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

(Portage version: 2.1.9.35/cvs/Linux x86_64)

3 files changed, 155 insertions, 1 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/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
+}