diff options
Diffstat (limited to 'sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch')
| -rw-r--r-- | sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch | 323 |
1 files changed, 0 insertions, 323 deletions
diff --git a/sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch deleted file mode 100644 index 1a55ad125d2a..000000000000 --- a/sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch +++ /dev/null @@ -1,323 +0,0 @@ -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 |