31 files changed, 0 insertions, 3096 deletions
diff --git a/sci-libs/balbes-db/Manifest b/sci-libs/balbes-db/Manifest
deleted file mode 100644
index 86fed7e6ab9e..000000000000
--- a/sci-libs/balbes-db/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ccp4-6.1.3-balbesdb-10-11-08.tar.gz 600856059 SHA256 5606fc5e131138b56fa3a1afce014225a6c07826b99587f132f6c337585f4f0d SHA512 5b7f3b3465312da72ff4816c96244252a6f0bf039fde8ff772ea683e6317053d903cdc2b3b86b78e8edbb1c766d1b3676048ac4e7d4d0db29ed7bf62dfb00ab2 WHIRLPOOL 9a01610c9767aece4c9cc052a8aa2fd5dff9c9967f11688f5e6e206a82e2714751e086a7ddbe6a99da23b70163c7b096f57d281eebe53b8dd7cdb18faed23d63
diff --git a/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild b/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild
deleted file mode 100644
index bd973c5120d7..000000000000
--- a/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-MY_P="ccp4-${PV}"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-VERSION="10-11-08"
-
-DESCRIPTION="The database for the BALBES automated crystallographic molecular replacement pipeline"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~fei/balbes/"
-SRC_URI="${SRC}/${PV}/${MY_P}-${PN/-/}-${VERSION}.tar.gz"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE=""
-
-RDEPEND="
-	>=dev-python/pyxml-0.8.4
-	sci-libs/monomer-db"
-DEPEND="${RDEPEND}"
-RESTRICT="binchecks strip"
-
-S="${WORKDIR}/${MY_P}"
-
-src_install() {
-	dodir /usr/share/balbes/BALBES_0.0.1
-	rm -rf share/balbes/BALBES_0.0.1/dic || die
-	# We don't want to wait around to copy all this, or suck up double
-	# the disk space
-	einfo "Installing files, which can take some time ..."
-	mv "${S}"/share/balbes/BALBES_0.0.1/* "${ED}"/usr/share/balbes/BALBES_0.0.1/ || die
-	# db files shouldn't be executable
-	find "${ED}"/usr/share/balbes/BALBES_0.0.1/ \
-		-type f \
-		-exec chmod 664 '{}' \; || die
-	dosym ../../ccp4/data/monomers /usr/share/balbes/BALBES_0.0.1/dic
-
-	cat >> "${T}"/20balbes <<- EOF
-	BALBES_ROOT="${EPREFIX}/usr/share/balbes/BALBES_0.0.1/"
-	EOF
-
-	doenvd "${T}"/20balbes
-}
diff --git a/sci-libs/balbes-db/metadata.xml b/sci-libs/balbes-db/metadata.xml
deleted file mode 100644
index 51fdedab1b38..000000000000
--- a/sci-libs/balbes-db/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-chemistry</herd>
-</pkgmetadata>
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
deleted file mode 100644
index 9d3fe2806365..000000000000
--- a/sci-libs/ccp4-libs/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild
deleted file mode 100644
index dcd741637048..000000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild
+++ /dev/null
@@ -1,359 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools eutils fortran-2 gnuconfig multilib python-single-r1 toolchain-funcs
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-
-DESCRIPTION="Protein X-ray crystallography toolkit - Libraries"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
-# patch tarball from upstream
-	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
-# patches created by us
-	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} https://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
-
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE="minimal"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	!<sci-chemistry/ccp4-6.1.3
-	!<sci-chemistry/ccp4-apps-${PV}-r10
-	app-shells/tcsh
-	dev-lang/tcl:0
-	>=sci-libs/cbflib-0.9.2.2
-	sci-libs/fftw:2.1
-	sci-libs/mmdb:0
-	sci-libs/monomer-db
-	sci-libs/ssm
-	virtual/jpeg:0=
-	virtual/lapack
-	virtual/blas"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${MY_P}"
-
-MAKEOPTS+=" -j1"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	tc-export PKG_CONFIG RANLIB AR
-
-	sed \
-		-e "/^AR/s:ar:$(tc-getAR):g" \
-		-i lib/src/Makefile.in src/Makefile.in src/ccp4mapwish_/Makefile.in lib/ccif/Makefile.in || die
-
-	einfo "Applying upstream patches ..."
-	for patch in $(seq $PATCH_TOT); do
-		base="PATCH${patch}"
-		dir=$(eval echo \${${base}[0]})
-		p=$(eval echo \${${base}[1]})
-		pushd "${dir}" >& /dev/null
-		ccp_patch "${DISTDIR}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-	# fix buffer overflows wrt bug 339706
-	ccp_patch "${FILESDIR}"/${PV}-overflows.patch
-
-	# it tries to create libdir, bindir etc on live system in configure
-	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
-	# make creation of libccif.so smooth
-	ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
-
-	# lets try to build libmmdb seperatly
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
-
-	# unbundle libjpeg and cbflib
-	ccp_patch "${FILESDIR}"/${PV}-unbundle-libs-ng2.patch
-
-	# Fix missing DESTIDR
-	# not installing during build
-	ccp_patch "${FILESDIR}"/${PV}-noinstall.patch
-	sed \
-		-e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \
-		-i configure || die
-
-	# Fix upstreams code
-	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
-
-	# use pkg-config to detect BLAS/LAPACK
-	ccp_patch "${FILESDIR}"/${PV}-lapack.patch
-
-	# proto type changing in version 0.9.2.2
-	ccp_patch "${FILESDIR}"/${PV}-cbf.patch
-
-	# proto type changing in version 0.9.2.2
-	ccp_patch "${FILESDIR}"/${PV}-no-pypath.patch
-
-	ccp_patch "${FILESDIR}"/${P}-force.patch
-
-	ccp_patch "${FILESDIR}"/${P}-format-security.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# not needed, we have it extra
-	rm -rf src/rapper/{libxml2,gc7.0} || die
-
-	sed \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		-e 's:-Wl,-rpath,$CLIB::g' \
-		-e 's: -rpath $CLIB::g' \
-		-e 's: -I${srcdir}/include/cpp_c_headers::g' \
-		-e 's:sleep 1:sleep .2:g' \
-		-i configure || die
-
-	gnuconfig_update
-
-	for i in lib/DiffractionImage src/rapper src/pisa; do
-		pushd ${i} > /dev/null
-			sed 's:-g::g' -i configure* || die
-			[[ -f configure.in ]] && mv configure.{in,ac}
-			eautoreconf
-		popd > /dev/null
-	done
-
-	## unbundle libssm
-	sed -e '/libdir/s:ssm::g' -i Makefile.in || die
-	find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete || die
-}
-
-src_configure() {
-	rm -rf lib/DiffractionImage/{jpg,CBFlib} || die
-
-	# Build system is broken if we set LDFLAGS
-	userldflags="${LDFLAGS}"
-	export SHARED_LIB_FLAGS="${LDFLAGS}"
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "$(tc-getFC)" = "ifort" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup || die
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure || die
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=$(tc-getFC)
-	export FOPTIM=${FFLAGS:- -O2}
-
-	export SHARE_LIB="\
-		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
-		$(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb) $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		--onlylibs \
-		--with-shared-libs \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-warnings \
-		--disable-cctbx \
-		--disable-clipper \
-		--disable-ssm \
-		--tmpdir="${TMPDIR}" \
-		--bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \
-		--libdir="${EPREFIX}/usr/$(get_libdir)" \
-		${GENTOO_OSNAME} || die "configure failed"
-}
-
-src_compile() {
-	emake DESTDIR="${D}" onlylib
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	emake \
-		DESTDIR="${D}" \
-		includedir="${EPREFIX}/usr/include" \
-		library_includedir="${EPREFIX}/usr/include" \
-		install
-
-	sed \
-		-e "330,1000d" \
-		-i "${S}"/include/ccp4.setup-sh || die
-
-	sed \
-		-e "378,1000d" \
-		-i "${S}"/include/ccp4.setup-csh || die
-
-	sed \
-		-e "s:-${PV/-r*/}::g" \
-		-e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \
-		-e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \
-		-e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \
-		-e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \
-		-e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
-		-e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
-		-e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \
-		-e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \
-		-e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
-		-e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
-		-e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
-		-e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
-		-e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \
-		-e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \
-		-e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \
-		-e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \
-		-e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
-		-e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
-		-e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \
-		-e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \
-		-e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \
-		-e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \
-		-e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
-		-e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
-		-e "s:\$CLIB/font84.dat:\"${EPREFIX}/usr/$(get_libdir)/font84.dat\":g" \
-		-e "s:\$CLIB/cif_mmdic.lib:\"${EPREFIX}/usr/$(get_libdir)/cif_mmdic.lib\":g" \
-		-e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \
-		-e '/CLIB=/d' \
-		-e '/CLIB /d' \
-		-e '/CLIBS=/d' \
-		-e '/CLIBS /d' \
-		-e "/alias/d" \
-		-e "/CCP4_HELPDIR/d" \
-		-e "/IMOSFLM_VERSION/d" \
-		-i "${S}"/include/ccp4.setup* || die
-
-	# Don't check for updates on every sourcing of /etc/profile
-	sed -i \
-		-e "s:\(eval python.*\):#\1:g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Libs
-	for file in "${S}"/lib/*; do
-		if [[ -d ${file} ]]; then
-			continue
-		elif [[ -x ${file} ]]; then
-			dolib.so ${file}
-		else
-			insinto /usr/$(get_libdir)
-			doins ${file}
-		fi
-	done
-
-	prune_libtool_files
-
-	sed \
-		-e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \
-		-i "${S}"/include/ccp4.setup-sh || die
-
-	if ! use minimal; then
-		# Setup scripts
-		insinto /etc/profile.d
-		newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh
-		newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh
-
-		# Data
-		insinto /usr/share/ccp4/data/
-		doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures}
-
-		# Environment files, setup scripts, etc.
-		rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die
-		insinto /usr/share/ccp4/
-		doins -r "${S}"/include
-	fi
-
-	rm -f "${S}"/include/ccp4.setup* || die
-
-	dodoc "${S}"/lib/data/*.doc
-	newdoc "${S}"/lib/data/README DATA-README
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this."
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
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 a77d9494a05c..000000000000
--- 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/6.1.3-cbf.patch b/sci-libs/ccp4-libs/files/6.1.3-cbf.patch
deleted file mode 100644
index 6930fcad766a..000000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-cbf.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- lib/DiffractionImage/DiffractionImageCBF.cpp |    2 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
-diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp
-index 69b32b0..3ffee26 100755
---- a/lib/DiffractionImage/DiffractionImageCBF.cpp
-+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp
-@@ -62,7 +62,7 @@ namespace DI
- 			int* tmpimg;
- 			tmpimg=new int[height*width];
- 			test= cbf_decompress_byte_offset ((void *)tmpimg,sizeof(int),sign,
--                               			nelements,&nread,0,32,sign,ccbbff,0,
-+                               			nelements,&nread,0,0,32,sign,ccbbff,0,
- 										byte_ord.c_str(),2,(size_t) width,
- 										(size_t) height,1,(size_t) padding);
- 			for(int i=0;i<height*width;i++)
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 ca18d75bc840..000000000000
--- 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 b3147ad81bbf..000000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in
-index c23f488..b32dd1e 100755
---- a/lib/src/Makefile.in
-+++ b/lib/src/Makefile.in
-@@ -176,7 +176,7 @@ $(mmdbsrcdir)/mmdb_sbase0.h    $(mmdbsrcdir)/hybrid_36.h
- 
- ##### Makefile targets ######
- 
--all:  fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
-+all:  fsplit $(LC) $(LF) $(SCRIPT_MODULES)
- # maybe create shared library
- 	$(SHARE_LIB)
- 
-@@ -717,10 +717,8 @@ uninstall-mmdbHEADERS:
- 	done
- 
- install : all install-ccp4HEADERS install-mmdbHEADERS
--	$(INSTALL_DATA) `pwd`/$(LMMDB) $(libdir)/$(LMMDB)
- 	$(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 583697cea0a1..000000000000
--- 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 6e3997647955..000000000000
--- 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-impl-dec.patch b/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch
deleted file mode 100644
index 8bfa7db8cbff..000000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch
+++ /dev/null
@@ -1,140 +0,0 @@
-diff --git a/lib/DiffractionImage/Bruker/FRM_LIB.c b/lib/DiffractionImage/Bruker/FRM_LIB.c
-index bfda882..f821e04 100755
---- a/lib/DiffractionImage/Bruker/FRM_LIB.c
-+++ b/lib/DiffractionImage/Bruker/FRM_LIB.c
-@@ -38,6 +38,8 @@ FRM_LIB: Routines for reading, writing, and handling frame files.
- #include "sys/types.h"  /* _open, etc. */
- #include "sys/stat.h"   /* _open, etc. */
- 
-+#include <unistd.h>
-+
- #ifndef _MSC_VER
- int min(int a, int b)
- 	{
-diff --git a/lib/DiffractionImage/MAR/mar300_header.c b/lib/DiffractionImage/MAR/mar300_header.c
-index 1a933de..1c40c32 100755
---- a/lib/DiffractionImage/MAR/mar300_header.c
-+++ b/lib/DiffractionImage/MAR/mar300_header.c
-@@ -23,6 +23,9 @@
-  */
- #include "mar300_header.h"
- 
-+#include <sys/types.h>
-+#include <unistd.h>
-+
- /*
-  * Local functions
-  */
-diff --git a/lib/DiffractionImage/MAR/mar345_header.c b/lib/DiffractionImage/MAR/mar345_header.c
-index a8351ea..16d0f7b 100755
---- a/lib/DiffractionImage/MAR/mar345_header.c
-+++ b/lib/DiffractionImage/MAR/mar345_header.c
-@@ -32,6 +32,9 @@
-  */
- #include "mar345_header.h"
- 
-+#include <sys/types.h>
-+#include <unistd.h>
-+
- /*
-  * Definitions
-  */
-diff --git a/lib/DiffractionImage/MAR/nb_header.c b/lib/DiffractionImage/MAR/nb_header.c
-index 07f2741..6364ca4 100755
---- a/lib/DiffractionImage/MAR/nb_header.c
-+++ b/lib/DiffractionImage/MAR/nb_header.c
-@@ -20,6 +20,8 @@
- #include <io.h>
- #endif
- 
-+#include <sys/types.h>
-+#include <unistd.h>
- /*
-  * mar software include files
-  */
-diff --git a/lib/DiffractionImage/MAR/swap.c b/lib/DiffractionImage/MAR/swap.c
-index 443bb8c..0d96b3f 100755
---- a/lib/DiffractionImage/MAR/swap.c
-+++ b/lib/DiffractionImage/MAR/swap.c
-@@ -10,6 +10,9 @@
-  *
-  **********************************************************************/
- 
-+#define _XOPEN_SOURCE
-+#include <unistd.h>
-+
- void swaplong();
- void swapshort();
- 
-diff --git a/lib/ccif/f_interface.c b/lib/ccif/f_interface.c
-index 0f6a6b7..a09dc48 100755
---- a/lib/ccif/f_interface.c
-+++ b/lib/ccif/f_interface.c
-@@ -25,6 +25,7 @@
- ********************************************************************/
- 
- #include "stdpccts.h"
-+#include <sys/mman.h>
- 
- /* This file is terribly organised, and badly needs re-doing. There is probably
-  * scope for splitting this into three modules:
-diff --git a/lib/src/ccp4_general_f.c b/lib/src/ccp4_general_f.c
-index 8b5d04f..74ee3f7 100755
---- a/lib/src/ccp4_general_f.c
-+++ b/lib/src/ccp4_general_f.c
-@@ -26,6 +26,7 @@
- #include <string.h>
- #include <stdlib.h>
- #include <math.h>
-+#include <time.h>
- #include "ccp4_errno.h"
- #include "ccp4_fortran.h"
- #include "ccp4_parser.h"
-diff --git a/lib/src/ccp4_program.c b/lib/src/ccp4_program.c
-index 3e83d4d..bb3e975 100755
---- a/lib/src/ccp4_program.c
-+++ b/lib/src/ccp4_program.c
-@@ -25,6 +25,7 @@
- #include <stdio.h>
- #include <stdlib.h>
- #include <string.h>
-+#include <time.h>
- #include "ccp4_program.h"
- #include "ccp4_parser.h"
- #include "ccp4_utils.h"
-diff --git a/lib/src/fsplit.c b/lib/src/fsplit.c
-index ee8af24..c6fb3cd 100755
---- a/lib/src/fsplit.c
-+++ b/lib/src/fsplit.c
-@@ -50,6 +50,7 @@ static char sccsid[] = "@(#)fsplit.c	5.5 (Berkeley) 3/12/91";
- #include <string.h>
- #include <sys/types.h>
- #include <sys/stat.h>
-+#include <unistd.h>
- 
- /*
-  *	usage:		fsplit [-e efile] ... [file]
-diff --git a/src/clipper_progs/src/pirate/compress42.c b/src/clipper_progs/src/pirate/compress42.c
-index ea52e96..30dbd56 100755
---- a/src/clipper_progs/src/pirate/compress42.c
-+++ b/src/clipper_progs/src/pirate/compress42.c
-@@ -142,6 +142,7 @@
- #include	<sys/types.h>
- #include	<sys/stat.h>
- #include	<errno.h>
-+#include	<unistd.h>
- 
- #ifdef DIRENT
- #	include	<dirent.h>
-diff --git a/src/mtz2cif_/mtz2cif.c b/src/mtz2cif_/mtz2cif.c
-index e224430..c7b82f4 100755
---- a/src/mtz2cif_/mtz2cif.c
-+++ b/src/mtz2cif_/mtz2cif.c
-@@ -28,6 +28,7 @@
- #include "cmtzlib.h"
- #include "ccp4_parser.h"
- #include "ccp4_general.h"
-+#include "ccp4_program.h"
- #include "csymlib.h"
- #include "mtz2cif_lib.h"
- 
diff --git a/sci-libs/ccp4-libs/files/6.1.3-lapack.patch b/sci-libs/ccp4-libs/files/6.1.3-lapack.patch
deleted file mode 100644
index 0463b3719525..000000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-lapack.patch
+++ /dev/null
@@ -1,597 +0,0 @@
-diff --git a/configure b/configure
-index 833f483..bcfa62d 100755
---- a/configure
-+++ b/configure
-@@ -3226,574 +3226,14 @@ else
-   echo
-   echo "Warning: this option has not been extensively tested!"
-   echo "Please report problems to ccp4@ccp4.ac.uk"
--  # Search for vendor LAPACK/BLAS first
--  if test ! "$with_netlib_lapack" ; then
--    # Initialise variables to blank
--    lapackdir=
--    XLAPACK_LIB=
--    # Possible directories to check for vendor or pre-existing LAPACK or
--    # BLAS - add to these if you want to test others
--    trydirs="`echo $LD_LIBRARY_PATH |sed -e s/:/\ /g` /lib /usr/lib /usr/local/lib"
--    # Possible library names
--    # These are the names like xxxx where the library will be libxxxx.a
--    # or libxxxx.so
--    echo
--    echo "Guessing names for native/vendor LAPACK and/or BLAS libraries"
--    echo "on this system"
--    case $system in
--      linux | linux64 | linux32 )
--        # linux users will usually have them in /usr/lib but don't call it
--        trylapack="lapack"
--        tryblas="blas"
--        # if code is non_shared then this can lead to problems. both blas and lapack
--        # need to be resolved even if they are not called!
--        if test "$non_shared" = yes; then
--          echo "You are compiling linux non_shared. This sometimes causes problems "
--          echo "  so checking for requirements." 
--          echo "Checking: try to link library against test program"
--          if test -f testlink.f || test -f testlink ; then
--            rm -f testlink*
--          fi 
--          cat > testlink.f <<EOF
--      PROGRAM TESTLINK
--C A bit of scala code to test the linking
--      real bf(3), bnorm
--c
--      integer maxbmt
--      parameter (maxbmt = 2)
--      double precision B(maxbmt,maxbmt), eigval(maxbmt),
--     $   eigvec(maxbmt,maxbmt), w(5*maxbmt)
--      integer m, ia, ix, istat
--c
--      B(1,1) = 1.00
--      B(1,2) = 1.00
--      B(2,1) = 1.00
--      B(2,2) = 1.00
--c
--      m = maxbmt
--      ia = maxbmt
--      ix = maxbmt
--      call dsyev('N', 'L', m, B, ia, eigval, w, 5*maxbmt, istat)
--      end
--EOF
--          #firstly test without -lblas
--          test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack"
--          echo $test_compile
--          if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then
--            # Compilation was okay
--            echo "... only -llapack needed"
--            XLAPACK_LIB="-llapack"
--            # Set the next two variables so that configure
--            # doesn't try to build netlib libraries
--            LAPACKLIB="lapack"
--            noblas=yes
--            trylapack=
--            tryblas=
--          else
--	    echo "more than just -llapack needed...."
--            test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas"
--            echo $test_compile
--            if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
--              # Compilation was okay
--              echo "...-llapack and -lblas were needed"
--              XLAPACK_LIB="-llapack -lblas"
--              # Set the next two variables so that configure
--              # doesn't try to build netlib libraries
--              LAPACKLIB="lapack blas"
--              noblas=no
--              trylapack=
--              tryblas=
--	    else
--              echo "....could not find either lapack or blas."
--	    fi
--          fi
--        fi
--        # add 64 bit libs
--        case $system in
--          linux64 ) trydirs="/usr/lib64 ${trydirs}" ;;
--        esac
--
--        ;;
--      osf1)
--        # OSF1 has dxml (old version) and cxml
--        # which should have both lapack and blas 
--        trylapack="dxml cxml"
--        tryblas=
--        trydirs="${trydirs} /usr/shlib"
--        ;;
--      irix)
--        # Additional search paths for IRIX
--        trydirs="${trydirs} /usr/lib32"
--        # SCSL should have both LAPACK and BLAS
--        trylapack="scs"
--        tryblas="blas"
--        ;;
--      irix64)
--        # Additional search paths for IRIX64
--        trydirs="${trydirs} /usr/lib64"
--        # SCSL should have both LAPACK and BLAS
--        trylapack="scs"
--        tryblas="blas"
--        # Extra compiler flags?
--        #XLAPACKFLAGS="-OPT:IEEE_NaN_inf=ON"
--        ;;
--      aix)
--        # Additional search paths for AIX
--        trydirs="${trydirs}" 
--        # AIX might have ESSL library - blas only I think
--        trylapack=
--        tryblas="essl"
--        ;;
--      hpux)
--        # Additional search paths for HPUX
--        trydirs="${trydirs} /opt/fortran/lib /opt/fortran/lib/pa2.0 /opt/mlib/lib/pa2.0"
--        # HPUX should have both LAPACK (part of mlib) and BLAS
--        trylapack="lapack"
--        tryblas="blas"
--        # Extra compiler flags?
--        # +U77 required for ETIME function - this is already in XFFLAGS
--        #XLAPACKFLAGS="+U77"
--        ;;
--
--      sunos | sunos64)
--        # Sun has libraries with BLAS and LAPACK invoked using
--        # -xlic_lib=sunperf
--        trylapack=
--        tryblas=
--        echo "SunOs can use the Sun Performance Library (if installed)"
--        echo "which has both BLAS and LAPACK 3.0"
--        echo 
--        echo "Looking for a valid library to use..."
--        echo
--	# Loop over the possible library names
--        try_libs="sunperf"
--        for testlib in $try_libs
--        do
--          if test ! "$XLAPACK_LIB" ; then
--            # Try running a test compile to see if this a valid library
--            if test -f testlink.f || test -f testlink ; then
--              rm -f testlink*
--            fi
--            cat > testlink.f <<EOF
--c Test fortran program to link against library
--      PROGRAM TESTLINK
--      IMPLICIT NONE
--      INTEGER A
--      A = 1
--      STOP
--      END
--EOF
--            test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -dalign -xlic_lib=$testlib"
--            echo $test_compile
--            if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
--              # Compilation was okay
--              echo "... -xlic_lib=$testlib is okay"
--              XLAPACK_LIB="-dalign -xlic_lib=$testlib"
--              # Set the next two variables so that configure
--              # doesn't try to build netlib libraries
--              LAPACKLIB="$testlib"
--              noblas=yes
--            else
--              # Compilation failed
--              echo "... cannot use -xlic_lib=$testlib"
--            fi
--            # End of test for testlib
--          fi
--          # End of loop over possible lib names
--        done
--	# Report if no suitable library was found
--        if test ! "$XLAPACK_LIB" ; then
--          echo
--          echo "No suitable LAPACK library was found."
--          echo "This may be because the Sun Performance Library is not"
--          echo "installed on your system"
--          echo "Contact your system administrator or Sun vendor"
--        fi
--        ;;
--      Darwin | Darwin32 | Darwin64 )
--        # Darwin has libraries with BLAS and LAPACK invoked using 
--        # -framework vecLib
--        echo "Darwin can use the vecLib Library (if installed)"
--        echo "which has both BLAS and LAPACK 3.0"
--        echo
--        # This is a special case so try running a test compile
--        echo "Checking: try to link library against test program"
--        if test -f testlink.f || test -f testlink ; then
--          rm -f testlink*
--        fi
--        cat > testlink.f <<EOF
--c Test fortran program to link against library
--      PROGRAM TESTLINK
--      IMPLICIT NONE     
--      INTEGER A
--      A = 1
--      STOP
--      END
--EOF
--        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -framework vecLib"
--        echo $test_compile
--        if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
--          # Compilation was okay
--          echo "... -framework vecLib is okay"
--          XLAPACK_LIB="-framework vecLib"
--          # Set the next two variables so that configure
--          # doesn't try to build netlib libraries
--          LAPACKLIB="vecLib"
--          noblas=yes
--        else
--#alternative linking for vecLib libraries
--          case `uname -sr` in
--            *Darwin\ 7.* ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic -Wl,-framework -Wl,vecLib" ;;
--            * ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" ;;
--          esac
--
--        echo $test_compile
--        if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
--          # Compilation was okay
--          echo "... -framework vecLib is okay"
--          XLAPACK_LIB="-Wl,-framework -Wl,vecLib"
--          # Set the next two variables so that configure
--          # doesn't try to build netlib libraries
--          LAPACKLIB="-Wl,-framework -Wl,vecLib"
--          noblas=yes
--        else
--          # Compilation failed
--          echo "... cannot use -framework vecLib"
--          echo
--         fi
--        fi
--        trylapack=
--        tryblas=
--# try the fink installation
--        trydirs="${trydirs} /sw"
--        ;;
--      Darwin_ibm_compilers )
--        # Darwin has libraries with BLAS and LAPACK invoked using
--        # -framework vecLib
--        echo "Darwin can use the vecLib Library (if installed)"
--        echo "which has both BLAS and LAPACK 3.0"
--        echo
--        # This is a special case so try running a test compile
--        echo "Checking: try to link library against test program"
--        if test -f testlink.f || test -f testlink ; then
--          rm -f testlink*
--        fi
--        cat > testlink.f <<EOF
--c Test fortran program to link against library
--      PROGRAM TESTLINK
--      IMPLICIT NONE
--      INTEGER A
--      A = 1
--      STOP
--      END
--EOF
--      case `uname -sr` in
--        Darwin\ 8* )
--        XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS"
--        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB"
--        ;;
--        Darwin\ 7* )
--        XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS"
--        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic $XLAPACK_LIB"
--        ;;
--        *)
--        XLAPACK_LIB="/System/Library/Frameworks/vecLib.Framework/Versions/Current/VecLib"
--        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB"
--        esac
--        echo $test_compile
--        if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
--          # Compilation was okay
--          echo "... -framework vecLib is okay"
--          # Set the next two variables so that configure
--          # doesn't try to build netlib libraries
--          LAPACKLIB="vecLib"
--          noblas=yes
--        else
--          # Compilation failed
--          XLAPACK_LIB=""
--          echo "... cannot use -framework vecLib"
--          echo
--        fi
--        trylapack=
--        tryblas=
--# try the fink installation
--        trydirs="${trydirs} /sw"
--        ;;
--
--      Darwin_intel_compilers)
--        # Darwin has libraries with BLAS and LAPACK invoked using
--        # -F vecLib
--        echo "Darwin can use the vecLib Library (if installed)"
--        echo "which has both BLAS and LAPACK 3.0"
--        echo
--        # This is a special case so try running a test compile
--        echo "Checking: try to link library against test program"
--        if test -f testlink.f || test -f testlink ; then
--          rm -f testlink*
--        fi
--        cat > testlink.f <<EOF
--c Test fortran program to link against library
--      PROGRAM TESTLINK
--      IMPLICIT NONE
--      INTEGER A
--      A = 1
--      STOP
--      END
--EOF
--        test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib"
--        echo $test_compile
--        if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
--          # Compilation was okay
--          # doesn't try to build netlib libraries
--          XLAPACK_LIB="-F /System/Library/Frameworks -Qoption,ld,-framework -Qoption,ld,vecLib"
--          LAPACKLIB="vecLib"
--          noblas=yes
--        else
--          # Compilation failed
--          echo "... cannot use -framework vecLib"
--          echo
--         fi
--        trylapack=
--        tryblas=
--# try the fink installation
--        trydirs="${trydirs} /sw"
--        ;;
--
--#       linux_ia64_sgi_altix)
--# SGI Japan
--      ia64_linux_intel) 
--        # Additional search paths for Linux/IA64
--        trydirs="${trydirs} /opt/scsl/lib /usr/lib /usr/local/lib"
--        # SCSL and MKL should have both LAPACK and BLAS
--        trylapack="mkl_lapack scs lapack"
--        tryblas="mkl scs blas"
--        ;;
--      linux_ibm_compilers )
--        trylapack="lapack"
--        tryblas="blas"
--        ;;
--      linux64_ibm_compilers )
--        trydirs="/usr/lib64 ${trydirs}"
--        trylapack="lapack"
--        tryblas="blas"
--        ;;
--      linux_intel_compilers )
--        trydirs="/usr/lib64 ${trydirs}"
--        trylapack="mkl_lapack lapack"
--        tryblas="mkl blas"
--        ;;
--      *)
--        echo "The guesses for this system may not be correct - please"
--        echo "e-mail ccp4@ccp4.ac.uk if you have any extra information"
--	echo
--        # Default guess is just libblas
--        trylapack="lapack"
--        tryblas="blas"
--        ;;
--    esac
--    #
--    # Search for LAPACK libraries
--    #
--    # Write out what the guesses are
--    if test "$trylapack" ; then
--      echo "Possible LAPACK library names for this system:"
--      for libname in $trylapack
--      do
--        echo "   lib$libname"
--      done
--      # Possible library name extensions
--      tryexts="a so dylib"
--      # Now loop over all the possibilities and see if anything
--      # turns up
--      echo
--      echo "Searching for libraries with LAPACK and BLAS:"
--      for testdir in $trydirs
--      do
--        for testlib in $trylapack
--        do
--          for ext in $tryexts
--          do
--            if test ! "$LAPACKLIB"; then
--              if test -s "$testdir/lib$testlib.$ext" ; then
--                echo "...found LAPACK library: $testdir/lib$testlib.$ext"
--                # Now try and link to a test program
--                # This is really for IRIX where libraries can be
--                # o32 or n32
--                echo "   Testing: try to link library against test program"
--                if test -f testlink.f || test -f testlink ; then
--                  rm -f testlink*
--                fi
--                cat > testlink.f <<EOF
--c Test fortran program to link against library
--      PROGRAM TESTLINK
--      IMPLICIT NONE
--      INTEGER A
--      A = 1
--      STOP
--      END
--EOF
--                test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
--                test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
--                echo $test_compile
--                if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
--                  have_lapack=yes
--                else
--# cover clapack option
--                  echo $test_ccompile
--                  if { (eval $test_ccompile ) 2>&1; } && test -s testlink ; then
--                    have_lapack=yes
--                  fi
--                fi
--                if test x$have_lapack = xyes ; then
--                # This one is okay
--                  LAPACKLIB="$testlib"
--                  LAPACKDIR="$testdir"
--                  echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR"
--		  #
--		  XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB"
--                  #
--                  # Test to see if we need BLAS too
--                  # Do this by trying to compile a test program
--                  # Use the LSAME test for now
--                  echo
--                  echo "   * Checking whether we need a separate BLAS library *"
--                  echo "   Testing: try linking library against test program"
--                  cd lib/lapack/test
--                  if test -f testlsame ; then
--                    rm -f testsame testlsame.o
--                  fi
--                  test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB"
--                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS"
--                  echo $test_compile
--                  if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then
--                    have_blas=yes
--                  else
--#cblas route
--                    echo $test_ccompile
--                    if { ( eval $test_ccompile) 2>&1;} && test -s testlsame ; then
--                      have_blas=yes
--                    fi
--                  fi
--                  if test x$have_blas = xyes ; then
--                    echo "Test program okay - additional separate BLAS not required"
--                    noblas=yes
--                  else
--                    echo "Test program failed - need a separate BLAS library"
--                  fi
--                  cd ../../..
--                else
--                # Keep looking
--                  echo "   link failed - cannot use lib$testlib"
--                fi
--              fi
--            fi
--          done
--        done
--        if test ! "$LAPACKLIB"; then
--          echo "...nothing in $testdir"
--        fi
--      done
--    fi
--
--    # If LAPACKLIB hasn't been set at this point then no LAPACK library
--    # was found 
--    if test ! "$LAPACKLIB" ; then
--      echo
--      echo "No pre-existing LAPACK library found - NetLib LAPACK will be built instead"
--      make_lapack=lapacklib
--    fi
--    # Look for possible BLAS
--    if test ! "$noblas" ; then
--      if test "$tryblas" ; then
--        echo
--        echo "Possible BLAS library names for this system:"
--        for libname in $tryblas
--        do
--          echo "   lib$libname"
--        done
--        # Possible library name extensions
--        tryexts="a so"
--        # Now loop over all the possibilities and see if anything
--        # turns up
--        echo
--        echo "Searching for libraries with BLAS:"
--        for testdir in $trydirs
--        do
--          for testlib in $tryblas
--          do
--            for ext in $tryexts
--            do
--              if test ! "$BLASLIB"; then
--                if test -s "$testdir/lib$testlib.$ext" ; then
--                  echo "...found BLAS library: $testdir/lib$testlib.$ext"
--                  # Now try and link to a test program
--                  # This is really for IRIX where libraries can be
--                  # o32 or n32
--                  echo "   Testing: try to link library against test program"
--                  if test -f testlink.f || test -f testlink ; then
--                    rm -f testlink*
--                  fi
--                  cat > testlink.f <<EOF
--c Test fortran program to link against library
--      PROGRAM TESTLINK
--      IMPLICIT NONE
--      INTEGER A
--      A = 1
--      STOP
--      END
--EOF
--                  test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
--                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
--                  echo $test_compile
--                  if { ( eval $test_compile) 2>&1;} && test -s testlink ; then
--                    have_blas=yes
--                  else
--                    echo $test_ccompile
--                    if { ( eval $test_compile) 2>&1;} && test -s testlink ; then
--                      have_blas=yes
--                    fi
--                  fi
--                  if test x$have_blas = xyes ; then
--                    # This one is okay
--                    BLASLIB="$testlib"
--                    BLASDIR="$testdir"
--                    BLASEXT="$ext"
--                    echo "Link ok - using lib$BLASLIB from $BLASDIR"
--		    XLAPACK_LIB="$XLAPACK_LIB -L$BLASDIR -l$BLASLIB"
--                  else
--                  # Keep looking
--                    echo "   link failed - cannot use lib$testlib"
--                  fi
--                fi
--              fi
--            done
--          done
--          if test ! "$BLASLIB"; then
--            echo "...nothing in $testdir"
--          fi
--        done
--      fi
--      # Do we need to build BLAS too?      
--      if test ! "$BLASLIB" ; then
--        echo
--        echo "No pre-existing BLAS library was found - NetLib BLAS will be built instead"
--        echo "This may result in poorer performance of the LAPACK routines"
--        make_blas=blaslib
--        BLASLIB=blas
--        BLASDIR="$srcdir/lib/lapack"
--        BLASEXT="a"
--      fi
--    fi
-+  # gentoo is clever
-+  make_blas=
-+  make_lapack=
-+  BLASLIB=$(${PKG_CONFIG} --libs lapack)
-+  LAPACKLIB=$(${PKG_CONFIG} --libs lapack)
-+  XLAPACK_LIB="${BLASLIB} ${LAPACKLIB}"
-+  XFFLAGS_LAPACK="$(${PKG_CONFIG} --cflags lapack blas)"
-   # Otherwise force building of NetLib BLAS and LAPACK libs
--  else
--    echo
--    echo "! Force building of NetLib BLAS and LAPACK..."
--    make_blas=blaslib
--    make_lapack=lapacklib
--    BLASLIB=blas
--    BLASDIR="$srcdir/lib/lapack"
--    BLASEXT="a"
--  fi
-   # need to know if we the lapack library was linked using the C or
-   # fortran linker
-   if test -f testlink.f || test -f testlink || test -f testlink.c ; then
-@@ -3916,8 +3356,8 @@ RANLIB   = ${RANLIB}
- INSTALL_DATA = ${INSTALL_DATA}
- libdir   = $libdir
- #
--BLASLIB     = lib${BLASLIB}.${BLASEXT}
--LAPACKLIB   = liblapack.a
-+BLASLIB     = ${BLASLIB}
-+LAPACKLIB   = ${LAPACKLIB}
- #
- # These variables define targets in the main Makefile
- blaslib   = ${make_blas}
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 24a0a2d8e4a2..000000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch
+++ /dev/null
@@ -1,230 +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
-+
- # 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-no-pypath.patch b/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch
deleted file mode 100644
index 6a0cb5be7c3d..000000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch
+++ /dev/null
@@ -1,87 +0,0 @@
- include/ccp4.setup-bash |  8 --------
- include/ccp4.setup-csh  | 11 -----------
- include/ccp4.setup-sh   |  8 --------
- include/ccp4.setup-zsh  | 10 ----------
- 4 files changed, 37 deletions(-)
-
-diff --git a/include/ccp4.setup-bash b/include/ccp4.setup-bash
-index 3a67791..80aef23 100755
---- a/include/ccp4.setup-bash
-+++ b/include/ccp4.setup-bash
-@@ -185,14 +185,6 @@ else
-   fi
- fi
- 
--#Python path for the subprocess fixed module
--
--if [ $ccp4_first_in_path -eq 1 ]; then
--    setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
--else
--    setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
--fi
--
- ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
- setenv PLOT_COMMAND   'lp -s -dmicrolaser'  
- setenv PRINT_COMMAND  'lp -s -denscript'    
-diff --git a/include/ccp4.setup-csh b/include/ccp4.setup-csh
-index 10d3ab8..72cc479 100755
---- a/include/ccp4.setup-csh
-+++ b/include/ccp4.setup-csh
-@@ -177,17 +177,6 @@ else
-   endif
- endif
- 
--#Python path for the subprocess fixed module
--if (${?PYTHONPATH}) then
--  if ($ccp4_first_in_path) then
--      setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
--  else
--      setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
--  endif
--else
--    setenv PYTHONPATH ${CCP4}/share/python
--endif
--
- ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
- setenv PLOT_COMMAND   'lp -s -dmicrolaser'  
- setenv PRINT_COMMAND  'lp -s -denscript'    
-diff --git a/include/ccp4.setup-sh b/include/ccp4.setup-sh
-index 2298bba..44643ab 100755
---- a/include/ccp4.setup-sh
-+++ b/include/ccp4.setup-sh
-@@ -225,14 +225,6 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg
- 
- ################### EXPERIENCED USERS STOP HERE #####################
- 
--#Python path for the subprocess fixed module
--
--if test $ccp4_first_in_path -eq 1; then
--    export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH}
--else
--    export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python
--fi
--
- ################### THE REST SHOULDN'T NEED EDITING #####################
- 
- ### dbCCP4i database handler setup ###
-diff --git a/include/ccp4.setup-zsh b/include/ccp4.setup-zsh
-index 660b35b..e453db9 100755
---- a/include/ccp4.setup-zsh
-+++ b/include/ccp4.setup-zsh
-@@ -154,16 +154,6 @@ export CCP4_BIN=$CBIN
- CLASSPATH=$CBIN:$CLASSPATH               # edit this if necessary
- export CLASSPATH
- 
--#Python path for the subprocess fixed module
--
--if ($ccp4_first_in_path) then
--    PYTHONPATH=${CCP4}/share/python:${PYTHONPATH}
--    export PYTHONPATH
--else
--    PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python
--    export PYTHONPATH
--fi
--
- ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
- export PLOT_COMMAND='lpr'  
- export PRINT_COMMAND='lpr'    
diff --git a/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch b/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch
deleted file mode 100644
index c1479f2b1155..000000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch
+++ /dev/null
@@ -1,142 +0,0 @@
-diff --git a/Makefile.in b/Makefile.in
-index ac552fe..fab1a87 100755
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -30,8 +30,7 @@ lapacklib : FORCE
- 
- cciflib : FORCE
- 	if test -n "$(ccifdir)"; then cd $(ccifdir); \
--	   $(MAKE) $(MFLAGS) $(MVARS); else true; fi; \
--           $(MAKE) install
-+	   $(MAKE) $(MFLAGS) $(MVARS); else true; fi
- 
- cctbx: FORCE
- 	if test -n "$(cctbxdir)"; then cd $(top_srcdir)/$(cctbxdir); \
-@@ -40,8 +39,7 @@ cctbx: FORCE
- libdir : FORCE lapacklib cciflib libccp4 clipper ssm diffractionImg
- 
- libccp4: FORCE
--	cd lib/src; $(MAKE) $(MFLAGS) $(MVARS) ; \
--	$(MAKE) install
-+	cd lib/src; $(MAKE) $(MFLAGS) $(MVARS)
- 
- share : FORCE
- 	cd share; $(MAKE) $(MFLAGS) $(MVARS)
-@@ -51,18 +49,15 @@ ccp4i : FORCE
- 
- clipper: FORCE fftw
- 	if test -n "$(clipperdir)"; then cd $(top_srcdir)/lib/clipper/clipper; \
--	$(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \
--	$(MAKE) install
-+	$(MAKE) -i $(MFLAGS) $(MVARS); else true; fi
- 
- diffractionImg: 
- 	if test -n "$(diffimdir)"; then cd $(top_srcdir)/$(diffimdir); \
--	$(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \
--        $(MAKE) install
-+	$(MAKE) -i $(MFLAGS) $(MVARS); else true; fi
- 
- ssm: 
- 	if test -n "$(ssmdir)"; then cd $(top_srcdir)/$(ssmdir); \
--	$(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \
--	$(MAKE) install
-+	$(MAKE) -i $(MFLAGS) $(MVARS); else true; fi
- 
- fftw: FORCE
- 	if test -n "$(fftwdir)"; then cd $(top_srcdir)/lib/fftw; \
-@@ -79,7 +74,7 @@ unsupported :  FORCE libdir
- 	   $(MAKE) $(MFLAGS) $(MVARS); else true; fi
- 
- datadir : FORCE libdir
--	cd lib/data; $(MAKE) $(MFLAGS) $(MVARS)
-+	cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) font84.dat
- 
- xwindir : FORCE libdir
- 	if test -f x-windows/Makefile; then cd x-windows; \
-diff --git a/lib/ccif/Makefile.in b/lib/ccif/Makefile.in
-index 975f1d9..75eda9f 100755
---- a/lib/ccif/Makefile.in
-+++ b/lib/ccif/Makefile.in
-@@ -371,11 +371,11 @@ condition.h condition_list.h: $(srcdir)/condition.list $(srcdir)/condition.awk
- #
- 
- install : all
--	$(INSTALL_DATA) `pwd`/$L $(libdir)/$L
--	$(INSTALL_DATA) `pwd`/$(CIFMMLIB) $(libdir)/$(CIFMMLIB)
--	$(RANLIB) $(libdir)/$L
-+	$(RANLIB) $L
-+	$(INSTALL_DATA) `pwd`/$L $(DESTDIR)/$(libdir)/$L
-+	$(INSTALL_DATA) `pwd`/$(CIFMMLIB) $(DESTDIR)$(libdir)/$(CIFMMLIB)
- 	if (test -f $(SHARED_LIB_NAME)); then \
--	  $(INSTALL_DATA) `pwd`/$(SHARED_LIB_NAME) $(libdir)/$(SHARED_LIB_NAME); \
-+	  $(INSTALL_DATA) `pwd`/$(SHARED_LIB_NAME) $(DESTDIR)/$(libdir)/$(SHARED_LIB_NAME); \
-         fi
- 
- uninstall :
-diff --git a/lib/data/Makefile.in b/lib/data/Makefile.in
-index cc25c5c..017502d 100755
---- a/lib/data/Makefile.in
-+++ b/lib/data/Makefile.in
-@@ -30,9 +30,9 @@ font84.dat : fontpack $(srcdir)/font84.ascii
- 
- install : all 
- 	-rm -f font84.dat
--	test -f font84.ascii || $(LNS) $(srcdir)/font84.ascii .
--	./fontpack
--	$(INSTALL) `pwd`/font84.dat $(libdir)/font84.dat 
-+	test -f font84.ascii || $(LNS) $(DESTDIR)/$(srcdir)/font84.ascii .
-+	LD_LIBRARY_PATH="../src:../ccif" ./fontpack
-+	$(INSTALL) `pwd`/font84.dat $(DESTDIR)/$(libdir)/font84.dat 
- 
- uninstall :
- 	-rm -f $(libdir)/font84.dat
-diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in
-index b32dd1e..6aa107d 100755
---- a/lib/src/Makefile.in
-+++ b/lib/src/Makefile.in
-@@ -685,7 +685,7 @@ testlib : $(srcdir)/testlib.f  $(LF)
- #
- 
- install-ccp4HEADERS: $(ccp4_HEADERS)
--	if test ! -d $(DESTDIR)$(includedir)/ccp4; then mkdir $(DESTDIR)$(includedir)/ccp4; fi
-+	if test ! -d $(DESTDIR)$(includedir)/ccp4; then mkdir -p $(DESTDIR)$(includedir)/ccp4; fi
- 	@list='$(ccp4_HEADERS)'; for p in $$list; do \
- 	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
- 	  f="`echo $$p | sed -e 's|^.*/||'`"; \
-@@ -716,11 +716,11 @@ uninstall-mmdbHEADERS:
- 	  rm -f $(DESTDIR)$(includedir)/mmdb/$$f; \
- 	done
- 
--install : all install-ccp4HEADERS install-mmdbHEADERS
--	$(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC)
--	$(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF)
--	$(RANLIB) $(libdir)/$(LC)
--	$(RANLIB) $(libdir)/$(LF)
-+install : all install-ccp4HEADERS
-+	$(RANLIB) $(LC)
-+	$(RANLIB) $(LF)
-+	$(INSTALL_DATA) `pwd`/$(LC) $(DESTDIR)/$(libdir)/$(LC)
-+	$(INSTALL_DATA) `pwd`/$(LF) $(DESTDIR)/$(libdir)/$(LF)
- 	$(SHARE_INST)
- 
- uninstall : uninstall-ccp4HEADERS uninstall-mmdbHEADERS
-diff --git a/lib/ssm/Makefile.in b/lib/ssm/Makefile.in
-index 27d3aa2..0a14fe5 100755
---- a/lib/ssm/Makefile.in
-+++ b/lib/ssm/Makefile.in
-@@ -375,12 +375,12 @@ distclean-libtool:
- uninstall-info-am:
- install-library_includeHEADERS: $(library_include_HEADERS)
- 	@$(NORMAL_INSTALL)
--	test -z "$(library_includedir)" || $(mkdir_p) "$(DESTDIR)$(library_includedir)"
-+	test -z "$(library_includedir)" || $(mkdir_p) "$(DESTDIR)$(library_includedir)/ssm"
- 	@list='$(library_include_HEADERS)'; for p in $$list; do \
- 	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
- 	  f=$(am__strip_dir) \
--	  echo " $(library_includeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(library_includedir)/$$f'"; \
--	  $(library_includeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(library_includedir)/$$f"; \
-+	  echo " $(library_includeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(library_includedir)/ssm/$$f'"; \
-+	  $(library_includeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(library_includedir)/ssm/$$f"; \
- 	done
- 
- uninstall-library_includeHEADERS:
diff --git a/sci-libs/ccp4-libs/files/6.1.3-overflows.patch b/sci-libs/ccp4-libs/files/6.1.3-overflows.patch
deleted file mode 100644
index 0e3c941d1cc2..000000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-overflows.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-Fix overflows and array subscript above array bounds
-
-http://bugs.gentoo.org/show_bug.cgi?id=339706
-
---- ccp4-6.1.3/lib/ccif/f_interface.c
-+++ ccp4-6.1.3/lib/ccif/f_interface.c
-@@ -926,7 +926,7 @@
- #endif
- 
- {
--  char logname_c[81];
-+  char logname_c[MAXFLEN];
-   size_t Length;
-   int unit;
-   CIF_FILE_LIST file_list_entry;
-@@ -4064,7 +4064,7 @@
- #endif
- 
- {
--   char lognam_c[81], *blknam_c;
-+   char lognam_c[MAXFLEN], *blknam_c;
-    size_t loglen, blklen;
-    int i, j, new;
-    
---- ccp4-6.1.3/lib/src/ccp4_diskio_f.c
-+++ ccp4-6.1.3/lib/src/ccp4_diskio_f.c
-@@ -705,7 +705,7 @@
-       log_name = strdup("diskio.dft"); 
-     if (!(file_name = getenv(log_name)))
-       file_name = log_name;
--    for ( *istrm = 1; *istrm == MAXFILES; *istrm++)
-+    for ( *istrm = 1; *istrm < MAXFILES; *istrm++)
-       if (!strcmp(file_name,_ioChannels[*istrm]->iobj->name)) break;
-   }
-   if (*istrm != MAXFILES) {
diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch
deleted file mode 100644
index 4271d5b76aec..000000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch
+++ /dev/null
@@ -1,367 +0,0 @@
-diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp
-index 69b32b0..602e35f 100755
---- a/lib/DiffractionImage/DiffractionImageCBF.cpp
-+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp
-@@ -6,10 +6,10 @@
- // images.
- 
- #include "DiffractionImage.h"
--#include "cbf.h"
--#include "cbf_simple.h" 
--#include "cbf_string.h"
--#include "cbf_byte_offset.h"
-+#include <cbflib/cbf.h>
-+#include <cbflib/cbf_simple.h>
-+#include <cbflib/cbf_string.h>
-+#include <cbflib/cbf_byte_offset.h>
- 
- 
- using namespace std;
-diff --git a/lib/DiffractionImage/MAR/Makefile.am b/lib/DiffractionImage/MAR/Makefile.am
-index fedb7ac..89a048e 100755
---- a/lib/DiffractionImage/MAR/Makefile.am
-+++ b/lib/DiffractionImage/MAR/Makefile.am
-@@ -2,7 +2,7 @@ AUTOMAKE_OPTIONS = gnu
- 
- noinst_LTLIBRARIES = libmar.la
- 
--AM_CPPFLAGS =-I../CBFlib/src -I../CBFlib/include
-+AM_CPPFLAGS =
- 
- libmar_la_SOURCES = mar300_header.c \
- 		    mar345_header.c \
-@@ -12,4 +12,3 @@ libmar_la_SOURCES = mar300_header.c \
- 		    utils.c \
- 		    pck.c
- 
--libmar_la_LDFLAGS = -static
-diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c
-index d3f4212..2c37108 100755
---- a/lib/DiffractionImage/MAR/marcif.c
-+++ b/lib/DiffractionImage/MAR/marcif.c
-@@ -31,8 +31,7 @@
- #include "marcif_header.h"
- #include "mar345_header.h"
- 
--#include <cbf.h>
--#include <img.h>
-+#include <cbflib/cbf.h>
- 
- #define printe(x) 	printf("%s: %s: %s\n",prg,f,x)
- #undef cbf_failnez
-diff --git a/lib/DiffractionImage/Makefile.am b/lib/DiffractionImage/Makefile.am
-index 189a1d7..6652576 100755
---- a/lib/DiffractionImage/Makefile.am
-+++ b/lib/DiffractionImage/Makefile.am
-@@ -1,7 +1,9 @@
- AUTOMAKE_OPTIONS = gnu
--SUBDIRS = CBFlib Bruker MAR Rigaku jpg
-+SUBDIRS = Bruker MAR Rigaku
- 
--AM_CPPFLAGS =-I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg
-+SYSLIBS = -ljpeg -lcbf
-+
-+AM_CPPFLAGS =-I./MAR
- lib_LTLIBRARIES = libDiffImage.la 
- 
- if WANT_PYTHONMOD
-@@ -35,48 +37,56 @@ libDiffImage_la_SOURCES =	DiffractionImageJpeg.cpp \
- 							Profile.cpp \
- 							Peak.cpp \
- 							dps_peaksearch_cn.c 
--libDiffImage_la_LDFLAGS = -static
-+libDiffImage_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS)
-+libDiffImage_la_LIBADD = $(SYSLIBS) \
-+                         ./MAR/libmar.la ./Bruker/libbruker.la \
-+                         ./Rigaku/librigaku.la
- 
--libDiffractionImage_la_DEPENDENCIES= libDiffImage.la ./CBFlib/src/libcbf.la \
-+libDiffractionImage_la_DEPENDENCIES= libDiffImage.la \
-                                      ./Bruker/libbruker.la ./MAR/libmar.la \
--                                     ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+                                     ./Rigaku/librigaku.la
- libDiffractionImage_la_SOURCES =  DiffractionImageTclInterface.cpp
--libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
--                                 ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
--				 				 ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
--								 --no-whole-archive -rpath '$(libdir)'
-+libDiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
-+libDiffractionImage_la_LIBADD = $(SYSLIBS) -ltcl \
-+                                libDiffImage.la \
-+                                 ./Bruker/libbruker.la \
-+				 				 ./MAR/libmar.la ./Rigaku/librigaku.la
- 
--lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
-+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \
-                                        ./Bruker/libbruker.la ./MAR/libmar.la \
--                                       ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+                                       ./Rigaku/librigaku.la
- lib_DiffractionImage_la_SOURCES =  DiffractionImagePythonInterface.cpp
--lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
--                                   ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
--				   			       ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
--								   --no-whole-archive -rpath '$(libdir)'
-+lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
-+lib_DiffractionImage_la_LIBADD = libDiffImage.la @PYLIB@ $(SYSLIBS) \
-+                                   ./Bruker/libbruker.la \
-+				   			       ./MAR/libmar.la ./Rigaku/librigaku.la
- 
--libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
-+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la  \
-                                        ./Bruker/libbruker.la ./MAR/libmar.la \
--                                       ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+                                       ./Rigaku/librigaku.la
- libDiffractionImaJ_la_SOURCES =  DiffractionImageJavaInterface.cpp
--libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
--                                   ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
--				                   ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
--								   --no-whole-archive -rpath '$(libdir)'
-+libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
-+libDiffractionImaJ_la_LIBADD = libDiffImage.la \
-+                                   ./Bruker/libbruker.la $(SYSLIBS) \
-+				                   ./MAR/libmar.la ./Rigaku/librigaku.la
- 
- bin_PROGRAMS = automask diffdump printpeaks diff2jpeg
--automask_LDADD =  libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
--                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+automask_LDADD =  libDiffImage.la ./Bruker/libbruker.la \
-+                  ./MAR/libmar.la ./Rigaku/librigaku.la  $(SYSLIBS)
- automask_SOURCES = automask.cpp
--diffdump_LDADD =  libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
--                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+automask_LDFLAGS = $(SHARED_LIB_FLAGS)
-+diffdump_LDADD =  libDiffImage.la ./Bruker/libbruker.la  $(SYSLIBS) \
-+                  ./MAR/libmar.la ./Rigaku/librigaku.la
- diffdump_SOURCES = diffdump.cpp
--printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
--                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+diffdump_LDFLAGS = $(SHARED_LIB_FLAGS)
-+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la \
-+                  ./MAR/libmar.la ./Rigaku/librigaku.la  $(SYSLIBS)
- printpeaks_SOURCES = printpeaks.cpp
--diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
--                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+printpeaks_LDFLAGS = $(SHARED_LIB_FLAGS)
-+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la \
-+                  ./MAR/libmar.la ./Rigaku/librigaku.la  $(SYSLIBS)
- diff2jpeg_SOURCES = diff2jpeg.cpp
-+diff2jpeg_LDFLAGS = $(SHARED_LIB_FLAGS)
- 
- install-data-local: 
- 			@INSTALL_DATA@ doc/DiffractionImage.doc ${CDOC}
-diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure
-index 3fb5784..fdf9683 100755
---- a/lib/DiffractionImage/configure
-+++ b/lib/DiffractionImage/configure
-@@ -21768,7 +21768,7 @@ _ACEOF
- fi
- 
- 
--ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile"
-+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile "
- 
- 
- cat >confcache <<\_ACEOF
-@@ -22407,12 +22407,9 @@ do
-   case $ac_config_target in
-     "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
-     "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
--    "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;;
--    "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;;
-     "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;;
-     "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;;
-     "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;;
--    "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;;
- 
-   *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
- echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
-diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in
-index 7f54b4b..16efc64 100755
---- a/lib/DiffractionImage/configure.in
-+++ b/lib/DiffractionImage/configure.in
-@@ -21,6 +21,8 @@ if test -n "${PYTHON}" ; then
-       HAVE_PYTHON=1
-       CPPFLAGS="${CPPFLAGS} -I${PYTHON_PREFIX}/include/python${PYTHON_VER}"
-     ])
-+  PYLIB="-lpython${PYTHON_VER}"
-+  AC_SUBST(PYLIB)
- fi
- AC_CHECK_HEADER([tcl.h], [HAVE_TCL=1])
- 
-@@ -65,11 +67,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z)
- AC_CHECK_LIB([m], [sqrt])
- 
- AC_CONFIG_FILES([Makefile
--                 CBFlib/Makefile
--                 CBFlib/src/Makefile
-                  MAR/Makefile
- 		 Rigaku/Makefile
--		 Bruker/Makefile
--		 jpg/Makefile])
-+		 Bruker/Makefile])
-                  
- AC_OUTPUT
-diff --git a/lib/ssm/Makefile.am b/lib/ssm/Makefile.am
-index e9554e1..a3ba33d 100755
---- a/lib/ssm/Makefile.am
-+++ b/lib/ssm/Makefile.am
-@@ -1,7 +1,11 @@
-+ACLOCAL_AMFLAGS = -I macros
- #libtool
- lib_LTLIBRARIES = libssm.la
-+libssm_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS)
-+libssm_la_CFLAGS = @MMDB_CFLAGS@
- libssm_la_SOURCES = ssm_superpose.cpp ss_csia.cpp ss_vxedge.cpp \
- ssm_align.cpp ss_graph.cpp
-+libssm_la_LIBADD = @MMDB_LIBS@
- 
- #non libtool
- #lib_LIBRARIES = libssm.a
-@@ -16,12 +20,10 @@ superpose_SOURCES = superpose.cpp
- 
- bin_PROGRAMS = superpose
- 
--INCLUDES = $(MMDB_CXXFLAGS)
--
--AM_LDFLAGS = $(MMDB_LIBS)
-+INCLUDES = @MMDB_CFLAGS@
- 
- EXTRA_DIST = macros/mmdb.m4
- 
--superpose_LDADD = libssm.la
-+superpose_LDADD = libssm.la @MMDB_LIBS@
- 
- libssm_a_AR = $(AR) $(AR_FLAGS)
-diff --git a/lib/ssm/configure.ac b/lib/ssm/configure.ac
-index 783cb46..d637d11 100755
---- a/lib/ssm/configure.ac
-+++ b/lib/ssm/configure.ac
-@@ -28,31 +28,10 @@ AC_ARG_ENABLE(debug,
-   [ac_cv_enable_debug=no ] )
- 
- dnl Optional: Check for MMDB.
--AM_PATH_MMDB(,
--  [ if test "x$mmdb_prefix" != x ; then
--      if test "x$ac_MMDB_CXXFLAGS" != x ; then 
--        case "$ac_MMDB_CXXFLAGS" in
--        *src/mmdb )
--        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g`
--        ;;
--        *include/mmdb )
--        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g`
--        ;;
--        *)
--        esac
--	MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS"
--        MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#`
--        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
--      else
--        MMDB_CXXFLAGS="-I$mmdb_prefix/lib/src/mmdb -I$mmdb_prefix/include/mmdb"
--        MMDB_LIBS="-L$mmdb_prefix/lib/src -L$mmdb_prefix/lib -lmmdb"
--        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
--      fi
--    else
--     AC_MSG_WARN([mmdb not found])
--    fi
--  ]
--)
-+
-+PKG_CHECK_MODULES([MMDB],[mmdb])
-+AC_SUBST([MMDB_CFLAGS])
-+AC_SUBST([MMDB_LIBS])
- 
- # Checks for typedefs, structures, and compiler characteristics.
- #
-@@ -67,6 +46,7 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
- # test for function in m
- AC_CHECK_LIB([m], [sqrt]) 
- 
-+
- AC_SUBST(AR_FLAGS)
- AC_SUBST(superpose_LDFLAGS)
- AM_CONDITIONAL(DEBUG, test "$ac_cv_enable_debug" = yes)
-diff --git a/src/pisa/Makefile.am b/src/pisa/Makefile.am
-index 094fd6b..922a131 100755
---- a/src/pisa/Makefile.am
-+++ b/src/pisa/Makefile.am
-@@ -1,3 +1,4 @@
-+ACLOCAL_AMFLAGS = -I macros
- SUBDIRS = molref pisastore sbase
- 
- pkgdatadir = $(datadir)/pisa
-@@ -20,8 +21,8 @@ pisa.cpp                pisa_lists.cpp          seq_superpose.cpp
- 
- bin_PROGRAMS = pisa
- 
--INCLUDES = $(MMDB_CXXFLAGS) $(SSM_CXXFLAGS)
-+INCLUDES = @MMDB_CFLAGS@ $(SSM_CXXFLAGS)
- 
--pisa_LDADD = $(SSM_LIBS) $(MMDB_LIBS)
-+pisa_LDADD = $(SSM_LIBS) @MMDB_LIBS@
- 
- EXTRA_DIST = macros/mmdb.m4 macros/ssm.m4 pisa.cfg.in
-diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac
-index 81afdda..4f99df6 100755
---- a/src/pisa/configure.ac
-+++ b/src/pisa/configure.ac
-@@ -32,35 +32,13 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
- AC_CHECK_LIB([m], [sqrt])
- 
- dnl Optional: Check for MMDB.
--AM_PATH_MMDB(,
--  [ if test "x$mmdb_prefix" != x ; then
--      if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then 
--        case "$ac_MMDB_CXXFLAGS" in
--        *src/mmdb )
--        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g`
--        ;;
--        *include/mmdb )
--        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g`
--        ;;
--        *)
--        esac
--	MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS"
--        MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#`
--        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
--      else
--        MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb"
--        MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb"
--        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
--      fi
--    else
--     AC_MSG_ERROR([mmdb not found])
--    fi
--  ]
--)
-+PKG_CHECK_MODULES([MMDB],[mmdb])
-+AC_SUBST([MMDB_CFLAGS])
-+AC_SUBST([MMDB_LIBS])
- 
- ac_saved_CXXFLAGS=$CXXFLAGS
- ac_saved_LIBS=$LIBS
--CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS"
-+CXXFLAGS="$CXXFLAGS $MMDB_CFLAGS"
- LIBS="$MMDB_LIBS $LIBS"
- AM_PATH_SSM(,
-   [ if test "x$ssm_prefix" != x ; then
-diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am
-index e78b10d..486b931 100755
---- a/src/rapper/Makefile.am
-+++ b/src/rapper/Makefile.am
-@@ -1,3 +1,3 @@
--SUBDIRS = libxml2 gc7.0 LOOP data
-+SUBDIRS = LOOP data
- 
- EXTRA_DIST =
-diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac
-index 5e4ef69..11b63ec 100755
---- a/src/rapper/configure.ac
-+++ b/src/rapper/configure.ac
-@@ -48,6 +48,6 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno)
- 
- AC_SUBST(rapper_LDFLAGS)
- 
--AC_CONFIG_SUBDIRS([gc7.0 libxml2])
-+#AC_CONFIG_SUBDIRS([gc7.0 libxml2])
- #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile)
- AC_OUTPUT(Makefile LOOP/Makefile data/Makefile)
diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch
deleted file mode 100644
index c787df903dfc..000000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch
+++ /dev/null
@@ -1,395 +0,0 @@
- lib/DiffractionImage/DiffractionImageCBF.cpp |    8 ++--
- lib/DiffractionImage/MAR/Makefile.am         |    3 +-
- lib/DiffractionImage/MAR/marcif.c            |    3 +-
- lib/DiffractionImage/Makefile.am             |   68 +++++++++++++++-----------
- lib/DiffractionImage/configure               |    5 +--
- lib/DiffractionImage/configure.in            |    7 +--
- lib/src/Makefile.in                          |    2 +-
- lib/ssm/Makefile.am                          |   10 ++--
- lib/ssm/configure.ac                         |   30 ++---------
- src/pisa/Makefile.am                         |    5 +-
- src/pisa/configure.ac                        |   30 ++----------
- src/rapper/Makefile.am                       |    2 +-
- src/rapper/configure.ac                      |    2 +-
- 13 files changed, 70 insertions(+), 105 deletions(-)
-
-diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp
-index 69b32b0..602e35f 100755
---- a/lib/DiffractionImage/DiffractionImageCBF.cpp
-+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp
-@@ -6,10 +6,10 @@
- // images.
- 
- #include "DiffractionImage.h"
--#include "cbf.h"
--#include "cbf_simple.h" 
--#include "cbf_string.h"
--#include "cbf_byte_offset.h"
-+#include <cbflib/cbf.h>
-+#include <cbflib/cbf_simple.h>
-+#include <cbflib/cbf_string.h>
-+#include <cbflib/cbf_byte_offset.h>
- 
- 
- using namespace std;
-diff --git a/lib/DiffractionImage/MAR/Makefile.am b/lib/DiffractionImage/MAR/Makefile.am
-index fedb7ac..89a048e 100755
---- a/lib/DiffractionImage/MAR/Makefile.am
-+++ b/lib/DiffractionImage/MAR/Makefile.am
-@@ -2,7 +2,7 @@ AUTOMAKE_OPTIONS = gnu
- 
- noinst_LTLIBRARIES = libmar.la
- 
--AM_CPPFLAGS =-I../CBFlib/src -I../CBFlib/include
-+AM_CPPFLAGS =
- 
- libmar_la_SOURCES = mar300_header.c \
- 		    mar345_header.c \
-@@ -12,4 +12,3 @@ libmar_la_SOURCES = mar300_header.c \
- 		    utils.c \
- 		    pck.c
- 
--libmar_la_LDFLAGS = -static
-diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c
-index d3f4212..2c37108 100755
---- a/lib/DiffractionImage/MAR/marcif.c
-+++ b/lib/DiffractionImage/MAR/marcif.c
-@@ -31,8 +31,7 @@
- #include "marcif_header.h"
- #include "mar345_header.h"
- 
--#include <cbf.h>
--#include <img.h>
-+#include <cbflib/cbf.h>
- 
- #define printe(x) 	printf("%s: %s: %s\n",prg,f,x)
- #undef cbf_failnez
-diff --git a/lib/DiffractionImage/Makefile.am b/lib/DiffractionImage/Makefile.am
-index 189a1d7..6652576 100755
---- a/lib/DiffractionImage/Makefile.am
-+++ b/lib/DiffractionImage/Makefile.am
-@@ -1,7 +1,9 @@
- AUTOMAKE_OPTIONS = gnu
--SUBDIRS = CBFlib Bruker MAR Rigaku jpg
-+SUBDIRS = Bruker MAR Rigaku
- 
--AM_CPPFLAGS =-I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg
-+SYSLIBS = -ljpeg -lcbf
-+
-+AM_CPPFLAGS =-I./MAR
- lib_LTLIBRARIES = libDiffImage.la 
- 
- if WANT_PYTHONMOD
-@@ -35,48 +37,56 @@ libDiffImage_la_SOURCES =	DiffractionImageJpeg.cpp \
- 							Profile.cpp \
- 							Peak.cpp \
- 							dps_peaksearch_cn.c 
--libDiffImage_la_LDFLAGS = -static
-+libDiffImage_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS)
-+libDiffImage_la_LIBADD = $(SYSLIBS) \
-+                         ./MAR/libmar.la ./Bruker/libbruker.la \
-+                         ./Rigaku/librigaku.la
- 
--libDiffractionImage_la_DEPENDENCIES= libDiffImage.la ./CBFlib/src/libcbf.la \
-+libDiffractionImage_la_DEPENDENCIES= libDiffImage.la \
-                                      ./Bruker/libbruker.la ./MAR/libmar.la \
--                                     ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+                                     ./Rigaku/librigaku.la
- libDiffractionImage_la_SOURCES =  DiffractionImageTclInterface.cpp
--libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
--                                 ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
--				 				 ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
--								 --no-whole-archive -rpath '$(libdir)'
-+libDiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
-+libDiffractionImage_la_LIBADD = $(SYSLIBS) -ltcl \
-+                                libDiffImage.la \
-+                                 ./Bruker/libbruker.la \
-+				 				 ./MAR/libmar.la ./Rigaku/librigaku.la
- 
--lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
-+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \
-                                        ./Bruker/libbruker.la ./MAR/libmar.la \
--                                       ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+                                       ./Rigaku/librigaku.la
- lib_DiffractionImage_la_SOURCES =  DiffractionImagePythonInterface.cpp
--lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
--                                   ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
--				   			       ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
--								   --no-whole-archive -rpath '$(libdir)'
-+lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
-+lib_DiffractionImage_la_LIBADD = libDiffImage.la @PYLIB@ $(SYSLIBS) \
-+                                   ./Bruker/libbruker.la \
-+				   			       ./MAR/libmar.la ./Rigaku/librigaku.la
- 
--libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
-+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la  \
-                                        ./Bruker/libbruker.la ./MAR/libmar.la \
--                                       ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+                                       ./Rigaku/librigaku.la
- libDiffractionImaJ_la_SOURCES =  DiffractionImageJavaInterface.cpp
--libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
--                                   ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
--				                   ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
--								   --no-whole-archive -rpath '$(libdir)'
-+libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
-+libDiffractionImaJ_la_LIBADD = libDiffImage.la \
-+                                   ./Bruker/libbruker.la $(SYSLIBS) \
-+				                   ./MAR/libmar.la ./Rigaku/librigaku.la
- 
- bin_PROGRAMS = automask diffdump printpeaks diff2jpeg
--automask_LDADD =  libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
--                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+automask_LDADD =  libDiffImage.la ./Bruker/libbruker.la \
-+                  ./MAR/libmar.la ./Rigaku/librigaku.la  $(SYSLIBS)
- automask_SOURCES = automask.cpp
--diffdump_LDADD =  libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
--                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+automask_LDFLAGS = $(SHARED_LIB_FLAGS)
-+diffdump_LDADD =  libDiffImage.la ./Bruker/libbruker.la  $(SYSLIBS) \
-+                  ./MAR/libmar.la ./Rigaku/librigaku.la
- diffdump_SOURCES = diffdump.cpp
--printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
--                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+diffdump_LDFLAGS = $(SHARED_LIB_FLAGS)
-+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la \
-+                  ./MAR/libmar.la ./Rigaku/librigaku.la  $(SYSLIBS)
- printpeaks_SOURCES = printpeaks.cpp
--diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
--                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+printpeaks_LDFLAGS = $(SHARED_LIB_FLAGS)
-+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la \
-+                  ./MAR/libmar.la ./Rigaku/librigaku.la  $(SYSLIBS)
- diff2jpeg_SOURCES = diff2jpeg.cpp
-+diff2jpeg_LDFLAGS = $(SHARED_LIB_FLAGS)
- 
- install-data-local: 
- 			@INSTALL_DATA@ doc/DiffractionImage.doc ${CDOC}
-diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure
-index 3fb5784..fdf9683 100755
---- a/lib/DiffractionImage/configure
-+++ b/lib/DiffractionImage/configure
-@@ -21768,7 +21768,7 @@ _ACEOF
- fi
- 
- 
--ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile"
-+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile "
- 
- 
- cat >confcache <<\_ACEOF
-@@ -22407,12 +22407,9 @@ do
-   case $ac_config_target in
-     "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
-     "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
--    "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;;
--    "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;;
-     "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;;
-     "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;;
-     "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;;
--    "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;;
- 
-   *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
- echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
-diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in
-index 7f54b4b..16efc64 100755
---- a/lib/DiffractionImage/configure.in
-+++ b/lib/DiffractionImage/configure.in
-@@ -21,6 +21,8 @@ if test -n "${PYTHON}" ; then
-       HAVE_PYTHON=1
-       CPPFLAGS="${CPPFLAGS} -I${PYTHON_PREFIX}/include/python${PYTHON_VER}"
-     ])
-+  PYLIB="-lpython${PYTHON_VER}"
-+  AC_SUBST(PYLIB)
- fi
- AC_CHECK_HEADER([tcl.h], [HAVE_TCL=1])
- 
-@@ -65,11 +67,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z)
- AC_CHECK_LIB([m], [sqrt])
- 
- AC_CONFIG_FILES([Makefile
--                 CBFlib/Makefile
--                 CBFlib/src/Makefile
-                  MAR/Makefile
- 		 Rigaku/Makefile
--		 Bruker/Makefile
--		 jpg/Makefile])
-+		 Bruker/Makefile])
-                  
- AC_OUTPUT
-diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in
-index c23f488..9579b3b 100755
---- a/lib/src/Makefile.in
-+++ b/lib/src/Makefile.in
-@@ -659,7 +659,7 @@ csymlib.o:        $(srcdir)/csymlib.c $(srcdir)/csymlib.h
- csymlib_f.o:      $(srcdir)/csymlib_f.c $(srcdir)/csymlib.h
- ccp4_unitcell.o:  $(srcdir)/ccp4_unitcell.c $(srcdir)/ccp4_unitcell.h
- ccp4_unitcell_f.o:  $(srcdir)/ccp4_unitcell_f.c $(srcdir)/ccp4_unitcell.h
--hybrid_36_f.o:    $(srcdir)/hybrid_36_f.c $(mmdbsrcdir)/hybrid_36.h
-+hybrid_36_f.o:    $(srcdir)/hybrid_36_f.c
- cvecmat.o:        $(srcdir)/cvecmat.c $(srcdir)/cvecmat.h
- cmtzlib_python_wrap.o: $(srcdir)/cmtzlib_python_wrap.c  $(srcdir)/mtzdata.h 
- cmaplib_python_wrap.o: $(srcdir)/cmaplib_python_wrap.c 
-diff --git a/lib/ssm/Makefile.am b/lib/ssm/Makefile.am
-index e9554e1..a3ba33d 100755
---- a/lib/ssm/Makefile.am
-+++ b/lib/ssm/Makefile.am
-@@ -1,7 +1,11 @@
-+ACLOCAL_AMFLAGS = -I macros
- #libtool
- lib_LTLIBRARIES = libssm.la
-+libssm_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS)
-+libssm_la_CFLAGS = @MMDB_CFLAGS@
- libssm_la_SOURCES = ssm_superpose.cpp ss_csia.cpp ss_vxedge.cpp \
- ssm_align.cpp ss_graph.cpp
-+libssm_la_LIBADD = @MMDB_LIBS@
- 
- #non libtool
- #lib_LIBRARIES = libssm.a
-@@ -16,12 +20,10 @@ superpose_SOURCES = superpose.cpp
- 
- bin_PROGRAMS = superpose
- 
--INCLUDES = $(MMDB_CXXFLAGS)
--
--AM_LDFLAGS = $(MMDB_LIBS)
-+INCLUDES = @MMDB_CFLAGS@
- 
- EXTRA_DIST = macros/mmdb.m4
- 
--superpose_LDADD = libssm.la
-+superpose_LDADD = libssm.la @MMDB_LIBS@
- 
- libssm_a_AR = $(AR) $(AR_FLAGS)
-diff --git a/lib/ssm/configure.ac b/lib/ssm/configure.ac
-index 783cb46..d637d11 100755
---- a/lib/ssm/configure.ac
-+++ b/lib/ssm/configure.ac
-@@ -28,31 +28,10 @@ AC_ARG_ENABLE(debug,
-   [ac_cv_enable_debug=no ] )
- 
- dnl Optional: Check for MMDB.
--AM_PATH_MMDB(,
--  [ if test "x$mmdb_prefix" != x ; then
--      if test "x$ac_MMDB_CXXFLAGS" != x ; then 
--        case "$ac_MMDB_CXXFLAGS" in
--        *src/mmdb )
--        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g`
--        ;;
--        *include/mmdb )
--        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g`
--        ;;
--        *)
--        esac
--	MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS"
--        MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#`
--        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
--      else
--        MMDB_CXXFLAGS="-I$mmdb_prefix/lib/src/mmdb -I$mmdb_prefix/include/mmdb"
--        MMDB_LIBS="-L$mmdb_prefix/lib/src -L$mmdb_prefix/lib -lmmdb"
--        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
--      fi
--    else
--     AC_MSG_WARN([mmdb not found])
--    fi
--  ]
--)
-+
-+PKG_CHECK_MODULES([MMDB],[mmdb])
-+AC_SUBST([MMDB_CFLAGS])
-+AC_SUBST([MMDB_LIBS])
- 
- # Checks for typedefs, structures, and compiler characteristics.
- #
-@@ -67,6 +46,7 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
- # test for function in m
- AC_CHECK_LIB([m], [sqrt]) 
- 
-+
- AC_SUBST(AR_FLAGS)
- AC_SUBST(superpose_LDFLAGS)
- AM_CONDITIONAL(DEBUG, test "$ac_cv_enable_debug" = yes)
-diff --git a/src/pisa/Makefile.am b/src/pisa/Makefile.am
-index 094fd6b..922a131 100755
---- a/src/pisa/Makefile.am
-+++ b/src/pisa/Makefile.am
-@@ -1,3 +1,4 @@
-+ACLOCAL_AMFLAGS = -I macros
- SUBDIRS = molref pisastore sbase
- 
- pkgdatadir = $(datadir)/pisa
-@@ -20,8 +21,8 @@ pisa.cpp                pisa_lists.cpp          seq_superpose.cpp
- 
- bin_PROGRAMS = pisa
- 
--INCLUDES = $(MMDB_CXXFLAGS) $(SSM_CXXFLAGS)
-+INCLUDES = @MMDB_CFLAGS@ $(SSM_CXXFLAGS)
- 
--pisa_LDADD = $(SSM_LIBS) $(MMDB_LIBS)
-+pisa_LDADD = $(SSM_LIBS) @MMDB_LIBS@
- 
- EXTRA_DIST = macros/mmdb.m4 macros/ssm.m4 pisa.cfg.in
-diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac
-index 81afdda..4f99df6 100755
---- a/src/pisa/configure.ac
-+++ b/src/pisa/configure.ac
-@@ -32,35 +32,13 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
- AC_CHECK_LIB([m], [sqrt])
- 
- dnl Optional: Check for MMDB.
--AM_PATH_MMDB(,
--  [ if test "x$mmdb_prefix" != x ; then
--      if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then 
--        case "$ac_MMDB_CXXFLAGS" in
--        *src/mmdb )
--        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g`
--        ;;
--        *include/mmdb )
--        ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g`
--        ;;
--        *)
--        esac
--	MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS"
--        MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#`
--        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
--      else
--        MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb"
--        MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb"
--        AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
--      fi
--    else
--     AC_MSG_ERROR([mmdb not found])
--    fi
--  ]
--)
-+PKG_CHECK_MODULES([MMDB],[mmdb])
-+AC_SUBST([MMDB_CFLAGS])
-+AC_SUBST([MMDB_LIBS])
- 
- ac_saved_CXXFLAGS=$CXXFLAGS
- ac_saved_LIBS=$LIBS
--CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS"
-+CXXFLAGS="$CXXFLAGS $MMDB_CFLAGS"
- LIBS="$MMDB_LIBS $LIBS"
- AM_PATH_SSM(,
-   [ if test "x$ssm_prefix" != x ; then
-diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am
-index e78b10d..486b931 100755
---- a/src/rapper/Makefile.am
-+++ b/src/rapper/Makefile.am
-@@ -1,3 +1,3 @@
--SUBDIRS = libxml2 gc7.0 LOOP data
-+SUBDIRS = LOOP data
- 
- EXTRA_DIST =
-diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac
-index 5e4ef69..11b63ec 100755
---- a/src/rapper/configure.ac
-+++ b/src/rapper/configure.ac
-@@ -48,6 +48,6 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno)
- 
- AC_SUBST(rapper_LDFLAGS)
- 
--AC_CONFIG_SUBDIRS([gc7.0 libxml2])
-+#AC_CONFIG_SUBDIRS([gc7.0 libxml2])
- #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile)
- AC_OUTPUT(Makefile LOOP/Makefile data/Makefile)
diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch
deleted file mode 100644
index 96978320163b..000000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch
+++ /dev/null
@@ -1,203 +0,0 @@
-diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp
-index 69b32b0..602e35f 100755
---- a/lib/DiffractionImage/DiffractionImageCBF.cpp
-+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp
-@@ -6,10 +6,10 @@
- // images.
- 
- #include "DiffractionImage.h"
--#include "cbf.h"
--#include "cbf_simple.h" 
--#include "cbf_string.h"
--#include "cbf_byte_offset.h"
-+#include <cbflib/cbf.h>
-+#include <cbflib/cbf_simple.h>
-+#include <cbflib/cbf_string.h>
-+#include <cbflib/cbf_byte_offset.h>
- 
- 
- using namespace std;
-diff --git a/lib/DiffractionImage/MAR/Makefile.in b/lib/DiffractionImage/MAR/Makefile.in
-index 4264696..00c4d8d 100755
---- a/lib/DiffractionImage/MAR/Makefile.in
-+++ b/lib/DiffractionImage/MAR/Makefile.in
-@@ -174,7 +174,7 @@ top_builddir = @top_builddir@
- top_srcdir = @top_srcdir@
- AUTOMAKE_OPTIONS = gnu
- noinst_LTLIBRARIES = libmar.la
--AM_CPPFLAGS = -I../CBFlib/src -I../CBFlib/include
-+AM_CPPFLAGS = 
- libmar_la_SOURCES = mar300_header.c \
- 		    mar345_header.c \
- 		    marcif.c \
-diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c
-index d3f4212..2c37108 100755
---- a/lib/DiffractionImage/MAR/marcif.c
-+++ b/lib/DiffractionImage/MAR/marcif.c
-@@ -31,8 +31,7 @@
- #include "marcif_header.h"
- #include "mar345_header.h"
- 
--#include <cbf.h>
--#include <img.h>
-+#include <cbflib/cbf.h>
- 
- #define printe(x) 	printf("%s: %s: %s\n",prg,f,x)
- #undef cbf_failnez
-diff --git a/lib/DiffractionImage/Makefile.in b/lib/DiffractionImage/Makefile.in
-index 8197956..807cf25 100755
---- a/lib/DiffractionImage/Makefile.in
-+++ b/lib/DiffractionImage/Makefile.in
-@@ -106,23 +106,19 @@ PROGRAMS = $(bin_PROGRAMS)
- am_automask_OBJECTS = automask.$(OBJEXT)
- automask_OBJECTS = $(am_automask_OBJECTS)
- automask_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \
--	./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \
--	./jpg/libjpeg.la
-+	./MAR/libmar.la ./Rigaku/librigaku.la
- am_diff2jpeg_OBJECTS = diff2jpeg.$(OBJEXT)
- diff2jpeg_OBJECTS = $(am_diff2jpeg_OBJECTS)
- diff2jpeg_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \
--	./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \
--	./jpg/libjpeg.la
-+	./MAR/libmar.la ./Rigaku/librigaku.la
- am_diffdump_OBJECTS = diffdump.$(OBJEXT)
- diffdump_OBJECTS = $(am_diffdump_OBJECTS)
- diffdump_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \
--	./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \
--	./jpg/libjpeg.la
-+	./MAR/libmar.la ./Rigaku/librigaku.la
- am_printpeaks_OBJECTS = printpeaks.$(OBJEXT)
- printpeaks_OBJECTS = $(am_printpeaks_OBJECTS)
- printpeaks_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \
--	./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \
--	./jpg/libjpeg.la
-+	./MAR/libmar.la ./Rigaku/librigaku.la
- DEFAULT_INCLUDES = -I.@am__isrc@
- depcomp = $(SHELL) $(top_srcdir)/depcomp
- am__depfiles_maybe = depfiles
-@@ -284,8 +280,8 @@ target_alias = @target_alias@
- top_builddir = @top_builddir@
- top_srcdir = @top_srcdir@
- AUTOMAKE_OPTIONS = gnu
--SUBDIRS = CBFlib Bruker MAR Rigaku jpg
--AM_CPPFLAGS = -I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg
-+SUBDIRS = Bruker MAR Rigaku
-+AM_CPPFLAGS = -I./MAR
- lib_LTLIBRARIES = libDiffImage.la $(am__append_1) $(am__append_2) \
- 	$(am__append_3)
- libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \
-@@ -311,50 +307,50 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \
- 							dps_peaksearch_cn.c 
- 
- libDiffImage_la_LDFLAGS = -static
--libDiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
-+libDiffractionImage_la_DEPENDENCIES = libDiffImage.la \
-                                      ./Bruker/libbruker.la ./MAR/libmar.la \
--                                     ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+                                     ./Rigaku/librigaku.la
- 
- libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp
- libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
--                                 ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
--				 				 ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
-+                                 -lcbf ./Bruker/libbruker.la \
-+				 				 ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \
- 								 --no-whole-archive -rpath '$(libdir)'
- 
--lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
-+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \
-                                        ./Bruker/libbruker.la ./MAR/libmar.la \
--                                       ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+                                       ./Rigaku/librigaku.la
- 
- lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp
- lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
--                                   ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
--				   			       ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
-+                                   -lcbf ./Bruker/libbruker.la \
-+				   			       ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \
- 								   --no-whole-archive -rpath '$(libdir)'
- 
--libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
-+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \
-                                        ./Bruker/libbruker.la ./MAR/libmar.la \
--                                       ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+                                       ./Rigaku/librigaku.la
- 
- libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp
- libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
--                                   ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
--				                   ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
-+                                   -lcbf ./Bruker/libbruker.la \
-+				                   ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \
- 								   --no-whole-archive -rpath '$(libdir)'
- 
--automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
--                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+automask_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \
-+                  ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg
- 
- automask_SOURCES = automask.cpp
--diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
--                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \
-+                  ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg
- 
- diffdump_SOURCES = diffdump.cpp
--printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
--                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \
-+                  ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg
- 
- printpeaks_SOURCES = printpeaks.cpp
--diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
--                  ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
-+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \
-+                  ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg
- 
- diff2jpeg_SOURCES = diff2jpeg.cpp
- all: all-recursive
-diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure
-index 3fb5784..fdf9683 100755
---- a/lib/DiffractionImage/configure
-+++ b/lib/DiffractionImage/configure
-@@ -21768,7 +21768,7 @@ _ACEOF
- fi
- 
- 
--ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile"
-+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile "
- 
- 
- cat >confcache <<\_ACEOF
-@@ -22407,12 +22407,9 @@ do
-   case $ac_config_target in
-     "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
-     "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
--    "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;;
--    "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;;
-     "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;;
-     "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;;
-     "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;;
--    "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;;
- 
-   *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
- echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
-diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in
-index 7f54b4b..69b10e1 100755
---- a/lib/DiffractionImage/configure.in
-+++ b/lib/DiffractionImage/configure.in
-@@ -65,11 +65,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z)
- AC_CHECK_LIB([m], [sqrt])
- 
- AC_CONFIG_FILES([Makefile
--                 CBFlib/Makefile
--                 CBFlib/src/Makefile
-                  MAR/Makefile
- 		 Rigaku/Makefile
--		 Bruker/Makefile
--		 jpg/Makefile])
-+		 Bruker/Makefile])
-                  
- AC_OUTPUT
diff --git a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch b/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch
deleted file mode 100644
index 367d53e3e4f6..000000000000
--- a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- Makefile.in | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/Makefile.in b/Makefile.in
-index 60033eb..13ddbd0 100755
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -53,7 +53,7 @@ clipper: FORCE fftw
- 
- diffractionImg: 
- 	if test -n "$(diffimdir)"; then cd $(top_srcdir)/$(diffimdir); \
--	$(MAKE) -i $(MFLAGS) $(MVARS); else true; fi
-+	$(MAKE) $(MFLAGS) $(MVARS); fi
- 
- ssm: 
- 	if test -n "$(ssmdir)"; then cd $(top_srcdir)/$(ssmdir); \
diff --git a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch b/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch
deleted file mode 100644
index caf62bb652e2..000000000000
--- a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- lib/DiffractionImage/DiffractionImagePythonInterface.cpp | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/lib/DiffractionImage/DiffractionImagePythonInterface.cpp b/lib/DiffractionImage/DiffractionImagePythonInterface.cpp
-index f729fc5..4c24e82 100755
---- a/lib/DiffractionImage/DiffractionImagePythonInterface.cpp
-+++ b/lib/DiffractionImage/DiffractionImagePythonInterface.cpp
-@@ -867,7 +867,7 @@ SWIG_Python_AddErrorMsg(const char* mesg)
-     Py_DECREF(old_str);
-     Py_DECREF(value);
-   } else {
--    PyErr_Format(PyExc_RuntimeError, mesg);
-+    PyErr_Format(PyExc_RuntimeError, "%s", mesg);
-   }
- }
- 
diff --git a/sci-libs/ccp4-libs/metadata.xml b/sci-libs/ccp4-libs/metadata.xml
deleted file mode 100644
index c0432fefe855..000000000000
--- 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@gentoo.org</email>
-    <name>Justin Lecher (jlec)</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-libs/clipper/clipper-2.1_p100511-r1.ebuild b/sci-libs/clipper/clipper-2.1_p100511-r1.ebuild
deleted file mode 100644
index 1757c6960b83..000000000000
--- a/sci-libs/clipper/clipper-2.1_p100511-r1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils eutils flag-o-matic
-
-MY_PV=${PV/_p/-}
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Object-oriented libraries for crystallographic data and crystallographic computation"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html"
-SRC_URI="http://www.ysbl.york.ac.uk/~cowtan/clipper/${MY_P}-ac.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE="debug static-libs"
-
-RDEPEND="
-	sci-libs/ccp4-libs
-	sci-libs/fftw
-	sci-libs/mmdb"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/${PN}-2.1
-
-PATCHES=(
-	"${FILESDIR}"/20091215-missing-var.patch
-	"${FILESDIR}"/${PV}-makefile.patch
-	"${FILESDIR}"/${P}-outofsourcebuild.patch
-	)
-
-src_configure() {
-	# Recommended on ccp4bb/coot ML to fix crashes when calculating maps
-	# on 64-bit systems
-	append-flags -fno-strict-aliasing
-
-	local myeconfargs=(
-		--enable-ccp4
-		--enable-cif
-		--enable-cns
-		--enable-contrib
-		--enable-minimol
-		--enable-mmdb
-		--enable-phs
-		--with-mmdb="${EPREFIX}/usr"
-		$(use_enable debug)
-		)
-	autotools-utils_src_configure
-}
-
-src_test() {
-	emake -C "${AUTOTOOLS_BUILD_DIR}"/examples check
-}
diff --git a/sci-libs/coot-data/coot-data-2-r1.ebuild b/sci-libs/coot-data/coot-data-2-r1.ebuild
deleted file mode 100644
index 1640d461d019..000000000000
--- a/sci-libs/coot-data/coot-data-2-r1.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-DESCRIPTION="Data for the Crystallographic Object-Oriented Toolkit"
-HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
-#SRC_URI="http://lmb.bioch.ox.ac.uk/coot/software/dependencies/reference-structures.tar.gz"
-SRC_URI="mirror://gentoo/reference-structures-${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE=""
-
-RESTRICT="binchecks strip"
-
-S="${WORKDIR}"
-
-src_install() {
-	insinto /usr/share/coot
-	doins -r reference-structures
-
-	# Coot looks in the wrong spot for the monomer library
-	# Listens to ccp4's CCP4_LIB rather than CLIBD_MON
-	cat >> "${T}"/coot <<- EOF
-	COOT_REFMAC_LIB_DIR="${EPREFIX}/usr/share/ccp4/"
-	COOT_REF_STRUCTS="${EPREFIX}/usr/share/coot/reference-structures/"
-	EOF
-
-	newenvd "${T}"/coot 20coot
-}
diff --git a/sci-libs/coot-data/coot-data-2.ebuild b/sci-libs/coot-data/coot-data-2.ebuild
deleted file mode 100644
index 2b7d33178adb..000000000000
--- a/sci-libs/coot-data/coot-data-2.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="3"
-
-DESCRIPTION="Data for the Crystallographic Object-Oriented Toolkit"
-HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
-#SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz"
-SRC_URI="mirror://gentoo/reference-structures-${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE=""
-
-RESTRICT="binchecks strip"
-
-S="${WORKDIR}"
-
-src_install() {
-	insinto /usr/share/coot
-	doins -r reference-structures || die
-
-	# Coot looks in the wrong spot for the monomer library
-	# Listens to ccp4's CCP4_LIB rather than CLIBD_MON
-	cat >> "${T}"/coot <<- EOF
-	COOT_REFMAC_LIB_DIR="${EPREFIX}/usr/share/ccp4/"
-	COOT_REF_STRUCTS="${EPREFIX}/usr/share/coot/reference-structures/"
-	EOF
-
-	newenvd "${T}"/coot 20coot || die
-}
diff --git a/sci-libs/mmdb/mmdb-1.24.ebuild b/sci-libs/mmdb/mmdb-1.24.ebuild
deleted file mode 100644
index f44a3ae67ee1..000000000000
--- a/sci-libs/mmdb/mmdb-1.24.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit autotools-utils
-
-DESCRIPTION="The Coordinate Library, designed to assist CCP4 developers in working with coordinate files"
-HOMEPAGE="https://launchpad.net/mmdb/"
-SRC_URI="
-	http://www.ysbl.york.ac.uk/~emsley/software/${P}.tar.gz
-	https://launchpad.net/mmdb/1.23/${PV}/+download/${P}.tar.gz"
-
-LICENSE="GPL-2 LGPL-3"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="static-libs"
-
-DEPEND="!<sci-libs/ccp4-libs-6.1.3"
-RDEPEND=""
-
-src_install() {
-	autotools-utils_src_install
-
-	# create missing mmdb.pc
-	cat >> "${T}"/mmdb.pc <<- EOF
-	prefix=${EPREFIX}/usr
-	exec_prefix=${EPREFIX}/usr
-	libdir=${EPREFIX}/usr/$(get_libdir)
-	includedir=${EPREFIX}/usr/include/mmdb
-
-	Name: ${PN}
-	Description: Macromolecular coordinate library
-	Version: ${PV}
-	Requires:
-	Conflicts:
-	Libs: -L"${EPREFIX}/usr/$(get_libdir)" -lmmdb
-	Cflags: -I"${EPREFIX}/usr/include/mmdb"
-
-	EOF
-
-	insinto /usr/$(get_libdir)/pkgconfig
-	doins "${T}"/mmdb.pc
-}
diff --git a/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild b/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild
index 8cae49d97a8c..6389827c63ee 100644
--- a/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild
+++ b/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild
@@ -15,7 +15,4 @@ SLOT="0"
 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 IUSE="static-libs"
 
-DEPEND="!<sci-libs/ccp4-libs-6.1.3"
-RDEPEND=""
-
 PATCHES=( "${FILESDIR}"/${P}-include-path.patch )
diff --git a/sci-libs/mmdb/mmdb-1.25.5.ebuild b/sci-libs/mmdb/mmdb-1.25.5.ebuild
deleted file mode 100644
index 9be8cec5a894..000000000000
--- a/sci-libs/mmdb/mmdb-1.25.5.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit autotools-utils
-
-DESCRIPTION="The Coordinate Library, designed to assist CCP4 developers in working with coordinate files"
-HOMEPAGE="https://launchpad.net/mmdb/"
-SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.gz"
-
-LICENSE="GPL-2 LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="static-libs"
-
-DEPEND="!<sci-libs/ccp4-libs-6.1.3"
-RDEPEND=""
diff --git a/sci-libs/monomer-db/monomer-db-0.090729.ebuild b/sci-libs/monomer-db/monomer-db-0.090729.ebuild
deleted file mode 100644
index 6513cbc0404c..000000000000
--- a/sci-libs/monomer-db/monomer-db-0.090729.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-DESCRIPTION="Monomer library used for macromolecular structure building and refinement"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-# SRC_URI="http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_dictionary.tar.gz"
-SRC_URI="https://dev.gentoo.org/~jlec/science-dist/${P}.tar.gz"
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="!<sci-chemistry/ccp4-6.1.3"
-DEPEND="${RDEPEND}"
-
-RESTRICT="binchecks strip"
-
-S="${WORKDIR}"/dic
-
-src_install() {
-	insinto /usr/share/ccp4/data/monomers/
-	for i in {a..z} {1..9} *list *.cif *.txt; do
-		doins -r ${i}
-	done
-	docinto html
-	dodoc *.html
-}
diff --git a/sci-libs/ssm/ssm-1.1.ebuild b/sci-libs/ssm/ssm-1.1.ebuild
deleted file mode 100644
index d247077313dd..000000000000
--- a/sci-libs/ssm/ssm-1.1.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit autotools eutils
-
-DESCRIPTION="A macromolecular coordinate superposition library"
-HOMEPAGE="https://launchpad.net/ssm"
-SRC_URI="https://launchpad.net/${PN}/trunk/${PV}/+download/${P}.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs"
-
-DEPEND=">=sci-libs/mmdb-1.23:0"
-RDEPEND="${DEPEND}
-	!<sci-libs/ccp4-libs-6.1.3-r10"
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${P}-mmdb.patch \
-		"${FILESDIR}"/${P}-pc.patch
-	eautoreconf
-}
-
-src_configure() {
-	econf $(use_enable static-libs static)
-}