sci-chemistry/coot: Version Bump, #437304; drop prereleases

Package-Manager: portage-2.2.0_alpha135/cvs/Linux x86_64

15 files changed, 32 insertions, 377 deletions

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 9af9cc16646a..dd59db687c3c 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -1,6 +1,22 @@
 # 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 1.53 2012/07/11 20:38:49 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.54 2012/10/06 16:19:58 jlec Exp $
+
+*coot-0.7 (06 Oct 2012)
+
+  06 Oct 2012; Justin Lecher <jlec@gentoo.org> -coot-0.7_pre4040.ebuild,
+  -coot-0.7_pre4266.ebuild, +coot-0.7.ebuild,
+  +files/coot-0.7-clipper-config.patch, +files/coot-0.7-goocanvas.patch,
+  +files/coot-0.7-mmdb-config.patch, +files/coot-0.7-ssm.patch,
+  -files/coot-0.7_pre4040-clipper-config.patch,
+  -files/coot-0.7_pre4040-gl.patch, -files/coot-0.7_pre4040-goocanvas.patch,
+  -files/coot-0.7_pre4040-libpng-1.5.patch,
+  -files/coot-0.7_pre4040-mmdb-config.patch, -files/coot-0.7_pre4040-ssm.patch,
+  -files/coot-0.7_pre4040-test.patch,
+  -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, #437304; drop prereleases
 
 *coot-0.7_pre4266 (11 Jul 2012)
 
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index c2dfad86edd7..89045251de5a 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -7,34 +7,24 @@ AUX 0.6.2-libpng15.patch 1396 SHA256 e1a1a172f92702aab5921943201baeba36643f9c5bb
 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
+AUX coot-0.7-clipper-config.patch 431 SHA256 9ae9129e733d845ad2e4dd505bc5e0987147fc3a5e5dd2457b5857643809db2f SHA512 5817da41b5c692b9d06e44ba8711922465285474ba18ce1d55e567f16f3487218229ae768b63b61a74f437f3d83e3dd49fb504bdd6bb4d9206a97f775b5765c2 WHIRLPOOL 87cc71ae030696a6fa99058aeaf29f66509756732b4f8dcf497e3aab01f395c3a4903c06e0d0e5f77441a7a886c472d77e5a3aa8d05b811e534446f33cceab93
+AUX coot-0.7-goocanvas.patch 702 SHA256 162b21a3afb2d523df315ec021faf7a6497eb3b4fe00f90f601527fe1c22621a SHA512 e083513ea21777c7db05ec59340b57ce70aad5f7acbf93545cee53ce7d595218804531aabf6bcc6d5a2ec72fe5528228478538a52cd61d020e5632f6dfed9b53 WHIRLPOOL 7a99136387924c292e3ea155082706b02f3633740d072c3c35dd26022bb7559397b2574d6707c000f0264e0704be266ae085fe25b25e99adacbb92c683a706de
+AUX coot-0.7-mmdb-config.patch 479 SHA256 0b7d61f9c5f9664672286e82a790d4dea1673ed1537ef62b59142ced97685d82 SHA512 a124943644761ed18e9906655e616c657f8e1a3930ff3fe11cc73f04456c6562a6c240c5bad887ffc26a49798bcd6ec3f40ce967fd06932bcc55ae5795f62433 WHIRLPOOL ceacb033bc7a87449f1dce6d5e3a09d90cd10f4445515622864df8f09c23000421680e6c13dbf1885d867901fbc38553d9008a0307085070b70ca4f30566319f
+AUX coot-0.7-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 coot-0.7.tar.gz 16172237 SHA256 e3d61d326ee906eb77081a6f646024cc6c5c92281f9508da3086fb937fb05aa2 SHA512 27fe0485240adcb7f370cf2daf116d8ea1c8e80e297c0975f1b2d2f78d4a5cd9314e06537e680993d465ef551ceba46a2b402c63acfabcbf599cca6bdb8f843f WHIRLPOOL cc919a7ec3731cfd482bb906c7fd9dc98d9ce2ba2f6bbaa91facf5e5195e27b3fe3f0e03e93668a1524bc2b2306ec23951e1db5033315ed1f26456768a5ac2a7
 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
+DIST greg-data-0.7.tar.gz 8202091 SHA256 b82743b1d3c2d3acaa4adb4901368d46e0638733364963ad62044f79111f21f7 SHA512 71ab00869df074660103b824130776ceeaad398b1df8bbc30c9fc41660cc08a66998a406c5cfc93f4605cc5052aae414bd79b6e6de2ae46acd9c6997dbd5361b WHIRLPOOL 87deff25e864f55b316f432b9a9b595e23352720d08257e2b69bbe7946bf8ab5d1fcc9d13205354a0edd3fbea89422952df5f6fa0c05f9707167b544494b2c14
 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
+EBUILD coot-0.7.ebuild 4298 SHA256 e1a0b5d7b32423d30d0416773fc425f7d2cfde03bf8b7ddbb3ea1fde9f845c69 SHA512 d9ecd88e6a2a1d04aad119c5c283f4f2e821816175efdae95692e5075b8b8c6031816c93d7ce92cdf9f28d67df0d2834dab7e216b69b0b0fbe38c028f0bbfa19 WHIRLPOOL 0ae0e74a973bd56dfcd68e676ed5fd28ceb9f104098a6cd9e5e3864e97f97838a17330a8516e7db62b396b11262135dffd816540e778a1732c07fc74e22b8e50
+MISC ChangeLog 9067 SHA256 4aa4043029992168d249a907f317fb390e31f142bee3533099e53069595b4133 SHA512 c923b9f7b6730a4e244729fb85d38cc5e063e2678c97eb3e4e577026e8479254a71a03ca71bef74052245c141a51de6dcc76730ab12d50144479a967ec202040 WHIRLPOOL 31fcd915abb190e965aa2de03095850b9859146f13568bdc191180ff3ebcc0390a453b76c530c06b38310679aa1be1bd38466607e5fdcada38f9749546d4627a
 MISC metadata.xml 167 SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8 SHA512 0f65f650c91edb15011884892b3e2447ec2342f207b6b71541ec25939fed33cd219b1fcd85dd06008b56a50622973febeb63c9c6158f62435c63c4fbd3ab93bd WHIRLPOOL 0823fd1d22e4aea50bcf78c359303d804128475e21e39514505ee6528c9c46376ceafc1f13bb1cc4e1143d434397fb4ef65dc028e924fdc831521947534fd93f
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 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/coot/coot-0.7_pre4266.ebuild b/sci-chemistry/coot/coot-0.7.ebuild
index 6d331ba735e8..bae7ef02dc0a 100644
--- a/sci-chemistry/coot/coot-0.7_pre4266.ebuild
+++ b/sci-chemistry/coot/coot-0.7.ebuild
@@ -1,6 +1,6 @@
 # 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 $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.7.ebuild,v 1.1 2012/10/06 16:19:58 jlec Exp $
 
 EAPI=4
 
@@ -19,7 +19,7 @@ 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/${P}.tar.xz
+	http://www.biop.ox.ac.uk/coot/software/source/releases/${MY_P}.tar.gz
 	test? ( http://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz  )"
 
 SLOT="0"
@@ -71,6 +71,8 @@ DEPEND="${RDEPEND}
 	sys-devel/bc
 	test? ( dev-scheme/greg )"
 
+S="${WORKDIR}/${MY_P}"
+
 pkg_setup() {
 	if use openmp; then
 		tc-has-openmp || die "Please use an OPENMP capable compiler"
@@ -92,14 +94,6 @@ src_prepare() {
 		-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() {
diff --git a/sci-chemistry/coot/coot-0.7_pre4040.ebuild b/sci-chemistry/coot/coot-0.7_pre4040.ebuild
deleted file mode 100644
index 2a7e3fccbfb3..000000000000
--- a/sci-chemistry/coot/coot-0.7_pre4040.ebuild
+++ /dev/null
@@ -1,174 +0,0 @@
-# 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_pre4040.ebuild,v 1.2 2012/03/07 19:33:39 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}-gl.patch
-	"${FILESDIR}"/${P}-mmdb-config.patch
-	"${FILESDIR}"/${P}-test.patch
-	"${FILESDIR}"/${P}-ssm.patch
-	"${FILESDIR}"/${P}-libpng-1.5.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_pre4040-clipper-config.patch b/sci-chemistry/coot/files/coot-0.7-clipper-config.patch
index 311b5e88d84e..311b5e88d84e 100644
--- a/sci-chemistry/coot/files/coot-0.7_pre4040-clipper-config.patch
+++ b/sci-chemistry/coot/files/coot-0.7-clipper-config.patch
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-goocanvas.patch b/sci-chemistry/coot/files/coot-0.7-goocanvas.patch
index ce0d4a00abba..ce0d4a00abba 100644
--- a/sci-chemistry/coot/files/coot-0.7_pre4040-goocanvas.patch
+++ b/sci-chemistry/coot/files/coot-0.7-goocanvas.patch
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-mmdb-config.patch b/sci-chemistry/coot/files/coot-0.7-mmdb-config.patch
index b3b66ab65786..b3b66ab65786 100644
--- a/sci-chemistry/coot/files/coot-0.7_pre4040-mmdb-config.patch
+++ b/sci-chemistry/coot/files/coot-0.7-mmdb-config.patch
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-ssm.patch b/sci-chemistry/coot/files/coot-0.7-ssm.patch
index c801da72410a..c801da72410a 100644
--- a/sci-chemistry/coot/files/coot-0.7_pre4040-ssm.patch
+++ b/sci-chemistry/coot/files/coot-0.7-ssm.patch
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-gl.patch b/sci-chemistry/coot/files/coot-0.7_pre4040-gl.patch
deleted file mode 100644
index bbd858c646df..000000000000
--- a/sci-chemistry/coot/files/coot-0.7_pre4040-gl.patch
+++ /dev/null
@@ -1,10 +0,0 @@
-Index: coot-surface/Makefile.am
-===================================================================
---- coot-surface/Makefile.am	(revision 3478)
-+++ coot-surface/Makefile.am	(working copy)
-@@ -29,4 +29,4 @@
- 
- libcoot_surface_la_LIBADD = \
- 	$(top_builddir)/surface/libccp4mg-surface.la \
--	$(GLUT_LIBS) $(CLIPPER_LIBS) $(MMDB_LIBS) 
-+	$(GLUT_LIBS) $(CLIPPER_LIBS) $(MMDB_LIBS) -lGL
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-libpng-1.5.patch b/sci-chemistry/coot/files/coot-0.7_pre4040-libpng-1.5.patch
deleted file mode 100644
index bddd251698de..000000000000
--- a/sci-chemistry/coot/files/coot-0.7_pre4040-libpng-1.5.patch
+++ /dev/null
@@ -1,29 +0,0 @@
---- ccp4mg-utils/ppmutil.cc
-+++ ccp4mg-utils/ppmutil.cc
-@@ -2494,15 +2494,21 @@
- 
-   pixels = new unsigned char[width*height*colourspace];
- 
-+  png_colorp palette;
-+  int num_trans;
-+#if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4
-+  png_bytep trans_alpha;
-+#endif
-+
-   for (int i=0; i<height; i++){
-     if(color_type==PNG_COLOR_TYPE_PALETTE){
-       for (int j=0; j<width; j++){
--        pixels[i*width*colourspace+j*colourspace] = png_ptr->palette[row_pointers[i][j]].red;
--        pixels[i*width*colourspace+j*colourspace+1] = png_ptr->palette[row_pointers[i][j]].green;
--        pixels[i*width*colourspace+j*colourspace+2] = png_ptr->palette[row_pointers[i][j]].blue;
--        if(row_pointers[i][j]<png_ptr->num_trans){
-+        pixels[i*width*colourspace+j*colourspace] = palette[row_pointers[i][j]].red;
-+        pixels[i*width*colourspace+j*colourspace+1] = palette[row_pointers[i][j]].green;
-+        pixels[i*width*colourspace+j*colourspace+2] = palette[row_pointers[i][j]].blue;
-+        if(row_pointers[i][j]<num_trans){
- #if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4
--         pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans_alpha[row_pointers[i][j]];
-+         pixels[i*width*colourspace+j*colourspace+3] = trans_alpha[row_pointers[i][j]];
- #else
-          pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans[row_pointers[i][j]];
- #endif
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4040-test.patch b/sci-chemistry/coot/files/coot-0.7_pre4040-test.patch
deleted file mode 100644
index 8cb79e65d767..000000000000
--- a/sci-chemistry/coot/files/coot-0.7_pre4040-test.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/testing.cc |    4 +++-
- 1 files changed, 3 insertions(+), 1 deletions(-)
-
-diff --git a/src/testing.cc b/src/testing.cc
-index f767bf6..097b9b9 100644
---- a/src/testing.cc
-+++ b/src/testing.cc
-@@ -86,6 +86,8 @@ std::string greg_test(const std::string &file_name) {
-    const char *c = getenv("COOT_TEST_DATA_DIR");
-    if (c) {
-       dd = c;
-+      dd += "/";
-+      dd += file_name;
-    } else { 
-       const char *d = getenv("HOME");
-       if (d) {
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
deleted file mode 100644
index 311b5e88d84e..000000000000
--- a/sci-chemistry/coot/files/coot-0.7_pre4266-clipper-config.patch
+++ /dev/null
@@ -1,17 +0,0 @@
- 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 $CLIPPER_LDOPTS"
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4266-goocanvas.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-goocanvas.patch
deleted file mode 100644
index ce0d4a00abba..000000000000
--- a/sci-chemistry/coot/files/coot-0.7_pre4266-goocanvas.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-Index: macros/goo-canvas.m4
-===================================================================
---- macros/goo-canvas.m4	(revision 3307)
-+++ macros/goo-canvas.m4	(working copy)
-@@ -56,9 +56,9 @@
-   fi
- fi
- 
--AC_MSG_CHECKING([for Goocanvas])
-+PKG_CHECK_MODULES(GOOCANVAS, goocanvas)
- 
--LIBS="$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], , :, [$1])
- 
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4266-mmdb-config.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-mmdb-config.patch
deleted file mode 100644
index b3b66ab65786..000000000000
--- a/sci-chemistry/coot/files/coot-0.7_pre4266-mmdb-config.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Index: macros/mmdb.m4
-===================================================================
---- macros/mmdb.m4	(revision 3579)
-+++ macros/mmdb.m4	(working copy)
-@@ -86,8 +86,12 @@
-  ac_MMDB_LDOPTS="-lmmdb -lm"
- fi
- 
--AC_MSG_CHECKING([for MMDB])
-+PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2])
-+ac_MMDB_LDOPTS="${MMDB_LIBS}"
-+ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}"
- 
-+AC_MSG_CHECKING([for CISPEP in MMDB])
-+
- 	LIBS="$save_LIBS $ac_MMDB_LDOPTS"
- 	CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS"
- 	#
diff --git a/sci-chemistry/coot/files/coot-0.7_pre4266-ssm.patch b/sci-chemistry/coot/files/coot-0.7_pre4266-ssm.patch
deleted file mode 100644
index c801da72410a..000000000000
--- a/sci-chemistry/coot/files/coot-0.7_pre4266-ssm.patch
+++ /dev/null
@@ -1,56 +0,0 @@
- macros/mmdb-ssm.m4 |   42 +-----------------------------------------
- 1 files changed, 1 insertions(+), 41 deletions(-)
-
-diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
-index 1937a16..6ef547c 100644
---- a/macros/mmdb-ssm.m4
-+++ b/macros/mmdb-ssm.m4
-@@ -22,47 +22,7 @@
- AC_DEFUN([AM_WITH_MMDBSSM],
- [AC_PROVIDE([AM_USE_MMDBSSM])
- 
--
--AC_ARG_WITH(ssmlib-prefix, 
--	AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ),
--	[ with_ssmlib_prefix="$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)