# ChangeLog for sci-biology/eugene
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/ChangeLog,v 1.13 2015/03/25 14:07:24 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/ChangeLog,v 1.14 2015/03/25 15:47:44 jlec Exp $
+
+ 25 Mar 2015; Justin Lecher <jlec@gentoo.org> -eugene-3.6-r1.ebuild:
+ Drop old
25 Mar 2015; Agostino Sarubbo <ago@gentoo.org> eugene-4.1.ebuild:
Stable for x86, wrt bug #543936
-----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
AUX eugene-3.6-overflow.patch 252 SHA256 cc8795d5f4525a299bc3e17da1e26c1e5fe3ef0c2371c5bf9de36b5037972fc7 SHA512 ed39c8d4aa73ba9e378a025e740c50f1b431fbb4590e3e9204f789081c8b22aef05fb4ce9ac7a0f22015ee03f73392730894a8dea5f6f16cd4533172e46776ce WHIRLPOOL 775e4167b0efa7dfd1539b01c20f4ce268666840d5c2766222deadacfcc21cf6697c177efde0e777c398ad4c888ee3df1b57113b451b1700ca5965b718c8432f
AUX eugene-3.6-plugins.patch 1784 SHA256 0ec9c0d2bf6009e89612c3d95711b211aefc267d3eb6b75bc6279318256bc46d SHA512 300601ee6abe469460ebbe29c45468d516e5e781ad4b0542e9590de38ba6e98e3697c5f6f92f83212a1aa6da5e0650636af279d82241277c0b43fb5472028fcc WHIRLPOOL 695b8efe382014c6e1c9c44bebab3ed417b7ad736fd7db5623911971926bab284e9bdfb2ee5061287c99a93433d060040285765f37e0b283ecd83717adca5359
AUX eugene-4.1-format-security.patch 609 SHA256 391521469ce4c6df425084d9b2df611efe2721f563b15843f495064ed72d4553 SHA512 f4eedd5b70309d4b8eedce8f3a4f79b65e595d407e88fd79e7f4f2f8c98880432366124b7f0a34c9032c9a498a1db607b0cac20304e84ec01f736589924ff362 WHIRLPOOL 5b703b25d049f9f9fb78d543e72cde8130f9f1e116aac26e1c748897fe6558507d22f2ce08fc7c4e65568f5213fe4fc7de111a58043c88ee94586c4aca3f71e0
-DIST eugene-3.6.tar.gz 5589654 SHA256 731757d65f182e2eb2a18ee1fb2e710519a705aa91ef268136053698e07cb227 SHA512 594ad23e215ece2b088a2177304f9eee25411d8b44f1a94dee2079a0a69847cac7053f8675e50dab1cad41bc61135057efb3dce674a9f42156d56acb2ea29968 WHIRLPOOL 50847357a80e3cd149575c569980b050e35997b7a5d3781b4f1cf48f79e05a88c358e186226ff80d56ae090d08ef82f5e9bea779911d96ffb5c983ccf36b09a6
DIST eugene-4.1.tar.gz 7393361 SHA256 faff769f68e1ab1fdec61be34ec7fef3c73805734199765ba11cf1ea9c02f800 SHA512 f4bcf63103754f8fb577d311d181375732411fa926fb0cef86fcd00c373ed5cc5637f1b55fa375a4bb14c5181f7de1dc244570f74cdd1887b6107d5c6cea37b3 WHIRLPOOL 32f4539456c243dd3c6a9d5a986fea210e53e5566aaa0849a26f34832957100623570a0814193059420d53e553247584360635706844ed0ec55c4cc65e235ad4
-EBUILD eugene-3.6-r1.ebuild 1133 SHA256 d2f29d0f837b5e8043db68b4590b93bb894be11a744c067a3333391bc0b1963d SHA512 88d997ee9a940591b827b2bb921711777177c5178d40b2fe02a161e16fb68c4a76f7e1a8c01da8d45b1330852622bf69c373ed95afe636da49369d903f03b92b WHIRLPOOL 9db7c3d98cc0e8a7f67d114e66ec338bf39bf4000a877258a2553fc4af2ebaf08c19eed736175743d603bc3de5297b7fde2e0c5da9fff4eff98c7b4a84e6e5ae
EBUILD eugene-4.1.ebuild 901 SHA256 b1a95371213c10847c8e772156ac58abddefd5e4cb8b868ef95eb02a53db6b5f SHA512 040922fc22bc51f16d3392f0acceed1db3fe993a1c579fec71bc95490964f4e8b853142eda12701d6ed5bff05d0ed7ff930ed092cd2cc6fcf1ed91e9c5db57ed WHIRLPOOL 87e252113cb06cf33ab6dd56999ae47b616de13b0c1ba9e52205aeb39564a77e0227b8392ee8c3f99fd11d225c0d2da7f80faf52b4ee535eef1e324eac230034
-MISC ChangeLog 1926 SHA256 38885546218ab0d989966faae95077b948b431f9f875b7e5e3aca5d2ba150957 SHA512 ca86a057e1e07fe322ecf370f18a282e01afe9aa100a755c2941fde22c30fe9a585afa75e716b8baf74a47ed848973c945b556ad051abf60126068f463ba095e WHIRLPOOL 289646f86a3771a2f71977bf7c642b7d91914543dac1952e6613552728b0123e273957a121672b8631e032b1d295a344823a0306ae58d8a820bd538f29734c4b
+MISC ChangeLog 2009 SHA256 9cc7672d01f3ea069e1465072396b59e81cd8aff667ccf3e5c06776e0bbc571b SHA512 4c25d7d81ca0f63765b8635bff0043d9736e6cec7bc0ed5a4481309851e69bb7a059348e7d5b9a3b0073d68b5e04c3890349a9d0ba92d56f1c319500c58802c6 WHIRLPOOL 664c9da77c8e2bc49b29633d4f04cd9a2e1f1ed7e8f62c276cbe9865c7918ad6903e9cc78b87ac8788e56e331fc08eba18cbf864c0efcf8a72721460d1a82b32
MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/eugene-3.6-r1.ebuild,v 1.5 2015/03/20 16:38:39 jlec Exp $
-
-EAPI=2
-
-inherit autotools eutils
-
-DESCRIPTION="Eukaryotic gene predictor"
-HOMEPAGE="http://www.inra.fr/mia/T/EuGene/"
-# self-signed https SRC_URI
-#SRC_URI="http://mulcyber.toulouse.inra.fr/gf/download/frsrelease/220/3675/${P}-1.tar.gz"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE="doc"
-KEYWORDS="amd64 x86"
-
-RESTRICT="test"
-
-DEPEND="media-libs/gd[png]
- media-libs/libpng:0
- doc? ( dev-lang/tcl:0
- dev-texlive/texlive-latex
- dev-texlive/texlive-latexrecommended
- dev-texlive/texlive-latexextra
- )"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
- # https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170
- epatch "${FILESDIR}"/${P}-overflow.patch \
- "${FILESDIR}"/${P}-plugins.patch
- if ( ! use doc ); then
- sed -i -e '/SUBDIRS/ s/doc//' \
- -e '/INSTALL.*doc/ s/\(.*\)//' \
- Makefile.am || die
- eautoreconf
- fi
-}
-
-src_install() {
- emake DESTDIR="${D}" install || die
-}
# ChangeLog for sci-biology/rebase
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/rebase/ChangeLog,v 1.147 2015/03/25 14:06:48 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/rebase/ChangeLog,v 1.148 2015/03/25 15:47:09 jlec Exp $
+
+ 25 Mar 2015; Justin Lecher <jlec@gentoo.org> -rebase-1412.ebuild,
+ -rebase-1501.ebuild:
+ Drop old
25 Mar 2015; Agostino Sarubbo <ago@gentoo.org> rebase-1502.ebuild:
Stable for x86, wrt bug #541512
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-DIST rebase-1501.tar.xz 66478008 SHA256 4ffba0e98524cb25389f6cb0079792a4efc1e0f95101961105ecd67209c79f94 SHA512 46656da15d297d3a58382559da16659f0c01611910cde4284ef45e3f0d181bcb7878ba32465ea154e45a3658b731d4cb2a5a25f62105a05daf284bbd78df3592 WHIRLPOOL 57fdd5ddf01842e0214f64231c9171234e7dedd06b7d1faeef996142c67bfbfa582cd0a85f0156f9f51f1c6c12e7603c2b1aba7c4edb8c6e5c11af6247b84e02
DIST rebase-1502.tar.xz 513837344 SHA256 9d579b7ea0c93a199defd94fc378871a87f1b238aacd87649a5ad3e63caa4c5b SHA512 945c884c0b940e374e47b41f53d2d24edbab3f627ac015ff6033e2fc1bab1599c20595d03c31ec60b9aaa9f25e9dad09012bfd347a152b2b2b27996e157b730a WHIRLPOOL a8b145ac4cbe2edff39fac9934d5d6d43bcf16a89988e9b5e82682911196adb33ba8681a2de65e3a6f7e136bc259476316bdb24f0e46d83ce5572effe99aaaac
DIST rebase-1503.tar.xz 67267924 SHA256 6f808fd86bcc13f92a6ca876fa910260fc50bce50ac4bbe04e8d87cd2f9a4822 SHA512 83f2b1f0b44cb674ca99e1a5a917cd55621d6cd33d2d4d0c635af1bc958c038e6e77f5d1e2d03623010eaecb2ae88d050829797d90cb7142b83f6baace4e4d96 WHIRLPOOL 2e267cd39c626d61d33b37625c9bc56f8f83a84bfa709ac37790b90a400bf2b6e5577c34d7ced6db747dc37fb2aa72071da1e254ba185e81574eac301abd42a6
-EBUILD rebase-1412.ebuild 1201 SHA256 90871577aaea008997ca6b2c806411617602c830ebe53a208ab98b70c15ad8e8 SHA512 15fb7f7c0e5078c6e75b1d96122dd091694878b469240b06ffa6d3157ed5af8edfa2e6e3e71febdce1d7081e7ec65b751b83007f7cff839c1b70d28620fb91e0 WHIRLPOOL f88be98e00587f486816de38da561042108d1b7916376f9dcf42d615f3b978e6861f2a6c05a1439898f3c2e5d29ab8198dd3ebeddfcc3ab19bbe01e20a4339c0
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EBUILD rebase-1502.ebuild 1201 SHA256 8254315ccf45f1d719edb055da9df005af439593655af0843e038b98816e6825 SHA512 8491d03cb395e4c8732b193dbf6bb3fb47cab25c5e234b8725d5c7c0f6ca41874d55aa9d35c6231d85ddb94cf00fe72654665e0161f92a09dc1c8588dc1b0d71 WHIRLPOOL e6075024c7606001da1ebfb4f481740e7fe921a5274f1f9ca94889b66045a4503c465ffa7333bdd4333fb762aaaee15ffd4accd18bd28d1a41bc5869dc0c4889
EBUILD rebase-1503.ebuild 1205 SHA256 4d342e674eeca2d57d45961809e267859f9b3f22ce997ac42aff9cd278469e2a SHA512 40ee04680fa34bd2ee6ad217c3a8fa6152780829b7a0b21d3a8b9c3b70e1f9f0377cf1bb018f01a7103eafc08e40270c50f147627e59e490ad1ff124fcf8c142 WHIRLPOOL 7055a6dcf3d00350f32dadb0a4543b1bfeab74e7f22557f40099314599533cdf76fd1bc9ffcaefac3d92b3ef9818254b5d5ffc17ed1886e1cef9304fd4204939
-MISC ChangeLog 18803 SHA256 91e4ee5d2468113259a50a002cf87a462cbb3aa6571c9cb56287e9ef00201d4e SHA512 67f5a63b685ef57c195f716debebf8663ae70a21c855f5d3abe15dc3f077310b330d4bf485d2bc4910822076c1d6410232ff0003719fe1aa5dc1ebf13496adb8 WHIRLPOOL b40be58620ee1d4de123949d322ef37239d8c322ced966375b49acab6b99965bc886273cabea3600176cb0ae18eb842592023ed7c177422b9c4c1979ff6eca68
+MISC ChangeLog 18907 SHA256 dbab24e8b773ec1f77f5edbf3fdf209d4009afa45d0b8560cc562a0f834ab6ac SHA512 d9aaf892505fa3bfa58a2379a771c463af560fc42330f9f92acefe42b327ce79bbce4f2fe3f3cf1d8f9c4b82acf0d176f30e9f872d82b9766157b769cda9a85a WHIRLPOOL 60efdf3df8f0a7628faa10b8f37fb280d07516cd4eb98e3076f1d007d180486edfed54f0e521e62260fec8760903f07c9de4c785c91d368dec67d8b833b4fa2f
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+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/rebase/rebase-1412.ebuild,v 1.4 2015/01/26 10:34:05 ago Exp $
-
-EAPI=5
-
-MY_PV=${PV#1}
-
-DESCRIPTION="A restriction enzyme database"
-HOMEPAGE="http://rebase.neb.com"
-SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
-
-SLOT="0"
-LICENSE="public-domain"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris"
-IUSE="emboss minimal"
-
-RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )"
-DEPEND="${RDEPEND}"
-
-RESTRICT="binchecks strip"
-
-src_compile() {
- if use emboss; then
- echo; einfo "Indexing Rebase for usage with EMBOSS."
- mkdir REBASE || die
- EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \
- -protofile proto.${MY_PV} -equivalences \
- || die "Indexing Rebase failed."
- echo
- fi
-}
-
-src_install() {
- if ! use minimal; then
- insinto /usr/share/${PN}
- doins withrefm.${MY_PV} proto.${MY_PV}
- fi
- newdoc REBASE.DOC README
- if use emboss; then
- insinto /usr/share/EMBOSS/data/REBASE
- doins REBASE/embossre.{enz,ref,sup}
- insinto /usr/share/EMBOSS/data
- doins REBASE/embossre.equ
- fi
-}
+++ /dev/null
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/rebase/rebase-1501.ebuild,v 1.1 2015/01/04 11:28:58 jlec Exp $
-
-EAPI=5
-
-MY_PV=${PV#1}
-
-DESCRIPTION="A restriction enzyme database"
-HOMEPAGE="http://rebase.neb.com"
-SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
-
-SLOT="0"
-LICENSE="public-domain"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris"
-IUSE="emboss minimal"
-
-RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )"
-DEPEND="${RDEPEND}"
-
-RESTRICT="binchecks strip"
-
-src_compile() {
- if use emboss; then
- echo; einfo "Indexing Rebase for usage with EMBOSS."
- mkdir REBASE || die
- EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \
- -protofile proto.${MY_PV} -equivalences \
- || die "Indexing Rebase failed."
- echo
- fi
-}
-
-src_install() {
- if ! use minimal; then
- insinto /usr/share/${PN}
- doins withrefm.${MY_PV} proto.${MY_PV}
- fi
- newdoc REBASE.DOC README
- if use emboss; then
- insinto /usr/share/EMBOSS/data/REBASE
- doins REBASE/embossre.{enz,ref,sup}
- insinto /usr/share/EMBOSS/data
- doins REBASE/embossre.equ
- fi
-}
projects / gentoo.git / commitdiff