InCvs

40 files changed, 0 insertions, 3337 deletions

diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
deleted file mode 100644
index aae7ba9c7..000000000
--- a/sci-libs/ccp4-libs/ChangeLog
+++ /dev/null
@@ -1,104 +0,0 @@
-# ChangeLog for sci-libs/ccp4-libs
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*ccp4-libs-6.1.3-r1 (30 Jan 2010)
-
-  30 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  -ccp4-libs-6.1.3.ebuild, +ccp4-libs-6.1.3-r1.ebuild:
-  Bad upstream, changed tarball w/o bumping
-
-*ccp4-libs-6.1.3 (22 Dec 2009)
-
-  22 Dec 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +files/6.1.3-ccif-shared.patch,
-  +files/6.1.3-dont-build-mmdb.patch,
-  +files/6.1.3-dont-make-dirs-in-configure.patch,
-  +files/6.1.3-glibc2.10.patch, +ccp4-libs-6.1.3.ebuild,
-  +files/6.1.3-link-proberly.patch:
-  Version bump
-
-*ccp4-libs-6.1.2-r1 (29 Oct 2009)
-
-  29 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +ccp4-libs-6.1.2-r1.ebuild, +files/6.1.2-64bit.patch:
-  64bit fix in diffdump
-
-  26 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  ccp4-libs-6.1.2.ebuild:
-  QA
-
-  13 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  ccp4-libs-6.1.2.ebuild:
-  Try to libmmdb build seperatly
-
-*ccp4-libs-6.1.2 (29 Jul 2009)
-
-  29 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +ccp4-libs-6.1.2.ebuild, +ccp4-libs-6.1.2.ebuild.save,
-  +files/6.1.2-dont-make-dirs-in-configure.patch,
-  +files/6.1.2-glibc2.10.patch, +files/6.1.2-link-proberly.patch:
-  Still not released 6.1.2
-
-*ccp4-libs-6.1.1-r7 (05 Jul 2009)
-
-  05 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +ccp4-libs-6.1.1-r7.ebuild:
-  Installs now some bins which come with the libs
-  superpose now is named superpose-ccp4
-
-*ccp4-libs-6.1.1-r6 (11 Jun 2009)
-
-  11 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +ccp4-libs-6.1.1-r6.ebuild:
-  missing libm in libccp4c.so
-  hopefully alinkings fixed now
-
-*ccp4-libs-6.1.1-r5 (10 Jun 2009)
-
-  10 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +files/6.1.1-glibc2.10.patch, +ccp4-libs-6.1.1-r5.ebuild:
-  Another linking fix
-
-  03 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  -ccp4-libs-6.1.1-r2.ebuild, -ccp4-libs-6.1.1-r3.ebuild:
-  cleaned up old versions
-
-*ccp4-libs-6.1.1-r4 (03 Jun 2009)
-
-  03 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +ccp4-libs-6.1.1-r4.ebuild:
-  glibc-2.10 getline fix
-  bug 270615
-
-*ccp4-libs-6.1.1-r3 (13 May 2009)
-
-  13 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +ccp4-libs-6.1.1-r3.ebuild:
-  Includes upstream updates src files from 03/04/09
-  fixes bug 269504
-
-*ccp4-libs-6.1.1-r2 (29 Apr 2009)
-
-  29 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  -ccp4-libs-6.1.1-r1.ebuild, +ccp4-libs-6.1.1-r2.ebuild:
-  Fixed Path of data dir
-
-*ccp4-libs-6.1.1-r1 (26 Apr 2009)
-
-  26 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +ccp4-libs-6.1.1-r1.ebuild:
-  excluded monomer-db to seperate ebuild
-  Some QA on data dir
-
-*sci-libs/ccp4-libs-6.1.1
- 
-  18 Feb 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  -sci-libs/ccp4-libs/files/6.0.99e-clipper-mmdbold-ggc-4.3.patch,
-  -sci-libs/ccp4-libs/files/6.0.99e-fix-setup-bash-incompatibility.patch,
-  +sci-libs/ccp4-libs/files/6.1.1-dont-make-dirs-in-configure.patch,
-  +sci-libs/ccp4-libs/files/6.1.1-clipper-mmdbold-ggc-4.3.patch,
-  -sci-libs/ccp4-libs/files/6.0.99e-dont-make-dirs-in-configure.patch,
-  +sci-libs/ccp4-libs/files/6.1.1-fix-setup-bash-incompatibility.patch:
-  bumped to revision 6.1.1
-  fix-setup-bash-incompatibility.patch now done by upstream
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
deleted file mode 100644
index cb5cca424..000000000
--- a/sci-libs/ccp4-libs/Manifest
+++ /dev/null
@@ -1,40 +0,0 @@
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diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r4.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r4.ebuild
deleted file mode 100644
index 201228553..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r4.ebuild
+++ /dev/null
@@ -1,209 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-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/"
-RESTRICT="mirror"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz
-	${SRC}/${PV}/updates/${MY_P}-src-patch-${UPDATE}.tar.gz
-	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/${!NAME}"
-done
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE=""
-RDEPEND="virtual/lapack
-	virtual/blas
-	=sci-libs/fftw-2*
-	app-shells/tcsh
-	!<sci-chemistry/ccp4-6.0.99
-	sci-libs/monomer-db"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${P/-libs}"
-
-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}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	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}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# glibc-2.10 getline fix
-	ls -l lib/src/fsplit.c
-	sed -e "s:getline:${PN/-libs}getline:g" -i lib/src/fsplit.c || die
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "${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/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}
-
-	# Fix linking
-	export SHARE_LIB="ld -shared -soname libmmdb.so --whole-archive -o libmmdb.so libmmdb.a ../libccif.a; \
-			  ld -shared -soname libccp4c.so --whole-archive -o libccp4c.so libccp4c.a ../libccif.a; \
-			  ld -shared -soname libccp4f.so --whole-archive -o libccp4f.so libccp4f.a libmmdb.a libccp4c.a ../libccif.a -lstdc++ $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		--onlylibs \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-cctbx \
-		--disable-clipper \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-	emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${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/$(get_libdir) /usr/bin
-
-#	make install || die "install failed"
-	einstall || die "install failed"
-
-	# Libs
-	for file in "${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/$(get_libdir)/*.la
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${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 mmdb; 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-6.1.1-r6.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r6.ebuild
deleted file mode 100644
index 31cbfd155..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r6.ebuild
+++ /dev/null
@@ -1,209 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-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/"
-RESTRICT="mirror"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz
-	${SRC}/${PV}/updates/${MY_P}-src-patch-${UPDATE}.tar.gz
-	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/${!NAME}"
-done
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE=""
-RDEPEND="virtual/lapack
-	virtual/blas
-	=sci-libs/fftw-2*
-	app-shells/tcsh
-	!<sci-chemistry/ccp4-6.0.99
-	sci-libs/monomer-db"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${P/-libs}"
-
-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}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	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}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# glibc-2.10 getline fix
-	sed -e "s:getline:${PN/-libs}getline:g" -i lib/src/fsplit.c || die
-	ccp_patch "${FILESDIR}"/${PV}-glibc2.10.patch
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "${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/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}
-
-	# Fix linking
-	export SHARE_LIB="ld -shared -soname libmmdb.so --whole-archive -o libmmdb.so libmmdb.a ../libccif.a $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
-			  ld -shared -soname libccp4c.so --whole-archive -o libccp4c.so libccp4c.a ../libccif.a -lm $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
-			  ld -shared -soname libccp4f.so --whole-archive -o libccp4f.so libccp4f.a libmmdb.a libccp4c.a ../libccif.a -lstdc++ -lgfortran $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		--onlylibs \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-cctbx \
-		--disable-clipper \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-	emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${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/$(get_libdir) /usr/bin
-
-#	make install || die "install failed"
-	einstall || die "install failed"
-
-	# Libs
-	for file in "${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/$(get_libdir)/*.la
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${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 mmdb; 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-6.1.1-r7.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r7.ebuild
deleted file mode 100644
index 43ddf853f..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r7.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-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/"
-RESTRICT="mirror"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz
-	${SRC}/${PV}/updates/${MY_P}-src-patch-${UPDATE}.tar.gz
-	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/${!NAME}"
-done
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE=""
-RDEPEND="virtual/lapack
-	virtual/blas
-	=sci-libs/fftw-2*
-	app-shells/tcsh
-	!<sci-chemistry/ccp4-6.0.99
-	sci-libs/monomer-db"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${P/-libs}"
-
-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}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	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}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# glibc-2.10 getline fix
-	sed -e "s:getline:${PN/-libs}getline:g" -i lib/src/fsplit.c || die
-	ccp_patch "${FILESDIR}"/${PV}-glibc2.10.patch
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "${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/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
-	export SHARE_LIB="ld -shared -soname libmmdb.so --whole-archive -o libmmdb.so libmmdb.a ../libccif.a $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
-			  ld -shared -soname libccp4c.so --whole-archive -o libccp4c.so libccp4c.a ../libccif.a -lm $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
-			  ld -shared -soname libccp4f.so --whole-archive -o libccp4f.so libccp4f.a libmmdb.a libccp4c.a ../libccif.a -lstdc++ -lgfortran $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		--onlylibs \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-cctbx \
-		--disable-clipper \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-	emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${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/$(get_libdir) /usr/bin
-
-#	make install || die "install failed"
-	einstall || die "install failed"
-
-	# Libs
-	for file in "${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\'/usr/$(get_libdir)\':g" \
-		"${D}"/usr/$(get_libdir)/*.la
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${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 mmdb; 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-6.1.1.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.1.ebuild
deleted file mode 100644
index 871bffab1..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.1.ebuild
+++ /dev/null
@@ -1,192 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit fortran eutils gnuconfig toolchain-funcs
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-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/"
-RESTRICT="mirror"
-SRC_URI="${SRC}/${PV}/${P/-libs}-core-src.tar.gz"
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE=""
-RDEPEND="virtual/lapack
-		virtual/blas
-		=sci-libs/fftw-2*
-		app-shells/tcsh
-	 !<sci-chemistry/ccp4-6.0.99"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${P/-libs}"
-
-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
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "${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/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}
-
-	# Fix linking
-	export SHARE_LIB="ld -shared -soname libmmdb.so --whole-archive -o libmmdb.so libmmdb.a ../libccif.a; \
-			  ld -shared -soname libccp4c.so --whole-archive -o libccp4c.so libccp4c.a ../libccif.a; \
-			  ld -shared -soname libccp4f.so --whole-archive -o libccp4f.so libccp4f.a libmmdb.a libccp4c.a ../libccif.a -lstdc++ $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		--onlylibs \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-cctbx \
-		--disable-clipper \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-	emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${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/$(get_libdir) /usr/bin
-
-#	make install || die "install failed"
-	einstall || die "install failed"
-
-	# Libs
-	for file in "${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/$(get_libdir)/*.la
-
-	# Data
-	insinto /usr/share/ccp4
-	doins -r "${S}"/lib/data || die
-
-	# Include files
-	insinto /usr/include
-	for i in ccp4 mmdb; do
-		doins -r "${S}"/include/${i} || die
-	done
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.2-r1.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.2-r1.ebuild
deleted file mode 100644
index 3d6ac6880..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.2-r1.ebuild
+++ /dev/null
@@ -1,213 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	app-shells/tcsh
-	!<sci-chemistry/ccp4-6.0.99
-	=sci-libs/fftw-2*
-	sci-libs/mmdb
-	sci-libs/monomer-db
-	virtual/lapack
-	virtual/blas"
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}/${MY_P}"
-
-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
-
-	[[ -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}"/${PV}-dont-build-mmdb.patch
-
-	# 64bit long -> int32_t patch
-	ccp_patch "${FILESDIR}"/${PV}-64bit.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	userldflags="${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/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", $i}') -lstdc++ -lgfortran -lm"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		--onlylibs \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-cctbx \
-		--disable-clipper \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-	emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${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\'/usr/$(get_libdir)\':g" \
-		"${D}"/usr/$(get_libdir)/*.la
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${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-6.1.2.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild
deleted file mode 100644
index 7191ff805..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild
+++ /dev/null
@@ -1,210 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	app-shells/tcsh
-	!<sci-chemistry/ccp4-6.0.99
-	=sci-libs/fftw-2*
-	sci-libs/mmdb
-	sci-libs/monomer-db
-	virtual/lapack
-	virtual/blas"
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}/${MY_P}"
-
-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
-
-	[[ -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}"/${PV}-dont-build-mmdb.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	userldflags="${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/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", $i}') -lstdc++ -lgfortran -lm"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		--onlylibs \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-cctbx \
-		--disable-clipper \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-	emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${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\'/usr/$(get_libdir)\':g" \
-		"${D}"/usr/$(get_libdir)/*.la
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${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-r1.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r1.ebuild
deleted file mode 100644
index 39015b67a..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r1.ebuild
+++ /dev/null
@@ -1,210 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	app-shells/tcsh
-	!<sci-chemistry/ccp4-6.0.99
-	=sci-libs/fftw-2*
-	sci-libs/mmdb
-	sci-libs/monomer-db
-	virtual/lapack
-	virtual/blas"
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}/${MY_P}"
-
-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
-
-	[[ -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}"/${PV}-dont-build-mmdb.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	gnuconfig_update
-}
-
-src_compile() {
-	# Build system is broken if we set LDFLAGS
-	userldflags="${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/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", $i}') -lstdc++ -lgfortran -lm"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		--onlylibs \
-		--with-shared-libs \
-		--with-fftw=/usr \
-		--with-warnings \
-		--disable-cctbx \
-		--disable-clipper \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-	emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${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\'/usr/$(get_libdir)\':g" \
-		"${D}"/usr/$(get_libdir)/*.la
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${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/files/6.0.2-ppc-double-define-gerror.patch b/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch
deleted file mode 100644
index a77d9494a..000000000
--- a/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-6.0.1.orig/lib/src/library_f.c	2006-06-12 07:06:22.000000000 -0700
-+++ ccp4-6.0.1/lib/src/library_f.c	2006-06-12 07:21:56.000000000 -0700
-@@ -716,7 +716,7 @@
- 
- #endif /* end of apple xlf support */
- 
--#if ( defined (__linux__) && defined (_CALL_SYSV) )
-+#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) )
- /* linuxppc xlf support */
- void gerror_ (str, Lstr)
- char *str;
diff --git a/sci-libs/ccp4-libs/files/6.1.1-dont-make-dirs-in-configure.patch b/sci-libs/ccp4-libs/files/6.1.1-dont-make-dirs-in-configure.patch
deleted file mode 100644
index 583697cea..000000000
--- a/sci-libs/ccp4-libs/files/6.1.1-dont-make-dirs-in-configure.patch
+++ /dev/null
@@ -1,87 +0,0 @@
---- ccp4-6.0.99e.orig/configure	2008-07-31 10:37:22.000000000 -0700
-+++ ccp4-6.0.99e/configure	2008-07-31 10:39:18.000000000 -0700
-@@ -643,45 +643,45 @@
- #     echo "! Beware -- the $system installation isn't properly tested." ; }
- syswarn='echo; echo "! Beware -- the $system installation is not properly tested."'
- 
--if test -z "$onlylibs" ; then 
--   for i in CCP4_SCR BINSORT_SCR; do
--     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
--     else
--       eval echo "! No directory \$$i and can\'t create it."
--       echo "  Check the value of $i."
--       badvar=1
--     fi
--   done
--
--   for i in libdir bindir includedir; do
--     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
--     else
--       eval echo "! No directory \$$i and can\'t create it."
--       echo "  Check the argument of --$i."
--       badvar=1
--     fi
--   done
--
--   for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
--     if test -d $i || mkdir $i; then :
--     else
--       eval echo "! No directory $i and can\'t create it."
--       badvar=1
--     fi
--   done
--else
--   # Kludge to fool the "Makefile" target in the top-level CCP4
--   # Makefile into not trying to remake src/Makefile.in
--   for i in $srcdir/src $srcdir/lib/src ; do
--     if test -d $i || mkdir $i; then
--       if ! test -f $i/Makefile.in ; then
--         echo
--         echo "onlylibs: making dummy file $i/Makefile.in"
--	 touch $i/Makefile.in
--       fi
--     fi
--   done
--fi
-+#if test -z "$onlylibs" ; then 
-+#   for i in CCP4_SCR BINSORT_SCR; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the value of $i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in libdir bindir includedir; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the argument of --$i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
-+#     if test -d $i || mkdir $i; then :
-+#     else
-+#       eval echo "! No directory $i and can\'t create it."
-+#       badvar=1
-+#     fi
-+#   done
-+#else
-+#   # Kludge to fool the "Makefile" target in the top-level CCP4
-+#   # Makefile into not trying to remake src/Makefile.in
-+#   for i in $srcdir/src $srcdir/lib/src ; do
-+#     if test -d $i || mkdir $i; then
-+#       if ! test -f $i/Makefile.in ; then
-+#         echo
-+#         echo "onlylibs: making dummy file $i/Makefile.in"
-+#	 touch $i/Makefile.in
-+#       fi
-+#     fi
-+#   done
-+#fi
- 
- ### sanity checks
- 
diff --git a/sci-libs/ccp4-libs/files/6.1.1-glibc2.10.patch b/sci-libs/ccp4-libs/files/6.1.1-glibc2.10.patch
deleted file mode 100644
index 6e3997647..000000000
--- a/sci-libs/ccp4-libs/files/6.1.1-glibc2.10.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- lib/ccif/configure.in	2009-06-10 13:52:59.000000000 +0200
-+++ lib/ccif/configure.in.new	2009-06-10 14:04:31.000000000 +0200
-@@ -363,7 +363,7 @@
-          fi
-          SHARED_LIB_CMD='$(LD) $(SHARED_LIB_FLAGS) -shared -soname $(SHARED_LIB_NAME) \\\
-                         --whole-archive '"$SHARED_LIB_RESTRICT"' $L \\\
--                        $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
-+                        $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
-          SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
-       fi
-    ;;
---- lib/ccif/configure	2009-06-10 14:26:58.000000000 +0200
-+++ lib/ccif/configure.new	2009-06-10 14:43:31.000000000 +0200
-@@ -1807,7 +1807,7 @@
-          SHARED_LIB_CMD='$(LD) $(SHARED_LIB_CFLAGS) -shared -soname \\\
- 				$(SHARED_LIB_NAME) \\\
-                                --whole-archive $L \\\
--                               -o $(SHARED_LIB_NAME)'
-+                               -o $(SHARED_LIB_NAME) -lm'
-          SHARED_LIB_EXPORTS_CMD=''
-       fi
-    ;;
diff --git a/sci-libs/ccp4-libs/files/6.1.1-link-proberly.patch b/sci-libs/ccp4-libs/files/6.1.1-link-proberly.patch
deleted file mode 100644
index 0780314f0..000000000
--- a/sci-libs/ccp4-libs/files/6.1.1-link-proberly.patch
+++ /dev/null
@@ -1,255 +0,0 @@
---- lib/src/Makefile.in	2009-03-02 17:53:15.000000000 +0100
-+++ lib/src/Makefile.in.new	2009-03-02 17:52:09.000000000 +0100
-@@ -172,9 +172,8 @@
- 
- ##### Makefile targets ######
- 
--all:  fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
-+all:  fsplit $(LMMDB) LMMDB_SO $(LC) LC_SO $(LF) LF_SO $(SCRIPT_MODULES)
- # maybe create shared library
--	$(SHARE_LIB)
- 
- $(LC) : $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS)
- 	$(AR) $(LC) $?
-@@ -186,6 +185,27 @@
- 	$(AR) $(LF) $(FINTERFACEOBJS)
- 	$(RANLIB) $@
- 
-+LMMDB_SO : 
-+	$(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o libmmdb.so.0.0.0 \
-+	$(MMDBOBJS) && \
-+	ln -sf libmmdb.so.0.0.0 libmmdb.so.0 && \
-+	ln -sf libmmdb.so.0.0.0 libmmdb.so
-+
-+LC_SO : 
-+	$(CC) $(COPTIM) -shared -Wl,-soname,libccp4c.so.0 -o libccp4c.so.0.0.0 \
-+	$(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
-+	ln -sf libccp4c.so.0.0.0 libccp4c.so.0 && \
-+	ln -sf libccp4c.so.0.0.0 libccp4c.so
-+
-+LF_SO : 
-+	$(FC) $(FOPTIM) -shared -Wl,-soname,libccp4f.so.0 -o libccp4f.so.0.0.0 \
-+	parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
-+	libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
-+	harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
-+	modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
-+	ln -sf libccp4f.so.0.0.0 libccp4f.so.0 && \
-+	ln -sf libccp4f.so.0.0.0 libccp4f.so
-+
-#@@ -186,6 +185,27 @@
-# 	$(AR) $(LF) $(FINTERFACEOBJS)
-# 	$(RANLIB) $@
-# 
-#+LMMDB_SO : 
-#+	$(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o ../libmmdb.so.0.0.0 \
-#+	$(MMDBOBJS) && \
-#+	ln -sf libmmdb.so.0.0.0 ../libmmdb.so.0 && \
-#+	ln -sf libmmdb.so.0.0.0 ../libmmdb.so
-#+
-#+LC_SO : 
-#+	$(CC) $(COPTIM) -shared -Wl,-soname,libccp4_c.so.0 -o ../libccp4_c.so.0.0.0 \
-#+	$(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
-#+	ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so.0 && \
-#+	ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so
-#+
-#+LF_SO : 
-#+	$(FC) $(FOPTIM) -shared -Wl,-soname,libccp4_f.so.0 -o ../libccp4_f.so.0.0.0 \
-#+	parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
-#+	libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
-#+	harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
-#+	modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
-#+	ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so.0 && \
-#+	ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so
-#+
- # cmtz library only
- 
- cmtz: $(LCMTZ)
-@@ -339,9 +356,7 @@
- 	fi
- 	cd parser.dir && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f parser.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- parser : parser.o
- 	$(RANLIB) $(LF)
- 
-@@ -351,9 +366,7 @@
- 	echo '      END' >> ccplib.dir/ccplib.$F
- 	cd ccplib.dir && $(fsplit_dir)/fsplit $(srcdir)/ccplib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f ccplib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- ccplib : ccplib.o
- 	$(RANLIB) $(LF)
- 
-@@ -364,9 +377,7 @@
- 	@$(SETFLAGS) ; \
- 	cd lgglib.dir && $(fsplit_dir)/fsplit $(srcdir)/lgglib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    eval $(FC) -c  $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f lgglib.dir/*.o
-+	    eval $(FC) -c  $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done
- lgglib : lgglib.o
- 	$(RANLIB) $(LF)
- 
-@@ -376,9 +387,7 @@
- 	echo '      END' >> plot84lib.dir/plot84lib.$F
- 	cd plot84lib.dir && $(fsplit_dir)/fsplit $(srcdir)/plot84lib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f plot84lib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- plot84lib : plot84lib.o
- 	$(RANLIB) $(LF)
- 
-@@ -388,9 +397,7 @@
- 	echo '      END' >> libhtml.dir/libhtml.$F
- 	cd libhtml.dir && $(fsplit_dir)/fsplit $(srcdir)/libhtml.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f libhtml.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- libhtml : libhtml.o
- 	$(RANLIB) $(LF)
- 
-@@ -400,9 +407,7 @@
- 	echo '      END' >> pxxml.dir/pxxml.$F
- 	cd pxxml.dir && $(fsplit_dir)/fsplit $(srcdir)/pxxml.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f pxxml.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- pxxml : pxxml.o
- 	$(RANLIB) $(LF)
- 
-@@ -412,9 +417,7 @@
- 	echo '      END' >> rwbrook.dir/rwbrook.$F
- 	cd rwbrook.dir && $(fsplit_dir)/fsplit $(srcdir)/rwbrook.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f rwbrook.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- rwbrook : rwbrook.o
- 	$(RANLIB) $(LF)
- 
-@@ -424,9 +427,7 @@
- 	echo '      END' >> cciflib.dir/cciflib.$F
- 	cd cciflib.dir && $(fsplit_dir)/fsplit $(srcdir)/cciflib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f cciflib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done
- cciflib : cciflib.o
- 	$(RANLIB) $(LF)
- 
-@@ -440,9 +441,7 @@
- 	  && $(AR) ../$(LF) *.o ; else \
- 	cd harvlib.dir && $(fsplit_dir)/fsplit $(srcdir)/harv_dummy.f >/dev/null && $(RMEMPTY) && \
- 	for i in `pwd`/*.$F; do \
--	  $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
--	  && $(AR) ../$(LF) *.o ; fi
--	rm -f harvlib.dir/*.o
-+	  $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done; fi
- harvlib : harvlib.o
- 	$(RANLIB) $(LF)
- 
-@@ -452,9 +451,7 @@
- 	echo '      END' >> keyparse.dir/keyparse.$F
- 	cd keyparse.dir && $(fsplit_dir)/fsplit $(srcdir)/keyparse.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f keyparse.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- keyparse : keyparse.o
- 	$(RANLIB) $(LF)
- 
-@@ -464,9 +461,7 @@
- 	echo '      END' >> dna_output.dir/dna_output.$F
- 	cd dna_output.dir && $(fsplit_dir)/fsplit $(srcdir)/dna_output.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f dna_output.dir/*.o
-+	    $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- dna_output : dna_output.o
- 	$(RANLIB) $(LF)
- 
-@@ -474,10 +469,9 @@
- #  for ipdisp. May be useful but could be moved. 
- $(LF)(pack_c.o):   $(srcdir)/pack_c.c $(srcdir)/pack_c.h
- 	$(CC) $(CFLAGS) $(SHARED_LIB_CFLAGS) -I$(srcdir) -c $(srcdir)/pack_c.c
--	$(AR) $(LF) pack_c.o && rm pack_c.o
-+	$(AR) $(LF) pack_c.o
- $(LF)(pack_f.o):   $(srcdir)/pack_f.f
--	$(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o \
--          && rm pack_f.o
-+	$(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o
- pack:   $(LF)(pack_c.o) $(LF)(pack_f.o)
- 	$(RANLIB) $(LF) 
- 
-@@ -488,9 +482,7 @@
- 	echo '      END' >> sorting_main.dir/sorting_main.$F
- 	cd sorting_main.dir && $(fsplit_dir)/fsplit $(srcdir)/sorting_main.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f sorting_main.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- sorting_main : sorting_main.o
- 	$(RANLIB) $(LF)
- 
-@@ -500,9 +492,7 @@
- 	echo '      END' >> plotsubs.dir/plotsubs.$F
- 	cd plotsubs.dir && $(fsplit_dir)/fsplit $(srcdir)/plotsubs.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f plotsubs.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- plotsubs : plotsubs.o
- 	$(RANLIB) $(LF)
- 
-@@ -512,9 +502,7 @@
- 	echo '      END' >> modlib.dir/modlib.$F
- 	cd modlib.dir && $(fsplit_dir)/fsplit $(srcdir)/modlib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f modlib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- modlib : modlib.o
- 	$(RANLIB) $(LF)
- 
-@@ -524,9 +512,7 @@
- 	echo '      END' >> fftlib.dir/fftlib.$F
- 	cd fftlib.dir && $(fsplit_dir)/fsplit $(srcdir)/fftlib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done \
--	  && $(AR) ../$(LF) *.o
--	rm -f fftlib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done 
- fftlib : fftlib.o
- 	$(RANLIB) $(LF)
- 
-@@ -541,9 +527,7 @@
- 	echo '      END' >> unix.dir/unix.f
- 	cd unix.dir && $(fsplit_dir)/fsplit ../unix.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f unix.dir/*.o 
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- unix : unix.o
- 	$(RANLIB) $(LF)
- 
diff --git a/sci-libs/ccp4-libs/files/6.1.2-64bit.patch b/sci-libs/ccp4-libs/files/6.1.2-64bit.patch
deleted file mode 100644
index 390600b71..000000000
--- a/sci-libs/ccp4-libs/files/6.1.2-64bit.patch
+++ /dev/null
@@ -1,205 +0,0 @@
-diff --git a/ccp4-6.1.2/lib/DiffractionImage/Rigaku/RaxisImage.h b/ccp4-6.1.2/lib/DiffractionImage/Rigaku/RaxisImage.h
-index e02b72b..8a9611c 100755
---- a/ccp4-6.1.2/lib/DiffractionImage/Rigaku/RaxisImage.h
-+++ b/ccp4-6.1.2/lib/DiffractionImage/Rigaku/RaxisImage.h
-@@ -50,6 +50,7 @@
- #include <iostream>
- #include <fstream>
- #include <sstream>
-+#include <stdint.h>
- 
- /****************************************************************************
-  *                               Definitions                                *
-@@ -92,7 +93,7 @@ struct RigakuHeader {
-    float crnt;         /* generator current (mA) */
-    char  focs[12];     /* focus info */
-    char  optc[80];     /* xray memo */
--   long  cyld;         /* IP shape, 0=flat,1=cylinder */
-+   int32_t  cyld;         /* IP shape, 0=flat,1=cylinder */
-    float weis;         /* Weissenberg oscillation 1 */
-    char  res2[56];     /* reserved space for future use */
- 
-@@ -101,7 +102,7 @@ struct RigakuHeader {
-    float phi0;         /* datum phi angle (deg) */
-    float phis;         /* phi oscillation start angle (deg) */
-    float phie;         /* phi oscillation end angle (deg) */
--   long  oscn;         /* frame number */
-+   int32_t  oscn;         /* frame number */
-    float fext;         /* exposure time (min) */
-    float drtx;         /* direct beam X position */
-    float drtz;         /* direct beam Z position */
-@@ -113,31 +114,31 @@ struct RigakuHeader {
-                        /* This space is now used for storing the scan
-                           template information - tlh, 01 Feb 1999 */
-    
--   long  xpxl;         /* number of pixels in X direction */
--   long  zpxl;         /* number of pixels in Z direction */
-+   int32_t  xpxl;         /* number of pixels in X direction */
-+   int32_t  zpxl;         /* number of pixels in Z direction */
-    float xsiz;         /* size of pixel in X direction (mm) */
-    float zsiz;         /* size of pixel in Z direction (mm) */
--   long  rlng;         /* record length (bytes) */
--   long  rnum;         /* number of records (lines) in image */
--   long  ipst;         /* starting line number */
--   long  ipnm;         /* IP number */
-+   int32_t  rlng;         /* record length (bytes) */
-+   int32_t  rnum;         /* number of records (lines) in image */
-+   int32_t  ipst;         /* starting line number */
-+   int32_t  ipnm;         /* IP number */
-    float rato;         /* photomultiplier output hi/lo ratio */
-    float ft_1;         /* fading time, end of exposure to start of read */
-    float ft_2;         /* fading time, end of exposure to end of read */
-    char  host[10];     /* type of computer (IRIS, VAX) => endian */
-    char  ip[10];       /* type of IP */
--   long  dr_x;         /* horizontal scanning code: 0=left->right, 1=>right->left */
--   long  dr_z;         /* vertical scanning code: 0=down->up, 1=up->down */
--   long  drxz;	        /* front/back scanning code: 0=front, 1=back */
-+   int32_t  dr_x;         /* horizontal scanning code: 0=left->right, 1=>right->left */
-+   int32_t  dr_z;         /* vertical scanning code: 0=down->up, 1=up->down */
-+   int32_t  drxz;	        /* front/back scanning code: 0=front, 1=back */
-    float shft;         /* pixel shift, R-AXIS V */
-    float ineo;         /* intensity ratio E/O R-AXIS V */
--   long  majc;         /* magic number to indicate next values are legit */
--   long  naxs;         /* Number of goniometer axes */
-+   int32_t  majc;         /* magic number to indicate next values are legit */
-+   int32_t  naxs;         /* Number of goniometer axes */
-    float gvec[5][3];   /* Goniometer axis vectors */
-    float gst[5];       /* Start angles for each of 5 axes */
-    float gend[5];      /* End angles for each of 5 axes */
-    float goff[5];      /* Offset values for each of 5 axes */
--   long  saxs;         /* Which axis is the scan axis? */
-+   int32_t  saxs;         /* Which axis is the scan axis? */
-    char  gnom[40];     /* Names of the axes (space or comma separated?) */
- 
- /*
-@@ -148,17 +149,17 @@ struct RigakuHeader {
-    char  file[16];     /* */
-    char  cmnt[20];     /* */
-    char  smpl[20];     /* */
--   long  iext;         /* */
--   long  reso;         /* */
--   long  save;         /* */
--   long  dint;         /* */
--   long  byte;         /* */
--   long  init;         /* */
--   long  ipus;         /* */
--   long  dexp;         /* */
--   long  expn;         /* */
--   long  posx[20];     /* */
--   long  posy[20];     /* */
-+   int32_t  iext;         /* */
-+   int32_t  reso;         /* */
-+   int32_t  save;         /* */
-+   int32_t  dint;         /* */
-+   int32_t  byte;         /* */
-+   int32_t  init;         /* */
-+   int32_t  ipus;         /* */
-+   int32_t  dexp;         /* */
-+   int32_t  expn;         /* */
-+   int32_t  posx[20];     /* */
-+   int32_t  posy[20];     /* */
-    int   xray;         /* */
-    char  res5[768];    /* reserved space for future use */
- };
-@@ -213,10 +214,10 @@ bool ReadImageBuffer(std::ifstream &InputFile,unsigned short * const pImageBuffe
-    // is 2 bytes.
- unsigned short Swap(unsigned short Value);
- 
--   // This routine swaps the long <VAR>Value</VAR> so that the endianness 
-+   // This routine swaps the int32_t <VAR>Value</VAR> so that the endianness 
-    // of <VAR>Value</VAR> is reversed and then returns the swapped value.
--   // This routine assumes that the size of a long is 4 bytes.
--long Swap(long Value);
-+   // This routine assumes that the size of a int32_t is 4 bytes.
-+int32_t Swap(int32_t Value);
- 
-    // This routine swaps the float <VAR>Value</VAR> so that the endianness 
-    // of <VAR>Value</VAR> is reversed and then returns the swapped value.
-@@ -225,14 +226,14 @@ long Swap(long Value);
- float Swap(float Value);
- 
-    // This routine swaps the values in a Rigaku-style header,
--   // <VAR>Header</VAR> so that the endianness of the <CODE>long</CODE>
-+   // <VAR>Header</VAR> so that the endianness of the <CODE>int32_t</CODE>
-    // and </CODE>float</CODE> is reversed.
- void Swap(RigakuHeader &Header);
-   
--   // This routine returns a long containing the actual value of a packed
-+   // This routine returns a int32_t containing the actual value of a packed
-    // R-AXIS image pixel, <VAR>PixelValue</VAR>.  The Rigaku-style header
-    // contains information concerning the packing scheme used.
--long UnPackPixelValue(const RigakuHeader &Header,
-+int32_t UnPackPixelValue(const RigakuHeader &Header,
-                       const unsigned short PixelValue);
- 
-    // This routine writes out pixel values for some prefined pixel positions
-diff --git a/ccp4-6.1.2/lib/DiffractionImage/Rigaku/ReadRAXISImages.cpp b/ccp4-6.1.2/lib/DiffractionImage/Rigaku/ReadRAXISImages.cpp
-index 882d93d..3df1918 100755
---- a/ccp4-6.1.2/lib/DiffractionImage/Rigaku/ReadRAXISImages.cpp
-+++ b/ccp4-6.1.2/lib/DiffractionImage/Rigaku/ReadRAXISImages.cpp
-@@ -87,7 +87,7 @@ bool ReadHeader(std::ifstream &InputFile,
- 
-    // Read the additional padding in the header
- 
--   long size = Header.rlng-MinimumRigakuHeaderLength;
-+   int32_t size = Header.rlng-MinimumRigakuHeaderLength;
-    p = new char [size];
-    InputFile.read(p,size);
-    delete [] p;
-@@ -108,7 +108,7 @@ bool ReadImageBuffer(std::ifstream &InputFile,unsigned short * const pImageBuffe
-    // 2 bytes/pixel.
-    RigakuHeader Header;
-    ReadHeader(InputFile, Header);
--   long size = Header.rlng*Header.rnum/2;
-+   int32_t size = Header.rlng*Header.rnum/2;
- 
-    // Read in the data.
- 
-@@ -153,9 +153,9 @@ unsigned short Swap(const unsigned short Value)
- 
- /****************************************************************************
-  ****************************************************************************/
--long Swap(const long Value)
-+int32_t Swap(const int32_t Value)
- {
--   long swap = Value;
-+   int32_t swap = Value;
-    char *p = reinterpret_cast<char *>(&swap);
- 
-    char tmp = p[0];
-@@ -192,7 +192,7 @@ float Swap(const float Value)
- void Swap(RigakuHeader &Header)
- {
- 
--// Swap the bytes in the long elements of the header.
-+// Swap the bytes in the int32_t elements of the header.
- 
-    Header.cyld = Swap(Header.cyld);
-    Header.oscn = Swap(Header.oscn);
-@@ -257,7 +257,7 @@ void Swap(RigakuHeader &Header)
- 
- /****************************************************************************
-  ****************************************************************************/
--long UnPackPixelValue(const RigakuHeader &Header,
-+int32_t UnPackPixelValue(const RigakuHeader &Header,
-                       const unsigned short PixelValue)
- {
-    // Pixels are packed so that if the most significant bit is set, then
-@@ -274,7 +274,7 @@ long UnPackPixelValue(const RigakuHeader &Header,
- 
-    // We only need to use the lower 15 bits of the value to uncompress it.
- 
--   long Value = 0x7fff&PixelValue;
-+   int32_t Value = 0x7fff&PixelValue;
- 
-    // Shift the value by the ratio in the header.
- 
-@@ -296,7 +296,7 @@ void OutputSamplePixelValues(const RigakuHeader &Header,
-    std::cout << "   First pixel (0," << Header.ipst << ") in image = " << 
-                 UnPackPixelValue(Header,*pImageBuffer) << std::endl;
- 
--   long index = (Header.rnum/2-1)*Header.xpxl+(Header.xpxl/2-1);
-+   int32_t index = (Header.rnum/2-1)*Header.xpxl+(Header.xpxl/2-1);
-    std::cout << "   Middle pixel (" << Header.xpxl/2 << ',' << 
-                  Header.rnum/2+Header.ipst << ") in image = " << 
-                  UnPackPixelValue(Header,pImageBuffer[index]) << std::endl;
diff --git a/sci-libs/ccp4-libs/files/6.1.2-ccif-shared.patch b/sci-libs/ccp4-libs/files/6.1.2-ccif-shared.patch
deleted file mode 100644
index ca18d75bc..000000000
--- a/sci-libs/ccp4-libs/files/6.1.2-ccif-shared.patch
+++ /dev/null
@@ -1,33 +0,0 @@
---- configure	2009-08-04 22:35:34.000000000 +0200
-+++ configure.new	2009-08-04 22:54:32.000000000 +0200
-@@ -3136,8 +3136,8 @@
-   fi
-   ( touch /tmp/$$.cache_file 2>/dev/null && \
-     cat /dev/null > /tmp/$$.cache_file && \
--    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \
--    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif
-+    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file --enable-shared-lib ) || \
-+    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --enable-shared-lib
-   rm -f /tmp/$$.cache_file
-   if [ "X$LIBFOPTIM" != "X" ]; then
-     FOPTIM=$FOPTIM_save
---- lib/ccif/configure	2009-08-04 22:35:37.000000000 +0200
-+++ lib/ccif/configure.new	2009-08-04 23:05:44.000000000 +0200
-@@ -5568,7 +5568,7 @@
-       enable_shared_lib=no
-    ;;
- 
--   i?86-unknown-linux | i?86-pc-linux-gnu )
-+   i?86-unknown-linux | i?86-pc-linux-gnu | x86_64-unknown-linux-gnu)
-       if test $enable_shared_lib = yes ; then
- 
-          SO_LOC_VAR='LD_LIBRARY_PATH'
-@@ -5585,7 +5585,7 @@
-          else
-            SHARED_LIB_PATH='LD_LIBRARY_PATH=`pwd`'
-          fi
--         SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
-+         SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
-          # SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
-          SHARED_LIB_EXPORTS_CMD=''
-       fi
diff --git a/sci-libs/ccp4-libs/files/6.1.2-dont-build-mmdb.patch b/sci-libs/ccp4-libs/files/6.1.2-dont-build-mmdb.patch
deleted file mode 100644
index b3fefacda..000000000
--- a/sci-libs/ccp4-libs/files/6.1.2-dont-build-mmdb.patch
+++ /dev/null
@@ -1,26 +0,0 @@
---- lib/src/Makefile.in	2009-06-18 15:44:08.000000000 +0200
-+++ lib/src/Makefile.in.new	2009-08-11 11:58:25.000000000 +0200
-@@ -176,7 +176,7 @@
- 
- ##### Makefile targets ######
- 
--all:  fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
-+all:  fsplit $(LC) $(LF) $(SCRIPT_MODULES)
- # maybe create shared library
- 	$(SHARE_LIB)
- 
---- lib/src/Makefile.in	2009-06-18 15:44:08.000000000 +0200
-+++ lib/src/Makefile.in.new	2009-08-11 12:17:53.000000000 +0200
-@@ -716,11 +716,9 @@
- 	  rm -f $(DESTDIR)$(includedir)/mmdb/$$f; \
- 	done
- 
--install : all install-ccp4HEADERS install-mmdbHEADERS
--	$(INSTALL_DATA) `pwd`/$(LMMDB) $(libdir)/$(LMMDB)
-+install : all install-ccp4HEADERS
- 	$(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC)
- 	$(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF)
--	$(RANLIB) $(libdir)/$(LMMDB)
- 	$(RANLIB) $(libdir)/$(LC)
- 	$(RANLIB) $(libdir)/$(LF)
- 	$(SHARE_INST)
diff --git a/sci-libs/ccp4-libs/files/6.1.2-dont-make-dirs-in-configure.patch b/sci-libs/ccp4-libs/files/6.1.2-dont-make-dirs-in-configure.patch
deleted file mode 100644
index 583697cea..000000000
--- a/sci-libs/ccp4-libs/files/6.1.2-dont-make-dirs-in-configure.patch
+++ /dev/null
@@ -1,87 +0,0 @@
---- ccp4-6.0.99e.orig/configure	2008-07-31 10:37:22.000000000 -0700
-+++ ccp4-6.0.99e/configure	2008-07-31 10:39:18.000000000 -0700
-@@ -643,45 +643,45 @@
- #     echo "! Beware -- the $system installation isn't properly tested." ; }
- syswarn='echo; echo "! Beware -- the $system installation is not properly tested."'
- 
--if test -z "$onlylibs" ; then 
--   for i in CCP4_SCR BINSORT_SCR; do
--     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
--     else
--       eval echo "! No directory \$$i and can\'t create it."
--       echo "  Check the value of $i."
--       badvar=1
--     fi
--   done
--
--   for i in libdir bindir includedir; do
--     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
--     else
--       eval echo "! No directory \$$i and can\'t create it."
--       echo "  Check the argument of --$i."
--       badvar=1
--     fi
--   done
--
--   for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
--     if test -d $i || mkdir $i; then :
--     else
--       eval echo "! No directory $i and can\'t create it."
--       badvar=1
--     fi
--   done
--else
--   # Kludge to fool the "Makefile" target in the top-level CCP4
--   # Makefile into not trying to remake src/Makefile.in
--   for i in $srcdir/src $srcdir/lib/src ; do
--     if test -d $i || mkdir $i; then
--       if ! test -f $i/Makefile.in ; then
--         echo
--         echo "onlylibs: making dummy file $i/Makefile.in"
--	 touch $i/Makefile.in
--       fi
--     fi
--   done
--fi
-+#if test -z "$onlylibs" ; then 
-+#   for i in CCP4_SCR BINSORT_SCR; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the value of $i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in libdir bindir includedir; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the argument of --$i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
-+#     if test -d $i || mkdir $i; then :
-+#     else
-+#       eval echo "! No directory $i and can\'t create it."
-+#       badvar=1
-+#     fi
-+#   done
-+#else
-+#   # Kludge to fool the "Makefile" target in the top-level CCP4
-+#   # Makefile into not trying to remake src/Makefile.in
-+#   for i in $srcdir/src $srcdir/lib/src ; do
-+#     if test -d $i || mkdir $i; then
-+#       if ! test -f $i/Makefile.in ; then
-+#         echo
-+#         echo "onlylibs: making dummy file $i/Makefile.in"
-+#	 touch $i/Makefile.in
-+#       fi
-+#     fi
-+#   done
-+#fi
- 
- ### sanity checks
- 
diff --git a/sci-libs/ccp4-libs/files/6.1.2-glibc2.10.patch b/sci-libs/ccp4-libs/files/6.1.2-glibc2.10.patch
deleted file mode 100644
index 6e3997647..000000000
--- a/sci-libs/ccp4-libs/files/6.1.2-glibc2.10.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- lib/ccif/configure.in	2009-06-10 13:52:59.000000000 +0200
-+++ lib/ccif/configure.in.new	2009-06-10 14:04:31.000000000 +0200
-@@ -363,7 +363,7 @@
-          fi
-          SHARED_LIB_CMD='$(LD) $(SHARED_LIB_FLAGS) -shared -soname $(SHARED_LIB_NAME) \\\
-                         --whole-archive '"$SHARED_LIB_RESTRICT"' $L \\\
--                        $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
-+                        $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
-          SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
-       fi
-    ;;
---- lib/ccif/configure	2009-06-10 14:26:58.000000000 +0200
-+++ lib/ccif/configure.new	2009-06-10 14:43:31.000000000 +0200
-@@ -1807,7 +1807,7 @@
-          SHARED_LIB_CMD='$(LD) $(SHARED_LIB_CFLAGS) -shared -soname \\\
- 				$(SHARED_LIB_NAME) \\\
-                                --whole-archive $L \\\
--                               -o $(SHARED_LIB_NAME)'
-+                               -o $(SHARED_LIB_NAME) -lm'
-          SHARED_LIB_EXPORTS_CMD=''
-       fi
-    ;;
diff --git a/sci-libs/ccp4-libs/files/6.1.2-link-proberly.patch b/sci-libs/ccp4-libs/files/6.1.2-link-proberly.patch
deleted file mode 100644
index 0780314f0..000000000
--- a/sci-libs/ccp4-libs/files/6.1.2-link-proberly.patch
+++ /dev/null
@@ -1,255 +0,0 @@
---- lib/src/Makefile.in	2009-03-02 17:53:15.000000000 +0100
-+++ lib/src/Makefile.in.new	2009-03-02 17:52:09.000000000 +0100
-@@ -172,9 +172,8 @@
- 
- ##### Makefile targets ######
- 
--all:  fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
-+all:  fsplit $(LMMDB) LMMDB_SO $(LC) LC_SO $(LF) LF_SO $(SCRIPT_MODULES)
- # maybe create shared library
--	$(SHARE_LIB)
- 
- $(LC) : $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS)
- 	$(AR) $(LC) $?
-@@ -186,6 +185,27 @@
- 	$(AR) $(LF) $(FINTERFACEOBJS)
- 	$(RANLIB) $@
- 
-+LMMDB_SO : 
-+	$(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o libmmdb.so.0.0.0 \
-+	$(MMDBOBJS) && \
-+	ln -sf libmmdb.so.0.0.0 libmmdb.so.0 && \
-+	ln -sf libmmdb.so.0.0.0 libmmdb.so
-+
-+LC_SO : 
-+	$(CC) $(COPTIM) -shared -Wl,-soname,libccp4c.so.0 -o libccp4c.so.0.0.0 \
-+	$(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
-+	ln -sf libccp4c.so.0.0.0 libccp4c.so.0 && \
-+	ln -sf libccp4c.so.0.0.0 libccp4c.so
-+
-+LF_SO : 
-+	$(FC) $(FOPTIM) -shared -Wl,-soname,libccp4f.so.0 -o libccp4f.so.0.0.0 \
-+	parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
-+	libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
-+	harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
-+	modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
-+	ln -sf libccp4f.so.0.0.0 libccp4f.so.0 && \
-+	ln -sf libccp4f.so.0.0.0 libccp4f.so
-+
-#@@ -186,6 +185,27 @@
-# 	$(AR) $(LF) $(FINTERFACEOBJS)
-# 	$(RANLIB) $@
-# 
-#+LMMDB_SO : 
-#+	$(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o ../libmmdb.so.0.0.0 \
-#+	$(MMDBOBJS) && \
-#+	ln -sf libmmdb.so.0.0.0 ../libmmdb.so.0 && \
-#+	ln -sf libmmdb.so.0.0.0 ../libmmdb.so
-#+
-#+LC_SO : 
-#+	$(CC) $(COPTIM) -shared -Wl,-soname,libccp4_c.so.0 -o ../libccp4_c.so.0.0.0 \
-#+	$(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
-#+	ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so.0 && \
-#+	ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so
-#+
-#+LF_SO : 
-#+	$(FC) $(FOPTIM) -shared -Wl,-soname,libccp4_f.so.0 -o ../libccp4_f.so.0.0.0 \
-#+	parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
-#+	libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
-#+	harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
-#+	modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
-#+	ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so.0 && \
-#+	ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so
-#+
- # cmtz library only
- 
- cmtz: $(LCMTZ)
-@@ -339,9 +356,7 @@
- 	fi
- 	cd parser.dir && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f parser.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- parser : parser.o
- 	$(RANLIB) $(LF)
- 
-@@ -351,9 +366,7 @@
- 	echo '      END' >> ccplib.dir/ccplib.$F
- 	cd ccplib.dir && $(fsplit_dir)/fsplit $(srcdir)/ccplib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f ccplib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- ccplib : ccplib.o
- 	$(RANLIB) $(LF)
- 
-@@ -364,9 +377,7 @@
- 	@$(SETFLAGS) ; \
- 	cd lgglib.dir && $(fsplit_dir)/fsplit $(srcdir)/lgglib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    eval $(FC) -c  $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f lgglib.dir/*.o
-+	    eval $(FC) -c  $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done
- lgglib : lgglib.o
- 	$(RANLIB) $(LF)
- 
-@@ -376,9 +387,7 @@
- 	echo '      END' >> plot84lib.dir/plot84lib.$F
- 	cd plot84lib.dir && $(fsplit_dir)/fsplit $(srcdir)/plot84lib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f plot84lib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- plot84lib : plot84lib.o
- 	$(RANLIB) $(LF)
- 
-@@ -388,9 +397,7 @@
- 	echo '      END' >> libhtml.dir/libhtml.$F
- 	cd libhtml.dir && $(fsplit_dir)/fsplit $(srcdir)/libhtml.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f libhtml.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- libhtml : libhtml.o
- 	$(RANLIB) $(LF)
- 
-@@ -400,9 +407,7 @@
- 	echo '      END' >> pxxml.dir/pxxml.$F
- 	cd pxxml.dir && $(fsplit_dir)/fsplit $(srcdir)/pxxml.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f pxxml.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- pxxml : pxxml.o
- 	$(RANLIB) $(LF)
- 
-@@ -412,9 +417,7 @@
- 	echo '      END' >> rwbrook.dir/rwbrook.$F
- 	cd rwbrook.dir && $(fsplit_dir)/fsplit $(srcdir)/rwbrook.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f rwbrook.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- rwbrook : rwbrook.o
- 	$(RANLIB) $(LF)
- 
-@@ -424,9 +427,7 @@
- 	echo '      END' >> cciflib.dir/cciflib.$F
- 	cd cciflib.dir && $(fsplit_dir)/fsplit $(srcdir)/cciflib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f cciflib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done
- cciflib : cciflib.o
- 	$(RANLIB) $(LF)
- 
-@@ -440,9 +441,7 @@
- 	  && $(AR) ../$(LF) *.o ; else \
- 	cd harvlib.dir && $(fsplit_dir)/fsplit $(srcdir)/harv_dummy.f >/dev/null && $(RMEMPTY) && \
- 	for i in `pwd`/*.$F; do \
--	  $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
--	  && $(AR) ../$(LF) *.o ; fi
--	rm -f harvlib.dir/*.o
-+	  $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done; fi
- harvlib : harvlib.o
- 	$(RANLIB) $(LF)
- 
-@@ -452,9 +451,7 @@
- 	echo '      END' >> keyparse.dir/keyparse.$F
- 	cd keyparse.dir && $(fsplit_dir)/fsplit $(srcdir)/keyparse.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f keyparse.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- keyparse : keyparse.o
- 	$(RANLIB) $(LF)
- 
-@@ -464,9 +461,7 @@
- 	echo '      END' >> dna_output.dir/dna_output.$F
- 	cd dna_output.dir && $(fsplit_dir)/fsplit $(srcdir)/dna_output.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f dna_output.dir/*.o
-+	    $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- dna_output : dna_output.o
- 	$(RANLIB) $(LF)
- 
-@@ -474,10 +469,9 @@
- #  for ipdisp. May be useful but could be moved. 
- $(LF)(pack_c.o):   $(srcdir)/pack_c.c $(srcdir)/pack_c.h
- 	$(CC) $(CFLAGS) $(SHARED_LIB_CFLAGS) -I$(srcdir) -c $(srcdir)/pack_c.c
--	$(AR) $(LF) pack_c.o && rm pack_c.o
-+	$(AR) $(LF) pack_c.o
- $(LF)(pack_f.o):   $(srcdir)/pack_f.f
--	$(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o \
--          && rm pack_f.o
-+	$(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o
- pack:   $(LF)(pack_c.o) $(LF)(pack_f.o)
- 	$(RANLIB) $(LF) 
- 
-@@ -488,9 +482,7 @@
- 	echo '      END' >> sorting_main.dir/sorting_main.$F
- 	cd sorting_main.dir && $(fsplit_dir)/fsplit $(srcdir)/sorting_main.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f sorting_main.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- sorting_main : sorting_main.o
- 	$(RANLIB) $(LF)
- 
-@@ -500,9 +492,7 @@
- 	echo '      END' >> plotsubs.dir/plotsubs.$F
- 	cd plotsubs.dir && $(fsplit_dir)/fsplit $(srcdir)/plotsubs.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f plotsubs.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- plotsubs : plotsubs.o
- 	$(RANLIB) $(LF)
- 
-@@ -512,9 +502,7 @@
- 	echo '      END' >> modlib.dir/modlib.$F
- 	cd modlib.dir && $(fsplit_dir)/fsplit $(srcdir)/modlib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f modlib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- modlib : modlib.o
- 	$(RANLIB) $(LF)
- 
-@@ -524,9 +512,7 @@
- 	echo '      END' >> fftlib.dir/fftlib.$F
- 	cd fftlib.dir && $(fsplit_dir)/fsplit $(srcdir)/fftlib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done \
--	  && $(AR) ../$(LF) *.o
--	rm -f fftlib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done 
- fftlib : fftlib.o
- 	$(RANLIB) $(LF)
- 
-@@ -541,9 +527,7 @@
- 	echo '      END' >> unix.dir/unix.f
- 	cd unix.dir && $(fsplit_dir)/fsplit ../unix.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f unix.dir/*.o 
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- unix : unix.o
- 	$(RANLIB) $(LF)
- 
diff --git a/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch b/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch
deleted file mode 100644
index ca18d75bc..000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch
+++ /dev/null
@@ -1,33 +0,0 @@
---- configure	2009-08-04 22:35:34.000000000 +0200
-+++ configure.new	2009-08-04 22:54:32.000000000 +0200
-@@ -3136,8 +3136,8 @@
-   fi
-   ( touch /tmp/$$.cache_file 2>/dev/null && \
-     cat /dev/null > /tmp/$$.cache_file && \
--    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \
--    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif
-+    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file --enable-shared-lib ) || \
-+    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --enable-shared-lib
-   rm -f /tmp/$$.cache_file
-   if [ "X$LIBFOPTIM" != "X" ]; then
-     FOPTIM=$FOPTIM_save
---- lib/ccif/configure	2009-08-04 22:35:37.000000000 +0200
-+++ lib/ccif/configure.new	2009-08-04 23:05:44.000000000 +0200
-@@ -5568,7 +5568,7 @@
-       enable_shared_lib=no
-    ;;
- 
--   i?86-unknown-linux | i?86-pc-linux-gnu )
-+   i?86-unknown-linux | i?86-pc-linux-gnu | x86_64-unknown-linux-gnu)
-       if test $enable_shared_lib = yes ; then
- 
-          SO_LOC_VAR='LD_LIBRARY_PATH'
-@@ -5585,7 +5585,7 @@
-          else
-            SHARED_LIB_PATH='LD_LIBRARY_PATH=`pwd`'
-          fi
--         SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
-+         SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
-          # SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
-          SHARED_LIB_EXPORTS_CMD=''
-       fi
diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch
deleted file mode 100644
index b3fefacda..000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch
+++ /dev/null
@@ -1,26 +0,0 @@
---- lib/src/Makefile.in	2009-06-18 15:44:08.000000000 +0200
-+++ lib/src/Makefile.in.new	2009-08-11 11:58:25.000000000 +0200
-@@ -176,7 +176,7 @@
- 
- ##### Makefile targets ######
- 
--all:  fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
-+all:  fsplit $(LC) $(LF) $(SCRIPT_MODULES)
- # maybe create shared library
- 	$(SHARE_LIB)
- 
---- lib/src/Makefile.in	2009-06-18 15:44:08.000000000 +0200
-+++ lib/src/Makefile.in.new	2009-08-11 12:17:53.000000000 +0200
-@@ -716,11 +716,9 @@
- 	  rm -f $(DESTDIR)$(includedir)/mmdb/$$f; \
- 	done
- 
--install : all install-ccp4HEADERS install-mmdbHEADERS
--	$(INSTALL_DATA) `pwd`/$(LMMDB) $(libdir)/$(LMMDB)
-+install : all install-ccp4HEADERS
- 	$(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC)
- 	$(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF)
--	$(RANLIB) $(libdir)/$(LMMDB)
- 	$(RANLIB) $(libdir)/$(LC)
- 	$(RANLIB) $(libdir)/$(LF)
- 	$(SHARE_INST)
diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch
deleted file mode 100644
index 583697cea..000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch
+++ /dev/null
@@ -1,87 +0,0 @@
---- ccp4-6.0.99e.orig/configure	2008-07-31 10:37:22.000000000 -0700
-+++ ccp4-6.0.99e/configure	2008-07-31 10:39:18.000000000 -0700
-@@ -643,45 +643,45 @@
- #     echo "! Beware -- the $system installation isn't properly tested." ; }
- syswarn='echo; echo "! Beware -- the $system installation is not properly tested."'
- 
--if test -z "$onlylibs" ; then 
--   for i in CCP4_SCR BINSORT_SCR; do
--     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
--     else
--       eval echo "! No directory \$$i and can\'t create it."
--       echo "  Check the value of $i."
--       badvar=1
--     fi
--   done
--
--   for i in libdir bindir includedir; do
--     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
--     else
--       eval echo "! No directory \$$i and can\'t create it."
--       echo "  Check the argument of --$i."
--       badvar=1
--     fi
--   done
--
--   for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
--     if test -d $i || mkdir $i; then :
--     else
--       eval echo "! No directory $i and can\'t create it."
--       badvar=1
--     fi
--   done
--else
--   # Kludge to fool the "Makefile" target in the top-level CCP4
--   # Makefile into not trying to remake src/Makefile.in
--   for i in $srcdir/src $srcdir/lib/src ; do
--     if test -d $i || mkdir $i; then
--       if ! test -f $i/Makefile.in ; then
--         echo
--         echo "onlylibs: making dummy file $i/Makefile.in"
--	 touch $i/Makefile.in
--       fi
--     fi
--   done
--fi
-+#if test -z "$onlylibs" ; then 
-+#   for i in CCP4_SCR BINSORT_SCR; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the value of $i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in libdir bindir includedir; do
-+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-+#     else
-+#       eval echo "! No directory \$$i and can\'t create it."
-+#       echo "  Check the argument of --$i."
-+#       badvar=1
-+#     fi
-+#   done
-+#
-+#   for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
-+#     if test -d $i || mkdir $i; then :
-+#     else
-+#       eval echo "! No directory $i and can\'t create it."
-+#       badvar=1
-+#     fi
-+#   done
-+#else
-+#   # Kludge to fool the "Makefile" target in the top-level CCP4
-+#   # Makefile into not trying to remake src/Makefile.in
-+#   for i in $srcdir/src $srcdir/lib/src ; do
-+#     if test -d $i || mkdir $i; then
-+#       if ! test -f $i/Makefile.in ; then
-+#         echo
-+#         echo "onlylibs: making dummy file $i/Makefile.in"
-+#	 touch $i/Makefile.in
-+#       fi
-+#     fi
-+#   done
-+#fi
- 
- ### sanity checks
- 
diff --git a/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch b/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch
deleted file mode 100644
index 6e3997647..000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- lib/ccif/configure.in	2009-06-10 13:52:59.000000000 +0200
-+++ lib/ccif/configure.in.new	2009-06-10 14:04:31.000000000 +0200
-@@ -363,7 +363,7 @@
-          fi
-          SHARED_LIB_CMD='$(LD) $(SHARED_LIB_FLAGS) -shared -soname $(SHARED_LIB_NAME) \\\
-                         --whole-archive '"$SHARED_LIB_RESTRICT"' $L \\\
--                        $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
-+                        $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
-          SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
-       fi
-    ;;
---- lib/ccif/configure	2009-06-10 14:26:58.000000000 +0200
-+++ lib/ccif/configure.new	2009-06-10 14:43:31.000000000 +0200
-@@ -1807,7 +1807,7 @@
-          SHARED_LIB_CMD='$(LD) $(SHARED_LIB_CFLAGS) -shared -soname \\\
- 				$(SHARED_LIB_NAME) \\\
-                                --whole-archive $L \\\
--                               -o $(SHARED_LIB_NAME)'
-+                               -o $(SHARED_LIB_NAME) -lm'
-          SHARED_LIB_EXPORTS_CMD=''
-       fi
-    ;;
diff --git a/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch b/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch
deleted file mode 100644
index 0780314f0..000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch
+++ /dev/null
@@ -1,255 +0,0 @@
---- lib/src/Makefile.in	2009-03-02 17:53:15.000000000 +0100
-+++ lib/src/Makefile.in.new	2009-03-02 17:52:09.000000000 +0100
-@@ -172,9 +172,8 @@
- 
- ##### Makefile targets ######
- 
--all:  fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
-+all:  fsplit $(LMMDB) LMMDB_SO $(LC) LC_SO $(LF) LF_SO $(SCRIPT_MODULES)
- # maybe create shared library
--	$(SHARE_LIB)
- 
- $(LC) : $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS)
- 	$(AR) $(LC) $?
-@@ -186,6 +185,27 @@
- 	$(AR) $(LF) $(FINTERFACEOBJS)
- 	$(RANLIB) $@
- 
-+LMMDB_SO : 
-+	$(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o libmmdb.so.0.0.0 \
-+	$(MMDBOBJS) && \
-+	ln -sf libmmdb.so.0.0.0 libmmdb.so.0 && \
-+	ln -sf libmmdb.so.0.0.0 libmmdb.so
-+
-+LC_SO : 
-+	$(CC) $(COPTIM) -shared -Wl,-soname,libccp4c.so.0 -o libccp4c.so.0.0.0 \
-+	$(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
-+	ln -sf libccp4c.so.0.0.0 libccp4c.so.0 && \
-+	ln -sf libccp4c.so.0.0.0 libccp4c.so
-+
-+LF_SO : 
-+	$(FC) $(FOPTIM) -shared -Wl,-soname,libccp4f.so.0 -o libccp4f.so.0.0.0 \
-+	parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
-+	libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
-+	harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
-+	modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
-+	ln -sf libccp4f.so.0.0.0 libccp4f.so.0 && \
-+	ln -sf libccp4f.so.0.0.0 libccp4f.so
-+
-#@@ -186,6 +185,27 @@
-# 	$(AR) $(LF) $(FINTERFACEOBJS)
-# 	$(RANLIB) $@
-# 
-#+LMMDB_SO : 
-#+	$(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o ../libmmdb.so.0.0.0 \
-#+	$(MMDBOBJS) && \
-#+	ln -sf libmmdb.so.0.0.0 ../libmmdb.so.0 && \
-#+	ln -sf libmmdb.so.0.0.0 ../libmmdb.so
-#+
-#+LC_SO : 
-#+	$(CC) $(COPTIM) -shared -Wl,-soname,libccp4_c.so.0 -o ../libccp4_c.so.0.0.0 \
-#+	$(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
-#+	ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so.0 && \
-#+	ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so
-#+
-#+LF_SO : 
-#+	$(FC) $(FOPTIM) -shared -Wl,-soname,libccp4_f.so.0 -o ../libccp4_f.so.0.0.0 \
-#+	parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
-#+	libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
-#+	harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
-#+	modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
-#+	ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so.0 && \
-#+	ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so
-#+
- # cmtz library only
- 
- cmtz: $(LCMTZ)
-@@ -339,9 +356,7 @@
- 	fi
- 	cd parser.dir && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f parser.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- parser : parser.o
- 	$(RANLIB) $(LF)
- 
-@@ -351,9 +366,7 @@
- 	echo '      END' >> ccplib.dir/ccplib.$F
- 	cd ccplib.dir && $(fsplit_dir)/fsplit $(srcdir)/ccplib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f ccplib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- ccplib : ccplib.o
- 	$(RANLIB) $(LF)
- 
-@@ -364,9 +377,7 @@
- 	@$(SETFLAGS) ; \
- 	cd lgglib.dir && $(fsplit_dir)/fsplit $(srcdir)/lgglib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    eval $(FC) -c  $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f lgglib.dir/*.o
-+	    eval $(FC) -c  $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done
- lgglib : lgglib.o
- 	$(RANLIB) $(LF)
- 
-@@ -376,9 +387,7 @@
- 	echo '      END' >> plot84lib.dir/plot84lib.$F
- 	cd plot84lib.dir && $(fsplit_dir)/fsplit $(srcdir)/plot84lib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f plot84lib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- plot84lib : plot84lib.o
- 	$(RANLIB) $(LF)
- 
-@@ -388,9 +397,7 @@
- 	echo '      END' >> libhtml.dir/libhtml.$F
- 	cd libhtml.dir && $(fsplit_dir)/fsplit $(srcdir)/libhtml.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f libhtml.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- libhtml : libhtml.o
- 	$(RANLIB) $(LF)
- 
-@@ -400,9 +407,7 @@
- 	echo '      END' >> pxxml.dir/pxxml.$F
- 	cd pxxml.dir && $(fsplit_dir)/fsplit $(srcdir)/pxxml.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f pxxml.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- pxxml : pxxml.o
- 	$(RANLIB) $(LF)
- 
-@@ -412,9 +417,7 @@
- 	echo '      END' >> rwbrook.dir/rwbrook.$F
- 	cd rwbrook.dir && $(fsplit_dir)/fsplit $(srcdir)/rwbrook.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f rwbrook.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- rwbrook : rwbrook.o
- 	$(RANLIB) $(LF)
- 
-@@ -424,9 +427,7 @@
- 	echo '      END' >> cciflib.dir/cciflib.$F
- 	cd cciflib.dir && $(fsplit_dir)/fsplit $(srcdir)/cciflib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f cciflib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done
- cciflib : cciflib.o
- 	$(RANLIB) $(LF)
- 
-@@ -440,9 +441,7 @@
- 	  && $(AR) ../$(LF) *.o ; else \
- 	cd harvlib.dir && $(fsplit_dir)/fsplit $(srcdir)/harv_dummy.f >/dev/null && $(RMEMPTY) && \
- 	for i in `pwd`/*.$F; do \
--	  $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
--	  && $(AR) ../$(LF) *.o ; fi
--	rm -f harvlib.dir/*.o
-+	  $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done; fi
- harvlib : harvlib.o
- 	$(RANLIB) $(LF)
- 
-@@ -452,9 +451,7 @@
- 	echo '      END' >> keyparse.dir/keyparse.$F
- 	cd keyparse.dir && $(fsplit_dir)/fsplit $(srcdir)/keyparse.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f keyparse.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- keyparse : keyparse.o
- 	$(RANLIB) $(LF)
- 
-@@ -464,9 +461,7 @@
- 	echo '      END' >> dna_output.dir/dna_output.$F
- 	cd dna_output.dir && $(fsplit_dir)/fsplit $(srcdir)/dna_output.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f dna_output.dir/*.o
-+	    $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- dna_output : dna_output.o
- 	$(RANLIB) $(LF)
- 
-@@ -474,10 +469,9 @@
- #  for ipdisp. May be useful but could be moved. 
- $(LF)(pack_c.o):   $(srcdir)/pack_c.c $(srcdir)/pack_c.h
- 	$(CC) $(CFLAGS) $(SHARED_LIB_CFLAGS) -I$(srcdir) -c $(srcdir)/pack_c.c
--	$(AR) $(LF) pack_c.o && rm pack_c.o
-+	$(AR) $(LF) pack_c.o
- $(LF)(pack_f.o):   $(srcdir)/pack_f.f
--	$(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o \
--          && rm pack_f.o
-+	$(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o
- pack:   $(LF)(pack_c.o) $(LF)(pack_f.o)
- 	$(RANLIB) $(LF) 
- 
-@@ -488,9 +482,7 @@
- 	echo '      END' >> sorting_main.dir/sorting_main.$F
- 	cd sorting_main.dir && $(fsplit_dir)/fsplit $(srcdir)/sorting_main.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f sorting_main.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- sorting_main : sorting_main.o
- 	$(RANLIB) $(LF)
- 
-@@ -500,9 +492,7 @@
- 	echo '      END' >> plotsubs.dir/plotsubs.$F
- 	cd plotsubs.dir && $(fsplit_dir)/fsplit $(srcdir)/plotsubs.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f plotsubs.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- plotsubs : plotsubs.o
- 	$(RANLIB) $(LF)
- 
-@@ -512,9 +502,7 @@
- 	echo '      END' >> modlib.dir/modlib.$F
- 	cd modlib.dir && $(fsplit_dir)/fsplit $(srcdir)/modlib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f modlib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- modlib : modlib.o
- 	$(RANLIB) $(LF)
- 
-@@ -524,9 +512,7 @@
- 	echo '      END' >> fftlib.dir/fftlib.$F
- 	cd fftlib.dir && $(fsplit_dir)/fsplit $(srcdir)/fftlib.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done \
--	  && $(AR) ../$(LF) *.o
--	rm -f fftlib.dir/*.o
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done 
- fftlib : fftlib.o
- 	$(RANLIB) $(LF)
- 
-@@ -541,9 +527,7 @@
- 	echo '      END' >> unix.dir/unix.f
- 	cd unix.dir && $(fsplit_dir)/fsplit ../unix.f >/dev/null && $(RMEMPTY) && \
- 	  for i in `pwd`/*.$F; do \
--	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
--	  && $(AR) ../$(LF) *.o
--	rm -f unix.dir/*.o 
-+	    $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- unix : unix.o
- 	$(RANLIB) $(LF)
- 
diff --git a/sci-libs/ccp4-libs/files/pass-clipper-enablevals.patch b/sci-libs/ccp4-libs/files/pass-clipper-enablevals.patch
deleted file mode 100644
index 3e1a8b0e6..000000000
--- a/sci-libs/ccp4-libs/files/pass-clipper-enablevals.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-5.99.5.orig/configure	2006-01-06 11:45:43.000000000 -0800
-+++ ccp4-5.99.5/configure	2006-01-06 11:46:53.000000000 -0800
-@@ -3210,7 +3210,7 @@
- #ccp4 setup
-   xopts="${xopts} --with-ccp4=${srcdir}"
- #interface setup
--  xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol"
-+  xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol --enable-mmdbold --enable-mtz --with-mccp4=/usr"
-   echo   
-   echo "********* CLIPPER CONFIGURATION ***********"
-   echo
diff --git a/sci-libs/ccp4-libs/metadata.xml b/sci-libs/ccp4-libs/metadata.xml
deleted file mode 100644
index c1ba80b18..000000000
--- a/sci-libs/ccp4-libs/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci-chemistry</herd>
-        <maintainer>
-                <email>jlec@j-schmitz.net</email>
-                <name>Justin Lecher (jlec)</name>
-        </maintainer>
-</pkgmetadata>
diff --git a/sci-libs/mmdb/ChangeLog b/sci-libs/mmdb/ChangeLog
deleted file mode 100644
index 842dbcbf9..000000000
--- a/sci-libs/mmdb/ChangeLog
+++ /dev/null
@@ -1,14 +0,0 @@
-# ChangeLog for sci-libs/mmdb
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  15 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> mmdb-1.21.ebuild:
-  buildtime blocker against <sci-libs/ccp4-libs-6.1.2 added
-
-*mmdb-1.21 (10 Aug 2009)
-
-  10 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mmdb-1.21.ebuild,
-  +metadata.xml:
-  version bump
-  license changed to GPL-2 LGPL-3
-
diff --git a/sci-libs/mmdb/Manifest b/sci-libs/mmdb/Manifest
deleted file mode 100644
index f8a8d6dfd..000000000
--- a/sci-libs/mmdb/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST mmdb-1.21.tar.gz 675301 RMD160 9feb5660ffb79289a796bde5e5effffc3e81a4af SHA1 cc17a4f12448e21ce9d0c772b269b42d417113fb SHA256 508dcb4bc3a8f9552d930edf019cd2a3750c5fa794d8a95e6a22eaeaeb5ab0be
-EBUILD mmdb-1.21.ebuild 541 RMD160 697f700e44d84fd2567fc5cbb7d1603ba182f56c SHA1 549797f40b7f2fe00b2a7c13ffa0354233a0223d SHA256 b11bd7421ae0befce86c38d3cf550411f7c4c346b17c1f9c86ffc9a211ec5c58
-MISC ChangeLog 419 RMD160 9f33d0073fd13df5eaf760d854802c0cebfa3209 SHA1 9abf2990b898adf322cc894c96bdc7677e425dbb SHA256 3b340f8a3dd53e806bbd98109f7361a4f4250db0d7e17d15356c9d45cb567233
-MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-libs/mmdb/metadata.xml b/sci-libs/mmdb/metadata.xml
deleted file mode 100644
index efb490d78..000000000
--- a/sci-libs/mmdb/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<maintainer>
-  <email>sci@gentoo.org</email>
-</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/mmdb/mmdb-1.21.ebuild b/sci-libs/mmdb/mmdb-1.21.ebuild
deleted file mode 100644
index c21944e4f..000000000
--- a/sci-libs/mmdb/mmdb-1.21.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-DESCRIPTION="The Coordinate Library is designed to assist CCP4 developers in working with coordinate files"
-HOMEPAGE="http://www.ebi.ac.uk/~keb/cldoc/"
-SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${P}.tar.gz"
-
-LICENSE="GPL-2 LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="!!<sci-libs/ccp4-libs-6.1.2"
-RDEPEND=""
-
-src_install() {
-	emake DESTDIR="${D}" install || die "emake install failed"
-}
diff --git a/x11-libs/libjwc_c/ChangeLog b/x11-libs/libjwc_c/ChangeLog
deleted file mode 100644
index ad87038af..000000000
--- a/x11-libs/libjwc_c/ChangeLog
+++ /dev/null
@@ -1,17 +0,0 @@
-# ChangeLog for x11-libs/libjwc_c
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*libjwc_c-1.1-r1 (17 Aug 2009)
-
-  17 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  -libjwc_c-1.1.ebuild, +libjwc_c-1.1-r1.ebuild,
-  +files/libjwc_c-1.1_p6.1.2.patch:
-  as-needed fix
-
-*libjwc_c-1.1 (27 Feb 2009)
-
-  27 Feb 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +metadata.xml,
-  +libjwc_c-1.1.ebuild:
-  Initial checkin
-
diff --git a/x11-libs/libjwc_c/Manifest b/x11-libs/libjwc_c/Manifest
deleted file mode 100644
index 7eb1ede73..000000000
--- a/x11-libs/libjwc_c/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX 612-gentoo.patch 804 RMD160 69c659d6e251b69740f72b229f24f1aa75ec5364 SHA1 c58d82b1d561fbd681bf9c98d19911e76b76054f SHA256 7772a77657832119f6051cf63185d46533004e4d612a7e089dba8b1ae85a92de
-DIST libjwc_c-1.1.tar.gz 253637 RMD160 a7cee4a3509f51720d0061d7134eb7fdbdccdea7 SHA1 5f689410136194d2972994fa2e78468dee6833a9 SHA256 4e3c5406347356ac4549b2b977c8011391926470cc3556e54148070b929d9ea9
-EBUILD libjwc_c-1.1-r1.ebuild 531 RMD160 ed6856ff72975825a02c5710df1d286336d8b8b2 SHA1 6db3212de3de1113035e6fb4956cc6517df2051b SHA256 def84279f6886757876fc235bb19624565392b8754955c90baede6c7e6d34d39
-MISC ChangeLog 453 RMD160 a809f9f4991e83cb8fa019548a4b981d339fde0d SHA1 0ea117d7c797bc3b226af92f91eec8a9501d17a9 SHA256 9248d5a01efe40e8c3c65e34a6637870777919f910ab0b011acc75201427ef41
-MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/x11-libs/libjwc_c/files/612-gentoo.patch b/x11-libs/libjwc_c/files/612-gentoo.patch
deleted file mode 100644
index af4a691fe..000000000
--- a/x11-libs/libjwc_c/files/612-gentoo.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-diff -Nu libjwc_c-1.1/imglib.c libjwc_c/imglib.c
---- libjwc_c-1.1/imglib.c	1999-08-17 15:58:11.000000000 +0200
-+++ libjwc_c/imglib.c	2004-06-03 14:24:05.000000000 +0200
-@@ -4259,7 +4259,7 @@
- {
- 
- /* Note: In this routine the first local axis is called 'x' and the
--         second logal axi is called 'y' */
-+         second local axis is called 'y' */
- 
-    int mxcent;                  /* Current max no. of elements in active 
-                                    spots array */
-@@ -4469,6 +4469,7 @@
- 
- /* skipping condition */
- 
-+               iymid = (actspots[j].iyend+actspots[j].iybeg)/2;
-                itmp = abs(iymid-actspots[j].iycent);
-                if (abs((actspots[j].iyend+actspots[j].iybeg) -(iel+ibl))>
-                    abs((actspots[j].iyend-actspots[j].iybeg) +(iel-ibl))&&
diff --git a/x11-libs/libjwc_c/libjwc_c-1.1-r1.ebuild b/x11-libs/libjwc_c/libjwc_c-1.1-r1.ebuild
deleted file mode 100644
index 71033f5c3..000000000
--- a/x11-libs/libjwc_c/libjwc_c-1.1-r1.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit autotools eutils
-
-PATCH="612"
-
-DESCRIPTION="additional c library for ccp4"
-HOMEPAGE="http://www.ccp4.ac.uk/main.html"
-SRC_URI="ftp://ftp.ccp4.ac.uk/jwc/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PATCH}-gentoo.patch
-	rm missing || die
-	eautoreconf
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die
-	dodoc README NEWS
-}
diff --git a/x11-libs/libjwc_c/metadata.xml b/x11-libs/libjwc_c/metadata.xml
deleted file mode 100644
index efb490d78..000000000
--- a/x11-libs/libjwc_c/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<maintainer>
-  <email>sci@gentoo.org</email>
-</maintainer>
-</pkgmetadata>
diff --git a/x11-libs/libjwc_f/ChangeLog b/x11-libs/libjwc_f/ChangeLog
deleted file mode 100644
index baf2ca0f1..000000000
--- a/x11-libs/libjwc_f/ChangeLog
+++ /dev/null
@@ -1,16 +0,0 @@
-# ChangeLog for x11-libs/libjwc_f
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*libjwc_f-1.1-r1 (17 Aug 2009)
-
-  17 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +files/612-gentoo.patch, -libjwc_f-1.1.ebuild, +libjwc_f-1.1-r1.ebuild:
-  add patch untill 6.1.2
-
-*libjwc_f-1.1 (27 Feb 2009)
-
-  27 Feb 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +metadata.xml,
-  +libjwc_f-1.1.ebuild:
-  Initial checkin
-
diff --git a/x11-libs/libjwc_f/Manifest b/x11-libs/libjwc_f/Manifest
deleted file mode 100644
index c039a1d69..000000000
--- a/x11-libs/libjwc_f/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX 612-gentoo.patch 2779 RMD160 8ea985d29ed03a5d7106b8f475ba629d523dc62f SHA1 b62d1c805455e69add3d457f78bfb897ea1a3801 SHA256 1320119153eb08c7bba844c7c320d9d63758ba2d816ad61c11b5ca2c65ef975e
-DIST libjwc_f-1.1.tar.gz 170973 RMD160 9fc0fc38aafa1611c13dfd963b903f4bd901e436 SHA1 f68c54e6062fec63f71eb612689626b4efc2e642 SHA256 9c05d5bac2a2e75d5fd490665c795ae31280da886e30f66cf39b3a32f2981199
-EBUILD libjwc_f-1.1-r1.ebuild 595 RMD160 084d06f14bbfb4090a992c2f695ed7f6d922846b SHA1 51befdb2c75e300d2d779d6f066d4f9ee6f4f3eb SHA256 5f5ab6f049c7986a0c197c1ba8c3442a8cbb576aff392519e7ae6ee2287f2271
-MISC ChangeLog 451 RMD160 8b934a8e0b7ea5b482702e66ab255c9a1e0abd60 SHA1 9759c6d5d3a8886cd6012f1feeeb754dea07b838 SHA256 18506d0e0415a45ee58886b394db63d19cd4df25360f9d858b8febfc53531a62
-MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/x11-libs/libjwc_f/files/612-gentoo.patch b/x11-libs/libjwc_f/files/612-gentoo.patch
deleted file mode 100644
index e687d8bec..000000000
--- a/x11-libs/libjwc_f/files/612-gentoo.patch
+++ /dev/null
@@ -1,100 +0,0 @@
-diff -Nu libjwc_f-1.1/configure.in ccp4-6.1.2/x-windows/libjwc/libjwc_f/configure.in
---- libjwc_f-1.1/configure.in	1999-10-21 16:07:14.000000000 +0200
-+++ ccp4-6.1.2/x-windows/libjwc/libjwc_f/configure.in	2004-03-11 17:31:45.000000000 +0100
-@@ -8,6 +8,7 @@
- AC_CANONICAL_SYSTEM
- 
- AM_INIT_AUTOMAKE(libjwc_f, 1.1)
-+AM_MAINTAINER_MODE
- 
- case ${with_g77} in
-   "yes" ) CC="gcc" GCC=yes F77=g77 ;;
-@@ -17,7 +18,7 @@
- AC_PROG_F77
- 
- AC_PROG_INSTALL
--AC_PROG_RANLIB
-+AC_PROG_LIBTOOL
- 
- case "$target" in
-   *irix6* )
-@@ -26,8 +27,9 @@
-       case "$FFLAGS" in
-       *-64* ) ;;   # assume they meant it
-       *-o32* | *-32* ) ;;   # presumably OK
--      * ) FFLAGS="$FFLAGS -o32 -O -g3"
--          CFLAGS=-32
-+      *-n32* ) ;;
-+      * ) FFLAGS="$FFLAGS -n32 -O -g3"
-+          CFLAGS=-n32
-           AC_MSG_WARN([
- 
- *** Using compiler flag -o32 for probable compatibility with
-@@ -47,8 +49,33 @@
- *** See the INSTALL file for more info.
- ])
-     fi ;;
-+  *linux*  )
-+    case $F77 in
-+    g77*)
-+     case "$FFLAGS" in
-+      *no-second-underscore* ) ;; # presumably OK
-+      * ) FFLAGS="$FFLAGS -fno-second-underscore -fno-globals" ;;
-+      esac
-+    esac ;;
-+  *darwin* ) 
-+    case $F77 in
-+    g77*)
-+     case "$FFLAGS" in
-+      *no-second-underscore* ) ;; # presumably OK
-+      * ) FFLAGS="$FFLAGS -fno-second-underscore -fno-globals" ;;
-+      esac
-+#mac g77 currently goes not handle -fno-common
-+    enable_shared=no;
-+    esac ;;
-   * ) 
- esac
-+# efc, version 7.1 at least does not support soname, so use CC
-+case "$F77" in
-+ *efc ) F77LD=${F77LD:-'${CC}'} ;;
-+ * ) F77LD=${F77LD:-'${F77}'}
-+esac
-+
-+AC_SUBST(F77LD)
- 
- AM_PROG_LIBTOOL
- 
-Common subdirectories: libjwc_f-1.1/doc and ccp4-6.1.2/x-windows/libjwc/libjwc_f/doc
-diff -Nu libjwc_f-1.1/opn_scr.f ccp4-6.1.2/x-windows/libjwc/libjwc_f/opn_scr.f
---- libjwc_f-1.1/opn_scr.f	1999-09-07 12:50:13.000000000 +0200
-+++ ccp4-6.1.2/x-windows/libjwc/libjwc_f/opn_scr.f	2000-10-25 13:03:09.000000000 +0200
-@@ -16,6 +16,6 @@
- C
- C====== Open the file
- C
--      OPEN (IUN_SCR, STATUS='SCRATCH')
--      RETURN
-+C     OPEN (IUN_SCR, STATUS='SCRATCH')
-+      CALL CCPDPN(IUN_SCR,'JWCSCR','SCRATCH','U',0, IFAIL) 
-       END
-diff -Nu libjwc_f-1.1/rpf_dstar.f ccp4-6.1.2/x-windows/libjwc/libjwc_f/rpf_dstar.f
---- libjwc_f-1.1/rpf_dstar.f	1999-07-09 13:39:38.000000000 +0200
-+++ ccp4-6.1.2/x-windows/libjwc/libjwc_f/rpf_dstar.f	2004-06-04 12:10:59.000000000 +0200
-@@ -376,7 +376,8 @@
-              INR_FLAG = 2
-              PHIW = 0.0
-           END IF
--        ELSE
-+          RETURN
-+        ENDIF
- C
- C---- Calculate distance of edge of spot from sphere at end of rotation
- Crotgen.for
-@@ -418,7 +419,6 @@
-             INR_FLAG = 4
-  40         RETURN
-           END IF
--        END IF
-       END IF
-       RETURN
-       END
diff --git a/x11-libs/libjwc_f/libjwc_f-1.1-r1.ebuild b/x11-libs/libjwc_f/libjwc_f-1.1-r1.ebuild
deleted file mode 100644
index 8a55f5297..000000000
--- a/x11-libs/libjwc_f/libjwc_f-1.1-r1.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit autotools eutils fortran
-
-FORTRAN="g77 gfortran ifc"
-
-PATCH="612"
-
-DESCRIPTION="additional c library for ccp4"
-HOMEPAGE="http://www.ccp4.ac.uk/main.html"
-SRC_URI="ftp://ftp.ccp4.ac.uk/jwc/${P}.tar.gz"
-
-LICENSE="GPL-2"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE=""
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PATCH}-gentoo.patch
-	eautoreconf
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die
-	dodoc NEWS README
-	dohtml doc/*
-}
diff --git a/x11-libs/libjwc_f/metadata.xml b/x11-libs/libjwc_f/metadata.xml
deleted file mode 100644
index efb490d78..000000000
--- a/x11-libs/libjwc_f/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<maintainer>
-  <email>sci@gentoo.org</email>
-</maintainer>
-</pkgmetadata>