diff options
| -rw-r--r-- | sci-chemistry/refmac/ChangeLog | 10 | ||||
| -rw-r--r-- | sci-chemistry/refmac/Manifest | 11 | ||||
| -rw-r--r-- | sci-chemistry/refmac/files/5.6.0097-allow-dynamic-linking.patch | 328 | ||||
| -rw-r--r-- | sci-chemistry/refmac/refmac-5.6.0097.ebuild | 71 |
4 files changed, 414 insertions, 6 deletions
diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog index e3b25b908b6e..1f05bf339c6b 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 1.31 2010/12/31 16:08:51 jlec Exp $ +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.32 2011/01/04 08:55:21 jlec Exp $ + +*refmac-5.6.0097 (04 Jan 2011) + + 04 Jan 2011; Justin Lecher <jlec@gentoo.org> + +files/5.6.0097-allow-dynamic-linking.patch, +refmac-5.6.0097.ebuild: + Version Bump 31 Dec 2010; Justin Lecher <jlec@gentoo.org> refmac-5.5.0110-r2.ebuild: Depend correct ccp4-libs version to make test work diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest index 2f45fd0c9c5d..97ee7e227c95 100644 --- a/sci-chemistry/refmac/Manifest +++ b/sci-chemistry/refmac/Manifest @@ -17,9 +17,11 @@ AUX 5.6.0089-allow-dynamic-linking.patch 15141 RMD160 9381d3cd8f9ca0d245fe40695c AUX 5.6.0092-allow-dynamic-linking.patch 15244 RMD160 c7d1313f9addc68a9fb3f1a3877d499bb319699b SHA1 dcd3c72e50fd70406cfc11e532076c85164d9302 SHA256 8c6553bb891baf53723c302e7063c8cf3bacd5565bc1bf2f40a4a58319ab895d AUX 5.6.0094-allow-dynamic-linking.patch 14253 RMD160 52c75acd769fc8df8c0c877457b558f7e1e4d52f SHA1 b2ce0c5adcd945037e2333818278fb4adfb15eb2 SHA256 629a7c10a8af3c5ddb8e6c5be65f121d3719f6d3298e2d41720dbecc16ea4d42 AUX 5.6.0096-allow-dynamic-linking.patch 15644 RMD160 a5918087c640f6b460da8f03e85da04618983d90 SHA1 6b40bf1401114102b4eccc775b2b08849765d275 SHA256 c01c2dcd9130e7e7e465b753416a62a495c16eac1cff56289cb2de070b2e62fc +AUX 5.6.0097-allow-dynamic-linking.patch 15960 RMD160 d5b0c7a0dcb3e3ca32d6c22b47cd20fd64e391e2 SHA1 b6cd3f6df9110670dba356acad31a3af56f65cd0 SHA256 4f1f5ed765c487f14b56d4386bb25a7f4dd069e49a5cb2b66c7c963c39c83812 DIST refmac5.6_source_v5.6.0093.tar.gz 1376999 RMD160 c7604eec1ac4a1b7bfede6ffcb5565bc1e437782 SHA1 e33cb346a5bebd0a8a95e28566d09ad43d24b9b4 SHA256 1ad6da34a2133a0489b1bf9138cb367f18cbb72a4da4038da2e97e69ee5fb29a DIST refmac5.6_source_v5.6.0094.tar.gz 1377162 RMD160 6fc3e22e82f7df8870d645323aa8cca446438cf0 SHA1 67ae1f389c54208c6e57c539d6c1c788cbb4c569 SHA256 e19a389bd5398529ab4cc1fde42f87d19919f91fee6819b0b13ccd755905a92d DIST refmac5.6_source_v5.6.0096.tar.gz 1378374 RMD160 11395e181c0e591983d81480acc9b36e03ee20e1 SHA1 ec1ff85e86461923a162228b35d158b50267b767 SHA256 0418177eea1eef1fd6ee48739fe21d8eaba13418449068fd8edde271e54fb62c +DIST refmac5.6_source_v5.6.0097.tar.gz 1385352 RMD160 794ec5b52fd3e59743a9a5f6e4e53e2b18b5eff7 SHA1 fee5a0b542f47c2f6c693489b2ca6bbc13b3a74d SHA256 127a260491cb8db7d670b6b9a48c74685bfd07e64e7819533b141ae7a90b055d 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 @@ -30,12 +32,13 @@ EBUILD refmac-5.5.0110.ebuild 1797 RMD160 12b3a0f9f8870f7f77d87ed633d080e6d81ca9 EBUILD refmac-5.6.0093.ebuild 1802 RMD160 27b6347e894ab8da82f34ca52bee12ed8595905a SHA1 aac4116505a948e1b4bc143b014750a2994f8862 SHA256 8e56838917d43cac17fc8f74981c1108662bdb5dd1f3b4b4423f1ee7c12576b5 EBUILD refmac-5.6.0094.ebuild 1799 RMD160 71f48ef1066f779e270549ba6cd40bbfab3c3766 SHA1 2446e7e61a944e34f1cc5b12a55e6327293b58fd SHA256 d059348d3794d0c658a61aba450646a4e02001e441182a3a1a797f8b8c7b8019 EBUILD refmac-5.6.0096.ebuild 1799 RMD160 ffb42954d3bfc7c4aef1a445c1695b6912dc3815 SHA1 cbc124f56cac7ef1102c3032b4da51d25e3a29fe SHA256 79c892bae3e446ef9501db1f5738c9c64b2c37b6b1867029621fc4e3efb06739 -MISC ChangeLog 5489 RMD160 b5ef9e464c48fe33c8d880fe4ce20d1f1f8aa564 SHA1 c46fdde63f65459d86963d776e636754c75cb0ba SHA256 fe569b7e824438f199183fba4218eeef1c1663f0449a2ff6ba27d97c2bd10fc9 +EBUILD refmac-5.6.0097.ebuild 1799 RMD160 1899571b277cda55d4e4173caa22b55c9e318e48 SHA1 c9f7971612754f8d37ee34af956738eec121d085 SHA256 d292711f5e700c2d895883f83f72ac536e8178fc2e25a37ba1c0fb4817468ff7 +MISC ChangeLog 5656 RMD160 7b823800e3401cc6d440a0f41c4a0efbbc758f4e SHA1 d49221bf142c4832c4f10becd9ca458932999c70 SHA256 34b9d3ea562d6994bd7ee57ba41b5c9ed11236d61fa3f4e4977d2f84eda8947d MISC metadata.xml 311 RMD160 df83b13d491a71b729455b664088d89ddbde1c8c SHA1 fffd2a5645181aa12ac9b6f74da9a011cdcf1b97 SHA256 782521c7e16d7eec82d7b7e7c43102806e7f72bc7366401808b1e1ac6e26045a -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.16 (GNU/Linux) -iEYEARECAAYFAk0eAB0ACgkQgAnW8HDreRYAcgCghvf1EgUenmxR3VpADnK9TgRS -/RcAn2OywE0dkJXL4dycGwDAX8oHZ1H9 -=nq1Z +iEYEARECAAYFAk0i4H4ACgkQgAnW8HDreRbTYgCeI96aqP3eHa5idw/vD+mXp66u +uAgAnRoNgQ3AbqE1z3K0xboXgKg9j6Gn +=DBOh -----END PGP SIGNATURE----- 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 new file mode 100644 index 000000000000..c2fe24e203cc --- /dev/null +++ b/sci-chemistry/refmac/files/5.6.0097-allow-dynamic-linking.patch @@ -0,0 +1,328 @@ +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/refmac-5.6.0097.ebuild b/sci-chemistry/refmac/refmac-5.6.0097.ebuild new file mode 100644 index 000000000000..44fd3c1415d2 --- /dev/null +++ b/sci-chemistry/refmac/refmac-5.6.0097.ebuild @@ -0,0 +1,71 @@ +# 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 1.1 2011/01/04 08:55:21 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}${MY_PV}.tar.gz + test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" + +SLOT="0" +LICENSE="ccp4" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + sci-libs/ccp4-libs + sci-libs/mmdb + >sci-libs/monomer-db-1 + virtual/blas + virtual/lapack" +DEPEND="${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 +} |