Unbundle sci-libs/ssm

Package-Manager: portage-2.2.0_alpha45/cvs/Linux x86_64

7 files changed, 171 insertions, 435 deletions

diff --git a/sci-chemistry/ccp4-apps/ChangeLog b/sci-chemistry/ccp4-apps/ChangeLog
index c4e298a446bf..9c7a26b9e5e3 100644
--- a/sci-chemistry/ccp4-apps/ChangeLog
+++ b/sci-chemistry/ccp4-apps/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/ccp4-apps
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.27 2011/06/21 16:07:38 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.28 2011/07/16 12:43:00 jlec Exp $
+
+*ccp4-apps-6.1.3-r10 (16 Jul 2011)
+
+  16 Jul 2011; Justin Lecher <jlec@gentoo.org> +files/6.1.3-unbundle.patch,
+  -ccp4-apps-6.1.3-r7.ebuild, -ccp4-apps-6.1.3-r8.ebuild,
+  ccp4-apps-6.1.3-r9.ebuild, +ccp4-apps-6.1.3-r10.ebuild, metadata.xml:
+  Unbundle sci-libs/ssm
 
   21 Jun 2011; Justin Lecher <jlec@gentoo.org> ccp4-apps-6.1.3-r7.ebuild,
   ccp4-apps-6.1.3-r8.ebuild, ccp4-apps-6.1.3-r9.ebuild:
diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest
index 47d9d2dd772f..f27df6535ef6 100644
--- a/sci-chemistry/ccp4-apps/Manifest
+++ b/sci-chemistry/ccp4-apps/Manifest
@@ -1,5 +1,5 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA512
 
 AUX 6.1.3-clipper-template.patch 2619 RMD160 a3a4998365c4e516325cf95472e8493729ee4b46 SHA1 f3d92469ac5ec4483818abbf50c32ac9b05a622c SHA256 a185a93f76c23ce06256866cfaf0e9854a5702b95a1e49e4d3a5f732e0d1e2a3
 AUX 6.1.3-dont-build-balbes.patch 489 RMD160 7ee9ad48afcd6dd261277321be681bb41ce73fbb SHA1 56f045d3ec8dbf4e0c83dc9df2ac478bd4c5268c SHA256 dfe1b810fb07bf536528b9c955e3162dc470a803513ae6fa69848ed6d64503c4
@@ -16,17 +16,17 @@ AUX 6.1.3-lapack.patch 21635 RMD160 a1243e5a7fb1f9982171b8362b764ccbd1799747 SHA
 AUX 6.1.3-pisa.patch 714 RMD160 9923901ec82dc0c7cd2a13f1eb6362a11576abd8 SHA1 8d7e0b730b9969d2d59a6b9441b7c3709b397e16 SHA256 42a581d2a9747239c1b129dbeffc76a2532de320629dd58112a42ffde669bf12
 AUX 6.1.3-pythonpath.patch 2716 RMD160 f46963e6c4c48cfab76062aaff8d58189f9d590b SHA1 24f6c9a051f97d9e5db5c4fb9ef457114fa7a951 SHA256 41ca8ed3fc1701caa18b30f44af7475d49fc0042ee058bae3d8c8617a6d9bcc2
 AUX 6.1.3-rename-rapper-ng.patch 2241 RMD160 63cda7686f10316f2a9d0a12346de9d41c95d6cc SHA1 a08d3176e8939619893d1007685dda9be5fc78be SHA256 7a476133860463b91b39189aa5628607f0404224cae1273b4da1c500a845dfdb
+AUX 6.1.3-unbundle.patch 5736 RMD160 5e1416c26a6ddb61f5d3aaa7a5d199dfdc6112ba SHA1 985e5e84d01329d7671a63d030337d77cc7a4bb7 SHA256 1d50917bdd3733d099cf64df651c8743ab40ce1ea19416bfacf806e324b2bea2
 DIST 6.1.3-oasis4.0.patch.bz2 946 RMD160 b448376114ba41e6999d533929fdb79812476f87 SHA1 7667aca14d28cec01bfa7d2eee9cbce11624f4fa SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b
 DIST ccp4-6.1.3-core-src.tar.gz 242134076 RMD160 e9b7deb0766fb95d5e8946881f20e086f0896fe9 SHA1 ee5ada892694db5dc9b2d7d2330b4ac694f56580 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324
-EBUILD ccp4-apps-6.1.3-r7.ebuild 10287 RMD160 bf54169c4f5960b10e2be1f1b61ae371f149f004 SHA1 fb1b291564ed7b23432206b16f553e58fbaad66d SHA256 73351df4bd762e713527d45423c0e0311a34487c4829f91e40b6c8e9141a87c3
-EBUILD ccp4-apps-6.1.3-r8.ebuild 10003 RMD160 2b9e756bf2dd5f9fe0877ac574fc2ca24cc282c1 SHA1 42932d20c0d3eb5e2ad32ba195548a0ca38c6c3a SHA256 b45f9ea152606c528ee14ca6b137dd3ee73d2986dd9407ade27a4810b7dc31a9
-EBUILD ccp4-apps-6.1.3-r9.ebuild 10087 RMD160 392d37a3975d7cac8250686769fe601c6e625b0f SHA1 6012d9ff8d775250f4e3bc59616c137e34269ccd SHA256 4eb6bd77101c7c83c8e9174328590bf986f51df2a17e36f2946d21bc279ad99b
-MISC ChangeLog 5286 RMD160 a176b4c3456e60217e2cfbe7ca7aad4c401361d4 SHA1 74e728ca135c7e34239f923bf737f8cbcb1015d3 SHA256 84ed6cff064566c817ce634a496dfb2ea70497da06af20aab59a0b5cbd1a6db0
-MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
+EBUILD ccp4-apps-6.1.3-r10.ebuild 9901 RMD160 33d2e6a143b7e1a7b59b57eb690252d8ad974909 SHA1 c4b60d500bd47d59d11f7f3a5710b3ba71475aee SHA256 d94ba5362cbf20b5fd2fb75233abc649db95769df408152a00b3cb4afc804625
+EBUILD ccp4-apps-6.1.3-r9.ebuild 9726 RMD160 bd75bc08053d5338286cd30ce63e15657698206b SHA1 8c5f6aad01c4ec3453f6966f4f2f6981cd1f65cc SHA256 a6c8fa348c4cd489e6ed759ceef749bae9259e10c7e8c0b9a5ba0e69c7e149be
+MISC ChangeLog 5553 RMD160 fa39d23f67b98f18ce7faf1225f96a640bcdf885 SHA1 35db0de08c74289aa7b93728a4d0a93ab39d0747 SHA256 47d8751c70a25b2dd2013644a12bfd4b490800258ce784a2fd3cc3e8089c56ff
+MISC metadata.xml 167 RMD160 ea4003a55d6e2079381a540c441fc59cde29025a SHA1 3bc6dc4dd68f7de22828138e62aa117387b1765d SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8
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-8XYAnAoDqyjz6vuGvEPGkmWP7NAs0vsh
-=bUg1
+iEYEAREKAAYFAk4hh1oACgkQgAnW8HDreRY/ZACgwxyVra43iHSs7kZgBiDg2xkM
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diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r8.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r10.ebuild
index c12d5892bf42..0d2f9fd07f05 100644
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r8.ebuild
+++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r10.ebuild
@@ -1,8 +1,8 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r8.ebuild,v 1.6 2011/06/21 16:07:38 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r10.ebuild,v 1.1 2011/07/16 12:43:00 jlec Exp $
 
-EAPI="3"
+EAPI=3
 
 PYTHON_DEPEND="2"
 
@@ -10,26 +10,14 @@ inherit autotools eutils fortran-2 flag-o-matic gnuconfig python toolchain-funcs
 
 MY_P="${PN/-apps}-${PV}"
 
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
 #UPDATE="04_03_09"
 #PATCHDATE="090511"
 
 PATCH_TOT="0"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-#PATCH1=( src/topp_
-#topp.f-r1.16.2.5-r1.16.2.6.diff )
-#PATCH2=( .
-#configure-r1.372.2.18-r1.372.2.19.diff )
 
 DESCRIPTION="Protein X-ray crystallography toolkit"
 HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
 SRC_URI="
 	${SRC}/${PV}/${MY_P}-core-src.tar.gz
 	http://dev.gentooexperimental.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2"
@@ -46,7 +34,7 @@ done
 
 LICENSE="ccp4"
 SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="examples X"
 
 X11DEPS="
@@ -71,6 +59,7 @@ SCILIBS="
 	sci-libs/clipper
 	sci-libs/fftw:2.1
 	sci-libs/mmdb
+	sci-libs/ssm
 	virtual/blas
 	virtual/lapack"
 
@@ -101,6 +90,8 @@ DEPEND="${RDEPEND}
 	)"
 PDEPEND="${SCIAPPS}"
 
+RESTRICT="mirror"
+
 S="${WORKDIR}/${MY_P}"
 
 pkg_setup() {
@@ -158,13 +149,21 @@ src_prepare() {
 	# Not renaming, but unbundling libs
 	ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch
 
+	# Use pkg-config to detect BLAS/LAPCK
+	ccp_patch "${FILESDIR}"/${PV}-lapack.patch
+
 	# Update things for oasis 4 usage
 	epatch "${WORKDIR}"/${PV}-oasis4.0.patch
 	sed 's: oasis : :g' -i src/Makefile.in || die
 
+	# unbundle libs
+	ccp_patch "${FILESDIR}"/${PV}-unbundle.patch
+
 	einfo "Done." # done applying Gentoo patches
 	echo
 
+	find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete
+
 	sed \
 		-e "s:/usr:${EPREFIX}/usr:g" \
 		-e 's:-Wl,-rpath,$CLIB::g' \
@@ -177,7 +176,7 @@ src_prepare() {
 		-exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \;
 
 	# Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version
-	sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure
+	sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die
 
 	# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
 	pushd src/rapper 2>/dev/null
@@ -258,6 +257,7 @@ src_configure() {
 		--disable-phaser \
 		--disable-diffractionImg \
 		--disable-clipper \
+		--disable-ssm \
 		--disable-mosflm \
 		--disable-mrbump \
 		--tmpdir="${TMPDIR}" \
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r7.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r7.ebuild
deleted file mode 100644
index 01a8ea4db73e..000000000000
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r7.ebuild
+++ /dev/null
@@ -1,392 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r7.ebuild,v 1.4 2011/06/21 16:07:38 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2"
-
-inherit autotools eutils fortran-2 flag-o-matic gnuconfig python toolchain-funcs
-
-MY_P="${PN/-apps}-${PV}"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-PATCH_TOT="0"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-#PATCH1=( src/topp_
-#topp.f-r1.16.2.5-r1.16.2.6.diff )
-#PATCH2=( .
-#configure-r1.372.2.18-r1.372.2.19.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-SRC_URI="
-	${SRC}/${PV}/${MY_P}-core-src.tar.gz
-	http://dev.gentooexperimental.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2"
-# patch tarball from upstream
-	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
-# patches created by us
-	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
-
-for i in $(seq $PATCH_TOT); do
-	NAME="PATCH${i}[1]"
-	SRC_URI="${SRC_URI}
-		${SRC}/${PV}/patches/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples X"
-
-X11DEPS="
-	x11-libs/libX11
-	x11-libs/libXaw
-	x11-libs/libXt
-	x11-libs/libxdl_view"
-
-TKDEPS="
-	>=dev-lang/tk-8.3
-	>=dev-tcltk/blt-2.4
-	dev-tcltk/iwidgets
-	dev-tcltk/itcl
-	dev-tcltk/itk
-	>=dev-tcltk/tdom-0.8
-	dev-tcltk/tkimg
-	dev-tcltk/tktreectrl"
-
-SCILIBS="
-	~sci-libs/ccp4-libs-${PV}
-	>=sci-libs/ccp4-libs-${PVR}
-	sci-libs/clipper
-	sci-libs/fftw:2.1
-	sci-libs/mmdb
-	virtual/blas
-	virtual/lapack"
-
-SCIAPPS="
-	sci-chemistry/pdb-extract
-	sci-chemistry/pymol
-	sci-chemistry/rasmol
-	>=sci-chemistry/oasis-4.0-r1"
-
-RDEPEND="
-	${TKDEPS}
-	${SCILIBS}
-	app-shells/tcsh
-	dev-python/pyxml
-	dev-libs/libxml2:2
-	dev-libs/libjwc_c
-	dev-libs/libjwc_f
-	dev-libs/boehm-gc
-	virtual/fortran
-	!app-office/sc
-	!<sci-chemistry/ccp4-6.1.3
-	X? ( ${X11DEPS} )"
-DEPEND="${RDEPEND}
-	X? (
-		x11-misc/imake
-		x11-proto/inputproto
-		x11-proto/xextproto
-	)"
-PDEPEND="${SCIAPPS}"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python_set_active_version 2
-}
-
-src_prepare() {
-	einfo "Applying upstream patches ..."
-	for patch in $(seq $PATCH_TOT); do
-		base="PATCH${patch}"
-		dir=$(eval echo \${${base}[0]})
-		p=$(eval echo \${${base}[1]})
-		pushd "${dir}" >& /dev/null
-		ccp_patch "${DISTDIR}/${p}"
-		popd >& /dev/null
-	done
-	einfo "Done."
-	echo
-
-	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
-	einfo "Applying Gentoo patches ..."
-
-	# it tries to create libdir, bindir etc on live system in configure
-	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
-	# We already have sci-chemistry/rasmol
-	# Also remember to create the bindir.
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch
-
-	# libraries come from sci-libs/ccp4-libs
-	ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
-
-	# coreutils fortran-2 installs a binary called truncate
-#	ccp_patch "${FILESDIR}"/${PV}-rename-truncate.patch
-#	mv ./doc/truncate.doc ./doc/ftruncate.doc || die
-#	mv ./html/truncate.html ./html/ftruncate.html || die
-
-	# conflicts with media-libs/raptor
-#	ccp_patch "${FILESDIR}"/${PV}-rename-rapper.patch
-#	mv ./doc/rapper.doc ./doc/rappermc.doc || die
-#	mv ./html/rapper.html ./html/rappermc.html || die
-
-	# We have seperate ebuilds for those
-	for bin in molref xia scala imosflm balbes; do
-		ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch
-	done
-
-	# don't configure what is not build
-	ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-pisa.patch
-
-	# Set python paths correctly
-	ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch
-
-	# Fix upstreams code
-	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
-
-	# Update things for oasis 4 usage
-	epatch "${WORKDIR}"/${PV}-oasis4.0.patch
-	sed 's: oasis : :g' -i src/Makefile.in || die
-
-	einfo "Done." # done applying Gentoo patches
-	echo
-
-	# Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version
-	sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure
-
-	# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
-	pushd src/rapper 2>/dev/null
-	sed -i \
-		-e '/^AC_CONFIG_SUBDIRS(\[gc7.0 libxml2\])/d' \
-		configure.ac
-	sed -i \
-		-e '/^SUBDIRS/s:libxml2 gc7.0::g' \
-		Makefile.am
-	sed -i \
-		-e '/^rapper_LDADD/s:../gc7.0/libgc.la ../libxml2/libxml2.la:-lgc -lxml2:g' \
-		LOOP/Makefile.am
-	sed -i \
-		-e "/^INCLUDES/s:-I../gc7.0/include -I../libxml2/include:-I${EPREFIX}/usr/include/gc -I${EPREFIX}/usr/include/libxml2:g" \
-		LOOP/Makefile.am
-	eautoreconf
-	popd 2>/dev/null
-
-	gnuconfig_update
-
-	python_convert_shebangs $(python_get_version) src/ccp4_pipeline_simple.py ./share/smartie/*.py
-}
-
-src_configure() {
-	# Build system is broken if we set LDFLAGS
-	unset LDFLAGS
-
-	# These are broken with ./src/procheck/ps.f
-	filter-flags "-floop-*"
-
-	# GENTOO_OSNAME can be one of:
-	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
-	# linux_compaq_compilers linux_intel_compilers generic Darwin
-	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
-	if [[ "$(tc-getFC)" = "ifort" ]]; then
-		if use ia64; then
-			GENTOO_OSNAME="ia64_linux_intel"
-		else
-			# Should be valid for x86, maybe amd64
-			GENTOO_OSNAME="linux_intel_compilers"
-		fi
-	else
-		# Should be valid for x86 and amd64, at least
-		GENTOO_OSNAME="linux"
-	fi
-
-	# Sets up env
-	ln -s \
-		ccp4.setup-bash \
-		"${S}"/include/ccp4.setup
-
-	# We agree to the license by emerging this, set in LICENSE
-	sed -i \
-		-e "s~^\(^agreed=\).*~\1yes~g" \
-		"${S}"/configure
-
-	# Fix up variables -- need to reset CCP4_MASTER at install-time
-	sed -i \
-		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
-		-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
-		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
-		"${S}"/include/ccp4.setup*
-
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	export CC=$(tc-getCC)
-	export CXX=$(tc-getCXX)
-	export COPTIM=${CFLAGS}
-	export CXXOPTIM=${CXXFLAGS}
-	# Default to -O2 if FFLAGS is unset
-	export FC=$(tc-getFC)
-	export FOPTIM=${FFLAGS:- -O2}
-	export BINSORT_SCR="${T}"
-	export CCP4_MASTER="${WORKDIR}"
-	export CCP4I_TCLTK="${EPREFIX}/usr/bin"
-
-	# Can't use econf, configure rejects unknown options like --prefix
-	./configure \
-		$(use_enable X x) \
-		--with-shared-libs \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-warnings \
-		--disable-pdb_extract \
-		--disable-cctbx \
-		--disable-phaser \
-		--disable-diffractionImg \
-		--disable-clipper \
-		--disable-mosflm \
-		--disable-mrbump \
-		--tmpdir="${TMPDIR}" \
-		${GENTOO_OSNAME} || die "econf failed"
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-	econf \
-		--prefix="${S}" \
-		--bindir="${ED}"/usr/libexec/ccp4/bin \
-		--with-ccp4="${S}" \
-		--with-clipper="${EPREFIX}/usr" \
-		--with-fftw="${EPREFIX}/usr" \
-		--with-mmdb="${EPREFIX}/usr" \
-		CXX=$(tc-getCXX)
-	popd 2>/dev/null
-}
-
-src_compile() {
-	# fsplit is required for the programs
-	pushd lib/src 2>/dev/null
-		emake fsplit -j1 || die
-	popd 2>/dev/null
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd src/clipper_progs 2>/dev/null
-		emake || die
-	popd 2>/dev/null
-
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	# Set up variables for build
-	source "${S}"/include/ccp4.setup-sh
-
-	# if we don't make this, a ton of programs fail to install
-	mkdir "${S}"/bin || die
-
-	# We do this manually, since disabling the clipper libraries also
-	# disables the clipper programs
-	pushd "${S}"/src/clipper_progs 2>/dev/null
-		emake install || die
-	popd 2>/dev/null
-
-	einstall || die "install failed"
-
-	# Collision with sci-chemistry/mrbump
-	rm -f "${S}"/bin/{mrbump,pydbviewer} || die
-
-	# Bins
-	exeinto /usr/libexec/ccp4/bin/
-	doexe "${S}"/bin/* || die
-
-	# Libs
-	for file in "${S}"/lib/*; do
-		if [[ -d ${file} ]]; then
-			continue
-		elif [[ -x ${file} ]]; then
-			dolib.so ${file} || die
-		else
-			insinto /usr/$(get_libdir)
-			doins ${file} || die
-		fi
-	done
-
-	rm -f "${S}"/include/ccp4.setup*
-
-	# smartie -- log parsing
-	insinto /usr/share/ccp4
-	doins -r "${S}"/share/smartie || die
-
-	# Install docs and examples
-	doman "${S}"/man/cat1/*
-
-	mv "${S}"/manual/README "${S}"/manual/README-manual
-	dodoc manual/* README CHANGES doc/* examples/README || die
-
-	rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.*
-	rm "${ED}"/usr/share/doc/${PF}/COPYING.*
-
-	dohtml -r "${S}"/html/*
-
-	if use examples; then
-		for i in data rnase toxd; do
-			docinto examples/${i}
-			dodoc "${S}"/examples/${i}/*
-		done
-
-		docinto examples/tutorial
-		dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css
-		for i in data results; do
-			docinto examples/tutorial/${i}
-			dodoc "${S}"/examples/tutorial/${i}/*
-		done
-
-		for i in non-runnable runnable; do
-			docinto examples/unix/${i}
-			dodoc "${S}"/examples/unix/${i}/*
-		done
-	fi
-	# Needed for ccp4i docs to work
-	dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die
-
-	# Fix overlaps with other packages
-	rm -f "${ED}"/usr/share/man/man1/rasmol.1* "${ED}"/usr/lib/font84.dat || die
-	mv "${ED}"/usr/share/man/man1/truncate{,-ccp4}.1 || die
-	mv "${ED}"/usr/share/man/man1/rapper{,-ccp4}.1 || die
-	mv "${ED}"/usr/share/man/man1/sc{,-ccp4}.1 || die
-
-	cat >> "${T}"/baubles <<- EOF
-	#!${EPREFIX}/bin/bash
-	exec $(PYTHON) \${CCP4}/share/ccp4/smartie/baubles.py
-	EOF
-
-	exeinto /usr/libexec/ccp4/bin/
-	doexe "${T}"/baubles || die
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
-	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r9.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r9.ebuild
index 41c9dad4ef92..3e9ae79f701e 100644
--- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r9.ebuild
+++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r9.ebuild
@@ -1,8 +1,8 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r9.ebuild,v 1.4 2011/06/21 16:07:38 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r9.ebuild,v 1.5 2011/07/16 12:43:00 jlec Exp $
 
-EAPI="3"
+EAPI=3
 
 PYTHON_DEPEND="2"
 
@@ -10,26 +10,14 @@ inherit autotools eutils fortran-2 flag-o-matic gnuconfig python toolchain-funcs
 
 MY_P="${PN/-apps}-${PV}"
 
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
 #UPDATE="04_03_09"
 #PATCHDATE="090511"
 
 PATCH_TOT="0"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-#PATCH1=( src/topp_
-#topp.f-r1.16.2.5-r1.16.2.6.diff )
-#PATCH2=( .
-#configure-r1.372.2.18-r1.372.2.19.diff )
 
 DESCRIPTION="Protein X-ray crystallography toolkit"
 HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
 SRC_URI="
 	${SRC}/${PV}/${MY_P}-core-src.tar.gz
 	http://dev.gentooexperimental.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2"
@@ -101,6 +89,8 @@ DEPEND="${RDEPEND}
 	)"
 PDEPEND="${SCIAPPS}"
 
+RESTRICT="mirror"
+
 S="${WORKDIR}/${MY_P}"
 
 pkg_setup() {
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch
new file mode 100644
index 000000000000..107cfd740238
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch
@@ -0,0 +1,131 @@
+ src/Makefile.in       |   14 +++++-----
+ src/pisa/configure.ac |   67 +++++++++----------------------------------------
+ 2 files changed, 19 insertions(+), 62 deletions(-)
+
+diff --git a/src/Makefile.in b/src/Makefile.in
+index 70781f3..b11db04 100755
+--- a/src/Makefile.in
++++ b/src/Makefile.in
+@@ -778,8 +778,8 @@ chainsaw : $(chainsawobjs)
+ 	eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o chainsaw $(chainsawobjs) $(LDCXXFLAGS)
+ pdbcur.o pcur_funcs.o ncont.o coord_format.o pdb_merge.o chainsaw.o: # dependencies at end
+ 	@$(SETFLAGS) xxx=1 ; \
+-	echo $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; 
+-	eval $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp
++	echo $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; 
++	eval $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp
+ 
+ ### bp3, afro, gcx
+ 
+@@ -813,8 +813,8 @@ gcx : libbp3 $(gcxobjs)
+ 
+ $(libbp3objs) $(bp3objs) $(afroobjs) $(gcxobjs) : # dependencies at end
+ 	@$(SETFLAGS) xxx=1 ; \
+-	echo $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \
+-	eval $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C
++	echo $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \
++	eval $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C
+ 
+ ### crunch2 pmf
+ 
+@@ -853,7 +853,7 @@ cif2xml : $(cif2xmlobjs)
+ cross_validate : $(cross_validateobjs)
+ 	@$(SETFLAGS); rm -f cross_validate; eval $(CXX) $${harvest_app_FLAGS-"$(CXXFLAGS)"} -o cross_validate $(cross_validateobjs) $(LDCXXFLAGS)
+ cif2xml.o cross_validate.o : # dependencies at end
+-	@$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) -I$(incdir)/mmdb $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp
++	@$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp
+ 
+ pdb_extractdir = $(srcdir)/harvest_app_/pdb_extract
+ pdb_extract_suite :
+@@ -873,8 +873,8 @@ $(dev_tools_ctargets) :
+ $(dev_tools_cxxtargets) :
+ 	@$(SETFLAGS) xxx=1; \
+ 	  rm -f $@; \
+-	  echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) ;\
+-	  eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS)
++	  echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) ;\
++	  eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS)
+ 
+ ### mlphare
+ mlphare:
+diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac
+index 81afdda..044b6f8 100755
+--- a/src/pisa/configure.ac
++++ b/src/pisa/configure.ac
+@@ -31,64 +31,21 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
+ # test for function in m
+ AC_CHECK_LIB([m], [sqrt])
+ 
+-dnl Optional: Check for MMDB.
+-AM_PATH_MMDB(,
+-  [ if test "x$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 $MMDB_CXXFLAGS])
+-      fi
+-    else
+-     AC_MSG_ERROR([mmdb not found])
+-    fi
+-  ]
+-)
++PKG_CHECK_MODULES([MMDB],[mmdb])
++PKG_CHECK_MODULES([SSM],[ssm])
++
++MMDB_CXXFLAGS=${MMDB_CFLAGS}
++
++AC_SUBST([MMDB_CFLAGS])
++AC_SUBST([MMDB_CXXFLAGS])
++AC_SUBST([SSM_CFLAGS])
++
++AC_SUBST([MMDB_LIBS])
++AC_SUBST([SSM_LIBS])
+ 
+-ac_saved_CXXFLAGS=$CXXFLAGS
+-ac_saved_LIBS=$LIBS
+ CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS"
+ LIBS="$MMDB_LIBS $LIBS"
+-AM_PATH_SSM(,
+-  [ if test "x$ssm_prefix" != x ; then
+-      if test "x$ac_SSM_CXXFLAGS" != x && test "x$ac_SSM_LDOPTS" = x ; then 
+-        case "$ac_SSM_CXXFLAGS" in
+-        *lib/ssm )
+-        ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#lib/ssm#lib#g`
+-        ;;
+-        *include/ssm )
+-        ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#include/ssm#lib#g`
+-        ;;
+-        *)
+-        esac
+-        SSM_CXXFLAGS="$ac_SSM_CXXFLAGS"
+-        SSM_LIBS=`echo "$ac_SSM_LDOPTS -lssm" | sed s#-I#-L#`
+-        AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS])
+-      else
+-        SSM_CXXFLAGS="-I$ssm_prefix/include/ssm -I$ssm_prefix/lib/ssm"
+-        SSM_LIBS="-L$ssm_prefix/lib -L$ssm_prefix/lib/ssm -lssm"
+-        AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS])
+-      fi
+-    else
+-     AC_MSG_ERROR([ssm not found])
+-    fi
+-  ]
+-)
+-CXXFLAGS=$ac_saved_CXXFLAGS
+-LIBS=$ac_saved_LIBS
++
+ 
+ # Checks for typedefs, structures, and compiler characteristics.
+ #
diff --git a/sci-chemistry/ccp4-apps/metadata.xml b/sci-chemistry/ccp4-apps/metadata.xml
index 9ac9ffdb3a41..e42d0af60f42 100644
--- a/sci-chemistry/ccp4-apps/metadata.xml
+++ b/sci-chemistry/ccp4-apps/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-chemistry</herd>
+	<herd>sci-chemistry</herd>
 </pkgmetadata>