diff options
Diffstat (limited to 'sci-chemistry/refmac')
| -rw-r--r-- | sci-chemistry/refmac/Manifest | 2 | ||||
| -rw-r--r-- | sci-chemistry/refmac/files/5.5-test.log.patch | 32 | ||||
| -rw-r--r-- | sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch | 84 | ||||
| -rw-r--r-- | sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch | 17 | ||||
| -rw-r--r-- | sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch | 341 | ||||
| -rw-r--r-- | sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch | 341 | ||||
| -rw-r--r-- | sci-chemistry/refmac/metadata.xml | 9 | ||||
| -rw-r--r-- | sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild | 85 |
8 files changed, 0 insertions, 911 deletions
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest deleted file mode 100644 index ba3def103020..000000000000 --- a/sci-chemistry/refmac/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST refmac_5.5.0110.tar.gz 1326832 SHA256 1353fb1042586ec8fa37d0a90f274890d0ccc02377af5216200662338dfe08ca SHA512 7e7fd1a7d2d11ef5f2e08cae61da62ecfe6978730ce4ca80f8b00be9bdad5e7d0ad493e1b8d57d64f1393f2017a87b8342e2607b08bc4018def798038a111728 WHIRLPOOL 587260eebd2df3115ba01ee03c11ab773d7316100a09af1f259f7795a139f978d94c569b8e4ab85982c2eeda628e643376231bdca5311fc8c7d2de5b65a033ac -DIST test-framework.tar.gz 130933173 SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605 SHA512 3ef8253f472c5a481f836291afb80746ad73858e130130b848851b6b5dc53ada3b78c9f853af1c46fa22f469f2ce2f3248f5f760950e118610922c0429a7da16 WHIRLPOOL 022c1b493ecd35e769b44d1e52a351b4883682ef9759626bac36e26cc61078d95de0ec2531ed706897c683c38727139fa7a13d06b64c597026817ed79612d16d 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 diff --git a/sci-chemistry/refmac/metadata.xml b/sci-chemistry/refmac/metadata.xml deleted file mode 100644 index c0432fefe855..000000000000 --- a/sci-chemistry/refmac/metadata.xml +++ /dev/null @@ -1,9 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-chemistry</herd> - <maintainer> - <email>jlec@gentoo.org</email> - <name>Justin Lecher (jlec)</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild deleted file mode 100644 index eb8e87018219..000000000000 --- a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild +++ /dev/null @@ -1,85 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -inherit eutils fortran-2 flag-o-matic toolchain-funcs versionator - -DESCRIPTION="Macromolecular crystallographic refinement program" -HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac" -SRC_URI=" - ${HOMEPAGE}/data/refmac_stable/refmac_${PV}.tar.gz - test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="test" - -RDEPEND=" - sci-chemistry/makecif - >=sci-libs/ccp4-libs-6.1.3-r7 - sci-libs/mmdb - <sci-libs/monomer-db-1 - virtual/blas - virtual/lapack" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -FORTRAN_STANDARD="77 90" - -S="${WORKDIR}" - -PATCHES=( - "${FILESDIR}"/${PV}-allow-dynamic-linking.patch - "${FILESDIR}"/${PV}-gcc4.6.patch - ) - -src_prepare() { - epatch ${PATCHES[@]} - - use test && epatch "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch - [[ ${FC} == *gfortran* ]] && \ - append-fflags -fno-second-underscore && \ - append-cflags -DGFORTRAN -DPROTOTYPE && \ - append-libs -lgfortran -lgfortranbegin -lstdc++ - [[ ${FC} == *ifort* ]] && \ - append-libs -lstdc++ -} - -src_compile() { - emake \ - FC=$(tc-getFC) \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - COPTIM="${CFLAGS}" \ - FOPTIM="${FFLAGS:- -O2}" \ - VERSION="" \ - XFFLAGS="" \ - XCFLAGS="" \ - LLIBCCP="-lccp4f -lccp4c -lccif $($(tc-getPKG_CONFIG) --libs mmdb)" \ - LLIBLAPACK="$($(tc-getPKG_CONFIG) --libs lapack blas)" \ - LLIBOTHERS="${LIBS}" \ - ${PN} libcheck -} - -src_test() { - einfo "Starting tests ..." - source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" - 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() { - exeinto /usr/libexec/ccp4/bin/ - doexe ${PN} - dosym refmac /usr/libexec/ccp4/bin/refmac5 - dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} - dosym refmac /usr/bin/refmac5 - dodoc refmac_keywords.pdf bugs_and_features.pdf -} |