[gentoo-commits] dev/dberkholz:master commit in: sci-chemistry/refmac/files/, sci-chemistry/refmac/

[Donnie Berkholz]

commit:     8eb267ed6a8d3439e4f9e0087b7f4cae28a49657
Author:     Donnie Berkholz <dberkholz <AT> gentoo <DOT> org>
AuthorDate: Thu May 26 14:01:55 2011 +0000
Commit:     Donnie Berkholz <dberkholz <AT> gentoo <DOT> org>
CommitDate: Thu May 26 14:03:04 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=dev/dberkholz.git;a=commit;h=8eb267ed

refmac: merged to main tree.

---
 sci-chemistry/refmac/ChangeLog                     |  207 +++++++++++++++++++-
 sci-chemistry/refmac/Manifest                      |   37 +++-
 .../refmac/files/5.6-allow-dynamic-linking.patch   |   43 ----
 sci-chemistry/refmac/files/5.6-test.log.patch      |   32 ---
 sci-chemistry/refmac/refmac-5.6.0069.ebuild        |   66 ------
 5 files changed, 237 insertions(+), 148 deletions(-)

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index 6383d68..4be8055 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -1,6 +1,209 @@
 # ChangeLog for sci-chemistry/refmac
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.3 2010/03/28 20:43:07 jlec Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.41 2011/01/28 15:39:11 jlec Exp $
+
+*refmac-5.6.0102 (28 Jan 2011)
+
+  28 Jan 2011; Justin Lecher <jlec@g.o>
+  +files/5.6.0102-allow-dynamic-linking.patch, +refmac-5.6.0102.ebuild:
+  Version Bump
+
+  20 Jan 2011; Markos Chandras <hwoarang@g.o> refmac-5.5.0110-r2.ebuild:
+  Stable on amd64 wrt bug #349587
+
+  16 Jan 2011; Thomas Kahle <tomka@g.o> refmac-5.5.0110-r2.ebuild:
+  x86 stable per bug 349587
+
+  16 Jan 2011; Justin Lecher <jlec@g.o> refmac-5.5.0110-r2.ebuild,
+  refmac-5.6.0097.ebuild, refmac-5.6.0098.ebuild, refmac-5.6.0099.ebuild:
+  Fix sourcing of ccp4 profile file for test
+
+  16 Jan 2011; Kacper Kowalik <xarthisius@g.o>
+  refmac-5.5.0110-r2.ebuild, refmac-5.6.0099.ebuild:
+  marked ~ppc wrt #303931
+
+  16 Jan 2011; Justin Lecher <jlec@g.o> refmac-5.5.0110-r2.ebuild,
+  refmac-5.6.0097.ebuild, refmac-5.6.0098.ebuild, refmac-5.6.0099.ebuild:
+  Source /etc/profile before testing
+
+*refmac-5.6.0099 (14 Jan 2011)
+
+  14 Jan 2011; Justin Lecher <jlec@g.o> +refmac-5.6.0099.ebuild:
+  Version Bump
+
+*refmac-5.6.0098 (11 Jan 2011)
+
+  11 Jan 2011; Justin Lecher <jlec@g.o>
+  +files/5.6.0098-allow-dynamic-linking.patch, +refmac-5.6.0098.ebuild:
+  Version Bump
+
+  10 Jan 2011; Justin Lecher <jlec@g.o> -refmac-5.5.0109.ebuild,
+  -refmac-5.5.0110.ebuild, -refmac-5.5.0110-r1.ebuild,
+  refmac-5.5.0110-r2.ebuild, -refmac-5.6.0093.ebuild, -refmac-5.6.0094.ebuild,
+  -refmac-5.6.0096.ebuild, refmac-5.6.0097.ebuild:
+  Moved the installation of profile files from sci-chemistry/ccp4-apps to
+  sci-libs/ccp4-libs, #349700
+
+*refmac-5.6.0097 (04 Jan 2011)
+
+  04 Jan 2011; Justin Lecher <jlec@g.o>
+  +files/5.6.0097-allow-dynamic-linking.patch, +refmac-5.6.0097.ebuild:
+  Version Bump
+
+  31 Dec 2010; Justin Lecher <jlec@g.o> refmac-5.5.0110-r2.ebuild:
+  Depend correct ccp4-libs version to make test work
+
+  25 Dec 2010; Justin Lecher <jlec@g.o> refmac-5.5.0110-r2.ebuild:
+  Removed installation of libcheck again, #349700
+
+*refmac-5.5.0110-r2 (24 Dec 2010)
+
+  24 Dec 2010; Justin Lecher <jlec@g.o>
+  files/5.5.0110-allow-dynamic-linking.patch, +refmac-5.5.0110-r2.ebuild:
+  Don't mix FLAGS
+
+*refmac-5.6.0096 (21 Dec 2010)
+
+  21 Dec 2010; Justin Lecher <jlec@g.o>
+  +files/5.6.0096-allow-dynamic-linking.patch, +refmac-5.6.0096.ebuild:
+  Version Bump
+
+  16 Dec 2010; Justin Lecher <jlec@g.o> refmac-5.5.0109.ebuild,
+  refmac-5.5.0110.ebuild, refmac-5.5.0110-r1.ebuild, refmac-5.6.0093.ebuild,
+  refmac-5.6.0094.ebuild:
+  Removal of fortran.eclass, #348851
+
+*refmac-5.6.0094 (07 Dec 2010)
+
+  07 Dec 2010; Justin Lecher <jlec@g.o>
+  +files/5.6.0094-allow-dynamic-linking.patch, -refmac-5.6.0085.ebuild,
+  -refmac-5.6.0086.ebuild, -refmac-5.6.0088.ebuild, -refmac-5.6.0089.ebuild,
+  -refmac-5.6.0090.ebuild, -refmac-5.6.0091.ebuild, -refmac-5.6.0092.ebuild,
+  +refmac-5.6.0094.ebuild:
+  Version Bump, cleaned old
+
+*refmac-5.6.0093 (17 Nov 2010)
+
+  17 Nov 2010; Justin Lecher <jlec@g.o> +refmac-5.6.0093.ebuild:
+  Version Bump
+
+*refmac-5.6.0092 (16 Nov 2010)
+
+  16 Nov 2010; Justin Lecher <jlec@g.o>
+  +files/5.6.0092-allow-dynamic-linking.patch, +refmac-5.6.0092.ebuild:
+  Version BUmp
+
+*refmac-5.6.0091 (06 Nov 2010)
+
+  06 Nov 2010; Justin Lecher <jlec@g.o> +refmac-5.6.0091.ebuild:
+  Version Bump
+
+*refmac-5.6.0090 (04 Nov 2010)
+
+  04 Nov 2010; Justin Lecher <jlec@g.o> +refmac-5.6.0090.ebuild:
+  Version Bump
+
+*refmac-5.6.0089 (04 Nov 2010)
+
+  04 Nov 2010; Justin Lecher <jlec@g.o>
+  +files/5.6.0089-allow-dynamic-linking.patch, +refmac-5.6.0089.ebuild:
+  Version Bump
+
+*refmac-5.6.0088 (03 Nov 2010)
+
+  03 Nov 2010; Justin Lecher <jlec@g.o>
+  +files/5.6.0088-allow-dynamic-linking.patch, +refmac-5.6.0088.ebuild:
+  Version Bump
+
+*refmac-5.6.0086 (20 Oct 2010)
+
+  20 Oct 2010; Justin Lecher <jlec@g.o>
+  +files/5.6.0086-allow-dynamic-linking.patch, -refmac-5.6.0083.ebuild,
+  -refmac-5.6.0084.ebuild, +refmac-5.6.0086.ebuild:
+  Version Bump, removed old
+
+*refmac-5.6.0085 (30 Sep 2010)
+
+  30 Sep 2010; Justin Lecher <jlec@g.o>
+  +files/5.6.0085-allow-dynamic-linking.patch, +refmac-5.6.0085.ebuild:
+  Version Bump
+
+*refmac-5.6.0084 (27 Sep 2010)
+
+  27 Sep 2010; Justin Lecher <jlec@g.o>
+  +files/5.6.0084-allow-dynamic-linking.patch, -refmac-5.6.0080.ebuild,
+  -refmac-5.6.0081.ebuild, +refmac-5.6.0084.ebuild:
+  Version Bump
+
+*refmac-5.6.0083 (24 Sep 2010)
+
+  24 Sep 2010; Justin Lecher <jlec@g.o>
+  +files/5.6.0083-allow-dynamic-linking.patch, +refmac-5.6.0083.ebuild:
+  Keyworded for ~-linux, Version Bump
+
+  06 Jul 2010; Justin Lecher <jlec@g.o>
+  +files/5.6.0081-allow-dynamic-linking.patch, refmac-5.6.0081.ebuild:
+  Fixed prll compilation
+
+*refmac-5.6.0081 (06 Jul 2010)
+
+  06 Jul 2010; Justin Lecher <jlec@g.o> -refmac-5.6.0077.ebuild,
+  -refmac-5.6.0078.ebuild, -refmac-5.6.0079.ebuild, +refmac-5.6.0081.ebuild:
+  Removed old, Version Bump
+
+*refmac-5.6.0080 (03 Jul 2010)
+
+  03 Jul 2010; Justin Lecher <jlec@g.o>
+  +files/5.6.0080-allow-dynamic-linking.patch, +refmac-5.6.0080.ebuild:
+  Version Bump, removed old
+
+*refmac-5.6.0079 (02 Jul 2010)
+
+  02 Jul 2010; Justin Lecher <jlec@g.o> +refmac-5.6.0079.ebuild:
+  Version Bump
+
+*refmac-5.6.0078 (28 Jun 2010)
+
+  28 Jun 2010; Justin Lecher <jlec@g.o>
+  +files/5.6.0078-allow-dynamic-linking.patch, -refmac-5.6.0076.ebuild,
+  +refmac-5.6.0078.ebuild:
+  Version Bump
+
+  16 Jun 2010; Justin Lecher <jlec@g.o> refmac-5.5.0109.ebuild,
+  refmac-5.5.0110.ebuild, refmac-5.5.0110-r1.ebuild, refmac-5.6.0076.ebuild,
+  refmac-5.6.0077.ebuild:
+  Added sci-libs/monomer-db DEP
+
+  15 Jun 2010; Justin Lecher <jlec@g.o> +refmac-5.5.0110-r1.ebuild:
+  Unbundled makecif into sci-chemistry/makecif
+
+*refmac-5.5.0110-r1 (15 Jun 2010)
+
+  15 Jun 2010; Justin Lecher <jlec@g.o> +refmac-5.5.0110-r1.ebuild:
+  Exclude makecif from refmac cause we have sci-chemistry/makecif now
+
+*refmac-5.6.0077 (27 May 2010)
+
+  27 May 2010; Justin Lecher <jlec@g.o> -refmac-5.6.0075.ebuild,
+  +refmac-5.6.0077.ebuild:
+  Version Bump
+
+*refmac-5.6.0076 (18 May 2010)
+
+  18 May 2010; Justin Lecher <jlec@g.o> +refmac-5.6.0076.ebuild:
+  Version Bump
+
+*refmac-5.6.0075 (16 May 2010)
+
+  16 May 2010; Justin Lecher <jlec@g.o>
+  +files/5.6.0075-allow-dynamic-linking.patch, +refmac-5.6.0075.ebuild:
+  Version bump
+
+*refmac-5.5.0110 (13 May 2010)
+
+  13 May 2010; Justin Lecher <jlec@g.o>
+  +files/5.5.0110-allow-dynamic-linking.patch, +refmac-5.5.0110.ebuild:
+  Version Bump, New CBIN location
 
   28 Mar 2010; Justin Lecher <jlec@g.o> refmac-5.5.0109.ebuild:
   Keyworded for ~x86-linux ~amd64-linux

diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
index 8ac6901..12a5f46 100644
--- a/sci-chemistry/refmac/Manifest
+++ b/sci-chemistry/refmac/Manifest
@@ -1,7 +1,34 @@
-AUX 5.6-allow-dynamic-linking.patch 1388 RMD160 80c5e2e9782e6494f80e7e4eed371aca79495530 SHA1 5951076662541f8bf8aee968da7c24fb4c30c21d SHA256 dfc6ae10d515d30ded38f78a6dbf0f6b907db5afbc3880c4b8099630b8fa674d
-AUX 5.6-test.log.patch 1146 RMD160 0ea6293e8ecde3b9ae12658a523e3c30a5c9f01b SHA1 d026fdea6a487754f7e48ec24bcf4851a613b6d1 SHA256 d2c2a09f44e525dc255bc2ac93ca4194b24ca1fe58c31f0e3b5c32e439dfe2e7
-DIST refmac5.6_source_v5.6.0069.tar.gz 1279124 RMD160 31b30844e134516a3ec1ce470399737f578d7a8f SHA1 01abede2d3004b430b3ac2a8f66bc9d973dcadaa SHA256 d6715c5d4571db806a2efddf5b89fff2515fcc8ee27338f38cf058eafc0f6403
+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 3254 RMD160 0136fa28503c10c07ae3e7b653c04cd1e03e3641 SHA1 8b896a003dad2ab840bd7310871fab8191930de6 SHA256 ad4c0feaefcdac5b834549f99ae69aa0b0b33c37332e7e385ee04258b4c51326
+AUX 5.6.0080-allow-dynamic-linking.patch 3680 RMD160 656b50c14ae3b8b886967c39bb73c22d5e8c9ea1 SHA1 bab840c675e4628ee2220c87859fd08f0e88b95b SHA256 1aa6c02ec0aa04e044c5627d649b09402d7d95c44752f9137f62e5d513b171d9
+AUX 5.6.0081-allow-dynamic-linking.patch 7251 RMD160 aba9b2cd1ace40020b59c6f320bae982191d450b SHA1 74e15ce9c68e38d2ad2541672c4184dca3f6fb84 SHA256 5c8f13cefafbf7df7dd86f5ca8134a5743cbb7b289da39b9d9f0b14a01cf9a04
+AUX 5.6.0083-allow-dynamic-linking.patch 9977 RMD160 d51728adbfe593832f71a6fe93593cd9affca7c3 SHA1 9a9571b615e444ac67b74c0f3a1b637fcfcf834e SHA256 b470bb10e67b30f5024e2b9c171583cf018b6a554e18115a570297e06905f26d
+AUX 5.6.0084-allow-dynamic-linking.patch 9851 RMD160 8e6a6116bc824452d9c9e377ca99fd345e0ba23f SHA1 b384d5e2d875d0d87dc62e250602d47a3658c0e8 SHA256 088fe80b3d7eb2910819f8b0f5fa83a1f25620fed88b7c4df2818a6edf440cb1
+AUX 5.6.0085-allow-dynamic-linking.patch 10030 RMD160 76ce00e00d978274cb1b5b585d583c27fff30e3f SHA1 53e2cac876c7d5420a6f7872a0dc8f1eeb9bc74d SHA256 c14115b5d50c7312c4e2cf5ca39f3c53810093555352f3d1bedd97a4aff38e4c
+AUX 5.6.0086-allow-dynamic-linking.patch 10030 RMD160 76ce00e00d978274cb1b5b585d583c27fff30e3f SHA1 53e2cac876c7d5420a6f7872a0dc8f1eeb9bc74d SHA256 c14115b5d50c7312c4e2cf5ca39f3c53810093555352f3d1bedd97a4aff38e4c
+AUX 5.6.0088-allow-dynamic-linking.patch 15141 RMD160 9381d3cd8f9ca0d245fe40695c36c9b4fcaf1c11 SHA1 5de5ef929af460d18908f78f6e3c81cad64e6556 SHA256 b5a9f7bce38f839a532c806dc47ee9d81d67cfda703ad2f3e3c31cb779e4ce98
+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
+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-5.6.0069.ebuild 1727 RMD160 1ccbed25be1676e6a06a546380b5f445cfcba114 SHA1 7dcbce5d2111a3d9115c003f5a8792236cc5eb0f SHA256 bd3bc07a164982c06be6473678b236281864647ad143f2e1ec21ef4f1247579c
-MISC ChangeLog 672 RMD160 debf5af13a4e8043ee87f5eec0ab8f350a9fe1da SHA1 acbd171de3cac9a91f421e21b3c51232d79f1d07 SHA256 f7e742ebab04dc7592ee15c5536fc360fd7da72ba695ac8116fe3c686b72ab13
+EBUILD refmac-5.5.0110-r2.ebuild 1882 RMD160 9090de535e3475370dd0581e80213e6e5d3169a6 SHA1 74866adf28c2695450bae403d5f38d87a07bb3a2 SHA256 a44037a5aebffd3b33067e7e764f02f7e97e4fe674f063b9eae7bae2e7722187
+EBUILD refmac-5.5.0110-r3.ebuild 1940 RMD160 7f528630ae13220c8d74befeb3c4324aa5018efd SHA1 b81ec52f5827dd189a9ebcbb439b7354ad22b379 SHA256 cea3460bb01b4c71858f9106e3305720e1fd973551e759084192f30073b90fa7
+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 1922 RMD160 e04fb847393a83c78d956546f3c3ace4f6360924 SHA1 942cb163aecc17237e51bfcee43e859099aa4111 SHA256 57d189ccee397edfe26202a0b614bf39c159d65e9623f4994245a65eff3c056b
+EBUILD refmac-5.6.0102.ebuild 1868 RMD160 480e226aa98f582ce692bab41d927cbfde830670 SHA1 8ae6e7946f62e0831111c84264953337dcaef75e SHA256 22e97a1e18982dc65118833101dedbcad9f1d5382d14cb9d94c12f96b8181b15
+MISC ChangeLog 7204 RMD160 21adccb54544f62a8bd1b57bbf752486d533ac88 SHA1 a12504c43ee3164987c6e5c2226c958c0111732b SHA256 efd098ca333be28e1d735d24644a866e2ab10d9fd515f34eb67582e4c27cfa31
 MISC metadata.xml 311 RMD160 df83b13d491a71b729455b664088d89ddbde1c8c SHA1 fffd2a5645181aa12ac9b6f74da9a011cdcf1b97 SHA256 782521c7e16d7eec82d7b7e7c43102806e7f72bc7366401808b1e1ac6e26045a

diff --git a/sci-chemistry/refmac/files/5.6-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6-allow-dynamic-linking.patch
deleted file mode 100644
index 6aa7697..0000000
--- a/sci-chemistry/refmac/files/5.6-allow-dynamic-linking.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff -ur refmac.orig//makefile_refmac.inc1 refmac//makefile_refmac.inc1
---- refmac.orig//makefile_refmac.inc1	2010-04-20 10:22:49.868462937 -0500
-+++ refmac//makefile_refmac.inc1	2010-04-20 10:29:37.378474391 -0500
-@@ -83,9 +83,7 @@
- bridge.o                    \
- i0.o                        \
- i1.o                        \
--chbevl.o                    \
--$(LLIBCIF)                  \
--$(LLIBLAPACK)
-+chbevl.o                    
- 
- 
- SUBL =                      \
-@@ -118,9 +116,7 @@
- iheap_sort.o                \
- linalgebra.o                \
- math_refmac.o               \
--subnumrec.o                 \
--$(LLIBLAPACK)               \
--$(LLIBCCP)
-+subnumrec.o                 
- 
- #--------------------------------------------------------------------------------
- 
-@@ -188,7 +184,7 @@
- 	$(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 +205,7 @@
- 	$(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) $(LLIBLAPACK)
- 
- clean:
- 	/bin/rm *.o

diff --git a/sci-chemistry/refmac/files/5.6-test.log.patch b/sci-chemistry/refmac/files/5.6-test.log.patch
deleted file mode 100644
index 61858be..0000000
--- a/sci-chemistry/refmac/files/5.6-test.log.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- test-framework/refmac5/test_refmac5.py	2009-06-29 15:45:37.000000000 +0200
-+++ test-framework/refmac5/test_refmac5.py.new	2009-06-29 15:48:05.000000000 +0200
-@@ -88,7 +88,8 @@
-              'make hydr no',
-              'labin IP=IMEAN SIGIP=SIGIMEAN FREE=FreeR_flag',
-              'labout FC=FC PHIC=PHIC'],
--            working_directory = self.test_dir)
-+            working_directory = self.test_dir,
-+            log_file = 'test_twinned_refinement.log')
- 
-         self.assertEqual(status, 0)
- 
-@@ -123,7 +124,8 @@
-              'weight auto',
-              'ncyc 20',
-              'labout FC=FC PHIC=PHIC'],
--            working_directory = self.test_dir)
-+            working_directory = self.test_dir,
-+            log_file = 'test_4_domain_tls.log')
- 
-         self.assertEqual(status, 0)
- 
-@@ -156,7 +158,8 @@
-              'anomalous form SE -9.9 3.9',
-              'anomalous wavelength 0.97966',
-              'labout FC=FC PHIC=PHIC'],
--            working_directory = self.test_dir)
-+            working_directory = self.test_dir,
-+            log_file = 'test_sad_refinement.log')
- 
-         self.assertEqual(status, 0)
- 

diff --git a/sci-chemistry/refmac/refmac-5.6.0069.ebuild b/sci-chemistry/refmac/refmac-5.6.0069.ebuild
deleted file mode 100644
index 66848c9..0000000
--- a/sci-chemistry/refmac/refmac-5.6.0069.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0109.ebuild,v 1.3 2010/03/28 20:43:07 jlec Exp $
-
-EAPI="2"
-
-inherit fortran base toolchain-funcs versionator
-
-DESCRIPTION="Macromolecular crystallographic refinement program"
-HOMEPAGE="http://www.ysbl.york.ac.uk/refmac/"
-SRC_URI="${HOMEPAGE}data/refmac_experimental/refmac5.6_source_v${PV}.tar.gz
-	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="
-	sci-libs/ccp4-libs
-	sci-libs/mmdb
-	virtual/blas
-	virtual/lapack"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"
-
-PATCHES=(
-	"${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-allow-dynamic-linking.patch
-	)
-
-src_prepare() {
-	base_src_prepare
-	use test && epatch "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch
-}
-
-src_compile() {
-	emake \
-		FC=$(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="-llapack -lblas" \
-		|| die
-}
-
-src_test() {
-	einfo "Starting tests ..."
-	export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}"
-	export CCP4_TEST="${WORKDIR}"/test-framework
-	export CCP4_SCR="${T}"
-	ln -sf refmac "${S}"/refmac5
-	sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb
-	ccp4-run-thorough-tests -v test_refmac5 || die
-}
-
-src_install() {
-	dobin refmac || die
-	dobin libcheck || die
-	dosym refmac /usr/bin/refmac5 || die
-#	dodoc refmac_keywords.pdf bugs_and_features.pdf || die
-}