refmac: bump to 5.6.0069, experimental version.

6 files changed, 178 insertions, 0 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
new file mode 100644
index 0000000..6383d68
--- /dev/null
+++ b/sci-chemistry/refmac/ChangeLog
@@ -0,0 +1,18 @@
+# ChangeLog for sci-chemistry/refmac
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.3 2010/03/28 20:43:07 jlec Exp $
+
+  28 Mar 2010; Justin Lecher <jlec@gentoo.org> refmac-5.5.0109.ebuild:
+  Keyworded for ~x86-linux ~amd64-linux
+
+  14 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  refmac-5.5.0109.ebuild:
+  Corrected wrong naming of patch
+
+*refmac-5.5.0109 (02 Feb 2010)
+
+  02 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/5.5-allow-dynamic-linking.patch, +files/5.5-test.log.patch,
+  +refmac-5.5.0109.ebuild, +metadata.xml:
+  refmac splitted from ccp4 package
+
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
new file mode 100644
index 0000000..8ac6901
--- /dev/null
+++ b/sci-chemistry/refmac/Manifest
@@ -0,0 +1,7 @@
+AUX 5.6-allow-dynamic-linking.patch 1388 RMD160 80c5e2e9782e6494f80e7e4eed371aca79495530 SHA1 5951076662541f8bf8aee968da7c24fb4c30c21d SHA256 dfc6ae10d515d30ded38f78a6dbf0f6b907db5afbc3880c4b8099630b8fa674d
+AUX 5.6-test.log.patch 1146 RMD160 0ea6293e8ecde3b9ae12658a523e3c30a5c9f01b SHA1 d026fdea6a487754f7e48ec24bcf4851a613b6d1 SHA256 d2c2a09f44e525dc255bc2ac93ca4194b24ca1fe58c31f0e3b5c32e439dfe2e7
+DIST refmac5.6_source_v5.6.0069.tar.gz 1279124 RMD160 31b30844e134516a3ec1ce470399737f578d7a8f SHA1 01abede2d3004b430b3ac2a8f66bc9d973dcadaa SHA256 d6715c5d4571db806a2efddf5b89fff2515fcc8ee27338f38cf058eafc0f6403
+DIST test-framework.tar.gz 130933173 RMD160 7122539dc713615dca2ddaddfd8d152cd22624d0 SHA1 1d3e3019a67afb9b2346e919c859d402d3250fea SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605
+EBUILD refmac-5.6.0069.ebuild 1727 RMD160 1ccbed25be1676e6a06a546380b5f445cfcba114 SHA1 7dcbce5d2111a3d9115c003f5a8792236cc5eb0f SHA256 bd3bc07a164982c06be6473678b236281864647ad143f2e1ec21ef4f1247579c
+MISC ChangeLog 672 RMD160 debf5af13a4e8043ee87f5eec0ab8f350a9fe1da SHA1 acbd171de3cac9a91f421e21b3c51232d79f1d07 SHA256 f7e742ebab04dc7592ee15c5536fc360fd7da72ba695ac8116fe3c686b72ab13
+MISC metadata.xml 311 RMD160 df83b13d491a71b729455b664088d89ddbde1c8c SHA1 fffd2a5645181aa12ac9b6f74da9a011cdcf1b97 SHA256 782521c7e16d7eec82d7b7e7c43102806e7f72bc7366401808b1e1ac6e26045a
diff --git a/sci-chemistry/refmac/files/5.6-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6-allow-dynamic-linking.patch
new file mode 100644
index 0000000..6aa7697
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.6-allow-dynamic-linking.patch
@@ -0,0 +1,43 @@
+diff -ur refmac.orig//makefile_refmac.inc1 refmac//makefile_refmac.inc1
+--- refmac.orig//makefile_refmac.inc1	2010-04-20 10:22:49.868462937 -0500
++++ refmac//makefile_refmac.inc1	2010-04-20 10:29:37.378474391 -0500
+@@ -83,9 +83,7 @@
+ bridge.o                    \
+ i0.o                        \
+ i1.o                        \
+-chbevl.o                    \
+-$(LLIBCIF)                  \
+-$(LLIBLAPACK)
++chbevl.o                    
+ 
+ 
+ SUBL =                      \
+@@ -118,9 +116,7 @@
+ iheap_sort.o                \
+ linalgebra.o                \
+ math_refmac.o               \
+-subnumrec.o                 \
+-$(LLIBLAPACK)               \
+-$(LLIBCCP)
++subnumrec.o                 
+ 
+ #--------------------------------------------------------------------------------
+ 
+@@ -188,7 +184,7 @@
+ 	$(FC) $(FFLAGS) -c linalgebra_f90.f90
+ 
+ refmac:	$(SUBR)
+-	$(FC) $(FFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
+ 
+ mol2_file.o:	mol2_file.f odb_files.f90
+ 	$(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f
+@@ -209,7 +205,7 @@
+ 	$(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f
+ 
+ libcheck:	$(SUBL)
+-	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBLAPACK)
+ 
+ clean:
+ 	/bin/rm *.o
diff --git a/sci-chemistry/refmac/files/5.6-test.log.patch b/sci-chemistry/refmac/files/5.6-test.log.patch
new file mode 100644
index 0000000..61858be
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.6-test.log.patch
@@ -0,0 +1,32 @@
+--- test-framework/refmac5/test_refmac5.py	2009-06-29 15:45:37.000000000 +0200
++++ test-framework/refmac5/test_refmac5.py.new	2009-06-29 15:48:05.000000000 +0200
+@@ -88,7 +88,8 @@
+              'make hydr no',
+              'labin IP=IMEAN SIGIP=SIGIMEAN FREE=FreeR_flag',
+              'labout FC=FC PHIC=PHIC'],
+-            working_directory = self.test_dir)
++            working_directory = self.test_dir,
++            log_file = 'test_twinned_refinement.log')
+ 
+         self.assertEqual(status, 0)
+ 
+@@ -123,7 +124,8 @@
+              'weight auto',
+              'ncyc 20',
+              'labout FC=FC PHIC=PHIC'],
+-            working_directory = self.test_dir)
++            working_directory = self.test_dir,
++            log_file = 'test_4_domain_tls.log')
+ 
+         self.assertEqual(status, 0)
+ 
+@@ -156,7 +158,8 @@
+              'anomalous form SE -9.9 3.9',
+              'anomalous wavelength 0.97966',
+              'labout FC=FC PHIC=PHIC'],
+-            working_directory = self.test_dir)
++            working_directory = self.test_dir,
++            log_file = 'test_sad_refinement.log')
+ 
+         self.assertEqual(status, 0)
+ 
diff --git a/sci-chemistry/refmac/metadata.xml b/sci-chemistry/refmac/metadata.xml
new file mode 100644
index 0000000..a4525fd
--- /dev/null
+++ b/sci-chemistry/refmac/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+  <email>sci@gentoo.org</email>
+</maintainer>
+<maintainer>
+ <email>jlec@gentoo.org</email>
+  <name>Justin Lecher (jlec)</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/refmac/refmac-5.6.0069.ebuild b/sci-chemistry/refmac/refmac-5.6.0069.ebuild
new file mode 100644
index 0000000..66848c9
--- /dev/null
+++ b/sci-chemistry/refmac/refmac-5.6.0069.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0109.ebuild,v 1.3 2010/03/28 20:43:07 jlec Exp $
+
+EAPI="2"
+
+inherit fortran base toolchain-funcs versionator
+
+DESCRIPTION="Macromolecular crystallographic refinement program"
+HOMEPAGE="http://www.ysbl.york.ac.uk/refmac/"
+SRC_URI="${HOMEPAGE}data/refmac_experimental/refmac5.6_source_v${PV}.tar.gz
+	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
+
+SLOT="0"
+LICENSE="ccp4"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+	sci-libs/ccp4-libs
+	sci-libs/mmdb
+	virtual/blas
+	virtual/lapack"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+PATCHES=(
+	"${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-allow-dynamic-linking.patch
+	)
+
+src_prepare() {
+	base_src_prepare
+	use test && epatch "${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="-llapack -lblas" \
+		|| die
+}
+
+src_test() {
+	einfo "Starting tests ..."
+	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() {
+	dobin refmac || die
+	dobin libcheck || die
+	dosym refmac /usr/bin/refmac5 || die
+#	dodoc refmac_keywords.pdf bugs_and_features.pdf || die
+}