diff options
-rw-r--r-- | sci-chemistry/refmac/ChangeLog | 8 | ||||
-rw-r--r-- | sci-chemistry/refmac/Manifest | 11 | ||||
-rw-r--r-- | sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch | 323 | ||||
-rw-r--r-- | sci-chemistry/refmac/refmac-5.6.0088.ebuild | 71 |
4 files changed, 408 insertions, 5 deletions
diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog index dd9092d9c7c4..256464fa799a 100644 --- a/sci-chemistry/refmac/ChangeLog +++ b/sci-chemistry/refmac/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-chemistry/refmac # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.19 2010/10/20 06:32:26 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.20 2010/11/03 19:01:51 jlec Exp $ + +*refmac-5.6.0088 (03 Nov 2010) + + 03 Nov 2010; Justin Lecher <jlec@gentoo.org> + +files/5.6.0088-allow-dynamic-linking.patch, +refmac-5.6.0088.ebuild: + Version Bump *refmac-5.6.0086 (20 Oct 2010) diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest index 4a40430763f7..d9a017a27de5 100644 --- a/sci-chemistry/refmac/Manifest +++ b/sci-chemistry/refmac/Manifest @@ -12,8 +12,10 @@ AUX 5.6.0083-allow-dynamic-linking.patch 9977 RMD160 d51728adbfe593832f71a6fe935 AUX 5.6.0084-allow-dynamic-linking.patch 9851 RMD160 8e6a6116bc824452d9c9e377ca99fd345e0ba23f SHA1 b384d5e2d875d0d87dc62e250602d47a3658c0e8 SHA256 088fe80b3d7eb2910819f8b0f5fa83a1f25620fed88b7c4df2818a6edf440cb1 AUX 5.6.0085-allow-dynamic-linking.patch 10030 RMD160 76ce00e00d978274cb1b5b585d583c27fff30e3f SHA1 53e2cac876c7d5420a6f7872a0dc8f1eeb9bc74d SHA256 c14115b5d50c7312c4e2cf5ca39f3c53810093555352f3d1bedd97a4aff38e4c AUX 5.6.0086-allow-dynamic-linking.patch 10030 RMD160 76ce00e00d978274cb1b5b585d583c27fff30e3f SHA1 53e2cac876c7d5420a6f7872a0dc8f1eeb9bc74d SHA256 c14115b5d50c7312c4e2cf5ca39f3c53810093555352f3d1bedd97a4aff38e4c +AUX 5.6.0088-allow-dynamic-linking.patch 15141 RMD160 9381d3cd8f9ca0d245fe40695c36c9b4fcaf1c11 SHA1 5de5ef929af460d18908f78f6e3c81cad64e6556 SHA256 b5a9f7bce38f839a532c806dc47ee9d81d67cfda703ad2f3e3c31cb779e4ce98 DIST refmac5.6_source_v5.6.0085.tar.gz 1276744 RMD160 968d0c18039a5ae19472df3c2b13a7f3c95df99b SHA1 56141b2c1c08194b24d00e444b802c86574505b1 SHA256 f4bc6a02f36c7a57e2a5ef03eb4040854806ff62f56b97cd2c9335ab73e9df70 DIST refmac5.6_source_v5.6.0086.tar.gz 1276868 RMD160 dae01bd49871ff483f8bc8058b191f1bd96612aa SHA1 4d0e0f30adb110cc3976aefcf5c0e08e80cf7045 SHA256 37a46cdfd1e0db31cd312bf267fc2983bf6683d0b775e32e3535d00601e70f69 +DIST refmac5.6_source_v5.6.0088.tar.gz 1376837 RMD160 aaf7c3bb8846ad28a04580af5bd78c7af0838d03 SHA1 23aae26208efe37020dd02a3825976c97fce8613 SHA256 d2b28f24890f6333359c7351ee8430103ad925343ce5c47803e794e03ea40141 DIST refmac_5.5.0109.tar.gz 1326779 RMD160 3b603c13638407cceb907bd43ac0a971b587c116 SHA1 3cc35a55df71bac4de3eec9cf0e690e221ae3c86 SHA256 38d416c94e1f86a0676d48d7ddaeb4af272970b8cd6b084e70aa38481327c59e DIST refmac_5.5.0110.tar.gz 1326832 RMD160 6613ca8b70e54e7827f8ff02b7d497560cb83e39 SHA1 ba2e38db6c88550bd901b474de881d6514b4d74e SHA256 1353fb1042586ec8fa37d0a90f274890d0ccc02377af5216200662338dfe08ca DIST test-framework.tar.gz 130933173 RMD160 7122539dc713615dca2ddaddfd8d152cd22624d0 SHA1 1d3e3019a67afb9b2346e919c859d402d3250fea SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605 @@ -22,12 +24,13 @@ EBUILD refmac-5.5.0110-r1.ebuild 1787 RMD160 9017aa6e2f7d9d764904eeeb624c4480255 EBUILD refmac-5.5.0110.ebuild 1805 RMD160 80e546666e72290365c99c542abcef90a3394bb8 SHA1 a1731838742679b66984018fb8d25b8dbb11ae29 SHA256 8f825fc7f75854d631d6c6b037398237b8231a9fdc162e9ab1c6a46490b0a957 EBUILD refmac-5.6.0085.ebuild 1786 RMD160 3f5bd9e12f1ad100a499794d1244b52a8b1bfdd2 SHA1 69ba8bd099d567ac209dfdc10e6505ffd97d9710 SHA256 d09f9c11f05ed5fd625bd04304538af95b796143f2f064cf5f1ec4f141f9b48b EBUILD refmac-5.6.0086.ebuild 1786 RMD160 2ed810e339b67e19c32cb5c08f51caffa0e4a6db SHA1 19af34f8491c8250033c5130ac97c9fb39b98269 SHA256 c12923fcaf984a2fd8506f00c475e74059bbffa8934dd0b33916359504b37a93 -MISC ChangeLog 3460 RMD160 7fa5280ce2a8217a7e2eede81cf812ed52025ff4 SHA1 a5ffa654055c68197a0258503901eadebd282ad7 SHA256 86c5870d4c3da404d06089d1bbdb1c5d95a0d709f966a4a54a70efc3721b0510 +EBUILD refmac-5.6.0088.ebuild 1807 RMD160 11669262e2dfa49b416c803408608aea19d13cd6 SHA1 52f78c5d4c9e3849e1e49fb1bec8b82f3e3703fc SHA256 73ba767ef2be57e9e6f4076f634715caf505344eefa126b2fcb4e34f76f0dbfc +MISC ChangeLog 3627 RMD160 6cfa331681230f85fc4cb7ea8d0122c3680bb9d5 SHA1 69c91ae156ed204b258fe3adcaaaa27d354882e9 SHA256 e2c0355c54a37c48f81da6c1762163bd1422d447bfd0a1546eba4ec239a6c458 MISC metadata.xml 311 RMD160 df83b13d491a71b729455b664088d89ddbde1c8c SHA1 fffd2a5645181aa12ac9b6f74da9a011cdcf1b97 SHA256 782521c7e16d7eec82d7b7e7c43102806e7f72bc7366401808b1e1ac6e26045a -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.16 (GNU/Linux) -iEYEARECAAYFAky+jQIACgkQgAnW8HDreRZEEQCgtBoO55rueQAgEhEnGXWFsyxs -cfwAmgKQrYCzdS68lxu0f8YEqDqgSQEf -=7qdp +iEYEARECAAYFAkzRsaQACgkQgAnW8HDreRZEXQCdFwK4FG/tiQozFJDhxZSPrRCY +RFUAoL9gZgdnJZysJ31BMx851zGhDOXH +=HEx1 -----END PGP SIGNATURE----- diff --git a/sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch new file mode 100644 index 000000000000..1a55ad125d2a --- /dev/null +++ b/sci-chemistry/refmac/files/5.6.0088-allow-dynamic-linking.patch @@ -0,0 +1,323 @@ +diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1 +index 80b199e..d3ab4c8 100644 +--- a/makefile_refmac.inc1 ++++ b/makefile_refmac.inc1 +@@ -93,9 +93,7 @@ messy_pdb.o \ + bridge.o \ + i0.o \ + i1.o \ +-chbevl.o \ +-$(LLIBCIF) \ +-$(LLIBLAPACK) ++chbevl.o + + + SUBL = \ +@@ -130,9 +128,7 @@ cell_symm_subrs.o \ + iheap_sort.o \ + linalgebra.o \ + math_refmac.o \ +-subnumrec.o \ +-$(LLIBLAPACK) \ +-$(LLIBCCP) ++subnumrec.o + + SUB_FREE = \ + freer_twin.o \ +@@ -142,9 +138,7 @@ subnumrec.o \ + libT.o \ + iheap_sort.o \ + cell_symm_subrs.o \ +-math_refmac.o \ +-$(LLIBLAPACK) \ +-$(LLIBCCP) ++math_refmac.o + + SUB_HEADER = header2matr.o + #-------------------------------------------------------------------------------- +@@ -179,32 +173,32 @@ rharvest_mod.o: rharvest_mod.f90 + twin77mod.o: twin77mod.f + $(FC) $(FFLAGS) -c twin77mod.f + +-max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f ++max_with_twins.o: restr_files.o max_with_twins.f ++ $(FC) $(FFLAGS) -c max_with_twins.f + +-merohedr_twin.o: restr_files.f90 merohedr_twin.f +- $(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f ++merohedr_twin.o: restr_files.o merohedr_twin.f ++ $(FC) $(FFLAGS) -c merohedr_twin.f + +-ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ls_scaling_twin_save.f ++ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f ++ $(FC) $(FFLAGS) -c ls_scaling_twin_save.f + +-ml_params_refine.o: restr_files.f90 ml_params_refine.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ml_params_refine.f ++ml_params_refine.o: restr_files.o ml_params_refine.f ++ $(FC) $(FFLAGS) -c ml_params_refine.f + +-optimise_solvent_all.o: optimise_solvent_all.f90 agreem.f90 +- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90 ++optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o ++ $(FC) $(FFLAGS) -c optimise_solvent_all.f90 + +-ncs_rest.o: restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f ++ncs_rest.o: restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o ++ $(FC) $(FFLAGS) -c ncs_rest.f + +-ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90 +- $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90 ++ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o ++ $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 + +-lsq_exp2.o: restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90 ++lsq_exp2.o: restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f weights.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c lsq_exp2.f + +-vdw_and_contacts.o: vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f ++vdw_and_contacts.o: vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o ++ $(FC) $(FFLAGS) -c vdw_and_contacts.f + + dist_routines.o: dist_routines.f90 + $(FC) $(FFLAGS) -c dist_routines.f90 +@@ -218,140 +212,137 @@ ridge.o: ridge.f90 + align_refmac.o: align_refmac.f90 + $(FC) $(FFLAGS) -c align_refmac.f90 + +-rigid_allocate.o: restr_files.f90 rigid_allocate.f agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f +- +-tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f ++rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o ++ $(FC) $(FFLAGS) -c rigid_allocate.f + +-hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \ +- restr_files.f90 weights.f90 agreem.f90 rharvest.f +- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \ +- hkon_secder_tch.f weights.f90 agreem.f90 rharvest.f ++tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o ++ $(FC) $(FFLAGS) -c tls_allocate.f + +-oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f ++hkon_secder_tch.o: hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \ ++ restr_files.o weights.o agreem.o rharvest.f ++ $(FC) $(FFLAGS) -c hkon_secder_tch.f + +-read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f ++oppro_allocate.o: oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o ++ $(FC) $(FFLAGS) -c oppro_allocate.f + +-coords.o: coords.f90 atomf77mod.f +- $(FC) $(FFLAGS) -c atomf77mod.f coords.f90 ++read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o ++ $(FC) $(FFLAGS) -c read_extra_restraints.f + ++coords.o: coords.f90 atomf77mod.o ++ $(FC) $(FFLAGS) -c coords.f90 + +-ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90 + +-fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90 +- $(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90 ++ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o ++ $(FC) $(FFLAGS) -c ls_scaling_double.f + +-calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90 ++fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o ++ $(FC) $(FFLAGS) -c fast_hessian_tabulation.f + +-refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f ++calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c calc_stats_twin.f + ++refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c refpre_twin.f + +-decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f +- $(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f ++decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f ++ $(FC) $(FFLAGS) -c decide_twin_opers_0.f + + automorphism.o: automorphism.f90 + $(FC) $(FFLAGS) -c automorphism.f90 + +-mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90 agreem.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f ++mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.o ++ $(FC) $(FFLAGS) -c mtz_write_twin.f + + filter_params.o: filter_params.f90 + $(FC) $(FFLAGS) -c filter_params.f90 + +-rcard_tor1.o: rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 \ +- agreem.f90 rharvest_mod.f90 ncs_constr.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \ +- agreem.f90 rharvest_mod.f90 ncs_constr.f90 rcard_tor1.f ++rcard_tor1.o: rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o weights.o \ ++ agreem.o rharvest_mod.o ncs_constr.o ++ $(FC) $(FFLAGS) -c rcard_tor1.f + +-inout_routines.o: restr_files.f90 inout_routines.f +- $(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f ++inout_routines.o: restr_files.o inout_routines.f ++ $(FC) $(FFLAGS) -c inout_routines.f + +-local_tls.o: local_tls.f90 linalgebra_f90.f90 +- $(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90 ++local_tls.o: local_tls.f90 linalgebra_f90.o ++ $(FC) $(FFLAGS) -c local_tls.f90 + + linalgebra_f90.o: linalgebra_f90.f90 + $(FC) $(FFLAGS) -c linalgebra_f90.f90 + +-make_refmac_dummy.o: make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f ++make_refmac_dummy.o: make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c make_refmac_dummy.f + +-ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f ++ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c ml_scaling_double.f + +-refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f ++refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c refall_twin.f + +-rharvest.o: rharvest.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 rharvest.f ++rharvest.o: rharvest.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c rharvest.f + +-solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 +- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f ++solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o ++ $(FC) $(FFLAGS) -c solvent_contr_mask.f + +-subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 +- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f ++subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o weights.o agreem.o rharvest_mod.o ncs_constr.o ++ $(FC) $(FFLAGS) -c subag_scale_hessian.f + +-aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90 +- $(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f ++aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o ++ $(FC) $(FFLAGS) -c aniso_ref_eigen.f + +-subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f ++subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c subcf_scale1.f + +-bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f +- $(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90 ++bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o ++ $(FC) $(FFLAGS) -c bvalue_routines.f90 + +-newentry_idealise.o:: newentry_idealise.f weights.f90 +- $(FC) $(FFLAGS) -c newentry_idealise.f weights.f90 ++newentry_idealise.o:: newentry_idealise.f weights.o ++ $(FC) $(FFLAGS) -c newentry_idealise.f + +-occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90 ++occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c occupancy_only_refine.f + +-refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90 +- $(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90 ++refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90 ++ $(FC) $(FFLAGS) -c refmac_completeness.f90 + +-refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90 +- $(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f ++refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o ++ $(FC) $(FFLAGS) -c refmac_xml.f + + hkl_pack.o: hkl_pack.f90 + $(FC) $(FFLAGS) -c hkl_pack.f90 + +-extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90 +- $(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90 ++extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o ++ $(FC) $(FFLAGS) -c extra_eigen.f + +-subvag.o: subvag.f hkl_pack.f90 ++subvag.o: subvag.f hkl_pack.o + $(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f + +-make_PDB.o: make_PDB.f ncs_constr.f90 +- $(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f ++make_PDB.o: make_PDB.f ncs_constr.o ++ $(FC) $(FFLAGS) -c make_PDB.f + + make_CIF.o: make_CIF.f ncs_constr.f90 +- $(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f ++ $(FC) $(FFLAGS) -c make_CIF.f + + refmac: $(SUBR) +- $(FC) $(FFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) + +-mol2_file.o: mol2_file.f odb_files.f90 +- $(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f ++mol2_file.o: mol2_file.f odb_files.o ++ $(FC) $(FFLAGS) -c mol2_file.f + +-odb_files.o: odb_files.f90 elements_module.f90 enerf77mod.f +- $(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90 ++odb_files.o: odb_files.f90 elements_module.o enerf77mod.o ++ $(FC) $(FFLAGS) -c odb_files.f90 + + elements_module.o: elements_module.f90 + $(FC) $(FFLAGS) -c elements_module.f90 + +-make_lib2.o: make_lib2.f odb_files.f90 +- $(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f ++make_lib2.o: make_lib2.f odb_files.o ++ $(FC) $(FFLAGS) -c make_lib2.f + + pdb2libcheck.o: pdb2libcheck.f90 + $(FC) $(FFLAGS) -c pdb2libcheck.f90 + +-libcheck.o: libcheck.f elements_module.f90 pdb2libcheck.f90 +- $(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f ++libcheck.o: libcheck.f elements_module.o pdb2libcheck.o ++ $(FC) $(FFLAGS) -c libcheck.f + + header2matr.o: header2matr.f90 + $(FC) $(FFLAGS) -c header2matr.f90 +@@ -360,16 +351,17 @@ freer_twin.o: freer_twin.f90 + $(FC) $(FFLAGS) -c freer_twin.f90 + + libcheck: $(SUBL) +- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) + + free_twin: $(SUB_FREE) +- $(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK) + + + header2matr: $(SUB_HEADER) +- $(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER) + + clean: + /bin/rm *.o *.mod + + bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h ++ $(CXX) $(CXXFLAGS) -c bridge.cpp diff --git a/sci-chemistry/refmac/refmac-5.6.0088.ebuild b/sci-chemistry/refmac/refmac-5.6.0088.ebuild new file mode 100644 index 000000000000..9d4ddfcedad5 --- /dev/null +++ b/sci-chemistry/refmac/refmac-5.6.0088.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0088.ebuild,v 1.1 2010/11/03 19:01:51 jlec Exp $ + +EAPI="2" + +inherit fortran base toolchain-funcs versionator + +MY_PV="$(get_version_component_range 1-2)_source_v${PV}" + +DESCRIPTION="Macromolecular crystallographic refinement program" +HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac/" +SRC_URI="${HOMEPAGE}data/refmac_experimental/${PN}${MY_PV}.tar.gz + test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" + +SLOT="0" +LICENSE="ccp4" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + sci-libs/ccp4-libs + sci-libs/mmdb + >sci-libs/monomer-db-1 + virtual/blas + virtual/lapack" +DEPEND="${RDEPEND}" + +S="${WORKDIR}" + +PATCHES=( + "${FILESDIR}"/${PV}-allow-dynamic-linking.patch + ) + +src_prepare() { + base_src_prepare + use test && epatch "${FILESDIR}"/5.5-test.log.patch +} + +src_compile() { + emake \ + FC=$(tc-getFC) \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + COPTIM="${CFLAGS}" \ + FOPTIM="${FFLAGS:- -O2}" \ + VERSION="" \ + XFFLAGS="-fno-second-underscore" \ + LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \ + LLIBLAPACK="$(pkg-config --libs lapack blas)" \ + || die +} + +src_test() { + einfo "Starting tests ..." + export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}" + export CCP4_TEST="${WORKDIR}"/test-framework + export CCP4_SCR="${T}" + ln -sf refmac "${S}"/refmac5 + sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb + ccp4-run-thorough-tests -v test_refmac5 || die +} + +src_install() { + for i in refmac libcheck FreeTwin header2matr; do + exeinto /usr/libexec/ccp4/bin/ + doexe ${i} || die + dosym ../libexec/ccp4/bin/${i} /usr/bin/${i} + done + dosym refmac /usr/bin/refmac5 || die +} |