diff options
58 files changed, 366 insertions, 760 deletions
diff --git a/sci-biology/embassy-cbstools/ChangeLog b/sci-biology/embassy-cbstools/ChangeLog index 6996907cd24b..1426e3265580 100644 --- a/sci-biology/embassy-cbstools/ChangeLog +++ b/sci-biology/embassy-cbstools/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-cbstools # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-cbstools/ChangeLog,v 1.8 2015/03/28 17:35:00 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-cbstools/ChangeLog,v 1.9 2015/03/28 17:54:39 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> + -embassy-cbstools-1.0.0-r1.ebuild, embassy-cbstools-1.0.0.650.ebuild: + Drop old *embassy-cbstools-1.0.0.650 (28 Mar 2015) diff --git a/sci-biology/embassy-cbstools/Manifest b/sci-biology/embassy-cbstools/Manifest index 8a69f0032818..3d5a55939837 100644 --- a/sci-biology/embassy-cbstools/Manifest +++ b/sci-biology/embassy-cbstools/Manifest @@ -3,31 +3,28 @@ Hash: SHA512 AUX embassy-cbstools-1.0.0.650_fix-build-system.patch 2586 SHA256 15692e00271d3d473d0591e7ee46eadca450b002188b795e22826f7e73ebb66f SHA512 38e4fbba5246a44d63b3ac695d8ed45ab6d0902fbe482007b0e206e7a61c0e2429108dbcbbfc1fed161571280a7d7656d6c385bd9cf85ea5a7bfa958e187c6fb WHIRLPOOL 37c54e3d75d457b8539f9e99c04bbb78eea1e1bfc4b31c012062bf8ff8956a78788ae5b93e15c0149745303ff837f7d81562bab69a98b813c417169a1258847c DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41 DIST embassy-6.0.1-cbstools-1.0.0.tar.gz 343812 SHA256 b61b6c19d18dd3a35eef248feb92ee68bcee0e9fc99af5185deee04a17fa3693 -DIST embassy-6.1.0-cbstools-1.0.0.tar.gz 356429 SHA256 de9e39838ee142ba4bb30a499c3326b35a1b86f07bcf1a6848f3f957fae69262 DIST embassy-cbstools-1.0.0.650.tar.gz 452594 SHA256 adb97baa5c7c44c1451537c8cb608024322435d5a4a2693a063a501e42f7127c SHA512 8f16f726220a36f998d8a0f1d8aec9ec6b2db8160b15bed7bafc5a65d57a937bd91ee831ecabe2e9aaa8cecaa18d050f16439a276a882730fde3fa4937bec384 WHIRLPOOL 82813e295f5576d30d474eb9294c2c2c75c577abb59f57baae35cc8cceaccd5a9216f50be43d61523feea80ad6212c955a084bcd9f84da9b5802d050cdc4092a -EBUILD embassy-cbstools-1.0.0-r1.ebuild 544 SHA256 9db4ff135b24e86fae98683e88d66bfc80b0204f0c29a1e3926037d56f1d50a1 SHA512 8b5f1f55daa97e181f23590e51189749af77e2fb40ec36caf4c492a84bed36d09e3e353e8267016f0a2d40d303bcbaca83edf5af7da27dbece3fd8d865695b9a WHIRLPOOL 0304ed650785ff9af4213bdf03b31cf29bdc015fd74904269e278308d30f3ab575499f954a0928d349594bfc4589ff9af3313d0a7f43bfa0b3c64263fda1d70f -EBUILD embassy-cbstools-1.0.0.650.ebuild 461 SHA256 43fc26e1a1f29d3ee96eed2e5cdeb952479cfcd94b39ae21b58bb93dd270c79f SHA512 9d3eaa981851c18547d6c90527a8561e1da08fa3ba39e1164f8d5a7e2239b6b5b63767fe2cd0b0cccd6019cf4bdec11cc802b6ba107344e46f0838d8ab49cd4d WHIRLPOOL ab4638036733586c3b5df12b4bc0e4ea6e7fb883ab8e2c4268545740ee5f30418e42cd68d4d16ae5fc0e375b5228649b5fb3f6543f1c85ff7cc486ba125ca155 +EBUILD embassy-cbstools-1.0.0.650.ebuild 463 SHA256 fce2ebfcf3d5bf074e3116ea46743e76b283ea7f685c3e4c9aa5d8c354945892 SHA512 24560a2063c17f1d2712621af56d440a050954b9511bbc070edfd4fde7fab3fa22798233e93e86fed01210880fb80587bb944326d399f067144a79f098363ede WHIRLPOOL 446bd4fc6024ef098306da267543187cf5d2a786dd662a2dab2f34538b43e7534a9592b37bc1770429874fbdb9ff49a86f516cd0936d3d03ccde39ee523b4ea9 EBUILD embassy-cbstools-1.0.0.ebuild 504 SHA256 71a95a9654810371b8e2520b4565df719bf8b83361cd3be05274bf880fa8621f SHA512 ab1b7aeedcb9470bc5e280f9803d3f9b8fc71daae758f36a64ef5bb15038143f49020984ade3369ed4ede377c46b81951d3c5a3e793710df220050f61b0915f1 WHIRLPOOL 2994eada7616e524ecbd5bc0e1c31400cb668d73b89858f3125cd91c789548462aa45b0cbb09162625e61e7caddaab5d92711778178a1cc30db9820e68979d39 -MISC ChangeLog 1508 SHA256 8513871a24824a3c0590926e806a2c83f6dca6872735b5b324cb0b12da08d987 SHA512 2286fca698ffacdc4a30d6e7271e1f270422624be2720bab28271d7ce02693e0a9727e67acdc2c7310fdf3c4d9e16da6149a8dca9aecf640b4254c88a5a41a75 WHIRLPOOL 7f471a2eda3d2bb57a9ef7a2d61ed019fc9b673963a42e6dff88616a58d8e705b14bad29113376fe2d0d431415898cc429965c54e3a172ec5b77287e86660d37 +MISC ChangeLog 1639 SHA256 8490dda298f827a92ea2e55a83b0569f0f0a8c19f12addc13e79692499fb81bb SHA512 38cbaabead69e29e96caccb4b6e8c7b9e3f69e5669dfba0eeeed741617d75539b47cecaa494adbfbadcc87e700f57f7e842ae0710f042c3ae73d77e0e4bc64aa WHIRLPOOL 59b3db0e82c69ff09070592697cbe4159147e59d903608f894db83ffc98e700118d8f5a650801e61486f590ab4336015051f1f19195855dd03bec039d53f797f MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0 -iQJ8BAEBCgBmBQJVFuZFXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w +iQJ8BAEBCgBmBQJVFurgXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w ZW5wZ3AuZmlmdGhob3JzZW1hbi5uZXQyQ0JDQjFGMzBDQ0UxMjFGNENDNDgxMDdC -OUQ0RjIzMUJEMTU1OEFCAAoJELnU8jG9FVirhUYP/3jK+NNpVkni+JneHFTyO6nf -WRT1ZH10Z4s9XYQM4HdiN4hvQ9QDtqJTmZ2FjhBVYpiqp09JYvQJqsKVhA0y2T2p -ggaDvDP9CUKqbi8TpdIrPcsZuIy0H8667F2CcK/BF6Si7Mm/JDaao94KScGFhFvI -buqiXPGo26VBslPOdJLyPPhhZXVkc8uoqKoSi1QWDasnZPMan2bXJcBxlLaBolWO -d3eqR6KfbYx/uSPDrvcgA+BDLdtSbaZWk9sPly3BAv5fEPFKJJfkbvurKWP9abq1 -7pe0OShpXFArSlU2awX/g9tM8/RMmKZT6opTTadBoez2W358dJfdo8rFOOeFMD8e -2d6yoU9JgSn5p21HfTabbS3dOzgl+dR6M1+kg2tWIuE4XYDN5YfuP6uu5E1jsJAT -xvPqRffFilDBVjBEBohK+hmK+/kSLrHiD41ci4MrAq7GkqLcVHFNy6D5Q8Nhc86M -OyePmCM2W3zj9RIMv4VVUTu71Xh22j/2BsKzvCw6qHQ7whfgSUMaM9zWb80KWEfk 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a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0-r1.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0-r1.ebuild deleted file mode 100644 index fbf01d165ae7..000000000000 --- a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0-r1.ebuild +++ /dev/null @@ -1,13 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0-r1.ebuild,v 1.4 2011/10/20 08:56:48 xarthisius Exp $ - -EBOV="6.1.0" - -inherit embassy - -DESCRIPTION="EMBOSS wrappers for applications from the CBS group" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild index 462183789f05..26446d870cd7 100644 --- a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild +++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild @@ -1,13 +1,15 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild,v 1.1 2015/03/28 17:35:00 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild,v 1.2 2015/03/28 17:54:39 jlec Exp $ EAPI=5 -EBO_DESCRIPTION="applications from the CBS group" +EBO_DESCRIPTION="Applications from the CBS group" -PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) AUTOTOOLS_AUTORECONF=1 + inherit emboss-r1 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-domainatrix/ChangeLog b/sci-biology/embassy-domainatrix/ChangeLog index 4ca9c278249c..e28526fd1b09 100644 --- a/sci-biology/embassy-domainatrix/ChangeLog +++ b/sci-biology/embassy-domainatrix/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-domainatrix # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/ChangeLog,v 1.33 2015/03/28 17:31:57 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/ChangeLog,v 1.34 2015/03/28 17:57:09 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> + -embassy-domainatrix-0.1.0-r4.ebuild, embassy-domainatrix-0.1.650.ebuild: + Drop old *embassy-domainatrix-0.1.650 (28 Mar 2015) diff --git a/sci-biology/embassy-domainatrix/Manifest b/sci-biology/embassy-domainatrix/Manifest index b1cd5e10a753..d8e129ec0faa 100644 --- a/sci-biology/embassy-domainatrix/Manifest +++ b/sci-biology/embassy-domainatrix/Manifest @@ -3,31 +3,28 @@ Hash: SHA512 AUX embassy-domainatrix-0.1.650_fix-build-system.patch 2388 SHA256 8b66b6a1499bb3700c23958726cf1ca92ed8387c0112ec3a2f426cfaa4cec281 SHA512 d607b1153113b503279a14478871f13a594fe8894daa14e4f558d6051971dc70bc4bedbcdaad20c9be85841d409eab494ecdeb3f8f73631e6acaa1911dd645b3 WHIRLPOOL 889a02a76695558290e8b1595197f8ebe5d28332fc02d1ad75e4062800730fff996cef58101105134b63b6f23a97b10cb3ed96d86353977e9d6e87695f2d2406 DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41 DIST embassy-6.0.1-domainatrix-0.1.0.tar.gz 420983 SHA256 7596e76b79f19d77e27b8ea8a75a3e1ba4c806aa548cb9675f23e2bb434a42b1 -DIST embassy-6.1.0-domainatrix-0.1.0.tar.gz 399655 SHA256 54f4aa2bd8753a261722f16098e42f01a9083467162c027e2f1738a740f880d3 DIST embassy-domainatrix-0.1.650.tar.gz 474066 SHA256 122cae02e529385eb98d51caa3a21b613545b5dbc763e17524afeab1f7d1cb18 SHA512 151e026445abb171a9141ae5576442307121646c66dc811320a6f73be1103203bf04d37b813e5c95ef0873be261cd474835f4dffd042f33f99d7dd4fda19be7b WHIRLPOOL 82689cbedec77da2c7eb62a78e4407e2153d9dc6e4c51608705bc4bfed3556516ca61619982a3fcb02cdf8e37eee68f87aeba9fec23d054b660dad15d81553c0 EBUILD embassy-domainatrix-0.1.0-r3.ebuild 511 SHA256 4a0293c37b1f414f8699767c029b3cbcfa51bccd847288155c5da33d48f71250 SHA512 f40d442c07a8049c1f9636c99f6a9e8580050b27f1d5c62b1e64f3648515e905cdf6c25b94e31b0607e5a0e2ba6df78f475874ef0a036ef1875c0194dde58e95 WHIRLPOOL 5db1ea0c39f2ec4e701f35c2f839ad73fe5a3f0aecabb53cad86f795512e1d795fb2525768286e3360efe519f954baaa575278e25554676458000b1fddede4e2 -EBUILD embassy-domainatrix-0.1.0-r4.ebuild 535 SHA256 af43b3014e915d3c71bccbe2142a63f005c04eea16db188ee3b6439acb4c6fd1 SHA512 92d23eceeb6dd88ae949df4f470a83439084d32faea38c196ca14d7114c6b6ae6dc8b5287083c6cf7bdfa46c05a47d13a0160fa2ebf05cb3118fbbeb18606a0f WHIRLPOOL 64bb5116ffdf8368d97e8710e13f96e3420a2f597720900a033deab5cc4db255c24ab283045cdd0eb204cf42fd09cb6339794c139143b6a327375fbb053aa0d4 -EBUILD embassy-domainatrix-0.1.650.ebuild 459 SHA256 ea47e42014cf7b3cd81b587f9e034a26f2587d4b2d6023354889f6727cfcfad5 SHA512 d2133bb4224daae332c1289e49b92351d69eb9c1eb4b324a5dffadaef3e161952c1d1bf66244c587c878de2ae94192af386a368c4b40e2f510855d4584db2eb5 WHIRLPOOL bfa5500cb637ee5a88c5f2e5c1ccbabdb5d972f439ce3d3ae7e8910d3de99fd0f05ae8619dd61554c5affecbab501144f9290977b32c1cb227577e9bfa8d20d5 -MISC ChangeLog 5508 SHA256 d923cc253a3103fdb9774e8c935aacbda574cedaa06848799b4e6541e194509f SHA512 1cbbd206595aae8b4799c02863f5e9405dfe56a2034afe016fb7ede063fef2a508498e581ea138af1f596f3ea1cac0f50b1f3bd1c0b62f4f3a6ec0391449e332 WHIRLPOOL 44472d22194f65641a0d1ac9c798bc6451baccbe68b015f52a6f67c76b8037ecc5d875a1279131dd85175a4bab32278c481735d4033130a52111f7f61cce7a80 +EBUILD embassy-domainatrix-0.1.650.ebuild 461 SHA256 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211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0 -iQJ8BAEBCgBmBQJVFuWOXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w +iQJ8BAEBCgBmBQJVFut2XxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w ZW5wZ3AuZmlmdGhob3JzZW1hbi5uZXQyQ0JDQjFGMzBDQ0UxMjFGNENDNDgxMDdC -OUQ0RjIzMUJEMTU1OEFCAAoJELnU8jG9FVirRosP/jhwQD+i/XIhy+THukJ2hbuB -gMp6GtEBdmgoMrS5f510t8Lpx7gTpW/og5iIhn1Nq7yAIC6svAqqgm/2rJkmkmoo -OMVyNnAB13CoryPrixJ4FFTKuTnhUwSDX9u5mBDxifclSJFI8boSVAE956DRVmMn -zqQboa45mHO4gWA63uYUzhhENnhpoMMLLh+G+2G7kSJ2sbF4F5tqotd+EqVvlTIJ -14Id/Dvu61sNDLdgXO+YgnyFhhAMjT7axy9lM0/KIwjAe3Xz7JFBPdIOrcOD0vlX -bcXARdFiOfKXTQ4E6YKzChN0YFIjawH0k9YxzpLfLaZZTSAMCQs12aK9SNd+ZCHO -Iz5wOfYLjFQHHjTG2WjSnh+lsD0pBz2hYgBoecmx0T3sJGIRIbaacj9dY7IwZI3/ -2m5Qx+XELLMUYn0jv+6Pl66Ecmi6PAq6qUlNxd86MQREd0b7WqasdM9WQm5ncoyK -GhlPwsZYqJS+odzI/slw1WpBqNljifYq8X7CT2Chu0s3McMUXNz//YG9LpbM1WuZ 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a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r4.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r4.ebuild deleted file mode 100644 index 970f98c5c5bf..000000000000 --- a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r4.ebuild +++ /dev/null @@ -1,13 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r4.ebuild,v 1.4 2011/10/20 08:57:09 xarthisius Exp $ - -EBOV="6.1.0" - -inherit embassy - -DESCRIPTION="Protein domain analysis add-on package for EMBOSS" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild index 0325abd696a0..b1113806b9e0 100644 --- a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild +++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild @@ -1,13 +1,15 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild,v 1.1 2015/03/28 17:31:57 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild,v 1.2 2015/03/28 17:57:09 jlec Exp $ EAPI=5 EBO_DESCRIPTION="Protein domain analysis add-on package" -PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) AUTOTOOLS_AUTORECONF=1 + inherit emboss-r1 KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-domalign/ChangeLog b/sci-biology/embassy-domalign/ChangeLog index cf25c5266a7c..7d020f1086dc 100644 --- a/sci-biology/embassy-domalign/ChangeLog +++ b/sci-biology/embassy-domalign/ChangeLog @@ -1,6 +1,9 @@ # ChangeLog for sci-biology/embassy-domalign # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/ChangeLog,v 1.24 2015/03/28 17:30:41 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/ChangeLog,v 1.25 2015/03/28 17:58:10 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> embassy-domalign-0.1.650.ebuild: + Drop old *embassy-domalign-0.1.650 (28 Mar 2015) diff --git a/sci-biology/embassy-domalign/Manifest b/sci-biology/embassy-domalign/Manifest index 0d00775cb901..7deb87e1edd5 100644 --- a/sci-biology/embassy-domalign/Manifest +++ b/sci-biology/embassy-domalign/Manifest @@ -9,25 +9,25 @@ DIST embassy-6.1.0-domalign-0.1.0.tar.gz 434640 SHA256 45ddc0ee932d2bc6387a0fef7 DIST embassy-domalign-0.1.650.tar.gz 498669 SHA256 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a/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild index 8152116b0539..d6e6e3352b2b 100644 --- a/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild +++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild @@ -1,13 +1,15 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild,v 1.1 2015/03/28 17:30:41 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild,v 1.2 2015/03/28 17:58:10 jlec Exp $ EAPI=5 EBO_DESCRIPTION="Protein domain alignment add-on package" -PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) AUTOTOOLS_AUTORECONF=1 + inherit emboss-r1 KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-domsearch/ChangeLog b/sci-biology/embassy-domsearch/ChangeLog index 56c0bc2ba631..2091b5e76712 100644 --- a/sci-biology/embassy-domsearch/ChangeLog +++ b/sci-biology/embassy-domsearch/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-domsearch # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/ChangeLog,v 1.23 2015/03/28 17:26:58 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/ChangeLog,v 1.24 2015/03/28 17:59:24 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> + -embassy-domsearch-0.1.0-r4.ebuild, embassy-domsearch-0.1.650.ebuild: + Drop old *embassy-domsearch-0.1.650 (28 Mar 2015) diff --git a/sci-biology/embassy-domsearch/Manifest b/sci-biology/embassy-domsearch/Manifest index 8be543dbdd4d..5e428e1f6992 100644 --- a/sci-biology/embassy-domsearch/Manifest +++ b/sci-biology/embassy-domsearch/Manifest @@ -3,31 +3,28 @@ Hash: SHA512 AUX embassy-domsearch-0.1.650_fix-build-system.patch 2410 SHA256 c18d9208dcb000e12fe023863180ac1d3643c236a8bf4259e930526ead7f8257 SHA512 d6e0ef61a009b5df0c8e3d4a61a366a0a202c73e47fa86917a0eb9c476f3bf77b1dda399f1db7e6fd6d504247f31b84b022496b230fe570867239c70584fa68f WHIRLPOOL ecbdb32b6dec691de7808aea25bb7b46bdbe80b219aa36a006bd839de50011801134cdab66b770a81a7dcf62e349a2197e67d830dec1fa6e9c1a0ae7c56f7928 DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41 DIST embassy-6.0.1-domsearch-0.1.0.tar.gz 470537 SHA256 fb34c1b2f668f89abe6912fe75e9828c53802820753aa8a1b952f37894939c95 -DIST embassy-6.1.0-domsearch-0.1.0.tar.gz 443681 SHA256 781461790a85d259a49130d5220a644213d5aaf352e9f72ab8fbb0dfaa331120 DIST embassy-domsearch-0.1.650.tar.gz 504183 SHA256 43c1d99723f42d0f79c4e9d11abaff084bed8262ec958f237a51465cd7afa168 SHA512 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cb039314f17c0bccde3a6485af538eab73c53b482a8a2d8361e8bbf0093bf0d1 SHA512 91e8b0082a8a8aa0b41606df26145d770dd371a04e7ae71974f0aa24367610875834a0f51d619fec9b2c65b480bf7bc99bf99179d639e53e7cd09ae0cd5732e8 WHIRLPOOL e20fa45658d9616060dd536f84f496ad9576ae48aa3049e40fb0680d4b5d2661d678fc67dc2c25820fd77a2bc9cf7b6452a7787d5e41dc963bab7b6a88f8dfc3 +MISC ChangeLog 3711 SHA256 2c74ffe75979077cae107a5447614cadf0671dc200754ecec5c655b1b4267d48 SHA512 ef798e8b1e9e5e5ec01ca6675e6a7e9249362a2bf643175ef6df7df892d2bbe2f48dfb757a311e973b7a99ade2b0bcb9afd916672599d9b38c3f1657626e3e78 WHIRLPOOL 2336d7199682e9873359d25a51904900e4caaf1c7d03649dacb2d070d2360a10ed1bf75eebcafc94184938d0b2e9e5bd38e7d05ecfe0b587ab2cc73ac44a8a2d MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0 -iQJ8BAEBCgBmBQJVFuRjXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w +iQJ8BAEBCgBmBQJVFuv9XxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w ZW5wZ3AuZmlmdGhob3JzZW1hbi5uZXQyQ0JDQjFGMzBDQ0UxMjFGNENDNDgxMDdC -OUQ0RjIzMUJEMTU1OEFCAAoJELnU8jG9FVirbYMP/21ZWWmgNfg9e0HpfNEPTadr -huKR0UntTlRMDht06N00quqR/pg/TYTgXl9kCaUAA1ibqEA3h2uLpn96MlJS+c3X -gD0LPzvnsIuBGbV4khoJATTHl0UP8sMMMM6BXKlLtMcMVZeNxK8SpIrWMYdZHNBG -MDgkhcEjgFr1VFoDfwtktSwMGEskCUNfGm14TBXl+FGugquFH/I+AuMeP8oDDuta -wmU27Nmo+4aAC3FtKHtERD2EnaolLSFrJ4E684+keUZlFgDXVhcrJTjcclrl2z9E -tY1d+ez6TvF1rrc1TlAXLYkZSdN2WaaE1idLRZUMI128+x6vqD3guzwBJ5wogl5i -zHqkd/Gqbw59QgioYmkDxl6EWv/cezrsbS+ZkYPGpSB9dgjnqrV269NhA0u0sSLn -lykT1rv1tj22WHYWx9ZEWQvVeUZ4oAZUBFkd49XGvuNXc6ROF9fsjnKYF2wkJ1zu -AqwWXs9e6YJzo1JZxsgDrBBJwW1a4s4jthXlswCr3f2GlSfJjN7H6qo6kvXONjXU 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a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r4.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r4.ebuild deleted file mode 100644 index 2915d2ab5fd4..000000000000 --- a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r4.ebuild +++ /dev/null @@ -1,13 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r4.ebuild,v 1.4 2011/10/20 08:55:04 xarthisius Exp $ - -EBOV="6.1.0" - -inherit embassy - -DESCRIPTION="Protein domain search add-on package for EMBOSS" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild index c1619bfd7f46..b3436fef4f4b 100644 --- a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild +++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild @@ -1,13 +1,15 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild,v 1.1 2015/03/28 17:26:58 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild,v 1.2 2015/03/28 17:59:24 jlec Exp $ EAPI=5 EBO_DESCRIPTION="Protein domain search add-on package" -PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) AUTOTOOLS_AUTORECONF=1 + inherit emboss-r1 KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-emnu/ChangeLog b/sci-biology/embassy-emnu/ChangeLog index e4f8e1310b0c..b53b1c3f5986 100644 --- a/sci-biology/embassy-emnu/ChangeLog +++ b/sci-biology/embassy-emnu/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-emnu # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/ChangeLog,v 1.33 2015/03/28 17:24:57 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/ChangeLog,v 1.34 2015/03/28 18:00:22 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-emnu-1.05-r6.ebuild, + embassy-emnu-1.05.650.ebuild: + Drop old *embassy-emnu-1.05.650 (28 Mar 2015) diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest index f21f17683ef2..5d8bf73faf7d 100644 --- a/sci-biology/embassy-emnu/Manifest +++ b/sci-biology/embassy-emnu/Manifest @@ -3,31 +3,28 @@ Hash: SHA512 AUX embassy-emnu-1.05.650_fix-build-system.patch 3455 SHA256 6f165662eb1e8d57eed8f51fa6c836b949f6be83327732bb7a7fa1b93373c763 SHA512 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1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/embassy-emnu-1.05-r6.ebuild,v 1.4 2011/10/20 08:54:43 xarthisius Exp $ - -EBOV="6.1.0" - -inherit embassy - -DESCRIPTION="EMBOSS Menu is Not UNIX - Simple menu of EMBOSS applications" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" - -RDEPEND="sys-libs/ncurses - ${RDEPEND}" - -DEPEND="sys-libs/ncurses - ${DEPEND}" diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild index 15daeda9d936..f3731b9b9203 100644 --- a/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild +++ b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild @@ -1,17 +1,19 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild,v 1.1 2015/03/28 17:24:57 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild,v 1.2 2015/03/28 18:00:22 jlec Exp $ EAPI=5 EBO_DESCRIPTION="Simple menu of EMBOSS applications" EBO_EXTRA_ECONF="$(use_enable ncurses curses)" -PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) AUTOTOOLS_AUTORECONF=1 + inherit emboss-r1 KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" IUSE+=" ncurses" RDEPEND+=" ncurses? ( sys-libs/ncurses )" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-esim4/ChangeLog b/sci-biology/embassy-esim4/ChangeLog index c7243b02282c..bef564a95604 100644 --- a/sci-biology/embassy-esim4/ChangeLog +++ b/sci-biology/embassy-esim4/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-esim4 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.32 2015/03/28 17:23:35 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.33 2015/03/28 18:01:21 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-esim4-1.0.0-r6.ebuild, + embassy-esim4-1.0.0.650.ebuild: + Drop old *embassy-esim4-1.0.0.650 (28 Mar 2015) diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest index 77980aa589b2..6872b54f4b76 100644 --- a/sci-biology/embassy-esim4/Manifest +++ b/sci-biology/embassy-esim4/Manifest @@ -3,31 +3,28 @@ Hash: SHA512 AUX embassy-esim4-1.0.0.650_fix-build-system.patch 2568 SHA256 b19e115c5e2585349cea1a67e10d2928eb57ec65d2d55d305145d942cf7592b3 SHA512 2205c7b6ddcbbb17be6ae7242ddc54240c8087f04be5b7b9b245ce5d14c16ac196e227589b579d9c10ec433eaef7d69af9acb0ba16795130f630ef4b597997c2 WHIRLPOOL 8e52232753759142512035c86753214bf40b1e4433bf643b6866e8802aa53125ec61b5c3387a259aa81cadb3ddc1854eaaf7e8d15e3ec4d68d5fa6209bd3b49d DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41 DIST embassy-6.0.1-esim4-1.0.0.tar.gz 431898 SHA256 219b3541e2a67d31fd62140c2c9c2b41e2d3d814dec6aaf691f764e337917577 -DIST embassy-6.1.0-esim4-1.0.0.tar.gz 405076 SHA256 ff4c01548a4a70f0e27b25df439588d25db417a6f80371590acc4254b3876b7c DIST embassy-esim4-1.0.0.650.tar.gz 473261 SHA256 ce2f8a4e802da7e11ac3cbaf24406d9b33d4aa488f1c68bbbc8e969ec7e0b671 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152 WHIRLPOOL ea34bd05cc41f8e1e4af8eebfca9f1c0888c96f0dbb11df79c2cd8966b27d72f019c8ec3043ca7c9e276e015232476165a77336590ace448766a45163f654d62 EBUILD embassy-esim4-1.0.0-r5.ebuild 519 SHA256 f8b35c9e3fd4c0b2b44501628a7daacb31a9ada8c58f029fa3dccd850928bdab SHA512 23b41eea8b3c0dd1f41887305afa18596cc82e6853e83355399a81545932c95c661760df2d926b1fd295bb04554e471f3926669808c0a625813216dc3e3750c3 WHIRLPOOL 47d8e921988c76e15d5a77adafe5df01b655be2a9d60201a139a098b2b45252b81befc23f6e5b8813bf71a64c6c843f676c99f194a7b2cb9b5e5902fd1388771 -EBUILD embassy-esim4-1.0.0-r6.ebuild 543 SHA256 1d0c45a80b4a3ff5b53edb353ccacd2778e20d331ce7a31fc24214aecf0f6460 SHA512 13e8a52f313123b41ba178feb8e44aa7f8607cebb7c1a3a700b22e31a6f057980edf9aea09b55dc300d404b1731590c05f3f9e4dd5a52ee9cd8c5d65a138b5ac WHIRLPOOL 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c1e3ab42f2f99f749d15086762a1bcdbb36171eab6ebe273d8ddbd526b0c0feb SHA512 b05a644e027aad996a7c4ff56bf9ba656129a76390933976a034f2adb703c727e2cfee5aa71cc4a2a2f09b832b5a050d22a931528ee13dc60d5e6f71b6fdb40d WHIRLPOOL 780dbb382eb59e718f1f10321071b90668b04e4c81f2c1ea7e3c988f2cfec54d869cccd341dc91600dd00c49c5591d71f01aa7559551d3572a842486963716dc +MISC ChangeLog 5018 SHA256 46a2f9032ecc0ff4e3c72e3819cb8ee3c2cca759380921e3a66d096473aa3395 SHA512 7867950cfa0cdcb2e4900e5e9673fabe969f596715896763560f0e629c2858d8e13c8ae030613d11354369f6d5ef526dbdffdb287ac2b5122c9ee48984da3e62 WHIRLPOOL 6e1032eacdab8e55a1cc0e8e1fc02da8bfba0f3c150078cae868acc73185a85d3340e860484b18508cbf60bc101d8bc7eee2b1776dc298fb933aeaba19285987 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0 -iQJ8BAEBCgBmBQJVFuOYXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w +iQJ8BAEBCgBmBQJVFuxyXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w ZW5wZ3AuZmlmdGhob3JzZW1hbi5uZXQyQ0JDQjFGMzBDQ0UxMjFGNENDNDgxMDdC -OUQ0RjIzMUJEMTU1OEFCAAoJELnU8jG9FVirv+YP/iO0BEco+kP/89BGw54+mBeV -39Ex3FhdTPCN8sHztKcyVswYpXFe7TpvI3sPllaHWUpVnDkABfdE/6tpfg4+M5AQ -BG8Eda7mm4szNEoVcuNIFmgJ7mChyZMP5xhAEG1VwNCXRhSz0B9UhAKkIK8GfDZs -Epr/6aUvlv8PFMoJQ/cZ2y8+CqROvYrb4dvKa1JJF/keywQKdvPlrB5Zw8QkcHkI -+NTKSuYvPawwuxiX745NiG1ODIurApb2v7/z7SK6Ef1+pnTzvPagddYHMlwcYz4G -JCqXJoU34UszJTLyNCe2o9ookgdelGcM2Fmei+8nyzJGGJMQLum+1WVNUj2TRbgu -+QgdQ5uIwymLw0NQJ0c8XN1YG5xCAwUcSwwsTUx337uJJiSXtq2ry8o3aAPuUjV5 -lizGnP+MLI6XV3N8r/J6M+tA9aXBil/4c1h0IduKqmlJWto1OmtruOgn8Hd5k54B -7lVDDP0H8z38IDRbplJGctV8rjXMmiDT9Dx50i5mxlDcL0yNvXPqDBIdxO67U1IL 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a/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r6.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r6.ebuild deleted file mode 100644 index 9e9c0681c4bc..000000000000 --- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r6.ebuild +++ /dev/null @@ -1,13 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r6.ebuild,v 1.4 2011/10/20 08:54:22 xarthisius Exp $ - -EBOV="6.1.0" - -inherit embassy - -DESCRIPTION="EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild index 218b569b4a1c..e5fcc989057a 100644 --- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild +++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild @@ -1,13 +1,15 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild,v 1.1 2015/03/28 17:23:35 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild,v 1.2 2015/03/28 18:01:21 jlec Exp $ EAPI=5 EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA" -PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) AUTOTOOLS_AUTORECONF=1 + inherit emboss-r1 KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-hmmer/ChangeLog b/sci-biology/embassy-hmmer/ChangeLog index df2f6f77c52a..e13c9d1a94ee 100644 --- a/sci-biology/embassy-hmmer/ChangeLog +++ b/sci-biology/embassy-hmmer/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-hmmer # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/ChangeLog,v 1.34 2015/03/28 17:21:22 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/ChangeLog,v 1.35 2015/03/28 18:02:43 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-hmmer-2.3.2-r3.ebuild, + embassy-hmmer-2.3.2.650.ebuild: + Drop old *embassy-hmmer-2.3.2.650 (28 Mar 2015) diff --git a/sci-biology/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest index 5edae00022f8..a274f84f59ec 100644 --- a/sci-biology/embassy-hmmer/Manifest +++ b/sci-biology/embassy-hmmer/Manifest @@ -3,31 +3,28 @@ Hash: SHA512 AUX embassy-hmmer-2.3.2.650_fix-build-system.patch 2371 SHA256 20427d58bfc422c6bed462720a5bc134d447afbab16f18971abd8f1cba514ebd SHA512 5dcae5146e86fe828bfd026ca95aecae1838b785d0b0b02f59193baa3966ebedb91cef4b7674353bc1935eb46f17aa9503f8c0a3cea69524f592a27d4de13b1e WHIRLPOOL 69ac46d89d397c4618aa753280a2606c5d5f8792e5d4366efc72e7c5032face31be1d7babcb1f6ed8a116050d6299538c01e4121f026d5233f7d7f733eec0c6c DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41 DIST embassy-6.0.1-hmmer-2.3.2.tar.gz 565686 SHA256 9b27f2b7a9059b017e3bd3d31de08f6fbf7d49c3e025d73abd83ff0567732258 -DIST embassy-6.1.0-hmmer-2.3.2.tar.gz 541801 SHA256 725d1b1f7b79a29b6b2a0569ce82fbd773c1199cd041b1c2360f66e4be78aaab DIST embassy-hmmer-2.3.2.650.tar.gz 587775 SHA256 1464ff5e87c7c429f2fc78ac3554f8bd32cdaf49b8bed095fce6268b9afd4f6a SHA512 eb2c037fec70f4113b9ab59cc4eca9a608e8d0971a7bcc4612d60b1e28556444dd3ecdea4ff7b8f8b34711ad9f655334857e7510e89060459c81994a3abcc02a WHIRLPOOL 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Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r3.ebuild,v 1.4 2011/10/20 08:54:01 xarthisius Exp $ - -EBOV="6.1.0" - -inherit embassy - -DESCRIPTION="EMBOSS wrappers for HMMER - Biological sequence analysis with profile HMMs" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" - -RDEPEND="~sci-biology/hmmer-2.3.2" - -src_install() { - embassy_src_install - insinto /usr/include/emboss/hmmer - doins src/*.h -} diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild index 9df99b843eb5..248f9e5c214f 100644 --- a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild +++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild @@ -1,15 +1,17 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild,v 1.1 2015/03/28 17:21:22 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild,v 1.2 2015/03/28 18:02:43 jlec Exp $ EAPI=5 -EBO_DESCRIPTION="wrappers for HMMER - Biological sequence analysis with profile HMMs" +EBO_DESCRIPTION="Wrappers for HMMER - Biological sequence analysis with profile HMMs" -PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) AUTOTOOLS_AUTORECONF=1 + inherit emboss-r1 KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" RDEPEND+="sci-biology/hmmer" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-iprscan/ChangeLog b/sci-biology/embassy-iprscan/ChangeLog index d58acceadb12..2bf7f0584ea8 100644 --- a/sci-biology/embassy-iprscan/ChangeLog +++ b/sci-biology/embassy-iprscan/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-iprscan # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/ChangeLog,v 1.8 2015/03/28 17:20:18 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/ChangeLog,v 1.9 2015/03/28 18:01:54 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-iprscan-4.3.1-r1.ebuild, + embassy-iprscan-4.3.1.650.ebuild: + Drop old *embassy-iprscan-4.3.1.650 (28 Mar 2015) diff --git a/sci-biology/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest index b246d609c6f0..91a255a7a273 100644 --- a/sci-biology/embassy-iprscan/Manifest +++ b/sci-biology/embassy-iprscan/Manifest @@ -3,31 +3,28 @@ Hash: SHA512 AUX embassy-iprscan-4.3.1.650_fix-build-system.patch 2580 SHA256 8027ce9bd9b318fc6bce543770ab59fc8bd50237a68b959bc05274cdb3caa282 SHA512 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+0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1-r1.ebuild,v 1.4 2011/10/20 08:53:38 xarthisius Exp $ - -EBOV="6.1.0" - -inherit embassy - -DESCRIPTION="InterProScan motif detection add-on package for EMBOSS" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild index 48ee401e232b..59602de4057c 100644 --- a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild +++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild @@ -1,13 +1,15 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild,v 1.1 2015/03/28 17:20:18 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild,v 1.2 2015/03/28 18:01:54 jlec Exp $ EAPI=5 EBO_DESCRIPTION="InterProScan motif detection add-on package" -PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) AUTOTOOLS_AUTORECONF=1 + inherit emboss-r1 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-mse/ChangeLog b/sci-biology/embassy-mse/ChangeLog index 601378dedd08..3e2233894889 100644 --- a/sci-biology/embassy-mse/ChangeLog +++ b/sci-biology/embassy-mse/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-mse # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.40 2015/03/28 17:29:44 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.41 2015/03/28 17:59:49 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-mse-1.0.0-r7.ebuild, + embassy-mse-3.0.0.650.ebuild: + Drop old 28 Mar 2015; Justin Lecher <jlec@gentoo.org> embassy-mse-3.0.0.650.ebuild: Call correct install function diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest index 17f678584c6f..6dc11a4a06f8 100644 --- a/sci-biology/embassy-mse/Manifest +++ b/sci-biology/embassy-mse/Manifest @@ -3,31 +3,28 @@ Hash: SHA512 AUX embassy-mse-3.0.0.650_fix-build-system.patch 3603 SHA256 929a1caf44f233ed5254e6df080370c2d876692508c523f0184373090024ac5b SHA512 a9448a5c0530abf9c596a5742e73e76d93a5aeca006b116b53b955f007983f0832fc7bf388e67a5c833c16fd9934dd9c17ba1870fe05f1062f0b9f2dc26191f3 WHIRLPOOL 63575045b844ebb8dadf9d772a9cdd46328e200f492ec0576fb275d2f5773784cd40544bdb05fe24b23f887ed35a6664d8c2bdfb5919c090bcb1cd96433da8ad DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41 DIST embassy-6.0.1-mse-1.0.0.tar.gz 445562 SHA256 9e3688ff3514b7ea6cf104fbd2a2e611fe726fb7ac4bebab6f3c103f05c08d90 -DIST embassy-6.1.0-mse-1.0.0.tar.gz 424839 SHA256 916e6cc772c499cb0519e1fa19e1f64f8d6502a1971239c08a55b8f0e3cf2c6a DIST embassy-mse-3.0.0.650.tar.gz 491747 SHA256 2744c2a447cc16d7ad4d9049c61793fc2803659b83b0666b3ca9c30648dac88c SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3 WHIRLPOOL 8d257e79161d5989ac2fe3fe5e55e073402b57795121693fd43ac0d2d348032abb7927d4e40faf2b4db182145f9bcdcc7ba5d7b0534df10dd844c256b8dacb9b EBUILD embassy-mse-1.0.0-r6.ebuild 598 SHA256 40ae8e6cb04fd32fcaa7d93c4a9b247d555f76fff212fb5b0ce2228ec46e4465 SHA512 fc8c501160f9d93eee5e5f72b2a3421fc8a290b66da5802f973c12102334050c8afb9727fd1a1598a1d8cefc6a05db926c1cd63ea94c82f6108959fa552989eb WHIRLPOOL e8368ff3f0e0d5f768964d84cc3c4934ecf6f45060a52e161030a93c160c88b848b0fa659ef84d10e2767f15b35dda53c263524cb3169d6b94f3adcda1d6c304 -EBUILD embassy-mse-1.0.0-r7.ebuild 622 SHA256 ba96c25c4e91946fc509113af0d4acca7409a293bb8ea757b3f8a63705736587 SHA512 bd742fee143508a9011a9a792f324af2fce01ef5d9c7d09d6165c305926a77df8aa21316ed04d914439aa134cc196b33e857de585f99aef4349b97f3d131c67a WHIRLPOOL 59eb19b7b117a13184da27d4e88ca48140f4ba0d51df291e37ca7298f23d16be768b3041a1384af898ab6c231fc7d166871b91d0c07abf89f769c97cd0410382 -EBUILD embassy-mse-3.0.0.650.ebuild 645 SHA256 2fe4f89cefadc2f866a527cc9b36fadcf957c3ea44bc8a85cd9b37e6290c61b8 SHA512 04f9ad9028214948a20c02326871b00c01f7f8b2f7488dd948c3c6381833e8cd28cead5df41be3f594e780da70b698f2a11611d4b59d5612535cf2d4b0934870 WHIRLPOOL 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08:52:56 xarthisius Exp $ - -EBOV="6.1.0" - -inherit embassy - -DESCRIPTION="EMBOSS integrated version of MSE - Multiple Sequence Screen Editor" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" - -src_install() { - embassy_src_install - insinto /usr/include/emboss/mse - doins h/*.h -} diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild index 7cde055b2310..063262a17ab1 100644 --- a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild +++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild @@ -1,14 +1,14 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild,v 1.2 2015/03/28 17:29:44 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild,v 1.3 2015/03/28 17:59:49 jlec Exp $ EAPI=5 EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor" EBO_EXTRA_ECONF="$(use_enable ncurses curses)" -PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) AUTOTOOLS_AUTORECONF=1 + inherit emboss-r1 KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" @@ -16,6 +16,8 @@ IUSE+=" ncurses" RDEPEND+=" ncurses? ( sys-libs/ncurses )" +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) + src_install() { autotools-utils_src_install insinto /usr/include/emboss/mse diff --git a/sci-biology/embassy-phylipnew/ChangeLog b/sci-biology/embassy-phylipnew/ChangeLog index 90c7fbada465..81bc2d6382c4 100644 --- a/sci-biology/embassy-phylipnew/ChangeLog +++ b/sci-biology/embassy-phylipnew/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-phylipnew # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/ChangeLog,v 1.16 2015/03/28 17:13:13 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/ChangeLog,v 1.17 2015/03/28 17:58:36 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-phylipnew-3.68.ebuild, + embassy-phylipnew-3.69.650.ebuild: + Drop old *embassy-phylipnew-3.69.650 (28 Mar 2015) diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest index 1b69d0ba825a..3e77749d83e3 100644 --- a/sci-biology/embassy-phylipnew/Manifest +++ b/sci-biology/embassy-phylipnew/Manifest @@ -3,31 +3,28 @@ Hash: SHA512 AUX embassy-phylipnew-3.69.650_fix-build-system.patch 2660 SHA256 7a8701647c510d04a710d6cb52042dcc516124a5209662dd362f7e49c3f50e2f SHA512 ca2211e53077954a07d1a8997cff015f7a08e569d4c6d032703a9113ccb25ac2b191e866d35046ed02c0374cd3c177d90f0aeb4d182ec04cf6a39d1beda5c04a WHIRLPOOL 271ad6d7663f6aaac5a38750b00f262ebe37bf4c51b81238114c2bfe87e71fc897849781c2c052d792d17b5076e147db8a74e14f54278a82082fa92e73b268d0 DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41 DIST embassy-6.0.1-phylipnew-3.67.tar.gz 1624802 SHA256 efbfdbff0109c62823caf13f20cb6462f54371d55899fcbbe29240e503584945 -DIST embassy-6.1.0-phylipnew-3.68.tar.gz 1626990 SHA256 b22ec1efdae59160073acdcb57c660b58e0bd04d57fa8a86d8b0f48ec77bce78 DIST embassy-phylipnew-3.69.650.tar.gz 1741298 SHA256 af385d01826e67e05295955f05721728abbd4feb9e11a944189414da6590bfeb SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5 WHIRLPOOL 94cbe384a1575c322c7e3cdba7ccdb79e3e24cec7bd24776872f3e7d425d85c64fdcdc1cae6c079b40ca943b84a039ba2c7c5c059c40ceaf95c5c2e11e4a3e58 EBUILD embassy-phylipnew-3.67.ebuild 542 SHA256 caaf16c790c0df32de03bb4b520cb123e9f544622b4fe8e0a75aff98f7d7f763 SHA512 b04ac52ba9068ae2ab2fe5e910ce6b3bb94e205a5c58bc8cba8a812992290299735bdb5138051287c3d98ee2db77f411e54a43da7259905e030b9dcfc4a8d400 WHIRLPOOL c7e7b02e801dfc48d692d6bd771684d4c66bed6dbdd7daa8761b359e5ea03a635ddd40d94c3b73af00e23bb928e668c123a7b5d148ec9741f17d57d9afa0955e -EBUILD embassy-phylipnew-3.68.ebuild 566 SHA256 9c922f05f8ab6810d898e78d53885356a37143f80116297382e0b077dec4dd98 SHA512 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51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0 -iQJ8BAEBCgBmBQJVFuErXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w +iQJ8BAEBCgBmBQJVFuvNXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w ZW5wZ3AuZmlmdGhob3JzZW1hbi5uZXQyQ0JDQjFGMzBDQ0UxMjFGNENDNDgxMDdC -OUQ0RjIzMUJEMTU1OEFCAAoJELnU8jG9FVirr9IQAJInci1YXGInRN9tJt3lMciC -HHZnmPGUZMR13lLvBc2Gv4cliFuoM1FMuOwHqCUc7mCHiO3OcSRJsbQMcnUygcBf -MiiK9DGMh5dFNMQbvhNyH7NRbjzTq5QKB/KKsyuD/NPXqCPEPfPKPZhevSm01Klr -S6g1FlDeV/i4lnk6OxwYTFbA08eVIxE1gNDSQZHbDA8X5P2HdHXGu1UZOaVnPkY7 -qo/5IpmevZEBo0D3DLzAS0p5oETkBpukX9qUOBuKgV0q1BKsmhnP5nJx4+Ny+B0v -2lj3KoKE/rfEzBQ4d01EylhknW5iynOugJBtzGOL0eWX2VCdi2Lu42y0+XYzTjDS -YcWyf+Vpf3JbRzXaK2oWmIyTfuaDDvkQk2cZz2893DhO3hca5c5bF+DLGW5NWVHY 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--git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild index f84223e5232b..26e939e7d366 100644 --- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild +++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild @@ -1,15 +1,17 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild,v 1.1 2015/03/28 17:13:13 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild,v 1.2 2015/03/28 17:58:36 jlec Exp $ EAPI=5 -EBO_DESCRIPTION="the Phylogeny Inference Package" +EBO_DESCRIPTION="The Phylogeny Inference Package" -PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) AUTOTOOLS_AUTORECONF=1 + inherit emboss-r1 LICENSE+=" freedist" KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-structure/ChangeLog b/sci-biology/embassy-structure/ChangeLog index 3478211e0740..d19f8e6ffdc2 100644 --- a/sci-biology/embassy-structure/ChangeLog +++ b/sci-biology/embassy-structure/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-structure # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/ChangeLog,v 1.23 2015/03/28 17:10:08 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/ChangeLog,v 1.24 2015/03/28 17:57:40 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> + -embassy-structure-0.1.0-r4.ebuild, embassy-structure-0.1.650.ebuild: + Drop old *embassy-structure-0.1.650 (28 Mar 2015) diff --git a/sci-biology/embassy-structure/Manifest b/sci-biology/embassy-structure/Manifest index f67fbf39a116..7d78d9fa4c1d 100644 --- a/sci-biology/embassy-structure/Manifest +++ b/sci-biology/embassy-structure/Manifest @@ -3,31 +3,28 @@ Hash: SHA512 AUX embassy-structure-0.1.650_fix-build-system.patch 2379 SHA256 167ed0cef4f275351dbdc52c7f0fb587527e62049edc987497e79c9d5c486ff0 SHA512 2ae3080fe28cd6ad03dfe02112e16a302ac2d2d65efd70b98676a137221d9897662930a6beb4eeae87cdbf66d29cacca4b4647314eedfe2aefdcb000c762af69 WHIRLPOOL 49d523d564afcb72db32eb475e4738706b7d60e2505bb309642cdb5b9b121d29370dcdf7571e9a02c9e699f79439b04a494cc22274aee7173ae73d03da03fcfe DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41 DIST embassy-6.0.1-structure-0.1.0.tar.gz 532035 SHA256 cd8b17947fe764e830bd14887deb85a5f196f490d25b9c6408aaca0c1baecd23 -DIST embassy-6.1.0-structure-0.1.0.tar.gz 519780 SHA256 014ac2d07fdd79a3e4ffbfc70aa808fdd039214021972f87165eaa18aeb58e3f DIST embassy-structure-0.1.650.tar.gz 588118 SHA256 06c3d07f495247d1427e91887fa00df053486e2b59f0ec722735bb0b957502f1 SHA512 56fb0ed975bfd95b1fbbccaf694e0617ec23971d53bdc230eeb6ca177907e784805697193e7630e4a513f1b4ee7a1a7974136520963557c452185be4ed22b641 WHIRLPOOL db988aab3f6d2165f44039385fd0a7ab2d6a7dce12906714d5932b411e3dfeac7e06a219af048ef120ea22acab3c1e958fefe68e6e1f19eec56de82c5c1b8c03 EBUILD embassy-structure-0.1.0-r3.ebuild 501 SHA256 0b292a276467ae04180ca9c25c5a75c72ef5938848322f1f08cff49aa0d72d30 SHA512 ac9e82e81e88a2d9a065366ac7ff1327e43e00e9a06591475f7faf30b87a16b194b921bf40a5e1a469a889998cd93cd19cde9e2ddda5c8b247c19c76193ce6ff WHIRLPOOL 3b998631a045721c65b84f9dd442251920618b90acbcb2c535cf4d22f6b3a7a51ea3db01fee272aa23dd90af81a85ae77edb904a31a485510e673bf8eabca852 -EBUILD embassy-structure-0.1.0-r4.ebuild 525 SHA256 15cbef4eaece14ffdfbf12b556c6551316903f1a9bfa33cac0807af821ebc743 SHA512 45379690cf87d9ab1b3fc5c8b2096a5b8cd426ce391de82f0e159887a60f8f34a1e3ab089691ac3a0b3aad4af5a4b5eaea480a17e2658ad0ef9c0502d33c6a2d WHIRLPOOL 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a/sci-biology/embassy-structure/embassy-structure-0.1.0-r4.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.0-r4.ebuild deleted file mode 100644 index 9939738081af..000000000000 --- a/sci-biology/embassy-structure/embassy-structure-0.1.0-r4.ebuild +++ /dev/null @@ -1,13 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/embassy-structure-0.1.0-r4.ebuild,v 1.4 2011/10/20 08:49:50 xarthisius Exp $ - -EBOV="6.1.0" - -inherit embassy - -DESCRIPTION="Protein structure add-on package for EMBOSS" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild index f15fc3921f65..efe720171e59 100644 --- a/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild +++ b/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild @@ -1,13 +1,15 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild,v 1.1 2015/03/28 17:10:08 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild,v 1.2 2015/03/28 17:57:40 jlec Exp $ EAPI=5 EBO_DESCRIPTION="Protein structure add-on package" -PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) AUTOTOOLS_AUTORECONF=1 + inherit emboss-r1 KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-topo/ChangeLog b/sci-biology/embassy-topo/ChangeLog index d7d450d14047..4f7b2d168b75 100644 --- a/sci-biology/embassy-topo/ChangeLog +++ b/sci-biology/embassy-topo/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-topo # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/ChangeLog,v 1.33 2015/03/28 17:08:46 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/ChangeLog,v 1.34 2015/03/28 17:56:40 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-topo-1.0.0-r6.ebuild, + embassy-topo-2.0.650.ebuild: + Drop old *embassy-topo-2.0.650 (28 Mar 2015) diff --git a/sci-biology/embassy-topo/Manifest b/sci-biology/embassy-topo/Manifest index 0f53cf5ac2e9..da7ef761df6b 100644 --- a/sci-biology/embassy-topo/Manifest +++ b/sci-biology/embassy-topo/Manifest @@ -3,31 +3,28 @@ Hash: SHA512 AUX embassy-topo-2.0.650_fix-build-system.patch 2550 SHA256 9ae3b09bd98c5d19e692bd5fdeeb6629b2ab74b5727a3d8e310d8db3c505a8ed SHA512 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Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/embassy-topo-1.0.0-r6.ebuild,v 1.4 2011/10/20 08:49:25 xarthisius Exp $ - -EBOV="6.1.0" - -inherit embassy - -DESCRIPTION="EMBOSS integrated version of TOPO - Transmembrane protein display" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild index 9408efa37d42..0f06ce435969 100644 --- a/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild +++ b/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild @@ -1,13 +1,15 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild,v 1.1 2015/03/28 17:08:46 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild,v 1.2 2015/03/28 17:56:40 jlec Exp $ EAPI=5 EBO_DESCRIPTION="Transmembrane protein display" -PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) AUTOTOOLS_AUTORECONF=1 + inherit emboss-r1 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-vienna/ChangeLog b/sci-biology/embassy-vienna/ChangeLog index 487329567511..2133af5a45c0 100644 --- a/sci-biology/embassy-vienna/ChangeLog +++ b/sci-biology/embassy-vienna/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-vienna # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.11 2015/03/28 17:07:04 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.12 2015/03/28 17:55:11 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-vienna-1.7.2-r1.ebuild, + embassy-vienna-1.7.2.650.ebuild: + Drop old *embassy-vienna-1.7.2.650 (28 Mar 2015) diff --git a/sci-biology/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest index cea1e6b6c0d2..359e45c5ce2b 100644 --- a/sci-biology/embassy-vienna/Manifest +++ b/sci-biology/embassy-vienna/Manifest @@ -3,31 +3,28 @@ Hash: SHA512 AUX embassy-vienna-1.7.2.650_fix-build-system.patch 2607 SHA256 4710a3477526134952cbaac58e373537ce5bed852052ee9d67ab8dffce9c86d2 SHA512 fcd14f06b2eebed9426a0ef8e47a7cf286529d5ae12a2cc145e8d755bf132ee0d157bedff9c81373c19f637449681de8977c9dce3725611fdbc27909dd437a10 WHIRLPOOL 1a7189d68244b7f3a436be3a12ba26fe855eacd3bfa67b54733e4bc92e8cfa18fa3d66f84dfef39f02d17bcd923d42dd18120b10faa1c322a63c9eff8cb63798 DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -DIST EMBOSS-6.1.0.tar.gz 21968220 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41 DIST embassy-6.0.1-vienna-1.7.2.tar.gz 682200 SHA256 7bed50f9992aec250f974f5c5fd9a42d49c24f05e0e9fac88bb94b2d76be25db -DIST embassy-6.1.0-vienna-1.7.2.tar.gz 634985 SHA256 c2be4279d7e666eac99a10b333a813fbcef4148140a6c9745f518c2d8667e727 DIST embassy-vienna-1.7.2.650.tar.gz 873165 SHA256 d3c9f64394a5c59151a345c3a2d8e2b3fcab3b59918584776316c204f0bb6c6d SHA512 1484ca419ebcb7776d8f92dd633d4fda1a752a73ccb5189b58f7417a5611e015e9b42cbb37b51f4d5c7a27df0d5cab2cdf1e95ebd70a8359ffc8fa1633d28103 WHIRLPOOL 78679a7aca7db9b67774c9a07e11ecb081b0297c3e9c23e0f98d08ee96f62bef7b861ae223f2962ff79f67b0d9582168e21d869ae0ef6c9c23beb53102a351d2 -EBUILD embassy-vienna-1.7.2-r1.ebuild 554 SHA256 10b2501f1e2f90c4fcbba97bfd259ad1e1bb5a6ee703e3e685cb33bc8b4dc1b3 SHA512 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/var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/embassy-vienna-1.7.2-r1.ebuild,v 1.4 2011/10/20 08:49:03 xarthisius Exp $ - -EBOV="6.1.0" - -inherit embassy - -DESCRIPTION="EMBOSS integrated version of the Vienna RNA package - RNA folding" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild index 9ca6ffa900ea..3decd280281c 100644 --- a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild +++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild @@ -1,13 +1,15 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild,v 1.1 2015/03/28 17:07:04 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild,v 1.2 2015/03/28 17:55:11 jlec Exp $ EAPI=5 EBO_DESCRIPTION="Vienna RNA package - RNA folding" -PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) AUTOTOOLS_AUTORECONF=1 + inherit emboss-r1 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy/ChangeLog b/sci-biology/embassy/ChangeLog index edaaffccfb53..60ddd1424312 100644 --- a/sci-biology/embassy/ChangeLog +++ b/sci-biology/embassy/ChangeLog @@ -1,6 +1,9 @@ # ChangeLog for sci-biology/embassy # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy/ChangeLog,v 1.36 2015/03/28 17:38:39 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy/ChangeLog,v 1.37 2015/03/28 17:52:58 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-6.1.0.ebuild: + Drop old *embassy-6.6.0 (28 Mar 2015) diff --git a/sci-biology/embassy/Manifest b/sci-biology/embassy/Manifest index 60f78412fb8c..6d3745ce8f0a 100644 --- a/sci-biology/embassy/Manifest +++ b/sci-biology/embassy/Manifest @@ -2,26 +2,25 @@ Hash: SHA512 EBUILD embassy-6.0.1.ebuild 1144 SHA256 e0cb11917f6852ebcff2a76781ae6a19f9d61dd3d7ebdb7e0bf4c8c25232f449 SHA512 dea7bac8927f96403898322b5a3cd491e5810bf6b67fa1ef784acddbb638333fe839d2f10d63fe8d2150ef9787693fe53cc5b32963ab3be0fc59c524e8d89171 WHIRLPOOL b9be1dbffc095bbd3a531fbce791b3559f02abd1339e5431ec17febe82e68427859e76ed9580fcb824cd63d740bafa9eb62bdaa54db2088901c81f6247a10b3e -EBUILD embassy-6.1.0.ebuild 1121 SHA256 09e481e48cd9365291e757fa4892812eb4df475bf8864365dbcf3dac076c2f6c SHA512 b290ce86e0e293baa68893ec875368426dd5aca0a556be5d9ff1a71db88e4bf5e6884b12bc7321f3494110032da503f60d478a10952f0e9eb0763cc25446de72 WHIRLPOOL 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meta-package for installing all EMBASSY packages (EMBOSS add-ons)" -HOMEPAGE="http://www.emboss.org/" -SRC_URI="" -LICENSE="GPL-2 freedist" - -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" -IUSE="" - -RDEPEND="!<sci-biology/emboss-6.1.0 - ~sci-biology/emboss-6.1.0 - =sci-biology/embassy-cbstools-1.0.0-r1 - =sci-biology/embassy-domainatrix-0.1.0-r4 - =sci-biology/embassy-domalign-0.1.0-r4 - =sci-biology/embassy-domsearch-0.1.0-r4 - =sci-biology/embassy-emnu-1.05-r6 - =sci-biology/embassy-esim4-1.0.0-r6 - =sci-biology/embassy-hmmer-2.3.2-r3 - =sci-biology/embassy-iprscan-4.3.1-r1 - =sci-biology/embassy-memenew-4.0.0 - =sci-biology/embassy-mira-2.8.2-r1 - =sci-biology/embassy-mse-1.0.0-r7 - =sci-biology/embassy-phylipnew-3.68 - =sci-biology/embassy-signature-0.1.0-r4 - =sci-biology/embassy-structure-0.1.0-r4 - =sci-biology/embassy-topo-1.0.0-r6 - =sci-biology/embassy-vienna-1.7.2-r1" diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog index 10c9731636aa..679413e0ad15 100644 --- a/sci-biology/emboss/ChangeLog +++ b/sci-biology/emboss/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/emboss # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.72 2015/03/28 17:03:16 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.73 2015/03/28 18:03:23 jlec Exp $ + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> -emboss-6.1.0-r1.ebuild, + -emboss-6.3.1_p4.ebuild: + Drop old *emboss-6.6.0 (28 Mar 2015) diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest index c362048584fe..7b459a97d399 100644 --- a/sci-biology/emboss/Manifest +++ b/sci-biology/emboss/Manifest @@ -14,33 +14,30 @@ AUX emboss-6.6.0_qa-implicit-declarations.patch 1324 SHA256 87de58d0a6225ba7f464 AUX emboss-README.Gentoo-1 1474 SHA256 e97558bbc8296f2e9395080061e494b282303ed69e1d6eb45554846617b47abd SHA512 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-inherit eutils - -DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" -HOMEPAGE="http://emboss.sourceforge.net/" -SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV}.tar.gz" -LICENSE="GPL-2 LGPL-2" - -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" -IUSE="X png minimal" - -DEPEND=" - X? ( x11-libs/libXt ) - png? ( - sys-libs/zlib - media-libs/libpng - media-libs/gd - ) - !minimal? ( - sci-biology/primer3 - sci-biology/clustalw - )" - -RDEPEND="${DEPEND} - !sys-devel/cons" - -PDEPEND=" - !minimal? ( - sci-biology/aaindex - sci-biology/cutg - sci-biology/prints - sci-biology/prosite - sci-biology/rebase - sci-biology/transfac - )" - -S="${WORKDIR}/EMBOSS-${PV}" - -src_prepare() { - epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch - - local link_string="$(pkg-config --libs x11)" - if use png; then - link_string="${link_string} -lgd $(pkg-config --libs libpng)" - fi - sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \ - || die "Failed to patch ajax Makefile" -} - -src_configure() { - local myconf - myconf="--includedir=${ED}/usr/include/emboss" - use X || myconf="${EXTRA_CONF} --without-x" - use png || myconf="${EXTRA_CONF} --without-pngdriver" - - econf ${myconf} - # Do not install the JEMBOSS component (the --without-java configure option - # does not work). JEMBOSS will eventually be available as a separate package. - sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \ - Makefile || die -} - -src_install() { - einstall || die "Failed to install program files." - - dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \ - || die "Failed to install documentation." - newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \ - || die "Failed to install Gentoo readme file." - - # Install env file for setting libplplot and acd files path. - cat <<- EOF > 22emboss - # plplot libs dir - PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/" - # ACD files location - EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" - EOF - doenvd 22emboss || die "Failed to install environment file." - - # Symlink preinstalled docs to "/usr/share/doc". - dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die - dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die - dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die - dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die - - # Remove frestdist documentation conflicting with the EMBASSY philypnew - # package. - rm "${ED}"/usr/share/EMBOSS/doc/programs/text/frestdist.txt || \ - die "Failed to remove duplicated documentation." - - # Clashes #330507 - mv "${ED}"/usr/bin/{digest,pepdigest} || die - - # Remove useless dummy files from the image. - find emboss/data -name dummyfile -delete || die "Failed to remove dummy files." - - # Move the provided codon files to a different directory. This will avoid - # user confusion and file collisions on case-insensitive file systems (see - # bug #115446). This change is documented in "README.Gentoo". - mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ - die "Failed to move CODON directory." - - # Move the provided restriction enzyme prototypes file to a different name. - # This avoids file collisions with versions of rebase that install their - # own enzyme prototypes file (see bug #118832). - mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ - die "Failed to move enzyme equivalence file." -} diff --git a/sci-biology/emboss/emboss-6.3.1_p4.ebuild b/sci-biology/emboss/emboss-6.3.1_p4.ebuild deleted file mode 100644 index 10bc72589c56..000000000000 --- a/sci-biology/emboss/emboss-6.3.1_p4.ebuild +++ /dev/null @@ -1,116 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1_p4.ebuild,v 1.9 2014/12/28 16:46:09 titanofold Exp $ - -EAPI="4" - -inherit autotools eutils - -MY_PATCH="4" - -DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" -HOMEPAGE="http://emboss.sourceforge.net/" -SRC_URI=" - ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV/_p${MY_PATCH}}.tar.gz - ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/fixes/patches/patch-1-${MY_PATCH}.gz -> ${P}.patch.gz" - -LICENSE="GPL-2 LGPL-2" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" -IUSE="doc minimal mysql pdf png postgres static-libs X" - -DEPEND=" - dev-libs/expat - dev-libs/libpcre:3 - sci-libs/plplot - sys-libs/zlib - mysql? ( virtual/mysql ) - pdf? ( media-libs/libharu ) - png? ( - sys-libs/zlib - media-libs/libpng - media-libs/gd - ) - postgres? ( dev-db/postgresql ) - !minimal? ( - sci-biology/primer3 - sci-biology/clustalw - ) - X? ( x11-libs/libXt )" -RDEPEND="${DEPEND} - !sys-devel/cons" -PDEPEND=" - !minimal? ( - sci-biology/aaindex - sci-biology/cutg - sci-biology/prints - sci-biology/prosite - sci-biology/rebase - sci-biology/transfac - )" - -S="${WORKDIR}/EMBOSS-${PV/_p${MY_PATCH}}" - -src_prepare() { - epatch "${WORKDIR}"/${P}.patch - epatch \ - "${FILESDIR}"/${PV}-unbundle-libs.patch - eautoreconf -} - -src_configure() { - econf \ - $(use_with X x) \ - $(use_with png pngdriver "${EPREFIX}/usr") \ - $(use_with doc docroot "${EPREFIX}/usr") \ - $(use_with pdf hpdf "${EPREFIX}/usr") \ - $(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config") \ - $(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config") \ - $(use_enable amd64 64) \ - $(use_enable static-libs static) \ - --without-java \ - --enable-large \ - --enable-systemlibs \ - --includedir="${ED}/usr/include/emboss" -} - -src_install() { - einstall || die "Failed to install program files." - - dodoc AUTHORS ChangeLog FAQ NEWS README THANKS - sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \ - dodoc README.Gentoo - - # Install env file for setting libplplot and acd files path. - cat <<- EOF > 22emboss - # plplot libs dir - PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/" - # ACD files location - EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" - EOF - doenvd 22emboss - - # Symlink preinstalled docs to "/usr/share/doc". - dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals - dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs - dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials - dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html - - # Clashes #330507 - mv "${ED}"/usr/bin/{digest,pepdigest} || die - - # Remove useless dummy files from the image. - find emboss/data -name dummyfile -delete || die "Failed to remove dummy files." - - # Move the provided codon files to a different directory. This will avoid - # user confusion and file collisions on case-insensitive file systems (see - # bug #115446). This change is documented in "README.Gentoo". - mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ - die "Failed to move CODON directory." - - # Move the provided restriction enzyme prototypes file to a different name. - # This avoids file collisions with versions of rebase that install their - # own enzyme prototypes file (see bug #118832). - mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ - die "Failed to move enzyme equivalence file." -} |