Fixed prll compilation

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

1 files changed, 184 insertions, 0 deletions

diff --git a/sci-chemistry/refmac/files/5.6.0081-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0081-allow-dynamic-linking.patch
new file mode 100644
index 000000000000..33defbfc7086
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.6.0081-allow-dynamic-linking.patch
@@ -0,0 +1,184 @@
+diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
+index 3f858c8..a8ab515 100644
+--- a/makefile_refmac.inc1
++++ b/makefile_refmac.inc1
+@@ -89,9 +89,7 @@ messy_pdb.o                 \
+ bridge.o                    \
+ i0.o                        \
+ i1.o                        \
+-chbevl.o                    \
+-$(LLIBCIF)                  \
+-$(LLIBLAPACK)
++chbevl.o
+ 
+ 
+ SUBL =                      \
+@@ -124,9 +122,7 @@ cell_symm_subrs.o           \
+ iheap_sort.o                \
+ linalgebra.o                \
+ math_refmac.o               \
+-subnumrec.o                 \
+-$(LLIBLAPACK)               \
+-$(LLIBCCP)
++subnumrec.o
+ 
+ #--------------------------------------------------------------------------------
+ 
+@@ -150,20 +146,20 @@ twin77mod.o:  twin77mod.f
+ 	$(FC) $(FFLAGS) -c twin77mod.f
+ 
+ 
+-optimise_solvent_all.o: optimise_solvent_all.f90
++optimise_solvent_all.o: optimise_solvent_all.f90 atomf77mod.o
+ 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90
+ 
+-ncs_rest.o: ncs_ncs_generate.f90 ncs_rest.f
+-	$(FC) $(FFLAGS) -c ncs_ncs_generate.f90 ncs_rest.f
++ncs_rest.o: ncs_ncs_generate.o ncs_rest.f
++	$(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: dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f
+-	$(FC) $(FFLAGS) -c dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90  lsq_exp2.f
++lsq_exp2.o: dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f
++	$(FC) $(FFLAGS) -c lsq_exp2.f
+ 
+-vdw_and_contacts.o: vdw_and_contacts.f local_tls.f90 ridge.f90 
+-	$(FC) $(FFLAGS) -c ridge.f90 local_tls.f90 vdw_and_contacts.f
++vdw_and_contacts.o: vdw_and_contacts.f local_tls.o ridge.o
++	$(FC) $(FFLAGS) -c vdw_and_contacts.f
+ 
+ dist_routines.o: dist_routines.f90
+ 	$(FC) $(FFLAGS) -c dist_routines.f90
+@@ -178,8 +174,8 @@ align_refmac.o: align_refmac.f90
+ 	$(FC) $(FFLAGS) -c align_refmac.f90
+ 
+ 
+-hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 hkon_secder_tch.f
++hkon_secder_tch.o: hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o optimise_solvent_all.o
++	$(FC) $(FFLAGS) -c hkon_secder_tch.f
+ 
+ oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90
+ 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 filter_params.f90 oppro_allocate.f
+@@ -187,50 +183,50 @@ oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90
+ coords.o: coords.f90 atomf77mod.f
+ 	$(FC) $(FFLAGS) -c atomf77mod.f coords.f90
+ 
+-refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90
+-	$(FC) $(FFLAGS) -c coords.f90 automorphism.f90 refpre_twin.f
++refpre_twin.o: refpre_twin.f coords.o automorphism.o
++	$(FC) $(FFLAGS) -c refpre_twin.f
+ 
+ automorphism.o: automorphism.f90
+ 	$(FC) $(FFLAGS) -c automorphism.f90
+ 
+-mtz_write_twin.o: mtz_write_twin.f filter_params.f90
+-	$(FC) $(FFLAGS) -c filter_params.f90 mtz_write_twin.f
++mtz_write_twin.o: mtz_write_twin.f filter_params.o
++	$(FC) $(FFLAGS) -c mtz_write_twin.f
+ 
+ filter_params.o: filter_params.f90
+ 	$(FC) $(FFLAGS) -c filter_params.f90
+ 
+-rcard_tor1.o: rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 rcard_tor1.f
++rcard_tor1.o: rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o
++	$(FC) $(FFLAGS) -c rcard_tor1.f
+ 
+-local_tls.o: local_tls.f90 linalgebra_f90.f90
+-	$(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90
++local_tls.o: local_tls.f90 linalgebra_f90.o
++	$(FC) $(FFLAGS) -c local_tls.f90
+ 
+ linalgebra_f90.o: linalgebra_f90.f90 
+ 	$(FC) $(FFLAGS) -c linalgebra_f90.f90
+ 
+-make_refmac_dummy.o: make_refmac_dummy.f optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 make_refmac_dummy.f
++make_refmac_dummy.o: make_refmac_dummy.f optimise_solvent_all.o
++	$(FC) $(FFLAGS) -c make_refmac_dummy.f
+ 
+-ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 ml_scaling_double.f
++ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o
++	$(FC) $(FFLAGS) -c ml_scaling_double.f
+ 
+-refall_twin.o: refall_twin.f optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 refall_twin.f
++refall_twin.o: refall_twin.f optimise_solvent_all.o
++	$(FC) $(FFLAGS) -c refall_twin.f
+ 
+-rharvest.o: rharvest.f optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 rharvest.f
++rharvest.o: rharvest.f optimise_solvent_all.o
++	$(FC) $(FFLAGS) -c rharvest.f
+ 
+-solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 solvent_contr_mask.f
++solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o atomf77mod.o
++	$(FC) $(FFLAGS) -c  atomf77mod.f solvent_contr_mask.f
+ 
+-subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 subag_scale_hessian.f
++subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o
++	$(FC) $(FFLAGS) -c subag_scale_hessian.f
+ 
+-subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 subcf_scale1.f
++subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o
++	$(FC) $(FFLAGS) -c subcf_scale1.f
+ 
+-refmac_xml.o: refmac_xml.f optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 refmac_xml.f
++refmac_xml.o: refmac_xml.f optimise_solvent_all.o
++	$(FC) $(FFLAGS) -c refmac_xml.f
+ 
+ hkl_pack.o:  hkl_pack.f90
+ 	$(FC) $(FFLAGS) -c hkl_pack.f90
+@@ -239,30 +235,31 @@ subvag.o: subvag.f hkl_pack.f90
+ 	$(FC) $(FFLAGS) -c hkl_pack.f90 subvag.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.f
++	$(FC) $(FFLAGS) -c enerf77mod.f 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
+ 
+ libcheck:	$(SUBL)
+-	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
+ 
+ clean:
+ 	/bin/rm *.o
+ 
+ bridge.o:			bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h
++	$(CXX) $(CXXFLAGS) -c bridge.cpp