Version Bump, removed old

(Portage version: 2.2_rc67/cvs/Linux x86_64)

3 files changed, 172 insertions, 1 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index 7cdbf97c470f..3a4af17923a4 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.12 2010/07/02 06:36:10 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.13 2010/07/03 08:33:57 jlec Exp $
+
+*refmac-5.6.0080 (03 Jul 2010)
+
+  03 Jul 2010; Justin Lecher <jlec@gentoo.org>
+  +files/5.6.0080-allow-dynamic-linking.patch, +refmac-5.6.0080.ebuild:
+  Version Bump, removed old
 
 *refmac-5.6.0079 (02 Jul 2010)
 
diff --git a/sci-chemistry/refmac/files/5.6.0080-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0080-allow-dynamic-linking.patch
new file mode 100644
index 000000000000..6f5d1c6efe98
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.6.0080-allow-dynamic-linking.patch
@@ -0,0 +1,94 @@
+diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
+index 3f858c8..04e6790 100644
+--- a/makefile_refmac.inc1
++++ b/makefile_refmac.inc1
+@@ -89,9 +89,7 @@ messy_pdb.o                 \
+ bridge.o                    \
+ i0.o                        \
+ i1.o                        \
+-chbevl.o                    \
+-$(LLIBCIF)                  \
+-$(LLIBLAPACK)
++chbevl.o
+ 
+ 
+ SUBL =                      \
+@@ -124,9 +122,7 @@ cell_symm_subrs.o           \
+ iheap_sort.o                \
+ linalgebra.o                \
+ math_refmac.o               \
+-subnumrec.o                 \
+-$(LLIBLAPACK)               \
+-$(LLIBCCP)
++subnumrec.o
+ 
+ #--------------------------------------------------------------------------------
+ 
+@@ -150,7 +146,7 @@ twin77mod.o:  twin77mod.f
+ 	$(FC) $(FFLAGS) -c twin77mod.f
+ 
+ 
+-optimise_solvent_all.o: optimise_solvent_all.f90
++optimise_solvent_all.o: optimise_solvent_all.f90 atomf77mod.o
+ 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90
+ 
+ ncs_rest.o: ncs_ncs_generate.f90 ncs_rest.f
+@@ -178,7 +174,7 @@ align_refmac.o: align_refmac.f90
+ 	$(FC) $(FFLAGS) -c align_refmac.f90
+ 
+ 
+-hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90
++hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 optimise_solvent_all.o
+ 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 hkon_secder_tch.f
+ 
+ oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90
+@@ -220,8 +216,8 @@ refall_twin.o: refall_twin.f optimise_solvent_all.f90
+ rharvest.o: rharvest.f optimise_solvent_all.f90
+ 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 rharvest.f
+ 
+-solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 solvent_contr_mask.f
++solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 atomf77mod.o
++	$(FC) $(FFLAGS) -c  atomf77mod.f optimise_solvent_all.f90 solvent_contr_mask.f
+ 
+ subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90
+ 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 subag_scale_hessian.f
+@@ -229,7 +225,7 @@ subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90
+ subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90
+ 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 subcf_scale1.f
+ 
+-refmac_xml.o: refmac_xml.f optimise_solvent_all.f90
++refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 optimise_solvent_all.o
+ 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 refmac_xml.f
+ 
+ hkl_pack.o:  hkl_pack.f90
+@@ -239,9 +235,9 @@ subvag.o: subvag.f hkl_pack.f90
+ 	$(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f
+ 
+ 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
++mol2_file.o:	mol2_file.f odb_files.o
+ 	$(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f
+ 
+ odb_files.o:	odb_files.f90 elements_module.f90 enerf77mod.f
+@@ -250,7 +246,7 @@ odb_files.o:	odb_files.f90 elements_module.f90 enerf77mod.f
+ elements_module.o:	elements_module.f90
+ 	$(FC) $(FFLAGS) -c elements_module.f90
+ 
+-make_lib2.o:	make_lib2.f odb_files.f90 
++make_lib2.o:	make_lib2.f odb_files.o
+ 	$(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f
+ 
+ pdb2libcheck.o:	pdb2libcheck.f90
+@@ -260,7 +256,7 @@ libcheck.o:	libcheck.f elements_module.f90 pdb2libcheck.f90
+ 	$(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) $(LLIBCIF) $(LLIBLAPACK)
+ 
+ clean:
+ 	/bin/rm *.o
diff --git a/sci-chemistry/refmac/refmac-5.6.0080.ebuild b/sci-chemistry/refmac/refmac-5.6.0080.ebuild
new file mode 100644
index 000000000000..8f6bdbfaa1ce
--- /dev/null
+++ b/sci-chemistry/refmac/refmac-5.6.0080.ebuild
@@ -0,0 +1,71 @@
+# 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-5.6.0080.ebuild,v 1.1 2010/07/03 08:33:57 jlec Exp $
+
+EAPI="2"
+
+inherit fortran 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}${MY_PV}.tar.gz
+	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
+
+SLOT="0"
+LICENSE="ccp4"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+	sci-libs/ccp4-libs
+	sci-libs/mmdb
+	>sci-libs/monomer-db-1
+	virtual/blas
+	virtual/lapack"
+DEPEND="${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 ..."
+	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; do
+		exeinto /usr/libexec/ccp4/bin/
+		doexe ${i} || die
+		dosym ../libexec/ccp4/bin/${i} /usr/bin/${i}
+	done
+	dosym refmac /usr/bin/refmac5 || die
+}