Version Bump

Package-Manager: portage-2.2.0_alpha3/cvs/Linux x86_64

1 files changed, 323 insertions, 0 deletions

diff --git a/sci-chemistry/refmac/files/5.6.0089-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0089-allow-dynamic-linking.patch
new file mode 100644
index 000000000000..1a55ad125d2a
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.6.0089-allow-dynamic-linking.patch
@@ -0,0 +1,323 @@
+diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
+index 80b199e..d3ab4c8 100644
+--- a/makefile_refmac.inc1
++++ b/makefile_refmac.inc1
+@@ -93,9 +93,7 @@ messy_pdb.o                 \
+ bridge.o                    \
+ i0.o                        \
+ i1.o                        \
+-chbevl.o                    \
+-$(LLIBCIF)                  \
+-$(LLIBLAPACK)
++chbevl.o
+ 
+ 
+ SUBL =                      \
+@@ -130,9 +128,7 @@ cell_symm_subrs.o           \
+ iheap_sort.o                \
+ linalgebra.o                \
+ math_refmac.o               \
+-subnumrec.o                 \
+-$(LLIBLAPACK)               \
+-$(LLIBCCP)
++subnumrec.o
+ 
+ SUB_FREE  =                 \
+ freer_twin.o                 \
+@@ -142,9 +138,7 @@ subnumrec.o                 \
+ libT.o                      \
+ iheap_sort.o                \
+ cell_symm_subrs.o           \
+-math_refmac.o               \
+-$(LLIBLAPACK)               \
+-$(LLIBCCP)
++math_refmac.o
+ 
+ SUB_HEADER = header2matr.o
+ #--------------------------------------------------------------------------------
+@@ -179,32 +173,32 @@ rharvest_mod.o:  rharvest_mod.f90
+ twin77mod.o:  twin77mod.f
+ 	$(FC) $(FFLAGS) -c twin77mod.f
+ 
+-max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f
++max_with_twins.o: restr_files.o max_with_twins.f
++	$(FC) $(FFLAGS) -c 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 weights.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.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 weights.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.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 agreem.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90
++optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o
++	$(FC) $(FFLAGS) -c optimise_solvent_all.f90
+ 
+-ncs_rest.o: restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f
++ncs_rest.o: restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o
++	$(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 weights.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90  lsq_exp2.f weights.f90 rharvest_mod.f90
++lsq_exp2.o: restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f weights.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c lsq_exp2.f
+ 
+-vdw_and_contacts.o: vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f
++vdw_and_contacts.o: vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o
++	$(FC) $(FFLAGS) -c vdw_and_contacts.f
+ 
+ dist_routines.o: dist_routines.f90
+ 	$(FC) $(FFLAGS) -c dist_routines.f90
+@@ -218,140 +212,137 @@ 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 agreem.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f
+-
+-tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f
++rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o
++	$(FC) $(FFLAGS) -c rigid_allocate.f
+ 
+-hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \
+-                   restr_files.f90 weights.f90 agreem.f90 rharvest.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \
+-	                   hkon_secder_tch.f weights.f90 agreem.f90 rharvest.f
++tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o
++	$(FC) $(FFLAGS) -c tls_allocate.f
+ 
+-oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f
++hkon_secder_tch.o: hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \
++                   restr_files.o weights.o agreem.o rharvest.f
++	$(FC) $(FFLAGS) -c hkon_secder_tch.f
+ 
+-read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f
++oppro_allocate.o: oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o
++	$(FC) $(FFLAGS) -c oppro_allocate.f
+ 
+-coords.o: coords.f90 atomf77mod.f
+-	$(FC) $(FFLAGS) -c atomf77mod.f coords.f90
++read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o
++	$(FC) $(FFLAGS) -c read_extra_restraints.f
+ 
++coords.o: coords.f90 atomf77mod.o
++	$(FC) $(FFLAGS) -c coords.f90
+ 
+-ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90
+ 
+-fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90 
+-	$(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90
++ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o
++	$(FC) $(FFLAGS) -c ls_scaling_double.f
+ 
+-calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
++fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o
++	$(FC) $(FFLAGS) -c fast_hessian_tabulation.f
+ 
+-refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f
++calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c calc_stats_twin.f
+ 
++refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.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 weights.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f
++mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.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 weights.f90 \
+-              agreem.f90 rharvest_mod.f90 ncs_constr.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \
+-	                   agreem.f90 rharvest_mod.f90 ncs_constr.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 weights.o \
++              agreem.o rharvest_mod.o ncs_constr.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 weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f
++make_refmac_dummy.o: make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c make_refmac_dummy.f
+ 
+-ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f
++ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c ml_scaling_double.f
+ 
+-refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90  weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f
++refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c refall_twin.f
+ 
+-rharvest.o: rharvest.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90  weights.f90 agreem.f90 rharvest_mod.f90 rharvest.f
++rharvest.o: rharvest.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c rharvest.f
+ 
+-solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f
++solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o
++	$(FC) $(FFLAGS) -c solvent_contr_mask.f
+ 
+-subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f
++subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o weights.o agreem.o rharvest_mod.o ncs_constr.o
++	$(FC) $(FFLAGS) -c subag_scale_hessian.f
+ 
+-aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90
+-	$(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f
++aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o
++	$(FC) $(FFLAGS) -c aniso_ref_eigen.f
+ 
+-subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f
++subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.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
+ 
+-newentry_idealise.o:: newentry_idealise.f weights.f90
+-	$(FC) $(FFLAGS) -c newentry_idealise.f weights.f90
++newentry_idealise.o:: newentry_idealise.f weights.o
++	$(FC) $(FFLAGS) -c newentry_idealise.f
+ 
+-occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90
++occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c occupancy_only_refine.f
+ 
+-refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90  refmac_completeness.f90
+-	$(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90
++refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90
++	$(FC) $(FFLAGS) -c refmac_completeness.f90
+ 
+-refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f
++refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c refmac_xml.f
+ 
+ hkl_pack.o:  hkl_pack.f90
+ 	$(FC) $(FFLAGS) -c hkl_pack.f90
+ 
+-extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90
+-	$(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90
++extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o
++	$(FC) $(FFLAGS) -c extra_eigen.f
+ 
+-subvag.o: subvag.f hkl_pack.f90
++subvag.o: subvag.f hkl_pack.o
+ 	$(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f
+ 
+-make_PDB.o: make_PDB.f ncs_constr.f90
+-	$(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f
++make_PDB.o: make_PDB.f ncs_constr.o
++	$(FC) $(FFLAGS) -c make_PDB.f
+ 
+ make_CIF.o: make_CIF.f ncs_constr.f90
+-	$(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f
++	$(FC) $(FFLAGS) -c make_CIF.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 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
+ 
+ header2matr.o:	header2matr.f90
+ 	$(FC) $(FFLAGS) -c header2matr.f90
+@@ -360,16 +351,17 @@ freer_twin.o:	freer_twin.f90
+ 	$(FC) $(FFLAGS) -c  freer_twin.f90
+ 
+ libcheck:	$(SUBL)
+-	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
+ 
+ free_twin:	$(SUB_FREE)
+-	$(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK)
+ 
+ 
+ header2matr:	$(SUB_HEADER)
+-	$(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
+ 
+ clean:
+ 	/bin/rm *.o *.mod
+ 
+ bridge.o:			bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h
++	$(CXX) $(CXXFLAGS) -c bridge.cpp