Version Bump

Package-Manager: portage-2.1.9.24/cvs/Linux x86_64

4 files changed, 408 insertions, 5 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index dd9092d9c7c4..256464fa799a 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/refmac
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.19 2010/10/20 06:32:26 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.20 2010/11/03 19:01:51 jlec Exp $
+
+*refmac-5.6.0088 (03 Nov 2010)
+
+  03 Nov 2010; Justin Lecher <jlec@gentoo.org>
+  +files/5.6.0088-allow-dynamic-linking.patch, +refmac-5.6.0088.ebuild:
+  Version Bump
 
 *refmac-5.6.0086 (20 Oct 2010)
 
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
index 4a40430763f7..d9a017a27de5 100644
--- a/sci-chemistry/refmac/Manifest
+++ b/sci-chemistry/refmac/Manifest
@@ -12,8 +12,10 @@ AUX 5.6.0083-allow-dynamic-linking.patch 9977 RMD160 d51728adbfe593832f71a6fe935
 AUX 5.6.0084-allow-dynamic-linking.patch 9851 RMD160 8e6a6116bc824452d9c9e377ca99fd345e0ba23f SHA1 b384d5e2d875d0d87dc62e250602d47a3658c0e8 SHA256 088fe80b3d7eb2910819f8b0f5fa83a1f25620fed88b7c4df2818a6edf440cb1
 AUX 5.6.0085-allow-dynamic-linking.patch 10030 RMD160 76ce00e00d978274cb1b5b585d583c27fff30e3f SHA1 53e2cac876c7d5420a6f7872a0dc8f1eeb9bc74d SHA256 c14115b5d50c7312c4e2cf5ca39f3c53810093555352f3d1bedd97a4aff38e4c
 AUX 5.6.0086-allow-dynamic-linking.patch 10030 RMD160 76ce00e00d978274cb1b5b585d583c27fff30e3f SHA1 53e2cac876c7d5420a6f7872a0dc8f1eeb9bc74d SHA256 c14115b5d50c7312c4e2cf5ca39f3c53810093555352f3d1bedd97a4aff38e4c
+AUX 5.6.0088-allow-dynamic-linking.patch 15141 RMD160 9381d3cd8f9ca0d245fe40695c36c9b4fcaf1c11 SHA1 5de5ef929af460d18908f78f6e3c81cad64e6556 SHA256 b5a9f7bce38f839a532c806dc47ee9d81d67cfda703ad2f3e3c31cb779e4ce98
 DIST refmac5.6_source_v5.6.0085.tar.gz 1276744 RMD160 968d0c18039a5ae19472df3c2b13a7f3c95df99b SHA1 56141b2c1c08194b24d00e444b802c86574505b1 SHA256 f4bc6a02f36c7a57e2a5ef03eb4040854806ff62f56b97cd2c9335ab73e9df70
 DIST refmac5.6_source_v5.6.0086.tar.gz 1276868 RMD160 dae01bd49871ff483f8bc8058b191f1bd96612aa SHA1 4d0e0f30adb110cc3976aefcf5c0e08e80cf7045 SHA256 37a46cdfd1e0db31cd312bf267fc2983bf6683d0b775e32e3535d00601e70f69
+DIST refmac5.6_source_v5.6.0088.tar.gz 1376837 RMD160 aaf7c3bb8846ad28a04580af5bd78c7af0838d03 SHA1 23aae26208efe37020dd02a3825976c97fce8613 SHA256 d2b28f24890f6333359c7351ee8430103ad925343ce5c47803e794e03ea40141
 DIST refmac_5.5.0109.tar.gz 1326779 RMD160 3b603c13638407cceb907bd43ac0a971b587c116 SHA1 3cc35a55df71bac4de3eec9cf0e690e221ae3c86 SHA256 38d416c94e1f86a0676d48d7ddaeb4af272970b8cd6b084e70aa38481327c59e
 DIST refmac_5.5.0110.tar.gz 1326832 RMD160 6613ca8b70e54e7827f8ff02b7d497560cb83e39 SHA1 ba2e38db6c88550bd901b474de881d6514b4d74e SHA256 1353fb1042586ec8fa37d0a90f274890d0ccc02377af5216200662338dfe08ca
 DIST test-framework.tar.gz 130933173 RMD160 7122539dc713615dca2ddaddfd8d152cd22624d0 SHA1 1d3e3019a67afb9b2346e919c859d402d3250fea SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605
@@ -22,12 +24,13 @@ EBUILD refmac-5.5.0110-r1.ebuild 1787 RMD160 9017aa6e2f7d9d764904eeeb624c4480255
 EBUILD refmac-5.5.0110.ebuild 1805 RMD160 80e546666e72290365c99c542abcef90a3394bb8 SHA1 a1731838742679b66984018fb8d25b8dbb11ae29 SHA256 8f825fc7f75854d631d6c6b037398237b8231a9fdc162e9ab1c6a46490b0a957
 EBUILD refmac-5.6.0085.ebuild 1786 RMD160 3f5bd9e12f1ad100a499794d1244b52a8b1bfdd2 SHA1 69ba8bd099d567ac209dfdc10e6505ffd97d9710 SHA256 d09f9c11f05ed5fd625bd04304538af95b796143f2f064cf5f1ec4f141f9b48b
 EBUILD refmac-5.6.0086.ebuild 1786 RMD160 2ed810e339b67e19c32cb5c08f51caffa0e4a6db SHA1 19af34f8491c8250033c5130ac97c9fb39b98269 SHA256 c12923fcaf984a2fd8506f00c475e74059bbffa8934dd0b33916359504b37a93
-MISC ChangeLog 3460 RMD160 7fa5280ce2a8217a7e2eede81cf812ed52025ff4 SHA1 a5ffa654055c68197a0258503901eadebd282ad7 SHA256 86c5870d4c3da404d06089d1bbdb1c5d95a0d709f966a4a54a70efc3721b0510
+EBUILD refmac-5.6.0088.ebuild 1807 RMD160 11669262e2dfa49b416c803408608aea19d13cd6 SHA1 52f78c5d4c9e3849e1e49fb1bec8b82f3e3703fc SHA256 73ba767ef2be57e9e6f4076f634715caf505344eefa126b2fcb4e34f76f0dbfc
+MISC ChangeLog 3627 RMD160 6cfa331681230f85fc4cb7ea8d0122c3680bb9d5 SHA1 69c91ae156ed204b258fe3adcaaaa27d354882e9 SHA256 e2c0355c54a37c48f81da6c1762163bd1422d447bfd0a1546eba4ec239a6c458
 MISC metadata.xml 311 RMD160 df83b13d491a71b729455b664088d89ddbde1c8c SHA1 fffd2a5645181aa12ac9b6f74da9a011cdcf1b97 SHA256 782521c7e16d7eec82d7b7e7c43102806e7f72bc7366401808b1e1ac6e26045a
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-=7qdp
+iEYEARECAAYFAkzRsaQACgkQgAnW8HDreRZEXQCdFwK4FG/tiQozFJDhxZSPrRCY
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diff --git a/sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch
new file mode 100644
index 000000000000..1a55ad125d2a
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch
@@ -0,0 +1,323 @@
+diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
+index 80b199e..d3ab4c8 100644
+--- a/makefile_refmac.inc1
++++ b/makefile_refmac.inc1
+@@ -93,9 +93,7 @@ messy_pdb.o                 \
+ bridge.o                    \
+ i0.o                        \
+ i1.o                        \
+-chbevl.o                    \
+-$(LLIBCIF)                  \
+-$(LLIBLAPACK)
++chbevl.o
+ 
+ 
+ SUBL =                      \
+@@ -130,9 +128,7 @@ cell_symm_subrs.o           \
+ iheap_sort.o                \
+ linalgebra.o                \
+ math_refmac.o               \
+-subnumrec.o                 \
+-$(LLIBLAPACK)               \
+-$(LLIBCCP)
++subnumrec.o
+ 
+ SUB_FREE  =                 \
+ freer_twin.o                 \
+@@ -142,9 +138,7 @@ subnumrec.o                 \
+ libT.o                      \
+ iheap_sort.o                \
+ cell_symm_subrs.o           \
+-math_refmac.o               \
+-$(LLIBLAPACK)               \
+-$(LLIBCCP)
++math_refmac.o
+ 
+ SUB_HEADER = header2matr.o
+ #--------------------------------------------------------------------------------
+@@ -179,32 +173,32 @@ rharvest_mod.o:  rharvest_mod.f90
+ twin77mod.o:  twin77mod.f
+ 	$(FC) $(FFLAGS) -c twin77mod.f
+ 
+-max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f
++max_with_twins.o: restr_files.o max_with_twins.f
++	$(FC) $(FFLAGS) -c max_with_twins.f
+ 
+-merohedr_twin.o: restr_files.f90 merohedr_twin.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f
++merohedr_twin.o: restr_files.o merohedr_twin.f
++	$(FC) $(FFLAGS) -c merohedr_twin.f
+ 
+-ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f weights.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ls_scaling_twin_save.f
++ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f
++	$(FC) $(FFLAGS) -c ls_scaling_twin_save.f
+ 
+-ml_params_refine.o: restr_files.f90 ml_params_refine.f weights.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ml_params_refine.f
++ml_params_refine.o: restr_files.o ml_params_refine.f
++	$(FC) $(FFLAGS) -c ml_params_refine.f
+ 
+-optimise_solvent_all.o: optimise_solvent_all.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90
++optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o
++	$(FC) $(FFLAGS) -c optimise_solvent_all.f90
+ 
+-ncs_rest.o: restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f
++ncs_rest.o: restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o
++	$(FC) $(FFLAGS) -c ncs_rest.f
+ 
+-ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90
+-	$(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90
++ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o
++	$(FC) $(FFLAGS) -c ncs_ncs_generate.f90
+ 
+-lsq_exp2.o: restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90  lsq_exp2.f weights.f90 rharvest_mod.f90
++lsq_exp2.o: restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f weights.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c lsq_exp2.f
+ 
+-vdw_and_contacts.o: vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f
++vdw_and_contacts.o: vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o
++	$(FC) $(FFLAGS) -c vdw_and_contacts.f
+ 
+ dist_routines.o: dist_routines.f90
+ 	$(FC) $(FFLAGS) -c dist_routines.f90
+@@ -218,140 +212,137 @@ ridge.o: ridge.f90
+ align_refmac.o: align_refmac.f90
+ 	$(FC) $(FFLAGS) -c align_refmac.f90
+ 
+-rigid_allocate.o: restr_files.f90 rigid_allocate.f agreem.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f
+-
+-tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f
++rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o
++	$(FC) $(FFLAGS) -c rigid_allocate.f
+ 
+-hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \
+-                   restr_files.f90 weights.f90 agreem.f90 rharvest.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \
+-	                   hkon_secder_tch.f weights.f90 agreem.f90 rharvest.f
++tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o
++	$(FC) $(FFLAGS) -c tls_allocate.f
+ 
+-oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f
++hkon_secder_tch.o: hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \
++                   restr_files.o weights.o agreem.o rharvest.f
++	$(FC) $(FFLAGS) -c hkon_secder_tch.f
+ 
+-read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f
++oppro_allocate.o: oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o
++	$(FC) $(FFLAGS) -c oppro_allocate.f
+ 
+-coords.o: coords.f90 atomf77mod.f
+-	$(FC) $(FFLAGS) -c atomf77mod.f coords.f90
++read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o
++	$(FC) $(FFLAGS) -c read_extra_restraints.f
+ 
++coords.o: coords.f90 atomf77mod.o
++	$(FC) $(FFLAGS) -c coords.f90
+ 
+-ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90
+ 
+-fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90 
+-	$(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90
++ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o
++	$(FC) $(FFLAGS) -c ls_scaling_double.f
+ 
+-calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
++fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o
++	$(FC) $(FFLAGS) -c fast_hessian_tabulation.f
+ 
+-refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f
++calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c calc_stats_twin.f
+ 
++refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c refpre_twin.f
+ 
+-decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f
++decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f
++	$(FC) $(FFLAGS) -c decide_twin_opers_0.f
+ 
+ automorphism.o: automorphism.f90
+ 	$(FC) $(FFLAGS) -c automorphism.f90
+ 
+-mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90 agreem.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f
++mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.o
++	$(FC) $(FFLAGS) -c mtz_write_twin.f
+ 
+ filter_params.o: filter_params.f90
+ 	$(FC) $(FFLAGS) -c filter_params.f90
+ 
+-rcard_tor1.o: rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 \
+-              agreem.f90 rharvest_mod.f90 ncs_constr.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \
+-	                   agreem.f90 rharvest_mod.f90 ncs_constr.f90 rcard_tor1.f
++rcard_tor1.o: rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o weights.o \
++              agreem.o rharvest_mod.o ncs_constr.o
++	$(FC) $(FFLAGS) -c rcard_tor1.f
+ 
+-inout_routines.o: restr_files.f90 inout_routines.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f
++inout_routines.o: restr_files.o inout_routines.f
++	$(FC) $(FFLAGS) -c inout_routines.f
+ 
+-local_tls.o: local_tls.f90 linalgebra_f90.f90
+-	$(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90
++local_tls.o: local_tls.f90 linalgebra_f90.o
++	$(FC) $(FFLAGS) -c local_tls.f90
+ 
+ linalgebra_f90.o: linalgebra_f90.f90 
+ 	$(FC) $(FFLAGS) -c linalgebra_f90.f90
+ 
+-make_refmac_dummy.o: make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f
++make_refmac_dummy.o: make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c make_refmac_dummy.f
+ 
+-ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f
++ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c ml_scaling_double.f
+ 
+-refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90  weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f
++refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c refall_twin.f
+ 
+-rharvest.o: rharvest.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90  weights.f90 agreem.f90 rharvest_mod.f90 rharvest.f
++rharvest.o: rharvest.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c rharvest.f
+ 
+-solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f
++solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o
++	$(FC) $(FFLAGS) -c solvent_contr_mask.f
+ 
+-subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
+-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f
++subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o weights.o agreem.o rharvest_mod.o ncs_constr.o
++	$(FC) $(FFLAGS) -c subag_scale_hessian.f
+ 
+-aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90
+-	$(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f
++aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o
++	$(FC) $(FFLAGS) -c aniso_ref_eigen.f
+ 
+-subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f
++subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c subcf_scale1.f
+ 
+-bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f
+-	$(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90
++bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o
++	$(FC) $(FFLAGS) -c bvalue_routines.f90
+ 
+-newentry_idealise.o:: newentry_idealise.f weights.f90
+-	$(FC) $(FFLAGS) -c newentry_idealise.f weights.f90
++newentry_idealise.o:: newentry_idealise.f weights.o
++	$(FC) $(FFLAGS) -c newentry_idealise.f
+ 
+-occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90
++occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c occupancy_only_refine.f
+ 
+-refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90  refmac_completeness.f90
+-	$(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90
++refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90
++	$(FC) $(FFLAGS) -c refmac_completeness.f90
+ 
+-refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90
+-	$(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f
++refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o
++	$(FC) $(FFLAGS) -c refmac_xml.f
+ 
+ hkl_pack.o:  hkl_pack.f90
+ 	$(FC) $(FFLAGS) -c hkl_pack.f90
+ 
+-extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90
+-	$(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90
++extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o
++	$(FC) $(FFLAGS) -c extra_eigen.f
+ 
+-subvag.o: subvag.f hkl_pack.f90
++subvag.o: subvag.f hkl_pack.o
+ 	$(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f
+ 
+-make_PDB.o: make_PDB.f ncs_constr.f90
+-	$(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f
++make_PDB.o: make_PDB.f ncs_constr.o
++	$(FC) $(FFLAGS) -c make_PDB.f
+ 
+ make_CIF.o: make_CIF.f ncs_constr.f90
+-	$(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f
++	$(FC) $(FFLAGS) -c make_CIF.f
+ 
+ refmac:	$(SUBR)
+-	$(FC) $(FFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
+ 
+-mol2_file.o:	mol2_file.f odb_files.f90
+-	$(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f
++mol2_file.o:	mol2_file.f odb_files.o
++	$(FC) $(FFLAGS) -c mol2_file.f
+ 
+-odb_files.o:	odb_files.f90 elements_module.f90 enerf77mod.f
+-	$(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90
++odb_files.o:	odb_files.f90 elements_module.o enerf77mod.o
++	$(FC) $(FFLAGS) -c odb_files.f90
+ 
+ elements_module.o:	elements_module.f90
+ 	$(FC) $(FFLAGS) -c elements_module.f90
+ 
+-make_lib2.o:	make_lib2.f odb_files.f90 
+-	$(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f
++make_lib2.o:	make_lib2.f odb_files.o
++	$(FC) $(FFLAGS) -c make_lib2.f
+ 
+ pdb2libcheck.o:	pdb2libcheck.f90
+ 	$(FC) $(FFLAGS) -c pdb2libcheck.f90
+ 
+-libcheck.o:	libcheck.f elements_module.f90 pdb2libcheck.f90
+-	$(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f
++libcheck.o:	libcheck.f elements_module.o pdb2libcheck.o
++	$(FC) $(FFLAGS) -c libcheck.f
+ 
+ header2matr.o:	header2matr.f90
+ 	$(FC) $(FFLAGS) -c header2matr.f90
+@@ -360,16 +351,17 @@ freer_twin.o:	freer_twin.f90
+ 	$(FC) $(FFLAGS) -c  freer_twin.f90
+ 
+ libcheck:	$(SUBL)
+-	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
+ 
+ free_twin:	$(SUB_FREE)
+-	$(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK)
+ 
+ 
+ header2matr:	$(SUB_HEADER)
+-	$(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
+ 
+ clean:
+ 	/bin/rm *.o *.mod
+ 
+ bridge.o:			bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h
++	$(CXX) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/refmac-5.6.0088.ebuild b/sci-chemistry/refmac/refmac-5.6.0088.ebuild
new file mode 100644
index 000000000000..9d4ddfcedad5
--- /dev/null
+++ b/sci-chemistry/refmac/refmac-5.6.0088.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0088.ebuild,v 1.1 2010/11/03 19:01:51 jlec Exp $
+
+EAPI="2"
+
+inherit fortran base toolchain-funcs versionator
+
+MY_PV="$(get_version_component_range 1-2)_source_v${PV}"
+
+DESCRIPTION="Macromolecular crystallographic refinement program"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac/"
+SRC_URI="${HOMEPAGE}data/refmac_experimental/${PN}${MY_PV}.tar.gz
+	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
+
+SLOT="0"
+LICENSE="ccp4"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+	sci-libs/ccp4-libs
+	sci-libs/mmdb
+	>sci-libs/monomer-db-1
+	virtual/blas
+	virtual/lapack"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-allow-dynamic-linking.patch
+	)
+
+src_prepare() {
+	base_src_prepare
+	use test && epatch "${FILESDIR}"/5.5-test.log.patch
+}
+
+src_compile() {
+	emake \
+		FC=$(tc-getFC) \
+		CC=$(tc-getCC) \
+		CXX=$(tc-getCXX) \
+		COPTIM="${CFLAGS}" \
+		FOPTIM="${FFLAGS:- -O2}" \
+		VERSION="" \
+		XFFLAGS="-fno-second-underscore" \
+		LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \
+		LLIBLAPACK="$(pkg-config --libs lapack blas)" \
+		|| die
+}
+
+src_test() {
+	einfo "Starting tests ..."
+	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() {
+	for i in refmac libcheck FreeTwin header2matr; do
+		exeinto /usr/libexec/ccp4/bin/
+		doexe ${i} || die
+		dosym ../libexec/ccp4/bin/${i} /usr/bin/${i}
+	done
+	dosym refmac /usr/bin/refmac5 || die
+}