Fixed prll compilation

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

4 files changed, 197 insertions, 8 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index 3bb87107b4ac..713e3301bd0c 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -1,6 +1,10 @@
 # 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 1.14 2010/07/06 06:34:38 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.15 2010/07/06 13:07:18 jlec Exp $
+
+  06 Jul 2010; Justin Lecher <jlec@gentoo.org>
+  +files/5.6.0081-allow-dynamic-linking.patch, refmac-5.6.0081.ebuild:
+  Fixed prll compilation
 
 *refmac-5.6.0081 (06 Jul 2010)
 
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
index f2425b97ed96..4915f12ad253 100644
--- a/sci-chemistry/refmac/Manifest
+++ b/sci-chemistry/refmac/Manifest
@@ -7,6 +7,7 @@ AUX 5.5.0110-allow-dynamic-linking.patch 2265 RMD160 191b90c619a3a0a6cd71b819b45
 AUX 5.6.0075-allow-dynamic-linking.patch 1447 RMD160 5b4eca9f5e03aa0dea24fe4e391c363b3600eb4a SHA1 a3e4989d6b68c77e69e1bfcb76ddbc98c6e7a157 SHA256 0e54d70ac56326422158d19268432772813d34b653b041554ac6e08981ff0140
 AUX 5.6.0078-allow-dynamic-linking.patch 3254 RMD160 0136fa28503c10c07ae3e7b653c04cd1e03e3641 SHA1 8b896a003dad2ab840bd7310871fab8191930de6 SHA256 ad4c0feaefcdac5b834549f99ae69aa0b0b33c37332e7e385ee04258b4c51326
 AUX 5.6.0080-allow-dynamic-linking.patch 3680 RMD160 656b50c14ae3b8b886967c39bb73c22d5e8c9ea1 SHA1 bab840c675e4628ee2220c87859fd08f0e88b95b SHA256 1aa6c02ec0aa04e044c5627d649b09402d7d95c44752f9137f62e5d513b171d9
+AUX 5.6.0081-allow-dynamic-linking.patch 7251 RMD160 aba9b2cd1ace40020b59c6f320bae982191d450b SHA1 74e15ce9c68e38d2ad2541672c4184dca3f6fb84 SHA256 5c8f13cefafbf7df7dd86f5ca8134a5743cbb7b289da39b9d9f0b14a01cf9a04
 DIST refmac5.6_source_v5.6.0080.tar.gz 1317431 RMD160 13f306092428bf87a29fa456c03f33c318183110 SHA1 17796be16dbbf4d442fed8814edbf6bb175a4aaf SHA256 cae4017c5a75b185c99a5460c96386978f7959c28c870b80ec9df272f9b3da53
 DIST refmac5.6_source_v5.6.0081.tar.gz 1317646 RMD160 5b9e04d8b48f6f1445b192c6f592b0a7870e94d6 SHA1 b664dbcba778852137bbc13012d1bb8bff214e6e SHA256 8004eef62d6b37975b83eb5f8a92d4779022823d7a1e2130c53e0a41ced29027
 DIST refmac_5.5.0109.tar.gz 1326779 RMD160 3b603c13638407cceb907bd43ac0a971b587c116 SHA1 3cc35a55df71bac4de3eec9cf0e690e221ae3c86 SHA256 38d416c94e1f86a0676d48d7ddaeb4af272970b8cd6b084e70aa38481327c59e
@@ -16,13 +17,13 @@ EBUILD refmac-5.5.0109.ebuild 1760 RMD160 7d38ec3480c3716698a1926815414c02dae4fe
 EBUILD refmac-5.5.0110-r1.ebuild 1787 RMD160 9017aa6e2f7d9d764904eeeb624c448025583701 SHA1 9252ba8e478ec48e5bba99678c8dde60f4d4ac2f SHA256 bdf76b64a98146b57cd6037473206041a181f893f19b6d0275b950d7560aa1a6
 EBUILD refmac-5.5.0110.ebuild 1805 RMD160 80e546666e72290365c99c542abcef90a3394bb8 SHA1 a1731838742679b66984018fb8d25b8dbb11ae29 SHA256 8f825fc7f75854d631d6c6b037398237b8231a9fdc162e9ab1c6a46490b0a957
 EBUILD refmac-5.6.0080.ebuild 1786 RMD160 5851ff9ac4b5fbb60bbc76baca5a2cf060ed5d69 SHA1 5eeaef1b03d2bda2be97fe43defd5e0602661750 SHA256 c891536606c9ad16198d181a6938012b2c1c6b0fde35bfedb96d44a6e1ec8eb5
-EBUILD refmac-5.6.0081.ebuild 1792 RMD160 9fb29278ced8c0031e1b45a376dc2a0a49ed48cc SHA1 edf2cc6c101a9858a879f69cb2a5fff84243f3bf SHA256 46d0434beb7b7b121bbbf96feea5c2b93cef3b5b7a3422195622ac539ad3798f
-MISC ChangeLog 2508 RMD160 dfd445e8e68a6c372d0a4e7e302a5dec6d15fee9 SHA1 d1c89e8c03b33b2807ebd586726a4b26083be375 SHA256 4c5549409faba32aba315bda80b512f0b04c26873876dc7cbebee2b2016abc58
+EBUILD refmac-5.6.0081.ebuild 1786 RMD160 455b1167da85251e933c0280305a005582df78cf SHA1 2480d78f1d6381263fbbcada040519f6baf90b1d SHA256 2f60016dd306075c73a2d2e4f60285f8302dc3b173d51b2ff5a30d3c19b3cf91
+MISC ChangeLog 2652 RMD160 c8ee6b54c7351c9352fdd475396541b4ce6ad069 SHA1 1a529b4964a840a3f11a38f7a62e1fc9a1320a30 SHA256 5eeb74271d676259556751fafe1ae45c805fa02119c972f8c5508bb2e17bc5b3
 MISC metadata.xml 311 RMD160 df83b13d491a71b729455b664088d89ddbde1c8c SHA1 fffd2a5645181aa12ac9b6f74da9a011cdcf1b97 SHA256 782521c7e16d7eec82d7b7e7c43102806e7f72bc7366401808b1e1ac6e26045a
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.15 (GNU/Linux)
 
-iEYEARECAAYFAkwyzoQACgkQgAnW8HDreRYaUQCgxA8SugKP2liw5lPaW1vbrRms
-MLwAoMM33rlsOSWR3SEdOu46+vyF/zMe
-=dk71
+iEYEARECAAYFAkwzKowACgkQgAnW8HDreRavaACdEQfRPXD1/EMTyYeo4s0VC+Xf
+imcAnjQkhOfAIHV3k2QpOFb0Gx5DnunS
+=SxuT
 -----END PGP SIGNATURE-----
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
new file mode 100644
index 000000000000..33defbfc7086
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.6.0081-allow-dynamic-linking.patch
@@ -0,0 +1,184 @@
+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/refmac-5.6.0081.ebuild b/sci-chemistry/refmac/refmac-5.6.0081.ebuild
index 19b0a2303aa7..85f3d85a551c 100644
--- a/sci-chemistry/refmac/refmac-5.6.0081.ebuild
+++ b/sci-chemistry/refmac/refmac-5.6.0081.ebuild
@@ -1,6 +1,6 @@
 # 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-5.6.0081.ebuild,v 1.1 2010/07/06 06:34:38 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0081.ebuild,v 1.2 2010/07/06 13:07:18 jlec Exp $
 
 EAPI="2"
 
@@ -29,7 +29,7 @@ DEPEND="${RDEPEND}"
 S="${WORKDIR}"
 
 PATCHES=(
-	"${FILESDIR}"/${PV/81/80}-allow-dynamic-linking.patch
+	"${FILESDIR}"/${PV}-allow-dynamic-linking.patch
 	)
 
 src_prepare() {