419517..000000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r2.ebuild
+++ /dev/null
@@ -1,220 +0,0 @@
-# Copyright 1999-2010 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-r2.ebuild,v 1.1 2010/05/22 10:04:27 jlec Exp $
-
-EAPI="3"
-
-inherit fortran eutils gnuconfig toolchain-funcs
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-# 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 )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-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.gentooexperimental.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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	media-libs/jpeg:0
-	app-shells/tcsh
-	!<sci-chemistry/ccp4-6.1.3
-	sci-libs/cbflib
-	=sci-libs/fftw-2*
-	sci-libs/mmdb
-	sci-libs/monomer-db
-	virtual/lapack
-	virtual/blas"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	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
-
-	# 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}"/${PV}-unbundle-libs.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	sed "s:/usr:${EPREFIX}/usr:g" -i configure || die
-
-	gnuconfig_update
-}
-
-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 [[ "${FORTRANC}" = "ifc" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${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${EPREFIX}/usr/bin~g" \
-		"${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=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=${FORTRANC}
-	export FOPTIM=${FFLAGS:- -O2}
-#	export CCP4_SCR="${T}"
-
-	# Fix linking
-#	$(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm -lstdc++ && \
-	export SHARE_LIB="\
-		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L.. -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
-		${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L.. -lccif -L. -lccp4c -lmmdb $(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 \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-}
-
-src_compile() {
-	emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-	einstall || die "install failed"
-
-	# 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
-
-	# Bins
-	exeinto /usr/libexec/ccp4/bin/
-	doexe bin/{automask,diff2jpeg,diffdump,printpeaks,superpose} || die
-
-	# Fix libdir in all *.la files
-	sed -i \
-		-e "s:^\(libdir=\).*:\1\'${EPREFIX}/usr/$(get_libdir)\':g" \
-		"${ED}"/usr/$(get_libdir)/*.la || die
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
-	dodoc "${S}"/lib/data/*.doc
-	newdoc "${S}"/lib/data/README DATA-README
-
-	# Include files
-	insinto /usr/include
-	for i in ccp4; do
-		doins -r "${S}"/include/${i} || die
-	done
-}
-
-# 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.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3.ebuild
deleted file mode 100644
index f0dc95152372..000000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3.ebuild
+++ /dev/null
@@ -1,210 +0,0 @@
-# Copyright 1999-2010 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.ebuild,v 1.2 2010/02/11 08:01:47 jlec Exp $
-
-EAPI="3"
-
-inherit fortran eutils gnuconfig toolchain-funcs
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-# 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 )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-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.gentooexperimental.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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	app-shells/tcsh
-	!<sci-chemistry/ccp4-6.1.3
-	=sci-libs/fftw-2*
-	sci-libs/mmdb
-	sci-libs/monomer-db
-	virtual/lapack
-	virtual/blas"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-	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
-
-	# 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}"/${PV}-dont-build-mmdb.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	gnuconfig_update
-}
-
-src_configure() {
-	# Build system is broken if we set LDFLAGS
-	userldflags="${LDFLAGS}"
-	export SHARED_LIB_FLAGS="${LDFLAGS}"
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "${FORTRANC}" = "ifc" ]]; 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${EPREFIX}/usr/bin~g" \
-		"${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=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=${FORTRANC}
-	export FOPTIM=${FFLAGS:- -O2}
-#	export CCP4_SCR="${T}"
-
-	# Fix linking
-#	$(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm -lstdc++ && \
-	export SHARE_LIB="\
-		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L.. -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
-		${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L.. -lccif -L. -lccp4c -lmmdb $(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 \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-}
-
-src_compile() {
-	emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup
-
-	einstall || die "install failed"
-
-	# 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
-
-	# Bins
-	dobin bin/{automask,diff2jpeg,diffdump,printpeaks} || die
-	newbin bin/superpose superpose-ccp4 || die
-
-	# Fix libdir in all *.la files
-	sed -i \
-		-e "s:^\(libdir=\).*:\1\'${EPREFIX}/usr/$(get_libdir)\':g" \
-		"${ED}"/usr/$(get_libdir)/*.la || die
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
-	dodoc "${S}"/lib/data/*.doc
-	newdoc "${S}"/lib/data/README DATA-README
-
-	# Include files
-	insinto /usr/include
-	for i in ccp4; do
-		doins -r "${S}"/include/${i} || die
-	done
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}