From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1QPbA1-00014f-CC for garchives@archives.gentoo.org; Thu, 26 May 2011 14:03:38 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 106A21C11A; Thu, 26 May 2011 14:03:29 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id A3A7A1C11A for ; Thu, 26 May 2011 14:03:29 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-CAMELLIA256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 24FCB1B4007 for ; Thu, 26 May 2011 14:03:29 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 558388050C for ; Thu, 26 May 2011 14:03:28 +0000 (UTC) From: "Donnie Berkholz" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Donnie Berkholz" Message-ID: <8eb267ed6a8d3439e4f9e0087b7f4cae28a49657.dberkholz@gentoo> Subject: [gentoo-commits] dev/dberkholz:master commit in: sci-chemistry/refmac/files/, sci-chemistry/refmac/ X-VCS-Repository: dev/dberkholz X-VCS-Files: sci-chemistry/refmac/ChangeLog sci-chemistry/refmac/Manifest sci-chemistry/refmac/files/5.6-allow-dynamic-linking.patch sci-chemistry/refmac/files/5.6-test.log.patch sci-chemistry/refmac/refmac-5.6.0069.ebuild X-VCS-Directories: sci-chemistry/refmac/files/ sci-chemistry/refmac/ X-VCS-Committer: dberkholz X-VCS-Committer-Name: Donnie Berkholz X-VCS-Revision: 8eb267ed6a8d3439e4f9e0087b7f4cae28a49657 Date: Thu, 26 May 2011 14:03:28 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: a2998111645c1ab7b5b7c044d5c63195 commit: 8eb267ed6a8d3439e4f9e0087b7f4cae28a49657 Author: Donnie Berkholz gentoo org> AuthorDate: Thu May 26 14:01:55 2011 +0000 Commit: Donnie Berkholz gentoo org> CommitDate: Thu May 26 14:03:04 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Ddev/dberkholz.git;= a=3Dcommit;h=3D8eb267ed 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/Change= Log 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 + +files/5.6.0102-allow-dynamic-linking.patch, +refmac-5.6.0102.ebuild: + Version Bump + + 20 Jan 2011; Markos Chandras refmac-5.5.0110-r2.= ebuild: + Stable on amd64 wrt bug #349587 + + 16 Jan 2011; Thomas Kahle refmac-5.5.0110-r2.ebuild= : + x86 stable per bug 349587 + + 16 Jan 2011; Justin Lecher 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 + refmac-5.5.0110-r2.ebuild, refmac-5.6.0099.ebuild: + marked ~ppc wrt #303931 + + 16 Jan 2011; Justin Lecher 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 +refmac-5.6.0099.ebuild: + Version Bump + +*refmac-5.6.0098 (11 Jan 2011) + + 11 Jan 2011; Justin Lecher + +files/5.6.0098-allow-dynamic-linking.patch, +refmac-5.6.0098.ebuild: + Version Bump + + 10 Jan 2011; Justin Lecher -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.e= build, + -refmac-5.6.0096.ebuild, refmac-5.6.0097.ebuild: + Moved the installation of profile files from sci-chemistry/ccp4-apps t= o + sci-libs/ccp4-libs, #349700 + +*refmac-5.6.0097 (04 Jan 2011) + + 04 Jan 2011; Justin Lecher + +files/5.6.0097-allow-dynamic-linking.patch, +refmac-5.6.0097.ebuild: + Version Bump + + 31 Dec 2010; Justin Lecher refmac-5.5.0110-r2.ebuild= : + Depend correct ccp4-libs version to make test work + + 25 Dec 2010; Justin Lecher 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 + 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 + +files/5.6.0096-allow-dynamic-linking.patch, +refmac-5.6.0096.ebuild: + Version Bump + + 16 Dec 2010; Justin Lecher refmac-5.5.0109.ebuild, + refmac-5.5.0110.ebuild, refmac-5.5.0110-r1.ebuild, refmac-5.6.0093.ebu= ild, + refmac-5.6.0094.ebuild: + Removal of fortran.eclass, #348851 + +*refmac-5.6.0094 (07 Dec 2010) + + 07 Dec 2010; Justin Lecher + +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.ebu= ild, + -refmac-5.6.0090.ebuild, -refmac-5.6.0091.ebuild, -refmac-5.6.0092.ebu= ild, + +refmac-5.6.0094.ebuild: + Version Bump, cleaned old + +*refmac-5.6.0093 (17 Nov 2010) + + 17 Nov 2010; Justin Lecher +refmac-5.6.0093.ebuild: + Version Bump + +*refmac-5.6.0092 (16 Nov 2010) + + 16 Nov 2010; Justin Lecher + +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 +refmac-5.6.0091.ebuild: + Version Bump + +*refmac-5.6.0090 (04 Nov 2010) + + 04 Nov 2010; Justin Lecher +refmac-5.6.0090.ebuild: + Version Bump + +*refmac-5.6.0089 (04 Nov 2010) + + 04 Nov 2010; Justin Lecher + +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 + +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 + +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 + +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 + +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 + +files/5.6.0083-allow-dynamic-linking.patch, +refmac-5.6.0083.ebuild: + Keyworded for ~-linux, Version Bump + + 06 Jul 2010; Justin Lecher + +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 -refmac-5.6.0077.ebuild, + -refmac-5.6.0078.ebuild, -refmac-5.6.0079.ebuild, +refmac-5.6.0081.ebu= ild: + Removed old, Version Bump + +*refmac-5.6.0080 (03 Jul 2010) + + 03 Jul 2010; Justin Lecher + +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 +refmac-5.6.0079.ebuild: + Version Bump + +*refmac-5.6.0078 (28 Jun 2010) + + 28 Jun 2010; Justin Lecher + +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 refmac-5.5.0109.ebuild, + refmac-5.5.0110.ebuild, refmac-5.5.0110-r1.ebuild, refmac-5.6.0076.ebu= ild, + refmac-5.6.0077.ebuild: + Added sci-libs/monomer-db DEP + + 15 Jun 2010; Justin Lecher +refmac-5.5.0110-r1.ebuil= d: + Unbundled makecif into sci-chemistry/makecif + +*refmac-5.5.0110-r1 (15 Jun 2010) + + 15 Jun 2010; Justin Lecher +refmac-5.5.0110-r1.ebuil= d: + Exclude makecif from refmac cause we have sci-chemistry/makecif now + +*refmac-5.6.0077 (27 May 2010) + + 27 May 2010; Justin Lecher -refmac-5.6.0075.ebuild, + +refmac-5.6.0077.ebuild: + Version Bump + +*refmac-5.6.0076 (18 May 2010) + + 18 May 2010; Justin Lecher +refmac-5.6.0076.ebuild: + Version Bump + +*refmac-5.6.0075 (16 May 2010) + + 16 May 2010; Justin Lecher + +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 + +files/5.5.0110-allow-dynamic-linking.patch, +refmac-5.5.0110.ebuild: + Version Bump, New CBIN location =20 28 Mar 2010; Justin Lecher refmac-5.5.0109.ebuild: Keyworded for ~x86-linux ~amd64-linux diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifes= t 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 80c5e2e9782e6494f80e7e4e= ed371aca79495530 SHA1 5951076662541f8bf8aee968da7c24fb4c30c21d SHA256 dfc= 6ae10d515d30ded38f78a6dbf0f6b907db5afbc3880c4b8099630b8fa674d -AUX 5.6-test.log.patch 1146 RMD160 0ea6293e8ecde3b9ae12658a523e3c30a5c9f= 01b SHA1 d026fdea6a487754f7e48ec24bcf4851a613b6d1 SHA256 d2c2a09f44e525dc= 255bc2ac93ca4194b24ca1fe58c31f0e3b5c32e439dfe2e7 -DIST refmac5.6_source_v5.6.0069.tar.gz 1279124 RMD160 31b30844e134516a3e= c1ce470399737f578d7a8f SHA1 01abede2d3004b430b3ac2a8f66bc9d973dcadaa SHA2= 56 d6715c5d4571db806a2efddf5b89fff2515fcc8ee27338f38cf058eafc0f6403 +AUX 5.5-allow-dynamic-linking.patch 2025 RMD160 b4324061b5468aedce6d37fc= 17049711231e677d SHA1 d04e47048302bd7df59d470a9657289871f42721 SHA256 410= ffe2a7dee8dd30376355298319f7cc413fa2ff0765a1f77f02cb975e4a23a +AUX 5.5-test.log.patch 1146 RMD160 0ea6293e8ecde3b9ae12658a523e3c30a5c9f= 01b SHA1 d026fdea6a487754f7e48ec24bcf4851a613b6d1 SHA256 d2c2a09f44e525dc= 255bc2ac93ca4194b24ca1fe58c31f0e3b5c32e439dfe2e7 +AUX 5.5.0110-allow-dynamic-linking.patch 2730 RMD160 3637d62986050317a14= 80e5074ecfac5307fb216 SHA1 c3035d478f22a9d9b95b70aaa3a357eb91d9375f SHA25= 6 72e782184abc94f8efa46082e3b0d30000e745c8ee9141affa2c178b1cf87d35 +AUX 5.6.0075-allow-dynamic-linking.patch 1447 RMD160 5b4eca9f5e03aa0dea2= 4fe4e391c363b3600eb4a SHA1 a3e4989d6b68c77e69e1bfcb76ddbc98c6e7a157 SHA25= 6 0e54d70ac56326422158d19268432772813d34b653b041554ac6e08981ff0140 +AUX 5.6.0078-allow-dynamic-linking.patch 3254 RMD160 0136fa28503c10c07ae= 3e7b653c04cd1e03e3641 SHA1 8b896a003dad2ab840bd7310871fab8191930de6 SHA25= 6 ad4c0feaefcdac5b834549f99ae69aa0b0b33c37332e7e385ee04258b4c51326 +AUX 5.6.0080-allow-dynamic-linking.patch 3680 RMD160 656b50c14ae3b8b8869= 67c39bb73c22d5e8c9ea1 SHA1 bab840c675e4628ee2220c87859fd08f0e88b95b SHA25= 6 1aa6c02ec0aa04e044c5627d649b09402d7d95c44752f9137f62e5d513b171d9 +AUX 5.6.0081-allow-dynamic-linking.patch 7251 RMD160 aba9b2cd1ace40020b5= 9c6f320bae982191d450b SHA1 74e15ce9c68e38d2ad2541672c4184dca3f6fb84 SHA25= 6 5c8f13cefafbf7df7dd86f5ca8134a5743cbb7b289da39b9d9f0b14a01cf9a04 +AUX 5.6.0083-allow-dynamic-linking.patch 9977 RMD160 d51728adbfe593832f7= 1a6fe93593cd9affca7c3 SHA1 9a9571b615e444ac67b74c0f3a1b637fcfcf834e SHA25= 6 b470bb10e67b30f5024e2b9c171583cf018b6a554e18115a570297e06905f26d +AUX 5.6.0084-allow-dynamic-linking.patch 9851 RMD160 8e6a6116bc824452d9c= 9e377ca99fd345e0ba23f SHA1 b384d5e2d875d0d87dc62e250602d47a3658c0e8 SHA25= 6 088fe80b3d7eb2910819f8b0f5fa83a1f25620fed88b7c4df2818a6edf440cb1 +AUX 5.6.0085-allow-dynamic-linking.patch 10030 RMD160 76ce00e00d978274cb= 1b5b585d583c27fff30e3f SHA1 53e2cac876c7d5420a6f7872a0dc8f1eeb9bc74d SHA2= 56 c14115b5d50c7312c4e2cf5ca39f3c53810093555352f3d1bedd97a4aff38e4c +AUX 5.6.0086-allow-dynamic-linking.patch 10030 RMD160 76ce00e00d978274cb= 1b5b585d583c27fff30e3f SHA1 53e2cac876c7d5420a6f7872a0dc8f1eeb9bc74d SHA2= 56 c14115b5d50c7312c4e2cf5ca39f3c53810093555352f3d1bedd97a4aff38e4c +AUX 5.6.0088-allow-dynamic-linking.patch 15141 RMD160 9381d3cd8f9ca0d245= fe40695c36c9b4fcaf1c11 SHA1 5de5ef929af460d18908f78f6e3c81cad64e6556 SHA2= 56 b5a9f7bce38f839a532c806dc47ee9d81d67cfda703ad2f3e3c31cb779e4ce98 +AUX 5.6.0089-allow-dynamic-linking.patch 15141 RMD160 9381d3cd8f9ca0d245= fe40695c36c9b4fcaf1c11 SHA1 5de5ef929af460d18908f78f6e3c81cad64e6556 SHA2= 56 b5a9f7bce38f839a532c806dc47ee9d81d67cfda703ad2f3e3c31cb779e4ce98 +AUX 5.6.0092-allow-dynamic-linking.patch 15244 RMD160 c7d1313f9addc68a9f= b3f1a3877d499bb319699b SHA1 dcd3c72e50fd70406cfc11e532076c85164d9302 SHA2= 56 8c6553bb891baf53723c302e7063c8cf3bacd5565bc1bf2f40a4a58319ab895d +AUX 5.6.0094-allow-dynamic-linking.patch 14253 RMD160 52c75acd769fc8df8c= 0c877457b558f7e1e4d52f SHA1 b2ce0c5adcd945037e2333818278fb4adfb15eb2 SHA2= 56 629a7c10a8af3c5ddb8e6c5be65f121d3719f6d3298e2d41720dbecc16ea4d42 +AUX 5.6.0096-allow-dynamic-linking.patch 15644 RMD160 a5918087c640f6b460= da8f03e85da04618983d90 SHA1 6b40bf1401114102b4eccc775b2b08849765d275 SHA2= 56 c01c2dcd9130e7e7e465b753416a62a495c16eac1cff56289cb2de070b2e62fc +AUX 5.6.0097-allow-dynamic-linking.patch 15960 RMD160 d5b0c7a0dcb3e3ca32= d6c22b47cd20fd64e391e2 SHA1 b6cd3f6df9110670dba356acad31a3af56f65cd0 SHA2= 56 4f1f5ed765c487f14b56d4386bb25a7f4dd069e49a5cb2b66c7c963c39c83812 +AUX 5.6.0098-allow-dynamic-linking.patch 16190 RMD160 748fad762e601897bd= 81ba936d50a0d213e5226f SHA1 25c320391370d8226bdbf163f973693205cdc25a SHA2= 56 a439334cf935321fb050c83b03faf6df212fcbb31255b4223db8a30215db09e3 +AUX 5.6.0102-allow-dynamic-linking.patch 16236 RMD160 d05f0bf2b9e59eb856= b0e3da8fc4648fe87a2c74 SHA1 5471e925f95a5e9fca44708f4bf0859e3f2a1932 SHA2= 56 7c1bddd203b116a3a17d41c17f9dc8707f20cee1ef5deade40b59b35cd20952b +DIST refmac5.6_source_v5.6.0097.tar.gz 1385352 RMD160 794ec5b52fd3e59743= a9a5f6e4e53e2b18b5eff7 SHA1 fee5a0b542f47c2f6c693489b2ca6bbc13b3a74d SHA2= 56 127a260491cb8db7d670b6b9a48c74685bfd07e64e7819533b141ae7a90b055d +DIST refmac5.6_source_v5.6.0098.tar.gz 1385701 RMD160 b0348e9b8c0e5a3318= d8d5fb589c9d62a41ae080 SHA1 c1484972ad783b56c948c50b49a351cce87241d6 SHA2= 56 dc38426128109148f1c2b066e5162487d94e5cc0dddc4a14ac244cd36d7fc007 +DIST refmac5.6_source_v5.6.0099.tar.gz 1386351 RMD160 7ddc195259e47462f7= 49a9ca06dae69eb159dbf7 SHA1 8460e6d30fdfeda4056559c0b93bc8562bdf5f94 SHA2= 56 d91da122372b2c0895f4c344bded6e4433d2948ed4320e40bf46783b1940a77e +DIST refmac5.6_source_v5.6.0102.tar.gz 1387462 RMD160 827f41b30609c4ade0= b11ebef6cb3f2bf435ed72 SHA1 7259a6686af1e71dc7f5290116a0b9ae74219982 SHA2= 56 a74d2173d15b65ec24dd745f852299bf38e150569a97e199f0cef31b990f01d3 +DIST refmac_5.5.0110.tar.gz 1326832 RMD160 6613ca8b70e54e7827f8ff02b7d49= 7560cb83e39 SHA1 ba2e38db6c88550bd901b474de881d6514b4d74e SHA256 1353fb10= 42586ec8fa37d0a90f274890d0ccc02377af5216200662338dfe08ca DIST test-framework.tar.gz 130933173 RMD160 7122539dc713615dca2ddaddfd8d= 152cd22624d0 SHA1 1d3e3019a67afb9b2346e919c859d402d3250fea SHA256 df050a2= a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605 -EBUILD refmac-5.6.0069.ebuild 1727 RMD160 1ccbed25be1676e6a06a546380b5f4= 45cfcba114 SHA1 7dcbce5d2111a3d9115c003f5a8792236cc5eb0f SHA256 bd3bc07a1= 64982c06be6473678b236281864647ad143f2e1ec21ef4f1247579c -MISC ChangeLog 672 RMD160 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--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 -050= 0 -+++ 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 =20 -=20 -=20 - SUBL =3D \ -@@ -118,9 +116,7 @@ - iheap_sort.o \ - linalgebra.o \ - math_refmac.o \ --subnumrec.o \ --$(LLIBLAPACK) \ --$(LLIBCCP) -+subnumrec.o =20 -=20 - #----------------------------------------------------------------------= ---------- -=20 -@@ -188,7 +184,7 @@ - $(FC) $(FFLAGS) -c linalgebra_f90.f90 -=20 - refmac: $(SUBR) -- $(FC) $(FFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) -+ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS)= $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) -=20 - 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 -=20 - libcheck: $(SUBL) -- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL) -+ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(= LLIBLAPACK) -=20 - clean: - /bin/rm *.o diff --git a/sci-chemistry/refmac/files/5.6-test.log.patch b/sci-chemistr= y/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 15:48:05.00000= 0000 +0200 -@@ -88,7 +88,8 @@ - 'make hydr no', - 'labin IP=3DIMEAN SIGIP=3DSIGIMEAN FREE=3DFreeR_flag', - 'labout FC=3DFC PHIC=3DPHIC'], -- working_directory =3D self.test_dir) -+ working_directory =3D self.test_dir, -+ log_file =3D 'test_twinned_refinement.log') -=20 - self.assertEqual(status, 0) -=20 -@@ -123,7 +124,8 @@ - 'weight auto', - 'ncyc 20', - 'labout FC=3DFC PHIC=3DPHIC'], -- working_directory =3D self.test_dir) -+ working_directory =3D self.test_dir, -+ log_file =3D 'test_4_domain_tls.log') -=20 - self.assertEqual(status, 0) -=20 -@@ -156,7 +158,8 @@ - 'anomalous form SE -9.9 3.9', - 'anomalous wavelength 0.97966', - 'labout FC=3DFC PHIC=3DPHIC'], -- working_directory =3D self.test_dir) -+ working_directory =3D self.test_dir, -+ log_file =3D 'test_sad_refinement.log') -=20 - self.assertEqual(status, 0) -=20 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=3D"2" - -inherit fortran base toolchain-funcs versionator - -DESCRIPTION=3D"Macromolecular crystallographic refinement program" -HOMEPAGE=3D"http://www.ysbl.york.ac.uk/refmac/" -SRC_URI=3D"${HOMEPAGE}data/refmac_experimental/refmac5.6_source_v${PV}.t= ar.gz - test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framewor= k.tar.gz )" - -SLOT=3D"0" -LICENSE=3D"ccp4" -KEYWORDS=3D"~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE=3D"test" - -RDEPEND=3D" - sci-libs/ccp4-libs - sci-libs/mmdb - virtual/blas - virtual/lapack" -DEPEND=3D"${RDEPEND}" - -S=3D"${WORKDIR}" - -PATCHES=3D( - "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-allow-dynamic-li= nking.patch - ) - -src_prepare() { - base_src_prepare - use test && epatch "${FILESDIR}"/$(get_version_component_range 1-2 ${PV= })-test.log.patch -} - -src_compile() { - emake \ - FC=3D$(tc-getFC) \ - CC=3D$(tc-getCC) \ - CXX=3D$(tc-getCXX) \ - COPTIM=3D"${CFLAGS}" \ - FOPTIM=3D"${FFLAGS:- -O2}" \ - VERSION=3D"" \ - XFFLAGS=3D"-fno-second-underscore" \ - LLIBCCP=3D"-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \ - LLIBLAPACK=3D"-llapack -lblas" \ - || die -} - -src_test() { - einfo "Starting tests ..." - export PATH=3D"${WORKDIR}/test-framework/scripts:${S}:${PATH}" - export CCP4_TEST=3D"${WORKDIR}"/test-framework - export CCP4_SCR=3D"${T}" - ln -sf refmac "${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 -}