Drop old

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

7 files changed, 32 insertions, 1077 deletions

diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
index 75e72fe3dbab..6131f33be497 100644
--- a/sci-libs/ccp4-libs/ChangeLog
+++ b/sci-libs/ccp4-libs/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-libs/ccp4-libs
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.60 2014/10/12 14:46:08 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.61 2015/03/09 13:35:48 jlec Exp $
+
+  09 Mar 2015; Justin Lecher <jlec@gentoo.org> -ccp4-libs-6.1.3-r12.ebuild,
+  -ccp4-libs-6.1.3-r13.ebuild, -ccp4-libs-6.1.3-r14.ebuild,
+  ccp4-libs-6.1.3-r11.ebuild, ccp4-libs-6.1.3-r15.ebuild:
+  Drop old
 
   12 Oct 2014; Justin Lecher <jlec@gentoo.org> ccp4-libs-6.1.3-r11.ebuild,
   ccp4-libs-6.1.3-r12.ebuild, ccp4-libs-6.1.3-r13.ebuild,
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
index 3bd10483d445..e69df6ad48a1 100644
--- a/sci-libs/ccp4-libs/Manifest
+++ b/sci-libs/ccp4-libs/Manifest
@@ -17,29 +17,26 @@ AUX 6.1.3-unbundle-libs-ng.patch 13925 SHA256 e24757ac37a173fc501f1036e283f048fa
 AUX 6.1.3-unbundle-libs-ng2.patch 15485 SHA256 ded20e7e5a3fd347bc852ca119b3cbe6cde22c8acae21d710d69da4ab12fa7a6 SHA512 4ba517c14a298a31cf894c26dafc713c1b3b5acc114c653874f914bf3d197fa2fec82305775357e343d809e8d240f5f2b0c6573859ecf2b89a7aa17e1f1c7554 WHIRLPOOL 52dbd8044f563d2ba2f4c8cef615067fd6fb9034b5e6fd543a0dc3830ced99b47347cb5bd57f5a246e744f67609883e800057b552831f75d6b4553726f7b764a
 AUX 6.1.3-unbundle-libs.patch 9063 SHA256 7e5fc919b5204e2d9141f7715afdd8a8b4e3e2a96e2bf95aa00fbd56046f1aa4 SHA512 3e4b2564e3870f024a95bbf556ad597c0de7f83309aaa0f3d3af80c05b616eb0cbec04abe94546951c316b172accb74580c74a16963e3213c5477c89d4fae85d WHIRLPOOL 64d9c5408a48b80a515e465d0ce59ffad3b61e6f9ab247cfd23ac17af40e723d387a7970d116ce8d4aae45a051ae5901de0e96ccbf21a6df84cc341c03a6224e
 DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
-EBUILD ccp4-libs-6.1.3-r11.ebuild 10954 SHA256 63f44f8b9ca3f4294967a6635b643653ca5efa3a4cc4f46b6a07a6e3db238af1 SHA512 5da7edaa04cdea1d87e6d20deb592e0c4789d5884c5edff152d92aaca3153002d2f55dc6c6c8d3a89c05c47f7e62a8c5d314b7d3953898ed14d08894c2003ad0 WHIRLPOOL 428cb5f1b1445e02cb22e599f1b6c8c05169bc4e16d6617c36c0a921e6b84ad8136455bc5d8f26ab93bf18c305b447130cd923b6f8aab5f923bad0847c5e520c
-EBUILD ccp4-libs-6.1.3-r12.ebuild 11210 SHA256 57c76ce5f440dc056b090433b5edb4adb017bdf3277a9c7be743c34da49be435 SHA512 3b6aed0b034c51941cd6f9a059ececa1b240fd9ccdf31b73ddf14c06dd7f58df3b580d18a0e197753215afffd9869fd4160c50380b0989fa368f38819f741af9 WHIRLPOOL aa513e94e0dc5b5be03f6d94da9daeeca6d2b9fb3bfd1e32e1954ea947c34016d1b30bd09691e1ff1f6437371092459d652ad255d4d31ba73076bde4caa34e59
-EBUILD ccp4-libs-6.1.3-r13.ebuild 11036 SHA256 44a60c5e6007ff7aebb9eeeb3bfca8216fa3ec28c692a358c5eaa8f7c588cc89 SHA512 c41eb9383271f45de4e86e910fd7b1b8776035ac6b1bd340ed82b7a5a7c1d86b5a6636ed1194d2e76a74c8da05a1134e6fb2b198606524821476cd2dbe7866f6 WHIRLPOOL f07f1162814e860a874118916110506e8f5606f114a4230b661d7f7221a74e9e96d955889165a3cf78b485f0b2c4f4e9211f9dffd9d3e700d8631e6c304cf4b1
-EBUILD ccp4-libs-6.1.3-r14.ebuild 11111 SHA256 241a9cf48736d3dc48f462ee0c42e345fa22e03f3d900f9cb9a8e9cf1323bac5 SHA512 7412315009fee862f4aecce7045c81303f0953a46388d7e55d986300bfc2714f3674e2a87926603cfe4df8c7b6df70f7adc26e35df2b185396f3175bffb2a1bc WHIRLPOOL cdc035cdc977df4f9edb7aa0bb4f4eb224554d5d98f55727c2ee16a759797a53cf6c0b0a303bfa8daf5bf0db4e4ec4c16a682a101110ac8715c683b43a61b799
-EBUILD ccp4-libs-6.1.3-r15.ebuild 11192 SHA256 7b0e34f670502cf96b36b67ae19e8c65898a098dd9f4dac852543d1131c0e182 SHA512 820603ed6a3e5c33c150857fe3b747cd5464b165746cd6de17badf94329dbdf6a60379df0f00369b798acb8f1385d516eaa3d15fe5f6122dc20353269ca69b15 WHIRLPOOL 7b13a6fe7b71f94abd2cdfa10f2204a2bebad4de732c72eeb680f7ef3d2457adb2493b0b17fcab5b80c92d070f9aa1a94cbf4d8e19838ca856a0c1c785e22ba0
-MISC ChangeLog 9096 SHA256 b926fb554fff2aa735ed524337a4b0cdee90b3b011d3910afbf49228c12680f8 SHA512 9014568c1f39351a317bd9c245bf14b60fa46a7c39dbef1e0b6f44bd46ce917e58ac8d69a842878ff572dbc72c5f417f9940dbc6449a1f45fba38b3044a2e964 WHIRLPOOL a0b07207f0b3c5c43d466380b60435d90e7c521b947355ce212ddc9ad3c2c76c14463895dbf5732598bc371187d69da68224ccc262ca7627fbe4120dc51f020d
+EBUILD ccp4-libs-6.1.3-r11.ebuild 10942 SHA256 5fbe4cf4b9056be38670f8dfa6ee4ff15a02ebd1651e92d393eeda8fa91de754 SHA512 bc163a58ceb913cbfe6854d6d0eaa24b4f0ae23b81fc7c72f88cfde6a2a3cc84d042da9b134c774a0d6d9545fe182e9db5883f5dc355e1a39623132587269f7b WHIRLPOOL 99f59454db2636e4aaae0d013b570578eae5e7830be00e724a3ee3e64e24158909f749925c7ed19d358c7a5d9bb1877affd6f4272f37ad6c7aecb573cc68b6fb
+EBUILD ccp4-libs-6.1.3-r15.ebuild 11177 SHA256 68db2f75c2d30931dbc7c9443fdf02ed74ca3c7a497dfd5af44db79e236d11c2 SHA512 a20b60341ac583c0951533c4098ad84e5bb699c83a4944518ae69328950251bd3a513497073896e52002668e0ba943858001333bae1de5d1369f3a70dd7019a3 WHIRLPOOL 2a872d3c0de3739df887c4e8001f4e9a0187c43e190593f8e02877fbea71036544bbc97cab3e50d87491f7402f9f0724429c91ea1d71ff2eecf5cef2c9cce220
+MISC ChangeLog 9302 SHA256 a04d066ddb2501df9973f758392107392cb8894e66d3794180a6392bdf73d981 SHA512 709217bf2332051b73fcae8bba3e0539ca303b12fd099940137dab978fff4a88892c4a98caacfaf261772baaf1da4df32f2a93634f55ac1a376bc8b5a03ab863 WHIRLPOOL e666267a13400f28e89ccd6336d6a36c5c342f12b3cd3f1e78444ddd90b91a393c26e5fcc8103a9f442723c4f2ece4e7ae1025f6596fec2a7c46e3f853708b83
 MISC metadata.xml 272 SHA256 464cdfad7e5470cd4897f4d81fb87220dfdb9b8645f720e2fcf5157a7a75fbec SHA512 3e8682fbb209895927a39021555e3a440c49e61dcce93ea1b13759e067b285c604328cff031843e3aac6528970384c8fdbf15c8edd76a421db111a3981825fa5 WHIRLPOOL fc8d5f3db9db73bb2026ca21c4448107558ac53d568c89c7c6ccc635fde460aec1bbd177a4ad770b20d35693b59fc0721c8d60aea997973db3efd6b3c3777eba
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diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild
index 9ac15932373c..6ce6dc0d77fa 100644
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild,v 1.11 2014/10/12 14:46:08 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r11.ebuild,v 1.12 2015/03/09 13:35:48 jlec Exp $
 
 EAPI=3
 
@@ -23,7 +23,7 @@ SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
 # patch tarball from upstream
 	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
 # patches created by us
-	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
+	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
 
 for i in $(seq $PATCH_TOT); do
 	NAME="PATCH${i}[1]"
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r12.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r12.ebuild
deleted file mode 100644
index 7ef561290595..000000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r12.ebuild
+++ /dev/null
@@ -1,348 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r12.ebuild,v 1.3 2014/10/12 14:46:08 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_6,2_7} )
-
-inherit autotools eutils fortran-2 gnuconfig multilib python-single-r1 toolchain-funcs
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-
-DESCRIPTION="Protein X-ray crystallography toolkit - Libraries"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
-# patch tarball from upstream
-	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
-# patches created by us
-	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
-
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	!<sci-chemistry/ccp4-6.1.3
-	!<sci-chemistry/ccp4-apps-${PV}-r10
-	app-shells/tcsh
-	dev-lang/tcl
-	>=sci-libs/cbflib-0.9.2.2
-	sci-libs/fftw:2.1
-	sci-libs/mmdb:0
-	sci-libs/monomer-db
-	sci-libs/ssm
-	virtual/jpeg
-	virtual/lapack
-	virtual/blas"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${MY_P}"
-
-MAKEOPTS+=" -j1"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	tc-export PKG_CONFIG RANLIB AR
-
-	sed \
-		-e "/^AR/s:ar:$(tc-getAR):g" \
-		-i lib/src/Makefile.in src/Makefile.in src/ccp4mapwish_/Makefile.in lib/ccif/Makefile.in || die
-
-	einfo "Applying upstream patches ..."
-	for patch in $(seq $PATCH_TOT); do
-		base="PATCH${patch}"
-		dir=$(eval echo \${${base}[0]})
-		p=$(eval echo \${${base}[1]})
-		pushd "${dir}" >& /dev/null
-		ccp_patch "${DISTDIR}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-	# fix buffer overflows wrt bug 339706
-	ccp_patch "${FILESDIR}"/${PV}-overflows.patch
-
-	# it tries to create libdir, bindir etc on live system in configure
-	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
-	# make creation of libccif.so smooth
-	ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
-
-	# lets try to build libmmdb seperatly
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
-
-	# unbundle libjpeg and cbflib
-	ccp_patch "${FILESDIR}"/${PV}-unbundle-libs-ng2.patch
-
-	# Fix missing DESTIDR
-	# not installing during build
-	ccp_patch "${FILESDIR}"/${PV}-noinstall.patch
-	sed \
-		-e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \
-		-i configure || die
-
-	# Fix upstreams code
-	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
-
-	# use pkg-config to detect BLAS/LAPACK
-	ccp_patch "${FILESDIR}"/${PV}-lapack.patch
-
-	# proto type changing in version 0.9.2.2
-	ccp_patch "${FILESDIR}"/${PV}-cbf.patch
-
-	# proto type changing in version 0.9.2.2
-	ccp_patch "${FILESDIR}"/${PV}-no-pypath.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# not needed, we have it extra
-	rm -rf src/rapper/{libxml2,gc7.0} || die
-
-	sed \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		-e 's:-Wl,-rpath,$CLIB::g' \
-		-e 's: -rpath $CLIB::g' \
-		-e 's: -I${srcdir}/include/cpp_c_headers::g' \
-		-e 's:sleep 1:sleep .2:g' \
-		-i configure || die
-
-	gnuconfig_update
-
-	for i in lib/DiffractionImage src/rapper src/pisa; do
-		pushd ${i} > /dev/null
-			sed 's:-g::g' -i configure* || die
-			eautoreconf
-		popd > /dev/null
-	done
-
-	## unbundle libssm
-	sed -e '/libdir/s:ssm::g' -i Makefile.in || die
-	find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete || die
-}
-
-src_configure() {
-	rm -rf lib/DiffractionImage/{jpg,CBFlib} || die
-
-	# Build system is broken if we set LDFLAGS
-	userldflags="${LDFLAGS}"
-	export SHARED_LIB_FLAGS="${LDFLAGS}"
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "$(tc-getFC)" = "ifort" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup || die
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure || die
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=$(tc-getFC)
-	export FOPTIM=${FFLAGS:- -O2}
-
-	export SHARE_LIB="\
-		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
-		$(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb) $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		--onlylibs \
-		--with-shared-libs \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-warnings \
-		--disable-cctbx \
-		--disable-clipper \
-		--disable-ssm \
-		--tmpdir="${TMPDIR}" \
-		--bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \
-		--libdir="${EPREFIX}/usr/$(get_libdir)" \
-		${GENTOO_OSNAME} || die "configure failed"
-}
-
-src_compile() {
-	emake DESTDIR="${D}" onlylib
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	emake \
-		DESTDIR="${D}" \
-		includedir="${EPREFIX}/usr/include" \
-		library_includedir="${EPREFIX}/usr/include" \
-		install
-
-	sed \
-		-e "330,1000d" \
-		-i "${S}"/include/ccp4.setup-sh || die
-
-	sed \
-		-e "378,1000d" \
-		-i "${S}"/include/ccp4.setup-csh || die
-
-	sed \
-		-e "s:-${PV/-r*/}::g" \
-		-e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \
-		-e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \
-		-e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \
-		-e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \
-		-e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
-		-e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
-		-e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \
-		-e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \
-		-e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
-		-e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
-		-e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
-		-e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
-		-e "s:^\(.*export CLIBS=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*setenv CLIBS \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*export CLIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*setenv CLIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \
-		-e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \
-		-e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \
-		-e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \
-		-e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
-		-e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
-		-e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \
-		-e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \
-		-e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \
-		-e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \
-		-e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
-		-e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
-		-e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \
-		-e "/CCP4_HELPDIR/d" \
-		-e "/IMOSFLM_VERSION/d" \
-		-i "${S}"/include/ccp4.setup* || die
-
-	# Don't check for updates on every sourcing of /etc/profile
-	sed -i \
-		-e "s:\(eval python.*\):#\1:g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Libs
-	for file in "${S}"/lib/*; do
-		if [[ -d ${file} ]]; then
-			continue
-		elif [[ -x ${file} ]]; then
-			dolib.so ${file}
-		else
-			insinto /usr/$(get_libdir)
-			doins ${file}
-		fi
-	done
-
-	prune_libtool_files
-
-	sed \
-		-e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \
-		-i "${S}"/include/ccp4.setup-sh || die
-
-	# Setup scripts
-	insinto /etc/profile.d
-	newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh
-	newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh
-	rm -f "${S}"/include/ccp4.setup*
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures}
-
-	# Environment files, setup scripts, etc.
-	rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die
-	insinto /usr/share/ccp4/
-	doins -r "${S}"/include
-
-	dodoc "${S}"/lib/data/*.doc
-	newdoc "${S}"/lib/data/README DATA-README
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this."
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r13.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r13.ebuild
deleted file mode 100644
index a5e63e29a737..000000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r13.ebuild
+++ /dev/null
@@ -1,349 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r13.ebuild,v 1.3 2014/10/12 14:46:08 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_6,2_7} )
-
-inherit autotools eutils fortran-2 gnuconfig multilib python-single-r1 toolchain-funcs
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-
-DESCRIPTION="Protein X-ray crystallography toolkit - Libraries"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
-# patch tarball from upstream
-	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
-# patches created by us
-	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
-
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	!<sci-chemistry/ccp4-6.1.3
-	!<sci-chemistry/ccp4-apps-${PV}-r10
-	app-shells/tcsh
-	dev-lang/tcl
-	>=sci-libs/cbflib-0.9.2.2
-	sci-libs/fftw:2.1
-	sci-libs/mmdb:0
-	sci-libs/monomer-db
-	sci-libs/ssm
-	virtual/jpeg
-	virtual/lapack
-	virtual/blas"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${MY_P}"
-
-MAKEOPTS+=" -j1"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	tc-export PKG_CONFIG RANLIB AR
-
-	sed \
-		-e "/^AR/s:ar:$(tc-getAR):g" \
-		-i lib/src/Makefile.in src/Makefile.in src/ccp4mapwish_/Makefile.in lib/ccif/Makefile.in || die
-
-	einfo "Applying upstream patches ..."
-	for patch in $(seq $PATCH_TOT); do
-		base="PATCH${patch}"
-		dir=$(eval echo \${${base}[0]})
-		p=$(eval echo \${${base}[1]})
-		pushd "${dir}" >& /dev/null
-		ccp_patch "${DISTDIR}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-	# fix buffer overflows wrt bug 339706
-	ccp_patch "${FILESDIR}"/${PV}-overflows.patch
-
-	# it tries to create libdir, bindir etc on live system in configure
-	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
-	# make creation of libccif.so smooth
-	ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
-
-	# lets try to build libmmdb seperatly
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
-
-	# unbundle libjpeg and cbflib
-	ccp_patch "${FILESDIR}"/${PV}-unbundle-libs-ng2.patch
-
-	# Fix missing DESTIDR
-	# not installing during build
-	ccp_patch "${FILESDIR}"/${PV}-noinstall.patch
-	sed \
-		-e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \
-		-i configure || die
-
-	# Fix upstreams code
-	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
-
-	# use pkg-config to detect BLAS/LAPACK
-	ccp_patch "${FILESDIR}"/${PV}-lapack.patch
-
-	# proto type changing in version 0.9.2.2
-	ccp_patch "${FILESDIR}"/${PV}-cbf.patch
-
-	# proto type changing in version 0.9.2.2
-	ccp_patch "${FILESDIR}"/${PV}-no-pypath.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# not needed, we have it extra
-	rm -rf src/rapper/{libxml2,gc7.0} || die
-
-	sed \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		-e 's:-Wl,-rpath,$CLIB::g' \
-		-e 's: -rpath $CLIB::g' \
-		-e 's: -I${srcdir}/include/cpp_c_headers::g' \
-		-e 's:sleep 1:sleep .2:g' \
-		-i configure || die
-
-	gnuconfig_update
-
-	for i in lib/DiffractionImage src/rapper src/pisa; do
-		pushd ${i} > /dev/null
-			sed 's:-g::g' -i configure* || die
-			eautoreconf
-		popd > /dev/null
-	done
-
-	## unbundle libssm
-	sed -e '/libdir/s:ssm::g' -i Makefile.in || die
-	find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete || die
-}
-
-src_configure() {
-	rm -rf lib/DiffractionImage/{jpg,CBFlib} || die
-
-	# Build system is broken if we set LDFLAGS
-	userldflags="${LDFLAGS}"
-	export SHARED_LIB_FLAGS="${LDFLAGS}"
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "$(tc-getFC)" = "ifort" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup || die
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure || die
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=$(tc-getFC)
-	export FOPTIM=${FFLAGS:- -O2}
-
-	export SHARE_LIB="\
-		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
-		$(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb) $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		--onlylibs \
-		--with-shared-libs \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-warnings \
-		--disable-cctbx \
-		--disable-clipper \
-		--disable-ssm \
-		--tmpdir="${TMPDIR}" \
-		--bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \
-		--libdir="${EPREFIX}/usr/$(get_libdir)" \
-		${GENTOO_OSNAME} || die "configure failed"
-}
-
-src_compile() {
-	emake DESTDIR="${D}" onlylib
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	emake \
-		DESTDIR="${D}" \
-		includedir="${EPREFIX}/usr/include" \
-		library_includedir="${EPREFIX}/usr/include" \
-		install
-
-	sed \
-		-e "330,1000d" \
-		-i "${S}"/include/ccp4.setup-sh || die
-
-	sed \
-		-e "378,1000d" \
-		-i "${S}"/include/ccp4.setup-csh || die
-
-	sed \
-		-e "s:-${PV/-r*/}::g" \
-		-e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \
-		-e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \
-		-e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \
-		-e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \
-		-e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
-		-e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
-		-e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \
-		-e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \
-		-e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
-		-e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
-		-e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
-		-e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
-		-e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \
-		-e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \
-		-e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \
-		-e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \
-		-e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
-		-e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
-		-e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \
-		-e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \
-		-e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \
-		-e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \
-		-e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
-		-e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
-		-e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \
-		-e '/CLIB=/d' \
-		-e '/CLIB /d' \
-		-e '/CLIBS=/d' \
-		-e '/CLIBS /d' \
-		-e "/alias/d" \
-		-e "/CCP4_HELPDIR/d" \
-		-e "/IMOSFLM_VERSION/d" \
-		-i "${S}"/include/ccp4.setup* || die
-
-	# Don't check for updates on every sourcing of /etc/profile
-	sed -i \
-		-e "s:\(eval python.*\):#\1:g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Libs
-	for file in "${S}"/lib/*; do
-		if [[ -d ${file} ]]; then
-			continue
-		elif [[ -x ${file} ]]; then
-			dolib.so ${file}
-		else
-			insinto /usr/$(get_libdir)
-			doins ${file}
-		fi
-	done
-
-	prune_libtool_files
-
-	sed \
-		-e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \
-		-i "${S}"/include/ccp4.setup-sh || die
-
-	# Setup scripts
-	insinto /etc/profile.d
-	newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh
-	newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh
-	rm -f "${S}"/include/ccp4.setup*
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures}
-
-	# Environment files, setup scripts, etc.
-	rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die
-	insinto /usr/share/ccp4/
-	doins -r "${S}"/include
-
-	dodoc "${S}"/lib/data/*.doc
-	newdoc "${S}"/lib/data/README DATA-README
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this."
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r14.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r14.ebuild
deleted file mode 100644
index 4cf29537697e..000000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r14.ebuild
+++ /dev/null
@@ -1,350 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r14.ebuild,v 1.2 2014/10/12 14:46:08 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_6,2_7} )
-
-inherit autotools eutils fortran-2 gnuconfig multilib python-single-r1 toolchain-funcs
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-
-DESCRIPTION="Protein X-ray crystallography toolkit - Libraries"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
-# patch tarball from upstream
-	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
-# patches created by us
-	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
-
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	!<sci-chemistry/ccp4-6.1.3
-	!<sci-chemistry/ccp4-apps-${PV}-r10
-	app-shells/tcsh
-	dev-lang/tcl
-	>=sci-libs/cbflib-0.9.2.2
-	sci-libs/fftw:2.1
-	sci-libs/mmdb:0
-	sci-libs/monomer-db
-	sci-libs/ssm
-	virtual/jpeg
-	virtual/lapack
-	virtual/blas"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${MY_P}"
-
-MAKEOPTS+=" -j1"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	tc-export PKG_CONFIG RANLIB AR
-
-	sed \
-		-e "/^AR/s:ar:$(tc-getAR):g" \
-		-i lib/src/Makefile.in src/Makefile.in src/ccp4mapwish_/Makefile.in lib/ccif/Makefile.in || die
-
-	einfo "Applying upstream patches ..."
-	for patch in $(seq $PATCH_TOT); do
-		base="PATCH${patch}"
-		dir=$(eval echo \${${base}[0]})
-		p=$(eval echo \${${base}[1]})
-		pushd "${dir}" >& /dev/null
-		ccp_patch "${DISTDIR}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-	# fix buffer overflows wrt bug 339706
-	ccp_patch "${FILESDIR}"/${PV}-overflows.patch
-
-	# it tries to create libdir, bindir etc on live system in configure
-	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# gerror_ gets defined twice on ppc if you're using gfortran/g95
-	ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
-	# make creation of libccif.so smooth
-	ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
-
-	# lets try to build libmmdb seperatly
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
-
-	# unbundle libjpeg and cbflib
-	ccp_patch "${FILESDIR}"/${PV}-unbundle-libs-ng2.patch
-
-	# Fix missing DESTIDR
-	# not installing during build
-	ccp_patch "${FILESDIR}"/${PV}-noinstall.patch
-	sed \
-		-e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \
-		-i configure || die
-
-	# Fix upstreams code
-	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
-
-	# use pkg-config to detect BLAS/LAPACK
-	ccp_patch "${FILESDIR}"/${PV}-lapack.patch
-
-	# proto type changing in version 0.9.2.2
-	ccp_patch "${FILESDIR}"/${PV}-cbf.patch
-
-	# proto type changing in version 0.9.2.2
-	ccp_patch "${FILESDIR}"/${PV}-no-pypath.patch
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# not needed, we have it extra
-	rm -rf src/rapper/{libxml2,gc7.0} || die
-
-	sed \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		-e 's:-Wl,-rpath,$CLIB::g' \
-		-e 's: -rpath $CLIB::g' \
-		-e 's: -I${srcdir}/include/cpp_c_headers::g' \
-		-e 's:sleep 1:sleep .2:g' \
-		-i configure || die
-
-	gnuconfig_update
-
-	for i in lib/DiffractionImage src/rapper src/pisa; do
-		pushd ${i} > /dev/null
-			sed 's:-g::g' -i configure* || die
-			eautoreconf
-		popd > /dev/null
-	done
-
-	## unbundle libssm
-	sed -e '/libdir/s:ssm::g' -i Makefile.in || die
-	find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete || die
-}
-
-src_configure() {
-	rm -rf lib/DiffractionImage/{jpg,CBFlib} || die
-
-	# Build system is broken if we set LDFLAGS
-	userldflags="${LDFLAGS}"
-	export SHARED_LIB_FLAGS="${LDFLAGS}"
-	unset LDFLAGS
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "$(tc-getFC)" = "ifort" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup || die
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure || die
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=$(tc-getFC)
-	export FOPTIM=${FFLAGS:- -O2}
-
-	export SHARE_LIB="\
-		$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
-		$(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb) $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		--onlylibs \
-		--with-shared-libs \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-warnings \
-		--disable-cctbx \
-		--disable-clipper \
-		--disable-ssm \
-		--tmpdir="${TMPDIR}" \
-		--bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \
-		--libdir="${EPREFIX}/usr/$(get_libdir)" \
-		${GENTOO_OSNAME} || die "configure failed"
-}
-
-src_compile() {
-	emake DESTDIR="${D}" onlylib
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	emake \
-		DESTDIR="${D}" \
-		includedir="${EPREFIX}/usr/include" \
-		library_includedir="${EPREFIX}/usr/include" \
-		install
-
-	sed \
-		-e "330,1000d" \
-		-i "${S}"/include/ccp4.setup-sh || die
-
-	sed \
-		-e "378,1000d" \
-		-i "${S}"/include/ccp4.setup-csh || die
-
-	sed \
-		-e "s:-${PV/-r*/}::g" \
-		-e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \
-		-e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \
-		-e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \
-		-e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \
-		-e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \
-		-e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
-		-e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \
-		-e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \
-		-e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \
-		-e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
-		-e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \
-		-e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \
-		-e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
-		-e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \
-		-e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \
-		-e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \
-		-e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \
-		-e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \
-		-e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
-		-e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \
-		-e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \
-		-e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \
-		-e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \
-		-e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \
-		-e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \
-		-e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
-		-e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \
-		-e "s:\$CLIB/font84.dat:\"${EPREFIX}/usr/$(get_libdir)/font84.dat\":g" \
-		-e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \
-		-e '/CLIB=/d' \
-		-e '/CLIB /d' \
-		-e '/CLIBS=/d' \
-		-e '/CLIBS /d' \
-		-e "/alias/d" \
-		-e "/CCP4_HELPDIR/d" \
-		-e "/IMOSFLM_VERSION/d" \
-		-i "${S}"/include/ccp4.setup* || die
-
-	# Don't check for updates on every sourcing of /etc/profile
-	sed -i \
-		-e "s:\(eval python.*\):#\1:g" \
-		"${S}"/include/ccp4.setup* || die
-
-	# Libs
-	for file in "${S}"/lib/*; do
-		if [[ -d ${file} ]]; then
-			continue
-		elif [[ -x ${file} ]]; then
-			dolib.so ${file}
-		else
-			insinto /usr/$(get_libdir)
-			doins ${file}
-		fi
-	done
-
-	prune_libtool_files
-
-	sed \
-		-e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \
-		-i "${S}"/include/ccp4.setup-sh || die
-
-	# Setup scripts
-	insinto /etc/profile.d
-	newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh
-	newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh
-	rm -f "${S}"/include/ccp4.setup*
-
-	# Data
-	insinto /usr/share/ccp4/data/
-	doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures}
-
-	# Environment files, setup scripts, etc.
-	rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die
-	insinto /usr/share/ccp4/
-	doins -r "${S}"/include
-
-	dodoc "${S}"/lib/data/*.doc
-	newdoc "${S}"/lib/data/README DATA-README
-}
-
-pkg_postinst() {
-	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
-	einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this."
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild
index 95be2810d6d4..a23602876a35 100644
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild
+++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild,v 1.2 2014/10/12 14:46:08 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r15.ebuild,v 1.3 2015/03/09 13:35:48 jlec Exp $
 
 EAPI=5
 
-PYTHON_COMPAT=( python{2_6,2_7} )
+PYTHON_COMPAT=( python2_7 )
 
 inherit autotools eutils fortran-2 gnuconfig multilib python-single-r1 toolchain-funcs
 
@@ -23,7 +23,7 @@ SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
 # patch tarball from upstream
 	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
 # patches created by us
-	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
+	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
 
 for i in $(seq $PATCH_TOT); do
 	NAME="PATCH${i}[1]"
@@ -49,7 +49,7 @@ RDEPEND="
 	sci-libs/mmdb:0
 	sci-libs/monomer-db
 	sci-libs/ssm
-	virtual/jpeg
+	virtual/jpeg:0=
 	virtual/lapack
 	virtual/blas"
 DEPEND="${RDEPEND}