sci-chemistry/coot: Version Bump, fixes compilation with gcc-4.7, #425836

Package-Manager: portage-2.2.0_alpha116/cvs/Linux x86_64

7 files changed, 331 insertions, 28 deletions

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 4bda510b5d15..9af9cc16646a 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/coot
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.52 2012/03/07 19:33:39 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.53 2012/07/11 20:38:49 jlec Exp $
+
+*coot-0.7_pre4266 (11 Jul 2012)
+
+  11 Jul 2012; Justin Lecher <jlec@gentoo.org> +coot-0.7_pre4266.ebuild,
+  +files/coot-0.7_pre4266-clipper-config.patch,
+  +files/coot-0.7_pre4266-goocanvas.patch,
+  +files/coot-0.7_pre4266-mmdb-config.patch, +files/coot-0.7_pre4266-ssm.patch:
+  Version Bump, fixes compilation with gcc-4.7, #425836
 
   07 Mar 2012; Justin Lecher <jlec@gentoo.org> coot-0.6.2.ebuild,
   coot-0.6.2-r1.ebuild, coot-0.7_pre4040.ebuild:
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index e1c3abc5f139..c2dfad86edd7 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -1,32 +1,40 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
+Hash: SHA256
 
-AUX 0.6.2-clipper-config.patch 431 RMD160 7a00939760bc4c062bbde1a65f53b9556b93c3bc SHA1 0d72c4c898fd29802c74d237b54f715444922956 SHA256 9ae9129e733d845ad2e4dd505bc5e0987147fc3a5e5dd2457b5857643809db2f
-AUX 0.6.2-gl.patch 383 RMD160 6460e87e4da57ff845f96f072dec1354ed117bee SHA1 00bc0bbfc7d4fb00ebc8477941469bef2ed6b670 SHA256 9d47a6cf2d0c7644b945f88acdc7af146df4f9a5a8f883a0e72e1bc8ccf8b380
-AUX 0.6.2-libpng15.patch 1396 RMD160 a7295bf9b312df0f19f82aec3f9458b4d7881606 SHA1 dfa904f324398cc4c7169ec223fb1cec9e72f482 SHA256 e1a1a172f92702aab5921943201baeba36643f9c5bbf1aa40151c4d4dd9dfee6
-AUX 0.6.2-mmdb-config.patch 432 RMD160 8418198b08d15af9ee5d80b15ea46bb9efd2b973 SHA1 3e6f5c888b476d8d37da4effa67a8053784a7a3c SHA256 41484424f2f7f61b0555c893a51884d02f7bd471e70c4c0903c8740dcc273f77
-AUX 0.6.2-ssm.patch 1276 RMD160 8c7eef0034efc2c57bd774fe8ebb1bd0ba9c7aa2 SHA1 8812f35fba16a45b21ecce5243fd26d6105e29e3 SHA256 42f1098b0d56f85125293ca24410061e7a9bee10c94ba6e9fd3496439368bf75
-AUX 0.6.2-test.patch 457 RMD160 1a3e0956d8b7f051fdd964524c0ba9eabf8c2aca SHA1 a8f9584be09cc58e7cb55801115e9649b05aa910 SHA256 494ef09e407c3047145c250c70b90c7679a1c5b9f84c57a680e40580bd980397
-AUX coot-0.7_pre4040-clipper-config.patch 431 RMD160 7a00939760bc4c062bbde1a65f53b9556b93c3bc SHA1 0d72c4c898fd29802c74d237b54f715444922956 SHA256 9ae9129e733d845ad2e4dd505bc5e0987147fc3a5e5dd2457b5857643809db2f
-AUX coot-0.7_pre4040-gl.patch 383 RMD160 6460e87e4da57ff845f96f072dec1354ed117bee SHA1 00bc0bbfc7d4fb00ebc8477941469bef2ed6b670 SHA256 9d47a6cf2d0c7644b945f88acdc7af146df4f9a5a8f883a0e72e1bc8ccf8b380
-AUX coot-0.7_pre4040-goocanvas.patch 702 RMD160 9b26975eb658f15dfd806e47be9c11bcb7f850db SHA1 37bb70847ced34b754fe7cf5fea878b93bb6ed12 SHA256 162b21a3afb2d523df315ec021faf7a6497eb3b4fe00f90f601527fe1c22621a
-AUX coot-0.7_pre4040-libpng-1.5.patch 1396 RMD160 a7295bf9b312df0f19f82aec3f9458b4d7881606 SHA1 dfa904f324398cc4c7169ec223fb1cec9e72f482 SHA256 e1a1a172f92702aab5921943201baeba36643f9c5bbf1aa40151c4d4dd9dfee6
-AUX coot-0.7_pre4040-mmdb-config.patch 479 RMD160 8026b5420940726547200e51db7ce82d7706702c SHA1 e1b1c9ea87fdb2fa5d6c7301d397986d6a9afc4a SHA256 0b7d61f9c5f9664672286e82a790d4dea1673ed1537ef62b59142ced97685d82
-AUX coot-0.7_pre4040-ssm.patch 1276 RMD160 8c7eef0034efc2c57bd774fe8ebb1bd0ba9c7aa2 SHA1 8812f35fba16a45b21ecce5243fd26d6105e29e3 SHA256 42f1098b0d56f85125293ca24410061e7a9bee10c94ba6e9fd3496439368bf75
-AUX coot-0.7_pre4040-test.patch 457 RMD160 1a3e0956d8b7f051fdd964524c0ba9eabf8c2aca SHA1 a8f9584be09cc58e7cb55801115e9649b05aa910 SHA256 494ef09e407c3047145c250c70b90c7679a1c5b9f84c57a680e40580bd980397
-DIST coot-0.6.2.tar.gz 13597123 RMD160 707eb3df47681a011f42874210b940329a748bc7 SHA1 46b663125cef4c01387330d144e49acb0b0b5709 SHA256 d2f55db4f75c721d120ea33a4ca42c1abf246dff29a75b7f189e604e32709e78
-DIST coot-0.7_pre4040.tar.xz 12318188 RMD160 cb92e4192ce8ede97b38791cd05e958205fca363 SHA1 b3b8c5260b6d67d401085756b0532dc76df0ffe6 SHA256 c1ca06199da2b1531cdff7ecc08b336b8d50d265b3c8ed9d37da656f6c4abf8a
-DIST greg-data-0.6.2.tar.gz 8044588 RMD160 065acee98384540d0c2ffaf2511dfd1aa400b11c SHA1 92cec24dab594d8024f41047af2bf6760e9e7d00 SHA256 c9fedf6e1fa60fda178753bbfb539671c274f64d4daca2b63ab49c59bd4c5856
-DIST greg-data-0.7_pre4040.tar.gz 8046573 RMD160 66219ccad8edf27088959a4d5e5a4d3d74452524 SHA1 2c9cf8edde7eaf3b623758022ccc1c29bcc9c1fc SHA256 c343ef4a5e4d70c5f1e5af70a7d26d8b66f579c11b208019256bf6478ddb309c
-EBUILD coot-0.6.2-r1.ebuild 4423 RMD160 da5157564ae8086cb18664f2d60c85ec6bd3366e SHA1 3e0c931aa38d18ba46539c1c3d5abfc09df2e414 SHA256 7164cf3fe4b9c35cbeee7f2f9893fbf2e1db9688d67345e10c6f52044b9c4292
-EBUILD coot-0.6.2.ebuild 4320 RMD160 49e73e0107e6d2c89fdf4efbd2c5aecb830d5cd2 SHA1 dc68f9b3ffd7333bcc961e7474487ff68d55526b SHA256 fd788d6aa77b5e6611ffcd4a0821a21c845a39f9e897d71427ba0a9e58fcc087
-EBUILD coot-0.7_pre4040.ebuild 4477 RMD160 55601d93fce5fcf910ed6cbf0cf51e6855195844 SHA1 1dfe0b25c9b3ec3adbdbed573ec8e30bee0f8529 SHA256 cbc01e21ce216b09f241a6ea54a13c375c538f0363639f896b59fe52900f63d1
-MISC ChangeLog 7951 RMD160 e1dc51dc984828455ce5be6f47cdcf30ba44d051 SHA1 a19a1fc61da31518a8d96b3a2bc7efe6895b8417 SHA256 58af055f6c3cca77abcc5b195498d902efaf08efe8999f07b0cc1a26e56d8df8
-MISC metadata.xml 167 RMD160 ea4003a55d6e2079381a540c441fc59cde29025a SHA1 3bc6dc4dd68f7de22828138e62aa117387b1765d SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8
+AUX 0.6.2-clipper-config.patch 431 SHA256 9ae9129e733d845ad2e4dd505bc5e0987147fc3a5e5dd2457b5857643809db2f SHA512 5817da41b5c692b9d06e44ba8711922465285474ba18ce1d55e567f16f3487218229ae768b63b61a74f437f3d83e3dd49fb504bdd6bb4d9206a97f775b5765c2 WHIRLPOOL 87cc71ae030696a6fa99058aeaf29f66509756732b4f8dcf497e3aab01f395c3a4903c06e0d0e5f77441a7a886c472d77e5a3aa8d05b811e534446f33cceab93
+AUX 0.6.2-gl.patch 383 SHA256 9d47a6cf2d0c7644b945f88acdc7af146df4f9a5a8f883a0e72e1bc8ccf8b380 SHA512 4c12df84530711cf173bd3074e39aef79ad5a88d00711e4d5c4dfe824f93098736d21eb988b88773ff1097f602366b4be5e34fd10a57c8eb1f4b24f9018091e7 WHIRLPOOL b6f90347087df03f8a76c52507bd764cf651b90f6ca5d1313929690e5bbf19439eb2d56e73b4bf09e0bfc2db1cdbdcd4eaf93c3c13d3c073331296aaa82cd93b
+AUX 0.6.2-libpng15.patch 1396 SHA256 e1a1a172f92702aab5921943201baeba36643f9c5bbf1aa40151c4d4dd9dfee6 SHA512 640ccd8a0cbde29a813bba6f6b17817a16168fb845e1bd7f2c377396d09b18306501db5098cc52402e1132877b9d74f7a4488b7cb22b3fabcb7989e583f0c1f7 WHIRLPOOL 567ab70f68273870110b74c2ec99039f1e5db141460fbad5d02ca104a89fc94be076f1a4b8b1381b1dba17f40640a52726a6e759a184d273295d5e21d01dcf0c
+AUX 0.6.2-mmdb-config.patch 432 SHA256 41484424f2f7f61b0555c893a51884d02f7bd471e70c4c0903c8740dcc273f77 SHA512 7813f2cd2f77c0afaf6164cf4111ca28f231616f4821650fcb6b1a64fb16271ac6c295fb8f8bc39c916f5f152861bddf3a5e94ff9902da34f69ae71ff5e7787d WHIRLPOOL 04a992e52809a20fc3f5bb90d21d68ca7b96b601f62fe50e941c30fcf12000c07652c1d40b6c51c183a3ca3945dbe1cdfb9f658a29f5e9103825248e18c16454
+AUX 0.6.2-ssm.patch 1276 SHA256 42f1098b0d56f85125293ca24410061e7a9bee10c94ba6e9fd3496439368bf75 SHA512 20ea4f2fa82858b67ce55fba1e07c5e1caae92df30050b96c95a8f8fdc467bdcecfcd2cef89fd6a406135f18a2d8bc0de4eedeca9a5c97680be3484a8eddac5e WHIRLPOOL 91aee135f0c1a73d74fe26bf38a2ccb5d9b082733fd4c70eef0c04385c829dae5bfe075ed0248f4634dbd366ef5acb4be574a302ac008723d11524fa28b60b30
+AUX 0.6.2-test.patch 457 SHA256 494ef09e407c3047145c250c70b90c7679a1c5b9f84c57a680e40580bd980397 SHA512 2e06222eb21f21741c9f03b1f00f25d239f83dee50d109911fa1dff820ac42a0007fd21e723957457fdf3eeab77db3627a83dc687426bbd1cb3719016b42c5ad WHIRLPOOL 15b63c5cae92f0d895a7c10425703f1db2d959a71d0cb38708e19413d42005827320e24e2898871b880dee9dd48ee16a3f550003a89d1233bcb25fbf29753a4d
+AUX coot-0.7_pre4040-clipper-config.patch 431 SHA256 9ae9129e733d845ad2e4dd505bc5e0987147fc3a5e5dd2457b5857643809db2f SHA512 5817da41b5c692b9d06e44ba8711922465285474ba18ce1d55e567f16f3487218229ae768b63b61a74f437f3d83e3dd49fb504bdd6bb4d9206a97f775b5765c2 WHIRLPOOL 87cc71ae030696a6fa99058aeaf29f66509756732b4f8dcf497e3aab01f395c3a4903c06e0d0e5f77441a7a886c472d77e5a3aa8d05b811e534446f33cceab93
+AUX coot-0.7_pre4040-gl.patch 383 SHA256 9d47a6cf2d0c7644b945f88acdc7af146df4f9a5a8f883a0e72e1bc8ccf8b380 SHA512 4c12df84530711cf173bd3074e39aef79ad5a88d00711e4d5c4dfe824f93098736d21eb988b88773ff1097f602366b4be5e34fd10a57c8eb1f4b24f9018091e7 WHIRLPOOL b6f90347087df03f8a76c52507bd764cf651b90f6ca5d1313929690e5bbf19439eb2d56e73b4bf09e0bfc2db1cdbdcd4eaf93c3c13d3c073331296aaa82cd93b
+AUX coot-0.7_pre4040-goocanvas.patch 702 SHA256 162b21a3afb2d523df315ec021faf7a6497eb3b4fe00f90f601527fe1c22621a SHA512 e083513ea21777c7db05ec59340b57ce70aad5f7acbf93545cee53ce7d595218804531aabf6bcc6d5a2ec72fe5528228478538a52cd61d020e5632f6dfed9b53 WHIRLPOOL 7a99136387924c292e3ea155082706b02f3633740d072c3c35dd26022bb7559397b2574d6707c000f0264e0704be266ae085fe25b25e99adacbb92c683a706de
+AUX coot-0.7_pre4040-libpng-1.5.patch 1396 SHA256 e1a1a172f92702aab5921943201baeba36643f9c5bbf1aa40151c4d4dd9dfee6 SHA512 640ccd8a0cbde29a813bba6f6b17817a16168fb845e1bd7f2c377396d09b18306501db5098cc52402e1132877b9d74f7a4488b7cb22b3fabcb7989e583f0c1f7 WHIRLPOOL 567ab70f68273870110b74c2ec99039f1e5db141460fbad5d02ca104a89fc94be076f1a4b8b1381b1dba17f40640a52726a6e759a184d273295d5e21d01dcf0c
+AUX coot-0.7_pre4040-mmdb-config.patch 479 SHA256 0b7d61f9c5f9664672286e82a790d4dea1673ed1537ef62b59142ced97685d82 SHA512 a124943644761ed18e9906655e616c657f8e1a3930ff3fe11cc73f04456c6562a6c240c5bad887ffc26a49798bcd6ec3f40ce967fd06932bcc55ae5795f62433 WHIRLPOOL ceacb033bc7a87449f1dce6d5e3a09d90cd10f4445515622864df8f09c23000421680e6c13dbf1885d867901fbc38553d9008a0307085070b70ca4f30566319f
+AUX coot-0.7_pre4040-ssm.patch 1276 SHA256 42f1098b0d56f85125293ca24410061e7a9bee10c94ba6e9fd3496439368bf75 SHA512 20ea4f2fa82858b67ce55fba1e07c5e1caae92df30050b96c95a8f8fdc467bdcecfcd2cef89fd6a406135f18a2d8bc0de4eedeca9a5c97680be3484a8eddac5e WHIRLPOOL 91aee135f0c1a73d74fe26bf38a2ccb5d9b082733fd4c70eef0c04385c829dae5bfe075ed0248f4634dbd366ef5acb4be574a302ac008723d11524fa28b60b30
+AUX coot-0.7_pre4040-test.patch 457 SHA256 494ef09e407c3047145c250c70b90c7679a1c5b9f84c57a680e40580bd980397 SHA512 2e06222eb21f21741c9f03b1f00f25d239f83dee50d109911fa1dff820ac42a0007fd21e723957457fdf3eeab77db3627a83dc687426bbd1cb3719016b42c5ad WHIRLPOOL 15b63c5cae92f0d895a7c10425703f1db2d959a71d0cb38708e19413d42005827320e24e2898871b880dee9dd48ee16a3f550003a89d1233bcb25fbf29753a4d
+AUX coot-0.7_pre4266-clipper-config.patch 431 SHA256 9ae9129e733d845ad2e4dd505bc5e0987147fc3a5e5dd2457b5857643809db2f SHA512 5817da41b5c692b9d06e44ba8711922465285474ba18ce1d55e567f16f3487218229ae768b63b61a74f437f3d83e3dd49fb504bdd6bb4d9206a97f775b5765c2 WHIRLPOOL 87cc71ae030696a6fa99058aeaf29f66509756732b4f8dcf497e3aab01f395c3a4903c06e0d0e5f77441a7a886c472d77e5a3aa8d05b811e534446f33cceab93
+AUX coot-0.7_pre4266-goocanvas.patch 702 SHA256 162b21a3afb2d523df315ec021faf7a6497eb3b4fe00f90f601527fe1c22621a SHA512 e083513ea21777c7db05ec59340b57ce70aad5f7acbf93545cee53ce7d595218804531aabf6bcc6d5a2ec72fe5528228478538a52cd61d020e5632f6dfed9b53 WHIRLPOOL 7a99136387924c292e3ea155082706b02f3633740d072c3c35dd26022bb7559397b2574d6707c000f0264e0704be266ae085fe25b25e99adacbb92c683a706de
+AUX coot-0.7_pre4266-mmdb-config.patch 479 SHA256 0b7d61f9c5f9664672286e82a790d4dea1673ed1537ef62b59142ced97685d82 SHA512 a124943644761ed18e9906655e616c657f8e1a3930ff3fe11cc73f04456c6562a6c240c5bad887ffc26a49798bcd6ec3f40ce967fd06932bcc55ae5795f62433 WHIRLPOOL ceacb033bc7a87449f1dce6d5e3a09d90cd10f4445515622864df8f09c23000421680e6c13dbf1885d867901fbc38553d9008a0307085070b70ca4f30566319f
+AUX coot-0.7_pre4266-ssm.patch 1276 SHA256 42f1098b0d56f85125293ca24410061e7a9bee10c94ba6e9fd3496439368bf75 SHA512 20ea4f2fa82858b67ce55fba1e07c5e1caae92df30050b96c95a8f8fdc467bdcecfcd2cef89fd6a406135f18a2d8bc0de4eedeca9a5c97680be3484a8eddac5e WHIRLPOOL 91aee135f0c1a73d74fe26bf38a2ccb5d9b082733fd4c70eef0c04385c829dae5bfe075ed0248f4634dbd366ef5acb4be574a302ac008723d11524fa28b60b30
+DIST coot-0.6.2.tar.gz 13597123 SHA256 d2f55db4f75c721d120ea33a4ca42c1abf246dff29a75b7f189e604e32709e78 SHA512 d19357a446c0654be286410d33a96aa961f53a3ed87745fe4454a601662ca58463e5f7eb782bf5bc5540c681abccf205c265351cb64a64f851f5e41fad0c433c WHIRLPOOL c4f57d8235f9bfa3db50ef9616424c8eb041c6fca136572e775339436e3f188763df12014cd484ebb32697a3962c456f05b6a99d79478344c34844444b37f097
+DIST coot-0.7_pre4040.tar.xz 12318188 SHA256 c1ca06199da2b1531cdff7ecc08b336b8d50d265b3c8ed9d37da656f6c4abf8a SHA512 34d8bd1b010b40a21fe6fa36efe9a0f01fed714a57dfc21785c4fc7842ec248049f372a8d501cd40e6ec8eec5ca414c90dd948636d05ed7143a87e7384b1ddcb WHIRLPOOL d65892a03f25bea03d493e42dd451aa97752684882fd4ecb93dce16d863e376d2356a7af528174bc504e8b6c53b30a8fff29da4b4d283a7497166b9d7484afb9
+DIST coot-0.7_pre4266.tar.xz 13011656 SHA256 a240fd3492bcde56e224aa637c2f1d7de24b979e56ed8c5c7cd46fbbd8217ae7 SHA512 2684163645070d61f0baa5707483ce8e5708fe435a61b037466ad72c2afcbae6afa72951e655ee6bda018a419c5130dd42fbf6ec2ee1919d9a0802a0e0fed3ae WHIRLPOOL 6ab3e007a8e44cc395115a8285db54ab490e5cb3413bbd640393fad3919d6eae344bb7e03faf78b4ab8e5853466d8b91b74dadad10d402e73ea44e8723811d8a
+DIST greg-data-0.6.2.tar.gz 8044588 SHA256 c9fedf6e1fa60fda178753bbfb539671c274f64d4daca2b63ab49c59bd4c5856
+DIST greg-data-0.7_pre4040.tar.gz 8046573 SHA256 c343ef4a5e4d70c5f1e5af70a7d26d8b66f579c11b208019256bf6478ddb309c
+DIST greg-data-0.7_pre4266.tar.gz 8046574 SHA256 6dd7b701b55dbdf406067449d0586fbb5a855316a9a4e012c17576af1e75eee8 SHA512 43cd57e146281f4b4e30f9c3d5ece0c689f222aa9672f0922052af56423607f86bf33e20e86a5435791a0109f5bfe6bf144d709905a6a28b0e15c9f8a63697cb WHIRLPOOL 1727ac06c09662f37f5cd416b13e22e749621ef8691fd1c121699d5ab049074e5ba2f7bd5e301504ea12f898f6346eec1bc8541bd63fb6bffcf9cca611b7366b
+EBUILD coot-0.6.2-r1.ebuild 4423 SHA256 7164cf3fe4b9c35cbeee7f2f9893fbf2e1db9688d67345e10c6f52044b9c4292 SHA512 cb02d3c8d6bbce6b1614bbcce57b62b3c3f39abf645a9f93fde2d502bb6b82993a3a8b89efddd422830437e4cb0f84ea748d10b0ccc489cabd6b80c6b36c88a0 WHIRLPOOL 0385f14f15ae9bb9d0e34614c1181ae6ccc288f46faf2759728c2852f14574007bf4dbe2067637f4e533fa0e74e588a992fe35528ea96f655638de82f8487aa1
+EBUILD coot-0.6.2.ebuild 4320 SHA256 fd788d6aa77b5e6611ffcd4a0821a21c845a39f9e897d71427ba0a9e58fcc087 SHA512 30e6a58e3ebd4bc943a25a88d29d54d1faed9f2580852be418a595577968a80088fe512bd5a9cee6ad70d1c9b26b0b216fd4ca109c1f940139cc19bdfaafe785 WHIRLPOOL 38cf7eaf56315bdbff78445385b37ff9a2744258527017a9fe718893b571867fcad59a055551b3e0a00e03395717f095ce1bc5bab84c6c7d44c7cadd1248d3a1
+EBUILD coot-0.7_pre4040.ebuild 4477 SHA256 cbc01e21ce216b09f241a6ea54a13c375c538f0363639f896b59fe52900f63d1 SHA512 84a2c112ae81cb8f635169c8967eee39c6d39908bb5ce90e199233ec14ec9c4c29cdb8f711511a4ac58ac13e7242f403d75df0f62fbc41eff10029756d49dc35 WHIRLPOOL 0755dc950dd705eff7a1d3fc431aa7accec0782fbb6b50ae98d26429d6dd8c2f59feff44a166c29abed489992f3f3eb91de8526afe55a7dbd7abe62a049e25c4
+EBUILD coot-0.7_pre4266.ebuild 4380 SHA256 6e0474a52949d4e6beaaa07fca5ad91ba452db7c626dd7eb5d1410b51b608d4a SHA512 864315d0f91b8f26a3a9d9c187b8593bc2bf1a92d35a90bf32de12d5beb94a64cedbca57454c80375e906484517f3a80f6f32728a226b306db7ab4e193836819 WHIRLPOOL 75e4c5e6aec76aa39dc07ffdc694bbb6e7e7d3ade609374c4eb4ff6ea303028310c7fe0c993a85f3767330a52253d5eef88bf2a69801b3c7eaadb6fbcd882c95
+MISC ChangeLog 8285 SHA256 a603a51424fb5750a42c9ceff6d0f9466c91acc7442dbd88f7935a9aa3c13bec SHA512 443269cfc341b65a53298e28c4654a71454b5f9bc1fbaad90a906cadcf89d83dd640736dae16f0806d7744d3e17e80db200460a89f179a62773ea5033529f748 WHIRLPOOL be791bede4bcf46643aeed4f6f4306f0953902244f0df0154c2b9463447242b0c85acd77e51b0f129460205da922dae415f483a5349ea44728dfdc7198a7a11e
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diff --git a/sci-chemistry/coot/coot-0.7_pre4266.ebuild b/sci-chemistry/coot/coot-0.7_pre4266.ebuild
new file mode 100644
index 000000000000..6d331ba735e8
--- /dev/null
+++ b/sci-chemistry/coot/coot-0.7_pre4266.ebuild
@@ -0,0 +1,171 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.7_pre4266.ebuild,v 1.1 2012/07/11 20:38:49 jlec Exp $
+
+EAPI=4
+
+PYTHON_DEPEND="2"
+
+AUTOTOOLS_AUTORECONF="true"
+
+inherit autotools-utils python toolchain-funcs versionator
+
+MY_S2_PV=$(replace_version_separator 2 - ${PV})
+MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
+MY_S_P=${MY_S2_P}-${PR/r/revision-}
+MY_PV=${PV}
+MY_P=${PN}-${MY_PV}
+
+DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
+HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
+SRC_URI="
+	http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz
+	test? ( http://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz  )"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+openmp static-libs test"
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+SCIDEPS="
+	>=sci-libs/ccp4-libs-6.1
+	>=sci-libs/clipper-20090520
+	>=sci-libs/coot-data-2
+	>=sci-libs/gsl-1.3
+	>=sci-libs/mmdb-1.23
+	sci-libs/ssm
+	<sci-libs/monomer-db-1
+	sci-chemistry/reduce
+	<sci-chemistry/refmac-5.6
+	sci-chemistry/probe"
+
+XDEPS="
+	gnome-base/libgnomecanvas
+	gnome-base/librsvg:2
+	media-libs/libpng
+	media-libs/freeglut
+	x11-libs/gtk+:2
+	x11-libs/goocanvas:0
+	x11-libs/gtkglext"
+
+SCHEMEDEPS="
+	dev-scheme/net-http
+	dev-scheme/guile-gui
+	>=dev-scheme/guile-lib-0.1.6
+	dev-scheme/guile-www
+	>=x11-libs/guile-gtk-2.1"
+
+RDEPEND="
+	${SCIDEPS}
+	${XDEPS}
+	${SCHEMEDEPS}
+	dev-python/pygtk:2
+	>=dev-libs/gmp-4.2.2-r2
+	>=net-misc/curl-7.19.6
+	net-dns/libidn"
+DEPEND="${RDEPEND}
+	>=sys-devel/libtool-2.4-r2
+	dev-lang/swig
+	sys-devel/bc
+	test? ( dev-scheme/greg )"
+
+pkg_setup() {
+	if use openmp; then
+		tc-has-openmp || die "Please use an OPENMP capable compiler"
+	fi
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+PATCHES=(
+	"${FILESDIR}"/${P}-clipper-config.patch
+	"${FILESDIR}"/${P}-goocanvas.patch
+	"${FILESDIR}"/${P}-mmdb-config.patch
+	"${FILESDIR}"/${P}-ssm.patch
+	)
+
+src_prepare() {
+	sed \
+		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-$(PYTHON)-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
+		-i configure.in || die
+
+	autotools-utils_src_prepare
+
+	cat >> src/svn-revision.cc <<- EOF
+	extern "C" {
+	int svn_revision() {
+		return  ${ESVN_WC_REVISION:-0};
+	}
+	}
+	EOF
+}
+
+src_configure() {
+	# All the --with's are used to activate various parts.
+	# Yes, this is broken behavior.
+	local myeconfargs=(
+		--includedir='${prefix}/include/coot'
+		--with-goocanvas-prefix="${EPREFIX}/usr"
+		--with-guile
+		--with-python="${EPREFIX}/usr"
+		--with-guile-gtk
+		--with-gtk2
+		--with-pygtk
+		$(use_enable openmp)
+		)
+	autotools-utils_src_configure
+}
+
+src_compile() {
+	autotools-utils_src_compile
+	python_convert_shebangs $(python_get_version) "${S}"/src/coot_gtk2.py
+	cp "${S}"/src/coot_gtk2.py python/coot.py || die
+}
+
+src_test() {
+	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
+	mkdir "${T}"/coot_test
+
+	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
+	export COOT_SCHEME_DIR="${S}/scheme/"
+	export COOT_RESOURCES_FILE="${S}/cootrc"
+	export COOT_PIXMAPS_DIR="${S}/pixmaps/"
+	export COOT_DATA_DIR="${S}/"
+	export COOT_PYTHON_DIR="${S}/python/"
+	export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
+	export PYTHONHOME="${EPREFIX}"/usr/
+	export CCP4_SCR="${T}"/coot_test/
+	export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/"
+	export SYMINFO="${S}/syminfo.lib"
+
+	export COOT_TEST_DATA_DIR="${WORKDIR}"/data/greg-data
+
+	cat > command-line-greg.scm <<- EOF
+	(use-modules (ice-9 greg))
+		(set! greg-tools (list "greg-tests"))
+			(set! greg-debug #t)
+			(set! greg-verbose 5)
+			(let ((r (greg-test-run)))
+				(if r
+				(coot-real-exit 0)
+				(coot-real-exit 1)))
+	EOF
+
+	einfo "Running test with following paths ..."
+	einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
+	einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
+	einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
+	einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
+	einfo "COOT_DATA_DIR $COOT_DATA_DIR"
+	einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
+	einfo "PYTHONPATH $PYTHONPATH"
+	einfo "PYTHONHOME $PYTHONHOME"
+	einfo "CCP4_SCR ${CCP4_SCR}"
+	einfo "CLIBD_MON ${CLIBD_MON}"
+	einfo "SYMINFO ${SYMINFO}"
+
+	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
+	"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
+}
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4266-clipper-config.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-clipper-config.patch
new file mode 100644
index 000000000000..311b5e88d84e
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7_pre4266-clipper-config.patch
@@ -0,0 +1,17 @@
+ macros/clipper.m4 |    3 +++
+ 1 files changed, 3 insertions(+), 0 deletions(-)
+
+diff --git a/macros/clipper.m4 b/macros/clipper.m4
+index 0bf087a..d0e8b6b 100644
+--- a/macros/clipper.m4
++++ b/macros/clipper.m4
+@@ -98,6 +98,9 @@ case $ac_cv_build_alias in
+         ;;
+ esac
+ 
++CLIPPER_CXXFLAGS=`clipper-config --cflags`
++CLIPPER_LDOPTS=`clipper-config --libs`
++
+ AC_MSG_CHECKING([for Clipper])
+ 
+ 	LIBS="$save_LIBS $CLIPPER_LDOPTS"
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4266-goocanvas.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-goocanvas.patch
new file mode 100644
index 000000000000..ce0d4a00abba
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7_pre4266-goocanvas.patch
@@ -0,0 +1,25 @@
+Index: macros/goo-canvas.m4
+===================================================================
+--- macros/goo-canvas.m4	(revision 3307)
++++ macros/goo-canvas.m4	(working copy)
+@@ -56,9 +56,9 @@
+   fi
+ fi
+ 
+-AC_MSG_CHECKING([for Goocanvas])
++PKG_CHECK_MODULES(GOOCANVAS, goocanvas)
+ 
+-LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
++LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
+ CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
+ #
+ # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
+@@ -76,7 +76,7 @@
+ if test x$have_goocanvas = xyes; then
+ 
+  GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"
+- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS"
++ GOOCANVAS_LIBS="$GOOCANVAS_LIBS"
+ 
+ ifelse([$1], , :, [$1])
+ 
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4266-mmdb-config.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-mmdb-config.patch
new file mode 100644
index 000000000000..b3b66ab65786
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7_pre4266-mmdb-config.patch
@@ -0,0 +1,18 @@
+Index: macros/mmdb.m4
+===================================================================
+--- macros/mmdb.m4	(revision 3579)
++++ macros/mmdb.m4	(working copy)
+@@ -86,8 +86,12 @@
+  ac_MMDB_LDOPTS="-lmmdb -lm"
+ fi
+ 
+-AC_MSG_CHECKING([for MMDB])
++PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2])
++ac_MMDB_LDOPTS="${MMDB_LIBS}"
++ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}"
+ 
++AC_MSG_CHECKING([for CISPEP in MMDB])
++
+ 	LIBS="$save_LIBS $ac_MMDB_LDOPTS"
+ 	CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS"
+ 	#
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4266-ssm.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-ssm.patch
new file mode 100644
index 000000000000..c801da72410a
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7_pre4266-ssm.patch
@@ -0,0 +1,56 @@
+ macros/mmdb-ssm.m4 |   42 +-----------------------------------------
+ 1 files changed, 1 insertions(+), 41 deletions(-)
+
+diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
+index 1937a16..6ef547c 100644
+--- a/macros/mmdb-ssm.m4
++++ b/macros/mmdb-ssm.m4
+@@ -22,47 +22,7 @@
+ AC_DEFUN([AM_WITH_MMDBSSM],
+ [AC_PROVIDE([AM_USE_MMDBSSM])
+ 
+-
+-AC_ARG_WITH(ssmlib-prefix, 
+-	AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ),
+-	[ with_ssmlib_prefix="$withval" ],
+- with_ssmlib_prefix="")
+-
+-AC_MSG_CHECKING([for SSMLib])
+-
+-if test x$with_ssmlib_prefix != x; then
+-
+-   MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
+-   MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
+-
+-ac_mmdb_dirs='
+-.
+-include
+-include/ssm
+-include/mmdb
+-lib
+-src
+-lib/src
+-lib/src/mmdb'
+-
+-   for ac_dir in $ac_mmdb_dirs; do
+-      if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then
+-         ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir"
+-         break
+-      fi
+-   done
+-
+-  MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
+-  
+-else 
+-
+-   MMDBSSM_CXXFLAGS=""
+-   MMDBSSM_LIBS=""
+-   with_ssmlib_prefix=no 
+-
+-fi
+-
+-AC_MSG_RESULT([$with_ssmlib_prefix])
++PKG_CHECK_MODULES([MMDBSSM],[ssm])
+ 
+ AC_SUBST(MMDBSSM_CXXFLAGS)
+ AC_SUBST(MMDBSSM_LIBS)