diff options
| 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/refmac | |
| parent | Version Bump (diff) | |
| download | gentoo-2-12c324dfa08e4f8527cdc4b857ec47838ff80e3c.tar.gz gentoo-2-12c324dfa08e4f8527cdc4b857ec47838ff80e3c.tar.bz2 gentoo-2-12c324dfa08e4f8527cdc4b857ec47838ff80e3c.zip | |
Version Bump, Cleanup, Fixes for gcc-4.6
(Portage version: 2.2.0_alpha30/cvs/Linux x86_64)
Diffstat (limited to 'sci-chemistry/refmac')
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 } |