Gentoo Archives: gentoo-commits

From: "Justin Lecher (jlec)" <jlec@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] gentoo-x86 commit in sci-chemistry/refmac/files: 5.6.0088-allow-dynamic-linking.patch
Date: Wed, 03 Nov 2010 19:02:00
Message-Id: 20101103190151.547F920054@flycatcher.gentoo.org
1 jlec 10/11/03 19:01:51
2
3 Added: 5.6.0088-allow-dynamic-linking.patch
4 Log:
5 Version Bump
6
7 (Portage version: 2.1.9.24/cvs/Linux x86_64)
8
9 Revision Changes Path
10 1.1 sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch
11
12 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch?rev=1.1&view=markup
13 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch?rev=1.1&content-type=text/plain
14
15 Index: 5.6.0088-allow-dynamic-linking.patch
16 ===================================================================
17 diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
18 index 80b199e..d3ab4c8 100644
19 --- a/makefile_refmac.inc1
20 +++ b/makefile_refmac.inc1
21 @@ -93,9 +93,7 @@ messy_pdb.o \
22 bridge.o \
23 i0.o \
24 i1.o \
25 -chbevl.o \
26 -$(LLIBCIF) \
27 -$(LLIBLAPACK)
28 +chbevl.o
29
30
31 SUBL = \
32 @@ -130,9 +128,7 @@ cell_symm_subrs.o \
33 iheap_sort.o \
34 linalgebra.o \
35 math_refmac.o \
36 -subnumrec.o \
37 -$(LLIBLAPACK) \
38 -$(LLIBCCP)
39 +subnumrec.o
40
41 SUB_FREE = \
42 freer_twin.o \
43 @@ -142,9 +138,7 @@ subnumrec.o \
44 libT.o \
45 iheap_sort.o \
46 cell_symm_subrs.o \
47 -math_refmac.o \
48 -$(LLIBLAPACK) \
49 -$(LLIBCCP)
50 +math_refmac.o
51
52 SUB_HEADER = header2matr.o
53 #--------------------------------------------------------------------------------
54 @@ -179,32 +173,32 @@ rharvest_mod.o: rharvest_mod.f90
55 twin77mod.o: twin77mod.f
56 $(FC) $(FFLAGS) -c twin77mod.f
57
58 -max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90
59 - $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f
60 +max_with_twins.o: restr_files.o max_with_twins.f
61 + $(FC) $(FFLAGS) -c max_with_twins.f
62
63 -merohedr_twin.o: restr_files.f90 merohedr_twin.f
64 - $(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f
65 +merohedr_twin.o: restr_files.o merohedr_twin.f
66 + $(FC) $(FFLAGS) -c merohedr_twin.f
67
68 -ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f weights.f90 agreem.f90
69 - $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ls_scaling_twin_save.f
70 +ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f
71 + $(FC) $(FFLAGS) -c ls_scaling_twin_save.f
72
73 -ml_params_refine.o: restr_files.f90 ml_params_refine.f weights.f90 agreem.f90
74 - $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ml_params_refine.f
75 +ml_params_refine.o: restr_files.o ml_params_refine.f
76 + $(FC) $(FFLAGS) -c ml_params_refine.f
77
78 -optimise_solvent_all.o: optimise_solvent_all.f90 agreem.f90
79 - $(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90
80 +optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o
81 + $(FC) $(FFLAGS) -c optimise_solvent_all.f90
82
83 -ncs_rest.o: restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90
84 - $(FC) $(FFLAGS) -c restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f
85 +ncs_rest.o: restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o
86 + $(FC) $(FFLAGS) -c ncs_rest.f
87
88 -ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90
89 - $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90
90 +ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o
91 + $(FC) $(FFLAGS) -c ncs_ncs_generate.f90
92
93 -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
94 - $(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
95 +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
96 + $(FC) $(FFLAGS) -c lsq_exp2.f
97
98 -vdw_and_contacts.o: vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90
99 - $(FC) $(FFLAGS) -c restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f
100 +vdw_and_contacts.o: vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o
101 + $(FC) $(FFLAGS) -c vdw_and_contacts.f
102
103 dist_routines.o: dist_routines.f90
104 $(FC) $(FFLAGS) -c dist_routines.f90
105 @@ -218,140 +212,137 @@ ridge.o: ridge.f90
106 align_refmac.o: align_refmac.f90
107 $(FC) $(FFLAGS) -c align_refmac.f90
108
109 -rigid_allocate.o: restr_files.f90 rigid_allocate.f agreem.f90
110 - $(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f
111 -
112 -tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90
113 - $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f
114 +rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o
115 + $(FC) $(FFLAGS) -c rigid_allocate.f
116
117 -hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \
118 - restr_files.f90 weights.f90 agreem.f90 rharvest.f
119 - $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \
120 - hkon_secder_tch.f weights.f90 agreem.f90 rharvest.f
121 +tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o
122 + $(FC) $(FFLAGS) -c tls_allocate.f
123
124 -oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90
125 - $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f
126 +hkon_secder_tch.o: hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \
127 + restr_files.o weights.o agreem.o rharvest.f
128 + $(FC) $(FFLAGS) -c hkon_secder_tch.f
129
130 -read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90
131 - $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f
132 +oppro_allocate.o: oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o
133 + $(FC) $(FFLAGS) -c oppro_allocate.f
134
135 -coords.o: coords.f90 atomf77mod.f
136 - $(FC) $(FFLAGS) -c atomf77mod.f coords.f90
137 +read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o
138 + $(FC) $(FFLAGS) -c read_extra_restraints.f
139
140 +coords.o: coords.f90 atomf77mod.o
141 + $(FC) $(FFLAGS) -c coords.f90
142
143 -ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90
144 - $(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90
145
146 -fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90
147 - $(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90
148 +ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o
149 + $(FC) $(FFLAGS) -c ls_scaling_double.f
150
151 -calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
152 - $(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
153 +fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o
154 + $(FC) $(FFLAGS) -c fast_hessian_tabulation.f
155
156 -refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
157 - $(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f
158 +calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o
159 + $(FC) $(FFLAGS) -c calc_stats_twin.f
160
161 +refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.o
162 + $(FC) $(FFLAGS) -c refpre_twin.f
163
164 -decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f
165 - $(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f
166 +decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f
167 + $(FC) $(FFLAGS) -c decide_twin_opers_0.f
168
169 automorphism.o: automorphism.f90
170 $(FC) $(FFLAGS) -c automorphism.f90
171
172 -mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90 agreem.f90
173 - $(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f
174 +mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.o
175 + $(FC) $(FFLAGS) -c mtz_write_twin.f
176
177 filter_params.o: filter_params.f90
178 $(FC) $(FFLAGS) -c filter_params.f90
179
180 -rcard_tor1.o: rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 \
181 - agreem.f90 rharvest_mod.f90 ncs_constr.f90
182 - $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \
183 - agreem.f90 rharvest_mod.f90 ncs_constr.f90 rcard_tor1.f
184 +rcard_tor1.o: rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o weights.o \
185 + agreem.o rharvest_mod.o ncs_constr.o
186 + $(FC) $(FFLAGS) -c rcard_tor1.f
187
188 -inout_routines.o: restr_files.f90 inout_routines.f
189 - $(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f
190 +inout_routines.o: restr_files.o inout_routines.f
191 + $(FC) $(FFLAGS) -c inout_routines.f
192
193 -local_tls.o: local_tls.f90 linalgebra_f90.f90
194 - $(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90
195 +local_tls.o: local_tls.f90 linalgebra_f90.o
196 + $(FC) $(FFLAGS) -c local_tls.f90
197
198 linalgebra_f90.o: linalgebra_f90.f90
199 $(FC) $(FFLAGS) -c linalgebra_f90.f90
200
201 -make_refmac_dummy.o: make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
202 - $(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f
203 +make_refmac_dummy.o: make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
204 + $(FC) $(FFLAGS) -c make_refmac_dummy.f
205
206 -ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
207 - $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f
208 +ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
209 + $(FC) $(FFLAGS) -c ml_scaling_double.f
210
211 -refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
212 - $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f
213 +refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o
214 + $(FC) $(FFLAGS) -c refall_twin.f
215
216 -rharvest.o: rharvest.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
217 - $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 rharvest.f
218 +rharvest.o: rharvest.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
219 + $(FC) $(FFLAGS) -c rharvest.f
220
221 -solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
222 - $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f
223 +solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o
224 + $(FC) $(FFLAGS) -c solvent_contr_mask.f
225
226 -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
227 - $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f
228 +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
229 + $(FC) $(FFLAGS) -c subag_scale_hessian.f
230
231 -aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90
232 - $(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f
233 +aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o
234 + $(FC) $(FFLAGS) -c aniso_ref_eigen.f
235
236 -subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
237 - $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f
238 +subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
239 + $(FC) $(FFLAGS) -c subcf_scale1.f
240
241 -bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f
242 - $(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90
243 +bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o
244 + $(FC) $(FFLAGS) -c bvalue_routines.f90
245
246 -newentry_idealise.o:: newentry_idealise.f weights.f90
247 - $(FC) $(FFLAGS) -c newentry_idealise.f weights.f90
248 +newentry_idealise.o:: newentry_idealise.f weights.o
249 + $(FC) $(FFLAGS) -c newentry_idealise.f
250
251 -occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90
252 - $(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90
253 +occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o
254 + $(FC) $(FFLAGS) -c occupancy_only_refine.f
255
256 -refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90
257 - $(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90
258 +refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90
259 + $(FC) $(FFLAGS) -c refmac_completeness.f90
260
261 -refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90
262 - $(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f
263 +refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o
264 + $(FC) $(FFLAGS) -c refmac_xml.f
265
266 hkl_pack.o: hkl_pack.f90
267 $(FC) $(FFLAGS) -c hkl_pack.f90
268
269 -extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90
270 - $(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90
271 +extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o
272 + $(FC) $(FFLAGS) -c extra_eigen.f
273
274 -subvag.o: subvag.f hkl_pack.f90
275 +subvag.o: subvag.f hkl_pack.o
276 $(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f
277
278 -make_PDB.o: make_PDB.f ncs_constr.f90
279 - $(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f
280 +make_PDB.o: make_PDB.f ncs_constr.o
281 + $(FC) $(FFLAGS) -c make_PDB.f
282
283 make_CIF.o: make_CIF.f ncs_constr.f90
284 - $(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f
285 + $(FC) $(FFLAGS) -c make_CIF.f
286
287 refmac: $(SUBR)
288 - $(FC) $(FFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
289 + $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
290
291 -mol2_file.o: mol2_file.f odb_files.f90
292 - $(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f
293 +mol2_file.o: mol2_file.f odb_files.o
294 + $(FC) $(FFLAGS) -c mol2_file.f
295
296 -odb_files.o: odb_files.f90 elements_module.f90 enerf77mod.f
297 - $(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90
298 +odb_files.o: odb_files.f90 elements_module.o enerf77mod.o
299 + $(FC) $(FFLAGS) -c odb_files.f90
300
301 elements_module.o: elements_module.f90
302 $(FC) $(FFLAGS) -c elements_module.f90
303
304 -make_lib2.o: make_lib2.f odb_files.f90
305 - $(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f
306 +make_lib2.o: make_lib2.f odb_files.o
307 + $(FC) $(FFLAGS) -c make_lib2.f
308
309 pdb2libcheck.o: pdb2libcheck.f90
310 $(FC) $(FFLAGS) -c pdb2libcheck.f90
311
312 -libcheck.o: libcheck.f elements_module.f90 pdb2libcheck.f90
313 - $(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f
314 +libcheck.o: libcheck.f elements_module.o pdb2libcheck.o
315 + $(FC) $(FFLAGS) -c libcheck.f
316
317 header2matr.o: header2matr.f90
318 $(FC) $(FFLAGS) -c header2matr.f90
319 @@ -360,16 +351,17 @@ freer_twin.o: freer_twin.f90
320 $(FC) $(FFLAGS) -c freer_twin.f90
321
322 libcheck: $(SUBL)
323 - $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
324 + $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
325
326 free_twin: $(SUB_FREE)
327 - $(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE)
328 + $(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK)
329
330
331 header2matr: $(SUB_HEADER)
332 - $(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
333 + $(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
334
335 clean:
336 /bin/rm *.o *.mod
337
338 bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h
339 + $(CXX) $(CXXFLAGS) -c bridge.cpp