Fix for ARP/wARP. It looked for Refmac in a location where we didn't have it, so make another symlink.

Package-Manager: portage-2.1.9.35/cvs/Linux x86_64

4 files changed, 162 insertions, 6 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index 4be8055aa360..b3b528407a98 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/refmac
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.41 2011/01/28 15:39:11 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.42 2011/01/31 21:14:39 dberkholz Exp $
+
+*refmac-5.6.0102-r1 (31 Jan 2011)
+*refmac-5.5.0110-r3 (31 Jan 2011)
+
+  31 Jan 2011; Donnie Berkholz <dberkholz@gentoo.org>;
+  +refmac-5.5.0110-r3.ebuild, +refmac-5.6.0102-r1.ebuild:
+  Fix for ARP/wARP. It looked for Refmac in a location where we didn't have it,
+  so make another symlink.
 
 *refmac-5.6.0102 (28 Jan 2011)
 
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
index 5ca3c1f8ac04..499b4efc56e8 100644
--- a/sci-chemistry/refmac/Manifest
+++ b/sci-chemistry/refmac/Manifest
@@ -27,16 +27,18 @@ DIST refmac5.6_source_v5.6.0102.tar.gz 1387462 RMD160 827f41b30609c4ade0b11ebef6
 DIST refmac_5.5.0110.tar.gz 1326832 RMD160 6613ca8b70e54e7827f8ff02b7d497560cb83e39 SHA1 ba2e38db6c88550bd901b474de881d6514b4d74e SHA256 1353fb1042586ec8fa37d0a90f274890d0ccc02377af5216200662338dfe08ca
 DIST test-framework.tar.gz 130933173 RMD160 7122539dc713615dca2ddaddfd8d152cd22624d0 SHA1 1d3e3019a67afb9b2346e919c859d402d3250fea SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605
 EBUILD refmac-5.5.0110-r2.ebuild 1882 RMD160 9090de535e3475370dd0581e80213e6e5d3169a6 SHA1 74866adf28c2695450bae403d5f38d87a07bb3a2 SHA256 a44037a5aebffd3b33067e7e764f02f7e97e4fe674f063b9eae7bae2e7722187
+EBUILD refmac-5.5.0110-r3.ebuild 1943 RMD160 2dbd47b154efbb205d5319aaba2a699dd8d571bf SHA1 19410c7fd751023c64ef0847139b3928669675a2 SHA256 94e51676c648a9e88b0a9a61b7485ec4913d7516ac5e9cf7023cfb9beacc5d57
 EBUILD refmac-5.6.0097.ebuild 1868 RMD160 0ab9127e0db43e1c51a8495f21d8654bbb61a078 SHA1 2f0ed51542001e9e697f9dd6db51c0c32dab0525 SHA256 af13cca63f2265b1e03733b6ddec12f7ab7f8d65f35bfd7b8663f5589efb65ec
 EBUILD refmac-5.6.0098.ebuild 1868 RMD160 f9fb038fcd1dc01ae5681dbd3aad03004592a3b3 SHA1 a880241edc1508f054b207744b9a2c3571992f6d SHA256 5719df2edca46720c816b57034938bdeaac11ff620f783218a6cff4bca7de6a2
 EBUILD refmac-5.6.0099.ebuild 1874 RMD160 a7341a8e09c29034d1379ca92a2ee850ad163225 SHA1 500118dd748f30ba71f85bd78878319605375b57 SHA256 271b1a3513eac2d99dc6af897ac201c04bbb3539e4dd58bb42f1b1c12eab643c
+EBUILD refmac-5.6.0102-r1.ebuild 1927 RMD160 381073c03926e0d50ee0e475c25ecd8342e67b53 SHA1 8a653fad867cf24a8d308de59aa92bf3de4fc772 SHA256 45c85c984eef6196101b4f9e92eff8fedacead89ec49a2abf379b53d1c6797dd
 EBUILD refmac-5.6.0102.ebuild 1868 RMD160 480e226aa98f582ce692bab41d927cbfde830670 SHA1 8ae6e7946f62e0831111c84264953337dcaef75e SHA256 22e97a1e18982dc65118833101dedbcad9f1d5382d14cb9d94c12f96b8181b15
-MISC ChangeLog 7204 RMD160 21adccb54544f62a8bd1b57bbf752486d533ac88 SHA1 a12504c43ee3164987c6e5c2226c958c0111732b SHA256 efd098ca333be28e1d735d24644a866e2ab10d9fd515f34eb67582e4c27cfa31
+MISC ChangeLog 7499 RMD160 e6ecfc0a1125df24d5bc03ca65f91dc61d3a6e46 SHA1 14c281669e4fc9308517c207feff5bdbc1cd8f91 SHA256 da8017c9c7e9b261890bbc3b9338d8dad268495bea269d812e75bb40838a9277
 MISC metadata.xml 311 RMD160 df83b13d491a71b729455b664088d89ddbde1c8c SHA1 fffd2a5645181aa12ac9b6f74da9a011cdcf1b97 SHA256 782521c7e16d7eec82d7b7e7c43102806e7f72bc7366401808b1e1ac6e26045a
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.16 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
 
-iEYEARECAAYFAk1C4yQACgkQgAnW8HDreRaG4gCeKdYsEGxe1t9+dIZmM6vJZRaC
-gKgAnRqCJO71f3aIm5IPpM4h0BNiqKPZ
-=EtE3
+iEYEARECAAYFAk1HJnAACgkQXVaO67S1rttDOQCffNFx7eho1yZhXCIMTR7LiJuS
+6lwAnigDdKv56whzSKXft5rB4duXDazA
+=KJaH
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild
new file mode 100644
index 000000000000..683dcf8cb2a7
--- /dev/null
+++ b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild,v 1.1 2011/01/31 21:14:39 dberkholz Exp $
+
+EAPI="2"
+
+inherit base toolchain-funcs versionator
+
+DESCRIPTION="Macromolecular crystallographic refinement program"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac"
+SRC_URI="
+	${HOMEPAGE}/data/refmac_stable/refmac_${PV}.tar.gz
+	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
+
+SLOT="0"
+LICENSE="ccp4"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+	sci-chemistry/makecif
+	>=sci-libs/ccp4-libs-6.1.3-r7
+	sci-libs/mmdb
+	<sci-libs/monomer-db-1
+	virtual/blas
+	virtual/lapack"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-allow-dynamic-linking.patch
+	)
+
+src_prepare() {
+	base_src_prepare
+	use test && epatch "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch
+}
+
+src_compile() {
+	emake \
+		FC=$(tc-getFC) \
+		CC=$(tc-getCC) \
+		CXX=$(tc-getCXX) \
+		COPTIM="${CFLAGS}" \
+		FOPTIM="${FFLAGS:- -O2}" \
+		VERSION="" \
+		XFFLAGS="-fno-second-underscore" \
+		LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \
+		LLIBLAPACK="$(pkg-config --libs lapack blas)" \
+		${PN} libcheck || die
+}
+
+src_test() {
+	einfo "Starting tests ..."
+	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
+	export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}"
+	export CCP4_TEST="${WORKDIR}"/test-framework
+	export CCP4_SCR="${T}"
+	ln -sf refmac "${S}"/refmac5
+	sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb
+	ccp4-run-thorough-tests -v test_refmac5 || die
+}
+
+src_install() {
+	exeinto /usr/libexec/ccp4/bin/
+	doexe ${PN} || die
+	dosym refmac /usr/libexec/ccp4/bin/refmac5 || die
+	dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} || die
+	dosym refmac /usr/bin/refmac5 || die
+	dodoc refmac_keywords.pdf bugs_and_features.pdf || die
+}
diff --git a/sci-chemistry/refmac/refmac-5.6.0102-r1.ebuild b/sci-chemistry/refmac/refmac-5.6.0102-r1.ebuild
new file mode 100644
index 000000000000..8415ebd6e428
--- /dev/null
+++ b/sci-chemistry/refmac/refmac-5.6.0102-r1.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0102-r1.ebuild,v 1.1 2011/01/31 21:14:39 dberkholz Exp $
+
+EAPI="2"
+
+inherit base toolchain-funcs versionator
+
+MY_PV="$(get_version_component_range 1-2)_source_v${PV}"
+
+DESCRIPTION="Macromolecular crystallographic refinement program"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac"
+SRC_URI="
+	${HOMEPAGE}/data/refmac_experimental/${PN}${MY_PV}.tar.gz
+	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
+
+SLOT="0"
+LICENSE="ccp4"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+	>=sci-libs/ccp4-libs-6.1.3-r7
+	sci-libs/mmdb
+	>sci-libs/monomer-db-1
+	virtual/blas
+	virtual/lapack"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-allow-dynamic-linking.patch
+	)
+
+src_prepare() {
+	base_src_prepare
+	use test && epatch "${FILESDIR}"/5.5-test.log.patch
+}
+
+src_compile() {
+	emake \
+		FC=$(tc-getFC) \
+		CC=$(tc-getCC) \
+		CXX=$(tc-getCXX) \
+		COPTIM="${CFLAGS}" \
+		FOPTIM="${FFLAGS:- -O2}" \
+		VERSION="" \
+		XFFLAGS="-fno-second-underscore" \
+		LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \
+		LLIBLAPACK="$(pkg-config --libs lapack blas)" \
+		|| die
+}
+
+src_test() {
+	einfo "Starting tests ..."
+	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
+	export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}"
+	export CCP4_TEST="${WORKDIR}"/test-framework
+	export CCP4_SCR="${T}"
+	ln -sf refmac "${S}"/refmac5
+	sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb
+	ccp4-run-thorough-tests -v test_refmac5 || die
+}
+
+src_install() {
+	for i in refmac libcheck FreeTwin header2matr; do
+		exeinto /usr/libexec/ccp4/bin/
+		doexe ${i} || die
+		dosym ../libexec/ccp4/bin/${i} /usr/bin/${i}
+	done
+	dosym refmac /usr/bin/refmac5 || die
+	dosym refmac /usr/libexec/ccp4/bin/refmac5 || die
+}