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364 lines
13 KiB
364 lines
13 KiB
# ChangeLog for sci-biology/emboss
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# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
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# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.75 2015/07/23 20:18:07 pacho Exp $
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23 Jul 2015; Pacho Ramos <pacho@gentoo.org> emboss-6.6.0.ebuild:
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ppc stable wrt bug #529038
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07 May 2015; Justin Lecher <jlec@gentoo.org> emboss-6.6.0.ebuild,
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files/emboss-6.6.0_fix-build-system.patch:
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Correct Licenses, bug #548810; make build with newer plplot, bug #548806; add
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missing dep, bug #544516
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28 Mar 2015; Justin Lecher <jlec@gentoo.org> -emboss-6.1.0-r1.ebuild,
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-emboss-6.3.1_p4.ebuild:
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Drop old
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*emboss-6.6.0 (28 Mar 2015)
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28 Mar 2015; Justin Lecher <jlec@gentoo.org> +emboss-6.6.0.ebuild,
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+files/README.gentoo, +files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch,
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+files/emboss-6.6.0_fix-build-system.patch,
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+files/emboss-6.6.0_plplot-declarations.patch,
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+files/emboss-6.6.0_qa-implicit-declarations.patch, metadata.xml:
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Import latest changes from science overlay, thanks Ted Tanberry for the work;
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fixes #504680
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28 Dec 2014; Aaron W. Swenson <titanofold@gentoo.org> emboss-6.3.1_p4.ebuild,
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emboss-6.3.1_p4-r1.ebuild:
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Rename virtual/postgresql to dev-db/postgresql
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03 Nov 2014; Aaron W. Swenson <titanofold@gentoo.org> emboss-6.3.1_p4.ebuild,
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emboss-6.3.1_p4-r1.ebuild:
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Update PostgreSQL dependencies and/or checks to virtual/postgresql.
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30 Jul 2014; Brian Evans <grknight@gentoo.org> emboss-6.0.1.ebuild,
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emboss-6.1.0-r1.ebuild, emboss-6.3.1_p4-r1.ebuild, emboss-6.3.1_p4.ebuild:
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Non-maintainer commit. Update to use virtual/mysql wrt bug 508802
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*emboss-6.3.1_p4-r1 (19 Nov 2012)
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19 Nov 2012; Justin Lecher <jlec@gentoo.org> +emboss-6.3.1_p4-r1.ebuild,
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+files/emboss-6.3.1_p4-r1_plcol.patch:
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Fix compilation problem with toplplot, #391669, thanks Juergen Rose for the
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patch
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26 Apr 2012; Justin Lecher <jlec@gentoo.org> -emboss-6.1.0.ebuild:
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Drop old
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20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> emboss-6.3.1_p4.ebuild,
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emboss-6.1.0.ebuild, emboss-6.1.0-r1.ebuild, emboss-6.0.1.ebuild:
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Fix SRC_URI
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26 Jul 2011; Kacper Kowalik <xarthisius@gentoo.org> emboss-6.0.1.ebuild,
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emboss-6.1.0.ebuild, emboss-6.1.0-r1.ebuild, emboss-6.3.1_p4.ebuild:
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ppc64 keyword dropped
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04 Apr 2011; Justin Lecher <jlec@gentoo.org> -emboss-4.0.0.ebuild,
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emboss-6.0.1.ebuild, emboss-6.1.0.ebuild:
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Dropped old, fix for wrong EAPI version, #361919
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11 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild,
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metadata.xml:
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Remove largefile USE support and default to it
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09 Mar 2011; Raúl Porcel <armin76@gentoo.org> emboss-4.0.0.ebuild,
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emboss-6.0.1.ebuild, emboss-6.1.0.ebuild, emboss-6.1.0-r1.ebuild,
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emboss-6.3.1_p4.ebuild:
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Drop sparc keywords
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09 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild:
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EAPI=4 takes three arguments on use_with
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*emboss-6.3.1_p4 (09 Mar 2011)
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09 Mar 2011; Justin Lecher <jlec@gentoo.org>
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+files/6.3.1_p4-unbundle-libs.patch, -files/6.3.1-unbundle-libs.patch,
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-emboss-6.3.1.ebuild, +emboss-6.3.1_p4.ebuild:
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Bump to latest upstream patches
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*emboss-6.3.1 (09 Mar 2011)
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09 Mar 2011; Justin Lecher <jlec@gentoo.org>
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+files/6.3.1-unbundle-libs.patch, +files/emboss-README.Gentoo-2,
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emboss-4.0.0.ebuild, emboss-6.0.1.ebuild, emboss-6.1.0-r1.ebuild,
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+emboss-6.3.1.ebuild, metadata.xml:
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Version Bump #335603, Unbundled libs, removed old, fix clash with
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/usr/bin/digest, #330507
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18 Jul 2010; <nixnut@gentoo.org> emboss-6.0.1.ebuild:
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ppc stable #325457
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09 Jul 2010; Samuli Suominen <ssuominen@gentoo.org> emboss-6.0.1.ebuild:
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ppc64 stable wrt #325457
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23 Jun 2010; Justin Lecher <jlec@gentoo.org> emboss-4.0.0.ebuild,
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emboss-6.0.1.ebuild, emboss-6.1.0.ebuild, emboss-6.1.0-r1.ebuild:
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Blocking sys-devel/cons, bug 248792
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*emboss-6.1.0-r1 (07 Mar 2010)
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07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org>
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+emboss-6.1.0-r1.ebuild:
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Moved to EAPI=3 for PREFIX support, imported prefix patches from overlay,
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keyworded as in overlay
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01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
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Giving up maintainership of this package.
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01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> emboss-6.1.0.ebuild:
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Remove documentation that conflicts with EMBASSY phylipnew.
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*emboss-6.1.0 (01 Sep 2009)
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01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> +emboss-6.1.0.ebuild:
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New upstream version.
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01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> emboss-6.0.1.ebuild:
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Stabilised on x86 and amd64.
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31 Aug 2009; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild,
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emboss-6.0.1.ebuild:
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Q.A. fixes, including better dependency on ClustalW.
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27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> -emboss-5.0.0.ebuild:
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Pruning version that will never be stabilised.
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27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild:
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Depend on ClustalW 1.83 since version 2.x will soon be added to Portage
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and is incompatible with EMBOSS wrapper programs.
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*emboss-6.0.1 (26 Aug 2008)
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26 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +emboss-6.0.1.ebuild:
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New upstream version.
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25 Jan 2008; Markus Dittrich <markusle@gentoo.org>
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+files/emboss-5.0.0-as-needed.patch, emboss-4.0.0.ebuild,
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emboss-5.0.0.ebuild:
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Fixed unresolved symbols with as-needed (see bug #207304).
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22 Jul 2007; Donnie Berkholz <dberkholz@gentoo.org>; emboss-4.0.0.ebuild:
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Drop virtual/x11 references.
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18 Jul 2007; Olivier Fisette <ribosome@gentoo.org>
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+files/emboss-README.Gentoo-1:
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Added updated Gentoo README file in reStructuredText format.
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*emboss-5.0.0 (18 Jul 2007)
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18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> +emboss-5.0.0.ebuild:
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New upstream version.
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09 Apr 2007; Jeff Gardner <je_fro@gentoo.org> +files/22emboss,
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-files/22emboss-r1, emboss-4.0.0.ebuild:
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Fixed to use doenvd wrt bug #173884
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10 Dec 2006; Olivier Fisette <ribosome@gentoo.org>
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-emboss-3.0.0-r1.ebuild, emboss-4.0.0.ebuild:
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Pruned old version. Removed ppc-macos keyword, as grobian said the
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package and its dependencies were fully moved into "prefix".
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20 Nov 2006; <blubb@gentoo.org> emboss-4.0.0.ebuild:
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stable on amd64
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15 Nov 2006; Markus Rothe <corsair@gentoo.org> emboss-4.0.0.ebuild:
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Stable on ppc64; bug #153766
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03 Nov 2006; nixnut <nixnut@gentoo.org> emboss-4.0.0.ebuild:
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Stable on ppc wrt bug 153766
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03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> emboss-3.0.0-r1.ebuild:
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Added ~sparc to emboss-3 for embassy-phylip-3.6b.
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02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild:
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Added to x86.
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18 Aug 2006; Jason Wever <weeve@gentoo.org> emboss-4.0.0.ebuild:
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Added ~sparc keyword wrt bug #144241.
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*emboss-4.0.0 (21 Jul 2006)
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21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +emboss-4.0.0.ebuild:
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New upstream version. See change log:
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"http://emboss.sourceforge.net/developers/changelog.html".
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20 Apr 2006; Olivier Fisette <ribosome@gentoo.org> -emboss-3.0.0.ebuild:
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Removed old revision.
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08 Apr 2006; Simon Stelling <blubb@gentoo.org> emboss-3.0.0-r1.ebuild:
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stable on amd64
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22 Feb 2006; Fabian Groffen <grobian@gentoo.org> ChangeLog:
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Marked ppc-macos stable (bug #123332)
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22 Feb 2006; <nixnut@gentoo.org> emboss-3.0.0-r1.ebuild:
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Stable on ppc. bug 123332
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21 Feb 2006; Markus Rothe <corsair@gentoo.org> emboss-3.0.0-r1.ebuild:
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Stable on ppc64; bug #123332
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20 Feb 2006; Joshua Jackson <tsunam@gentoo.org> emboss-3.0.0-r1.ebuild:
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Stable on x86; bug #123332
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19 Feb 2006; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0-r1.ebuild:
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Block old versions of pscan to avoid file collisions (see bug #116236).
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23 Jan 2006; Olivier Fisette <ribosome@gentoo.org> +files/README.Gentoo:
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Added missing README file (fixes bug #120071).
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*emboss-3.0.0-r1 (21 Jan 2006)
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21 Jan 2006; Olivier Fisette <ribosome@gentoo.org>
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+emboss-3.0.0-r1.ebuild:
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Install codons and restriction enzyme equivalence files in alternative
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directories. This avoids file collisions on case insensitive filesystems
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(see bug #115446), allows the installation of an updated enzyme prototypes
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file that will give more consistent results (see bug #118832).
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14 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; emboss-3.0.0.ebuild:
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Add modular X dependencies.
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19 Nov 2005; Simon Stelling <blubb@gentoo.org> emboss-3.0.0.ebuild:
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stable on amd64
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04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -emboss-2.10.0.ebuild:
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Removed obsolete version.
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03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild:
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Stable on ppc-macos (with j4rg0n's permission, bug #102420).
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02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> emboss-3.0.0.ebuild:
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Stable on ppc.
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24 Sep 2005; Markus Rothe <corsair@gentoo.org> emboss-3.0.0.ebuild:
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Stable on ppc64
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21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild:
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Added to x86.
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04 Sep 2005; Simon Stelling <blubb@gentoo.org> emboss-3.0.0.ebuild:
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added ~amd64 keyword
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13 Aug 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild,
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emboss-2.10.0.ebuild:
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Fixed Prosite dependency.
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*emboss-3.0.0 (06 Aug 2005)
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06 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +emboss-3.0.0.ebuild:
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New version.
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28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> -emboss-2.9.0.ebuild:
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Removed old version.
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25 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.10.0.ebuild:
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Stable ppc-macos
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24 Jun 2005; Joseph Jezak <josejx@gentoo.org> emboss-2.10.0.ebuild:
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Marked ppc stable for bug #96819.
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19 Jun 2005; Markus Rothe <corsair@gentoo.org> emboss-2.10.0.ebuild:
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Stable on ppc64
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13 May 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.10.0.ebuild:
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Added to x86.
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02 May 2005; Omkhar Arasaratnam <omkhar@gentoo.org> emboss-2.10.0.ebuild:
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Added ~ppc64
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02 May 2005; Michael Hanselmann <hansmi@gentoo.org> emboss-2.9.0.ebuild:
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Stable on ppc.
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*emboss-2.10.0 (22 Mar 2005)
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22 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +emboss-2.10.0.ebuild:
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New version.
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22 Feb 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild:
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Added support for minimal build.
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09 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.9.0.ebuild:
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Stable ppc-macos
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30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild:
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Ebuild cleanup.
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01 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.9.0.ebuild:
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Unstable ppc-macos.
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*emboss-2.9.0 (23 Dec 2004)
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23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
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+files/22emboss-r1, +emboss-2.9.0.ebuild:
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Moved from app-sci/emboss to sci-biology/emboss.
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31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild,
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-emboss-2.8.0-r3.ebuild:
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Removed old version. Added 2.9.0 to x86.
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10 Aug 2004; Olivier Fisette <ribosome@gentoo.org>
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emboss-2.8.0-r3.ebuild:
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Added to x86.
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emboss-2.8.0-r2.ebuild:
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Removed obsolete ebuild.
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21 Jul 2004; David Holm <dholm@gentoo.org> emboss-2.9.0.ebuild:
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Added to ~ppc.
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20 Jul 2004; Olivier Fisette <ribosome@gentoo.org>
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emboss-2.8.0-r3.ebuild, emboss-2.9.0.ebuild:
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Removed icc support since no patching is needed.
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19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild:
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Version bump. Changed the configuration and install steps a bit to
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reflect the fact that header files are now installed automatically.
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14 Jul 2004; Olivier Fisette <ribosome@gentoo.org>
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emboss-2.8.0-r3.ebuild: Modified configuration step to make the X and png
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USE flags independent; Added support for icc; Added primer3 and clustalw
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to the dependencies since some EMBOSS programs won't work without them;
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Added support for the biological databases aaindex, cutg, prints, prosite,
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rebase and transfac, which are needed for many EMBOSS programs (the databases
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are PDEPENDencies since they all must be indexed with an EMBOSS program before
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use) (this database support is optional); Added header files installation for
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EMBOSS development.
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emboss-2.8.0-r2.ebuild: Added to x86.
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emboss-2.8.0-r1.ebuild, emboss-2.8.0.ebuild, emboss-2.7.1.ebuild: Removed files.
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metadata.xml: Added long description; Set myself as maintainer.
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02 Jun 2004; Aron Griffis <agriffis@gentoo.org> emboss-2.8.0-r1.ebuild,
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emboss-2.8.0-r2.ebuild:
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Fix use invocation
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12 May 2004; David Holm <dholm@gentoo.org> emboss-2.8.0-r2.ebuild:
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Added to ~ppc.
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*emboss-2.8.0-r2 (11 May 2004)
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11 May 2004; Patrick Kursawe <phosphan@gentoo.org> emboss-2.8.0-r2.ebuild,
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files/22emboss-r1:
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Adjusted value of PLPLOT_LIB, see bug #50176
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*emboss-2.8.0-r1 (30 Jan 2004)
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30 Jan 2004; Stephen Diener <sediener@gentoo.org> emboss-2.8.0-r1.ebuild:
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Modified to use X and png properly for servers
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28 Jan 2004; Stephen Diener <sediener@gentoo.org> emboss-2.8.0.ebuild:
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Modified 2.8.0 ebuild to require X not just USE it.
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*emboss-2.8.0 (13 Dec 2003)
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13 Dec 2003; Stephen Diener <sediener@gentoo.org> emboss-2.7.1.ebuild,
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emboss-2.8.0.ebuild:
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Version bump...
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20 Oct 2003; George Shapovalov <george@gentoo.org> metdata.xml :
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added metadata.xml, marked ebuild stable
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*emboss-2.7.1 (03 Sep 2003)
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03 Sep 2003; <sediener@gentoo.org> emboss-2.7.1.ebuild:
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Initial ebuild
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