Version Bump, Cleanup, Fixes for gcc-4.6

(Portage version: 2.2.0_alpha30/cvs/Linux x86_64)
author: Justin Lecher <jlec@gentoo.org> 2011-04-21 07:08:54 +0000
committer: Justin Lecher <jlec@gentoo.org> 2011-04-21 07:08:54 +0000
commit: 12c324dfa08e4f8527cdc4b857ec47838ff80e3c (patch)
tree: 8ad53c52e16ada3729599321505b3a1e5e629c83 /sci-chemistry
parent: Version Bump (diff)
download: gentoo-2-12c324dfa08e4f8527cdc4b857ec47838ff80e3c.tar.gz
gentoo-2-12c324dfa08e4f8527cdc4b857ec47838ff80e3c.tar.bz2
gentoo-2-12c324dfa08e4f8527cdc4b857ec47838ff80e3c.zip
27 files changed, 74 insertions, 3660 deletions
diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index 892f4241ba48..76798b925a0f 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -1,6 +1,31 @@
 # ChangeLog for sci-chemistry/refmac
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.43 2011/02/26 11:30:08 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.44 2011/04/21 07:08:54 jlec Exp $
+
+*refmac-5.6.0116 (21 Apr 2011)
+
+  21 Apr 2011; Justin Lecher <jlec@gentoo.org> +files/5.5.0110-gcc4.6.patch,
+  refmac-5.5.0110-r3.ebuild, +files/5.6.0110-allow-dynamic-linking.patch,
+  -refmac-5.6.0097.ebuild, +files/5.6.0116-allow-dynamic-linking.patch,
+  refmac-5.5.0110-r2.ebuild, -refmac-5.6.0098.ebuild, -refmac-5.6.0099.ebuild,
+  -refmac-5.6.0102.ebuild, -files/5.5-allow-dynamic-linking.patch,
+  -refmac-5.6.0102-r1.ebuild, -files/5.6.0102-allow-dynamic-linking.patch,
+  refmac-5.6.0110.ebuild, -files/5.6.0075-allow-dynamic-linking.patch,
+  +refmac-5.6.0116.ebuild, -files/5.6.0078-allow-dynamic-linking.patch,
+  -files/5.6.0080-allow-dynamic-linking.patch,
+  -files/5.6.0081-allow-dynamic-linking.patch,
+  -files/5.6.0083-allow-dynamic-linking.patch,
+  -files/5.6.0084-allow-dynamic-linking.patch,
+  -files/5.6.0085-allow-dynamic-linking.patch,
+  -files/5.6.0086-allow-dynamic-linking.patch,
+  -files/5.6.0088-allow-dynamic-linking.patch,
+  -files/5.6.0089-allow-dynamic-linking.patch,
+  -files/5.6.0092-allow-dynamic-linking.patch,
+  -files/5.6.0094-allow-dynamic-linking.patch,
+  -files/5.6.0096-allow-dynamic-linking.patch,
+  -files/5.6.0097-allow-dynamic-linking.patch,
+  -files/5.6.0098-allow-dynamic-linking.patch:
+  Version Bump, Cleanup, Fixes for gcc-4.6
 
 *refmac-5.6.0110 (26 Feb 2011)
 
diff --git a/sci-chemistry/refmac/files/5.5-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5-allow-dynamic-linking.patch
deleted file mode 100644
index 415ba9d08cb0..000000000000
--- a/sci-chemistry/refmac/files/5.5-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,66 +0,0 @@
---- makefile_refmac.inc1.orig	2008-08-01 22:17:14.000000000 -0700
-+++ makefile_refmac.inc1	2008-08-01 22:18:46.000000000 -0700
-@@ -69,9 +69,7 @@
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(LLIBCIF)                  \
--$(LLIBLAPACK)
-+chbevl.o                    
- #$(LLIBCCP)                  \
- #crt0.o                      \
- 
-@@ -95,8 +93,7 @@
- emin.o                      \
- libcheck_min.o              \
- mol2_file.o                 \
--sdf_files.o                 \
--$(LLIBCCP)
-+sdf_files.o                 
- 
- SUBM =                      \
- main_makecif.o              \
-@@ -116,9 +113,7 @@
- make_PDB.o                  \
- makecif.o                   \
- make_unix_ccp4.o            \
--make_vdw.o                  \
--$(LLIBCCP)                  \
--$(LLIBCIF)
-+make_vdw.o                  
- 
- SUBT =                      \
- tlsgroups.o                 \
-@@ -142,9 +137,7 @@
- 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
-@@ -154,16 +147,16 @@
- all:	refmac libcheck makecif
- 
- refmac:	$(SUBR)
--	$(FC) $(FFLAGS) -o refmac${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) $(LLIBCIF)
- 
- clean:
- 	/bin/rm *.o
diff --git a/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch b/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch
new file mode 100644
index 000000000000..3969cc9c8586
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch
@@ -0,0 +1,17 @@
+ hkon_secder_tch.f |    3 ++-
+ 1 files changed, 2 insertions(+), 1 deletions(-)
+
+diff --git a/hkon_secder_tch.f b/hkon_secder_tch.f
+index 31794b0..86d2cdf 100644
+--- a/hkon_secder_tch.f
++++ b/hkon_secder_tch.f
+@@ -3724,7 +3724,8 @@ c---External functions and subprutines
+       INTEGER NWORKSPACE
+       REAL*8 TOLER
+       REAL*8 WORKSPACE(300)
+-      REAL LSTLSQ,D2DF_WEIGHT
++      REAL*8 D2DF_WEIGHT
++      REAL LSTLSQ
+ C
+       INTEGER IBIN,IBIN_S
+       INTEGER I,J,K
diff --git a/sci-chemistry/refmac/files/5.6.0075-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0075-allow-dynamic-linking.patch
deleted file mode 100644
index e86a3a69dfd8..000000000000
--- a/sci-chemistry/refmac/files/5.6.0075-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 97791e0..6c43c5d 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -83,9 +83,7 @@ messy_pdb.o                 \
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(LLIBCIF)                  \
--$(LLIBLAPACK)
-+chbevl.o
- 
- 
- SUBL =                      \
-@@ -118,9 +116,8 @@ cell_symm_subrs.o           \
- iheap_sort.o                \
- linalgebra.o                \
- math_refmac.o               \
--subnumrec.o                 \
--$(LLIBLAPACK)               \
--$(LLIBCCP)
-+subnumrec.o
-+
- 
- #--------------------------------------------------------------------------------
- 
-@@ -188,7 +185,7 @@ linalgebra_f90.o: linalgebra_f90.f90
- 	$(FC) $(FFLAGS) -c linalgebra_f90.f90
- 
- 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
-@@ -209,7 +206,7 @@ libcheck.o:	libcheck.f elements_module.f90 pdb2libcheck.f90
- 	$(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f
- 
- libcheck:	$(SUBL)
--	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
- 
- clean:
- 	/bin/rm *.o
diff --git a/sci-chemistry/refmac/files/5.6.0078-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0078-allow-dynamic-linking.patch
deleted file mode 100644
index b1d74de4bbb5..000000000000
--- a/sci-chemistry/refmac/files/5.6.0078-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 3f858c8..8b32cab 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -89,9 +89,7 @@ messy_pdb.o                 \
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(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
- 
- #--------------------------------------------------------------------------------
- 
-@@ -150,7 +146,7 @@ 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
-@@ -178,7 +174,7 @@ 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
-+hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 optimise_solvent_all.o
- 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 hkon_secder_tch.f
- 
- oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90
-@@ -220,8 +216,8 @@ refall_twin.o: refall_twin.f optimise_solvent_all.f90
- rharvest.o: rharvest.f optimise_solvent_all.f90
- 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 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.f90 atomf77mod.o
-+	$(FC) $(FFLAGS) -c  atomf77mod.f optimise_solvent_all.f90 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
-@@ -229,7 +225,7 @@ subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90
- subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90
- 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 subcf_scale1.f
- 
--refmac_xml.o: refmac_xml.f optimise_solvent_all.f90
-+refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 optimise_solvent_all.o
- 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 refmac_xml.f
- 
- hkl_pack.o:  hkl_pack.f90
-@@ -239,7 +235,7 @@ 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
-@@ -260,7 +256,7 @@ libcheck.o:	libcheck.f elements_module.f90 pdb2libcheck.f90
- 	$(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f
- 
- libcheck:	$(SUBL)
--	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
- 
- clean:
- 	/bin/rm *.o
diff --git a/sci-chemistry/refmac/files/5.6.0080-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0080-allow-dynamic-linking.patch
deleted file mode 100644
index 6f5d1c6efe98..000000000000
--- a/sci-chemistry/refmac/files/5.6.0080-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,94 +0,0 @@
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 3f858c8..04e6790 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -89,9 +89,7 @@ messy_pdb.o                 \
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(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
- 
- #--------------------------------------------------------------------------------
- 
-@@ -150,7 +146,7 @@ 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
-@@ -178,7 +174,7 @@ 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
-+hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 optimise_solvent_all.o
- 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 hkon_secder_tch.f
- 
- oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90
-@@ -220,8 +216,8 @@ refall_twin.o: refall_twin.f optimise_solvent_all.f90
- rharvest.o: rharvest.f optimise_solvent_all.f90
- 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 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.f90 atomf77mod.o
-+	$(FC) $(FFLAGS) -c  atomf77mod.f optimise_solvent_all.f90 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
-@@ -229,7 +225,7 @@ subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90
- subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90
- 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 subcf_scale1.f
- 
--refmac_xml.o: refmac_xml.f optimise_solvent_all.f90
-+refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 optimise_solvent_all.o
- 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 refmac_xml.f
- 
- hkl_pack.o:  hkl_pack.f90
-@@ -239,9 +235,9 @@ 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
-+mol2_file.o:	mol2_file.f odb_files.o
- 	$(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f
- 
- odb_files.o:	odb_files.f90 elements_module.f90 enerf77mod.f
-@@ -250,7 +246,7 @@ odb_files.o:	odb_files.f90 elements_module.f90 enerf77mod.f
- elements_module.o:	elements_module.f90
- 	$(FC) $(FFLAGS) -c elements_module.f90
- 
--make_lib2.o:	make_lib2.f odb_files.f90 
-+make_lib2.o:	make_lib2.f odb_files.o
- 	$(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f
- 
- pdb2libcheck.o:	pdb2libcheck.f90
-@@ -260,7 +256,7 @@ libcheck.o:	libcheck.f elements_module.f90 pdb2libcheck.f90
- 	$(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f
- 
- libcheck:	$(SUBL)
--	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
- 
- clean:
- 	/bin/rm *.o
diff --git a/sci-chemistry/refmac/files/5.6.0081-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0081-allow-dynamic-linking.patch
deleted file mode 100644
index 33defbfc7086..000000000000
--- a/sci-chemistry/refmac/files/5.6.0081-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,184 +0,0 @@
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 3f858c8..a8ab515 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -89,9 +89,7 @@ messy_pdb.o                 \
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(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) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.6.0083-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0083-allow-dynamic-linking.patch
deleted file mode 100644
index 6ffe2cf9a6c6..000000000000
--- a/sci-chemistry/refmac/files/5.6.0083-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,237 +0,0 @@
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 3626812..26b2607 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -91,9 +91,7 @@ messy_pdb.o                 \
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(LLIBCIF)                  \
--$(LLIBLAPACK)
-+chbevl.o
- 
- 
- SUBL =                      \
-@@ -127,9 +125,7 @@ cell_symm_subrs.o           \
- iheap_sort.o                \
- linalgebra.o                \
- math_refmac.o               \
--subnumrec.o                 \
--$(LLIBLAPACK)               \
--$(LLIBCCP)
-+subnumrec.o
- 
- #--------------------------------------------------------------------------------
- 
-@@ -155,35 +151,35 @@ twin77mod.o:  twin77mod.f
- 	$(FC) $(FFLAGS) -c twin77mod.f
- 
- 
--max_with_twins.o: restr_files.f90 max_with_twins.f
--	$(FC) $(FFLAGS) -c restr_files.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
--	$(FC) $(FFLAGS) -c restr_files.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
--	$(FC) $(FFLAGS) -c restr_files.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
- 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90
- 
--ncs_rest.o: restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f
--	$(FC) $(FFLAGS) -c restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f
-+ncs_rest.o: restr_files.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: restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f
--	$(FC) $(FFLAGS) -c restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90  lsq_exp2.f
-+lsq_exp2.o: restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f
-+	$(FC) $(FFLAGS) -c lsq_exp2.f
- 
--enm_restraints.o: restr_files.f90 enm_restraints.f
--	$(FC) $(FFLAGS) -c restr_files.f90 enm_restraints.f
-+enm_restraints.o: restr_files.o enm_restraints.f
-+	$(FC) $(FFLAGS) -c enm_restraints.f
- 
--vdw_and_contacts.o: vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 ridge.f90 local_tls.f90 vdw_and_contacts.f
-+vdw_and_contacts.o: vdw_and_contacts.f local_tls.o ridge.o restr_files.o
-+	$(FC) $(FFLAGS) -c vdw_and_contacts.f
- 
- dist_routines.o: dist_routines.f90
- 	$(FC) $(FFLAGS) -c dist_routines.f90
-@@ -197,17 +193,17 @@ 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
--	$(FC) $(FFLAGS) -c restr_files.f90 rigid_allocate.f
-+rigid_allocate.o: restr_files.o rigid_allocate.f
-+	$(FC) $(FFLAGS) -c rigid_allocate.f
- 
--tls_allocate.o: restr_files.f90 tls_allocate.f
--	$(FC) $(FFLAGS) -c restr_files.f90 tls_allocate.f
-+tls_allocate.o: restr_files.o tls_allocate.f
-+	$(FC) $(FFLAGS) -c tls_allocate.f
- 
--hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 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 restr_files.o
-+	$(FC) $(FFLAGS) -c hkon_secder_tch.f
- 
- oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 filter_params.f90 oppro_allocate.f
-+	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 filter_params.f90 oppro_allocate.f
- 
- read_extra_restraints.o: restr_files.f90 read_extra_restraints.f
- 	$(FC) $(FFLAGS) -c restr_files.f90 read_extra_restraints.f
-@@ -215,59 +211,59 @@ read_extra_restraints.o: restr_files.f90 read_extra_restraints.f
- coords.o: coords.f90 atomf77mod.f
- 	$(FC) $(FFLAGS) -c atomf77mod.f coords.f90
- 
--refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 refpre_twin.f
-+refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.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
--	$(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 mtz_write_twin.f
-+mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.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
--	$(FC) $(FFLAGS) -c restr_files.f90 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 restr_files.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
--	$(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 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 refall_twin.f
-+refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.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
-+	$(FC) $(FFLAGS) -c solvent_contr_mask.f
- 
--subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 subag_scale_hessian.f
-+subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.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
- 
--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.f
-+	$(FC) $(FFLAGS) -c bvalue_routines.f90
- 
--refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90
--	$(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 refmac_xml.f
-+refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o
-+	$(FC) $(FFLAGS) -c refmac_xml.f
- 
- hkl_pack.o:  hkl_pack.f90
- 	$(FC) $(FFLAGS) -c hkl_pack.f90
-@@ -276,30 +272,31 @@ 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) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.6.0084-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0084-allow-dynamic-linking.patch
deleted file mode 100644
index ad335bf469bc..000000000000
--- a/sci-chemistry/refmac/files/5.6.0084-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,235 +0,0 @@
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 5263df1..62ccd3b 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -90,9 +90,7 @@ messy_pdb.o                 \
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(LLIBCIF)                  \
--$(LLIBLAPACK)
-+chbevl.o
- 
- 
- SUBL =                      \
-@@ -126,9 +124,7 @@ cell_symm_subrs.o           \
- iheap_sort.o                \
- linalgebra.o                \
- math_refmac.o               \
--subnumrec.o                 \
--$(LLIBLAPACK)               \
--$(LLIBCCP)
-+subnumrec.o
- 
- #--------------------------------------------------------------------------------
- 
-@@ -154,32 +150,32 @@ twin77mod.o:  twin77mod.f
- 	$(FC) $(FFLAGS) -c twin77mod.f
- 
- 
--max_with_twins.o: restr_files.f90 max_with_twins.f
--	$(FC) $(FFLAGS) -c restr_files.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
--	$(FC) $(FFLAGS) -c restr_files.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
--	$(FC) $(FFLAGS) -c restr_files.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
- 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90
- 
--ncs_rest.o: restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f
--	$(FC) $(FFLAGS) -c restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f
-+ncs_rest.o: restr_files.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: restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f
--	$(FC) $(FFLAGS) -c restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90  lsq_exp2.f
-+lsq_exp2.o: restr_files.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 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 ridge.f90 local_tls.f90 vdw_and_contacts.f
-+vdw_and_contacts.o: vdw_and_contacts.f local_tls.o ridge.o restr_files.o
-+	$(FC) $(FFLAGS) -c vdw_and_contacts.f
- 
- dist_routines.o: dist_routines.f90
- 	$(FC) $(FFLAGS) -c dist_routines.f90
-@@ -193,77 +189,77 @@ 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
--	$(FC) $(FFLAGS) -c restr_files.f90 rigid_allocate.f
-+rigid_allocate.o: restr_files.o rigid_allocate.f
-+	$(FC) $(FFLAGS) -c rigid_allocate.f
- 
--tls_allocate.o: restr_files.f90 tls_allocate.f
--	$(FC) $(FFLAGS) -c restr_files.f90 tls_allocate.f
-+tls_allocate.o: restr_files.o tls_allocate.f
-+	$(FC) $(FFLAGS) -c tls_allocate.f
- 
--hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 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 restr_files.o
-+	$(FC) $(FFLAGS) -c hkon_secder_tch.f
- 
--oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 filter_params.f90 oppro_allocate.f
-+oppro_allocate.o: oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o
-+	$(FC) $(FFLAGS) -c oppro_allocate.f
- 
--read_extra_restraints.o: restr_files.f90 read_extra_restraints.f
--	$(FC) $(FFLAGS) -c restr_files.f90 read_extra_restraints.f
-+read_extra_restraints.o: restr_files.o read_extra_restraints.f
-+	$(FC) $(FFLAGS) -c read_extra_restraints.f
- 
- coords.o: coords.f90 atomf77mod.f
- 	$(FC) $(FFLAGS) -c atomf77mod.f coords.f90
- 
--refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 refpre_twin.f
-+refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.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
--	$(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 mtz_write_twin.f
-+mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.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
--	$(FC) $(FFLAGS) -c restr_files.f90 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 restr_files.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
--	$(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 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 refall_twin.f
-+refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.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
-+	$(FC) $(FFLAGS) -c solvent_contr_mask.f
- 
--subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 subag_scale_hessian.f
-+subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.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
- 
--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.f
-+	$(FC) $(FFLAGS) -c bvalue_routines.f90
- 
--refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90
--	$(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 refmac_xml.f
-+refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o
-+	$(FC) $(FFLAGS) -c refmac_xml.f
- 
- hkl_pack.o:  hkl_pack.f90
- 	$(FC) $(FFLAGS) -c hkl_pack.f90
-@@ -272,30 +268,31 @@ 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) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.6.0085-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0085-allow-dynamic-linking.patch
deleted file mode 100644
index 2134cc63ec67..000000000000
--- a/sci-chemistry/refmac/files/5.6.0085-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,241 +0,0 @@
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 5263df1..6b96e5e 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -90,9 +90,7 @@ messy_pdb.o                 \
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(LLIBCIF)                  \
--$(LLIBLAPACK)
-+chbevl.o
- 
- 
- SUBL =                      \
-@@ -126,9 +124,7 @@ cell_symm_subrs.o           \
- iheap_sort.o                \
- linalgebra.o                \
- math_refmac.o               \
--subnumrec.o                 \
--$(LLIBLAPACK)               \
--$(LLIBCCP)
-+subnumrec.o
- 
- #--------------------------------------------------------------------------------
- 
-@@ -153,33 +149,32 @@ rharvest77mod.o:  rharvest77mod.f
- twin77mod.o:  twin77mod.f
- 	$(FC) $(FFLAGS) -c twin77mod.f
- 
-+max_with_twins.o: restr_files.o max_with_twins.f
-+	$(FC) $(FFLAGS) -c max_with_twins.f
- 
--max_with_twins.o: restr_files.f90 max_with_twins.f
--	$(FC) $(FFLAGS) -c restr_files.f90 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
--	$(FC) $(FFLAGS) -c restr_files.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
--	$(FC) $(FFLAGS) -c restr_files.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
-+optimise_solvent_all.o: optimise_solvent_all.f90 atomf77mod.o
- 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90
- 
--ncs_rest.o: restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f
--	$(FC) $(FFLAGS) -c restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f
-+ncs_rest.o: restr_files.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: restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f
--	$(FC) $(FFLAGS) -c restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90  lsq_exp2.f
-+lsq_exp2.o: restr_files.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 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 ridge.f90 local_tls.f90 vdw_and_contacts.f
-+vdw_and_contacts.o: vdw_and_contacts.f local_tls.o ridge.o restr_files.o
-+	$(FC) $(FFLAGS) -c vdw_and_contacts.f
- 
- dist_routines.o: dist_routines.f90
- 	$(FC) $(FFLAGS) -c dist_routines.f90
-@@ -193,109 +188,110 @@ 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
--	$(FC) $(FFLAGS) -c restr_files.f90 rigid_allocate.f
-+rigid_allocate.o: restr_files.o rigid_allocate.f
-+	$(FC) $(FFLAGS) -c rigid_allocate.f
- 
--tls_allocate.o: restr_files.f90 tls_allocate.f
--	$(FC) $(FFLAGS) -c restr_files.f90 tls_allocate.f
-+tls_allocate.o: restr_files.o tls_allocate.f
-+	$(FC) $(FFLAGS) -c tls_allocate.f
- 
--hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 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 restr_files.o
-+	$(FC) $(FFLAGS) -c hkon_secder_tch.f
- 
--oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 filter_params.f90 oppro_allocate.f
-+oppro_allocate.o: oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o
-+	$(FC) $(FFLAGS) -c oppro_allocate.f
- 
--read_extra_restraints.o: restr_files.f90 read_extra_restraints.f
--	$(FC) $(FFLAGS) -c restr_files.f90 read_extra_restraints.f
-+read_extra_restraints.o: restr_files.o read_extra_restraints.f
-+	$(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
- 
--refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 refpre_twin.f
-+refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.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
--	$(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 mtz_write_twin.f
-+mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.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
--	$(FC) $(FFLAGS) -c restr_files.f90 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 restr_files.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
--	$(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 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 refall_twin.f
-+refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.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
-+	$(FC) $(FFLAGS) -c solvent_contr_mask.f
- 
--subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 subag_scale_hessian.f
-+subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.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
- 
--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
- 
--refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90
--	$(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 refmac_xml.f
-+refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o
-+	$(FC) $(FFLAGS) -c refmac_xml.f
- 
- hkl_pack.o:  hkl_pack.f90
- 	$(FC) $(FFLAGS) -c hkl_pack.f90
- 
--subvag.o: subvag.f hkl_pack.f90
-+subvag.o: subvag.f hkl_pack.o
- 	$(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.o
-+	$(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) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.6.0086-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0086-allow-dynamic-linking.patch
deleted file mode 100644
index 2134cc63ec67..000000000000
--- a/sci-chemistry/refmac/files/5.6.0086-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,241 +0,0 @@
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 5263df1..6b96e5e 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -90,9 +90,7 @@ messy_pdb.o                 \
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(LLIBCIF)                  \
--$(LLIBLAPACK)
-+chbevl.o
- 
- 
- SUBL =                      \
-@@ -126,9 +124,7 @@ cell_symm_subrs.o           \
- iheap_sort.o                \
- linalgebra.o                \
- math_refmac.o               \
--subnumrec.o                 \
--$(LLIBLAPACK)               \
--$(LLIBCCP)
-+subnumrec.o
- 
- #--------------------------------------------------------------------------------
- 
-@@ -153,33 +149,32 @@ rharvest77mod.o:  rharvest77mod.f
- twin77mod.o:  twin77mod.f
- 	$(FC) $(FFLAGS) -c twin77mod.f
- 
-+max_with_twins.o: restr_files.o max_with_twins.f
-+	$(FC) $(FFLAGS) -c max_with_twins.f
- 
--max_with_twins.o: restr_files.f90 max_with_twins.f
--	$(FC) $(FFLAGS) -c restr_files.f90 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
--	$(FC) $(FFLAGS) -c restr_files.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
--	$(FC) $(FFLAGS) -c restr_files.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
-+optimise_solvent_all.o: optimise_solvent_all.f90 atomf77mod.o
- 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90
- 
--ncs_rest.o: restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f
--	$(FC) $(FFLAGS) -c restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f
-+ncs_rest.o: restr_files.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: restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f
--	$(FC) $(FFLAGS) -c restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90  lsq_exp2.f
-+lsq_exp2.o: restr_files.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 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 ridge.f90 local_tls.f90 vdw_and_contacts.f
-+vdw_and_contacts.o: vdw_and_contacts.f local_tls.o ridge.o restr_files.o
-+	$(FC) $(FFLAGS) -c vdw_and_contacts.f
- 
- dist_routines.o: dist_routines.f90
- 	$(FC) $(FFLAGS) -c dist_routines.f90
-@@ -193,109 +188,110 @@ 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
--	$(FC) $(FFLAGS) -c restr_files.f90 rigid_allocate.f
-+rigid_allocate.o: restr_files.o rigid_allocate.f
-+	$(FC) $(FFLAGS) -c rigid_allocate.f
- 
--tls_allocate.o: restr_files.f90 tls_allocate.f
--	$(FC) $(FFLAGS) -c restr_files.f90 tls_allocate.f
-+tls_allocate.o: restr_files.o tls_allocate.f
-+	$(FC) $(FFLAGS) -c tls_allocate.f
- 
--hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 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 restr_files.o
-+	$(FC) $(FFLAGS) -c hkon_secder_tch.f
- 
--oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 filter_params.f90 oppro_allocate.f
-+oppro_allocate.o: oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o
-+	$(FC) $(FFLAGS) -c oppro_allocate.f
- 
--read_extra_restraints.o: restr_files.f90 read_extra_restraints.f
--	$(FC) $(FFLAGS) -c restr_files.f90 read_extra_restraints.f
-+read_extra_restraints.o: restr_files.o read_extra_restraints.f
-+	$(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
- 
--refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 refpre_twin.f
-+refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.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
--	$(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 mtz_write_twin.f
-+mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.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
--	$(FC) $(FFLAGS) -c restr_files.f90 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 restr_files.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
--	$(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 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 refall_twin.f
-+refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.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
-+	$(FC) $(FFLAGS) -c solvent_contr_mask.f
- 
--subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90
--	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 subag_scale_hessian.f
-+subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.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
- 
--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
- 
--refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90
--	$(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 refmac_xml.f
-+refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o
-+	$(FC) $(FFLAGS) -c refmac_xml.f
- 
- hkl_pack.o:  hkl_pack.f90
- 	$(FC) $(FFLAGS) -c hkl_pack.f90
- 
--subvag.o: subvag.f hkl_pack.f90
-+subvag.o: subvag.f hkl_pack.o
- 	$(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.o
-+	$(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) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch
deleted file mode 100644
index 1a55ad125d2a..000000000000
--- a/sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,323 +0,0 @@
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 80b199e..d3ab4c8 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -93,9 +93,7 @@ messy_pdb.o                 \
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(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) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.6.0089-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0089-allow-dynamic-linking.patch
deleted file mode 100644
index 1a55ad125d2a..000000000000
--- a/sci-chemistry/refmac/files/5.6.0089-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,323 +0,0 @@
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 80b199e..d3ab4c8 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -93,9 +93,7 @@ messy_pdb.o                 \
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(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) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.6.0092-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0092-allow-dynamic-linking.patch
deleted file mode 100644
index 5d83ca93e97d..000000000000
--- a/sci-chemistry/refmac/files/5.6.0092-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,323 +0,0 @@
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index ebf3cc1..627623e 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -93,9 +93,7 @@ messy_pdb.o                 \
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(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 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: 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_mod.f90
--	$(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_mod.f90
-+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_mod.o
-+	$(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_subr.o: rharvest_subr.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_subr.f
-+rharvest_subr.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
-+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) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.6.0094-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0094-allow-dynamic-linking.patch
deleted file mode 100644
index 6ef5737e6b4d..000000000000
--- a/sci-chemistry/refmac/files/5.6.0094-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,302 +0,0 @@
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 40fb746..155e653 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -94,9 +94,7 @@ bridge.o                    \
- i0.o                        \
- i1.o                        \
- chbevl.o                    \
--make_unix_ccp4.o            \
--$(LLIBCIF)                  \
--$(LLIBLAPACK)
-+make_unix_ccp4.o
- 
- 
- SUBL =                      \
-@@ -131,9 +129,7 @@ cell_symm_subrs.o           \
- iheap_sort.o                \
- linalgebra.o                \
- math_refmac.o               \
--subnumrec.o                 \
--$(LLIBLAPACK)               \
--$(LLIBCCP)
-+subnumrec.o
- 
- SUB_FREE  =                 \
- freer_twin.o                 \
-@@ -143,9 +139,7 @@ subnumrec.o                 \
- libT.o                      \
- iheap_sort.o                \
- cell_symm_subrs.o           \
--math_refmac.o               \
--$(LLIBLAPACK)               \
--$(LLIBCCP)
-+math_refmac.o
- 
- SUB_HEADER = header2matr.o
- #--------------------------------------------------------------------------------
-@@ -180,32 +174,32 @@ 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 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: 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
-@@ -219,32 +213,31 @@ 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: 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 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: 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: 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
-+oppro_allocate.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
-@@ -265,94 +258,93 @@ mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90
- 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_subr.o: rharvest_subr.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_subr.f
-+rharvest_subr.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
-+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
-@@ -361,16 +353,17 @@ 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) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.6.0096-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0096-allow-dynamic-linking.patch
deleted file mode 100644
index 37e7f439132e..000000000000
--- a/sci-chemistry/refmac/files/5.6.0096-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,323 +0,0 @@
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 94eb0db..4f96dfe 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -95,9 +95,7 @@ bridge.o                    \
- i0.o                        \
- i1.o                        \
- chbevl.o                    \
--make_unix_ccp4.o            \
--$(LLIBCIF)                  \
--$(LLIBLAPACK)
-+make_unix_ccp4.o
- 
- 
- SUBL =                      \
-@@ -132,9 +130,7 @@ cell_symm_subrs.o           \
- iheap_sort.o                \
- linalgebra.o                \
- math_refmac.o               \
--subnumrec.o                 \
--$(LLIBLAPACK)               \
--$(LLIBCCP)
-+subnumrec.o
- 
- SUB_FREE  =                 \
- freer_twin.o                 \
-@@ -144,9 +140,7 @@ subnumrec.o                 \
- libT.o                      \
- iheap_sort.o                \
- cell_symm_subrs.o           \
--math_refmac.o               \
--$(LLIBLAPACK)               \
--$(LLIBCCP)
-+math_refmac.o
- 
- SUB_HEADER = header2matr.o
- #--------------------------------------------------------------------------------
-@@ -184,32 +178,32 @@ 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 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
-@@ -223,140 +217,138 @@ 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: 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 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: 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: ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f
-+make_refmac_dummy.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
-+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
-@@ -365,16 +357,17 @@ 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) $(CXXFLAGS) -c bridge.cpp
diff --git a/sci-chemistry/refmac/files/5.6.0097-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0097-allow-dynamic-linking.patch
deleted file mode 100644
index c2fe24e203cc..000000000000
--- a/sci-chemistry/refmac/files/5.6.0097-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,328 +0,0 @@
-diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index e10752d..f5ffa4e 100644
---- a/makefile_refmac.inc1
-+++ b/makefile_refmac.inc1
-@@ -96,9 +96,7 @@ bridge.o                    \
- i0.o                        \
- i1.o                        \
- chbevl.o                    \
--make_unix_ccp4.o            \
--$(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
- #--------------------------------------------------------------------------------
-@@ -185,35 +179,35 @@ 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
-@@ -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: ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f
-+make_refmac_dummy.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
-+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
-@@ -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/5.6.0102-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch
index 54861a5247e1..9998b759c664 100644
--- a/sci-chemistry/refmac/files/5.6.0102-allow-dynamic-linking.patch
+++ b/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch
@@ -1,5 +1,8 @@
+ makefile_refmac.inc1 |  215 ++++++++++++++++++++++++--------------------------
+ 1 files changed, 104 insertions(+), 111 deletions(-)
+
 diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 0f8bd63..21b51aa 100644
+index 0f8bd63..e59fbfb 100644
 --- a/makefile_refmac.inc1
 +++ b/makefile_refmac.inc1
 @@ -96,9 +96,7 @@ bridge.o                    \
@@ -269,16 +272,18 @@ index 0f8bd63..21b51aa 100644
 +	$(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 hkl_pack.f90 subvag.f
++	$(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
+-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)
diff --git a/sci-chemistry/refmac/files/5.6.0098-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch
index 635f0d34b6e0..9998b759c664 100644
--- a/sci-chemistry/refmac/files/5.6.0098-allow-dynamic-linking.patch
+++ b/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch
@@ -1,5 +1,8 @@
+ makefile_refmac.inc1 |  215 ++++++++++++++++++++++++--------------------------
+ 1 files changed, 104 insertions(+), 111 deletions(-)
+
 diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
-index 44a6771..e7c74a0 100644
+index 0f8bd63..e59fbfb 100644
 --- a/makefile_refmac.inc1
 +++ b/makefile_refmac.inc1
 @@ -96,9 +96,7 @@ bridge.o                    \
@@ -195,9 +198,9 @@ index 44a6771..e7c74a0 100644
  linalgebra_f90.o: linalgebra_f90.f90 
  	$(FC) $(FFLAGS) -c linalgebra_f90.f90
  
--make_refmac_dummy.o: ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
--	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f
-+make_refmac_dummy.o: ncs_rest_mod.o make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
+-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
@@ -269,16 +272,18 @@ index 44a6771..e7c74a0 100644
 +	$(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 hkl_pack.f90 subvag.f
++	$(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
+-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)
diff --git a/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild b/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild
index 53e23ce80f42..70a7ca889896 100644
--- a/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild
+++ b/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild,v 1.9 2011/01/20 12:12:25 hwoarang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild,v 1.10 2011/04/21 07:08:54 jlec Exp $
 
 EAPI="2"
 
@@ -46,7 +46,7 @@ src_compile() {
 		FOPTIM="${FFLAGS:- -O2}" \
 		VERSION="" \
 		XFFLAGS="-fno-second-underscore" \
-		LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \
+		LLIBCCP="-lccp4f -lccp4c -lccif $(pkg-config --libs mmdb) -lstdc++" \
 		LLIBLAPACK="$(pkg-config --libs lapack blas)" \
 		${PN} libcheck || die
 }
diff --git a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild
index 683dcf8cb2a7..285a12ebfdf4 100644
--- a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild
+++ b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild,v 1.1 2011/01/31 21:14:39 dberkholz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild,v 1.2 2011/04/21 07:08:54 jlec Exp $
 
 EAPI="2"
 
@@ -30,6 +30,7 @@ S="${WORKDIR}"
 
 PATCHES=(
 	"${FILESDIR}"/${PV}-allow-dynamic-linking.patch
+	"${FILESDIR}"/${PV}-gcc4.6.patch
 	)
 
 src_prepare() {
@@ -46,7 +47,7 @@ src_compile() {
 		FOPTIM="${FFLAGS:- -O2}" \
 		VERSION="" \
 		XFFLAGS="-fno-second-underscore" \
-		LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \
+		LLIBCCP="-lccp4f -lccp4c -lccif $(pkg-config --libs mmdb) -lstdc++" \
 		LLIBLAPACK="$(pkg-config --libs lapack blas)" \
 		${PN} libcheck || die
 }
diff --git a/sci-chemistry/refmac/refmac-5.6.0097.ebuild b/sci-chemistry/refmac/refmac-5.6.0097.ebuild
deleted file mode 100644
index f30378311e9c..000000000000
--- a/sci-chemistry/refmac/refmac-5.6.0097.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0097.ebuild,v 1.4 2011/01/16 18:01:12 jlec Exp $
-
-EAPI="2"
-
-inherit 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}${MY_PV}.tar.gz
-	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="
-	>=sci-libs/ccp4-libs-6.1.3-r7
-	sci-libs/mmdb
-	>sci-libs/monomer-db-1
-	virtual/blas
-	virtual/lapack"
-DEPEND="${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 ..."
-	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() {
-	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
-}
diff --git a/sci-chemistry/refmac/refmac-5.6.0098.ebuild b/sci-chemistry/refmac/refmac-5.6.0098.ebuild
deleted file mode 100644
index c678a7457fb5..000000000000
--- a/sci-chemistry/refmac/refmac-5.6.0098.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0098.ebuild,v 1.3 2011/01/16 18:01:12 jlec Exp $
-
-EAPI="2"
-
-inherit 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}${MY_PV}.tar.gz
-	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="
-	>=sci-libs/ccp4-libs-6.1.3-r7
-	sci-libs/mmdb
-	>sci-libs/monomer-db-1
-	virtual/blas
-	virtual/lapack"
-DEPEND="${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 ..."
-	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() {
-	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
-}
diff --git a/sci-chemistry/refmac/refmac-5.6.0099.ebuild b/sci-chemistry/refmac/refmac-5.6.0099.ebuild
deleted file mode 100644
index 59d26a27a257..000000000000
--- a/sci-chemistry/refmac/refmac-5.6.0099.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0099.ebuild,v 1.4 2011/01/16 18:01:12 jlec Exp $
-
-EAPI="2"
-
-inherit 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}${MY_PV}.tar.gz
-	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="
-	>=sci-libs/ccp4-libs-6.1.3-r7
-	sci-libs/mmdb
-	>sci-libs/monomer-db-1
-	virtual/blas
-	virtual/lapack"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"
-
-PATCHES=(
-	"${FILESDIR}"/${PV/99/98}-allow-dynamic-linking.patch
-	)
-
-src_prepare() {
-	base_src_prepare
-	use test && epatch "${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 ..."
-	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() {
-	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
-}
diff --git a/sci-chemistry/refmac/refmac-5.6.0102.ebuild b/sci-chemistry/refmac/refmac-5.6.0102.ebuild
deleted file mode 100644
index 6f00bbf10220..000000000000
--- a/sci-chemistry/refmac/refmac-5.6.0102.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0102.ebuild,v 1.1 2011/01/28 15:39:11 jlec Exp $
-
-EAPI="2"
-
-inherit 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}${MY_PV}.tar.gz
-	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="
-	>=sci-libs/ccp4-libs-6.1.3-r7
-	sci-libs/mmdb
-	>sci-libs/monomer-db-1
-	virtual/blas
-	virtual/lapack"
-DEPEND="${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 ..."
-	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() {
-	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
-}
diff --git a/sci-chemistry/refmac/refmac-5.6.0110.ebuild b/sci-chemistry/refmac/refmac-5.6.0110.ebuild
index 0222f07faf31..63bb36965c7a 100644
--- a/sci-chemistry/refmac/refmac-5.6.0110.ebuild
+++ b/sci-chemistry/refmac/refmac-5.6.0110.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0110.ebuild,v 1.1 2011/02/26 11:30:08 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0110.ebuild,v 1.2 2011/04/21 07:08:54 jlec Exp $
 
 EAPI="2"
 
@@ -30,8 +30,8 @@ DEPEND="${RDEPEND}"
 S="${WORKDIR}"
 
 PATCHES=(
-#	"${FILESDIR}"/${PV}-allow-dynamic-linking.patch
-	"${FILESDIR}"/5.6.0102-allow-dynamic-linking.patch
+	"${FILESDIR}"/${PV}-allow-dynamic-linking.patch
+
 	)
 
 src_prepare() {
@@ -48,7 +48,7 @@ src_compile() {
 		FOPTIM="${FFLAGS:- -O2}" \
 		VERSION="" \
 		XFFLAGS="-fno-second-underscore -fwhole-file" \
-		LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \
+		LLIBCCP="-lccp4f -lccp4c -lccif $(pkg-config --libs mmdb) -lstdc++" \
 		LLIBLAPACK="$(pkg-config --libs lapack blas)" \
 		|| die
 }
diff --git a/sci-chemistry/refmac/refmac-5.6.0102-r1.ebuild b/sci-chemistry/refmac/refmac-5.6.0116.ebuild
index 8415ebd6e428..e55483c44b75 100644
--- a/sci-chemistry/refmac/refmac-5.6.0102-r1.ebuild
+++ b/sci-chemistry/refmac/refmac-5.6.0116.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0102-r1.ebuild,v 1.1 2011/01/31 21:14:39 dberkholz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0116.ebuild,v 1.1 2011/04/21 07:08:54 jlec Exp $
 
 EAPI="2"
 
@@ -46,8 +46,8 @@ src_compile() {
 		COPTIM="${CFLAGS}" \
 		FOPTIM="${FFLAGS:- -O2}" \
 		VERSION="" \
-		XFFLAGS="-fno-second-underscore" \
-		LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \
+		XFFLAGS="-fno-second-underscore -fwhole-file" \
+		LLIBCCP="-lccp4f -lccp4c -lccif $(pkg-config --libs mmdb) -lstdc++" \
 		LLIBLAPACK="$(pkg-config --libs lapack blas)" \
 		|| die
 }
author	Justin Lecher <jlec@gentoo.org>	2011-04-21 07:08:54 +0000
committer	Justin Lecher <jlec@gentoo.org>	2011-04-21 07:08:54 +0000
commit	12c324dfa08e4f8527cdc4b857ec47838ff80e3c (patch)
tree	8ad53c52e16ada3729599321505b3a1e5e629c83 /sci-chemistry
parent	Version Bump (diff)
download	gentoo-2-12c324dfa08e4f8527cdc4b857ec47838ff80e3c.tar.gz gentoo-2-12c324dfa08e4f8527cdc4b857ec47838ff80e3c.tar.bz2 gentoo-2-12c324dfa08e4f8527cdc4b857ec47838ff80e3c.zip