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-rw-r--r--sci-chemistry/refmac/files/5.5-test.log.patch32
-rw-r--r--sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch84
-rw-r--r--sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch17
-rw-r--r--sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch341
-rw-r--r--sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch341
5 files changed, 0 insertions, 815 deletions
diff --git a/sci-chemistry/refmac/files/5.5-test.log.patch b/sci-chemistry/refmac/files/5.5-test.log.patch
deleted file mode 100644
index 61858be357a0..000000000000
--- a/sci-chemistry/refmac/files/5.5-test.log.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- 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/files/5.5.0110-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch
deleted file mode 100644
index 1efbaa04d9e6..000000000000
--- a/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,84 +0,0 @@
-diff --git a/makefile b/makefile
-index 66d4cee..5270677 100644
---- a/makefile
-+++ b/makefile
-@@ -9,7 +9,7 @@ XFFLAGS = -fno-second-underscore -static
- XCFLAGS = -DGFORTRAN -DPROTOTYPE
- FFLAGS = $(FOPTIM) $(XFFLAGS)
- CFLAGS = $(COPTIM) $(XCFLAGS)
--CPPFLAGS = $(CFLAGS)
-+CPPFLAGS = $(CXXFLAGS) $(XCFLAGS)
-
- LLIBCIF =
- LLIBCCP = $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 371d84d..557077f 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -68,9 +68,7 @@ messy_pdb.o \
- bridge.o \
- i0.o \
- i1.o \
--chbevl.o \
--$(LLIBCIF) \
--$(LLIBLAPACK)
-+chbevl.o
- #$(LLIBCCP) \
- #crt0.o \
- #heavy.o \
-@@ -95,8 +93,7 @@ make_unix_ccp4.o \
- emin.o \
- libcheck_min.o \
- mol2_file.o \
--sdf_files.o \
--$(LLIBCCP)
-+sdf_files.o
-
- SUBM = \
- main_makecif.o \
-@@ -116,9 +113,7 @@ make_rst2.o \
- make_PDB.o \
- makecif.o \
- make_unix_ccp4.o \
--make_vdw.o \
--$(LLIBCCP) \
--$(LLIBCIF)
-+make_vdw.o
-
- SUBT = \
- tlsgroups.o \
-@@ -142,9 +137,7 @@ make_refmac_dummy.o \
- inout_routines.o \
- errwrt_1.o \
- linalgebra.o \
--subnumrec.o \
--$(LLIBCCP) \
--$(LLIBCIF)
-+subnumrec.o
- #--------------------------------------------------------------------------------
-
- ed = echo 'g/^CMDW-5.0/s// /@w@q@' | tr "@" "\012" | ed -s
-@@ -154,18 +147,19 @@ ed = echo 'g/^CMDW-5.0/s// /@w@q@' | tr "@" "\012" | ed -s
- all: refmac libcheck makecif
-
- refmac: $(SUBR)
-- $(FC) $(FFLAGS) $(LDFLAGF)-o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
-
- libcheck: $(SUBL)
-- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP)
-
- makecif: $(SUBM)
-- $(FC) $(FFLAGS) -o makecif${VERSION} $(SUBM)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o makecif${VERSION} $(SUBM) $(LLIBCCP) $(LLIBCIF)
-
- tlsgroups: $(SUBT)
-- $(FC) $(FFLAGS) -o tlsgroups${VERSION} $(SUBT)
-+ $(FC) $(FFLAGS) $(LDFLAGS) -o tlsgroups${VERSION} $(SUBT) $(LLIBCCP) $(LLIBCIF)
-
- clean:
- /bin/rm *.o
-
- bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h
-+ $(CXX) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch b/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch
deleted file mode 100644
index 3969cc9c8586..000000000000
--- a/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch
+++ /dev/null
@@ -1,17 +0,0 @@
- hkon_secder_tch.f | 3 ++-
- 1 files changed, 2 insertions(+), 1 deletions(-)
-
-diff --git a/hkon_secder_tch.f b/hkon_secder_tch.f
-index 31794b0..86d2cdf 100644
---- a/hkon_secder_tch.f
-+++ b/hkon_secder_tch.f
-@@ -3724,7 +3724,8 @@ c---External functions and subprutines
- INTEGER NWORKSPACE
- REAL*8 TOLER
- REAL*8 WORKSPACE(300)
-- REAL LSTLSQ,D2DF_WEIGHT
-+ REAL*8 D2DF_WEIGHT
-+ REAL LSTLSQ
- C
- INTEGER IBIN,IBIN_S
- INTEGER I,J,K
diff --git a/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch
deleted file mode 100644
index 9998b759c664..000000000000
--- a/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,341 +0,0 @@
- makefile_refmac.inc1 | 215 ++++++++++++++++++++++++--------------------------
- 1 files changed, 104 insertions(+), 111 deletions(-)
-
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 0f8bd63..e59fbfb 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -96,9 +96,7 @@ bridge.o \
- i0.o \
- i1.o \
- chbevl.o \
--make_unix_ccp4.o \
--$(LLIBCIF) \
--$(LLIBLAPACK)
-+make_unix_ccp4.o
-
-
- SUBL = \
-@@ -133,9 +131,7 @@ cell_symm_subrs.o \
- iheap_sort.o \
- linalgebra.o \
- math_refmac.o \
--subnumrec.o \
--$(LLIBLAPACK) \
--$(LLIBCCP)
-+subnumrec.o
-
- SUB_FREE = \
- freer_twin.o \
-@@ -145,9 +141,7 @@ subnumrec.o \
- libT.o \
- iheap_sort.o \
- cell_symm_subrs.o \
--math_refmac.o \
--$(LLIBLAPACK) \
--$(LLIBCCP)
-+math_refmac.o
-
- SUB_HEADER = header2matr.o
- #--------------------------------------------------------------------------------
-@@ -185,41 +179,41 @@ rharvest_mod.o: rharvest_mod.f90
- twin77mod.o: twin77mod.f
- $(FC) $(FFLAGS) -c twin77mod.f
-
--gibbs_gm_sampler.o: linalgebra_f90.f90 gibbs_gm_sampler.f90
-- $(FC) $(FFLAGS) -c linalgebra_f90.f90 gibbs_gm_sampler.f90
-+gibbs_gm_sampler.o: linalgebra_f90.o gibbs_gm_sampler.f90
-+ $(FC) $(FFLAGS) -c gibbs_gm_sampler.f90
-
--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 weights.o agreem.o
-+ $(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 weights.o agreem.o
-+ $(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 weights.o agreem.o
-+ $(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: ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f
-+ncs_rest.o: ncs_rest_mod.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: ncs_rest_mod.f90 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 ncs_rest_mod.f90 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: ncs_rest_mod.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: ncs_rest_mod.f90 vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f
-+vdw_and_contacts.o: ncs_rest_mod.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
-
--ncs_simil.o: ncs_rest_mod.f90 ncs_simil.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 ncs_simil.f90
-+ncs_simil.o: ncs_rest_mod.o ncs_simil.f90
-+ $(FC) $(FFLAGS) -c ncs_simil.f90
-
- ridge.o: ridge.f90
- $(FC) $(FFLAGS) -c ridge.f90
-@@ -227,140 +221,138 @@ 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
-+rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o
-+ $(FC) $(FFLAGS) -c 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
-+tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o
-+ $(FC) $(FFLAGS) -c tls_allocate.f
-
--hkon_secder_tch.o: ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \
-- restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \
-- hkon_secder_tch.f weights.f90 agreem.f90 rharvest_mod.f90
-+hkon_secder_tch.o: ridge.o gibbs_gm_sampler.o ncs_rest_mod.o hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \
-+ restr_files.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c hkon_secder_tch.f
-
--oppro_allocate.o: ncs_rest_mod.f90 oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f
-+oppro_allocate.o: ncs_rest_mod.o oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o
-+ $(FC) $(FFLAGS) -c oppro_allocate.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
-+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.f
-- $(FC) $(FFLAGS) -c atomf77mod.f coords.f90
-+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
-+ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o
-+ $(FC) $(FFLAGS) -c ls_scaling_double.f
-
--fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90
-- $(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90
-+fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o
-+ $(FC) $(FFLAGS) -c fast_hessian_tabulation.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
-+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.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
-+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: ncs_rest_mod.f90 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 ncs_rest_mod.f90 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: ncs_rest_mod.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: restr_files.f90 ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f
-+make_refmac_dummy.o: restr_files.o ncs_rest_mod.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_subr.o: ncs_rest_mod.f90 rharvest_subr.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 rharvest_subr.f
-+rharvest_subr.o: ncs_rest_mod.o rharvest_subr.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c rharvest_subr.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
-- $(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f
-+subvag.o: subvag.f hkl_pack.o
-+ $(FC) $(FFLAGS) -c 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
-+make_CIF.o: make_CIF.f ncs_constr.o
-+ $(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
-@@ -369,16 +361,17 @@ 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) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch
deleted file mode 100644
index 9998b759c664..000000000000
--- a/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,341 +0,0 @@
- makefile_refmac.inc1 | 215 ++++++++++++++++++++++++--------------------------
- 1 files changed, 104 insertions(+), 111 deletions(-)
-
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 0f8bd63..e59fbfb 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -96,9 +96,7 @@ bridge.o \
- i0.o \
- i1.o \
- chbevl.o \
--make_unix_ccp4.o \
--$(LLIBCIF) \
--$(LLIBLAPACK)
-+make_unix_ccp4.o
-
-
- SUBL = \
-@@ -133,9 +131,7 @@ cell_symm_subrs.o \
- iheap_sort.o \
- linalgebra.o \
- math_refmac.o \
--subnumrec.o \
--$(LLIBLAPACK) \
--$(LLIBCCP)
-+subnumrec.o
-
- SUB_FREE = \
- freer_twin.o \
-@@ -145,9 +141,7 @@ subnumrec.o \
- libT.o \
- iheap_sort.o \
- cell_symm_subrs.o \
--math_refmac.o \
--$(LLIBLAPACK) \
--$(LLIBCCP)
-+math_refmac.o
-
- SUB_HEADER = header2matr.o
- #--------------------------------------------------------------------------------
-@@ -185,41 +179,41 @@ rharvest_mod.o: rharvest_mod.f90
- twin77mod.o: twin77mod.f
- $(FC) $(FFLAGS) -c twin77mod.f
-
--gibbs_gm_sampler.o: linalgebra_f90.f90 gibbs_gm_sampler.f90
-- $(FC) $(FFLAGS) -c linalgebra_f90.f90 gibbs_gm_sampler.f90
-+gibbs_gm_sampler.o: linalgebra_f90.o gibbs_gm_sampler.f90
-+ $(FC) $(FFLAGS) -c gibbs_gm_sampler.f90
-
--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 weights.o agreem.o
-+ $(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 weights.o agreem.o
-+ $(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 weights.o agreem.o
-+ $(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: ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f
-+ncs_rest.o: ncs_rest_mod.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: ncs_rest_mod.f90 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 ncs_rest_mod.f90 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: ncs_rest_mod.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: ncs_rest_mod.f90 vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f
-+vdw_and_contacts.o: ncs_rest_mod.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
-
--ncs_simil.o: ncs_rest_mod.f90 ncs_simil.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 ncs_simil.f90
-+ncs_simil.o: ncs_rest_mod.o ncs_simil.f90
-+ $(FC) $(FFLAGS) -c ncs_simil.f90
-
- ridge.o: ridge.f90
- $(FC) $(FFLAGS) -c ridge.f90
-@@ -227,140 +221,138 @@ 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
-+rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o
-+ $(FC) $(FFLAGS) -c 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
-+tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o
-+ $(FC) $(FFLAGS) -c tls_allocate.f
-
--hkon_secder_tch.o: ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \
-- restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \
-- hkon_secder_tch.f weights.f90 agreem.f90 rharvest_mod.f90
-+hkon_secder_tch.o: ridge.o gibbs_gm_sampler.o ncs_rest_mod.o hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \
-+ restr_files.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c hkon_secder_tch.f
-
--oppro_allocate.o: ncs_rest_mod.f90 oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f
-+oppro_allocate.o: ncs_rest_mod.o oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o
-+ $(FC) $(FFLAGS) -c oppro_allocate.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
-+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.f
-- $(FC) $(FFLAGS) -c atomf77mod.f coords.f90
-+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
-+ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o
-+ $(FC) $(FFLAGS) -c ls_scaling_double.f
-
--fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90
-- $(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90
-+fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o
-+ $(FC) $(FFLAGS) -c fast_hessian_tabulation.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
-+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.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
-+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: ncs_rest_mod.f90 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 ncs_rest_mod.f90 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: ncs_rest_mod.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: restr_files.f90 ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c restr_files.f90 ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f
-+make_refmac_dummy.o: restr_files.o ncs_rest_mod.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_subr.o: ncs_rest_mod.f90 rharvest_subr.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 rharvest_subr.f
-+rharvest_subr.o: ncs_rest_mod.o rharvest_subr.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
-+ $(FC) $(FFLAGS) -c rharvest_subr.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
-- $(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f
-+subvag.o: subvag.f hkl_pack.o
-+ $(FC) $(FFLAGS) -c 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
-+make_CIF.o: make_CIF.f ncs_constr.o
-+ $(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
-@@ -369,16 +361,17 @@ 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