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 | 4586202bc4f86db7487e1137457c6bcd8e13fa7a (patch) | |
| tree | 7daae4d247884b9b9d4ae3e0c1b87bfa696a70b1 /sci-chemistry | |
| parent | Version Bump (diff) | |
| download | historical-4586202bc4f86db7487e1137457c6bcd8e13fa7a.tar.gz historical-4586202bc4f86db7487e1137457c6bcd8e13fa7a.tar.bz2 historical-4586202bc4f86db7487e1137457c6bcd8e13fa7a.zip | |
Version Bump, Cleanup, Fixes for gcc-4.6
Package-Manager: portage-2.2.0_alpha30/cvs/Linux x86_64
Diffstat (limited to 'sci-chemistry')
28 files changed, 86 insertions, 3693 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/Manifest b/sci-chemistry/refmac/Manifest index e3e1bb6f3d51..5f9f88d2c7eb 100644 --- a/sci-chemistry/refmac/Manifest +++ b/sci-chemistry/refmac/Manifest @@ -1,46 +1,25 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 -AUX 5.5-allow-dynamic-linking.patch 2025 RMD160 b4324061b5468aedce6d37fc17049711231e677d SHA1 d04e47048302bd7df59d470a9657289871f42721 SHA256 410ffe2a7dee8dd30376355298319f7cc413fa2ff0765a1f77f02cb975e4a23a AUX 5.5-test.log.patch 1146 RMD160 0ea6293e8ecde3b9ae12658a523e3c30a5c9f01b SHA1 d026fdea6a487754f7e48ec24bcf4851a613b6d1 SHA256 d2c2a09f44e525dc255bc2ac93ca4194b24ca1fe58c31f0e3b5c32e439dfe2e7 AUX 5.5.0110-allow-dynamic-linking.patch 2730 RMD160 3637d62986050317a1480e5074ecfac5307fb216 SHA1 c3035d478f22a9d9b95b70aaa3a357eb91d9375f SHA256 72e782184abc94f8efa46082e3b0d30000e745c8ee9141affa2c178b1cf87d35 -AUX 5.6.0075-allow-dynamic-linking.patch 1447 RMD160 5b4eca9f5e03aa0dea24fe4e391c363b3600eb4a SHA1 a3e4989d6b68c77e69e1bfcb76ddbc98c6e7a157 SHA256 0e54d70ac56326422158d19268432772813d34b653b041554ac6e08981ff0140 -AUX 5.6.0078-allow-dynamic-linking.patch 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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 -AUX 5.6.0089-allow-dynamic-linking.patch 15141 RMD160 9381d3cd8f9ca0d245fe40695c36c9b4fcaf1c11 SHA1 5de5ef929af460d18908f78f6e3c81cad64e6556 SHA256 b5a9f7bce38f839a532c806dc47ee9d81d67cfda703ad2f3e3c31cb779e4ce98 -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 -AUX 5.6.0098-allow-dynamic-linking.patch 16190 RMD160 748fad762e601897bd81ba936d50a0d213e5226f SHA1 25c320391370d8226bdbf163f973693205cdc25a SHA256 a439334cf935321fb050c83b03faf6df212fcbb31255b4223db8a30215db09e3 -AUX 5.6.0102-allow-dynamic-linking.patch 16236 RMD160 d05f0bf2b9e59eb856b0e3da8fc4648fe87a2c74 SHA1 5471e925f95a5e9fca44708f4bf0859e3f2a1932 SHA256 7c1bddd203b116a3a17d41c17f9dc8707f20cee1ef5deade40b59b35cd20952b -DIST refmac5.6_source_v5.6.0097.tar.gz 1385352 RMD160 794ec5b52fd3e59743a9a5f6e4e53e2b18b5eff7 SHA1 fee5a0b542f47c2f6c693489b2ca6bbc13b3a74d SHA256 127a260491cb8db7d670b6b9a48c74685bfd07e64e7819533b141ae7a90b055d -DIST refmac5.6_source_v5.6.0098.tar.gz 1385701 RMD160 b0348e9b8c0e5a3318d8d5fb589c9d62a41ae080 SHA1 c1484972ad783b56c948c50b49a351cce87241d6 SHA256 dc38426128109148f1c2b066e5162487d94e5cc0dddc4a14ac244cd36d7fc007 -DIST refmac5.6_source_v5.6.0099.tar.gz 1386351 RMD160 7ddc195259e47462f749a9ca06dae69eb159dbf7 SHA1 8460e6d30fdfeda4056559c0b93bc8562bdf5f94 SHA256 d91da122372b2c0895f4c344bded6e4433d2948ed4320e40bf46783b1940a77e -DIST refmac5.6_source_v5.6.0102.tar.gz 1387462 RMD160 827f41b30609c4ade0b11ebef6cb3f2bf435ed72 SHA1 7259a6686af1e71dc7f5290116a0b9ae74219982 SHA256 a74d2173d15b65ec24dd745f852299bf38e150569a97e199f0cef31b990f01d3 +AUX 5.5.0110-gcc4.6.patch 473 RMD160 9912c28fec294080ee8e26f27067eaf40317f41d SHA1 e666295b8ddeaa07dc5485660210d001798e46ac SHA256 a33de3aa7236a6b711d5f578fea549da03130eabb061252c40b57e8ce3fe1778 +AUX 5.6.0110-allow-dynamic-linking.patch 16438 RMD160 149cfb8af3f35afc61c26d99d42992f6baa2f265 SHA1 dc5e1b2a95311b043afbd0de5e2b606ee5d42cf8 SHA256 ac854d5e755b05809d4015763b6ea8552f1733d5bc5073778ce82c812083624b +AUX 5.6.0116-allow-dynamic-linking.patch 16438 RMD160 149cfb8af3f35afc61c26d99d42992f6baa2f265 SHA1 dc5e1b2a95311b043afbd0de5e2b606ee5d42cf8 SHA256 ac854d5e755b05809d4015763b6ea8552f1733d5bc5073778ce82c812083624b DIST refmac5.6_source_v5.6.0110.tar.gz 1395208 RMD160 7d29ac54bc2178f0e47e0164f49a8d1567fa44f6 SHA1 6a7abe0190e8f6c74241934f98655b16678cad38 SHA256 5e16f95f374a8df2698644bc334b58474dacc418728542f00ce59d3fa47fbc34 +DIST refmac5.6_source_v5.6.0116.tar.gz 1397818 RMD160 2231e343cf103a4f6b10b9ded1d94626ea27c661 SHA1 daee72506fc67e2a572f4b8134e596df09fdc404 SHA256 c328ad373d3e41c2bd3c0a3343645859020dc008b2f7d071b24c55fe9e182b0d 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 -EBUILD refmac-5.5.0110-r2.ebuild 1882 RMD160 9090de535e3475370dd0581e80213e6e5d3169a6 SHA1 74866adf28c2695450bae403d5f38d87a07bb3a2 SHA256 a44037a5aebffd3b33067e7e764f02f7e97e4fe674f063b9eae7bae2e7722187 -EBUILD refmac-5.5.0110-r3.ebuild 1943 RMD160 2dbd47b154efbb205d5319aaba2a699dd8d571bf SHA1 19410c7fd751023c64ef0847139b3928669675a2 SHA256 94e51676c648a9e88b0a9a61b7485ec4913d7516ac5e9cf7023cfb9beacc5d57 -EBUILD refmac-5.6.0097.ebuild 1868 RMD160 0ab9127e0db43e1c51a8495f21d8654bbb61a078 SHA1 2f0ed51542001e9e697f9dd6db51c0c32dab0525 SHA256 af13cca63f2265b1e03733b6ddec12f7ab7f8d65f35bfd7b8663f5589efb65ec -EBUILD refmac-5.6.0098.ebuild 1868 RMD160 f9fb038fcd1dc01ae5681dbd3aad03004592a3b3 SHA1 a880241edc1508f054b207744b9a2c3571992f6d SHA256 5719df2edca46720c816b57034938bdeaac11ff620f783218a6cff4bca7de6a2 -EBUILD refmac-5.6.0099.ebuild 1874 RMD160 a7341a8e09c29034d1379ca92a2ee850ad163225 SHA1 500118dd748f30ba71f85bd78878319605375b57 SHA256 271b1a3513eac2d99dc6af897ac201c04bbb3539e4dd58bb42f1b1c12eab643c -EBUILD refmac-5.6.0102-r1.ebuild 1927 RMD160 381073c03926e0d50ee0e475c25ecd8342e67b53 SHA1 8a653fad867cf24a8d308de59aa92bf3de4fc772 SHA256 45c85c984eef6196101b4f9e92eff8fedacead89ec49a2abf379b53d1c6797dd -EBUILD refmac-5.6.0102.ebuild 1868 RMD160 480e226aa98f582ce692bab41d927cbfde830670 SHA1 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93f2233c8ae19db2228a762901259ebd00f52afc SHA256 6e944158ee8f96965053b93b47f0560d740aac02ebadb6c59893080210cbc301 +EBUILD refmac-5.6.0116.ebuild 1951 RMD160 aafd41a425939d485ebcf73663ace016f1ea99ac SHA1 0a93fb7e6b12fb3c481dccf907e4d9045701d914 SHA256 06b1c637c3404ff565eea5282ec8051e64b265f8bc98c9d49fe628a62e606e33 +MISC ChangeLog 8888 RMD160 08928fe7ca279a5a415c051f02c621010be262f6 SHA1 c5ef3117a0912235a8fa2920d0231a2fc057dfd5 SHA256 6c3d55e0c6f0977de13ffb227f75de22adb61276386d06dbbbac3024717a3063 MISC metadata.xml 311 RMD160 df83b13d491a71b729455b664088d89ddbde1c8c SHA1 fffd2a5645181aa12ac9b6f74da9a011cdcf1b97 SHA256 782521c7e16d7eec82d7b7e7c43102806e7f72bc7366401808b1e1ac6e26045a -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk1o5EYACgkQgAnW8HDreRZBFwCgnY4SvL1dIVvpBsKjnGmcAGk3 -RccAoI5SW90y2Q0e0O6eyRZ22m9RG2zM -=sFd8 +iEYEARECAAYFAk2v2AsACgkQgAnW8HDreRZNfACdFVB4ZdEeBamUwaz5HykkLRHX +9LQAn201KbntniCyO1rHVB+Hs3eUQzde +=V3qB -----END PGP SIGNATURE----- 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 } |