Version Bump, removed old

(Portage version: 2.2_rc98/cvs/Linux x86_64)

4 files changed, 250 insertions, 73 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index df2869d0f704..dd9092d9c7c4 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -1,6 +1,13 @@
 # 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 1.18 2010/09/30 08:06:44 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.19 2010/10/20 06:32:26 jlec Exp $
+
+*refmac-5.6.0086 (20 Oct 2010)
+
+  20 Oct 2010; Justin Lecher <jlec@gentoo.org>
+  +files/5.6.0086-allow-dynamic-linking.patch, -refmac-5.6.0083.ebuild,
+  -refmac-5.6.0084.ebuild, +refmac-5.6.0086.ebuild:
+  Version Bump, removed old
 
 *refmac-5.6.0085 (30 Sep 2010)
 
diff --git a/sci-chemistry/refmac/files/5.6.0086-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0086-allow-dynamic-linking.patch
new file mode 100644
index 000000000000..2134cc63ec67
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.6.0086-allow-dynamic-linking.patch
@@ -0,0 +1,241 @@
+diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
+index 5263df1..6b96e5e 100644
+--- a/makefile_refmac.inc1
++++ b/makefile_refmac.inc1
+@@ -90,9 +90,7 @@ messy_pdb.o                 \
+ bridge.o                    \
+ i0.o                        \
+ i1.o                        \
+-chbevl.o                    \
+-$(LLIBCIF)                  \
+-$(LLIBLAPACK)
++chbevl.o
+ 
+ 
+ SUBL =                      \
+@@ -126,9 +124,7 @@ cell_symm_subrs.o           \
+ iheap_sort.o                \
+ linalgebra.o                \
+ math_refmac.o               \
+-subnumrec.o                 \
+-$(LLIBLAPACK)               \
+-$(LLIBCCP)
++subnumrec.o
+ 
+ #--------------------------------------------------------------------------------
+ 
+@@ -153,33 +149,32 @@ rharvest77mod.o:  rharvest77mod.f
+ twin77mod.o:  twin77mod.f
+ 	$(FC) $(FFLAGS) -c twin77mod.f
+ 
++max_with_twins.o: restr_files.o max_with_twins.f
++	$(FC) $(FFLAGS) -c max_with_twins.f
+ 
+-max_with_twins.o: restr_files.f90 max_with_twins.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 max_with_twins.f
+-
+-merohedr_twin.o: restr_files.f90 merohedr_twin.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f
++merohedr_twin.o: restr_files.o merohedr_twin.f
++	$(FC) $(FFLAGS) -c merohedr_twin.f
+ 
+-ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 ls_scaling_twin_save.f
++ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f
++	$(FC) $(FFLAGS) -c ls_scaling_twin_save.f
+ 
+-ml_params_refine.o: restr_files.f90 ml_params_refine.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 ml_params_refine.f
++ml_params_refine.o: restr_files.o ml_params_refine.f
++	$(FC) $(FFLAGS) -c ml_params_refine.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: restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f
++ncs_rest.o: restr_files.o ncs_ncs_generate.o ncs_rest.f
++	$(FC) $(FFLAGS) -c ncs_rest.f
+ 
+-ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90
+-	$(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90
++ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o
++	$(FC) $(FFLAGS) -c ncs_ncs_generate.f90
+ 
+-lsq_exp2.o: restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90  lsq_exp2.f
++lsq_exp2.o: restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f
++	$(FC) $(FFLAGS) -c lsq_exp2.f
+ 
+-vdw_and_contacts.o: vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 ridge.f90 local_tls.f90 vdw_and_contacts.f
++vdw_and_contacts.o: vdw_and_contacts.f local_tls.o ridge.o restr_files.o
++	$(FC) $(FFLAGS) -c vdw_and_contacts.f
+ 
+ dist_routines.o: dist_routines.f90
+ 	$(FC) $(FFLAGS) -c dist_routines.f90
+@@ -193,109 +188,110 @@ ridge.o: ridge.f90
+ align_refmac.o: align_refmac.f90
+ 	$(FC) $(FFLAGS) -c align_refmac.f90
+ 
+-rigid_allocate.o: restr_files.f90 rigid_allocate.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 rigid_allocate.f
++rigid_allocate.o: restr_files.o rigid_allocate.f
++	$(FC) $(FFLAGS) -c rigid_allocate.f
+ 
+-tls_allocate.o: restr_files.f90 tls_allocate.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 tls_allocate.f
++tls_allocate.o: restr_files.o tls_allocate.f
++	$(FC) $(FFLAGS) -c tls_allocate.f
+ 
+-hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 restr_files.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 hkon_secder_tch.f
++hkon_secder_tch.o: hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o restr_files.o
++	$(FC) $(FFLAGS) -c hkon_secder_tch.f
+ 
+-oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 filter_params.f90 oppro_allocate.f
++oppro_allocate.o: oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o
++	$(FC) $(FFLAGS) -c oppro_allocate.f
+ 
+-read_extra_restraints.o: restr_files.f90 read_extra_restraints.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 read_extra_restraints.f
++read_extra_restraints.o: restr_files.o read_extra_restraints.f
++	$(FC) $(FFLAGS) -c read_extra_restraints.f
+ 
+-coords.o: coords.f90 atomf77mod.f
+-	$(FC) $(FFLAGS) -c atomf77mod.f coords.f90
++coords.o: coords.f90 atomf77mod.o
++	$(FC) $(FFLAGS) -c coords.f90
+ 
+-refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 refpre_twin.f
++refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o
++	$(FC) $(FFLAGS) -c refpre_twin.f
+ 
+-decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f
++decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f
++	$(FC) $(FFLAGS) -c decide_twin_opers_0.f
+ 
+ automorphism.o: automorphism.f90
+ 	$(FC) $(FFLAGS) -c automorphism.f90
+ 
+-mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 mtz_write_twin.f
++mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o
++	$(FC) $(FFLAGS) -c mtz_write_twin.f
+ 
+ filter_params.o: filter_params.f90
+ 	$(FC) $(FFLAGS) -c filter_params.f90
+ 
+-rcard_tor1.o: rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 rcard_tor1.f
++rcard_tor1.o: rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o
++	$(FC) $(FFLAGS) -c rcard_tor1.f
+ 
+-inout_routines.o: restr_files.f90 inout_routines.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f
++inout_routines.o: restr_files.o inout_routines.f
++	$(FC) $(FFLAGS) -c inout_routines.f
+ 
+-local_tls.o: local_tls.f90 linalgebra_f90.f90
+-	$(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90
++local_tls.o: local_tls.f90 linalgebra_f90.o
++	$(FC) $(FFLAGS) -c local_tls.f90
+ 
+ linalgebra_f90.o: linalgebra_f90.f90 
+ 	$(FC) $(FFLAGS) -c linalgebra_f90.f90
+ 
+-make_refmac_dummy.o: make_refmac_dummy.f optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 make_refmac_dummy.f
++make_refmac_dummy.o: make_refmac_dummy.f optimise_solvent_all.o
++	$(FC) $(FFLAGS) -c make_refmac_dummy.f
+ 
+-ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 ml_scaling_double.f
++ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o
++	$(FC) $(FFLAGS) -c ml_scaling_double.f
+ 
+-refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 refall_twin.f
++refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.o
++	$(FC) $(FFLAGS) -c refall_twin.f
+ 
+-rharvest.o: rharvest.f optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 rharvest.f
++rharvest.o: rharvest.f optimise_solvent_all.o
++	$(FC) $(FFLAGS) -c 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.o
++	$(FC) $(FFLAGS) -c solvent_contr_mask.f
+ 
+-subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 subag_scale_hessian.f
++subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o
++	$(FC) $(FFLAGS) -c subag_scale_hessian.f
+ 
+-subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 subcf_scale1.f
++subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o
++	$(FC) $(FFLAGS) -c subcf_scale1.f
+ 
+-bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90
++bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o
++	$(FC) $(FFLAGS) -c bvalue_routines.f90
+ 
+-refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90
+-	$(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 refmac_xml.f
++refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o
++	$(FC) $(FFLAGS) -c refmac_xml.f
+ 
+ hkl_pack.o:  hkl_pack.f90
+ 	$(FC) $(FFLAGS) -c hkl_pack.f90
+ 
+-subvag.o: subvag.f hkl_pack.f90
++subvag.o: subvag.f hkl_pack.o
+ 	$(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
+-	$(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f
++mol2_file.o:	mol2_file.f odb_files.o
++	$(FC) $(FFLAGS) -c mol2_file.f
+ 
+-odb_files.o:	odb_files.f90 elements_module.f90 enerf77mod.f
+-	$(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90
++odb_files.o:	odb_files.f90 elements_module.o enerf77mod.o
++	$(FC) $(FFLAGS) -c enerf77mod.f odb_files.f90
+ 
+ elements_module.o:	elements_module.f90
+ 	$(FC) $(FFLAGS) -c elements_module.f90
+ 
+-make_lib2.o:	make_lib2.f odb_files.f90 
+-	$(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f
++make_lib2.o:	make_lib2.f odb_files.o
++	$(FC) $(FFLAGS) -c make_lib2.f
+ 
+ pdb2libcheck.o:	pdb2libcheck.f90
+ 	$(FC) $(FFLAGS) -c pdb2libcheck.f90
+ 
+-libcheck.o:	libcheck.f elements_module.f90 pdb2libcheck.f90
+-	$(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f
++libcheck.o:	libcheck.f elements_module.o pdb2libcheck.o
++	$(FC) $(FFLAGS) -c libcheck.f
+ 
+ libcheck:	$(SUBL)
+-	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
+ 
+ clean:
+ 	/bin/rm *.o
+ 
+ bridge.o:			bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h
++	$(CXX) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/refmac-5.6.0084.ebuild b/sci-chemistry/refmac/refmac-5.6.0084.ebuild
deleted file mode 100644
index ea210304031b..000000000000
--- a/sci-chemistry/refmac/refmac-5.6.0084.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# 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-5.6.0084.ebuild,v 1.1 2010/09/27 15:09:53 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
-}
diff --git a/sci-chemistry/refmac/refmac-5.6.0083.ebuild b/sci-chemistry/refmac/refmac-5.6.0086.ebuild
index 4a83de4cf265..3d4040027147 100644
--- a/sci-chemistry/refmac/refmac-5.6.0083.ebuild
+++ b/sci-chemistry/refmac/refmac-5.6.0086.ebuild
@@ -1,6 +1,6 @@
 # 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-5.6.0083.ebuild,v 1.1 2010/09/24 10:55:08 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0086.ebuild,v 1.1 2010/10/20 06:32:26 jlec Exp $
 
 EAPI="2"