diff options
Diffstat (limited to 'sci-biology')
153 files changed, 13380 insertions, 0 deletions
diff --git a/sci-biology/ApE/ChangeLog b/sci-biology/ApE/ChangeLog new file mode 100644 index 00000000..30663296 --- /dev/null +++ b/sci-biology/ApE/ChangeLog @@ -0,0 +1,48 @@ +# ChangeLog for sci-biology/ApE +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ApE/ChangeLog,v 1.10 2015/03/20 15:39:09 jlec Exp $ + + 20 Mar 2015; Justin Lecher <jlec@gentoo.org> -ApE-2.0.7.ebuild, + ApE-2.0.7-r1.ebuild, metadata.xml: + Fix tcl/tk slotting;drop old; Bump EAPI + +*ApE-2.0.7-r1 (31 Dec 2012) + + 31 Dec 2012; Jeff Gardner <je_fro@gentoo.org> +ApE-2.0.7-r1.ebuild: + Forward command line arguments to ApE startup script, thanks to Markus Meier + in bug #375919 + + 25 Apr 2012; Jeff Gardner <je_fro@gentoo.org> ApE-2.0.7.ebuild: + Fix SRC_URI thanks to Horea Christian in bug #405367. + +*ApE-2.0.7 (15 Jun 2011) + + 15 Jun 2011; Jeff Gardner <je_fro@gentoo.org> ApE-1.17.ebuild, + +ApE-2.0.7.ebuild: + New version, fix bugs raised in #371473, thanks to Piotr Szymaniak and Jeroen + Roovers. + + 14 Nov 2009; Jeff Gardner <je_fro@gentoo.org> Manifest: + Update digest thanks to a bump from Martin Mokrejs and Stefanie D. Hueber + in bug #292789. + +*ApE-1.17 (17 Feb 2009) + + 17 Feb 2009; Jeff Gardner <je_fro@gentoo.org> -ApE-1.12.ebuild, + +ApE-1.17.ebuild: + Bump to latest version. Thanks to Sascha Lucas on bug #259267. + + 30 Dec 2008; Jeff Gardner <je_fro@gentoo.org> Manifest: + Fix manifest + + 02 Nov 2008; Jorge Manuel B. S. Vicetto <jmbsvicetto@gentoo.org> + metadata.xml: + Fixed the broken herd by adding no-herd to metadata.xml. + + 09 Jul 2008; Jeff Gardner <je_fro@gentoo.org> ApE-1.12.ebuild: + RESTRICT=mirror, thanks to tove who caught it. + +*ApE-1.12 (09 Jul 2008) + + 09 Jul 2008; Jeff Gardner <je_fro@gentoo.org> +ApE-1.12.ebuild: + Initial import, thanks to Marek Miller on bug #231231. diff --git a/sci-biology/GBrowse/ChangeLog b/sci-biology/GBrowse/ChangeLog new file mode 100644 index 00000000..a997416c --- /dev/null +++ b/sci-biology/GBrowse/ChangeLog @@ -0,0 +1,49 @@ +# ChangeLog for sci-biology/GBrowse +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/GBrowse/ChangeLog,v 1.10 2015/06/13 19:38:55 dilfridge Exp $ + + 13 Jun 2015; Andreas K. Huettel <dilfridge@gentoo.org> GBrowse-2.48-r1.ebuild: + Module::Build is no longer part of core Perl and has been moved to dev-perl + + 19 Dec 2014; Andreas K. Huettel <dilfridge@gentoo.org> metadata.xml: + Drop perl herd from metadata + + 25 Oct 2014; Andreas K. Huettel <dilfridge@gentoo.org> + -GBrowse-2.44-r1.ebuild: + Remove old due to old EAPI + +*GBrowse-2.48-r1 (27 Aug 2014) + + 27 Aug 2014; Ian Stakenvicius (_AxS_) <axs@gentoo.org> + +GBrowse-2.48-r1.ebuild, -GBrowse-2.48.ebuild: + bumped EAPI to 5 to support dev-lang/perl upgrades + + 19 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + herd is now sci-biology + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*GBrowse-2.48 (27 Feb 2012) + + 27 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> -GBrowse-2.39.ebuild, + +GBrowse-2.48.ebuild: + Version bump + +*GBrowse-2.44-r1 (02 Jan 2012) + + 02 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> -GBrowse-2.44.ebuild, + +GBrowse-2.44-r1.ebuild: + Disable webapp autoslotting, bug 396085 + +*GBrowse-2.44 (26 Dec 2011) + + 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +GBrowse-2.44.ebuild: + Version bump + +*GBrowse-2.39 (20 Jul 2011) + + 20 Jul 2011; Andrey Kislyuk <weaver@gentoo.org> +GBrowse-2.39.ebuild, + +files/GBrowseInstall.pm-2.39.patch, +metadata.xml: + Import from sci overlay, rename and rewrite; thanks to Martin Mokrejs + <mmokrejs@fold.natur.cuni.cz> and Justin Lecher <jlec@gentoo.org> diff --git a/sci-biology/aaindex/ChangeLog b/sci-biology/aaindex/ChangeLog new file mode 100644 index 00000000..f1294b43 --- /dev/null +++ b/sci-biology/aaindex/ChangeLog @@ -0,0 +1,106 @@ +# ChangeLog for sci-biology/aaindex +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/aaindex/ChangeLog,v 1.27 2011/08/09 15:36:16 xarthisius Exp $ + + 09 Aug 2011; Kacper Kowalik <xarthisius@gentoo.org> aaindex-9.1.ebuild: + ppc64 keyword dropped + + 09 Mar 2011; Raúl Porcel <armin76@gentoo.org> aaindex-9.1.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> aaindex-9.1.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> -aaindex-7.0.ebuild: + Pruned old version. + + 20 Nov 2006; <blubb@gentoo.org> aaindex-9.1.ebuild: + stable on amd64 + + 15 Nov 2006; Markus Rothe <corsair@gentoo.org> aaindex-9.1.ebuild: + Stable on ppc64; bug #153766 + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> aaindex-7.0.ebuild, + aaindex-9.1.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> aaindex-9.1.ebuild: + Added to x86. + +*aaindex-9.1 (13 Sep 2006) + + 13 Sep 2006; Olivier Fisette <ribosome@gentoo.org> +aaindex-9.1.ebuild: + New upstream version. + + 18 Aug 2006; Jason Wever <weeve@gentoo.org> aaindex-7.0.ebuild: + Added ~sparc keyword wrt bug #144241. + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> -aaindex-6.0.ebuild: + Removed obsolete version. + + 14 Jan 2006; Fabian Groffen <grobian@gentoo.org> aaindex-7.0.ebuild: + Marked ppc-macos stable for bug #115449 + + 24 Dec 2005; Simon Stelling <blubb@gentoo.org> aaindex-7.0.ebuild: + stable on amd64 + + 23 Dec 2005; Tobias Scherbaum <dertobi123@gentoo.org> aaindex-7.0.ebuild: + Marked ppc stable, #115449 + + 15 Dec 2005; Olivier Fisette <ribosome@gentoo.org> aaindex-7.0.ebuild: + Added to x86. + + 13 Dec 2005; Markus Rothe <corsair@gentoo.org> aaindex-7.0.ebuild: + Stable on ppc64; bug #115449 + + 19 Nov 2005; Simon Stelling <blubb@gentoo.org> aaindex-6.0.ebuild: + stable on amd64 + +*aaindex-7.0 (18 Oct 2005) + + 18 Oct 2005; Olivier Fisette <ribosome@gentoo.org> +aaindex-7.0.ebuild: + New version. + + 04 Sep 2005; Simon Stelling <blubb@gentoo.org> aaindex-6.0.ebuild: + added ~amd64 keyword + + 19 Jun 2005; Daniel Ostrow <dostrow@gentoo.org> aaindex-6.0.ebuild: + Stable on ppc64. + + 02 May 2005; Michael Hanselmann <hansmi@gentoo.org> aaindex-6.0.ebuild: + Stable on ppc. + + 27 Apr 2005; Markus Rothe <corsair@gentoo.org> aaindex-6.0.ebuild: + Added ~ppc64 to KEYWORDS; bug #89856 + + 22 Feb 2005; Olivier Fisette <ribosome@gentoo.org> aaindex-6.0.ebuild: + Added support for the "emboss" and "minimal" "USE" flags. + + 14 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> aaindex-6.0.ebuild: + Stable ppc-macos. + +*aaindex-6.0 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +aaindex-6.0.ebuild: + Moved from app-sci/aaindex to sci-biology/aaindex. + + 2 Nov 2004; Lina Pezzella <j4rg0n@gentoo.org> aaindex-6.0.ebuild: + Keyworded ~ppc-macos. + + 10 Aug 2004; Olivier Fisette <ribosome@gentoo.org> aaindex-6.0.ebuild: + Added to x86. + + 26 Jun 2004; David Holm <dholm@gentoo.org> aaindex-6.0.ebuild: + Added to ~ppc. + +*aaindex-6.0 (24 Jun 2004) + + 24 Jun 2004; Olivier Fisette <ribosome@gentoo.org> + aaindex-6.0.ebuild, metadata.xml : + Initial import. Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>. + Reference: Gentoo Bugzilla, bug #54319 + diff --git a/sci-biology/abyss/ChangeLog b/sci-biology/abyss/ChangeLog new file mode 100644 index 00000000..19599d30 --- /dev/null +++ b/sci-biology/abyss/ChangeLog @@ -0,0 +1,99 @@ +# ChangeLog for sci-biology/abyss +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/ChangeLog,v 1.21 2015/04/07 14:31:56 jlec Exp $ + + 06 Jul 2014; Justin Lecher <jlec@gentoo.org> abyss-1.3.6.ebuild: + Add missing dep on boost, #515156 + +*abyss-1.3.6 (11 Aug 2013) + + 11 Aug 2013; Justin Lecher <jlec@gentoo.org> abyss-1.3.3.ebuild, + abyss-1.3.4.ebuild, +abyss-1.3.6.ebuild, +files/abyss-1.3.3-ac_prog_ar.patch, + +files/abyss-1.3.6-ac_prog_ar.patch, +files/abyss-1.3.6-gcc-4.7.patch: + Version Bump, respect AR, #477580 + + 11 Aug 2013; Justin Lecher <jlec@gentoo.org> -abyss-1.2.3.ebuild, + -abyss-1.2.7.ebuild, -abyss-1.3.0.ebuild: + Drop old + + 27 Jul 2013; Agostino Sarubbo <ago@gentoo.org> abyss-1.3.3.ebuild: + Stable for x86, wrt bug #477144 + + 21 Jul 2013; Agostino Sarubbo <ago@gentoo.org> abyss-1.3.3.ebuild: + Stable for amd64, wrt bug #477144 + + 17 Jul 2013; Justin Lecher <jlec@gentoo.org> abyss-1.3.4.ebuild: + Moved to autotools-utils.eclass + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*abyss-1.3.4 (20 Jun 2012) + + 20 Jun 2012; Justin Lecher <jlec@gentoo.org> abyss-1.3.0.ebuild, + abyss-1.3.3.ebuild, +files/abyss-1.3.3-gcc-4.7.patch, +abyss-1.3.4.ebuild, + +files/abyss-1.3.4-gcc-4.7.patch: + Fix compilation with gcc-4.7, #422599; install docs inside /usr/share/doc/, + #297205 + +*abyss-1.3.3 (29 May 2012) + + 29 May 2012; Andrey Kislyuk <weaver@gentoo.org> +abyss-1.3.3.ebuild: + version bump + +*abyss-1.3.0 (24 Sep 2011) + + 24 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +abyss-1.3.0.ebuild: + Version bump + + 28 Apr 2011; Justin Lecher <jlec@gentoo.org> abyss-1.2.3.ebuild, + abyss-1.2.7.ebuild: + Added openmp USE + +*abyss-1.2.7 (28 Apr 2011) + + 28 Apr 2011; Kacper Kowalik <xarthisius@gentoo.org> -abyss-1.2.0.ebuild, + +abyss-1.2.7.ebuild: + Version bump. Remove -Werror wrt #365195 by Diego Elio Pettenò + <flameeyes@gentoo.org>. Fix doc paths. Drop old. + + 11 Feb 2011; Markos Chandras <hwoarang@gentoo.org> abyss-1.2.3.ebuild: + Stable on amd64 wrt bug #335370 + + 07 Feb 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> abyss-1.2.3.ebuild: + x86 stable wrt bug #353570 + +*abyss-1.2.3 (26 Sep 2010) + + 26 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> +abyss-1.2.3.ebuild: + Version bump + +*abyss-1.2.0 (23 Jun 2010) + + 23 Jun 2010; Andrey Kislyuk <weaver@gentoo.org> -abyss-1.1.2.ebuild, + +abyss-1.2.0.ebuild: + Version bump + +*abyss-1.1.2 (26 Mar 2010) + + 26 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> -abyss-1.1.1.ebuild, + +abyss-1.1.2.ebuild: + Version bump + +*abyss-1.1.1 (26 Jan 2010) + + 26 Jan 2010; Andrey Kislyuk <weaver@gentoo.org> -abyss-1.1.0.ebuild, + +abyss-1.1.1.ebuild: + Version bump + +*abyss-1.1.0 (04 Jan 2010) + + 04 Jan 2010; Andrey Kislyuk <weaver@gentoo.org> -abyss-1.0.16.ebuild, + +abyss-1.1.0.ebuild: + Version bump + +*abyss-1.0.16 (24 Nov 2009) + + 24 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +abyss-1.0.16.ebuild: + New package, ebuild written by me diff --git a/sci-biology/allpathslg/ChangeLog b/sci-biology/allpathslg/ChangeLog new file mode 100644 index 00000000..19e4feed --- /dev/null +++ b/sci-biology/allpathslg/ChangeLog @@ -0,0 +1,89 @@ +# ChangeLog for sci-biology/allpathslg +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpathslg/ChangeLog,v 1.20 2015/04/07 14:32:01 jlec Exp $ + +*allpathslg-52415 (31 Mar 2015) + + 31 Mar 2015; Justin Lecher <jlec@gentoo.org> +allpathslg-52415.ebuild: + Version Bump; move to EAPI=5 and autotools-utils.eclass; thanks Martin Mokrejs + for preparing the bump + + 31 Mar 2015; Justin Lecher <jlec@gentoo.org> allpathslg-47093.ebuild: + prefix love + + 31 Mar 2015; Justin Lecher <jlec@gentoo.org> + +files/allpathslg-47093-gcc4.9.patch, allpathslg-47093.ebuild: + Fix for newer gcc, bug #514654 + + 13 Nov 2013; Patrick Lauer <patrick@gentoo.org> allpathslg-42337.ebuild, + allpathslg-47093.ebuild: + Removing x86 keyword as dependency sci-biology/vaal does not work on x86 + +*allpathslg-47093 (17 Jul 2013) + + 17 Jul 2013; Justin Lecher <jlec@gentoo.org> allpathslg-42337.ebuild, + +allpathslg-47093.ebuild: + Version Bump + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 20 Feb 2013; Justin Lecher <jlec@gentoo.org> -allpathslg-37578.ebuild: + Drop old + + 20 Feb 2013; Agostino Sarubbo <ago@gentoo.org> allpathslg-42337.ebuild: + Stable for amd64, wrt bug #458106 + + 18 Feb 2013; Justin Lecher <jlec@gentoo.org> -allpathslg-41839.ebuild, + metadata.xml: + Drop old + + 14 Dec 2012; Ulrich Müller <ulm@gentoo.org> allpathslg-37578.ebuild, + allpathslg-41839.ebuild, allpathslg-42337.ebuild: + Fix LICENSE, MIT (Expat) according to COPYING file. + + 19 Nov 2012; Justin Lecher <jlec@gentoo.org> allpathslg-37578.ebuild, + allpathslg-41839.ebuild, allpathslg-42337.ebuild: + Block sci-biology/allpaths due to file collision, #443740 + +*allpathslg-42337 (09 Jul 2012) + + 09 Jul 2012; Justin Lecher <jlec@gentoo.org> +allpathslg-42337.ebuild: + Version bump, fix compilation errors with gcc-4.7, #425472 + +*allpathslg-41839 (29 May 2012) + + 29 May 2012; Andrey Kislyuk <weaver@gentoo.org> -allpathslg-38573.ebuild, + -allpathslg-40063.ebuild, +allpathslg-41839.ebuild: + version bump + +*allpathslg-40063 (28 Dec 2011) + + 28 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> + -allpathslg-35725-r1.ebuild, +allpathslg-40063.ebuild: + Version bump, remove old + + 15 Oct 2011; Markos Chandras <hwoarang@gentoo.org> allpathslg-37578.ebuild: + Stable on amd64 wrt bug #384379 + +*allpathslg-38573 (25 Sep 2011) + + 25 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +allpathslg-38573.ebuild: + Version bump + +*allpathslg-37578 (20 Jun 2011) + + 20 Jun 2011; Andrey Kislyuk <weaver@gentoo.org> +allpathslg-37578.ebuild: + Version bump + +*allpathslg-35725-r1 (27 Jan 2011) + + 27 Jan 2011; Andrey Kislyuk <weaver@gentoo.org> -allpathslg-35725.ebuild, + +allpathslg-35725-r1.ebuild: + Drop ~x86, avoid collision with sci-biology/vaal + +*allpathslg-35725 (25 Jan 2011) + + 25 Jan 2011; Andrey Kislyuk <weaver@gentoo.org> +allpathslg-35725.ebuild, + +metadata.xml: + Package move from sci-biology/allpaths and version bump diff --git a/sci-biology/amap/ChangeLog b/sci-biology/amap/ChangeLog new file mode 100644 index 00000000..943c3a54 --- /dev/null +++ b/sci-biology/amap/ChangeLog @@ -0,0 +1,48 @@ +# ChangeLog for sci-biology/amap +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/ChangeLog,v 1.7 2011/03/26 10:56:00 xarthisius Exp $ + +*amap-2.2-r2 (26 Mar 2011) + + 26 Mar 2011; Kacper Kowalik <xarthisius@gentoo.org> -amap-2.2-r1.ebuild, + +amap-2.2-r2.ebuild, -files/amap-2.2-cxxflags.patch, + -files/amap-2.2-gcc4.3.patch, +files/amap-2.2-includes.patch, + +files/amap-2.2-makefile.patch: + Clean java bits thanks to sera. General cleanup, fix linking order, fix + building with gcc 4.6 wrt #360517. Drop old. + + 10 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org> + -files/2.0-fix-cxxflags.patch, -amap-2.0.ebuild, -amap-2.2.ebuild, + -files/2.1-fix-cxxflags.patch, -amap-2.1.ebuild, amap-2.2-r1.ebuild: + Respect LDFLAGS wrt bug 332009. Thanks to Diego for report. Remove old. + +*amap-2.2-r1 (27 Jul 2009) + + 27 Jul 2009; Donnie Berkholz <dberkholz@gentoo.org>; +amap-2.2-r1.ebuild: + Someone wasn't reading the upstream changelogs ... add an option to build + the Java GUI. + +*amap-2.2 (17 Apr 2008) + + 17 Apr 2008; Markus Dittrich <markusle@gentoo.org> + +files/amap-2.2-cxxflags.patch, +files/amap-2.2-gcc4.3.patch, + +amap-2.2.ebuild: + Version bump and gcc-4.3 compatibility patch (fixes bug #217921). Thanks + much to Peter Alfredsen <peter.alfredsen@gmail.com> for his patches. + + 15 Oct 2007; Jeff Gardner <je_fro@gentoo.org> amap-2.1.ebuild: + Adding ~amd64 + +*amap-2.1 (13 Oct 2007) + + 13 Oct 2007; Markus Dittrich <markusle@gentoo.org> + +files/2.1-fix-cxxflags.patch, +amap-2.1.ebuild: + Version bump (fixes bug #191861). + +*amap-2.0 (11 Dec 2006) + + 11 Dec 2006; Donnie Berkholz <dberkholz@gentoo.org>; + +files/2.0-fix-cxxflags.patch, +metadata.xml, +amap-2.0.ebuild: + New package: Protein multiple-alignment-based sequence annealing. It's based + on ProbCons and adds sequence annealing. See the homepage for details. + diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog new file mode 100644 index 00000000..9246bc87 --- /dev/null +++ b/sci-biology/amos/ChangeLog @@ -0,0 +1,82 @@ +# ChangeLog for sci-biology/amos +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/ChangeLog,v 1.20 2015/04/08 18:20:42 mgorny Exp $ + + 08 Apr 2015; Michał Górny <mgorny@gentoo.org> amos-3.1.0-r1.ebuild: + Drop old Python implementations + +*amos-3.1.0-r1 (29 Dec 2013) + + 29 Dec 2013; Justin Lecher <jlec@gentoo.org> +amos-3.1.0-r1.ebuild, + +files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch: + Fix python support + + 19 Mar 2013; Justin Lecher <jlec@gentoo.org> amos-3.1.0.ebuild, metadata.xml: + Change USE name from qt to qt4, #462218 + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 02 Mar 2013; Markos Chandras <hwoarang@gentoo.org> amos-3.1.0.ebuild: + Move Qt dependencies to the new category + + 08 Jul 2012; Justin Lecher <jlec@gentoo.org> -amos-2.0.8-r1.ebuild, + -files/amos-2.0.8-gcc44.patch, -amos-3.0.0.ebuild, -amos-3.0.1.ebuild, + amos-3.1.0.ebuild, +files/amos-3.1.0-gcc-4.7.patch: + Add fix for gcc-4.7, #425264; cleaned old + + 05 Oct 2011; Justin Lecher <jlec@gentoo.org> amos-3.1.0.ebuild, metadata.xml: + Another simplification + + 01 Oct 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> amos-3.1.0.ebuild: + x86 stable wrt bug #384343 + + 25 Sep 2011; Tony Vroon <chainsaw@gentoo.org> amos-3.1.0.ebuild: + Marked stable on AMD64 based on arch testing by Agostino "ago" Sarubbo & + Elijah "Armageddon" El Lazkani in bug #384343. + +*amos-3.1.0 (12 Aug 2011) +*amos-3.0.1 (12 Aug 2011) + + 12 Aug 2011; Andrey Kislyuk <weaver@gentoo.org> +amos-3.0.1.ebuild, + +amos-3.1.0.ebuild: + Version bump + + 28 May 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> amos-3.0.0.ebuild: + x86 stable wrt bug #368287 + + 23 May 2011; Markos Chandras <hwoarang@gentoo.org> amos-3.0.0.ebuild: + Stable on amd64 wrt bug #368287 + +*amos-3.0.0 (03 Feb 2011) + + 03 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> +amos-3.0.0.ebuild: + Version bump + + 11 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> -amos-2.0.8.ebuild: + Drop old ebuild + +*amos-2.0.8-r1 (11 Feb 2010) + + 11 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> +amos-2.0.8-r1.ebuild: + Remove qt3 dependency per bug 304467 + + 30 Jul 2009; Samuli Suominen <ssuominen@gentoo.org> amos-2.0.8.ebuild, + +files/amos-2.0.8-gcc44.patch: + Fix building with GCC 4.4 and GLIBC 2.10+ wrt #279572. + + 15 Mar 2009; Markus Meier <maekke@gentoo.org> amos-2.0.8.ebuild: + amd64/x86 stable, bug #261786 + +*amos-2.0.8 (26 Aug 2008) + + 26 Aug 2008; weaver <weaver@gentoo.org> +amos-2.0.8.ebuild: + Bump to 2.0.8, drop patch + + 17 Jun 2008; weaver <weaver@gentoo.org> ChangeLog: + Bump to 2.0.7 and add gcc-4.3 patch, bug 227597, thanks to Marek Miller + +*amos-2.0.5 (26 May 2008) + + 26 May 2008; weaver <weaver@gentoo.org> +metadata.xml, +amos-2.0.5.ebuild: + Initial commit. New package from sunrise, bug 175293 diff --git a/sci-biology/arb/ChangeLog b/sci-biology/arb/ChangeLog new file mode 100644 index 00000000..d960d881 --- /dev/null +++ b/sci-biology/arb/ChangeLog @@ -0,0 +1,54 @@ +# ChangeLog for sci-biology/arb +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/arb/ChangeLog,v 1.11 2015/04/07 14:32:08 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 24 Oct 2012; Ulrich Müller <ulm@gentoo.org> arb-5.1-r1.ebuild, + arb-5.2.ebuild, arb-5.3.ebuild: + Update dependency after package move from x11-libs/openmotif to + x11-libs/motif. + +*arb-5.3 (14 Aug 2012) + + 14 Aug 2012; Justin Lecher <jlec@gentoo.org> arb-5.2.ebuild, + +files/arb-5.2-gcc-47.patch, +arb-5.3.ebuild: + Version Bump; add fix for gcc-4.7, #431228 + + 04 Mar 2012; Justin Lecher <jlec@gentoo.org> arb-5.1-r1.ebuild, + arb-5.2.ebuild: + Adopt deps to unbundled x11-libs/libGLw situation + + 11 Aug 2011; Kacper Kowalik <xarthisius@gentoo.org> + +files/5.2-libpng15.patch, arb-5.2.ebuild: + Add missing dependency on sys-process/time and fix building with libpng-1.5 + wrt #378353. Thanks to Diego Elio Pettenò <flameeyes@gentoo.org> for the + report and Samuli Suominen <ssuominen@gentoo.org> for the patch + +*arb-5.2 (20 Jun 2011) + + 20 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/5.1-bfr-overflow.patch, + arb-5.1-r1.ebuild, +arb-5.2.ebuild: + Version Bump, fix buffer overflow, make gcc46 resistent, fix build failure, + #314665,340579,362633 + + 10 Oct 2010; Ulrich Mueller <ulm@gentoo.org> arb-5.1-r1.ebuild: + Fix openmotif dependency. + + 16 Sep 2010; Tomáš Chvátal <scarabeus@gentoo.org> arb-5.1-r1.ebuild: + virtual/glut -> media-libs/glut + +*arb-5.1-r1 (13 Mar 2010) + + 13 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> +files/5.1-libs.patch, + -arb-5.1.ebuild, +arb-5.1-r1.ebuild: + Fixed compilation w/ glibc-2.10, #294876 + Respecting LDFLAGS + +*arb-5.1 (03 Oct 2009) + + 03 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +arb-5.1.ebuild: + Import from Science overlay and version bump + diff --git a/sci-biology/ariadne/ChangeLog b/sci-biology/ariadne/ChangeLog new file mode 100644 index 00000000..68e04892 --- /dev/null +++ b/sci-biology/ariadne/ChangeLog @@ -0,0 +1,54 @@ +# ChangeLog for sci-biology/ariadne +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ariadne/ChangeLog,v 1.12 2013/04/11 18:42:50 ulm Exp $ + + 11 Apr 2013; Ulrich Müller <ulm@gentoo.org> ariadne-1.3-r1.ebuild, + ariadne-1.3-r2.ebuild: + Fix LICENSE, see README and notices in source files. + + 14 Jun 2012; Justin Lecher <jlec@gentoo.org> ariadne-1.3-r1.ebuild, + ariadne-1.3-r2.ebuild: + Correct deps, bump EAPI, handle static-libs + +*ariadne-1.3-r2 (15 Mar 2011) + + 15 Mar 2011; Kacper Kowalik <xarthisius@gentoo.org> +ariadne-1.3-r2.ebuild, + +files/ariadne-1.3-implicits.patch: + Fix implicits, add missing explicit RDEPEND, respect LDFLAGS wrt #359045. + Thanks to Diego for the report. + + 30 Sep 2008; Jeremy Olexa <darkside@gentoo.org> ariadne-1.3-r1.ebuild: + add ~amd64 kw based on Chad's testing. bug #239159 + + 25 Mar 2007; Danny van Dyk <kugelfang@gentoo.org> ariadne-1.3-r1.ebuild: + QA: Removed redundant src_compile phase. + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Stepping down from maintainership. + + 12 Sep 2006; Olivier Fisette <ribosome@gentoo.org> + +files/ariadne-1.3-gcc4.patch, ariadne-1.3-r1.ebuild: + Fixed a GCC4 compilation issue (see bug #138833). + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> ariadne-1.3-r1.ebuild: + Ebuild clean-up. + + 04 Jan 2006; Olivier Fisette <ribosome@gentoo.org> ariadne-1.3-r1.ebuild: + Do not depend on "virtual/libc" (package not in system target). + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> ariadne-1.3-r1.ebuild: + Added to x86. + +*ariadne-1.3-r1 (06 Mar 2005) + + 06 Mar 2005; Olivier Fisette <ribosome@gentoo.org> -files/ariadne-env, + +ariadne-1.3-r1.ebuild, -ariadne-1.3.ebuild: + Package no longer sets the "BLASTMAT" environment variable. (This is now + done by the "ncbi-tools" package.) + +*ariadne-1.3 (05 Mar 2005) + + 05 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +files/ariadne-env, +ariadne-1.3.ebuild: + Initial import. + diff --git a/sci-biology/augustus/ChangeLog b/sci-biology/augustus/ChangeLog new file mode 100644 index 00000000..ee07f163 --- /dev/null +++ b/sci-biology/augustus/ChangeLog @@ -0,0 +1,78 @@ +# ChangeLog for sci-biology/augustus +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/ChangeLog,v 1.19 2013/03/11 14:37:00 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 31 Jan 2013; Justin Lecher <jlec@gentoo.org> -augustus-2.3.1.ebuild, + -augustus-2.4.ebuild, -augustus-2.5.ebuild, metadata.xml: + Drop old, fixes multiple QA issues, #454822 + + 31 Jan 2013; Agostino Sarubbo <ago@gentoo.org> augustus-2.5.5.ebuild: + Stable for x86, wrt bug #454842 + + 31 Jan 2013; Agostino Sarubbo <ago@gentoo.org> augustus-2.5.5.ebuild: + Stable for amd64, wrt bug #454842 + +*augustus-2.5.5 (23 Jun 2011) + + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> augustus-2.3.1.ebuild, + augustus-2.4.ebuild, augustus-2.5.ebuild, +augustus-2.5.5.ebuild, + +files/augustus-2.5.5-sane-build.patch: + Version Bump, respect LDFLAGS, #337655 + + 09 Mar 2011; Markos Chandras <hwoarang@gentoo.org> augustus-2.4.ebuild: + Stable on amd64 wrt bug #353573 + + 09 Mar 2011; Thomas Kahle <tomka@gentoo.org> augustus-2.4.ebuild: + x86 stable per bug 353573 + + 04 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> augustus-2.4.ebuild, + augustus-2.5.ebuild: + Respect LDFLAGS + +*augustus-2.5 (03 Feb 2011) + + 03 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> augustus-2.4.ebuild, + +augustus-2.5.ebuild: + Version bump, update SRC_URI + +*augustus-2.4 (26 Sep 2010) + + 26 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> -augustus-2.1.ebuild, + -files/augustus-2.1-glibc-2.10.patch, +augustus-2.4.ebuild: + Version bump, drop old + + 09 Feb 2010; Pacho Ramos <pacho@gentoo.org> augustus-2.3.1.ebuild: + amd64 stable, bug 298767 + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> + augustus-2.3.1.ebuild: + stable x86, bug 298767 + +*augustus-2.3.1 (16 Nov 2009) + + 16 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> +augustus-2.3.1.ebuild: + Version bump + + 31 Oct 2009; Markus Meier <maekke@gentoo.org> augustus-2.1.ebuild: + amd64/x86 stable, bug #290924 + + 09 Aug 2009; Samuli Suominen <ssuominen@gentoo.org> augustus-2.1.ebuild, + +files/augustus-2.1-glibc-2.10.patch: + Fix building with GLIBC 2.10+ wrt #276719. + +*augustus-2.1 (19 Mar 2009) + + 19 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> + -files/augustus-2.0.3-cflags.patch, -files/augustus-2.0.3-gcc4.3.patch, + -augustus-2.0.3.ebuild, +augustus-2.1.ebuild: + Version bump + +*augustus-2.0.3 (04 Jan 2009) + + 04 Jan 2009; weaver <weaver@gentoo.org> + +files/augustus-2.0.3-cflags.patch, +files/augustus-2.0.3-gcc4.3.patch, + +metadata.xml, +augustus-2.0.3.ebuild: + Initial commit, ebuild written by me diff --git a/sci-biology/bamtools/ChangeLog b/sci-biology/bamtools/ChangeLog new file mode 100644 index 00000000..095aee2c --- /dev/null +++ b/sci-biology/bamtools/ChangeLog @@ -0,0 +1,57 @@ +# ChangeLog for sci-biology/bamtools +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bamtools/ChangeLog,v 1.10 2013/09/17 15:37:30 jlec Exp $ + +*bamtools-2.3.0 (17 Sep 2013) + + 17 Sep 2013; Justin Lecher <jlec@gentoo.org> -bamtools-2.2.3.ebuild, + +bamtools-2.3.0.ebuild, +files/bamtools-2.3.0-unbundle.patch: + Version Bump, drop old, #482636; thanks Martin Mokrejš for the patch + + 27 Aug 2013; Jeroen Roovers <jer@gentoo.org> metadata.xml: + Update e-mail address. + + 17 Mar 2013; Markos Chandras <hwoarang@gentoo.org> metadata.xml: + Add proxy-maintainers to metadata.xml + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 01 Mar 2013; Justin Lecher <jlec@gentoo.org> bamtools-2.2.3.ebuild, + files/bamtools-2.2.3-unbundle.patch: + Update script and correct dep on jsoncpp + + 28 Feb 2013; Pawel Hajdan jr <phajdan.jr@gentoo.org> bamtools-2.2.3.ebuild: + Update jsoncpp dependency, bug #452234. + +*bamtools-2.2.3 (28 Jan 2013) + + 28 Jan 2013; Justin Lecher <jlec@gentoo.org> +bamtools-2.2.3.ebuild, + +files/bamtools-2.2.3-unbundle.patch, metadata.xml: + Version Bump; #452234; unbundles dev-libs/jsoncpp + + 26 Apr 2012; Justin Lecher <jlec@gentoo.org> bamtools-1.0.2.ebuild: + Remove unnecessary die + + 23 Apr 2012; Michał Górny <mgorny@gentoo.org> bamtools-1.0.2.ebuild: + Use mirror://github. + + 25 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> +bamtools-1.0.2.ebuild, + +metadata.xml: + Import from Science overlay + +*bamtools-1.0.2 (10 Sep 2011) + + 10 Sep 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +bamtools-1.0.2.ebuild, bamtools-9999.ebuild, -bamtools-20101215.ebuild, + metadata.xml: + moved to new release download link and version bump, documented that included + JsonCPP is a modified version bamtools-20101215.ebuild bamtools-1.0.2.ebuild + bamtools-9999.ebuild + + 08 Sep 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + bamtools-9999.ebuild, bamtools-20101215.ebuild: + Point to current HOMEPAGE bamtools-20101215.ebuild bamtools-9999.ebuild + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> bamtools-9999.ebuild: + Moved from 'git' to 'git-2' diff --git a/sci-biology/beast-mcmc/ChangeLog b/sci-biology/beast-mcmc/ChangeLog new file mode 100644 index 00000000..4793a8cc --- /dev/null +++ b/sci-biology/beast-mcmc/ChangeLog @@ -0,0 +1,31 @@ +# ChangeLog for sci-biology/beast-mcmc +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/beast-mcmc/ChangeLog,v 1.6 2013/03/11 14:38:27 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*beast-mcmc-1.7.5 (18 Feb 2013) + + 18 Feb 2013; Justin Lecher <jlec@gentoo.org> +beast-mcmc-1.7.5.ebuild, + metadata.xml: + Version Bump, fixes missing package, #374277 + + 20 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> -beast-mcmc-1.5.1.ebuild: + Drop old version + +*beast-mcmc-1.5.2 (19 Oct 2009) + + 19 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +beast-mcmc-1.5.2.ebuild: + Version bump + + 18 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> beast-mcmc-9999.ebuild: + Address upstream changes in live ebuild + +*beast-mcmc-9999 (02 Oct 2009) +*beast-mcmc-1.5.1 (02 Oct 2009) + + 02 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +beast-mcmc-1.5.1.ebuild, +beast-mcmc-9999.ebuild: + Import from Science overlay and rewrite + diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog new file mode 100644 index 00000000..25a1de82 --- /dev/null +++ b/sci-biology/bedtools/ChangeLog @@ -0,0 +1,37 @@ +# ChangeLog for sci-biology/bedtools +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bedtools/ChangeLog,v 1.7 2014/05/30 20:16:25 swift Exp $ + +*bedtools-2.20.1 (30 May 2014) + + 30 May 2014; Sven Vermeulen <swift@gentoo.org> +bedtools-2.20.1.ebuild: + Add bedtools 2.20.1 thanks to Martin Mokrejs (bug #505538) + + 24 Mar 2014; Jeroen Roovers <jer@gentoo.org> metadata.xml: + New e-mail address. + + 17 Mar 2013; Markos Chandras <hwoarang@gentoo.org> metadata.xml: + Add proxy-maintainers to metadata.xml + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*bedtools-2.16.2 (29 May 2012) + + 29 May 2012; Andrey Kislyuk <weaver@gentoo.org> +bedtools-2.16.2.ebuild, + -bedtools-2.13.3.ebuild, -bedtools-2.15.0.ebuild: + version bump + +*bedtools-2.15.0 (02 Jan 2012) + + 02 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> +bedtools-2.15.0.ebuild: + Version bump + +*bedtools-2.13.3 (09 Oct 2011) + + 09 Oct 2011; Andrey Kislyuk <weaver@gentoo.org> +bedtools-2.13.3.ebuild, + +metadata.xml: + Import from Science overlay and rewrite + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> bedtools-2.10.1.ebuild: + SOme ebuild cleaning diff --git a/sci-biology/bfast/ChangeLog b/sci-biology/bfast/ChangeLog new file mode 100644 index 00000000..76925776 --- /dev/null +++ b/sci-biology/bfast/ChangeLog @@ -0,0 +1,57 @@ +# ChangeLog for sci-biology/bfast +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bfast/ChangeLog,v 1.10 2013/03/11 14:42:24 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 17 Feb 2013; Justin Lecher <jlec@gentoo.org> bfast-0.7.0a.ebuild: + Build in source for tests + + 17 Feb 2013; Justin Lecher <jlec@gentoo.org> -bfast-0.6.5a.ebuild, + -bfast-0.6.5a-r1.ebuild, bfast-0.7.0a.ebuild, metadata.xml: + Drop old; move to autotools-utils; install docs in right place, #304603 + +*bfast-0.7.0a (28 Nov 2011) + + 28 Nov 2011; Andrey Kislyuk <weaver@gentoo.org> +bfast-0.7.0a.ebuild: + Version bump + +*bfast-0.6.5a-r1 (06 Oct 2011) + + 06 Oct 2011; Justin Lecher <jlec@gentoo.org> +bfast-0.6.5a-r1.ebuild: + Respect CFLAGS, #384369 + + 15 Jul 2011; Kacper Kowalik <xarthisius@gentoo.org> -bfast-0.6.4c.ebuild, + -bfast-0.6.4d.ebuild: + Drop old. Files not available upstream anymore + +*bfast-0.6.5a (18 May 2011) + + 18 May 2011; Andrey Kislyuk <weaver@gentoo.org> -bfast-0.6.4b.ebuild, + +bfast-0.6.4d.ebuild, +bfast-0.6.5a.ebuild: + Version bump + +*bfast-0.6.4d (11 Jul 2010) + + 11 Jul 2010; Andrey Kislyuk <weaver@gentoo.org> -bfast-0.6.4b.ebuild, + +bfast-0.6.4d.ebuild: + Version bump + +*bfast-0.6.4c (07 May 2010) + + 07 May 2010; Andrey Kislyuk <weaver@gentoo.org> -bfast-0.6.2a.ebuild, + +bfast-0.6.4c.ebuild: + Version bump + +*bfast-0.6.4b (18 Apr 2010) + + 18 Apr 2010; Andrey Kislyuk <weaver@gentoo.org> +bfast-0.6.4b.ebuild: + Version bump + +*bfast-0.6.2a (21 Jan 2010) + + 21 Jan 2010; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +bfast-0.6.2a.ebuild: + New package, ebuild written by me + diff --git a/sci-biology/biogrep/ChangeLog b/sci-biology/biogrep/ChangeLog new file mode 100644 index 00000000..7badc467 --- /dev/null +++ b/sci-biology/biogrep/ChangeLog @@ -0,0 +1,22 @@ +# ChangeLog for sci-biology/biogrep +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biogrep/ChangeLog,v 1.2 2010/10/10 17:43:49 jlec Exp $ + +*biogrep-1.0-r1 (10 Oct 2010) + + 10 Oct 2010; Justin Lecher <jlec@gentoo.org> +biogrep-1.0-r1.ebuild, + metadata.xml: + Package taken, respect CC now + +*biogrep-1.0 (04 Jun 2010) + + 04 Jun 2010; Markos Chandras <hwoarang@gentoo.org> +biogrep-1.0.ebuild, + +metadata.xml: + Moved from sunrise overlay. Fixes bug #235952. + Thanks to Chad A Simmons (CCIEChad) <chad.simmons@member.fsf.org> + for the ebuild + + 27 Aug 2008; Chad A Simmons (CCIEChad) <chad.simmons@member.fsf.org> + +biogrep-1.0.ebuild, +metadata.xml: + New Ebuild for bug 235952 thanks to Tommy and gentoofan23 for the review. + diff --git a/sci-biology/biojava/ChangeLog b/sci-biology/biojava/ChangeLog new file mode 100644 index 00000000..6077e528 --- /dev/null +++ b/sci-biology/biojava/ChangeLog @@ -0,0 +1,30 @@ +# ChangeLog for sci-biology/biojava +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biojava/ChangeLog,v 1.2 2015/08/05 21:01:52 monsieurp Exp $ + + 05 Aug 2015; Patrice Clement <monsieurp@gentoo.org> biojava-1.6.ebuild, + biojava-1.7.ebuild: + Fix year of copyright and silence QA warning. + + 24 May 2014; Pacho Ramos <pacho@gentoo.org> metadata.xml: + Cleanup due #199047 + + 20 Mar 2010; Petteri Räty <betelgeuse@gentoo.org> biojava-1.7.ebuild: + Keyword ~x86. + +*biojava-1.7 (10 Jul 2009) + + 10 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +biojava-1.7.ebuild: + Version bump + + 07 Feb 2009; weaver <weaver@gentoo.org> metadata.xml: + Assume ownership + +*biojava-1.6 (25 Jan 2009) + + 25 Jan 2009; weaver <weaver@gentoo.org> +metadata.xml, + +biojava-1.6.ebuild: + Import from Java overlay, thanks to serkan + + 22 Jan 2009; Alistair Bush <ali_bush@gentoo.org> ChangeLog: + Add ChangeLog for QA. diff --git a/sci-biology/bioperl-db/ChangeLog b/sci-biology/bioperl-db/ChangeLog new file mode 100644 index 00000000..7e4543c6 --- /dev/null +++ b/sci-biology/bioperl-db/ChangeLog @@ -0,0 +1,62 @@ +# ChangeLog for sci-biology/bioperl-db +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-db/ChangeLog,v 1.15 2015/06/13 19:16:38 dilfridge Exp $ + + 13 Jun 2015; Andreas K. Huettel <dilfridge@gentoo.org> + bioperl-db-1.6.9.ebuild, bioperl-db-9999-r1.ebuild: + Module::Build is no longer part of core Perl and has been moved to dev-perl + + 27 May 2015; Justin Lecher <jlec@gentoo.org> -bioperl-db-1.6.0.ebuild: + Drop old + + 27 May 2015; Agostino Sarubbo <ago@gentoo.org> bioperl-db-1.6.9.ebuild: + Stable for amd64, wrt bug #539426 + + 26 Apr 2015; Pacho Ramos <pacho@gentoo.org> bioperl-db-1.6.9.ebuild: + x86 stable wrt bug #539426 + + 09 Aug 2014; Mikle Kolyada <zlogene@gentoo.org> bioperl-db-1.6.0.ebuild, + bioperl-db-1.6.9.ebuild, bioperl-db-9999-r1.ebuild: + Bump to EAPI=5 (bug #478714) + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 23 Jun 2012; Justin Lecher <jlec@gentoo.org> bioperl-db-1.6.9.ebuild: + Add missing DEP on dev-perl/DBD-mysql, #422999 + + 12 Apr 2012; Torsten Veller <tove@gentoo.org> metadata.xml: + Fix cpan distribution in metadata.xml + + 20 Sep 2011; Michał Górny <mgorny@gentoo.org> bioperl-db-9999-r1.ebuild: + Migrate to git-2. + +*bioperl-db-1.6.9 (18 Jul 2011) + + 18 Jul 2011; Andrey Kislyuk <weaver@gentoo.org> +bioperl-db-1.6.9.ebuild: + Version bump, drop old + +*bioperl-db-9999-r1 (17 Oct 2010) + + 17 Oct 2010; Andrey Kislyuk <weaver@gentoo.org> -bioperl-db-9999.ebuild, + +bioperl-db-9999-r1.ebuild: + Update live ebuild for upstream svm->github migration, bug 338362. Thanks + to Joel Berendzen + + 11 Jun 2009; Markus Meier <maekke@gentoo.org> bioperl-db-1.6.0.ebuild: + amd64 stable, bug #270580 + + 02 Jun 2009; Christian Faulhammer <fauli@gentoo.org> + bioperl-db-1.6.0.ebuild: + stable x86, bug 270580 + + 13 May 2009; Andrey Kislyuk <weaver@gentoo.org> bioperl-db-1.6.0.ebuild, + bioperl-db-9999.ebuild: + Remove module-build from RDEPEND (bug 246942) + +*bioperl-db-9999 (16 Mar 2009) +*bioperl-db-1.6.0 (16 Mar 2009) + + 16 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +bioperl-db-1.6.0.ebuild, +bioperl-db-9999.ebuild: + New package, dependency for sci-biology/bioperl. Ebuild written by me. diff --git a/sci-biology/bioperl-network/ChangeLog b/sci-biology/bioperl-network/ChangeLog new file mode 100644 index 00000000..886caf90 --- /dev/null +++ b/sci-biology/bioperl-network/ChangeLog @@ -0,0 +1,62 @@ +# ChangeLog for sci-biology/bioperl-network +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-network/ChangeLog,v 1.14 2015/06/13 19:15:52 dilfridge Exp $ + + 13 Jun 2015; Andreas K. Huettel <dilfridge@gentoo.org> + bioperl-network-1.6.9.ebuild, bioperl-network-9999-r1.ebuild: + Module::Build is no longer part of core Perl and has been moved to dev-perl + + 27 May 2015; Justin Lecher <jlec@gentoo.org> -bioperl-network-1.6.0.ebuild: + Drop old + + 27 May 2015; Agostino Sarubbo <ago@gentoo.org> bioperl-network-1.6.9.ebuild: + Stable for amd64, wrt bug #539426 + + 26 Apr 2015; Pacho Ramos <pacho@gentoo.org> bioperl-network-1.6.9.ebuild: + x86 stable wrt bug #539426 + + 09 Aug 2014; Mikle Kolyada <zlogene@gentoo.org> bioperl-network-1.6.0.ebuild, + bioperl-network-1.6.9.ebuild, bioperl-network-9999-r1.ebuild: + Bump to EAPI=5 (bug #478714) + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 12 Apr 2012; Torsten Veller <tove@gentoo.org> metadata.xml: + Fix cpan distribution in metadata.xml + + 20 Sep 2011; Michał Górny <mgorny@gentoo.org> + bioperl-network-9999-r1.ebuild: + Migrate to git-2. + +*bioperl-network-1.6.9 (18 Jul 2011) + + 18 Jul 2011; Andrey Kislyuk <weaver@gentoo.org> + +bioperl-network-1.6.9.ebuild: + Version bump, drop old + +*bioperl-network-9999-r1 (17 Oct 2010) + + 17 Oct 2010; Andrey Kislyuk <weaver@gentoo.org> + -bioperl-network-9999.ebuild, +bioperl-network-9999-r1.ebuild: + Update live ebuild for upstream svm->github migration, bug 338362. Thanks + to Joel Berendzen + + 11 Jun 2009; Markus Meier <maekke@gentoo.org> + bioperl-network-1.6.0.ebuild: + amd64 stable, bug #270583 + + 02 Jun 2009; Christian Faulhammer <fauli@gentoo.org> + bioperl-network-1.6.0.ebuild: + stable x86, bug 270583 + + 13 May 2009; Andrey Kislyuk <weaver@gentoo.org> + bioperl-network-1.6.0.ebuild, bioperl-network-9999.ebuild: + Remove module-build from RDEPEND (bug 246942) + +*bioperl-network-9999 (16 Mar 2009) +*bioperl-network-1.6.0 (16 Mar 2009) + + 16 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +bioperl-network-1.6.0.ebuild, +bioperl-network-9999.ebuild: + New package, dependency for sci-biology/bioperl. Ebuild written by me. diff --git a/sci-biology/bioperl-run/ChangeLog b/sci-biology/bioperl-run/ChangeLog new file mode 100644 index 00000000..f0485edb --- /dev/null +++ b/sci-biology/bioperl-run/ChangeLog @@ -0,0 +1,142 @@ +# ChangeLog for sci-biology/bioperl-run +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/ChangeLog,v 1.29 2015/06/13 19:15:04 dilfridge Exp $ + + 13 Jun 2015; Andreas K. Huettel <dilfridge@gentoo.org> + bioperl-run-1.6.9.ebuild, bioperl-run-9999-r1.ebuild: + Module::Build is no longer part of core Perl and has been moved to dev-perl + + 27 May 2015; Justin Lecher <jlec@gentoo.org> -bioperl-run-1.6.1.ebuild, + metadata.xml: + Drop old + + 27 May 2015; Agostino Sarubbo <ago@gentoo.org> bioperl-run-1.6.9.ebuild: + Stable for amd64, wrt bug #539426 + + 26 Apr 2015; Pacho Ramos <pacho@gentoo.org> bioperl-run-1.6.9.ebuild: + x86 stable wrt bug #539426 + + 09 Aug 2014; Mikle Kolyada <zlogene@gentoo.org> bioperl-run-1.6.1.ebuild, + bioperl-run-1.6.9.ebuild, bioperl-run-9999-r1.ebuild: + Bump to EAPI=5 (bug #478714) + + 02 Nov 2012; Justin Lecher <jlec@gentoo.org> -bioperl-run-1.5.1.ebuild: + Dropped old + + 12 Apr 2012; Torsten Veller <tove@gentoo.org> metadata.xml: + Fix cpan distribution in metadata.xml + + 20 Sep 2011; Michał Górny <mgorny@gentoo.org> bioperl-run-9999-r1.ebuild: + Migrate to git-2. + +*bioperl-run-1.6.9 (18 Jul 2011) + + 18 Jul 2011; Andrey Kislyuk <weaver@gentoo.org> -bioperl-run-1.4.ebuild, + +bioperl-run-1.6.9.ebuild: + Version bump, drop old + +*bioperl-run-9999-r1 (17 Oct 2010) + + 17 Oct 2010; Andrey Kislyuk <weaver@gentoo.org> -bioperl-run-9999.ebuild, + +bioperl-run-9999-r1.ebuild: + Update live ebuild for upstream svm->github migration, bug 338362. Thanks + to Joel Berendzen + + 11 Jun 2009; Markus Meier <maekke@gentoo.org> bioperl-run-1.6.1.ebuild: + amd64 stable, bug #270582 + + 02 Jun 2009; Christian Faulhammer <fauli@gentoo.org> + bioperl-run-1.6.1.ebuild: + stable x86, bug 270582 + + 01 Jun 2009; Andrey Kislyuk <weaver@gentoo.org> bioperl-run-1.6.1.ebuild, + bioperl-run-9999.ebuild: + Disable tests until testsuite troubleshooting is complete + + 13 May 2009; Andrey Kislyuk <weaver@gentoo.org> bioperl-run-1.6.1.ebuild, + bioperl-run-9999.ebuild: + Remove module-build from RDEPEND (bug 246942) + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*bioperl-run-9999 (16 Mar 2009) +*bioperl-run-1.6.1 (16 Mar 2009) + + 16 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> +bioperl-run-1.6.1.ebuild, + +bioperl-run-9999.ebuild: + Version bump + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 22 Oct 2006; Olivier Fisette <ribosome@gentoo.org> bioperl-run-1.4.ebuild, + bioperl-run-1.5.1.ebuild: + Link bioperl-run versions to the correspond bioperl-core. + + 22 Oct 2006; Olivier Fisette <ribosome@gentoo.org> bioperl-run-1.4.ebuild, + bioperl-run-1.5.1.ebuild: + Fixed description. + + 13 Sep 2006; Olivier Fisette <ribosome@gentoo.org> + bioperl-run-1.5.1.ebuild: + Added missing dependency on bioperl. + +*bioperl-run-1.5.1 (13 Sep 2006) + + 13 Sep 2006; Olivier Fisette <ribosome@gentoo.org> + +bioperl-run-1.5.1.ebuild: + New upstream version. Added test cases. + + 13 Feb 2006; Michael Cummings <mcummings@gentoo.org> + bioperl-run-1.4.ebuild: + Virtuals for perl-core + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> + -bioperl-run-1.2.2.ebuild, bioperl-run-1.4.ebuild: + Removed obsolete versions. Ebuild clean-up. + + 28 Nov 2005; <mcumming@gentoo.org> bioperl-run-1.2.2.ebuild, + bioperl-run-1.4.ebuild: + Switched from perl-module to perl-app eclass + + 19 Sep 2005; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Maintainer changed from Stephen Diener (MIA) to Olivier Fisette. + + 25 May 2005; Michael Cummings <mcummings@gentoo.org> bioperl-run-1.4.ebuild: + dev-perl/File-Temp => perl-core/File-Temp migration + + 25 May 2005; Michael Cummings <mcummings@gentoo.org> + bioperl-run-1.2.2.ebuild: + dev-perl/File-Temp => perl-core/File-Temp migration + +*bioperl-run-1.2.2 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +files/bioperl-run-Pise-test-patch.diff, +bioperl-run-1.2.2.ebuild, + +bioperl-run-1.4.ebuild: + Moved from app-sci/bioperl-run to sci-biology/bioperl-run. + + 23 Sep 2004; Stephen Diener <sediener@gentoo.org> bioperl-run-1.4.ebuild: + Bumped 1.4 to stable on x86 + + 03 Aug 2004; David Holm <dholm@gentoo.org> bioperl-run-1.4.ebuild: + Added to ~ppc. + + 22 Mar 2004; Patrick Kursawe <phosphan@gentoo.org> bioperl-run-1.2.2.ebuild, + bioperl-run-1.4.ebuild: + removing DEPEND="${RDEPEND}" + +*bioperl-run-1.4 (08 Jan 2004) + + 08 Jan 2004; Stephen Diener <sediener@gentoo.org> bioperl-run-1.4.ebuild: + version bump to 1.4 + + 14 Dec 2003; Stephen Diener <sediener@gentoo.org> bioperl-run-1.2.2.ebuild: + Bump to stable + +*bioperl-run-1.2.2 (29 Sep 2003) + + 29 Sep 2003; <sediener@gentoo.org> bioperl-run-1.2.2.ebuild, metadata.xml, + files/bioperl-run-Pise-test-patch.diff: + Initial Import. Built of of the bioperl ebuild from Gontran Zepeda. diff --git a/sci-biology/bioperl/ChangeLog b/sci-biology/bioperl/ChangeLog new file mode 100644 index 00000000..ff99d4a4 --- /dev/null +++ b/sci-biology/bioperl/ChangeLog @@ -0,0 +1,289 @@ +# ChangeLog for sci-biology/bioperl +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/ChangeLog,v 1.60 2015/06/13 19:19:59 dilfridge Exp $ + + 13 Jun 2015; Andreas K. Huettel <dilfridge@gentoo.org> bioperl-1.6.9.ebuild, + bioperl-9999-r1.ebuild: + Module::Build is no longer part of core Perl and has been moved to dev-perl + + 27 May 2015; Justin Lecher <jlec@gentoo.org> -bioperl-1.6.0-r2.ebuild: + Drop old + + 27 May 2015; Agostino Sarubbo <ago@gentoo.org> bioperl-1.6.9.ebuild: + Stable for amd64, wrt bug #539426 + + 26 Apr 2015; Pacho Ramos <pacho@gentoo.org> bioperl-1.6.9.ebuild: + x86 stable wrt bug #539426 + + 18 Apr 2015; Andreas K. Huettel <dilfridge@gentoo.org> bioperl-1.6.9.ebuild: + Use REQUIRED_USE instead of dieing on invalid use-flag combination, bug + 547022 + + 08 Apr 2015; Justin Lecher <jlec@gentoo.org> bioperl-1.6.9.ebuild, + bioperl-9999-r1.ebuild, metadata.xml: + Add missing deps, bug #545472 + + 09 Aug 2014; Mikle Kolyada <zlogene@gentoo.org> bioperl-1.6.0-r2.ebuild, + bioperl-1.6.9.ebuild, bioperl-9999-r1.ebuild: + Bump to EAPI=5 (bug #478714) + + 10 Jul 2014; Andreas K. Huettel <dilfridge@gentoo.org> bioperl-1.6.9.ebuild: + Depend on virtual/perl-x instead of perl-core/x + + 28 Oct 2012; Justin Lecher <jlec@gentoo.org> -bioperl-1.5.1-r1.ebuild, + -bioperl-1.6.1.ebuild: + Drop versions with unsolvable dep sets + + 12 Apr 2012; Torsten Veller <tove@gentoo.org> metadata.xml: + Fix cpan distribution in metadata.xml + + 24 Mar 2012; Raúl Porcel <armin76@gentoo.org> bioperl-1.5.1-r1.ebuild: + Drop alpha/ia64/sparc keywords + + 20 Sep 2011; Michał Górny <mgorny@gentoo.org> bioperl-9999-r1.ebuild: + Migrate to git-2. + +*bioperl-1.6.9 (18 Jul 2011) + + 18 Jul 2011; Andrey Kislyuk <weaver@gentoo.org> -bioperl-1.4.ebuild, + +bioperl-1.6.9.ebuild: + Version bump, drop old + +*bioperl-9999-r1 (17 Oct 2010) + + 17 Oct 2010; Andrey Kislyuk <weaver@gentoo.org> -bioperl-9999.ebuild, + +bioperl-9999-r1.ebuild: + Update live ebuild for upstream svm->github migration, bug 338362. Thanks + to Joel Berendzen + + 02 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> bioperl-1.6.1.ebuild: + Fix typo + + 01 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> bioperl-1.6.1.ebuild: + Fix typo + +*bioperl-1.6.1 (01 Oct 2009) + + 01 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +bioperl-1.6.1.ebuild: + Version bump + + 11 Jun 2009; Markus Meier <maekke@gentoo.org> bioperl-1.6.0-r2.ebuild: + amd64 stable, bug #270585 + + 02 Jun 2009; Christian Faulhammer <fauli@gentoo.org> + bioperl-1.6.0-r2.ebuild: + stable x86, bug 270585 + + 24 May 2009; Andrey Kislyuk <weaver@gentoo.org> bioperl-1.6.0-r2.ebuild, + bioperl-9999.ebuild: + Moved Bio-ASN1-EntrezGene to PDEPEND per bug 269583 + + 13 May 2009; Andrey Kislyuk <weaver@gentoo.org> bioperl-9999.ebuild: + Override depend on perl 5.10 + + 13 May 2009; Andrey Kislyuk <weaver@gentoo.org> bioperl-1.6.0-r2.ebuild, + bioperl-9999.ebuild: + Remove module-build from RDEPEND (bug 246942) + +*bioperl-1.6.0-r2 (08 Apr 2009) + + 08 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> -bioperl-1.6.0-r1.ebuild, + +bioperl-1.6.0-r2.ebuild, bioperl-9999.ebuild: + Revision bump - add missing dependencies + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*bioperl-9999 (16 Mar 2009) +*bioperl-1.6.0-r1 (16 Mar 2009) + + 16 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> -bioperl-1.6.0.ebuild, + +bioperl-1.6.0-r1.ebuild, +bioperl-9999.ebuild: + Rewrite, commit split 1.6.0 packages and live ebuilds for packages in 1.6.0 + release. Bug 179110. + +*bioperl-1.6.0 (12 Mar 2009) + + 12 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> +bioperl-1.6.0.ebuild: + Testing release for revision bump + + 15 Jul 2008; Raúl Porcel <armin76@gentoo.org> bioperl-1.5.1-r1.ebuild: + x86 stable wrt #222727 + + 06 Jul 2008; Olivier Fisette <ribosome@gentoo.org> + bioperl-1.5.1-r1.ebuild: + Stable on amd64. + + 06 Jul 2008; Olivier Fisette <ribosome@gentoo.org> + bioperl-1.5.1-r1.ebuild: + Fixed test suite. + + 06 Jul 2008; Olivier Fisette <ribosome@gentoo.org> + bioperl-1.5.1-r1.ebuild: + Fixed dependency on io_lib. + + 02 Jan 2008; Raúl Porcel <armin76@gentoo.org> bioperl-1.5.1-r1.ebuild: + Re-add ~alpha/~ia64 + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> + bioperl-1.5.1-r1.ebuild: + Fixed Perl dependencies (see bug #157672). + + 22 Oct 2006; Olivier Fisette <ribosome@gentoo.org> bioperl-1.4.ebuild, + -bioperl-1.5.1.ebuild, bioperl-1.5.1-r1.ebuild: + Fixed description. Removed old ebuild. + + 30 Sep 2006; Jason Wever <weeve@gentoo.org> bioperl-1.5.1.ebuild, + bioperl-1.5.1-r1.ebuild: + Added ~sparc keyword wrt bug #149577. + + 30 Sep 2006; Olivier Fisette <ribosome@gentoo.org> + bioperl-1.5.1-r1.ebuild: + Fixing dependency on io_lib (thanks to Weeve for pointing this out). + +*bioperl-1.5.1-r1 (30 Sep 2006) + + 30 Sep 2006; Olivier Fisette <ribosome@gentoo.org> + +bioperl-1.5.1-r1.ebuild: + Added dependency on io_lib for the Staden extensions. Dropping ~alpha, ~ia64 + and ~sparc keywords (see bug #149577). + +*bioperl-1.5.1 (13 Sep 2006) + + 13 Sep 2006; Olivier Fisette <ribosome@gentoo.org> +bioperl-1.5.1.ebuild: + New upstream version. Thanks to Greg Wilson <gdw1@cornell.edu>, Martin + Mokrejs <mmokrejs@ribosome.natur.cuni.cz> and Neil Shephard + <nshephard@gmail.com> for their work (see bug #79459). + + 18 Aug 2006; Michael Cummings <mcummings@gentoo.org> bioperl-1.4.ebuild: + Marking amd64 stable + + 30 Mar 2006; Aron Griffis <agriffis@gentoo.org> bioperl-1.4.ebuild: + Mark 1.4 ~ia64 + + 13 Feb 2006; Michael Cummings <mcummings@gentoo.org> bioperl-1.4.ebuild: + Virtuals for perl-core + + 28 Nov 2005; <mcumming@gentoo.org> bioperl-1.0.2.ebuild, + bioperl-1.2.2.ebuild, bioperl-1.2.3.ebuild, bioperl-1.2.ebuild, + bioperl-1.4.ebuild: + Switched from perl-module to perl-app eclass + + 19 Sep 2005; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Maintainer changed from Stephen Diener (MIA) to Olivier Fisette. + + 05 Aug 2005; Herbie Hopkins <herbs@gentoo.org> bioperl-1.4.ebuild: + Marked ~amd64 wrt bug #101339. + + 25 May 2005; Michael Cummings <mcummings@gentoo.org> bioperl-1.4.ebuild: + dev-perl/Storable => perl-core/Storable migration + + 25 May 2005; Michael Cummings <mcummings@gentoo.org> bioperl-1.2.ebuild: + dev-perl/Storable => perl-core/Storable migration + + 25 May 2005; Michael Cummings <mcummings@gentoo.org> bioperl-1.2.3.ebuild: + dev-perl/Storable => perl-core/Storable migration + + 25 May 2005; Michael Cummings <mcummings@gentoo.org> bioperl-1.2.2.ebuild: + dev-perl/Storable => perl-core/Storable migration + + 25 May 2005; Michael Cummings <mcummings@gentoo.org> bioperl-1.0.2.ebuild: + dev-perl/Storable => perl-core/Storable migration + + 25 May 2005; Michael Cummings <mcummings@gentoo.org> bioperl-1.4.ebuild: + dev-perl/File-Temp => perl-core/File-Temp migration + + 25 May 2005; Michael Cummings <mcummings@gentoo.org> bioperl-1.2.ebuild: + dev-perl/File-Temp => perl-core/File-Temp migration + + 25 May 2005; Michael Cummings <mcummings@gentoo.org> bioperl-1.2.3.ebuild: + dev-perl/File-Temp => perl-core/File-Temp migration + + 25 May 2005; Michael Cummings <mcummings@gentoo.org> bioperl-1.2.2.ebuild: + dev-perl/File-Temp => perl-core/File-Temp migration + + 25 May 2005; Michael Cummings <mcummings@gentoo.org> bioperl-1.0.2.ebuild: + dev-perl/File-Temp => perl-core/File-Temp migration + + 30 Mar 2005; Gustavo Zacarias <gustavoz@gentoo.org> bioperl-1.4.ebuild: + Keyworded ~sparc + + 09 Jan 2005; Olivier Fisette <ribosome@gentoo.org> bioperl-1.4.ebuild: + Added regression test support. Fixes bug #38169. + + 29 Dec 2004; Ciaran McCreesh <ciaranm@gentoo.org> : + Change encoding to UTF-8 for GLEP 31 compliance + +*bioperl-1.2 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +files/biodbgff-enable-1.2.2.patch, +files/biodbgff-enable-1.2.3.patch, + +files/bioperl-1.2-manpage.diff, +files/domanpages-1.2.2.patch, + +bioperl-1.0.2.ebuild, +bioperl-1.2.2.ebuild, +bioperl-1.2.3.ebuild, + +bioperl-1.2.ebuild, +bioperl-1.4.ebuild: + Moved from app-sci/bioperl to sci-biology/bioperl. + + 30 Oct 2004; Olivier Fisette <ribosome@gentoo.org> bioperl-1.4.ebuild, + bioperl-1.0.2.ebuild: + Q.A.: Fixed RDEPEND=$DEPEND, fixed LICENSE. + + 03 Aug 2004; David Holm <dholm@gentoo.org> bioperl-1.4.ebuild: + Added to ~ppc. + + 03 Jul 2004; Bryan Østergaard <kloeri@gentoo.org> bioperl-1.4.ebuild: + Stable on alpha. + + 02 Jun 2004; Aron Griffis <agriffis@gentoo.org> bioperl-1.2.2.ebuild, + bioperl-1.2.3.ebuild: + Fix use invocation + + 05 May 2004; Stephen Diener <sediener@gentoo.org> bioperl-1.4.ebuild: + bumped 1.4 to stable + + 05 May 2004; Bryan Østergaard <kloeri@gentoo.org> bioperl-1.2.ebuild: + Stable on alpha. + + 20 Apr 2004; Bryan Østergaard <kloeri@gentoo.org> bioperl-1.4.ebuild: + Added ~alpha to keywords. + + 14 Jan 2004; Stephen Diener <sediener@gentoo.org> bioperl-1.4.ebuild: + removed src_test; fixes bug #38169, or at least works around it + +*bioperl-1.4 (08 Jan 2004) + + 08 Jan 2004; Stephen Diener <sediener@gentoo.org> bioperl-1.4.ebuild: + version bump + + 24 Nov 2003; Stephen Diener <sediener@gentoo.org> bioperl-1.2.3.ebuild: + bump to stable. + +*bioperl-1.2.3 (24 Oct 2003) + + 24 Oct 2003; <sediener@gentoo.org> bioperl-1.2.3.ebuild: + new release added. + +*bioperl-1.2.2 (28 Aug 2003) + + 28 Aug 2003; Stephen Diener <sediener@gentoo.org> bioperl-1.2.2.ebuild: + Bumped to stable x86 + +*bioperl-1.2.2 (02 Aug 2003) + + 02 Aug 2003; Stephen Diener <sediener@gentoo.org> bioperl-1.2.2.ebuild, + files/biodbgff-enable-1.2.2.patch, files/domanpages-1.2.2.patch: + New Version thanks to Gontran Zepeda <gontran@gontran.net> in bug# 24467 : + Also fixes bug# 25079 + +*bioperl-1.2 (24 Apr 2003) + + 24 Apr 2003; Jon Portnoy <avenj@gentoo.org> bioperl-1.2.ebuild : + Version bump, ebuild submitted by Gontran Zepeda <gontran@gontran.net> + in bug #13826 + +*bioperl-1.0.2 (21 Dec 2002) + + 21 Dec 2002; Michael Cummings <mcummings@gentoo.org> + bioperl-1.0.2.ebuild: + + Initial import. Ebuild submitted by Gontran Zepeda <gontran@gontran.net> + Bug 11498 diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog new file mode 100644 index 00000000..bede7dbe --- /dev/null +++ b/sci-biology/biopython/ChangeLog @@ -0,0 +1,393 @@ +# ChangeLog for sci-biology/biopython +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.85 2015/04/07 14:32:18 jlec Exp $ + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> -biopython-1.57.ebuild, + -biopython-1.64.ebuild, -files/SffIO_broken_padding.patch, + -files/SffIO_error_in_check_eof.patch, -files/biopython-1.51-flex.patch, + -files/biopython-1.62-SffIO.patch: + Drop old + + 28 Mar 2015; Agostino Sarubbo <ago@gentoo.org> biopython-1.65.ebuild: + Stable for ppc, wrt bug #544544 + + 27 Mar 2015; Agostino Sarubbo <ago@gentoo.org> biopython-1.65.ebuild: + Stable for x86, wrt bug #544544 + + 27 Mar 2015; Agostino Sarubbo <ago@gentoo.org> biopython-1.65.ebuild: + Stable for amd64, wrt bug #544544 + + 26 Mar 2015; Justin Lecher <jlec@gentoo.org> + +files/biopython-1.65-test-fix-backport.patch, biopython-1.65.ebuild: + Backport test fix + + 26 Mar 2015; Justin Lecher <jlec@gentoo.org> biopython-1.65.ebuild: + Add note for embos support, bug #543510 + + 03 Mar 2015; Justin Lecher <jlec@gentoo.org> -biopython-1.58.ebuild, + -biopython-1.59.ebuild, -biopython-1.61.ebuild, -biopython-1.62-r1.ebuild, + -biopython-1.62.ebuild, -biopython-1.63-r1.ebuild, -biopython-1.63.ebuild, + biopython-1.64.ebuild: + Drop old + +*biopython-1.65 (03 Mar 2015) + + 03 Mar 2015; Justin Lecher <jlec@gentoo.org> +biopython-1.65.ebuild: + Version Bump; add py3 and pypy support + +*biopython-1.64 (03 Jun 2014) + + 03 Jun 2014; Justin Lecher <jlec@gentoo.org> +biopython-1.64.ebuild: + Version Bump, thanks Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> preparing + the ebuild + +*biopython-1.63-r1 (07 May 2014) + + 07 May 2014; Justin Lecher <jlec@gentoo.org> +biopython-1.63-r1.ebuild, + +files/SffIO_broken_padding.patch, +files/SffIO_error_in_check_eof.patch: + Import changes from sci overlay + +*biopython-1.63 (30 Jan 2014) + + 30 Jan 2014; Justin Lecher <jlec@gentoo.org> +biopython-1.63.ebuild: + Version Bump + +*biopython-1.62-r1 (29 Dec 2013) + + 29 Dec 2013; Justin Lecher <jlec@gentoo.org> +biopython-1.62-r1.ebuild, + +files/biopython-1.62-SffIO.patch: + Add additional patch from Martin Mokrejš + +*biopython-1.62 (17 Sep 2013) + + 17 Sep 2013; Justin Lecher <jlec@gentoo.org> +biopython-1.62.ebuild: + Version Bump + + 02 Jul 2013; Justin Lecher <jlec@gentoo.org> biopython-1.61.ebuild: + Fix deps for python + + 06 Jun 2013; Justin Lecher <jlec@gentoo.org> biopython-1.61.ebuild: + Keyword ~-linux + +*biopython-1.61 (26 Apr 2013) + + 26 Apr 2013; Justin Lecher <jlec@gentoo.org> +biopython-1.61.ebuild, + metadata.xml: + Version Bump + + 14 Dec 2012; Ulrich Müller <ulm@gentoo.org> biopython-1.57.ebuild, + biopython-1.58.ebuild, biopython-1.59.ebuild: + Update LICENSE, HPND according to LICENSE file. + +*biopython-1.59 (27 Feb 2012) + + 27 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.59.ebuild: + Version bump + + 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.58.ebuild: + Version bump + +*biopython-1.58 (26 Dec 2011) + + 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.58.ebuild: + Version bump + + 23 Jun 2011; Markos Chandras <hwoarang@gentoo.org> -biopython-1.56.ebuild: + Remove old ebuilds. Requested by Arfrever + + 28 May 2011; Brent Baude <ranger@gentoo.org> biopython-1.57.ebuild: + Marking biopython-1.57 ppc for bug 365877 + + 24 May 2011; Markus Meier <maekke@gentoo.org> biopython-1.57.ebuild: + x86 stable, bug #365877 + + 06 May 2011; Justin Lecher <jlec@gentoo.org> biopython-1.56.ebuild, + biopython-1.57.ebuild: + Cleaned DESCRIPTION + + 05 May 2011; Markos Chandras <hwoarang@gentoo.org> biopython-1.57.ebuild: + Stable on amd64 wrt bug #365877 + +*biopython-1.57 (03 Apr 2011) + + 03 Apr 2011; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org> + +biopython-1.57.ebuild: + Version bump. + + 30 Jan 2011; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org> + -biopython-1.55.ebuild: + Delete. + + 30 Jan 2011; Raúl Porcel <armin76@gentoo.org> biopython-1.55.ebuild, + biopython-1.56.ebuild: + Drop alpha/sparc keywords + + 15 Jan 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> + biopython-1.56.ebuild: + x86 stable wrt bug #351498 + + 14 Jan 2011; Brent Baude <ranger@gentoo.org> biopython-1.56.ebuild: + stable ppc, bug 351498 + + 13 Jan 2011; Markos Chandras <hwoarang@gentoo.org> biopython-1.56.ebuild: + Stable on amd64 wrt bug #351498 + + 06 Jan 2011; Brent Baude <ranger@gentoo.org> biopython-1.55.ebuild: + Marking biopython-1.55 ppc for bug 341519 + +*biopython-1.56 (13 Dec 2010) + + 13 Dec 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org> + -biopython-1.53.ebuild, -biopython-1.54.ebuild, +biopython-1.56.ebuild: + Version bump. + + 31 Oct 2010; Raúl Porcel <armin76@gentoo.org> biopython-1.55.ebuild: + alpha/sparc stable wrt #341519 + + 21 Oct 2010; Thomas Kahle <tomka@gentoo.org> biopython-1.55.ebuild: + x86 stable per bug 341519 + + 19 Oct 2010; Markos Chandras <hwoarang@gentoo.org> biopython-1.55.ebuild: + Stable on amd64 wrt bug #341519 + + 15 Oct 2010; Brent Baude <ranger@gentoo.org> biopython-1.54.ebuild: + stable ppc, bug 327151 + + 10 Oct 2010; Raúl Porcel <armin76@gentoo.org> biopython-1.54.ebuild: + sparc stable wrt #327151 + +*biopython-1.55 (17 Sep 2010) + + 17 Sep 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org> + +biopython-1.55.ebuild: + Version bump. + + 12 Sep 2010; Tobias Klausmann <klausman@gentoo.org> biopython-1.54.ebuild: + Stable on alpha, bug #327151 + + 12 Jul 2010; Christian Faulhammer <fauli@gentoo.org> + biopython-1.54.ebuild: + stable x86, bug 327151 + + 06 Jul 2010; Markos Chandras <hwoarang@gentoo.org> biopython-1.54.ebuild: + Stable on amd64 wrt bug #327151 + +*biopython-1.54 (05 Jun 2010) + + 05 Jun 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org> + -biopython-1.49.ebuild, -files/biopython-1.49-flex.patch, + -biopython-1.51.ebuild, -biopython-1.52.ebuild, +biopython-1.54.ebuild: + Version bump. + + 13 Feb 2010; Raúl Porcel <armin76@gentoo.org> biopython-1.53.ebuild: + alpha/sparc stable wrt #301964 + + 07 Feb 2010; Markus Meier <maekke@gentoo.org> biopython-1.53.ebuild: + amd64/x86 stable, bug #301964 + + 24 Jan 2010; Brent Baude <ranger@gentoo.org> biopython-1.53.ebuild: + stable ppc, bug 301964 + +*biopython-1.53 (21 Dec 2009) + + 21 Dec 2009; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org> + +biopython-1.53.ebuild: + Version bump. Set SUPPORT_PYTHON_ABIS. + + 31 Oct 2009; Markus Meier <maekke@gentoo.org> biopython-1.52.ebuild: + amd64/x86 stable, bug #290931 + +*biopython-1.52 (23 Sep 2009) + + 23 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.52.ebuild: + Version bump + +*biopython-1.51 (09 Sep 2009) + + 09 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> + +files/biopython-1.51-flex.patch, +biopython-1.51.ebuild: + Version bump + + 26 Aug 2009; Christian Faulhammer <fauli@gentoo.org> metadata.xml: + remove now unused flag description + + 26 Aug 2009; Christian Faulhammer <fauli@gentoo.org> + -biopython-1.42.ebuild, -files/biopython-1.43-buildkdtree.patch, + -biopython-1.44.ebuild, -files/biopython-1.44-sequtils-complement.patch, + -biopython-1.47.ebuild, -files/biopython-1.47-kdtree.patch: + clean up + + 26 Aug 2009; Tobias Klausmann <klausman@gentoo.org> biopython-1.49.ebuild: + Stable on alpha, bug #277822 + + 02 Aug 2009; nixnut <nixnut@gentoo.org> biopython-1.49.ebuild: + ppc stable #277822 + + 20 Jul 2009; Jeremy Olexa <darkside@gentoo.org> biopython-1.49.ebuild: + amd64 stable, bug 277822 + + 17 Jul 2009; Ferris McCormick <fmccor@gentoo.org> biopython-1.49.ebuild: + Sparc stable --- bug #277822 --- ran tests successfully. + + 14 Jul 2009; Christian Faulhammer <fauli@gentoo.org> + biopython-1.49.ebuild: + stable x86, bug 277822 + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*biopython-1.49 (16 Jan 2009) + + 16 Jan 2009; Olivier Fisette <ribosome@gentoo.org> + +files/biopython-1.49-flex.patch, +biopython-1.49.ebuild: + Version bump. Thanks to Juan Aguado <juantxorena@gmail.com> for his work. + Fixes bug #248799. + + 06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml: + Add USE flag description to metadata wrt GLEP 56. + + 14 Jul 2008; nixnut <nixnut@gentoo.org> biopython-1.44.ebuild: + Stable on ppc wrt bug 221159 + + 07 Jul 2008; Raúl Porcel <armin76@gentoo.org> biopython-1.44.ebuild: + alpha/sparc/x86 stable wrt #221159 + +*biopython-1.47 (06 Jul 2008) + + 06 Jul 2008; Olivier Fisette <ribosome@gentoo.org> + +files/biopython-1.47-kdtree.patch, +biopython-1.47.ebuild: + New version. Better documentation installation. Added scripts and test + suite. KDTree now enabled by default (requires switching to EAPI 1). + + 06 Jul 2008; Olivier Fisette <ribosome@gentoo.org> biopython-1.44.ebuild: + Stable on amd64. + + 30 Jan 2008; Olivier Fisette <ribosome@gentoo.org> biopython-1.42.ebuild, + biopython-1.44.ebuild: + Q.A.: Quoted variables. + + 30 Jan 2008; Olivier Fisette <ribosome@gentoo.org> -biopython-1.43.ebuild: + Removed buggy version (see bug #202602). + +*biopython-1.44 (30 Jan 2008) + + 30 Jan 2008; Olivier Fisette <ribosome@gentoo.org> + +files/biopython-1.44-sequtils-complement.patch, +biopython-1.44.ebuild: + Fixed six_frame_translations function. Thanks to JTRiley + <justin.t.riley@gmail.com> for his patch. (Fixes bug #202606.) + +*biopython-1.43 (17 May 2007) + + 17 May 2007; Olivier Fisette <ribosome@gentoo.org> + +files/biopython-1.43-buildkdtree.patch, -biopython-1.40b.ebuild, + +biopython-1.43.ebuild: + New upstream version. Ebuild clean-up. Pruned old version. + + 16 May 2007; Raúl Porcel <armin76@gentoo.org> biopython-1.42.ebuild: + alpha stable wrt #153774 + + 05 Nov 2006; Christian Faulhammer <opfer@gentoo.org> + biopython-1.42.ebuild: + stabled x86, bug #153774 + + 03 Nov 2006; <blubb@gentoo.org> biopython-1.42.ebuild: + stable on amd64 + + 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> -biopython-1.41.ebuild: + Pruned old version. + + 02 Nov 2006; nixnut <nixnut@gentoo.org> biopython-1.42.ebuild: + Stable on ppc wrt bug 153774 + + 02 Nov 2006; Jason Wever <weeve@gentoo.org> biopython-1.42.ebuild: + Stable on SPARC wrt bug #153774. + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Taking over maintainership. + +*biopython-1.42 (12 Sep 2006) + + 12 Sep 2006; Olivier Fisette <ribosome@gentoo.org> +biopython-1.42.ebuild: + New upstream version. + + 19 Jan 2006; George Shapovalov <george@gentoo.org> +biopython-1.41.ebuild: + new version, cleaned up install + + 30 Aug 2005; Olivier Fisette <ribosome@gentoo.org> -biopython-1.24.ebuild, + -biopython-1.30.ebuild: + Removed obsolete versions. + + 12 Jun 2005; Bryan Østergaard <kloeri@gentoo.org> biopython-1.40b.ebuild: + Stable on alpha. + + 21 May 2005; Jason Wever <weeve@gentoo.org> biopython-1.40b.ebuild: + Stable on SPARC. + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> -biopython-1.10.ebuild, + -biopython-1.21.ebuild, -biopython-1.23.ebuild, biopython-1.40b.ebuild: + Removed obsolete versions. Added 1.40b to x86. + +*biopython-1.40b (19 Feb 2005) + + 19 Feb 2005; Olivier Fisette <ribosome@gentoo.org> + +biopython-1.40b.ebuild: + New version. Should fix bug #82498. + + 29 Dec 2004; Ciaran McCreesh <ciaranm@gentoo.org> : + Change encoding to UTF-8 for GLEP 31 compliance + +*biopython-1.23 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +biopython-1.10.ebuild, +biopython-1.21.ebuild, +biopython-1.23.ebuild, + +biopython-1.24.ebuild, +biopython-1.30.ebuild: + Moved from app-sci/biopython to sci-biology/biopython. + + 13 Dec 2004; Jason Wever <weeve@gentoo.org> biopython-1.24.ebuild: + Stable on sparc. + +*biopython-1.30 (07 Oct 2004) + + 07 Oct 2004; George Shapovalvo <george@gentoo.org> biopython-1.30.ebuild : + new version (#51833) + amd64 has problems with KDTree, will try to look into this more later + + 05 May 2004; Bryan Østergaard <kloeri@gentoo.org> biopython-1.24.ebuild: + Stable on alpha. + + 03 Apr 2004; Peter Bienstman <pbienst@gentoo.org> biopython-1.24.ebuild: + Marked stable on x86 + +*biopython-1.24 (29 Feb 2004) + + 29 Feb 2004; Peter Bienstman <pbienst@gentoo.org> biopython-1.24.ebuild : + version bump + +*biopython-1.23 (30 Dec 2003) + + 29 Feb 2004; Peter Bienstman <pbienst@gentoo.org> biopython-1.23.ebuild : + marked stable on x86 + + 30 Dec 2003; George Shapovalvo <george@gentoo.org> biopython-1.23.ebuild : + new version, reworked to use distutils. Thanks to + Peter Bienstman <Peter.Bienstman@rug.ac.be> for an update (#35727) + + 02 Sep 2003; Alastair Tse <liquidx@gentoo.org> biopython-1.10.ebuild, + biopython-1.21.ebuild: + moved dev-python/Numeric to dev-python/numeric + +*biopython-1.21 (08 Aug 2003) + + 08 Aug 2003; George Shapovalov <george@gentoo.org> biopython-1.21.ebuild : + new version, added few docs (#25428) + thanks to Daniel Jaeggi <daniel@jaeggi.co.uk> for notification + + 04 Jul 2003; Alastair Tse <liquidx@gentoo.org> biopython-1.10.ebuild: + renamed reportlab dep + +*biopython-1.10 (18 Feb 2003) + + 18 Feb 2003; George Shapovalov <george@gentoo.org> ChangeLog, biopython-1.10.ebuild, files/digest-biopython-1.10 : + initial release (#11617) + Biopython - python module for Computational Moelcular Biology + ebuild submitted by Daniel Jaeggi <daniel@jaeggi.co.uk> diff --git a/sci-biology/bioruby/ChangeLog b/sci-biology/bioruby/ChangeLog new file mode 100644 index 00000000..ef3c3b4c --- /dev/null +++ b/sci-biology/bioruby/ChangeLog @@ -0,0 +1,100 @@ +# ChangeLog for sci-biology/bioruby +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioruby/ChangeLog,v 1.22 2014/05/07 19:06:28 mrueg Exp $ + + 07 May 2014; Manuel Rüger <mrueg@gentoo.org> bioruby-1.4.3.0001-r1.ebuild, + bioruby-9999.ebuild: + Remove ruby18 target. + + 15 Dec 2013; Manuel Rüger <mrueg@gentoo.org> -bioruby-1.3.1.ebuild, + -bioruby-1.4.3.0001.ebuild: + Cleanup old. + + 15 Dec 2013; Agostino Sarubbo <ago@gentoo.org> bioruby-1.4.3.0001-r1.ebuild: + Stable for amd64, wrt bug #488414 + + 07 Dec 2013; Johannes Huber <johu@gentoo.org> bioruby-1.4.3.0001-r1.ebuild: + x86 stable, bug #488414 + +*bioruby-1.4.3.0001-r1 (25 Nov 2013) + + 25 Nov 2013; Manuel Rüger <mrueg@gentoo.org> +bioruby-1.4.3.0001-r1.ebuild, + +files/bioruby-1.4.3.0001-fix-tests.patch, bioruby-9999.ebuild: + NMU: Add missing dependency on libxml and ruby20 support. Fix tests see bug + #489712 + + 24 Oct 2013; Tony Vroon <chainsaw@gentoo.org> bioruby-1.4.3.0001.ebuild: + Marked stable on AMD64 based on arch testing by Elijah "Armageddon" El + Lazkani in bug #488414. + + 14 Sep 2013; Manuel Rüger <mrueg@gentoo.org> bioruby-9999.ebuild: + NMU: Fix whitespace. + +*bioruby-1.4.3.0001 (14 Sep 2013) + + 14 Sep 2013; Manuel Rüger <mrueg@gentoo.org> +bioruby-1.4.3.0001.ebuild, + -bioruby-1.1.0.ebuild, -bioruby-1.3.0.ebuild, -bioruby-1.4.2.ebuild, + bioruby-9999.ebuild: + NMU: Version bump. Migrate to ruby-ng eclass. Cleanup old. See bug #475310. + +*bioruby-1.4.2 (28 Nov 2011) + + 28 Nov 2011; Andrey Kislyuk <weaver@gentoo.org> +bioruby-1.4.2.ebuild: + Version bump + + 20 Sep 2011; Michał Górny <mgorny@gentoo.org> bioruby-9999.ebuild: + Migrate to git-2. + + 21 Sep 2009; Markus Meier <maekke@gentoo.org> bioruby-1.3.1.ebuild: + amd64/x86 stable, bug #285626 + +*bioruby-9999 (19 Sep 2009) +*bioruby-1.3.1 (19 Sep 2009) + + 19 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> -bioruby-1.0.0.ebuild, + +bioruby-1.3.1.ebuild, +bioruby-9999.ebuild: + Version bumps, remove old, and add test stage + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*bioruby-1.3.0 (04 Mar 2009) + + 04 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> +bioruby-1.3.0.ebuild: + Version bump. + +*bioruby-1.1.0 (16 Sep 2007) + + 16 Sep 2007; Markus Dittrich <markusle@gentoo.org> +bioruby-1.1.0.ebuild: + Version bump. Fixes bug #191863. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> -bioruby-0.6.2.ebuild, + -bioruby-0.6.4.ebuild, -bioruby-0.7.1.ebuild, bioruby-1.0.0.ebuild: + Added to x86. Pruned old versions. + +*bioruby-1.0.0 (13 Sep 2006) + + 13 Sep 2006; Olivier Fisette <ribosome@gentoo.org> +bioruby-1.0.0.ebuild: + New upstream version. + +*bioruby-0.7.1 (21 Jan 2006) + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> +bioruby-0.7.1.ebuild: + New version. + +*bioruby-0.6.4 (18 Oct 2005) + + 18 Oct 2005; Olivier Fisette <ribosome@gentoo.org> +bioruby-0.6.4.ebuild: + New version. + + 30 Aug 2005; Olivier Fisette <ribosome@gentoo.org> bioruby-0.6.2.ebuild: + Added to x86. + + 20 Jun 2005; David Holm <dholm@gentoo.org> bioruby-0.6.2.ebuild: + Added to ~ppc. + +*bioruby-0.6.2 (20 Jun 2005) + + 20 Jun 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +bioruby-0.6.2.ebuild: + Initial import. diff --git a/sci-biology/biosql/ChangeLog b/sci-biology/biosql/ChangeLog new file mode 100644 index 00000000..1b350cd4 --- /dev/null +++ b/sci-biology/biosql/ChangeLog @@ -0,0 +1,22 @@ +# ChangeLog for sci-biology/biosql +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biosql/ChangeLog,v 1.5 2013/03/11 14:52:40 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 02 Jun 2009; Christian Faulhammer <fauli@gentoo.org> biosql-1.0.1.ebuild: + stable x86, bug 270587 + + 29 May 2009; Steve Dibb <beandog@gentoo.org> biosql-1.0.1.ebuild: + amd64 stable, bug 270587 + + 16 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> biosql-1.0.1.ebuild: + Fix typo + +*biosql-1.0.1 (16 Mar 2009) + + 16 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +biosql-1.0.1.ebuild: + New package, dependency for sci-biology/bioperl. Ebuild written by me. + diff --git a/sci-biology/blat/ChangeLog b/sci-biology/blat/ChangeLog new file mode 100644 index 00000000..c696b404 --- /dev/null +++ b/sci-biology/blat/ChangeLog @@ -0,0 +1,24 @@ +# ChangeLog for sci-biology/blat +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/blat/ChangeLog,v 1.5 2013/03/11 14:53:02 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 04 Aug 2011; Fabian Groffen <grobian@gentoo.org> blat-34-r1.ebuild: + Marked ~x64-macos, bug #375521 + +*blat-34-r1 (20 Jun 2011) + + 20 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/34-gentoo.patch, + +blat-34-r1.ebuild: + Respect LDFLAGS, #337438 + + 22 Mar 2009; Markus Meier <maekke@gentoo.org> blat-34.ebuild: + amd64/x86 stable, bug #263045 + +*blat-34 (23 May 2008) + + 23 May 2008; weaver <weaver@gentoo.org> +blat-34.ebuild: + Initial commit. New package from sunrise, bug 135307 + diff --git a/sci-biology/blossoc/ChangeLog b/sci-biology/blossoc/ChangeLog new file mode 100644 index 00000000..5ccccd69 --- /dev/null +++ b/sci-biology/blossoc/ChangeLog @@ -0,0 +1,21 @@ +# ChangeLog for sci-biology/blossoc +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/blossoc/ChangeLog,v 1.5 2013/03/11 14:53:22 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 20 Jun 2010; Kacper Kowalik <xarthisius@gentoo.org> blossoc-1.4.0.ebuild, + +files/blossoc-1.4.0-gcc43.patch: + Fixing build with gcc-4.3. Thanks Sebastian Luther + <SebastianLuther@gmx.de> for report and patch + + 25 May 2009; Markus Meier <maekke@gentoo.org> blossoc-1.4.0.ebuild: + amd64/x86 stable, bug #269969 + + 24 May 2009; Andrey Kislyuk <weaver@gentoo.org> blossoc-1.4.0.ebuild: + Disabled one of the tests per bug 269969 + + 07 Feb 2009; weaver <weaver@gentoo.org> ChangeLog: + New package, ebuild written by me + diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog new file mode 100644 index 00000000..f48c1662 --- /dev/null +++ b/sci-biology/bowtie/ChangeLog @@ -0,0 +1,90 @@ +# ChangeLog for sci-biology/bowtie +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/ChangeLog,v 1.20 2013/09/18 06:50:27 jlec Exp $ + + 18 Sep 2013; Justin Lecher <jlec@gentoo.org> bowtie-1.0.0.ebuild: + Fix location of html files, #484620 + + 11 Aug 2013; Justin Lecher <jlec@gentoo.org> -bowtie-0.12.3.ebuild, + -bowtie-0.12.5.ebuild, -bowtie-0.12.7.ebuild: + Drop old + + 27 Jul 2013; Agostino Sarubbo <ago@gentoo.org> bowtie-0.12.8.ebuild: + Stable for x86, wrt bug #477134 + + 21 Jul 2013; Agostino Sarubbo <ago@gentoo.org> bowtie-0.12.8.ebuild: + Stable for amd64, wrt bug #477134 + +*bowtie-1.0.0 (17 Jul 2013) + + 17 Jul 2013; Justin Lecher <jlec@gentoo.org> +bowtie-1.0.0.ebuild: + Version Bump + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*bowtie-0.12.8 (19 Jun 2012) + + 19 Jun 2012; Justin Lecher <jlec@gentoo.org> +bowtie-0.12.8.ebuild, + +files/bowtie-0.12.8-gcc-47.patch: + Version Bump, Fix compilation with gcc-4.7, #421919 + +*bowtie-0.12.7 (06 Mar 2011) + + 06 Mar 2011; Justin Lecher <jlec@gentoo.org> -bowtie-0.10.1.ebuild, + +bowtie-0.12.7.ebuild: + Version Bump, respect *FLAGS, #337426 & #354927 + + 30 Sep 2010; Fabian Groffen <grobian@gentoo.org> bowtie-0.12.5.ebuild: + Marked ~x64-macos, bug #339187 + + 16 Jul 2010; Markos Chandras <hwoarang@gentoo.org> bowtie-0.12.3.ebuild: + Stable on amd64 wrt bug #328413 + + 16 Jul 2010; Christian Faulhammer <fauli@gentoo.org> bowtie-0.12.3.ebuild: + stable x86, bug 328413 + +*bowtie-0.12.5 (15 Jul 2010) + + 15 Jul 2010; Andrey Kislyuk <weaver@gentoo.org> +bowtie-0.12.5.ebuild: + Version bump + +*bowtie-0.12.3 (23 Mar 2010) + + 23 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> -bowtie-0.9.9.2.ebuild, + -bowtie-0.10.0.ebuild, +bowtie-0.12.3.ebuild: + Version bump, drop old versions + + 22 Sep 2009; Markus Meier <maekke@gentoo.org> bowtie-0.10.1.ebuild: + x86 stable, bug #282110 + + 06 Sep 2009; Jeremy Olexa <darkside@gentoo.org> bowtie-0.10.1.ebuild: + amd64 stable, bug 282110 + +*bowtie-0.10.1 (27 Jul 2009) + + 27 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +bowtie-0.10.1.ebuild: + Version bump + +*bowtie-0.10.0 (21 Jun 2009) + + 21 Jun 2009; Andrey Kislyuk <weaver@gentoo.org> -bowtie-0.9.9.1.ebuild, + +bowtie-0.10.0.ebuild: + Version bump + +*bowtie-0.9.9.2 (02 May 2009) + + 02 May 2009; Andrey Kislyuk <weaver@gentoo.org> +bowtie-0.9.9.2.ebuild: + Version bump + + 23 Apr 2009; Markus Meier <maekke@gentoo.org> bowtie-0.9.9.1: + amd64/x86 stable, bug #266869 + +*bowtie-0.9.9.1 (15 Mar 2009) + + 15 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +bowtie-0.9.9.1.ebuild: + Import from Science overlay + + 27 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: + New package sci-biology/bowtie, ebuild written by me diff --git a/sci-biology/bwa/ChangeLog b/sci-biology/bwa/ChangeLog new file mode 100644 index 00000000..17f8a489 --- /dev/null +++ b/sci-biology/bwa/ChangeLog @@ -0,0 +1,85 @@ +# ChangeLog for sci-biology/bwa +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bwa/ChangeLog,v 1.19 2015/04/20 20:21:41 jlec Exp $ + + 20 Apr 2015; Justin Lecher <jlec@gentoo.org> -bwa-0.5.0.ebuild, + -bwa-0.6.2.ebuild: + Drop old + + 19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> bwa-0.7.12.ebuild: + Stable for x86, wrt bug #544944 + + 08 Apr 2015; Agostino Sarubbo <ago@gentoo.org> bwa-0.7.12.ebuild: + Stable for amd64, wrt bug #544944 + + 03 Mar 2015; Justin Lecher <jlec@gentoo.org> -bwa-0.5.0-r1.ebuild, + -bwa-0.5.9.ebuild, -bwa-0.6.1.ebuild: + Drop old + +*bwa-0.7.12 (03 Mar 2015) + + 03 Mar 2015; Justin Lecher <jlec@gentoo.org> +bwa-0.7.12.ebuild, + +files/bwa-0.7.12-Makefile.patch: + Version Bump; thanks Ted Tanberry + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*bwa-0.6.2 (21 Jan 2013) + + 21 Jan 2013; Andrey Kislyuk <weaver@gentoo.org> +bwa-0.6.2.ebuild: + Version bump + +*bwa-0.6.1 (30 Nov 2011) + + 30 Nov 2011; Andrey Kislyuk <weaver@gentoo.org> -bwa-0.5.8a.ebuild, + +bwa-0.6.1.ebuild: + Version bump + +*bwa-0.5.9 (01 May 2011) + + 01 May 2011; Justin Lecher <jlec@gentoo.org> +bwa-0.5.9.ebuild: + Version Bump, #354925 + +*bwa-0.5.8a (09 Oct 2010) + + 09 Oct 2010; Andrey Kislyuk <weaver@gentoo.org> +bwa-0.5.8a.ebuild: + Version bump + +*bwa-0.5.0-r1 (07 Sep 2010) + + 07 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org> -bwa-0.4.6.ebuild, + +bwa-0.5.0-r1.ebuild: + Respect LDFLAGS wrt bug 336348. Thanks to Diego for the report. Add proper + pthread support, drop empty DEPENDs. Drop old. + + 23 May 2010; Pacho Ramos <pacho@gentoo.org> bwa-0.5.0.ebuild: + stable amd64, bug 314907 + + 26 Apr 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org> bwa-0.5.0.ebuild: + x86 stable wrt bug #314907 + +*bwa-0.5.0 (28 Oct 2009) + + 28 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +bwa-0.5.0.ebuild: + Version bump + + 12 Jun 2009; Christian Faulhammer <fauli@gentoo.org> bwa-0.4.6.ebuild: + respect CFLAGS, thus removing the hard 64bit build and other niceties + upstream hard forces on users, see bug 273065 by flameeyes; restore ~x86 + KEYWORD + + 07 Jun 2009; Diego E. Pettenò <flameeyes@gentoo.org> bwa-0.4.6.ebuild: + Remove ~x86 keyword, see bug #273065. + +*bwa-0.4.6 (20 Apr 2009) + + 20 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> -bwa-0.4.5.ebuild, + +bwa-0.4.6.ebuild: + Version bump + +*bwa-0.4.5 (26 Feb 2009) + + 26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +bwa-0.4.5.ebuild: + New package, ebuild written by me. diff --git a/sci-biology/cd-hit/ChangeLog b/sci-biology/cd-hit/ChangeLog new file mode 100644 index 00000000..90f4c75d --- /dev/null +++ b/sci-biology/cd-hit/ChangeLog @@ -0,0 +1,23 @@ +# ChangeLog for sci-biology/cd-hit +# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/ChangeLog,v 1.3 2012/06/20 18:39:24 jlec Exp $ + +*cd-hit-4.6 (20 Jun 2012) + + 20 Jun 2012; Justin Lecher <jlec@gentoo.org> +files/4.6-gentoo.patch, + cd-hit-4.5.1.ebuild, cd-hit-4.5.4.ebuild, +cd-hit-4.6.ebuild, metadata.xml: + Version Bump, which fixes compilation problems with gcc 4.7, #422569; add + missing eutils.eclass + +*cd-hit-4.5.4 (12 May 2011) + + 12 May 2011; Justin Lecher <jlec@gentoo.org> +files/4.5.4-gentoo.patch, + cd-hit-4.5.1.ebuild, +cd-hit-4.5.4.ebuild: + Version Bump, thanks for the notification by Martin Mokrejs + +*cd-hit-4.5.1 (01 Feb 2011) + + 01 Feb 2011; Justin Lecher <jlec@gentoo.org> +files/4.5.1-gentoo.patch, + +cd-hit-4.5.1.ebuild, +metadata.xml: + New addition, written by me + diff --git a/sci-biology/clustal-omega/ChangeLog b/sci-biology/clustal-omega/ChangeLog new file mode 100644 index 00000000..b2a8a32a --- /dev/null +++ b/sci-biology/clustal-omega/ChangeLog @@ -0,0 +1,28 @@ +# ChangeLog for sci-biology/clustal-omega +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustal-omega/ChangeLog,v 1.6 2015/04/07 14:32:30 jlec Exp $ + +*clustal-omega-1.2.1 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> +clustal-omega-1.2.1.ebuild, + -clustal-omega-1.0.3.ebuild, -clustal-omega-1.1.0.ebuild: + Version Bump; drop old + +*clustal-omega-1.2.0 (06 Jan 2014) + + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> +clustal-omega-1.2.0.ebuild: + Version Bump + +*clustal-omega-1.1.0 (26 Apr 2013) + + 26 Apr 2013; Justin Lecher <jlec@gentoo.org> +clustal-omega-1.1.0.ebuild: + Version Bump + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*clustal-omega-1.0.3 (25 Sep 2011) + + 25 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> + +clustal-omega-1.0.3.ebuild, +metadata.xml: + New package, ebuild written by me diff --git a/sci-biology/clustalw-mpi/ChangeLog b/sci-biology/clustalw-mpi/ChangeLog new file mode 100644 index 00000000..0737af62 --- /dev/null +++ b/sci-biology/clustalw-mpi/ChangeLog @@ -0,0 +1,34 @@ +# ChangeLog for sci-biology/clustalw-mpi +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw-mpi/ChangeLog,v 1.7 2011/06/19 10:00:09 jlec Exp $ + +*clustalw-mpi-0.13-r1 (19 Jun 2011) + + 19 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/0.13-gentoo.patch, + -clustalw-mpi-0.13.ebuild, +clustalw-mpi-0.13-r1.ebuild: + Respect LDFLAGS, #335232 + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml: + Add USE flag description to metadata wrt GLEP 56. + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + clustalw-mpi-0.13.ebuild: + Fixed description and home page. + + 04 Jan 2006; Olivier Fisette <ribosome@gentoo.org> + clustalw-mpi-0.13.ebuild: + Do not depend on "virtual/libc" (package not in system target). + +*clustalw-mpi-0.13 (19 Nov 2005) + + 19 Nov 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +clustalw-mpi-0.13.ebuild: + Initial import. Original ebuild submitted by Brady Catherman + <bradyc@uidaho.edu> (bug #112769). + diff --git a/sci-biology/clustalw/ChangeLog b/sci-biology/clustalw/ChangeLog new file mode 100644 index 00000000..66569bf8 --- /dev/null +++ b/sci-biology/clustalw/ChangeLog @@ -0,0 +1,171 @@ +# ChangeLog for sci-biology/clustalw +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/ChangeLog,v 1.37 2014/01/27 07:23:44 jlec Exp $ + + 27 Jan 2014; Justin Lecher <jlec@gentoo.org> -clustalw-1.83-r2.ebuild: + Drop old + + 26 Jan 2014; Agostino Sarubbo <ago@gentoo.org> clustalw-1.83-r3.ebuild: + Stable for sparc, wrt bug #497214 + + 19 Jan 2014; Agostino Sarubbo <ago@gentoo.org> clustalw-1.83-r3.ebuild: + Stable for ppc64, wrt bug #497214 + + 18 Jan 2014; Agostino Sarubbo <ago@gentoo.org> clustalw-1.83-r3.ebuild: + Stable for alpha, wrt bug #497214 + + 14 Jan 2014; Agostino Sarubbo <ago@gentoo.org> clustalw-1.83-r3.ebuild: + Stable for ppc, wrt bug #497214 + + 14 Jan 2014; Agostino Sarubbo <ago@gentoo.org> clustalw-1.83-r3.ebuild: + Stable for x86, wrt bug #497214 + + 12 Jan 2014; Pacho Ramos <pacho@gentoo.org> clustalw-1.83-r3.ebuild: + amd64 stable, bug #497214 + + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> +clustalw-1.83-r2.ebuild, + +clustalw-1.83-r3.ebuild: + Readd SLOT=1 ebuild; punt base.eclass usage; bump to EAPI=5 + + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -clustalw-1.83-r2.ebuild, + -clustalw-1.83-r3.ebuild, -clustalw-2.0.11.ebuild, -clustalw-2.0.12.ebuild: + Drop old and clean base.eclass usage + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 13 Jun 2012; Johannes Huber <johu@gentoo.org> clustalw-2.1.ebuild: + Stable for x86, wrt bug #416891 + + 04 Jun 2012; Agostino Sarubbo <ago@gentoo.org> clustalw-2.1.ebuild: + Stable for amd64, wrt bug #416891 + +*clustalw-2.1 (22 Apr 2012) + + 22 Apr 2012; Kacper Kowalik <xarthisius@gentoo.org> +clustalw-2.1.ebuild: + Version bump + + 02 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + clustalw-1.83-r3.ebuild: + Transfer Prefix keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + clustalw-2.0.12.ebuild: + Transfer Prefix keywords + +*clustalw-2.0.12 (18 Oct 2009) + + 18 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +clustalw-2.0.12.ebuild: + Version bump + + 22 Sep 2009; Markus Meier <maekke@gentoo.org> clustalw-2.0.11.ebuild: + x86 stable, bug #282109 + + 06 Sep 2009; Jeremy Olexa <darkside@gentoo.org> clustalw-2.0.11.ebuild: + amd64 stable, bug 282109 + + 18 Aug 2009; Andrey Kislyuk <weaver@gentoo.org> clustalw-1.83-r2.ebuild: + Fix Manifest + + 18 Aug 2009; Andrey Kislyuk <weaver@gentoo.org> +clustalw-1.83-r2.ebuild: + Avoid dropping stable keywords until stablereqs are done + +*clustalw-1.83-r3 (18 Aug 2009) + + 18 Aug 2009; Andrey Kislyuk <weaver@gentoo.org> + +files/1.83-as-needed.patch, -clustalw-1.83-r2.ebuild, + +clustalw-1.83-r3.ebuild: + Fix bug 281734, thanks to Justin Lecher (jlec) + +*clustalw-2.0.11 (28 Apr 2009) + + 28 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> -clustalw-2.0.9.ebuild, + +clustalw-2.0.11.ebuild: + Version bump, remove old, assume maintainership + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 09 Sep 2008; Markus Dittrich <markusle@gentoo.org> clustalw-2.0.9.ebuild: + Keyworded amd64 since it works just fine. + +*clustalw-2.0.9 (28 Aug 2008) + + 28 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +clustalw-2.0.9.ebuild: + New upstream major version (complete rewrite, removing keywords). Slotted + to cohexist with version 1.x. + +*clustalw-1.83-r2 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -clustalw-1.83-r1.ebuild, +clustalw-1.83-r2.ebuild: + Forcing bump to start using slots as ClustalW 2 should coexist with 1.83. + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> clustalw-1.83-r1.ebuild: + Dropped ppc-macos, see you in prefix. + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Taking over maintainership. + + 04 Jan 2006; Olivier Fisette <ribosome@gentoo.org> + clustalw-1.83-r1.ebuild: + Do not depend on "virtual/libc" (package not in system target). + + 11 Oct 2005; Luis Medinas <metalgod@gentoo.org> clustalw-1.83-r1.ebuild: + Marked Stable on amd64. + + 19 Jun 2005; Markus Rothe <corsair@gentoo.org> clustalw-1.83-r1.ebuild: + Stable on ppc64 + + 02 May 2005; Omkhar Arasaratnam <omkhar@gentoo.org> + clustalw-1.83-r1.ebuild: + Added ~ppc64 + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> + clustalw-1.83-r1.ebuild: + Ebuild cleanup. + + 14 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> clustalw-1.83-r1.ebuild: + Stable ppc-macos. + + 02 Jan 2005; Olivier Fisette <ribosome@gentoo.org> + clustalw-1.83-r1.ebuild: + Use the toolchain-funcs rather than the gcc eclass. + +*clustalw-1.83-r1 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +clustalw-1.83-r1.ebuild: + Moved from app-sci/clustalw to sci-biology/clustalw. + + 21 Nov 2004; Karol Wojtaszek <sekretarz@gentoo.org> + clustalw-1.83-r1.ebuild: + Added to ~amd64, bug #71865 + + 14 Oct 2004; Olivier Fisette <ribosome@gentoo.org> clustalw-1.83-r1.ebuild: + Fixed gcc with gcc.eclass. gongloo left some mistakes. + + 14 Oct 2004; Hasan Khalil <gongloo@gentoo.org> clustalw-1.83-r1.ebuild: + Fixed gcc with gcc.eclass. Keyworded ~ppc-macos. + + 05 Oct 2004; Olivier Fisette <ribosome@gentoo.org> clustalw-1.83-r1.ebuild: + Fixed overly verbose description. + +*clustalw-1.83-r1 (29 Sep 2004) + + 29 Sep 2004; Olivier Fisette <ribosome@gentoo.org> +clustalw-1.83-r1.ebuild, + -clustalw-1.83.ebuild: + Fixed bugs pertaining to "CFLAGS" and help files. + + 01 Jul 2004; Jeremy Huddleston <eradicator@gentoo.org> clustalw-1.83.ebuild: + virtual/glibc -> virtual/libc + + 19 Apr 2004; Patrick Kursawe <phosphan@gentoo.org> clustalw-1.83.ebuild: + Bumped to stable, using epatch now + +*clustalw-1.83 (04 Apr 2003) + + 04 Apr 2003; Michael Imhof <tantive@gentoo.org> : + Initial release. + This ebuild was submitted by Gontran Zepeda <gontran@gontran.net>. + Should close #18679. diff --git a/sci-biology/clustalx/ChangeLog b/sci-biology/clustalx/ChangeLog new file mode 100644 index 00000000..7d4baba9 --- /dev/null +++ b/sci-biology/clustalx/ChangeLog @@ -0,0 +1,149 @@ +# ChangeLog for sci-biology/clustalx +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalx/ChangeLog,v 1.33 2015/04/20 20:22:12 jlec Exp $ + + 20 Apr 2015; Justin Lecher <jlec@gentoo.org> -clustalx-2.1.ebuild: + Drop old + + 19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> clustalx-2.1-r1.ebuild: + Stable for x86, wrt bug #544936 + + 08 Apr 2015; Agostino Sarubbo <ago@gentoo.org> clustalx-2.1-r1.ebuild: + Stable for amd64, wrt bug #544936 + +*clustalx-2.1-r1 (06 Jan 2014) + + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> +clustalx-2.1-r1.ebuild: + Make sure only system libs are used + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> -clustalx-1.83-r2.ebuild, + metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly; + drop old ebuild because of missing deps + + 02 Mar 2013; Markos Chandras <hwoarang@gentoo.org> clustalx-2.1.ebuild: + Move Qt dependencies to the new category + + 24 Oct 2012; Ulrich Müller <ulm@gentoo.org> clustalx-1.83-r2.ebuild: + Update dependency after package move from x11-libs/openmotif to + x11-libs/motif. + + 13 Jun 2012; Justin Lecher <jlec@gentoo.org> clustalx-1.83-r2.ebuild: + Cleaned old + + 13 Jun 2012; Johannes Huber <johu@gentoo.org> -clustalx-2.0.11.ebuild: + Remove old wrt bug #311481. + + 13 Jun 2012; Johannes Huber <johu@gentoo.org> clustalx-2.1.ebuild: + Stable for x86, wrt bug #416891 + + 04 Jun 2012; Agostino Sarubbo <ago@gentoo.org> clustalx-2.1.ebuild: + Stable for amd64, wrt bug #416891 + +*clustalx-2.1 (22 Apr 2012) + + 22 Apr 2012; Kacper Kowalik <xarthisius@gentoo.org> +clustalx-2.1.ebuild: + Version bump wrt #410163 by Michael (kensington) <gentoo@scribeofthenile.com> + + 10 Oct 2010; Ulrich Mueller <ulm@gentoo.org> clustalx-1.83-r2.ebuild: + Fix openmotif dependency. + + 31 Oct 2009; Markus Meier <maekke@gentoo.org> clustalx-2.0.11.ebuild: + amd64/x86 stable, bug #290938 + +*clustalx-2.0.11 (28 Apr 2009) + + 28 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> + -files/clustalx-2.0.9-gcc4.3.patch, metadata.xml, -clustalx-2.0.9.ebuild, + +clustalx-2.0.11.ebuild: + Version bump, fix bug 261278, remove old, assume maintainership + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 09 Sep 2008; Markus Dittrich <markusle@gentoo.org> + +files/clustalx-2.0.9-gcc4.3.patch, clustalx-2.0.9.ebuild: + Added patch to fix gcc-4.3 header issue (bug #237077). Relaxed + dependency on full qt:4 to qt-gui:4 only which should be + sufficient. Finally, keyworded the 2.0.9 ebuild amd64 since it + works fine. + +*clustalx-2.0.9 (28 Aug 2008) + + 28 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +clustalx-2.0.9.ebuild: + New upstream version (complete rewrite based on Qt). + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + clustalx-1.83-r2.ebuild: + Depend on ClustalW 1.x as ClustalX 2.x will soon enter Portage. + + 26 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + clustalx-1.83-r2.ebuild: + Added missing libXpm dependency. Fixes bug #233046. + + 27 Jun 2008; Ulrich Mueller <ulm@gentoo.org> clustalx-1.83-r2.ebuild: + Change dependency from virtual/motif to x11-libs/openmotif, bug 224749. + + 24 Oct 2006; Jeff Gardner <je_fro@gentoo.org> clustalx-1.83-r2.ebuild: + Keywording ~sparc + + 01 Feb 2006; Donnie Berkholz <spyderous@gentoo.org>; + clustalx-1.83-r2.ebuild: + Fix deps for modular X. + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> + -clustalx-1.83-r1.ebuild: + Removed obsolete version. + + 23 Dec 2005; Simon Stelling <blubb@gentoo.org> clustalx-1.83-r2.ebuild: + stable on amd64 + + 15 Dec 2005; Joshua Jackson <tsunam@gentoo.org> clustalx-1.83-r2.ebuild: + Stable on x86 for bug #115442 + +*clustalx-1.83-r2 (13 Nov 2005) + + 13 Nov 2005; Olivier Fisette <ribosome@gentoo.org> + +clustalx-1.83-r2.ebuild: + Added check for X support in the NCBI toolkit, as suggested by Brady + Catherman <bradyc@uidaho.edu> (fixes bug #112336). + + 02 Jun 2005; Olivier Fisette <ribosome@gentoo.org> + clustalx-1.83-r1.ebuild: + Use "virtual/motif" instead of "x11-libs/openmotif". + +*clustalx-1.83-r1 (16 Feb 2005) + + 16 Feb 2005; Olivier Fisette <ribosome@gentoo.org> + +clustalx-1.83-r1.ebuild, -clustalx-1.83.ebuild: + Fixes bug #82211: ClustalX is incompatible with OpenMotif 2.2. + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> clustalx-1.83.ebuild: + Ebuild cleanup. + + 18 Jan 2005; Olivier Fisette <ribosome@gentoo.org> clustalx-1.83.ebuild: + Added to x86. + +*clustalx-1.83 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +clustalx-1.83.ebuild: + Moved from app-sci/clustalx to sci-biology/clustalx. + + 22 Nov 2004; Karol Wojtaszek <sekretarz@gentoo.org> clustalx-1.83.ebuild: + Added to ~amd64, bug #72084 + + 18 Nov 2004; Michael Sterrett <mr_bones_@gentoo.org> clustalx-1.83.ebuild: + needs stable app-sci/ncbi-tools first + + 17 Nov 2004; Olivier Fisette <ribosome@gentoo.org> clustalx-1.83.ebuild: + Added to x86. Use toolchain-funcs rather than the gcc eclass. + + 14 Oct 2004; Olivier Fisette <ribosome@gentoo.org> clustalx-1.83.ebuild: + Use gcc.eclass rather than ${CC}. + +*clustalx-1.83 (06 Oct 2004) + + 06 Oct 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +clustalx-1.83.ebuild: + Initial import. diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog new file mode 100644 index 00000000..b6e3c6c1 --- /dev/null +++ b/sci-biology/consed/ChangeLog @@ -0,0 +1,44 @@ +# ChangeLog for sci-biology/consed +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.8 2014/10/26 16:13:23 jlec Exp $ + +*consed-27 (26 Oct 2014) + + 26 Oct 2014; Justin Lecher <jlec@gentoo.org> -consed-19-r1.ebuild, + +consed-27.ebuild: + Import to tree; drop old EPAI=1 version, #526742 + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 17 Feb 2013; Justin Lecher <jlec@gentoo.org> consed-19-r2.ebuild, + metadata.xml: + Quote EPREFIX, thanks Martin Mokrejš for the patch + + 24 Oct 2012; Ulrich Müller <ulm@gentoo.org> consed-19-r1.ebuild, + consed-19-r2.ebuild: + Update dependency after package move from x11-libs/openmotif to + x11-libs/motif. + + 10 Oct 2010; Ulrich Mueller <ulm@gentoo.org> consed-19-r1.ebuild, + consed-19-r2.ebuild: + Fix openmotif dependency. + +*consed-19-r2 (22 May 2010) + + 22 May 2010; Justin Lecher <jlec@gentoo.org> consed-19-r1.ebuild, + +consed-19-r2.ebuild: + removed PHRED_PARAMETER_FILE env, #253451, some QA + +*consed-19-r1 (15 Mar 2009) + + 15 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> -consed-19.ebuild, + +consed-19-r1.ebuild: + Revision bump fixes several issues in installation of supplementary files + +*consed-19 (18 Feb 2009) + + 18 Feb 2009; weaver <weaver@gentoo.org> +metadata.xml, +consed-19.ebuild: + New package sci-biology/consed, bug 253451. Ebuild written by Martin Mokrejs + <mmokrejs@ribosome.natur.cuni.cz> and me. + diff --git a/sci-biology/cufflinks/ChangeLog b/sci-biology/cufflinks/ChangeLog new file mode 100644 index 00000000..281a6b27 --- /dev/null +++ b/sci-biology/cufflinks/ChangeLog @@ -0,0 +1,50 @@ +# ChangeLog for sci-biology/cufflinks +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/cufflinks/ChangeLog,v 1.12 2015/04/07 14:32:37 jlec Exp $ + + 17 Feb 2015; Justin Lecher <jlec@gentoo.org> cufflinks-2.2.1-r1.ebuild: + Drop missing patch + + 08 Jan 2015; Justin Lecher <jlec@gentoo.org> cufflinks-1.3.0-r1.ebuild, + cufflinks-2.2.1.ebuild, cufflinks-2.2.1-r1.ebuild: + Add upper limit for boost dep as forced by upstream, #535716 + +*cufflinks-2.2.1-r1 (02 Oct 2014) + + 02 Oct 2014; Justin Lecher <jlec@gentoo.org> +cufflinks-2.2.1-r1.ebuild, + +files/cufflinks-2.2.1-flags.patch, +files/cufflinks-2.2.1-hts.patch: + Drop debugging flags, fix compatibility with newer samtools, #524252 + +*cufflinks-2.2.1 (25 Sep 2014) + + 25 Sep 2014; Justin Lecher <jlec@gentoo.org> +cufflinks-2.2.1.ebuild: + Version Bump + + 25 Sep 2014; Justin Lecher <jlec@gentoo.org> cufflinks-1.3.0-r1.ebuild: + Fix dep due to uncompatible samtools release + +*cufflinks-1.3.0-r1 (05 Feb 2014) + + 05 Feb 2014; Sergey Popov <pinkbyte@gentoo.org> -cufflinks-1.3.0.ebuild, + +cufflinks-1.3.0-r1.ebuild, files/cufflinks-1.3.0-autotools.patch: + Revision bump: EAPI 5, add subslot to Boost dependency, fix compatibility + with Automake 1.14, wrt bug #499046. Drop old revision + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 10 Nov 2012; Justin Lecher <jlec@gentoo.org> cufflinks-1.3.0.ebuild, + +files/cufflinks-1.3.0-autotools.patch, +files/cufflinks-1.3.0-boost.patch, + +files/cufflinks-1.3.0-gcc-4.7.patch: + Drop hard version dep for boost, #440630, and fix compatibility with version + 1.5*; Fix gcc-4.7 problems; Fix underlinking problem + + 31 Oct 2012; Diego E. Pettenò <flameeyes@gentoo.org> cufflinks-1.3.0.ebuild: + Avoid using a slot depend since now boost is unslotted; remove pointless + filter-ldflags for --as-needed. + +*cufflinks-1.3.0 (05 Feb 2012) + + 05 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> +cufflinks-1.3.0.ebuild, + +metadata.xml: + New package, ebuild written by me diff --git a/sci-biology/cutg/ChangeLog b/sci-biology/cutg/ChangeLog new file mode 100644 index 00000000..63ffdea5 --- /dev/null +++ b/sci-biology/cutg/ChangeLog @@ -0,0 +1,255 @@ +# ChangeLog for sci-biology/cutg +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/ChangeLog,v 1.62 2015/03/29 09:35:00 jlec Exp $ + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> -cutg-151.ebuild, + -cutg-160.ebuild: + Drop old + + 28 Mar 2015; Agostino Sarubbo <ago@gentoo.org> cutg-160-r1.ebuild: + Stable for ppc, wrt bug #542246 + + 25 Mar 2015; Agostino Sarubbo <ago@gentoo.org> cutg-160-r1.ebuild: + Stable for x86, wrt bug #542246 + + 09 Mar 2015; Agostino Sarubbo <ago@gentoo.org> cutg-160-r1.ebuild: + Stable for amd64, wrt bug #542246 + + 07 Mar 2015; Justin Lecher <jlec@gentoo.org> cutg-160-r1.ebuild: + Fix broken doc installations, #542348 + +*cutg-160-r1 (05 Mar 2015) + + 05 Mar 2015; Justin Lecher <jlec@gentoo.org> +cutg-160-r1.ebuild, + metadata.xml: + Bump to EAPI=5 and host tarball instead of just mirror it + + 09 Aug 2011; Kacper Kowalik <xarthisius@gentoo.org> cutg-151.ebuild, + cutg-160.ebuild: + ppc64 keyword dropped + + 06 Apr 2011; Justin Lecher <jlec@gentoo.org> cutg-151.ebuild, + cutg-160.ebuild: + Removed checks for DB only packages + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> cutg-151.ebuild, + cutg-160.ebuild: + Drop sparc keywords + + 07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> cutg-160.ebuild: + Moved to EAPI=3 for PREFIX support, imported prefix patches from overlay, + keyworded as in overlay + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 31 Aug 2009; Olivier Fisette <ribosome@gentoo.org> cutg-160.ebuild: + Stabilised on x86 and amd64. + +*cutg-160 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +cutg-160.ebuild: + New upstream version. + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> -cutg-150.ebuild: + Pruned old version. + + 20 Nov 2006; <blubb@gentoo.org> cutg-151.ebuild: + stable on amd64 + + 15 Nov 2006; Markus Rothe <corsair@gentoo.org> cutg-151.ebuild: + Stable on ppc64; bug #153766 + + 03 Nov 2006; nixnut <nixnut@gentoo.org> cutg-151.ebuild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> -cutg-148.ebuild, + -cutg-149.ebuild: + Pruned old versions. + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> cutg-148.ebuild, + cutg-149.ebuild, cutg-150.ebuild, cutg-151.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> cutg-151.ebuild: + Added to x86. + + 18 Aug 2006; Jason Wever <weeve@gentoo.org> cutg-151.ebuild: + Added ~sparc keyword wrt bug #144241. + +*cutg-151 (26 Jun 2006) + + 26 Jun 2006; Olivier Fisette <ribosome@gentoo.org> +cutg-151.ebuild: + New version. + + 08 Apr 2006; Simon Stelling <blubb@gentoo.org> cutg-150.ebuild: + stable on amd64 + + 22 Feb 2006; Fabian Groffen <grobian@gentoo.org> cutg-150.ebuild: + Marked ppc-macos stable (bug #123333) + + 22 Feb 2006; <nixnut@gentoo.org> cutg-150.ebuild: + Stable on ppc. bug 123333 + + 21 Feb 2006; Markus Rothe <corsair@gentoo.org> cutg-150.ebuild: + Stable on ppc64; bug #123333 + + 20 Feb 2006; Joshua Jackson <tsunam@gentoo.org> cutg-150.ebuild: + Stable on x86; bug #123333 + + 24 Dec 2005; Simon Stelling <blubb@gentoo.org> cutg-149.ebuild: + stable on amd64 + + 23 Dec 2005; Tobias Scherbaum <dertobi123@gentoo.org> cutg-149.ebuild: + Marked ppc stable, #115446 + + 13 Dec 2005; Markus Rothe <corsair@gentoo.org> cutg-149.ebuild: + Stable on ppc64; bug #115446 + +*cutg-150 (13 Dec 2005) + + 13 Dec 2005; Olivier Fisette <ribosome@gentoo.org> cutg-149.ebuild, + +cutg-150.ebuild: + Added 149 to x86. New version. + + 19 Nov 2005; Simon Stelling <blubb@gentoo.org> cutg-148.ebuild: + stable on amd64 + +*cutg-149 (18 Oct 2005) + + 18 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -cutg-147-r1.ebuild, + +cutg-149.ebuild: + New version. Pruned old version. + + 08 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> cutg-148.ebuild: + Stable on ppc. + + 08 Oct 2005; Lina Pezzella <j4rg0n@gentoo.org> cutg-148.ebuild: + Stable ppc-macos, as per Bug 108332 + + 07 Oct 2005; Brent Baude <ranger@gentoo.org> cutg-148.ebuild: + Marking cutg-148 stable ppc64 for bug 108332 + + 07 Oct 2005; Olivier Fisette <ribosome@gentoo.org> cutg-148.ebuild: + Stable on x86. + + 04 Sep 2005; Simon Stelling <blubb@gentoo.org> cutg-148.ebuild: + added ~amd64 keyword + + 31 Aug 2005; Olivier Fisette <ribosome@gentoo.org> -cutg-146.ebuild: + Removed obsolete versions. + + 29 Aug 2005; Lina Pezzella <j4rg0n@gentoo.org> cutg-147-r1.ebuild: + Stable ppc-macos + + 13 Aug 2005; Michael Hanselmann <hansmi@gentoo.org> cutg-147-r1.ebuild: + Stable on ppc. + + 09 Aug 2005; Markus Rothe <corsair@gentoo.org> cutg-147-r1.ebuild: + Stable on ppc64 + +*cutg-148 (06 Aug 2005) + + 06 Aug 2005; Olivier Fisette <ribosome@gentoo.org> -cutg-145.ebuild, + -cutg-147.ebuild, cutg-147-r1.ebuild, +cutg-148.ebuild: + New version: 148. Added 147-r1 to x86. Removed old versions. + + 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> cutg-146.ebuild: + Stable ppc-macos + +*cutg-147-r1 (25 Jun 2005) + + 25 Jun 2005; Olivier Fisette <ribosome@gentoo.org> +cutg-147-r1.ebuild: + Trying to fix some ppc-macos bug reported in #96819. + +*cutg-147 (19 Jun 2005) + + 19 Jun 2005; Olivier Fisette <ribosome@gentoo.org> +cutg-147.ebuild: + New version. + + 18 Jun 2005; Olivier Fisette <ribosome@gentoo.org> -cutg-144.ebuild: + Removed obsolete version. + + 18 Jun 2005; Markus Rothe <corsair@gentoo.org> cutg-146.ebuild: + Stable on ppc64 + + 17 Jun 2005; Michael Hanselmann <hansmi@gentoo.org> cutg-146.ebuild: + Stable on ppc. + + 16 Jun 2005; Olivier Fisette <ribosome@gentoo.org> cutg-146.ebuild: + Added to x86. + + 31 May 2005; Lina Pezzella <j4rg0n@gentoo.org> cutg-145.ebuild: + Stable ppc-macos + +*cutg-146 (10 May 2005) + + 10 May 2005; Olivier Fisette <ribosome@gentoo.org> cutg-145.ebuild, + +cutg-146.ebuild: + New version: 146. Added 145 to x86. + + 02 May 2005; Michael Hanselmann <hansmi@gentoo.org> cutg-144.ebuild: + Stable on ppc. + + 05 Mar 2005; Markus Rothe <corsair@gentoo.org> cutg-144.ebuild: + Stable on ppc64 + +*cutg-145 (27 Feb 2005) + + 27 Feb 2005; Olivier Fisette <ribosome@gentoo.org> +cutg-145.ebuild: + New version. + + 22 Feb 2005; Olivier Fisette <ribosome@gentoo.org> -cutg-143.ebuild, + cutg-144.ebuild: + Added support for the "emboss" and "minimal" "USE" flags. + + 02 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> cutg-144.ebuild: + Stable ppc-macos + + 18 Jan 2005; Olivier Fisette <ribosome@gentoo.org> cutg-144.ebuild: + Added to x86. + + 01 Jan 2005; Markus Rothe <corsair@gentoo.org> cutg-144.ebuild: + Added ~ppc64 to KEYWORDS + + 01 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> cutg-144.ebuild: + Unstable ppc-macos. + +*cutg-143 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +cutg-143.ebuild, +cutg-144.ebuild: + Moved from app-sci/cutg to sci-biology/cutg. + +*cutg-144 (23 Nov 2004) + + 23 Nov 2004; Olivier Fisette <ribosome@gentoo.org> +cutg-144.ebuild: + New version. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> -cutg-142.ebuild, + cutg-143.ebuild: + Removed old version. Added 143 to x86. + +*cutg-143 (29 Sep 2004) + + 29 Sep 2004; Olivier Fisette <ribosome@gentoo.org> -cutg-141.0.ebuild, + cutg-142.ebuild, +cutg-143.ebuild: + Added 142 to x86. Added new version 142. Removed old version. + +*cutg-142 (10 Aug 2004) + + 10 Aug 2004; Olivier Fisette <ribosome@gentoo.org> + cutg-141.0.ebuild: + Added to x86. + cutg-142.ebuild: + Updated package. + + 26 Jun 2004; David Holm <dholm@gentoo.org> cutg-141.0.ebuild: + Added to ~ppc. + +*cutg-141.0 (24 Jun 2004) + + 24 Jun 2004; Olivier Fisette <ribosome@gentoo.org> + cutg-141.0.ebuild, metadata.xml : + Initial import. Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>. + Reference: Gentoo Bugzilla, bug #54322 diff --git a/sci-biology/dialign-tx/ChangeLog b/sci-biology/dialign-tx/ChangeLog new file mode 100644 index 00000000..c61581ec --- /dev/null +++ b/sci-biology/dialign-tx/ChangeLog @@ -0,0 +1,73 @@ +# ChangeLog for sci-biology/dialign-tx +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/dialign-tx/ChangeLog,v 1.8 2015/04/20 20:24:44 jlec Exp $ + + 20 Apr 2015; Justin Lecher <jlec@gentoo.org> -dialign-tx-1.0.2.ebuild, + dialign-tx-1.0.2-r1.ebuild: + Drop old + + 19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> dialign-tx-1.0.2-r1.ebuild: + Stable for x86, wrt bug #544948 + + 08 Apr 2015; Agostino Sarubbo <ago@gentoo.org> dialign-tx-1.0.2-r1.ebuild: + Stable for amd64, wrt bug #544948 + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*dialign-tx-1.0.2-r1 (09 Sep 2010) + + 09 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org> + +dialign-tx-1.0.2-r1.ebuild, +files/dialign-tx-1.0.2-implicits.patch: + Respect LDFLAGS wrt bug 336533. Thanks to Diego for the report. Fix + implicit function declarations. + + 09 Feb 2010; Pacho Ramos <pacho@gentoo.org> dialign-tx-1.0.2.ebuild: + amd64 stable, bug 298774 + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> + dialign-tx-1.0.2.ebuild: + stable x86, bug 298774 + +*dialign-tx-1.0.2 (06 Nov 2009) + + 06 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +dialign-tx-1.0.2.ebuild: + Version bump and move to dialign-tx, take ownership + + 17 Feb 2008; Christian Faulhammer <opfer@gentoo.org> + dialign-t-0.2.2.ebuild: + stable amd64, bug 207109 + + 17 Feb 2008; Christian Faulhammer <opfer@gentoo.org> + dialign-t-0.2.2.ebuild: + quote variables + + 17 Feb 2008; Christian Faulhammer <opfer@gentoo.org> + dialign-t-0.2.2.ebuild: + stable x86, bug 207109 + +*dialign-t-0.2.2 (12 Jul 2007) + + 12 Jul 2007; Jeff Gardner <je_fro@gentoo.org> +dialign-t-0.2.2.ebuild: + New version, add amd64. + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 01 Oct 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml: + Remove myself as maintainer so it goes to all of the sci-biology team. + + 09 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; + dialign-t-0.2.1.ebuild: + x86 stable. + + 07 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml: + Update to my new email address. + +*dialign-t-0.2.1 (21 Feb 2006) + + 21 Feb 2006; Donnie Berkholz <dberkholz@gentoo.org>; +metadata.xml, + +dialign-t-0.2.1.ebuild: + New multiple sequence alignment package. Perhaps the most accurate and + fastest local aligner. diff --git a/sci-biology/dialign2/ChangeLog b/sci-biology/dialign2/ChangeLog new file mode 100644 index 00000000..d2cd172e --- /dev/null +++ b/sci-biology/dialign2/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/dialign2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/dialign2/ChangeLog,v 1.1 2015/03/29 14:22:43 jlec Exp $ + +*dialign2-2.2.1 (29 Mar 2015) + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> +dialign2-2.2.1.ebuild, + +metadata.xml: + New addition written by me diff --git a/sci-biology/diya/ChangeLog b/sci-biology/diya/ChangeLog new file mode 100644 index 00000000..f1f7decd --- /dev/null +++ b/sci-biology/diya/ChangeLog @@ -0,0 +1,15 @@ +# ChangeLog for sci-biology/diya +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/diya/ChangeLog,v 1.3 2014/07/15 12:59:44 zlogene Exp $ + + 15 Jul 2014; Mikle Kolyada <zlogene@gentoo.org> diya-1.0_rc4.ebuild: + Bump to EAPI=5 + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*diya-1.0_rc4 (27 Sep 2009) + + 27 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +diya-1.0_rc4.ebuild: + New package, ebuild written by me diff --git a/sci-biology/elph/ChangeLog b/sci-biology/elph/ChangeLog new file mode 100644 index 00000000..ee5cfdf2 --- /dev/null +++ b/sci-biology/elph/ChangeLog @@ -0,0 +1,71 @@ +# ChangeLog for sci-biology/elph +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/elph/ChangeLog,v 1.15 2010/08/09 18:24:26 xarthisius Exp $ + + 09 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org> elph-1.0.1.ebuild: + Respect LDFLAGS wrt bug 331881. Thanks to Diego for report. + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> elph-1.0.1.ebuild: + Transfer Prefix keywords + + 29 Jun 2008; Torsten Veller <tove@gentoo.org> elph-0.1.5.ebuild, + elph-1.0.1.ebuild: + Add missing die: || "..." -> || die "..." + + 07 Feb 2008; Fabian Groffen <grobian@gentoo.org> elph-0.1.5.ebuild, + elph-1.0.1.ebuild: + Dropped ppc-macos keyword, see you in prefix + +*elph-1.0.1 (27 Jan 2008) + + 27 Jan 2008; Markus Dittrich <markusle@gentoo.org> +elph-1.0.1.ebuild: + Version bump (see bug #191864). + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Stepping down from maintainership. + + 18 Oct 2005; Olivier Fisette <ribosome@gentoo.org> elph-0.1.5.ebuild: + Ebuild clean-up. Corrected home page. + + 04 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> elph-0.1.5.ebuild + Stable ppc-macos + + 01 Mar 2005; Olivier Fisette <ribosome@gentoo.org> -elph-0.1.4.ebuild, + elph-0.1.5.ebuild: + Added 0.1.5 to x86. Removed old version. + + 30 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> elph-0.1.5.ebuild: + Unstable ppc-macos + + 27 Jan 2005; Olivier Fisette <ribosome@gentoo.org> elph-0.1.5.ebuild: + Ebuild clean-up. + +*elph-0.1.5 (27 Jan 2005) + + 27 Jan 2005; Olivier Fisette <ribosome@gentoo.org> + +files/elph-0.1.5-usage.patch, +elph-0.1.5.ebuild: + New version. + +*elph-0.1.4 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +files/elph-0.1.4-usage.patch, +elph-0.1.4.ebuild: + Moved from app-sci/elph to sci-biology/elph. + + 07 Nov 2004; Olivier Fisette <ribosome@gentoo.org> metadata.xml, + -elph-0.1.2.ebuild, elph-0.1.4.ebuild: + Removed buggy version (0.1.2). Added 0.1.4 to x86. Set myself as + maintainer. Added long description. + + 30 Oct 2004; Olivier Fisette <ribosome@gentoo.org> +elph-0.1.4.ebuild + +files/elph-0.1.4-usage.patch : + New version. + +*elph-0.1.2 (22 May 2003) + + 22 May 2003; Jon Portnoy <avenj@gentoo.org> elph-0.1.2.ebuild : + Initial import. Ebuild submitted by Stephen Diener in bug + #21308. diff --git a/sci-biology/embassy-cbstools/ChangeLog b/sci-biology/embassy-cbstools/ChangeLog new file mode 100644 index 00000000..d8f40e7a --- /dev/null +++ b/sci-biology/embassy-cbstools/ChangeLog @@ -0,0 +1,50 @@ +# 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 1.10 2015/06/21 08:31:31 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-cbstools-1.0.0.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 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) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> + +embassy-cbstools-1.0.0.650.ebuild, + +files/embassy-cbstools-1.0.0.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-cbstools-1.0.0.ebuild, embassy-cbstools-1.0.0-r1.ebuild: + Fix SRC_URI for emboss + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> embassy-cbstools-1.0.0.ebuild, + embassy-cbstools-1.0.0-r1.ebuild: + Drop sparc keywords + + 15 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-cbstools-1.0.0-r1.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-cbstools-1.0.0-r1 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-cbstools-1.0.0-r1.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-cbstools-1.0.0.ebuild: + Stabilised on amd64 and x86. + +*embassy-cbstools-1.0.0 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-cbstools-1.0.0.ebuild: + Initial import for EMBASSY 6.0.1. diff --git a/sci-biology/embassy-clustalomega/ChangeLog b/sci-biology/embassy-clustalomega/ChangeLog new file mode 100644 index 00000000..d95b3943 --- /dev/null +++ b/sci-biology/embassy-clustalomega/ChangeLog @@ -0,0 +1,19 @@ +# ChangeLog for sci-biology/embassy-clustalomega +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-clustalomega/ChangeLog,v 1.3 2015/06/21 08:41:14 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-clustalomega-1.1.0_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> + embassy-clustalomega-1.1.0.ebuild: + Clean global scope + +*embassy-clustalomega-1.1.0 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> + +embassy-clustalomega-1.1.0.ebuild, + +files/embassy-clustalomega-1.1.0_fix-build-system.patch, +metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 diff --git a/sci-biology/embassy-domainatrix/ChangeLog b/sci-biology/embassy-domainatrix/ChangeLog new file mode 100644 index 00000000..20d34e51 --- /dev/null +++ b/sci-biology/embassy-domainatrix/ChangeLog @@ -0,0 +1,174 @@ +# 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 1.35 2015/06/21 08:46:54 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-domainatrix-0.1.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 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) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> + +embassy-domainatrix-0.1.650.ebuild, + +files/embassy-domainatrix-0.1.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-domainatrix-0.1.0-r3.ebuild, embassy-domainatrix-0.1.0-r4.ebuild: + Fix SRC_URI for emboss + + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> + -embassy-domainatrix-0.1.0-r1.ebuild: + Dropped old, due to unsatisfied deps + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> + embassy-domainatrix-0.1.0-r1.ebuild, embassy-domainatrix-0.1.0-r3.ebuild, + embassy-domainatrix-0.1.0-r4.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-domainatrix-0.1.0-r4.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-domainatrix-0.1.0-r4 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-domainatrix-0.1.0-r4.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-domainatrix-0.1.0-r3.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-domainatrix-0.1.0-r2.ebuild: + Pruning version that will never be stabilised. + +*embassy-domainatrix-0.1.0-r3 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +embassy-domainatrix-0.1.0-r3.ebuild: + New upstream version/package for EMBASSY 6.0.1. + +*embassy-domainatrix-0.1.0-r2 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> + +embassy-domainatrix-0.1.0-r2.ebuild: + New upstream packaging for EMBOSS 5.0.0. + + 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> + embassy-domainatrix-0.1.0-r1.ebuild: + Added ~amd64. + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> + -embassy-domainatrix-0.1.0.ebuild: + Pruning old version. + + 03 Nov 2006; nixnut <nixnut@gentoo.org> + embassy-domainatrix-0.1.0-r1.ebuild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Fabian Groffen <grobian@gentoo.org> + embassy-domainatrix-0.1.0.ebuild, embassy-domainatrix-0.1.0-r1.ebuild: + Dropped ppc-macos, see you in prefix. + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> + embassy-domainatrix-0.1.0-r1.ebuild: + Added ~sparc + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-domainatrix-0.1.0-r1.ebuild: + Added to x86. + +*embassy-domainatrix-0.1.0-r1 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + +embassy-domainatrix-0.1.0-r1.ebuild: + New upstream version building against EMBOSS 4.0.0. + + 20 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-domainatrix-0.1.0.ebuild: + Fixed download URL (silent upstream repackaging). + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + -files/embassy-domainatrix-1.0.0-r1.patch, + -embassy-domainatrix-1.0.0-r1.ebuild: + Removed obsolete version. + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-domainatrix-0.1.0.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> + embassy-domainatrix-0.1.0.ebuild: + Stable on ppc. + + 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-domainatrix-0.1.0.ebuild: + Added to x86. + +*embassy-domainatrix-0.1.0 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> + +embassy-domainatrix-0.1.0.ebuild, embassy-domainatrix-1.0.0-r1.ebuild: + Ported version 1.0.0-r1 to the improved embassy.eclass. Version 0.1.0 is + really an upgrade; it is normal to be required to downgrade from 1.0.0 to + 0.1.0 to upgrade to EMBASSY 3.0.0. This is an issue with upstream's + versionning scheme. + + 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> + -embassy-domainatrix-1.0.0.ebuild: + Removed old version. + + 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> + embassy-domainatrix-1.0.0-r1.ebuild: + Stable ppc-macos + + 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> + embassy-domainatrix-1.0.0-r1.ebuild: + Marked ppc stable. + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-domainatrix-1.0.0-r1.ebuild: + Added to x86. + +*embassy-domainatrix-1.0.0-r1 (25 Mar 2005) + + 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> + +files/embassy-domainatrix-1.0.0-r1.patch, + +embassy-domainatrix-1.0.0-r1.ebuild: + Patched version for EMBOSS-2.10. + + 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> + embassy-domainatrix-1.0.0.ebuild: + Stable ppc-macos + + 25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-domainatrix-1.0.0.ebuild: + Unstable ppc-macos. + +*embassy-domainatrix-1.0.0 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-domainatrix-1.0.0.ebuild: + Moved from app-sci/embassy-domainatrix to sci-biology/embassy-domainatrix. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> + embassy-domainatrix-1.0.0.ebuild: + Added to x86. + + 21 Jul 2004; David Holm <dholm@gentoo.org> embassy-domainatrix-1.0.0.ebuild: + Added to ~ppc. + +* domainatrix-1.0.0 (19 Jul 2004) + + 14 Jul 2004; Olivier Fisette <ribosome@gentoo.org> + embassy-domainatrix-1.0.0.ebuild, metadata.xml, ChangeLog + Initial import. diff --git a/sci-biology/embassy-domalign/ChangeLog b/sci-biology/embassy-domalign/ChangeLog new file mode 100644 index 00000000..06d2bf99 --- /dev/null +++ b/sci-biology/embassy-domalign/ChangeLog @@ -0,0 +1,119 @@ +# 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 1.27 2015/06/21 08:48:40 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-domalign-0.1.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> + -embassy-domalign-0.1.0-r4.ebuild: + Drop old + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> embassy-domalign-0.1.650.ebuild: + Drop old + +*embassy-domalign-0.1.650 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-domalign-0.1.650.ebuild, + +files/embassy-domalign-0.1.650_fix-build-system.patch, metadata.xml: + Call correct install function + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-domalign-0.1.0-r4.ebuild, embassy-domalign-0.1.0-r3.ebuild: + Fix SRC_URI for emboss + + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> + -embassy-domalign-0.1.0-r1.ebuild: + Dropped old, due to unsatisfied deps + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> + embassy-domalign-0.1.0-r1.ebuild, embassy-domalign-0.1.0-r3.ebuild, + embassy-domalign-0.1.0-r4.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-domalign-0.1.0-r4.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-domalign-0.1.0-r4 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-domalign-0.1.0-r4.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-domalign-0.1.0-r3.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-domalign-0.1.0-r2.ebuild: + Pruning version that will never be stabilised. + +*embassy-domalign-0.1.0-r3 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +embassy-domalign-0.1.0-r3.ebuild: + New upstream version/package for EMBASSY 6.0.1. + +*embassy-domalign-0.1.0-r2 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> + +embassy-domalign-0.1.0-r2.ebuild: + New upstream packaging for EMBOSS 5.0.0. + + 16 Feb 2007; Jeff Gardner <je_fro@gentoo.org> + embassy-domalign-0.1.0-r1.ebuild: + Added ~amd64. + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> + -embassy-domalign-0.1.0.ebuild: + Pruning old version. + + 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-domalign-0.1.0-r1.ebuild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> ChangeLog: + Removed hidden file .#embassy-domalign-0.1.0-r1.ebuild.1.2 + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> ChangeLog: + Added ~sparc + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> + embassy-domalign-0.1.0.ebuild, embassy-domalign-0.1.0-r1.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-domalign-0.1.0-r1.ebuild: + Added to x86. + +*embassy-domalign-0.1.0-r1 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + +embassy-domalign-0.1.0-r1.ebuild: + New upstream version building against EMBOSS 4.0.0. + + 20 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-domalign-0.1.0.ebuild: + Fixed download URL (silent upstream repackaging). + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-domalign-0.1.0.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> + embassy-domalign-0.1.0.ebuild: + Stable on ppc. + + 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-domalign-0.1.0.ebuild: + Added to x86. + +*embassy-domalign-0.1.0 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-domalign-0.1.0.ebuild: + Initial import. Part of EMBASSY 3.0.0. diff --git a/sci-biology/embassy-domsearch/ChangeLog b/sci-biology/embassy-domsearch/ChangeLog new file mode 100644 index 00000000..2ed7232e --- /dev/null +++ b/sci-biology/embassy-domsearch/ChangeLog @@ -0,0 +1,116 @@ +# 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 1.25 2015/06/21 08:50:38 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-domsearch-0.1.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 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) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> + +embassy-domsearch-0.1.650.ebuild, + +files/embassy-domsearch-0.1.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-domsearch-0.1.0-r4.ebuild, embassy-domsearch-0.1.0-r3.ebuild: + Fix SRC_URI for emboss + + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> + -embassy-domsearch-0.1.0-r1.ebuild: + Dropped old, due to unsatisfied deps + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> + embassy-domsearch-0.1.0-r1.ebuild, embassy-domsearch-0.1.0-r3.ebuild, + embassy-domsearch-0.1.0-r4.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-domsearch-0.1.0-r4.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-domsearch-0.1.0-r4 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-domsearch-0.1.0-r4.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-domsearch-0.1.0-r3.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-domsearch-0.1.0-r2.ebuild: + Pruning version that will never be stabilised. + +*embassy-domsearch-0.1.0-r3 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +embassy-domsearch-0.1.0-r3.ebuild: + New upstream version/package for EMBASSY 6.0.1. + +*embassy-domsearch-0.1.0-r2 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> + +embassy-domsearch-0.1.0-r2.ebuild: + New upstream packaging for EMBOSS 5.0.0. + + 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> + embassy-domsearch-0.1.0-r1.ebuild: + Added ~amd64. + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> + -embassy-domsearch-0.1.0.ebuild: + Pruning old version. + + 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-domsearch-0.1.0-r1.ebuild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Fabian Groffen <grobian@gentoo.org> + embassy-domsearch-0.1.0.ebuild, embassy-domsearch-0.1.0-r1.ebuild: + Dropped ppc-macos, see you in prefix. + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> + embassy-domsearch-0.1.0-r1.ebuild: + Added ~sparc + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-domsearch-0.1.0-r1.ebuild: + Added to x86. + +*embassy-domsearch-0.1.0-r1 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + +embassy-domsearch-0.1.0-r1.ebuild: + New upstream version building against EMBOSS 4.0.0. + + 20 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-domsearch-0.1.0.ebuild: + Fixed download URL (silent upstream repackaging). + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-domsearch-0.1.0.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> + embassy-domsearch-0.1.0.ebuild: + Stable on ppc. + + 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-domsearch-0.1.0.ebuild: + Added to x86. + +*embassy-domsearch-0.1.0 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-domsearch-0.1.0.ebuild: + Initial import. Part of EMBASSY 3.0.0. diff --git a/sci-biology/embassy-emnu/ChangeLog b/sci-biology/embassy-emnu/ChangeLog new file mode 100644 index 00000000..e90ae769 --- /dev/null +++ b/sci-biology/embassy-emnu/ChangeLog @@ -0,0 +1,161 @@ +# 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 1.35 2015/06/21 08:56:06 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-emnu-1.05.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 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) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-emnu-1.05.650.ebuild, + +files/embassy-emnu-1.05.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-emnu-1.05-r5.ebuild, embassy-emnu-1.05-r6.ebuild: + Fix SRC_URI for emboss + + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> -embassy-emnu-1.05-r3.ebuild: + Dropped old, due to unsatisfied deps + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> embassy-emnu-1.05-r3.ebuild, + embassy-emnu-1.05-r5.ebuild, embassy-emnu-1.05-r6.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-emnu-1.05-r6.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-emnu-1.05-r6 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-emnu-1.05-r6.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-emnu-1.05-r5.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-emnu-1.05-r4.ebuild: + Pruning version that will never be stabilised. + +*embassy-emnu-1.05-r5 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +embassy-emnu-1.05-r5.ebuild: + New upstream version/package for EMBASSY 6.0.1. + +*embassy-emnu-1.05-r4 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> + +embassy-emnu-1.05-r4.ebuild: + New upstream packaging for EMBOSS 5.0.0. + + 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> embassy-emnu-1.05-r3.ebuild: + Added ~amd64. + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> + -embassy-emnu-1.05-r2.ebuild: + Pruning old version. + + 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-emnu-1.05-r3.ebuild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Fabian Groffen <grobian@gentoo.org> + embassy-emnu-1.05-r2.ebuild, embassy-emnu-1.05-r3.ebuild: + Dropped ppc-macos, see you in prefix. + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> embassy-emnu-1.05-r3.ebuild: + Added ~sparc + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-emnu-1.05-r3.ebuild: + Added to x86. + +*embassy-emnu-1.05-r3 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + +embassy-emnu-1.05-r3.ebuild: + New upstream version building against EMBOSS 4.0.0. + + 20 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-emnu-1.05-r2.ebuild: + Fixed digest mismatch due to silent upstream repackaging. + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + -files/embassy-emnu-1.05-r1.patch, -embassy-emnu-1.05-r1.ebuild: + Removed obsolete version. + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-emnu-1.05-r2.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> + embassy-emnu-1.05-r2.ebuild: + Stable on ppc. + + 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-emnu-1.05-r2.ebuild: + Added to x86. + +*embassy-emnu-1.05-r2 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-emnu-1.05-r1.ebuild, +embassy-emnu-1.05-r2.ebuild: + Ported 1.05-r1 to the improved embassy.eclass. The new version is part of + EMBASSY 3.0.0. + + 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> + -embassy-emnu-1.05.ebuild: + Removed old version. + + 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> + embassy-emnu-1.05-r1.ebuild: + Stable ppc-macos + + 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> embassy-emnu-1.05-r1.ebuild: + Marked ppc stable. + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-emnu-1.05-r1.ebuild: + Added to x86. + +*embassy-emnu-1.05-r1 (25 Mar 2005) + + 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> + +files/embassy-emnu-1.05-r1.patch, +embassy-emnu-1.05-r1.ebuild: + Patched version for EMBOSS 2.10. + + 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-emnu-1.05.ebuild: + Stable ppc-macos + + 25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-emnu-1.05.ebuild: + Unstable ppc-macos. + +*embassy-emnu-1.05 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-emnu-1.05.ebuild: + Moved from app-sci/embassy-emnu to sci-biology/embassy-emnu. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> embassy-emnu-1.05.ebuild: + Added to x86. + + 21 Jul 2004; David Holm <dholm@gentoo.org> embassy-emnu-1.05.ebuild: + Added to ~ppc. + +* embassy-emnu-1.05 (19 Jul 2004) + + 14 Jul 2004; Olivier Fisette <ribosome@gentoo.org> + embassy-emnu-1.05.ebuild, metadata.xml, ChangeLog + Initial import. diff --git a/sci-biology/embassy-esim4/ChangeLog b/sci-biology/embassy-esim4/ChangeLog new file mode 100644 index 00000000..b3da1f88 --- /dev/null +++ b/sci-biology/embassy-esim4/ChangeLog @@ -0,0 +1,162 @@ +# 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 1.34 2015/06/21 09:01:36 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-esim4-1.0.0.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 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) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-esim4-1.0.0.650.ebuild, + +files/embassy-esim4-1.0.0.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-esim4-1.0.0-r6.ebuild, embassy-esim4-1.0.0-r5.ebuild: + Fix SRC_URI for emboss + + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> -embassy-esim4-1.0.0-r3.ebuild: + Dropped old, due to unsatisfied deps + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> embassy-esim4-1.0.0-r3.ebuild, + embassy-esim4-1.0.0-r5.ebuild, embassy-esim4-1.0.0-r6.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-esim4-1.0.0-r6.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-esim4-1.0.0-r6 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-esim4-1.0.0-r6.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-esim4-1.0.0-r5.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-esim4-1.0.0-r4.ebuild: + Pruning version that will never be stabilised. + +*embassy-esim4-1.0.0-r5 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +embassy-esim4-1.0.0-r5.ebuild: + New upstream version/package for EMBASSY 6.0.1. + +*embassy-esim4-1.0.0-r4 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> + +embassy-esim4-1.0.0-r4.ebuild: + New upstream packaging for EMBOSS 5.0.0. + + 16 Feb 2007; Jeff Gardner <je_fro@gentoo.org> + embassy-esim4-1.0.0-r3.ebuild: + Added ~amd64. + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> + -embassy-esim4-1.0.0-r2.ebuild: + Pruning old version. + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> + embassy-esim4-1.0.0-r3.ebuild: + Marked ~sparc + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> + embassy-esim4-1.0.0-r2.ebuild, embassy-esim4-1.0.0-r3.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-esim4-1.0.0-r3.ebuild: + Added to x86. + +*embassy-esim4-1.0.0-r3 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + +embassy-esim4-1.0.0-r3.ebuild: + New upstream version building against EMBOSS 4.0.0. + + 20 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-esim4-1.0.0-r2.ebuild: + Fixed digest mismatch due to silent upstream repackaging. + + 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + -embassy-esim4-1.0.0-r1.ebuild: + Removed obsolete version. + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-esim4-1.0.0-r2.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> + embassy-esim4-1.0.0-r2.ebuild: + Stable on ppc. + + 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-esim4-1.0.0-r2.ebuild: + Added to x86. + +*embassy-esim4-1.0.0-r2 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-esim4-1.0.0-r1.ebuild, +embassy-esim4-1.0.0-r2.ebuild: + Ported 1.0.0-r1 to the improved embassy.eclass. The new version is part of + EMBASSY 3.0.0. + + 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> + -embassy-esim4-1.0.0.ebuild: + Removed old version. + + 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> + embassy-esim4-1.0.0-r1.ebuild: + Stable ppc-macos + + 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> + embassy-esim4-1.0.0-r1.ebuild: + Marked ppc stable. + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-esim4-1.0.0-r1.ebuild: + Added to x86. + +*embassy-esim4-1.0.0-r1 (25 Mar 2005) + + 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> + +embassy-esim4-1.0.0-r1.ebuild: + Build against the EMBOSS 2.10 source tree. + + 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-esim4-1.0.0.ebuild: + Stable ppc-macos + + 25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-esim4-1.0.0.ebuild: + Unstable ppc-macos. + +*embassy-esim4-1.0.0 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-esim4-1.0.0.ebuild: + Moved from app-sci/embassy-esim4 to sci-biology/embassy-esim4. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> + embassy-esim4-1.0.0.ebuild: + Added to x86. + + 21 Jul 2004; David Holm <dholm@gentoo.org> embassy-esim4-1.0.0.ebuild: + Added to ~ppc. + +* embassy-esim4-1.0.0 (19 Jul 2004) + + 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> + embassy-esim4-1.0.0.ebuild, metadata.xml, ChangeLog + Initial import. diff --git a/sci-biology/embassy-hmmer/ChangeLog b/sci-biology/embassy-hmmer/ChangeLog new file mode 100644 index 00000000..174dac9f --- /dev/null +++ b/sci-biology/embassy-hmmer/ChangeLog @@ -0,0 +1,168 @@ +# 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 1.36 2015/06/21 09:05:41 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-hmmer-2.3.2.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 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) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-hmmer-2.3.2.650.ebuild, + +files/embassy-hmmer-2.3.2.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-hmmer-2.3.2-r3.ebuild, embassy-hmmer-2.3.2-r2.ebuild: + Fix SRC_URI for emboss + + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> -embassy-hmmer-2.3.2.ebuild: + Dropped old, due to unsatisfied deps + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> embassy-hmmer-2.3.2.ebuild, + embassy-hmmer-2.3.2-r2.ebuild, embassy-hmmer-2.3.2-r3.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-hmmer-2.3.2-r3.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-hmmer-2.3.2-r3 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-hmmer-2.3.2-r3.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-hmmer-2.3.2-r2.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-hmmer-2.3.2-r1.ebuild: + Pruning version that will never be stabilised. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + embassy-hmmer-2.3.2-r1.ebuild, embassy-hmmer-2.3.2-r2.ebuild: + Fixed description. Added dependency on HMMER. + +*embassy-hmmer-2.3.2-r2 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +embassy-hmmer-2.3.2-r2.ebuild: + New upstream version/package for EMBASSY 6.0.1. + +*embassy-hmmer-2.3.2-r1 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> + +embassy-hmmer-2.3.2-r1.ebuild: + New upstream packaging for EMBOSS 5.0.0. + + 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> embassy-hmmer-2.3.2.ebuild: + Added ~amd64 + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> + -embassy-hmmer-2.1.1-r2.ebuild: + Pruning old version. + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> embassy-hmmer-2.3.2.ebuild: + Added ~sparc + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> + embassy-hmmer-2.1.1-r2.ebuild, embassy-hmmer-2.3.2.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-hmmer-2.3.2.ebuild: + Added to x86. + +*embassy-hmmer-2.3.2 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-hmmer-2.1.1-r2.ebuild, +embassy-hmmer-2.3.2.ebuild: + New upstream version building against EMBOSS 4.0.0. + + 20 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-hmmer-2.1.1-r2.ebuild: + Fixed download URL (silent upstream repackaging). + + 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + -embassy-hmmer-2.1.1-r1.ebuild: + Removed obsolete version. + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-hmmer-2.1.1-r2.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> + embassy-hmmer-2.1.1-r2.ebuild: + Stable on ppc. + + 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-hmmer-2.1.1-r2.ebuild: + Added to x86. + +*embassy-hmmer-2.1.1-r2 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-hmmer-2.1.1-r1.ebuild, +embassy-hmmer-2.1.1-r2.ebuild: + Ported 2.1.1-r1 to the improved embassy.eclass. The new version is part of + EMBASSY 3.0.0. + + 30 Jul 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-hmmer-2.1.1-r1.ebuild: + Fixed bug #100672. + + 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> + -embassy-hmmer-2.1.1.ebuild: + Removed old version. + + 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> + embassy-hmmer-2.1.1-r1.ebuild: + Stable ppc-macos Bug 96819 + + 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> + embassy-hmmer-2.1.1-r1.ebuild: + Marked ppc stable. + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-hmmer-2.1.1-r1.ebuild: + Added to x86. + +*embassy-hmmer-2.1.1-r1 (25 Mar 2005) + + 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> + +embassy-hmmer-2.1.1-r1.ebuild: + Build against the EMBOSS 2.10 source tree. + + 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-hmmer-2.1.1.ebuild: + Stable ppc-macos + + 25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-hmmer-2.1.1.ebuild: + Unstable ppc-macos + +*embassy-hmmer-2.1.1 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-hmmer-2.1.1.ebuild: + Moved from app-sci/embassy-hmmer to sci-biology/embassy-hmmer. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> + embassy-hmmer-2.1.1.ebuild: + Added to x86. + + 21 Jul 2004; David Holm <dholm@gentoo.org> embassy-hmmer-2.1.1.ebuild: + Added to ~ppc. + +* embassy-hmmer-2.1.1 (19 Jul 2004) + + 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> + embassy-hmmer-2.1.1.ebuild, metadata.xml, ChangeLog + Initial import. diff --git a/sci-biology/embassy-iprscan/ChangeLog b/sci-biology/embassy-iprscan/ChangeLog new file mode 100644 index 00000000..b9ccb62a --- /dev/null +++ b/sci-biology/embassy-iprscan/ChangeLog @@ -0,0 +1,50 @@ +# 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 1.10 2015/06/21 09:07:32 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-iprscan-4.3.1.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 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) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> + +embassy-iprscan-4.3.1.650.ebuild, + +files/embassy-iprscan-4.3.1.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-iprscan-4.3.1-r1.ebuild, embassy-iprscan-4.3.1.ebuild: + Fix SRC_URI for emboss + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> embassy-iprscan-4.3.1.ebuild, + embassy-iprscan-4.3.1-r1.ebuild: + Drop sparc keywords + + 15 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-iprscan-4.3.1-r1.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-iprscan-4.3.1-r1 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-iprscan-4.3.1-r1.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-iprscan-4.3.1.ebuild: + Stabilised on amd64 and x86. + +*embassy-iprscan-4.3.1 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-iprscan-4.3.1.ebuild: + Initial import for EMBASSY 6.0.1. diff --git a/sci-biology/embassy-meme/ChangeLog b/sci-biology/embassy-meme/ChangeLog new file mode 100644 index 00000000..c5ddb1ff --- /dev/null +++ b/sci-biology/embassy-meme/ChangeLog @@ -0,0 +1,17 @@ +# ChangeLog for sci-biology/embassy-meme +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-meme/ChangeLog,v 1.24 2015/06/21 09:09:22 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-meme-4.7.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> embassy-meme-4.7.650.ebuild: + Clean global scope + +*embassy-meme-4.7.650 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-meme-4.7.650.ebuild, + +files/embassy-meme-4.7.650_fix-build-system.patch, +metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 diff --git a/sci-biology/embassy-memenew/ChangeLog b/sci-biology/embassy-memenew/ChangeLog new file mode 100644 index 00000000..4eb2e750 --- /dev/null +++ b/sci-biology/embassy-memenew/ChangeLog @@ -0,0 +1,68 @@ +# ChangeLog for sci-biology/embassy-memenew +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-memenew/ChangeLog,v 1.15 2015/03/29 08:43:37 jlec Exp $ + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-memenew-4.0.0.ebuild, + metadata.xml: + Drop old + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-memenew-0.1.0-r1.ebuild, embassy-memenew-4.0.0.ebuild: + Fix SRC_URI for emboss + + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> -embassy-memenew-0.1.0.ebuild: + Dropped old, due to unsatisfied deps + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> embassy-memenew-0.1.0.ebuild, + embassy-memenew-0.1.0-r1.ebuild, embassy-memenew-4.0.0.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-memenew-4.0.0.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-memenew-4.0.0 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-memenew-4.0.0.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-memenew-0.1.0-r1.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + embassy-memenew-0.1.0.ebuild, embassy-memenew-0.1.0-r1.ebuild: + Fixed description. + +*embassy-memenew-0.1.0-r1 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +embassy-memenew-0.1.0-r1.ebuild: + New upstream version/package for EMBASSY 6.0.1. + + 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> + embassy-memenew-0.1.0.ebuild: + Added ~amd64. + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> + embassy-memenew-0.1.0.ebuild: + Added ~sparc + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> + embassy-memenew-0.1.0.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-memenew-0.1.0.ebuild: + Added to x86. + +*embassy-memenew-0.1.0 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-memenew-0.1.0.ebuild: + Initial import. This package will probably replace EMBASSY-MEME in new + EMBASSY releases. diff --git a/sci-biology/embassy-mira/ChangeLog b/sci-biology/embassy-mira/ChangeLog new file mode 100644 index 00000000..5e47fd93 --- /dev/null +++ b/sci-biology/embassy-mira/ChangeLog @@ -0,0 +1,38 @@ +# ChangeLog for sci-biology/embassy-mira +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mira/ChangeLog,v 1.8 2015/03/29 08:35:07 jlec Exp $ + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> -embassy-mira-2.8.2-r1.ebuild, + metadata.xml: + Drop old + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-mira-2.8.2.ebuild, embassy-mira-2.8.2-r1.ebuild: + Fix SRC_URI for emboss wrt #387299 + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> embassy-mira-2.8.2.ebuild, + embassy-mira-2.8.2-r1.ebuild: + Drop sparc keywords + + 15 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-mira-2.8.2-r1.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-mira-2.8.2-r1 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-mira-2.8.2-r1.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-mira-2.8.2.ebuild: + Stabilised on amd64 and x86. + +*embassy-mira-2.8.2 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-mira-2.8.2.ebuild: + Initial import for EMBASSY 6.0.1. diff --git a/sci-biology/embassy-mse/ChangeLog b/sci-biology/embassy-mse/ChangeLog new file mode 100644 index 00000000..ed526bcd --- /dev/null +++ b/sci-biology/embassy-mse/ChangeLog @@ -0,0 +1,193 @@ +# 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 1.42 2015/06/21 09:10:58 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-mse-3.0.0.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 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 + +*embassy-mse-3.0.0.650 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-mse-3.0.0.650.ebuild, + +files/embassy-mse-3.0.0.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-mse-1.0.0-r6.ebuild, embassy-mse-1.0.0-r7.ebuild: + Fix SRC_URI for emboss + + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> -embassy-mse-1.0.0-r3.ebuild, + -embassy-mse-1.0.0-r4.ebuild: + Dropped old, due to unsatisfied deps + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> embassy-mse-1.0.0-r3.ebuild, + embassy-mse-1.0.0-r4.ebuild, embassy-mse-1.0.0-r6.ebuild, + embassy-mse-1.0.0-r7.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-mse-1.0.0-r7.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-mse-1.0.0-r7 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-mse-1.0.0-r7.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-mse-1.0.0-r6.ebuild: + Stabilised on amd64 and x86. + + 28 Aug 2008; Olivier Fisette <ribosome@gentoo.org> ChangeLog: + Fixing broken Manifest. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-mse-1.0.0-r5.ebuild: + Pruning version that will never be stabilised. + +*embassy-mse-1.0.0-r6 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +embassy-mse-1.0.0-r6.ebuild: + New upstream version/package for EMBASSY 6.0.1. + + 07 Aug 2007; Olivier Fisette <ribosome@gentoo.org> + embassy-mse-1.0.0-r5.ebuild: + Removed multilib-strict fix, as it was moved to the embassy eclass. + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> + +embassy-mse-1.0.0-r4.ebuild: + We still need an AMD64 ebuild for EMBOSS 4.0.0 (my mistake). + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> + -embassy-mse-1.0.0-r4.ebuild: + Pruned old version that will never be stabilised. + +*embassy-mse-1.0.0-r5 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> + +embassy-mse-1.0.0-r5.ebuild: + New upstream packaging for EMBOSS 5.0.0. + + 17 Feb 2007; Olivier Fisette <ribosome@gentoo.org> + embassy-mse-1.0.0-r4.ebuild: + Added to ~amd64. + +*embassy-mse-1.0.0-r4 (17 Feb 2007) + + 17 Feb 2007; Olivier Fisette <ribosome@gentoo.org> + +embassy-mse-1.0.0-r4.ebuild: + Added a fix for multilib-strict on AMD64 suggested by Jeff Gardner + <je_fro@gentoo.org>. + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> + -embassy-mse-1.0.0-r2.ebuild: + Pruning old version. + + 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-mse-1.0.0-r3.ebuild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> embassy-mse-1.0.0-r3.ebuild: + Added ~sparc + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> + embassy-mse-1.0.0-r2.ebuild, embassy-mse-1.0.0-r3.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-mse-1.0.0-r3.ebuild: + Added to x86. + +*embassy-mse-1.0.0-r3 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + +embassy-mse-1.0.0-r3.ebuild: + New upstream version building against EMBOSS 4.0.0. + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-mse-1.0.0-r2.ebuild: + Fixed download URL (silent upstream repackaging). + + 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + -embassy-mse-1.0.0-r1.ebuild: + Removed obsolete version. + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-mse-1.0.0-r2.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> + embassy-mse-1.0.0-r2.ebuild: + Stable on ppc. + + 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-mse-1.0.0-r2.ebuild: + Added to x86. + +*embassy-mse-1.0.0-r2 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-mse-1.0.0-r1.ebuild, +embassy-mse-1.0.0-r2.ebuild: + Ported 1.0.0-r1 to the improved embassy.eclass. The new version is part of + EMBASSY 3.0.0. + + 30 Jul 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-mse-1.0.0-r1.ebuild: + Fixed bug #100672. + + 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> + -embassy-mse-1.0.0.ebuild: + Removed old version. + + 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> + embassy-mse-1.0.0-r1.ebuild: + Stable ppc-macos Bug 96819 + + 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> embassy-mse-1.0.0-r1.ebuild: + Marked ppc stable. + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-mse-1.0.0-r1.ebuild: + Added to x86. + +*embassy-mse-1.0.0-r1 (25 Mar 2005) + + 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> + +embassy-mse-1.0.0-r1.ebuild: + Build against the EMBOSS 2.10 source tree. + + 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-mse-1.0.0.ebuild: + Stable ppc-macos + + 25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-mse-1.0.0.ebuild: + Unstable ppc-macos + +*embassy-mse-1.0.0 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-mse-1.0.0.ebuild: + Moved from app-sci/embassy-mse to sci-biology/embassy-mse. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> embassy-mse-1.0.0.ebuild: + Added to x86. + + 21 Jul 2004; David Holm <dholm@gentoo.org> embassy-mse-1.0.0.ebuild: + Added to ~ppc. + +* embassy-mse-1.0.0 (19 Jul 2004) + + 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> + embassy-mse-1.0.0.ebuild, metadata.xml, ChangeLog + Initial import. diff --git a/sci-biology/embassy-phylipnew/ChangeLog b/sci-biology/embassy-phylipnew/ChangeLog new file mode 100644 index 00000000..9550a755 --- /dev/null +++ b/sci-biology/embassy-phylipnew/ChangeLog @@ -0,0 +1,83 @@ +# 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 1.18 2015/06/21 09:12:29 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-phylipnew-3.69.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 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) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> + +embassy-phylipnew-3.69.650.ebuild, + +files/embassy-phylipnew-3.69.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-phylipnew-3.68.ebuild, embassy-phylipnew-3.67.ebuild: + Fix SRC_URI for emboss + + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> -embassy-phylipnew-3.6b.ebuild: + Dropped old, due to unsatisfied deps + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> embassy-phylipnew-3.6b.ebuild, + embassy-phylipnew-3.67.ebuild, embassy-phylipnew-3.68.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-phylipnew-3.68.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-phylipnew-3.68 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-phylipnew-3.68.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-phylipnew-3.67.ebuild: + Stabilised on amd64 and x86. + +*embassy-phylipnew-3.67 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +embassy-phylipnew-3.67.ebuild: + New upstream version/package for EMBASSY 6.0.1. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + embassy-phylipnew-3.6b.ebuild: + Fixed description. + + 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> + embassy-phylipnew-3.6b.ebuild: + Adding ~amd64. + + 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-phylipnew-3.6b.ebuild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> + embassy-phylipnew-3.6b.ebuild: + Added ~sparc + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> + embassy-phylipnew-3.6b.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-phylipnew-3.6b.ebuild: + Added to x86. + +*embassy-phylipnew-3.6b (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-phylipnew-3.6b.ebuild: + Initial import. This package will probably replace EMBASSY-PHYLIP in new + EMBASSY releases. diff --git a/sci-biology/embassy-signature/ChangeLog b/sci-biology/embassy-signature/ChangeLog new file mode 100644 index 00000000..57c35be3 --- /dev/null +++ b/sci-biology/embassy-signature/ChangeLog @@ -0,0 +1,116 @@ +# ChangeLog for sci-biology/embassy-signature +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-signature/ChangeLog,v 1.25 2015/06/21 09:13:51 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-signature-0.1.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> + -embassy-signature-0.1.0-r4.ebuild: + Drop old + +*embassy-signature-0.1.650 (28 Mar 2015) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> + +embassy-signature-0.1.650.ebuild, + +files/embassy-signature-0.1.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-signature-0.1.0-r3.ebuild, embassy-signature-0.1.0-r4.ebuild: + Fix SRC_URI for emboss + + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> + -embassy-signature-0.1.0-r1.ebuild: + Dropped old, due to unsatisfied deps + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> + embassy-signature-0.1.0-r1.ebuild, embassy-signature-0.1.0-r3.ebuild, + embassy-signature-0.1.0-r4.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-signature-0.1.0-r4.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-signature-0.1.0-r4 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-signature-0.1.0-r4.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-signature-0.1.0-r3.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-signature-0.1.0-r2.ebuild: + Pruning version that will never be stabilised. + +*embassy-signature-0.1.0-r3 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +embassy-signature-0.1.0-r3.ebuild: + New upstream version/package for EMBASSY 6.0.1. + +*embassy-signature-0.1.0-r2 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> + +embassy-signature-0.1.0-r2.ebuild: + New upstream packaging for EMBOSS 5.0.0. + + 16 Feb 2007; Jeff Gardner <je_fro@gentoo.org> + embassy-signature-0.1.0-r1.ebuild: + Added ~amd64. + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> + -embassy-signature-0.1.0.ebuild: + Pruning old version. + + 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-signature-0.1.0-r1.ebuild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> + embassy-signature-0.1.0-r1.ebuild: + Added ~sparc + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> + embassy-signature-0.1.0.ebuild, embassy-signature-0.1.0-r1.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-signature-0.1.0-r1.ebuild: + Added to x86. + +*embassy-signature-0.1.0-r1 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + +embassy-signature-0.1.0-r1.ebuild: + New upstream version building against EMBOSS 4.0.0. + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-signature-0.1.0.ebuild: + Fixed download URL (silent upstream repackaging). + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-signature-0.1.0.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> + embassy-signature-0.1.0.ebuild: + Stable on ppc. + + 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-signature-0.1.0.ebuild: + Added to x86. + +*embassy-signature-0.1.0 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-signature-0.1.0.ebuild: + New import. This package is part of the EMBASSY 3.0.0 distribution. diff --git a/sci-biology/embassy-structure/ChangeLog b/sci-biology/embassy-structure/ChangeLog new file mode 100644 index 00000000..c7e3b80c --- /dev/null +++ b/sci-biology/embassy-structure/ChangeLog @@ -0,0 +1,116 @@ +# 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 1.25 2015/06/21 09:15:24 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-structure-0.1.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 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) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> + +embassy-structure-0.1.650.ebuild, + +files/embassy-structure-0.1.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-structure-0.1.0-r4.ebuild, embassy-structure-0.1.0-r3.ebuild: + Fix SRC_URI for emboss + + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> + -embassy-structure-0.1.0-r1.ebuild: + Dropped old, due to unsatisfied deps + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> + embassy-structure-0.1.0-r1.ebuild, embassy-structure-0.1.0-r3.ebuild, + embassy-structure-0.1.0-r4.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-structure-0.1.0-r4.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-structure-0.1.0-r4 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-structure-0.1.0-r4.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-structure-0.1.0-r3.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-structure-0.1.0-r2.ebuild: + Pruning version that will never be stabilised. + +*embassy-structure-0.1.0-r3 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +embassy-structure-0.1.0-r3.ebuild: + New upstream version/package for EMBASSY 6.0.1. + +*embassy-structure-0.1.0-r2 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> + +embassy-structure-0.1.0-r2.ebuild: + New upstream packaging for EMBOSS 5.0.0. + + 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> + embassy-structure-0.1.0-r1.ebuild: + Added ~amd64. + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> + -embassy-structure-0.1.0.ebuild: + Pruning old version. + + 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-structure-0.1.0-r1.ebuild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> + embassy-structure-0.1.0-r1.ebuild: + Added ~sparc + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> + embassy-structure-0.1.0.ebuild, embassy-structure-0.1.0-r1.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-structure-0.1.0-r1.ebuild: + Added to x86. + +*embassy-structure-0.1.0-r1 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + +embassy-structure-0.1.0-r1.ebuild: + New upstream version building against EMBOSS 4.0.0. + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-structure-0.1.0.ebuild: + Fixed download URL (silent upstream repackaging). + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-structure-0.1.0.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> + embassy-structure-0.1.0.ebuild: + Stable on ppc. + + 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-structure-0.1.0.ebuild: + Added to x86. + +*embassy-structure-0.1.0 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-structure-0.1.0.ebuild: + New import. This package is part of the EMBASSY 3.0.0 distribution. diff --git a/sci-biology/embassy-topo/ChangeLog b/sci-biology/embassy-topo/ChangeLog new file mode 100644 index 00000000..a4bb7482 --- /dev/null +++ b/sci-biology/embassy-topo/ChangeLog @@ -0,0 +1,164 @@ +# 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 1.35 2015/06/21 09:16:49 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-topo-2.0.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 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) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-topo-2.0.650.ebuild, + +files/embassy-topo-2.0.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-topo-1.0.0-r5.ebuild, embassy-topo-1.0.0-r6.ebuild: + Fix SRC_URI for emboss + + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> -embassy-topo-1.0.0-r3.ebuild: + Dropped old, due to unsatisfied deps + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> embassy-topo-1.0.0-r3.ebuild, + embassy-topo-1.0.0-r5.ebuild, embassy-topo-1.0.0-r6.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-topo-1.0.0-r6.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-topo-1.0.0-r6 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-topo-1.0.0-r6.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-topo-1.0.0-r5.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-topo-1.0.0-r4.ebuild: + Pruning version that will never be stabilised. + +*embassy-topo-1.0.0-r5 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +embassy-topo-1.0.0-r5.ebuild: + New upstream version/package for EMBASSY 6.0.1. + +*embassy-topo-1.0.0-r4 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> + +embassy-topo-1.0.0-r4.ebuild: + New upstream packaging for EMBOSS 5.0.0. + + 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> + embassy-topo-1.0.0-r3.ebuild: + Adding ~amd64 + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> + -embassy-topo-1.0.0-r2.ebuild: + Pruning old version. + + 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-topo-1.0.0-r3.ebuild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> + embassy-topo-1.0.0-r3.ebuild: + Marked ~sparc + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> + embassy-topo-1.0.0-r2.ebuild, embassy-topo-1.0.0-r3.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-topo-1.0.0-r3.ebuild: + Added to x86. + +*embassy-topo-1.0.0-r3 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + +embassy-topo-1.0.0-r3.ebuild: + New upstream version building against EMBOSS 4.0.0. + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> + embassy-topo-1.0.0-r2.ebuild: + Fixed download URL (silent upstream repackaging). + + 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + -embassy-topo-1.0.0-r1.ebuild: + Removed obsolete version. + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-topo-1.0.0-r2.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> + embassy-topo-1.0.0-r2.ebuild: + Stable on ppc. + + 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-topo-1.0.0-r2.ebuild: + Added to x86. + +*embassy-topo-1.0.0-r2 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-topo-1.0.0-r1.ebuild, +embassy-topo-1.0.0-r2.ebuild: + Ported 1.0.0-r1 to the improved embassy.eclass. The new version is part of + EMBASSY 3.0.0. + + 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> + -embassy-topo-1.0.0.ebuild: + Removed old version. + + 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> + embassy-topo-1.0.0-r1.ebuild: + Stable ppc-macos Bug 96819 + + 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> + embassy-topo-1.0.0-r1.ebuild: + Marked ppc stable. + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> + embassy-topo-1.0.0-r1.ebuild: + Added to x86. + +*embassy-topo-1.0.0-r1 (25 Mar 2005) + + 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> + +embassy-topo-1.0.0-r1.ebuild: + Build against the EMBOSS 2.10 source tree. + + 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-topo-1.0.0.ebuild: + Stable ppc-macos + + 25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-topo-1.0.0.ebuild: + Unstable ppc-macos + +*embassy-topo-1.0.0 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-topo-1.0.0.ebuild: + Moved from app-sci/embassy-topo to sci-biology/embassy-topo. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> embassy-topo-1.0.0.ebuild: + Added to x86. + + 21 Jul 2004; David Holm <dholm@gentoo.org> embassy-topo-1.0.0.ebuild: + Added to ~ppc. + +* embassy-topo-1.0.0 (19 Jul 2004) + + 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> + embassy-topo-1.0.0.ebuild, metadata.xml, ChangeLog + Initial import. diff --git a/sci-biology/embassy-vienna/ChangeLog b/sci-biology/embassy-vienna/ChangeLog new file mode 100644 index 00000000..ec10ac28 --- /dev/null +++ b/sci-biology/embassy-vienna/ChangeLog @@ -0,0 +1,63 @@ +# 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 1.13 2015/06/21 09:18:26 jlec Exp $ + + 21 Jun 2015; Justin Lecher <jlec@gentoo.org> + files/embassy-vienna-1.7.2.650_fix-build-system.patch: + Update buildsystem for latest plplot, bug #552492 + + 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) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-vienna-1.7.2.650.ebuild, + +files/embassy-vienna-1.7.2.650_fix-build-system.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> + embassy-vienna-1.7.2.ebuild, embassy-vienna-1.7.2-r1.ebuild: + Fix SRC_URI for emboss + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> embassy-vienna-1.7.2.ebuild, + embassy-vienna-1.7.2-r1.ebuild: + Drop sparc keywords + + 15 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + embassy-vienna-1.7.2-r1.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-vienna-1.7.2-r1 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + +embassy-vienna-1.7.2-r1.ebuild: + Updated version for EMBASSY 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> + embassy-vienna-1.7.2.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-vienna-1.6.ebuild: + Pruning version that will never be stabilised. + +*embassy-vienna-1.7.2 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +embassy-vienna-1.7.2.ebuild: + New upstream version/package for EMBASSY 6.0.1. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + embassy-vienna-1.6.ebuild: + Fixed description. + +*embassy-vienna-1.6 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> + +embassy-vienna-1.6.ebuild: + Initial import. diff --git a/sci-biology/embassy/ChangeLog b/sci-biology/embassy/ChangeLog new file mode 100644 index 00000000..60ddd142 --- /dev/null +++ b/sci-biology/embassy/ChangeLog @@ -0,0 +1,146 @@ +# 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 1.37 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) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-6.6.0.ebuild, + metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #335603 + + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> -embassy-4.0.0.ebuild: + Dropped old, due to unsatisfied deps + + 09 Mar 2011; Raúl Porcel <armin76@gentoo.org> embassy-4.0.0.ebuild, + embassy-6.0.1.ebuild, embassy-6.1.0.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> embassy-6.1.0.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*embassy-6.1.0 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> +embassy-6.1.0.ebuild: + New meta-package for EMBASSY packages building against EMBOSS 6.1.0. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> embassy-6.0.1.ebuild: + Stabilised on amd64 and x86. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> -embassy-5.0.0.ebuild: + Pruning version that will never be stabilised. + +*embassy-6.0.1 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +embassy-6.0.1.ebuild: + New meta-package for EMBASSY packages building against EMBOSS 6.0.1. + +*embassy-5.0.0 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> +embassy-5.0.0.ebuild: + New meta-package for EMBASSY packages building against EMBOSS 5.0.0. + + 17 Feb 2007; Olivier Fisette <ribosome@gentoo.org> embassy-4.0.0.ebuild: + Added to ~amd64. + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> -embassy-3.0.0.ebuild: + Pruning old version. + + 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-4.0.0.ebuild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> embassy-4.0.0.ebuild: + Added ~sparc + + 03 Nov 2006; Fabian Groffen <grobian@gentoo.org> embassy-3.0.0.ebuild, + embassy-4.0.0.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> embassy-4.0.0.ebuild: + Added to x86. + +*embassy-4.0.0 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +embassy-4.0.0.ebuild: + New meta-package for EMBASSY packages building against EMBOSS 4.0.0. + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -embassy-2.10.0.ebuild: + Removed obsolete version. + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> embassy-3.0.0.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> embassy-3.0.0.ebuild: + Stable on ppc. + + 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> embassy-3.0.0.ebuild: + Added to x86. + +*embassy-3.0.0 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +embassy-3.0.0.ebuild: + New version. This meta-package is for EMBASSY software distributed with + EMBOSS 3.0.0. + + 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> -embassy-2.9.0.ebuild: + Removed old version. + + 27 Jul 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-2.10.0.ebuild: + Stable ppc-macos + + 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-2.10.0.ebuild: + Testing ppc-macos due to embassy-construct being testing. + + 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> embassy-2.10.0.ebuild: + Marked ppc stable. + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> embassy-2.10.0.ebuild: + Added to x86. + + 06 May 2005; David Holm <dholm@gentoo.org> embassy-2.10.0.ebuild: + Added to ~ppc. + + 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> embassy-2.10.0.ebuild: + Added patched versions of DOMAINATRIX and EMNU that work with EMBOSS 2.10. + +*embassy-2.10.0 (25 Mar 2005) + + 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> embassy-2.9.0.ebuild, + +embassy-2.10.0.ebuild: + Ebuilds for the 2.9 and 2.10 branches of EMBOSS. + + 23 Mar 2005; Olivier Fisette <ribosome@gentoo.org> embassy-2.9.0.ebuild: + EMBOSS 2.10 is incompatible with EMBASSY 2.9 packages. + + 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-2.9.0.ebuild: + Stable ppc-macos + + 25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-2.9.0.ebuild: + Unstable ppc-macos + +*embassy-2.9.0 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +embassy-2.9.0.ebuild: + Moved from app-sci/embassy to sci-biology/embassy. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> embassy-2.9.0.ebuild: + Added to x86. + + 04 Sep 2004; Thomas Matthijs <axxo@gentoo.org> embassy-2.9.0.ebuild: + fix depend syntax 58347 + + 21 Jul 2004; David Holm <dholm@gentoo.org> embassy-2.9.0.ebuild: + Added to ~ppc. + +* embassy-2.9.0 (19 Jul 2004) + + 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> + embassy-2.9.0.ebuild, metadata.xml, ChangeLog + Initial import. diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog new file mode 100644 index 00000000..c0a7b718 --- /dev/null +++ b/sci-biology/emboss/ChangeLog @@ -0,0 +1,363 @@ +# 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 1.75 2015/07/23 20:18:07 pacho Exp $ + + 23 Jul 2015; Pacho Ramos <pacho@gentoo.org> emboss-6.6.0.ebuild: + ppc stable wrt bug #529038 + + 07 May 2015; Justin Lecher <jlec@gentoo.org> emboss-6.6.0.ebuild, + files/emboss-6.6.0_fix-build-system.patch: + Correct Licenses, bug #548810; make build with newer plplot, bug #548806; add + missing dep, bug #544516 + + 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) + + 28 Mar 2015; Justin Lecher <jlec@gentoo.org> +emboss-6.6.0.ebuild, + +files/README.gentoo, +files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch, + +files/emboss-6.6.0_fix-build-system.patch, + +files/emboss-6.6.0_plplot-declarations.patch, + +files/emboss-6.6.0_qa-implicit-declarations.patch, metadata.xml: + Import latest changes from science overlay, thanks Ted Tanberry for the work; + fixes #504680 + + 28 Dec 2014; Aaron W. Swenson <titanofold@gentoo.org> emboss-6.3.1_p4.ebuild, + emboss-6.3.1_p4-r1.ebuild: + Rename virtual/postgresql to dev-db/postgresql + + 03 Nov 2014; Aaron W. Swenson <titanofold@gentoo.org> emboss-6.3.1_p4.ebuild, + emboss-6.3.1_p4-r1.ebuild: + Update PostgreSQL dependencies and/or checks to virtual/postgresql. + + 30 Jul 2014; Brian Evans <grknight@gentoo.org> emboss-6.0.1.ebuild, + emboss-6.1.0-r1.ebuild, emboss-6.3.1_p4-r1.ebuild, emboss-6.3.1_p4.ebuild: + Non-maintainer commit. Update to use virtual/mysql wrt bug 508802 + +*emboss-6.3.1_p4-r1 (19 Nov 2012) + + 19 Nov 2012; Justin Lecher <jlec@gentoo.org> +emboss-6.3.1_p4-r1.ebuild, + +files/emboss-6.3.1_p4-r1_plcol.patch: + Fix compilation problem with toplplot, #391669, thanks Juergen Rose for the + patch + + 26 Apr 2012; Justin Lecher <jlec@gentoo.org> -emboss-6.1.0.ebuild: + Drop old + + 20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> emboss-6.3.1_p4.ebuild, + emboss-6.1.0.ebuild, emboss-6.1.0-r1.ebuild, emboss-6.0.1.ebuild: + Fix SRC_URI + + 26 Jul 2011; Kacper Kowalik <xarthisius@gentoo.org> emboss-6.0.1.ebuild, + emboss-6.1.0.ebuild, emboss-6.1.0-r1.ebuild, emboss-6.3.1_p4.ebuild: + ppc64 keyword dropped + + 04 Apr 2011; Justin Lecher <jlec@gentoo.org> -emboss-4.0.0.ebuild, + emboss-6.0.1.ebuild, emboss-6.1.0.ebuild: + Dropped old, fix for wrong EAPI version, #361919 + + 11 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild, + metadata.xml: + Remove largefile USE support and default to it + + 09 Mar 2011; Raúl Porcel <armin76@gentoo.org> emboss-4.0.0.ebuild, + emboss-6.0.1.ebuild, emboss-6.1.0.ebuild, emboss-6.1.0-r1.ebuild, + emboss-6.3.1_p4.ebuild: + Drop sparc keywords + + 09 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild: + EAPI=4 takes three arguments on use_with + +*emboss-6.3.1_p4 (09 Mar 2011) + + 09 Mar 2011; Justin Lecher <jlec@gentoo.org> + +files/6.3.1_p4-unbundle-libs.patch, -files/6.3.1-unbundle-libs.patch, + -emboss-6.3.1.ebuild, +emboss-6.3.1_p4.ebuild: + Bump to latest upstream patches + +*emboss-6.3.1 (09 Mar 2011) + + 09 Mar 2011; Justin Lecher <jlec@gentoo.org> + +files/6.3.1-unbundle-libs.patch, +files/emboss-README.Gentoo-2, + emboss-4.0.0.ebuild, emboss-6.0.1.ebuild, emboss-6.1.0-r1.ebuild, + +emboss-6.3.1.ebuild, metadata.xml: + Version Bump #335603, Unbundled libs, removed old, fix clash with + /usr/bin/digest, #330507 + + 18 Jul 2010; <nixnut@gentoo.org> emboss-6.0.1.ebuild: + ppc stable #325457 + + 09 Jul 2010; Samuli Suominen <ssuominen@gentoo.org> emboss-6.0.1.ebuild: + ppc64 stable wrt #325457 + + 23 Jun 2010; Justin Lecher <jlec@gentoo.org> emboss-4.0.0.ebuild, + emboss-6.0.1.ebuild, emboss-6.1.0.ebuild, emboss-6.1.0-r1.ebuild: + Blocking sys-devel/cons, bug 248792 + +*emboss-6.1.0-r1 (07 Mar 2010) + + 07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> + +emboss-6.1.0-r1.ebuild: + Moved to EAPI=3 for PREFIX support, imported prefix patches from overlay, + keyworded as in overlay + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> emboss-6.1.0.ebuild: + Remove documentation that conflicts with EMBASSY phylipnew. + +*emboss-6.1.0 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> +emboss-6.1.0.ebuild: + New upstream version. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> emboss-6.0.1.ebuild: + Stabilised on x86 and amd64. + + 31 Aug 2009; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild, + emboss-6.0.1.ebuild: + Q.A. fixes, including better dependency on ClustalW. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> -emboss-5.0.0.ebuild: + Pruning version that will never be stabilised. + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild: + Depend on ClustalW 1.83 since version 2.x will soon be added to Portage + and is incompatible with EMBOSS wrapper programs. + +*emboss-6.0.1 (26 Aug 2008) + + 26 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +emboss-6.0.1.ebuild: + New upstream version. + + 25 Jan 2008; Markus Dittrich <markusle@gentoo.org> + +files/emboss-5.0.0-as-needed.patch, emboss-4.0.0.ebuild, + emboss-5.0.0.ebuild: + Fixed unresolved symbols with as-needed (see bug #207304). + + 22 Jul 2007; Donnie Berkholz <dberkholz@gentoo.org>; emboss-4.0.0.ebuild: + Drop virtual/x11 references. + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> + +files/emboss-README.Gentoo-1: + Added updated Gentoo README file in reStructuredText format. + +*emboss-5.0.0 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> +emboss-5.0.0.ebuild: + New upstream version. + + 09 Apr 2007; Jeff Gardner <je_fro@gentoo.org> +files/22emboss, + -files/22emboss-r1, emboss-4.0.0.ebuild: + Fixed to use doenvd wrt bug #173884 + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> + -emboss-3.0.0-r1.ebuild, emboss-4.0.0.ebuild: + Pruned old version. Removed ppc-macos keyword, as grobian said the + package and its dependencies were fully moved into "prefix". + + 20 Nov 2006; <blubb@gentoo.org> emboss-4.0.0.ebuild: + stable on amd64 + + 15 Nov 2006; Markus Rothe <corsair@gentoo.org> emboss-4.0.0.ebuild: + Stable on ppc64; bug #153766 + + 03 Nov 2006; nixnut <nixnut@gentoo.org> emboss-4.0.0.ebuild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> emboss-3.0.0-r1.ebuild: + Added ~sparc to emboss-3 for embassy-phylip-3.6b. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild: + Added to x86. + + 18 Aug 2006; Jason Wever <weeve@gentoo.org> emboss-4.0.0.ebuild: + Added ~sparc keyword wrt bug #144241. + +*emboss-4.0.0 (21 Jul 2006) + + 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +emboss-4.0.0.ebuild: + New upstream version. See change log: + "http://emboss.sourceforge.net/developers/changelog.html". + + 20 Apr 2006; Olivier Fisette <ribosome@gentoo.org> -emboss-3.0.0.ebuild: + Removed old revision. + + 08 Apr 2006; Simon Stelling <blubb@gentoo.org> emboss-3.0.0-r1.ebuild: + stable on amd64 + + 22 Feb 2006; Fabian Groffen <grobian@gentoo.org> ChangeLog: + Marked ppc-macos stable (bug #123332) + + 22 Feb 2006; <nixnut@gentoo.org> emboss-3.0.0-r1.ebuild: + Stable on ppc. bug 123332 + + 21 Feb 2006; Markus Rothe <corsair@gentoo.org> emboss-3.0.0-r1.ebuild: + Stable on ppc64; bug #123332 + + 20 Feb 2006; Joshua Jackson <tsunam@gentoo.org> emboss-3.0.0-r1.ebuild: + Stable on x86; bug #123332 + + 19 Feb 2006; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0-r1.ebuild: + Block old versions of pscan to avoid file collisions (see bug #116236). + + 23 Jan 2006; Olivier Fisette <ribosome@gentoo.org> +files/README.Gentoo: + Added missing README file (fixes bug #120071). + +*emboss-3.0.0-r1 (21 Jan 2006) + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> + +emboss-3.0.0-r1.ebuild: + Install codons and restriction enzyme equivalence files in alternative + directories. This avoids file collisions on case insensitive filesystems + (see bug #115446), allows the installation of an updated enzyme prototypes + file that will give more consistent results (see bug #118832). + + 14 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; emboss-3.0.0.ebuild: + Add modular X dependencies. + + 19 Nov 2005; Simon Stelling <blubb@gentoo.org> emboss-3.0.0.ebuild: + stable on amd64 + + 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -emboss-2.10.0.ebuild: + Removed obsolete version. + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> emboss-3.0.0.ebuild: + Stable on ppc. + + 24 Sep 2005; Markus Rothe <corsair@gentoo.org> emboss-3.0.0.ebuild: + Stable on ppc64 + + 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild: + Added to x86. + + 04 Sep 2005; Simon Stelling <blubb@gentoo.org> emboss-3.0.0.ebuild: + added ~amd64 keyword + + 13 Aug 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild, + emboss-2.10.0.ebuild: + Fixed Prosite dependency. + +*emboss-3.0.0 (06 Aug 2005) + + 06 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +emboss-3.0.0.ebuild: + New version. + + 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> -emboss-2.9.0.ebuild: + Removed old version. + + 25 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.10.0.ebuild: + Stable ppc-macos + + 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> emboss-2.10.0.ebuild: + Marked ppc stable for bug #96819. + + 19 Jun 2005; Markus Rothe <corsair@gentoo.org> emboss-2.10.0.ebuild: + Stable on ppc64 + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.10.0.ebuild: + Added to x86. + + 02 May 2005; Omkhar Arasaratnam <omkhar@gentoo.org> emboss-2.10.0.ebuild: + Added ~ppc64 + + 02 May 2005; Michael Hanselmann <hansmi@gentoo.org> emboss-2.9.0.ebuild: + Stable on ppc. + +*emboss-2.10.0 (22 Mar 2005) + + 22 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +emboss-2.10.0.ebuild: + New version. + + 22 Feb 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild: + Added support for minimal build. + + 09 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.9.0.ebuild: + Stable ppc-macos + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild: + Ebuild cleanup. + + 01 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.9.0.ebuild: + Unstable ppc-macos. + +*emboss-2.9.0 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +files/22emboss-r1, +emboss-2.9.0.ebuild: + Moved from app-sci/emboss to sci-biology/emboss. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild, + -emboss-2.8.0-r3.ebuild: + Removed old version. Added 2.9.0 to x86. + + 10 Aug 2004; Olivier Fisette <ribosome@gentoo.org> + emboss-2.8.0-r3.ebuild: + Added to x86. + emboss-2.8.0-r2.ebuild: + Removed obsolete ebuild. + + 21 Jul 2004; David Holm <dholm@gentoo.org> emboss-2.9.0.ebuild: + Added to ~ppc. + + 20 Jul 2004; Olivier Fisette <ribosome@gentoo.org> + emboss-2.8.0-r3.ebuild, emboss-2.9.0.ebuild: + Removed icc support since no patching is needed. + + 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild: + Version bump. Changed the configuration and install steps a bit to + reflect the fact that header files are now installed automatically. + + 14 Jul 2004; Olivier Fisette <ribosome@gentoo.org> + emboss-2.8.0-r3.ebuild: Modified configuration step to make the X and png + USE flags independent; Added support for icc; Added primer3 and clustalw + to the dependencies since some EMBOSS programs won't work without them; + Added support for the biological databases aaindex, cutg, prints, prosite, + rebase and transfac, which are needed for many EMBOSS programs (the databases + are PDEPENDencies since they all must be indexed with an EMBOSS program before + use) (this database support is optional); Added header files installation for + EMBOSS development. + emboss-2.8.0-r2.ebuild: Added to x86. + emboss-2.8.0-r1.ebuild, emboss-2.8.0.ebuild, emboss-2.7.1.ebuild: Removed files. + metadata.xml: Added long description; Set myself as maintainer. + + 02 Jun 2004; Aron Griffis <agriffis@gentoo.org> emboss-2.8.0-r1.ebuild, + emboss-2.8.0-r2.ebuild: + Fix use invocation + + 12 May 2004; David Holm <dholm@gentoo.org> emboss-2.8.0-r2.ebuild: + Added to ~ppc. + +*emboss-2.8.0-r2 (11 May 2004) + + 11 May 2004; Patrick Kursawe <phosphan@gentoo.org> emboss-2.8.0-r2.ebuild, + files/22emboss-r1: + Adjusted value of PLPLOT_LIB, see bug #50176 + +*emboss-2.8.0-r1 (30 Jan 2004) + + 30 Jan 2004; Stephen Diener <sediener@gentoo.org> emboss-2.8.0-r1.ebuild: + Modified to use X and png properly for servers + + 28 Jan 2004; Stephen Diener <sediener@gentoo.org> emboss-2.8.0.ebuild: + Modified 2.8.0 ebuild to require X not just USE it. + +*emboss-2.8.0 (13 Dec 2003) + + 13 Dec 2003; Stephen Diener <sediener@gentoo.org> emboss-2.7.1.ebuild, + emboss-2.8.0.ebuild: + Version bump... + + 20 Oct 2003; George Shapovalov <george@gentoo.org> metdata.xml : + added metadata.xml, marked ebuild stable + +*emboss-2.7.1 (03 Sep 2003) + + 03 Sep 2003; <sediener@gentoo.org> emboss-2.7.1.ebuild: + Initial ebuild diff --git a/sci-biology/eugene/ChangeLog b/sci-biology/eugene/ChangeLog new file mode 100644 index 00000000..e610158d --- /dev/null +++ b/sci-biology/eugene/ChangeLog @@ -0,0 +1,60 @@ +# 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 1.14 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 + + 24 Mar 2015; Agostino Sarubbo <ago@gentoo.org> eugene-4.1.ebuild: + Stable for amd64, wrt bug #543936 + + 20 Mar 2015; Justin Lecher <jlec@gentoo.org> + +files/eugene-4.1-format-security.patch, -eugene-3.5g.ebuild, + eugene-3.6-r1.ebuild, eugene-4.1.ebuild: + Drop old; fix for format-security; drop broken doc generation, bug #461000 + +*eugene-4.1 (09 Mar 2013) + + 09 Mar 2013; Justin Lecher <jlec@gentoo.org> +eugene-4.1.ebuild, + metadata.xml: + Version Bump; drop maintainer + + 11 Feb 2011; Markos Chandras <hwoarang@gentoo.org> eugene-3.6-r1.ebuild: + Stable on amd64 wrt bug #353575 + + 07 Feb 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> eugene-3.6-r1.ebuild: + x86 stable wrt bug #353575 + +*eugene-3.6-r1 (10 Sep 2010) + + 10 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org> -eugene-3.6.ebuild, + +eugene-3.6-r1.ebuild, +files/eugene-3.6-overflow.patch, + +files/eugene-3.6-plugins.patch: + Fix overflows wrt bug 336607 and install path wrt bug 297536. Thanks to + Diego for the reports. + +*eugene-3.6 (07 May 2010) + + 07 May 2010; Andrey Kislyuk <weaver@gentoo.org> -eugene-3.5d.ebuild, + +eugene-3.6.ebuild: + Version bump + + 31 Oct 2009; Markus Meier <maekke@gentoo.org> eugene-3.5g.ebuild: + amd64/x86 stable, bug #290937 + +*eugene-3.5g (09 Sep 2009) + + 09 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> eugene-3.5d.ebuild, + +eugene-3.5g.ebuild: + Version bump and address bug 277226 + + 18 Apr 2009; Markus Meier <maekke@gentoo.org> eugene-3.5d: + amd64/x86 stable, bug #263041 + +*eugene-3.5d (04 Jan 2009) + + 04 Jan 2009; weaver <weaver@gentoo.org> +eugene-3.5d.ebuild: + Initial commit, ebuild written by me diff --git a/sci-biology/exonerate/ChangeLog b/sci-biology/exonerate/ChangeLog new file mode 100644 index 00000000..b7b4122e --- /dev/null +++ b/sci-biology/exonerate/ChangeLog @@ -0,0 +1,38 @@ +# ChangeLog for sci-biology/exonerate +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/exonerate/ChangeLog,v 1.7 2014/07/09 21:04:13 dilfridge Exp $ + + 09 Jul 2014; Andreas K. Huettel <dilfridge@gentoo.org> + -exonerate-2.2.0.ebuild: + Remove old + + 25 Jan 2013; Justin Lecher <jlec@gentoo.org> exonerate-2.2.0-r1.ebuild, + metadata.xml: + We need USE=utils for testing, #453978; move to autotool-utils.eclass + + 13 Dec 2011; Justin Lecher <jlec@gentoo.org> exonerate-2.2.0-r1.ebuild: + Respect CFLAGS and CC, #394545 + + 22 Jun 2011; Fabian Groffen <grobian@gentoo.org> exonerate-2.2.0-r1.ebuild: + Marked ~ppc-macos and ~x64-macos for bug #372327 + + 10 Mar 2011; Justin Lecher <jlec@gentoo.org> exonerate-2.2.0.ebuild, + exonerate-2.2.0-r1.ebuild, metadata.xml: + Remove largefile USE support and default to it + +*exonerate-2.2.0-r1 (20 Jun 2010) + + 20 Jun 2010; Kacper Kowalik <xarthisius@gentoo.org> + +exonerate-2.2.0-r1.ebuild, +files/exonerate-2.2.0-asneeded.patch: + Fixing --as-needed issues wrt bug 268094, adding threads flag, adding more + docs + +*exonerate-2.2.0 (01 May 2009) + + 01 May 2009; Jeff Gardner <je_fro@gentoo.org> +exonerate-2.2.0.ebuild, + +metadata.xml: + Bump and move to portage. + + 18 Jan 2008; Jeff Gardner <je_fro@gentoo.org> +exonerate-1.4.0.ebuild: + Initial import thanks to dawe on bug #206521 + diff --git a/sci-biology/express/ChangeLog b/sci-biology/express/ChangeLog new file mode 100644 index 00000000..2c271407 --- /dev/null +++ b/sci-biology/express/ChangeLog @@ -0,0 +1,30 @@ +# ChangeLog for sci-biology/express +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/express/ChangeLog,v 1.7 2015/04/07 14:32:44 jlec Exp $ + +*express-1.5.1 (13 Oct 2014) + + 13 Oct 2014; Justin Lecher <jlec@gentoo.org> +express-1.5.1.ebuild, + +files/express-1.5.1-buildsystem.patch: + Version Bump; thanks Michael Schubert for the initial patch, #525188 + +*express-0.9.5-r1 (05 Feb 2014) + + 05 Feb 2014; Sergey Popov <pinkbyte@gentoo.org> +express-0.9.5-r1.ebuild: + Revision bump: EAPI 5, add subslot to Boost dependency, fix underlinking on + Boost components, wrt bug #499038 + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 09 Nov 2012; Justin Lecher <jlec@gentoo.org> express-0.9.5.ebuild: + Keyworded for ~x86; drop needless version restriction of boost, #440634 + + 31 Oct 2012; Diego E. Pettenò <flameeyes@gentoo.org> express-0.9.5.ebuild: + Avoid using a slot depend since now boost is unslotted. + +*express-0.9.5 (25 Feb 2012) + + 25 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> +express-0.9.5.ebuild, + +metadata.xml: + New package, ebuild written by me diff --git a/sci-biology/fasta/ChangeLog b/sci-biology/fasta/ChangeLog new file mode 100644 index 00000000..bc5cb52d --- /dev/null +++ b/sci-biology/fasta/ChangeLog @@ -0,0 +1,41 @@ +# ChangeLog for sci-biology/fasta +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasta/ChangeLog,v 1.11 2015/04/07 14:32:54 jlec Exp $ + + 29 Jan 2015; Michał Górny <mgorny@gentoo.org> fasta-35.4.10.ebuild, + fasta-36.3.5e.ebuild: + Convert to CPU_FLAGS_X86. + +*fasta-36.3.5e (11 May 2013) + + 11 May 2013; Justin Lecher <jlec@gentoo.org> +fasta-36.3.5e.ebuild, + +files/fasta-36.3.5e-ldflags.patch: + Version Bump + + 10 Dec 2012; Justin Lecher <jlec@gentoo.org> fasta-35.4.10.ebuild, + metadata.xml: + Drop hardwired icc support + + 21 Nov 2011; Justin Lecher <jlec@gentoo.org> fasta-35.4.10.ebuild: + keyworded for ~x86-macos ~x64-macos, tested by Johan Hattne #390123 + + 18 Jan 2011; Thomas Kahle <tomka@gentoo.org> fasta-35.4.10.ebuild: + x86 stable per bug 351758 + + 18 Jan 2011; Justin Lecher <jlec@gentoo.org> fasta-35.4.10.ebuild: + Warn for incompatible CFLAGS with USE=icc, #351758 + + 18 Jan 2011; Markos Chandras <hwoarang@gentoo.org> fasta-35.4.10.ebuild: + Stable on amd64 wrt bug #351758 + + 16 Jan 2011; Kacper Kowalik <xarthisius@gentoo.org> fasta-35.4.10.ebuild: + marked ~ppc wrt #303931 + + 15 Jun 2010; Justin Lecher <jlec@gentoo.org> fasta-35.4.10.ebuild: + keyworded for ~amd64-linux ~x86-linux + +*fasta-35.4.10 (06 Feb 2010) + + 06 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org> + +files/35.4.10-ldflags.patch, +fasta-35.4.10.ebuild, +metadata.xml: + Initial import, thanks to Jose Maria Fernandez Gonzalez diff --git a/sci-biology/fasttree/ChangeLog b/sci-biology/fasttree/ChangeLog new file mode 100644 index 00000000..32bfaae5 --- /dev/null +++ b/sci-biology/fasttree/ChangeLog @@ -0,0 +1,40 @@ +# ChangeLog for sci-biology/fasttree +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/ChangeLog,v 1.9 2015/04/19 10:00:40 ago Exp $ + + 19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> fasttree-2.1.7.ebuild: + Stable for x86, wrt bug #544950 + + 08 Apr 2015; Agostino Sarubbo <ago@gentoo.org> fasttree-2.1.7.ebuild: + Stable for amd64, wrt bug #544950 + +*fasttree-2.1.8 (29 Mar 2015) + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> +fasttree-2.1.8.ebuild, + +files/fasttree-2.1.7-format-security.patch, + +files/fasttree-2.1.8-format-security.patch, -fasttree-2.0.1.ebuild, + -files/fasttree-2.0.1-asneeded.patch, fasttree-2.1.7.ebuild: + Version Bump; drop old + + 29 Jan 2015; Michał Górny <mgorny@gentoo.org> fasttree-2.1.7.ebuild: + Switch to CPU_FLAGS_X86. + +*fasttree-2.1.7 (20 Dec 2013) + + 20 Dec 2013; Justin Lecher <jlec@gentoo.org> +fasttree-2.1.7.ebuild, + +files/CMakeLists.txt, metadata.xml: + Version Bump, #494662 + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 20 Jun 2010; Kacper Kowalik <xarthisius@gentoo.org> fasttree-2.0.1.ebuild, + +files/fasttree-2.0.1-asneeded.patch: + Respect FLAGS and fix as-needed issues wrt bug 295199. Thanks Diego for + reporting. + +*fasttree-2.0.1 (10 Sep 2009) + + 10 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +fasttree-2.0.1.ebuild: + New package, ebuild written by me diff --git a/sci-biology/finchtv/ChangeLog b/sci-biology/finchtv/ChangeLog new file mode 100644 index 00000000..09a4aacc --- /dev/null +++ b/sci-biology/finchtv/ChangeLog @@ -0,0 +1,45 @@ +# ChangeLog for sci-biology/finchtv +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/finchtv/ChangeLog,v 1.11 2015/04/20 20:24:42 jlec Exp $ + + 20 Apr 2015; Justin Lecher <jlec@gentoo.org> -finchtv-1.3.1-r1.ebuild: + Drop old + + 19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> finchtv-1.3.1-r2.ebuild: + Stable for x86, wrt bug #545798 + + 08 Apr 2015; Agostino Sarubbo <ago@gentoo.org> finchtv-1.3.1-r2.ebuild: + Stable for amd64, wrt bug #545798 + +*finchtv-1.3.1-r2 (07 Apr 2015) + + 07 Apr 2015; Justin Lecher <jlec@gentoo.org> +finchtv-1.3.1-r2.ebuild, + metadata.xml: + EAPI bump + + 24 Jul 2012; Justin Lecher <jlec@gentoo.org> finchtv-1.3.1-r1.ebuild, + metadata.xml: + Use QA_PREBUILT for binary packages + + 06 Aug 2011; Markus Meier <maekke@gentoo.org> finchtv-1.3.1-r1.ebuild: + x86 stable, bug #375933 + + 24 Jul 2011; Markos Chandras <hwoarang@gentoo.org> finchtv-1.3.1-r1.ebuild: + Stable on amd64 wrt bug #375933 + + 15 Oct 2010; Justin Lecher <jlec@gentoo.org> -finchtv-1.3.1.ebuild, + finchtv-1.3.1-r1.ebuild: + Cleaned old versions and curent ebuild; keyworded for ~-linux prefix + +*finchtv-1.3.1-r1 (20 Dec 2008) + + 20 Dec 2008; Jeff Gardner <je_fro@gentoo.org> +finchtv-1.3.1-r1.ebuild: + Install in /opt fog bug #251613 + + 31 Dec 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog: + fixing my email addy in Changelog + +*finchtv-1.3.1 (30 Dec 2007) + + 30 Dec 2007; <je_fro@gentoo.org> +metadata.xml, +finchtv-1.3.1.ebuild: + Initial import from the science overlay. diff --git a/sci-biology/flower/ChangeLog b/sci-biology/flower/ChangeLog new file mode 100644 index 00000000..c53233cd --- /dev/null +++ b/sci-biology/flower/ChangeLog @@ -0,0 +1,18 @@ +# ChangeLog for sci-biology/flower +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/flower/ChangeLog,v 1.3 2015/01/19 22:44:09 slyfox Exp $ + + 19 Jan 2015; Sergei Trofimovich <slyfox@gentoo.org> + +files/flower-0.7.2-ghc-7.8.patch, -flower-0.7-r1.ebuild, flower-0.7.2.ebuild: + Port to ghc-7.8 (bug #537052 by Toralf Förster). + +*flower-0.7.2 (22 Sep 2013) + + 22 Sep 2013; Heather Cynede <cynede@gentoo.org> +flower-0.7.2.ebuild: + flower version bump + +*flower-0.7-r1 (12 Sep 2013) + + 12 Sep 2013; Sergei Trofimovich <slyfox@gentoo.org> +flower-0.7-r1.ebuild, + +metadata.xml: + Analyze 454 flowgrams (.SFF files) (requested by Martin MOKREJŠ). diff --git a/sci-biology/foldingathome/ChangeLog b/sci-biology/foldingathome/ChangeLog new file mode 100644 index 00000000..37cfa737 --- /dev/null +++ b/sci-biology/foldingathome/ChangeLog @@ -0,0 +1,324 @@ +# ChangeLog for sci-biology/foldingathome +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/foldingathome/ChangeLog,v 1.44 2014/08/10 20:31:38 slyfox Exp $ + + 10 Aug 2014; Sergei Trofimovich <slyfox@gentoo.org> + foldingathome-7.3.6-r2.ebuild, foldingathome-7.4.4.ebuild: + QA: drop trailing '.' from DESCRIPTION + +*foldingathome-7.4.4 (16 Jul 2014) + + 16 Jul 2014; Ian Stakenvicius (_AxS_) <axs@gentoo.org> + +foldingathome-7.4.4.ebuild: + version bump; license changed, is slightly more lax now + + 13 May 2013; Ian Stakenvicius <axs@gentoo.org> foldingathome-7.3.6-r2.ebuild: + showing special permission during pkg_setup so that we 'display this notice.' + + 13 May 2013; Ian Stakenvicius <axs@gentoo.org> foldingathome-7.3.6-r2.ebuild: + put back mirror restriction (was too excited about dropping fetch, forgot to + re-add) + + 13 May 2013; Ian Stakenvicius <axs@gentoo.org> foldingathome-7.3.6-r2.ebuild: + Dropped fetch restriction and amended license, as Gentoo has been granted + special permissions + +*foldingathome-7.3.6-r2 (20 Apr 2013) + + 20 Apr 2013; Ian Stakenvicius <axs@gentoo.org> +foldingathome-7.3.6-r2.ebuild, + -foldingathome-7.3.6-r1.ebuild: + restricted strip as technically that modifies the binaries, and we want to be + as safe as possible wrt to the EULA + +*foldingathome-7.3.6-r1 (16 Apr 2013) + + 16 Apr 2013; Ian Stakenvicius <axs@gentoo.org> +foldingathome-7.3.6-r1.ebuild, + -foldingathome-7.3.6.ebuild, files/7.3/fah-init, files/7.3/folding-conf.d: + minor fixes to conf.d and init.d files + +*foldingathome-7.3.6 (16 Apr 2013) + + 16 Apr 2013; Ian Stakenvicius <axs@gentoo.org> +files/7.3/fah-init, + +files/7.3/folding-conf.d, +files/7.3/initfolding, + +foldingathome-7.3.6.ebuild, -files/6.34/fah-init, -files/6.34/folding-conf.d, + -files/6.34/initfolding, -foldingathome-6.34-r1.ebuild, + -foldingathome-6.34-r2.ebuild, metadata.xml: + version bump, remove old; updated license and added RESTRICT as per license + requirements, also added 32bit variant + + 24 Sep 2012; Mike Frysinger <vapier@gentoo.org> foldingathome-6.34-r1.ebuild, + foldingathome-6.34-r2.ebuild: + QA_DT_HASH (old/deprecated) -> QA_FLAGS_IGNORED (new hotness). + + 14 Feb 2012; Torsten Veller <tove@gentoo.org> foldingathome-6.34-r2.ebuild: + Fix ebuild header (#398773) + +*foldingathome-6.34-r2 (20 Sep 2011) + + 20 Sep 2011; Jeff Gardner <je_fro@gentoo.org> files/6.34/fah-init, + +foldingathome-6.34-r2.ebuild: + Change opts to extra_commands in init script. + +*foldingathome-6.34-r1 (28 Jun 2011) + + 28 Jun 2011; Jeff Gardner <je_fro@gentoo.org> files/6.34/fah-init, + -foldingathome-6.34.ebuild, +foldingathome-6.34-r1.ebuild: + Change init script to use 'user' instead of 'chuid' for new openrc. + + 15 Jun 2011; Jeff Gardner <je_fro@gentoo.org> + -files/copy_client_config-5.0.2-r1, -files/init-5.0.2-r3, + -files/init-5.0.2-r5, -foldingathome-5.0.2-r5.ebuild, + -foldingathome-6.02-r1.ebuild, -foldingathome-6.29.ebuild, + -files/folding-conf.d-r1, -files/initfolding-r2: + Remove broken old versions. + +*foldingathome-6.34 (15 Jun 2011) + + 15 Jun 2011; Jeff Gardner <je_fro@gentoo.org> +files/6.34/fah-init, + +files/6.34/folding-conf.d, +files/6.34/initfolding, + +foldingathome-6.34.ebuild: + New version, fixes issues that prevented running FAH on newer GNU/Linux + systems. + + 24 Jun 2010; Justin Lecher <jlec@gentoo.org> + -foldingathome-5.0.2-r3.ebuild: + Cleaned uneeded version + + 22 Jun 2010; Justin Lecher <jlec@gentoo.org> foldingathome-6.29.ebuild: + Dropping ~x86 as upstream only provides 64bit for this version, 324611 + + +*foldingathome-6.29 (17 Jun 2010) + + 17 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/6.29/fah-init, + +files/6.29/folding-conf.d, +files/6.29/initfolding, + +foldingathome-6.29.ebuild: + Version Bump, 270458, fixes for prestripped files. #252033 + + 30 Nov 2008; Jeff Gardner <je_fro@gentoo.org> files/6.02/folding-conf.d: + Removing smp from default opts to hopefully fix bug #248896 + Thanks to Vladimir Berezhnoy. + + 22 Nov 2008; Jeff Gardner <je_fro@gentoo.org> + foldingathome-6.02-r1.ebuild: + Add shameless plug for my folding group. + +*foldingathome-6.02-r1 (22 Nov 2008) + + 22 Nov 2008; Jeff Gardner <je_fro@gentoo.org> -foldingathome-6.02.ebuild, + +foldingathome-6.02-r1.ebuild: + Bumping for init script fix and add back ~x86. + + 22 Nov 2008; Jeff Gardner <je_fro@gentoo.org> files/6.02/fah-init: + Changing to use init script from Constantin Baranov on bug #218331 + + 03 Aug 2008; Jeff Gardner <je_fro@gentoo.org> -files/6.02_beta1/fah-init, + -files/6.02_beta1/folding-conf.d, -files/6.02_beta1/initfolding, + -foldingathome-6.02_beta1.ebuild: + remove dead beta + +*foldingathome-6.02 (03 Aug 2008) + + 03 Aug 2008; Jeff Gardner <je_fro@gentoo.org> +files/6.02/fah-init, + +files/6.02/folding-conf.d, +files/6.02/initfolding, + +foldingathome-6.02.ebuild: + Latest version, thanks to Nicolas Schlumberger, closes bug #233751 + + 15 Jun 2008; Jeff Gardner <je_fro@gentoo.org> + files/6.02_beta1/folding-conf.d: + Add smp option thanks to Timon Van Overveldt in bug #194423 + +*foldingathome-6.02_beta1 (14 Jun 2008) + + 14 Jun 2008; Jeff Gardner <je_fro@gentoo.org> -files/5.91_beta/fah-init, + -files/5.91_beta/initfolding, -files/5.91_beta/folding-conf.d, + +files/6.02_beta1/fah-init, +files/6.02_beta1/folding-conf.d, + +files/6.02_beta1/initfolding, -foldingathome-5.91_beta.ebuild, + +foldingathome-6.02_beta1.ebuild: + Latest beta client + + 12 Jul 2007; Christoph Mende <angelos@gentoo.org> + foldingathome-5.0.2-r5.ebuild: + Stable on amd64 wrt bug #164823 + + 12 Jul 2007; Christian Faulhammer <opfer@gentoo.org> + foldingathome-5.0.2-r5.ebuild: + stable x86, bug 164823 + + 03 Jul 2007; Jeff Gardner <je_fro@gentoo.org> + foldingathome-5.91_beta.ebuild: + foldingathome-5.91_beta has expired. Removing KEYWORDS until the next + release arrives. + + 02 Jul 2007; Piotr Jaroszyński <peper@gentoo.org> + foldingathome-5.0.2-r3.ebuild, foldingathome-5.0.2-r5.ebuild: + (QA) RESTRICT clean up. + + 21 Apr 2007; Jeff Gardner <je_fro@gentoo.org> + foldingathome-5.0.2-r3.ebuild, foldingathome-5.0.2-r5.ebuild: + Use newconfd wrt bug #174266 + + 11 Apr 2007; Jeff Gardner <je_fro@gentoo.org> + foldingathome-5.91_beta.ebuild: + Fixed to better install files under /etc. + +*foldingathome-5.91_beta (10 Apr 2007) + + 10 Apr 2007; Jeff Gardner <je_fro@gentoo.org> +files/5.91_beta/fah-init, + +files/5.91_beta/folding-conf.d, +files/5.91_beta/initfolding, + +foldingathome-5.91_beta.ebuild: + Adding the amd64-smp client for testing. Thanks to John Gibson. + + 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> -files/init-5.0.2-r4, + -foldingathome-5.0.2-r4.ebuild: + Pruned old version. + +*foldingathome-5.0.2-r5 (16 Jun 2006) + + 16 Jun 2006; Patrick Kursawe <phosphan@gentoo.org> +files/init-5.0.2-r5, + +foldingathome-5.0.2-r5.ebuild: + Adding --chdir to start-stop-daemon because of bug #109707 + +*foldingathome-5.0.2-r4 (14 Aug 2005) + + 14 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +files/init-5.0.2-r4, + +foldingathome-5.0.2-r4.ebuild: + Fixed bug #95697: license is now correct and the binaries are no longer + stripped since we are not allowed to modify them. Thanks to Ian Kelly + <kellyia@udel.edu>. Fixed bugs #90247 and #93047: Foldingathome init script + now uses start-stop-daemon. Thanks to James Lademann + <jwlademann@myrealbox.com>. + + 22 Apr 2005; Danny van Dyk <kugelfang@gentoo.org> + foldingathome-5.0.2-r3.ebuild: + Marked stable on amd64. + + 03 Mar 2005; Brandon Low <lostlogic@gentoo.org> -files/folding-conf.d, + -files/folding-init.d, -files/folding-init.d-r1, -files/folding-init.d-r3, + -files/folding.sh, files/init-5.0.2-r3, -files/initfolding, + -files/initfolding-r1, -foldingathome-4.0.0-r2.ebuild, + -foldingathome-4.0.0.ebuild: + Fix bug 82345, nice 20 doesn't exist. + Remove old ebuilds and files. + + 08 Feb 2005; Brandon Low <lostlogic@gentoo.org> + foldingathome-5.0.2-r3.ebuild: + Mark stable on x86 + + 05 Feb 2005; Brandon Low <lostlogic@gentoo.org> -files/copy_client_config, + -files/folding-init.d-r2, -files/folding-init.d-r4, -files/init-5.0.2-r1, + -files/init-5.0.2-r2, -foldingathome-5.0.2-r1.ebuild, + -foldingathome-5.0.2-r2.ebuild, -foldingathome-5.0.2.ebuild: + Clean up some cruft + +*foldingathome-5.0.2-r3 (05 Feb 2005) + + 05 Feb 2005; Brandon Low <lostlogic@gentoo.org> +files/init-5.0.2-r3, + +foldingathome-5.0.2-r3.ebuild: + Fix bug #80778 + +*foldingathome-5.0.2-r2 (04 Feb 2005) + + 04 Feb 2005; Brandon Low <lostlogic@gentoo.org> +files/init-5.0.2-r2, + +foldingathome-5.0.2-r2.ebuild: + Fix bug #79574. Add unitinfo target to initscript to get the status of each + core on the system. Thanks to Yosef Meller <yosefm@gmail.com> for the idea + and initial patch + +*foldingathome-5.0.2-r1 (03 Feb 2005) + + 03 Feb 2005; Brandon Low <lostlogic@gentoo.org> + +files/copy_client_config-5.0.2-r1, +files/init-5.0.2-r1, + +foldingathome-5.0.2-r1.ebuild: + Fix bug 71700 hopefully. Use bash not python for copy_client_config. Update + the init script to do more sane things and not fail to stop on multi-cpu + systems. + +*foldingathome-4.0.0-r2 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +files/copy_client_config, +files/folding-conf.d, +files/folding-conf.d-r1, + +files/folding-init.d, +files/folding-init.d-r1, +files/folding-init.d-r2, + +files/folding-init.d-r3, +files/folding-init.d-r4, +files/folding.sh, + +files/initfolding, +files/initfolding-r1, +files/initfolding-r2, + +foldingathome-4.0.0-r2.ebuild, +foldingathome-4.0.0.ebuild, + +foldingathome-5.0.2.ebuild: + Moved from app-sci/foldingathome to sci-biology/foldingathome. + + 13 Dec 2004; Patrick Kursawe <phosphan@gentoo.org> + -foldingathome-4.0.0-r1.ebuild: + Cleanup + +*foldingathome-5.0.2 (09 Nov 2004) + + 09 Nov 2004; Steve Arnold <nerdboy@gentoo.org> +files/copy_client_config, + +files/folding-conf.d-r1, +files/folding-init.d-r4, +files/initfolding-r2, + +foldingathome-5.0.2.ebuild: + bumped to current version (bug 60318) with ebuild from Gregory P. Smith + <greg-gentoo@electricrain.com>. Gentoo team config. + + 12 Jun 2004; Danny van Dyk <kugelfang@gentoo.org> + foldingathome-4.0.0-r2.ebuild: + Marked ~amd64. + +*foldingathome-4.0.0-r2 (07 Jun 2004) + + 07 Jun 2004; Patrick Kursawe <phosphan@gentoo.org> + foldingathome-3.24-r1.ebuild, foldingathome-3.24.ebuild, + foldingathome-4.0.0-r2.ebuild, files/folding-init.d-r3: + No longer redirecting output to a redundand log file, see bug #51489 + Cleanup, removing 3.x versions. + + 23 Apr 2004; David Holm <dholm@gentoo.org> foldingathome-4.0.0-r1.ebuild: + Added to ~ppc. + +*foldingathome-4.0.0-r1 (22 Apr 2004) + + 22 Apr 2004; Patrick Kursawe <phosphan@gentoo.org> + foldingathome-4.0.0-r1.ebuild, files/folding-conf.d, + files/folding-init.d-r2, files/initfolding-r1: + Added support to run multiple clients for those with multiprocessors + and the ability to pass options to the Folding clients. + Based on bug #47526 (by Mike Caley <mjcaley@darkarctic.com>) + + 26 Mar 2004; Patrick Kursawe <phosphan@gentoo.org> + foldingathome-3.14.ebuild, foldingathome-3.24-r1.ebuild, + foldingathome-3.24.ebuild, foldingathome-4.0.0.ebuild: + Setting IUSE, removing S= where not necessary, declaring 4.0.0 stable for x86 + + 09 Mar 2004; Daniel Ahlberg <aliz@gentoo.org> foldingathome-4.0.0.ebuild: + Adding amd64 keyword. Closing #43779. + +*foldingathome-4.0.0 (03 Mar 2004) + + 03 Mar 2004; Patrick Kursawe <phosphan@gentoo.org> + foldingathome-4.0.0.ebuild: + Version bump inspired by bug #34859 + +*foldingathome-3.24-r1 (01 Mar 2004) + + 01 Mar 2004; Patrick Kursawe <phosphan@gentoo.org> + foldingathome-3.24-r1.ebuild, files/folding-init.d-r1, files/folding.sh, + files/initfolding: + Running as seperate user now. + + 05 May 2003; Daniel Ahlberg <aliz@gentoo.org> files/folding-init.d : + Fixed stop() in init script. Fix by + Roderick van Domburg <r.s.a.vandomburg@student.utwente.nl> in #20327. + + 23 Apr 2003; Daniel Ahlberg <aliz@gentoo.org> foldingathome-3.2.4.ebuild, files/folding-init.d : + Now has the version number in SRC_URI and also uses the newer client if we're running >=glibc-2.3.0. + Also updated init script. Closes #19709 and #17715. + +*foldingathome-3.24 (27 Feb 2003) + + 27 Feb 2003; Daniel Ahlberg <aliz@gentoo.org> foldingathome-3.24.ebuild : + Version bump. + + 27 Feb 2003; Daniel Ahlberg <aliz@gentoo.org> files/folding-init.d : + Start the daemon with nice, closes #12950. + +*foldingathome-3.14 (04 Nov 2002) + + 04 Nov 2002; Daniel Ahlberg <aliz@gentoo.org> : + Initial import. Ebuild contributed by Ryan Shaw <ryan.shaw@stanfordalumni.org> in #9535. diff --git a/sci-biology/gatk/ChangeLog b/sci-biology/gatk/ChangeLog new file mode 100644 index 00000000..f3680501 --- /dev/null +++ b/sci-biology/gatk/ChangeLog @@ -0,0 +1,42 @@ +# ChangeLog for sci-biology/gatk +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/ChangeLog,v 1.8 2015/04/07 14:33:05 jlec Exp $ + +*gatk-2.4 (11 Mar 2013) + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> -gatk-1.6.ebuild, + +gatk-2.4.ebuild, gatk-9999.ebuild: + Version Bump and move to MIT license + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*gatk-1.6 (30 Sep 2012) + + 30 Sep 2012; Andrey Kislyuk <weaver@gentoo.org> -gatk-1.4.ebuild, + -gatk-1.5.ebuild, +gatk-1.6.ebuild: + Version bump, remove old, add git dep + +*gatk-1.5 (07 Apr 2012) + + 07 Apr 2012; Andrey Kislyuk <weaver@gentoo.org> -gatk-1.2.ebuild, + -gatk-1.3.ebuild, +gatk-1.5.ebuild: + Version bump, drop old + +*gatk-1.4 (29 Jan 2012) + + 29 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> +gatk-1.4.ebuild: + Version bump, resolves bug 400885 + +*gatk-1.3 (26 Dec 2011) + + 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +gatk-1.3.ebuild: + Version bump + +*gatk-9999 (31 Oct 2011) +*gatk-1.2 (31 Oct 2011) + + 31 Oct 2011; Andrey Kislyuk <weaver@gentoo.org> +gatk-1.2.ebuild, + +gatk-9999.ebuild, +metadata.xml: + New package, ebuild written by me + diff --git a/sci-biology/gibbs/ChangeLog b/sci-biology/gibbs/ChangeLog new file mode 100644 index 00000000..0ee2a35d --- /dev/null +++ b/sci-biology/gibbs/ChangeLog @@ -0,0 +1,49 @@ +# ChangeLog for sci-biology/gibbs +# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/gibbs/ChangeLog,v 1.9 2012/04/26 16:17:09 jlec Exp $ + + 26 Apr 2012; Justin Lecher <jlec@gentoo.org> gibbs-3.1.ebuild, + -gibbs-1995.9.ebuild: + Move to EAPI=4, drop old + + 28 Dec 2009; Markus Meier <maekke@gentoo.org> gibbs-3.1.ebuild: + x86 stable, bug #290933 + + 24 Dec 2009; Pacho Ramos <pacho@gentoo.org> gibbs-3.1.ebuild: + amd64 stable, bug 290933 + + 30 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> gibbs-1995.9.ebuild: + Drop keyword for old version. Versions 3.1 and 1995.9 are different + packages. I will keep 1995.9 in tree without keywords for hysterical + raisins. + +*gibbs-3.1 (29 Sep 2009) + + 29 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> +gibbs-3.1.ebuild: + Version bump, rewrite ebuild (package rewritten) + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 04 Jan 2006; Olivier Fisette <ribosome@gentoo.org> gibbs-1995.9.ebuild: + Do not depend on "virtual/libc" (package not in system target). + +*gibbs-1995.9 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +files/gibbs-demo, +gibbs-1995.9.ebuild: + Moved from app-sci/gibbs to sci-biology/gibbs. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> gibbs-1995.9.ebuild: + Added to x86. + + 01 Jul 2004; Jeremy Huddleston <eradicator@gentoo.org> gibbs-1995.9.ebuild: + virtual/glibc -> virtual/libc + +*gibbs-1995.9 (27 May 2004) + + 27 May 2004; Patrick Kursawe <phosphan@gentoo.org> gibbs-1995.9.ebuild, + metadata.xml, files/gibbs-demo: + Initial import, ebuild by Frank Vernaillen <fr_ve@hotmail.com> and + olivier.fisette@sympatico.ca in bug #28808 + diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog new file mode 100644 index 00000000..9ce25e18 --- /dev/null +++ b/sci-biology/glimmer/ChangeLog @@ -0,0 +1,65 @@ +# ChangeLog for sci-biology/glimmer +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.14 2015/05/27 16:32:11 jlec Exp $ + + 27 May 2015; Justin Lecher <jlec@gentoo.org> -glimmer-3.02-r2.ebuild: + Drop old + + 27 May 2015; Agostino Sarubbo <ago@gentoo.org> glimmer-3.02-r3.ebuild: + Stable for x86, wrt bug #550436 + + 27 May 2015; Agostino Sarubbo <ago@gentoo.org> glimmer-3.02-r3.ebuild: + Stable for amd64, wrt bug #550436 + +*glimmer-3.02b (26 May 2015) +*glimmer-3.02-r3 (26 May 2015) + + 26 May 2015; Justin Lecher <jlec@gentoo.org> + +files/glimmer-3.02b-jobserver-fix.patch, +files/glimmer-3.02b-ldflags.patch, + +files/glimmer-3.02b-rename_extract.patch, +glimmer-3.02-r3.ebuild, + +glimmer-3.02b.ebuild, -glimmer-3.02-r1.ebuild: + Version Bump and patch for file collision, thanks Martin Mokrejs for the fix, + bug #247394; Respect CXX, CXXFLAGS and LDFLAGS + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 16 Jul 2010; Markos Chandras <hwoarang@gentoo.org> glimmer-3.02-r2.ebuild: + Stable on amd64 wrt bug #328415 + + 16 Jul 2010; Christian Faulhammer <fauli@gentoo.org> + glimmer-3.02-r2.ebuild: + stable x86, bug 328415 + +*glimmer-3.02-r2 (03 Apr 2010) + + 03 Apr 2010; Justin Lecher <jlec@gentoo.org> +glimmer-3.02-r2.ebuild, + +files/glimmer-3.02-jobserver-fix.patch: + jobserver fix, #299482, Thanks Myckel Habets + LDFLAGS/CFLAGS etc repected + + 03 Jan 2010; Pacho Ramos <pacho@gentoo.org> glimmer-3.02-r1.ebuild: + amd64 stable, bug 298762 + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> + glimmer-3.02-r1.ebuild: + stable x86, bug 298762 + + 28 Dec 2009; Andrey Kislyuk <weaver@gentoo.org> + +files/glimmer-3.02-glibc210.patch, glimmer-3.02-r1.ebuild: + QA fixes, including bug 298223 + +*glimmer-3.02-r1 (04 Jan 2009) + + 04 Jan 2009; weaver <weaver@gentoo.org> -glimmer-3.02.ebuild, + +glimmer-3.02-r1.ebuild: + Collision block, bug 247394 + + 30 Sep 2008; Jeremy Olexa <darkside@gentoo.org> glimmer-3.02.ebuild: + add ~amd64 kw based on Chad's testing. bug #239162 + +*glimmer-3.02 (07 Sep 2008) + + 07 Sep 2008; weaver <weaver@gentoo.org> +metadata.xml, + +glimmer-3.02.ebuild: + Import from science overlay diff --git a/sci-biology/glimmerhmm/ChangeLog b/sci-biology/glimmerhmm/ChangeLog new file mode 100644 index 00000000..e872b42b --- /dev/null +++ b/sci-biology/glimmerhmm/ChangeLog @@ -0,0 +1,40 @@ +# ChangeLog for sci-biology/glimmerhmm +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmerhmm/ChangeLog,v 1.10 2014/01/17 14:50:43 jer Exp $ + + 17 Jan 2014; Jeroen Roovers <jer@gentoo.org> glimmerhmm-3.0.1-r1.ebuild: + Spelling. + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 18 Oct 2012; Justin Lecher <jlec@gentoo.org> -glimmerhmm-3.0.1.ebuild: + Drop old + + 17 Oct 2012; Pawel Hajdan jr <phajdan.jr@gentoo.org> + glimmerhmm-3.0.1-r1.ebuild: + x86 stable wrt bug #430524 + + 14 Sep 2012; Agostino Sarubbo <ago@gentoo.org> glimmerhmm-3.0.1-r1.ebuild: + Stable for amd64, wrt bug #430524 + +*glimmerhmm-3.0.1-r1 (20 Jun 2011) + + 20 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/3.0.1-gentoo.patch, + glimmerhmm-3.0.1.ebuild, +glimmerhmm-3.0.1-r1.ebuild: + Respect LDFLAGS and CFLAGS, do not install ELF in usr/share, #297061 & 335257 + + 22 Sep 2009; Markus Meier <maekke@gentoo.org> glimmerhmm-3.0.1.ebuild: + x86 stable, bug #282107 + + 06 Sep 2009; Jeremy Olexa <darkside@gentoo.org> glimmerhmm-3.0.1.ebuild: + amd64 stable, bug 282107 + + 19 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: + QA, keyword ~amd64 + +*glimmerhmm-3.0.1 (07 Sep 2008) + + 07 Sep 2008; weaver <weaver@gentoo.org> +metadata.xml, + +glimmerhmm-3.0.1.ebuild: + Import from science overlay diff --git a/sci-biology/gmap/ChangeLog b/sci-biology/gmap/ChangeLog new file mode 100644 index 00000000..c6c6eb52 --- /dev/null +++ b/sci-biology/gmap/ChangeLog @@ -0,0 +1,64 @@ +# ChangeLog for sci-biology/gmap +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/gmap/ChangeLog,v 1.13 2013/03/11 15:20:23 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*gmap-2012.07.20 (05 Oct 2012) + + 05 Oct 2012; Andrey Kislyuk <weaver@gentoo.org> -gmap-2010.07.27.ebuild, + -gmap-2011.03.28.ebuild, -gmap-2011.09.14.ebuild, +gmap-2012.07.20.ebuild: + Version bump, remove old + +*gmap-2011.10.07 (08 Oct 2011) + + 08 Oct 2011; Andrey Kislyuk <weaver@gentoo.org> -gmap-2007.09.28.ebuild, + -gmap-2010.03.09.ebuild, +gmap-2011.10.07.ebuild: + Version bump, drop old + +*gmap-2011.09.14 (25 Sep 2011) + + 25 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +gmap-2011.09.14.ebuild: + Version bump + + 21 May 2011; Andrey Kislyuk <weaver@gentoo.org> +gmap-2011.03.28.ebuild: + Version bump + +*gmap-2011.03.28 (02 Apr 2011) + + 02 Apr 2011; Andrey Kislyuk <weaver@gentoo.org> +gmap-2011.03.28.ebuild: + Version bump + + 12 Oct 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org> + gmap-2010.07.27.ebuild: + x86 stable wrt bug #340371 + + 11 Oct 2010; Markos Chandras <hwoarang@gentoo.org> gmap-2010.07.27.ebuild: + Stable on amd64 wrt bug #340371 + +*gmap-2010.07.27 (26 Sep 2010) + + 26 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> +gmap-2010.07.27.ebuild: + Version bump + + 16 Jul 2010; Markos Chandras <hwoarang@gentoo.org> gmap-2010.03.09.ebuild: + Stable on amd64 wrt bug #328417 + + 16 Jul 2010; Christian Faulhammer <fauli@gentoo.org> + gmap-2010.03.09.ebuild: + stable x86, bug 328417 + +*gmap-2010.03.09 (23 Mar 2010) + + 23 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> +gmap-2010.03.09.ebuild: + Version bump + + 22 Mar 2009; Markus Meier <maekke@gentoo.org> gmap-2007.09.28.ebuild: + amd64/x86 stable, bug #263044 + +*gmap-2007.09.28 (23 May 2008) + + 23 May 2008; weaver <weaver@gentoo.org> +gmap-2007.09.28.ebuild: + New package from sunrise, bug 135103 + diff --git a/sci-biology/goby-cpp/ChangeLog b/sci-biology/goby-cpp/ChangeLog new file mode 100644 index 00000000..d31c9f8e --- /dev/null +++ b/sci-biology/goby-cpp/ChangeLog @@ -0,0 +1,27 @@ +# ChangeLog for sci-biology/goby-cpp +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/goby-cpp/ChangeLog,v 1.5 2015/04/13 08:26:36 jlec Exp $ + + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> +files/Alignments.proto, + +files/Reads.proto, +files/goby-cpp-2.0.1-underlinking.patch, + goby-cpp-2.0.1.ebuild: + Regenerate protocols, bug #514556 + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*goby-cpp-2.0.1 (19 Jul 2012) + + 19 Jul 2012; Justin Lecher <jlec@gentoo.org> +goby-cpp-2.0.1.ebuild: + Version Bump, handle static-libs + +*goby-cpp-1.9.8.1 (05 Jan 2012) + + 05 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> +goby-cpp-1.9.8.1.ebuild: + Version bump + +*goby-cpp-1.9.7.3 (25 Sep 2011) + + 25 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +goby-cpp-1.9.7.3.ebuild, + +metadata.xml: + New package, ebuild written by me diff --git a/sci-biology/goby/ChangeLog b/sci-biology/goby/ChangeLog new file mode 100644 index 00000000..83a736ee --- /dev/null +++ b/sci-biology/goby/ChangeLog @@ -0,0 +1,18 @@ +# ChangeLog for sci-biology/goby +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/goby/ChangeLog,v 1.3 2013/03/11 15:20:46 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*goby-1.9.8.1 (05 Jan 2012) + + 05 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> +goby-1.9.8.1.ebuild: + Version bump + +*goby-1.9.7.3 (25 Sep 2011) + + 25 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +goby-1.9.7.3.ebuild, + +metadata.xml: + New package, ebuild written by me + diff --git a/sci-biology/hmmer/ChangeLog b/sci-biology/hmmer/ChangeLog new file mode 100644 index 00000000..2e075ba3 --- /dev/null +++ b/sci-biology/hmmer/ChangeLog @@ -0,0 +1,162 @@ +# ChangeLog for sci-biology/hmmer +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.38 2015/01/29 21:21:18 mgorny Exp $ + + 29 Jan 2015; Michał Górny <mgorny@gentoo.org> hmmer-3.0.ebuild: + Switch to CPU_FLAGS_X86. + + 19 Oct 2014; Patrick Lauer <patrick@gentoo.org> hmmer-3.0.ebuild: + Fix header + + 28 Jun 2012; Justin Lecher <jlec@gentoo.org> hmmer-3.0.ebuild, + -files/hmmer-3.0-perl-5.16.patch: + Fix the patch, thanks xarthisius and bonsaikitten for help + + 28 Jun 2012; Justin Lecher <jlec@gentoo.org> files/hmmer-3.0-perl-5.16.patch: + Fix patch, screwed VCS tags, #423983 + + 25 Jun 2012; Justin Lecher <jlec@gentoo.org> hmmer-3.0.ebuild, + +files/hmmer-3.0-perl-5.16.patch, metadata.xml: + Fix for build with perl-5.16, #421799; handle static-libs + + 18 Jul 2010; Christian Faulhammer <fauli@gentoo.org> hmmer-3.0.ebuild: + stable x86, bug 328419 + + 18 Jul 2010; Kacper Kowalik <xarthisius@gentoo.org> hmmer-2.3.2-r1.ebuild, + hmmer-2.3.2-r2.ebuild, hmmer-3.0.ebuild, +files/hmmer-3.0-fix_tests.patch: + Fix tests that use gsl. Make repoman happy. + + 16 Jul 2010; Markos Chandras <hwoarang@gentoo.org> hmmer-3.0.ebuild: + Stable on amd64 wrt bug #328419 + +*hmmer-3.0 (28 Mar 2010) + + 28 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> -hmmer-3.0_beta2.ebuild, + +hmmer-3.0.ebuild: + Version bump + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + hmmer-3.0_beta2.ebuild: + Transfer Prefix keywords + +*hmmer-3.0_beta2 (30 Aug 2009) + + 30 Aug 2009; Andrey Kislyuk <weaver@gentoo.org> +hmmer-3.0_beta2.ebuild: + Bump and add parallel make workaround, bug 282813 + +*hmmer-3.0_beta1 (21 Jun 2009) + + 21 Jun 2009; Andrey Kislyuk <weaver@gentoo.org> -hmmer-3.0_alpha2.ebuild, + +hmmer-3.0_beta1.ebuild: + Version bump + +*hmmer-3.0_alpha2 (02 May 2009) + + 02 May 2009; Andrey Kislyuk <weaver@gentoo.org> +hmmer-3.0_alpha2.ebuild: + Version bump (pre-release) + + 06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml: + Add USE flag description to metadata wrt GLEP 56. + + 07 Feb 2008; Fabian Groffen <grobian@gentoo.org> hmmer-2.3.2-r1.ebuild, + hmmer-2.3.2-r2.ebuild: + Dropped ppc-macos keyword, see you in prefix + + 02 Jan 2008; Raúl Porcel <armin76@gentoo.org> hmmer-2.3.2-r2.ebuild: + Re-add ~ia64 + + 13 Nov 2007; Raúl Porcel <armin76@gentoo.org> hmmer-2.3.2-r2.ebuild: + Add ~alpha + + 22 May 2007; Olivier Fisette <ribosome@gentoo.org> hmmer-2.3.2-r1.ebuild, + hmmer-2.3.2-r2.ebuild: + Updated home page. Stabilised bug-fix release on x86 and amd64. + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Stepping down from maintaining this package. + + 07 May 2006; Markus Rothe <corsair@gentoo.org> hmmer-2.3.2-r2.ebuild: + Stable on ppc64 + + 06 Apr 2006; Thomas Cort <tcort@gentoo.org> hmmer-2.3.2-r1.ebuild: + Added ~alpha keyword. + + 29 Mar 2006; Aron Griffis <agriffis@gentoo.org> hmmer-2.3.2-r1.ebuild: + Mark 2.3.2-r1 stable on ia64 + + 23 Feb 2006; Aron Griffis <agriffis@gentoo.org> hmmer-2.3.2-r1.ebuild: + Mark 2.3.2-r1 ~ia64 + + 24 Jan 2006; Markus Rothe <corsair@gentoo.org> hmmer-2.3.2-r2.ebuild: + Added ~ppc64; bug #119723 + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> + -files/Makefile-hmmer-2.2g.patch, -hmmer-2.3.2.ebuild: + Removed obsolete version. + +*hmmer-2.3.2-r2 (21 Jan 2006) + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> +hmmer-2.3.2-r2.ebuild: + Fixed compilation problem on ppc64 (see bug #119723). + + 04 Jan 2006; Olivier Fisette <ribosome@gentoo.org> hmmer-2.3.2-r1.ebuild: + Do not depend on "virtual/libc" (package not in system target). + + 19 Sep 2005; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Maintainer changed from Stephen Diener (MIA) to Olivier Fisette. + + 26 Aug 2005; Carlos Silva <r3pek@gentoo.org> hmmer-2.3.2-r1.ebuild: + Marked amd64 + + 21 May 2005; Jason Wever <weeve@gentoo.org> hmmer-2.3.2-r1.ebuild: + Added ~sparc keyword. + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> hmmer-2.3.2-r1.ebuild: + Added to x86. + +*hmmer-2.3.2-r1 (06 Mar 2005) + + 06 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +hmmer-2.3.2-r1.ebuild: + Install header files, support for LFS, optional support for PVM and threads. + + 07 Feb 2005; <augustus@gentoo.org> hmmer-2.3.2.ebuild: + Marked amd64. + +*hmmer-2.3.2 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +files/Makefile-hmmer-2.2g.patch, +hmmer-2.3.2.ebuild: + Moved from app-sci/hmmer to sci-biology/hmmer. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> -hmmer-2.3.1.ebuild, + hmmer-2.3.2.ebuild: + Added 2.3.2 to x86. Removed old version. + + 17 Oct 2004; David Holm <dholm@gentoo.org> hmmer-2.3.2.ebuild: + Added to ~ppc. + + 14 Oct 2004; Hasan Khalil <gongloo@gentoo.org> hmmer-2.3.2.ebuild: + Keyworded ~ppc-macos. + +*hmmer-2.3.2 (29 Sep 2004) + + 29 Sep 2004; Olivier Fisette <ribosome@gentoo.org> -hmmer-2.2g.ebuild, + +hmmer-2.3.2.ebuild: + New version 2.3.2. Removed old version. + + 18 Nov 2003; Stephen Diener <sediener@gentoo.org> hmmer-2.3.1.ebuild: + ~x86 -> x86 + +*hmmer-2.3.1 (28 Aug 2003) + + 28 Aug 2003; <sediener@gentoo.org> hmmer-2.3.1.ebuild: + Version bump + +*hmmer-2.2g (07 May 2003) + + 07 May 2003; Jon Portnoy <avenj@gentoo.org> hmmer-2.2g.ebuild : + Initial import. Ebuild submitted by Steve Diener and Gontran Zepeda + in bug #20449. diff --git a/sci-biology/iedera/ChangeLog b/sci-biology/iedera/ChangeLog new file mode 100644 index 00000000..3d2298a1 --- /dev/null +++ b/sci-biology/iedera/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for sci-biology/iedera +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/iedera/ChangeLog,v 1.2 2013/03/11 15:25:03 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*iedera-1.04 (18 Jun 2010) + + 18 Jun 2010; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +iedera-1.04.ebuild: + New package, ebuild written by me + diff --git a/sci-biology/infernal/ChangeLog b/sci-biology/infernal/ChangeLog new file mode 100644 index 00000000..49449a02 --- /dev/null +++ b/sci-biology/infernal/ChangeLog @@ -0,0 +1,71 @@ +# ChangeLog for sci-biology/infernal +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/infernal/ChangeLog,v 1.15 2014/07/06 11:34:46 jlec Exp $ + + 06 Jul 2014; Justin Lecher <jlec@gentoo.org> infernal-1.0.2-r1.ebuild, + +files/infernal-1.0.2-perl-5.16-2.patch, + -files/infernal-1.0.2-perl-5.16.patch: + Add patch as binary to prevent CVS magics, #431076 + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 15 Jul 2012; Justin Lecher <jlec@gentoo.org> -infernal-1.0.2.ebuild: + Cleaned old + + 15 Jul 2012; Justin Lecher <jlec@gentoo.org> + files/infernal-1.0.2-perl-5.16.patch: + Fix cvs updates of commiter names in patches, #426588 + + 25 Jun 2012; Justin Lecher <jlec@gentoo.org> infernal-1.0.2-r1.ebuild, + +files/infernal-1.0.2-perl-5.16.patch: + Fix for perl-5.16, #422561; move to EAPI=4 + + 11 Feb 2011; Markos Chandras <hwoarang@gentoo.org> infernal-1.0.2-r1.ebuild: + Stable on amd64 wrt bug #353571 + + 07 Feb 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> + infernal-1.0.2-r1.ebuild: + x86 stable wrt bug #353571 + +*infernal-1.0.2-r1 (04 Nov 2010) + + 04 Nov 2010; Kacper Kowalik <xarthisius@gentoo.org> -infernal-1.0.ebuild, + +infernal-1.0.2-r1.ebuild, +files/infernal-1.0.2-ldflags.patch, + +files/infernal-1.0.2-overflows.patch, + +files/infernal-1.0.2-parallel-build.patch: + Fix parallel build wrt bug 311919. Thanks to Myckel Habets + <m.e.j.habets@biology.leidenuniv.nl> for patch and report. Fix buffer + overflow wrt bug 338179 and respect LDFLAGS wrt bug 338177. Thanks to + Diego Elio Pettenò for the reports. Drop old. + + 05 Apr 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org> + infernal-1.0.2.ebuild: + x86 stable wrt bug #311837 + + 29 Mar 2010; Pacho Ramos <pacho@gentoo.org> infernal-1.0.2.ebuild: + amd64 stable, bug 311837 + +*infernal-1.0.2 (27 Jan 2010) + + 27 Jan 2010; Andrey Kislyuk <weaver@gentoo.org> +infernal-1.0.2.ebuild: + Version bump + + 22 Sep 2009; Markus Meier <maekke@gentoo.org> infernal-1.0.ebuild: + x86 stable, bug #282114 + + 06 Sep 2009; Jeremy Olexa <darkside@gentoo.org> infernal-1.0.ebuild: + amd64 stable, bug 282114 + + 20 Aug 2009; Andrey Kislyuk <weaver@gentoo.org> infernal-1.0.ebuild: + Tweak SRC_URI to include version + +*infernal-1.0 (09 Jul 2009) + + 09 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +infernal-1.0.ebuild: + Import from Science overlay + + 08 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: + New package, ebuild written by me + diff --git a/sci-biology/iqpnni/ChangeLog b/sci-biology/iqpnni/ChangeLog new file mode 100644 index 00000000..0676bb11 --- /dev/null +++ b/sci-biology/iqpnni/ChangeLog @@ -0,0 +1,29 @@ +# ChangeLog for sci-biology/iqpnni +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/iqpnni/ChangeLog,v 1.5 2013/03/11 15:25:40 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*iqpnni-3.3.2 (25 Sep 2011) + + 25 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +iqpnni-3.3.2.ebuild: + Version bump + + 24 May 2009; Markus Meier <maekke@gentoo.org> iqpnni-3.3.1.ebuild: + amd64/x86 stable, bug #269965 + +*iqpnni-3.3.1 (05 Jan 2009) + + 05 Jan 2009; weaver <weaver@gentoo.org> +files/iqpnni-3.3.1-gcc4.3.patch, + +iqpnni-3.3.1.ebuild: + Version bump + +*iqpnni-3.2 (30 Oct 2008) + + 30 Oct 2008; weaver <weaver@gentoo.org> +metadata.xml, +iqpnni-3.2.ebuild: + Import from science overlay + + 03 Sep 2008; weaver <weaver@gentoo.org> +metadata.xml, +iqpnni-3.2.ebuild: + Initial commit for bug 221965, thanks to Marek Miller <mlm@ngc17.pl> + diff --git a/sci-biology/kalign/ChangeLog b/sci-biology/kalign/ChangeLog new file mode 100644 index 00000000..f9b99984 --- /dev/null +++ b/sci-biology/kalign/ChangeLog @@ -0,0 +1,34 @@ +# ChangeLog for sci-biology/kalign +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/kalign/ChangeLog,v 1.8 2013/03/11 15:42:47 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 18 Dec 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> kalign-2.03-r1.ebuild: + x86 stable wrt bug #393791 + + 16 Dec 2011; Agostino Sarubbo <ago@gentoo.org> kalign-2.03-r1.ebuild: + Stable for AMD64, wrt bug #393791 + + 16 Dec 2011; Justin Lecher <jlec@gentoo.org> kalign-2.03-r1.ebuild: + Move to EAPI=4 + +*kalign-2.03-r1 (04 Sep 2010) + + 04 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org> + +kalign-2.03-r1.ebuild: + Respect CC,LDFLAGS wrt bug 335952. Thanks to Diego for the report and Ross + Smith <gaurdro@gmail.com> for the patch. + + 21 Mar 2009; Raúl Porcel <armin76@gentoo.org> kalign-2.03.ebuild: + x86 stable, bug #263043 + + 19 Mar 2009; Thomas Anderson <gentoofan23@gentoo.org> kalign-2.03.ebuild: + stable amd64, bug 263043 + +*kalign-2.03 (20 Jun 2008) + + 20 Jun 2008; weaver <weaver@gentoo.org> +kalign-2.03.ebuild: + New package from sunrise, bug 175116 + diff --git a/sci-biology/lagan/ChangeLog b/sci-biology/lagan/ChangeLog new file mode 100644 index 00000000..b7952fe4 --- /dev/null +++ b/sci-biology/lagan/ChangeLog @@ -0,0 +1,28 @@ +# ChangeLog for sci-biology/lagan +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/lagan/ChangeLog,v 1.4 2013/03/11 16:05:05 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*lagan-2.0-r2 (12 Sep 2010) + + 12 Sep 2010; Justin Lecher <jlec@gentoo.org> +lagan-2.0-r2.ebuild, + +files/lagan-2.0-flags.patch: + Fix respect of FLAGS, 334951; do not install ELF in /usr/share, 296021 + +*lagan-2.0-r1 (21 Jul 2009) + + 21 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> -lagan-2.0.ebuild, + +lagan-2.0-r1.ebuild: + Fix compilation with glibc-2.10, bug 273988 + +*lagan-2.0 (26 Feb 2009) + + 26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> + +files/lagan-2.0-gcc4.3.patch, +metadata.xml, +lagan-2.0.ebuild: + Import from Science overlay + + 04 Feb 2009; weaver <weaver@gentoo.org> ChangeLog: + New package sci-biology/lagan, bug 257667 + diff --git a/sci-biology/last/ChangeLog b/sci-biology/last/ChangeLog new file mode 100644 index 00000000..0718e9b3 --- /dev/null +++ b/sci-biology/last/ChangeLog @@ -0,0 +1,110 @@ +# ChangeLog for sci-biology/last +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/last/ChangeLog,v 1.27 2015/04/08 18:20:42 mgorny Exp $ + + 08 Apr 2015; Michał Górny <mgorny@gentoo.org> last-299.ebuild: + Drop old Python implementations + + 11 Aug 2013; Justin Lecher <jlec@gentoo.org> -last-146.ebuild, + -last-162-r1.ebuild, -last-184.ebuild, -last-192.ebuild: + Drop old + + 07 Aug 2013; Agostino Sarubbo <ago@gentoo.org> last-230.ebuild: + Stable for x86, wrt bug #477140 + + 28 Jul 2013; Chema Alonso <nimiux@gentoo.org> last-230.ebuild: + Stable for amd64 wrt bug #477140 + +*last-299 (17 Jul 2013) + + 17 Jul 2013; Justin Lecher <jlec@gentoo.org> +last-299.ebuild: + Version Bump + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*last-230 (20 Jun 2012) + + 20 Jun 2012; Justin Lecher <jlec@gentoo.org> +last-230.ebuild: + Version Bump, allows to compile with gcc-4.7, #422573 + +*last-192 (10 Feb 2012) + + 10 Feb 2012; Justin Lecher <jlec@gentoo.org> +last-192.ebuild: + Version Bump, #402941 + + 15 Dec 2011; Agostino Sarubbo <ago@gentoo.org> last-162-r1.ebuild: + Stable for AMD64, wrt bug #391545 + + 28 Nov 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> last-162-r1.ebuild: + x86 stable wrt bug #391545 + + 23 Nov 2011; Justin Lecher <jlec@gentoo.org> -last-162.ebuild, + last-184.ebuild: + Dropped old, respect LDFLAGS + +*last-184 (25 Sep 2011) + + 25 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +last-184.ebuild: + Version bump + + 25 Apr 2011; Justin Lecher <jlec@gentoo.org> +files/162-gcc46.patch, + last-162.ebuild, last-162-r1.ebuild: + Fix for gcc-4.6, #3624783 + +*last-162-r1 (08 Apr 2011) + + 08 Apr 2011; Justin Lecher <jlec@gentoo.org> +files/162-ldflags.patch, + +last-162-r1.ebuild: + Install lastex, #362525 + + 02 Apr 2011; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: + drop old + +*last-162 (02 Apr 2011) + + 02 Apr 2011; Andrey Kislyuk <weaver@gentoo.org> +last-162.ebuild: + Version bump + + 11 Feb 2011; Markos Chandras <hwoarang@gentoo.org> last-146.ebuild: + Stable on amd64 wrt bug #353567 + + 07 Feb 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> last-146.ebuild: + x86 stable wrt bug #353567 + +*last-146 (29 Nov 2010) + + 29 Nov 2010; Andrey Kislyuk <weaver@gentoo.org> +last-146.ebuild: + Version bump + +*last-128-r1 (15 Sep 2010) + + 15 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org> -last-103.ebuild, + -last-128.ebuild, +last-128-r1.ebuild: + Respect CXX,CXXFLAGS,LDFLAGS wrt bug 337525. Thanks to Diego for the + report. Drop old. + +*last-128 (15 Jul 2010) + + 15 Jul 2010; Andrey Kislyuk <weaver@gentoo.org> +last-128.ebuild: + Version bump + +*last-103 (07 May 2010) + + 07 May 2010; Andrey Kislyuk <weaver@gentoo.org> +last-103.ebuild: + Version bump + + 05 Apr 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org> last-96.ebuild: + x86 stable wrt bug #311831 + + 29 Mar 2010; Pacho Ramos <pacho@gentoo.org> last-96.ebuild: + amd64 stable, bug 311831 + + 09 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> last-96.ebuild: + Add unzip dependency + +*last-96 (09 Feb 2010) + + 09 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +last-96.ebuild: + New package, ebuild written by me diff --git a/sci-biology/mafft/ChangeLog b/sci-biology/mafft/ChangeLog new file mode 100644 index 00000000..1685e508 --- /dev/null +++ b/sci-biology/mafft/ChangeLog @@ -0,0 +1,117 @@ +# ChangeLog for sci-biology/mafft +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.24 2015/04/19 10:01:14 ago Exp $ + + 19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> mafft-7.050.ebuild: + Stable for x86, wrt bug #544952 + + 08 Apr 2015; Agostino Sarubbo <ago@gentoo.org> mafft-7.050.ebuild: + Stable for amd64, wrt bug #544952 + +*mafft-7.215 (29 Mar 2015) + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> +mafft-7.215.ebuild, + -files/mafft-6.240-mktemp.patch: + Version Bump; drop obsolete patch + + 19 Jul 2013; Justin Lecher <jlec@gentoo.org> mafft-7.050.ebuild: + Keyword for ~-linux + +*mafft-7.050 (03 Jul 2013) + + 03 Jul 2013; Justin Lecher <jlec@gentoo.org> -mafft-6.240-r1.ebuild, + -mafft-6.707.ebuild, -mafft-6.811.ebuild, -mafft-7.037.ebuild, + -mafft-7.040.ebuild, -mafft-7.043.ebuild, -mafft-7.045.ebuild, + -mafft-7.046.ebuild, -mafft-7.047.ebuild, +mafft-7.050.ebuild: + Drop old; Bump version + +*mafft-7.047 (24 Jun 2013) + + 24 Jun 2013; Justin Lecher <jlec@gentoo.org> +mafft-7.047.ebuild: + Version Bump + +*mafft-7.046 (12 Jun 2013) + + 12 Jun 2013; Justin Lecher <jlec@gentoo.org> +mafft-7.046.ebuild: + version Bump + + 06 Jun 2013; Justin Lecher <jlec@gentoo.org> Manifest: + Update to new upstream tarball + +*mafft-7.045 (06 Jun 2013) + + 06 Jun 2013; Justin Lecher <jlec@gentoo.org> +mafft-7.045.ebuild: + Version Bump + + 26 May 2013; Justin Lecher <jlec@gentoo.org> mafft-7.043.ebuild: + Use append-cppflags for preprocessor flags + +*mafft-7.043 (26 May 2013) + + 26 May 2013; Justin Lecher <jlec@gentoo.org> mafft-7.040.ebuild, + +mafft-7.043.ebuild: + Version Bump, add test function + +*mafft-7.040 (21 May 2013) + + 21 May 2013; Justin Lecher <jlec@gentoo.org> mafft-7.037.ebuild, + +mafft-7.040.ebuild: + Version Bump, drop unnecessary die + + 29 Apr 2013; Justin Lecher <jlec@gentoo.org> mafft-7.037.ebuild: + Fix USE=threads make flag magic + +*mafft-7.037 (29 Apr 2013) + + 29 Apr 2013; Justin Lecher <jlec@gentoo.org> +mafft-7.037.ebuild, + +files/mafft-7.037-respect.patch, metadata.xml: + Version Bump + + 21 Nov 2011; Justin Lecher <jlec@gentoo.org> mafft-6.811.ebuild: + keyworded for ~x86-macos ~x64-macos, tested by Johan Hattne #390123 + + 24 Jun 2010; Justin Lecher <jlec@gentoo.org> mafft-6.240-r1.ebuild, + mafft-6.707.ebuild, mafft-6.811.ebuild: + Fix installpath for manpages, #278571 + +*mafft-6.811 (15 Jun 2010) + + 15 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/6.811-respect.patch, + +mafft-6.811.ebuild: + Version Bump, keyworded for prefix, repecting multilib and LDFLAGS + +*mafft-6.707 (27 Jul 2009) + + 27 Jul 2009; Donnie Berkholz <dberkholz@gentoo.org>; +mafft-6.707.ebuild: + Bump to latest. Use no-extensions version because the extensions rely on a + bunch of bundled packages. That means you don't get RNA structural + alignment, sorry. + + 27 Jul 2009; Donnie Berkholz <dberkholz@gentoo.org>; + mafft-6.240-r1.ebuild: + Keyword ~amd64. + +*mafft-6.240-r1 (23 Sep 2008) + + 23 Sep 2008; Markus Dittrich <markusle@gentoo.org> + +files/mafft-6.240-mktemp.patch, -mafft-5.861-r1.ebuild, + -mafft-6.240.ebuild, +mafft-6.240-r1.ebuild: + Added patch to fix insecure tempfile handling (see bug #235804). + Removed ebuilds for vulnerable versions. + + 08 Oct 2007; Markus Dittrich <markusle@gentoo.org> mafft-5.861-r1.ebuild, +mafft-6.240.ebuild: + Fixed wrongs SRC_URI and HOMEPAGE (see bug #195080). Also bumped + package to the most recent version. + +*mafft-5.861-r1 (09 Nov 2006) + + 09 Nov 2006; Donnie Berkholz <dberkholz@gentoo.org>; -mafft-5.861.ebuild, + +mafft-5.861-r1.ebuild: + (#154545) Install to correct locations and set PREFIX so it finds the + binaries automatically. + +*mafft-5.861 (21 Oct 2006) + + 21 Oct 2006; Donnie Berkholz <dberkholz@gentoo.org>; +metadata.xml, + +mafft-5.861.ebuild: + New package: Multiple sequence alignments using a variety of algorithms. diff --git a/sci-biology/mammoth/ChangeLog b/sci-biology/mammoth/ChangeLog new file mode 100644 index 00000000..9b62db4a --- /dev/null +++ b/sci-biology/mammoth/ChangeLog @@ -0,0 +1,34 @@ +# ChangeLog for sci-biology/mammoth +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mammoth/ChangeLog,v 1.7 2015/03/05 11:07:15 jlec Exp $ + +*mammoth-1.0-r1 (05 Mar 2015) + + 05 Mar 2015; Justin Lecher <jlec@gentoo.org> +mammoth-1.0-r1.ebuild, + -mammoth-1.0.ebuild, metadata.xml: + EAPI Bump + + 19 Oct 2012; Justin Lecher <jlec@gentoo.org> mammoth-1.0.ebuild, + metadata.xml: + Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the + updated fortran-2.eclass + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> mammoth-1.0.ebuild: + Add dependency on virtual/fortran + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> mammoth-1.0.ebuild: + Added fortran-2.eclass support + + 16 Dec 2010; Justin Lecher <jlec@gentoo.org> mammoth-1.0.ebuild: + Removal of fortran.eclass, #348851 + + 13 Sep 2010; Markos Chandras <hwoarang@gentoo.org> mammoth-1.0.ebuild: + Keyworded for amd64. Bug #335605 + +*mammoth-1.0 (10 Dec 2007) + + 10 Dec 2007; Donnie Berkholz <dberkholz@gentoo.org>; + +files/1.0-consistent-system-intrinsic.patch, +metadata.xml, + +mammoth-1.0.ebuild: + Add mammoth, a nice structural alignment program. It contains the MaxSub + algorithm, which is used by lots of people. diff --git a/sci-biology/maq/ChangeLog b/sci-biology/maq/ChangeLog new file mode 100644 index 00000000..3dd1be09 --- /dev/null +++ b/sci-biology/maq/ChangeLog @@ -0,0 +1,42 @@ +# ChangeLog for sci-biology/maq +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/maq/ChangeLog,v 1.11 2013/03/11 16:05:48 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 23 Jun 2012; Justin Lecher <jlec@gentoo.org> maq-0.7.1-r1.ebuild, + +files/maq-0.7.1-gcc-4.7.patch: + Add patch for gcc-4.7, #422869 + + 18 Dec 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> maq-0.7.1-r1.ebuild: + x86 stable wrt bug #393759 + + 15 Dec 2011; Justin Lecher <jlec@gentoo.org> maq-0.7.1-r1.ebuild: + Add missing dependency on sys-libs/zlib + + 15 Dec 2011; Agostino Sarubbo <ago@gentoo.org> maq-0.7.1-r1.ebuild: + Stable for AMD64, wrt bug #393759 + + 15 Dec 2011; Justin Lecher <jlec@gentoo.org> maq-0.7.1-r1.ebuild: + Respect multilib, keyworded for prefix linux, remove additionally die + +*maq-0.7.1-r1 (14 Apr 2011) + + 14 Apr 2011; Justin Lecher <jlec@gentoo.org> +maq-0.7.1-r1.ebuild, + +files/maq-0.7.1-bfr-overfl.patch, +files/maq-0.7.1-flags.patch: + Fix for _FORTIFY_SOURCE indicates presence of overflow, #363537; Don't mix + FLAGS + + 04 Apr 2009; Markus Meier <maekke@gentoo.org> maq-0.7.1.ebuild: + amd64/x86 stable, bug #263735 + + 26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> maq-0.7.1.ebuild: + Install calibration data + + 26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> maq-0.7.1.ebuild: + Install documentation + + 26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: + New package, bug 231339. Ebuild written by me. + diff --git a/sci-biology/maqview/ChangeLog b/sci-biology/maqview/ChangeLog new file mode 100644 index 00000000..a4dfd593 --- /dev/null +++ b/sci-biology/maqview/ChangeLog @@ -0,0 +1,46 @@ +# ChangeLog for sci-biology/maqview +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/maqview/ChangeLog,v 1.11 2013/08/11 13:35:14 jlec Exp $ + + 11 Aug 2013; Justin Lecher <jlec@gentoo.org> -maqview-0.2.5.ebuild, + -maqview-0.2.5-r1.ebuild: + Drop old + + 27 Jul 2013; Agostino Sarubbo <ago@gentoo.org> maqview-0.2.5-r2.ebuild: + Stable for x86, wrt bug #477186 + + 21 Jul 2013; Agostino Sarubbo <ago@gentoo.org> maqview-0.2.5-r2.ebuild: + Stable for amd64, wrt bug #477186 + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*maqview-0.2.5-r2 (23 Jan 2013) + + 23 Jan 2013; Justin Lecher <jlec@gentoo.org> +maqview-0.2.5-r2.ebuild, + +files/maqview-0.2.5-gcc4.7.patch, metadata.xml: + Fix compilation with gcc-4.7, #451438 + + 11 May 2011; Christoph Mende <angelos@gentoo.org> maqview-0.2.5-r1.ebuild: + Stable on amd64 wrt bug #298094 + + 09 May 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> maqview-0.2.5-r1.ebuild: + x86 stable wrt security bug #298094 + +*maqview-0.2.5-r1 (06 May 2011) + + 06 May 2011; Justin Lecher <jlec@gentoo.org> +files/0.2.5-ldflags.patch, + +files/0.2.5-zlib.patch, +maqview-0.2.5-r1.ebuild: + Resepct LDFLAGS, do not link static, unbundle zlib, #298094, #337658, #366197 + + 16 Sep 2010; Tomáš Chvátal <scarabeus@gentoo.org> maqview-0.2.5.ebuild: + virtual/glut -> media-libs/glut + + 04 Apr 2009; Markus Meier <maekke@gentoo.org> maqview-0.2.5.ebuild: + amd64/x86 stable, bug #263736 + +*maqview-0.2.5 (26 Feb 2009) + + 26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +maqview-0.2.5.ebuild: + New package, bug 231339. Ebuild written by me. diff --git a/sci-biology/mauve/ChangeLog b/sci-biology/mauve/ChangeLog new file mode 100644 index 00000000..6344ef75 --- /dev/null +++ b/sci-biology/mauve/ChangeLog @@ -0,0 +1,19 @@ +# ChangeLog for sci-biology/mauve +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mauve/ChangeLog,v 1.4 2015/08/05 14:04:32 monsieurp Exp $ + + 05 Aug 2015; Patrice Clement <monsieurp@gentoo.org> mauve-9999.ebuild: + pkgmove from dev-java/ to sci-biology/: update dependencies. + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 09 Mar 2010; Jonathan Callen <abcd@gentoo.org> mauve-9999.ebuild: + QA: Do not use absolute path to icon when in standard dirs (in + make_desktop_entry()) + +*mauve-9999 (09 Dec 2009) + + 09 Dec 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +mauve-9999.ebuild: + New package, ebuild written by me. Stable snapshot pending. diff --git a/sci-biology/mauvealigner/ChangeLog b/sci-biology/mauvealigner/ChangeLog new file mode 100644 index 00000000..4540dfbb --- /dev/null +++ b/sci-biology/mauvealigner/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for sci-biology/mauvealigner +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mauvealigner/ChangeLog,v 1.2 2013/03/11 16:09:32 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*mauvealigner-9999 (17 Apr 2009) + + 17 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +mauvealigner-9999.ebuild: + New package, ebuild written by me + diff --git a/sci-biology/mcl/ChangeLog b/sci-biology/mcl/ChangeLog new file mode 100644 index 00000000..280fe57c --- /dev/null +++ b/sci-biology/mcl/ChangeLog @@ -0,0 +1,25 @@ +# ChangeLog for sci-biology/mcl +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mcl/ChangeLog,v 1.5 2015/04/07 14:33:23 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*mcl-12.135 (17 Feb 2013) + + 17 Feb 2013; Justin Lecher <jlec@gentoo.org> mcl-08.312.ebuild, + +mcl-12.135.ebuild, metadata.xml: + Version Bump; move to autotools-utils; install docs in right place, #296893 + + 26 Apr 2012; Justin Lecher <jlec@gentoo.org> mcl-08.312.ebuild, metadata.xml: + Move to EAPI=4 + +*mcl-08.312 (04 Apr 2009) + + 04 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +mcl-08.312.ebuild: + Import from Science overlay, version bump + + 07 Sep 2008; weaver <weaver@gentoo.org> +metadata.xml, +mcl-08.157.ebuild: + New package, bug 236954 + diff --git a/sci-biology/meme/ChangeLog b/sci-biology/meme/ChangeLog new file mode 100644 index 00000000..a164b15c --- /dev/null +++ b/sci-biology/meme/ChangeLog @@ -0,0 +1,122 @@ +# ChangeLog for sci-biology/meme +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.28 2014/10/19 03:59:15 patrick Exp $ + + 19 Oct 2014; Patrick Lauer <patrick@gentoo.org> meme-4.8.1-r2.ebuild: + Fix header + + 19 Mar 2013; Justin Lecher <jlec@gentoo.org> meme-4.8.1-r2.ebuild: + Fix renaming procedure, #460372 + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 08 Mar 2013; Justin Lecher <jlec@gentoo.org> meme-4.8.1-r2.ebuild: + Fix missing command, #460372 + +*meme-4.8.1-r2 (01 Mar 2013) + + 01 Mar 2013; Justin Lecher <jlec@gentoo.org> -meme-4.8.1.ebuild, + -meme-4.8.1-r1.ebuild, +meme-4.8.1-r2.ebuild: + Rename all binaries to meme-*; should fix all collisions in future, #458208; + drop old + +*meme-4.8.1-r1 (01 Feb 2013) + + 01 Feb 2013; Justin Lecher <jlec@gentoo.org> meme-4.8.1.ebuild, + +meme-4.8.1-r1.ebuild: + Resolve file collision with app-text and sci-biology/readseq, #455010 + + 31 Jan 2013; Justin Lecher <jlec@gentoo.org> -meme-4.3.0.ebuild, + meme-4.8.1.ebuild: + Drop old, fixes bug 297070 & bug 454662 + + 30 Jan 2013; Agostino Sarubbo <ago@gentoo.org> meme-4.8.1.ebuild: + Stable for x86, wrt bug #454698 + + 30 Jan 2013; Agostino Sarubbo <ago@gentoo.org> meme-4.8.1.ebuild: + Stable for amd64, wrt bug #454698 + + 30 Jan 2013; Justin Lecher <jlec@gentoo.org> -meme-4.3.0-r1.ebuild, + -meme-4.4.0.ebuild, meme-4.8.1.ebuild, metadata.xml: + Drop old; add examples handling + +*meme-4.8.1 (26 Aug 2012) + + 26 Aug 2012; Justin Lecher <jlec@gentoo.org> +meme-4.8.1.ebuild, + +files/meme-4.8.1-Makefile.am.patch: + Version Bump; respect CFLAGS, #430774 + + 02 Mar 2011; Justin Lecher <jlec@gentoo.org> meme-4.3.0.ebuild, + meme-4.3.0-r1.ebuild, meme-4.4.0.ebuild: + Correct Slots for gtk 3 introduction to tree + + 17 Jun 2010; Justin Bronder <jsbronder@gentoo.org> -meme-3.5.4-r1.ebuild, + -meme-3.5.7.ebuild: + Removing outdated meme-3.5.x + +*meme-4.4.0 (07 May 2010) + + 07 May 2010; Andrey Kislyuk <weaver@gentoo.org> -meme-4.2.0.ebuild, + +meme-4.4.0.ebuild: + Version bump + +*meme-4.3.0-r1 (07 Mar 2010) + + 07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> +meme-4.3.0-r1.ebuild: + Moved to EAPI=3 for PREFIX support, imported prefix patches from overlay, + keyworded as in overlay + + 03 Jan 2010; Pacho Ramos <pacho@gentoo.org> meme-4.3.0.ebuild: + amd64 stable, bug 298760 + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> meme-4.3.0.ebuild: + stable x86, bug 298760 + + 15 Dec 2009; Diego E. Pettenò <flameeyes@gentoo.org> meme-4.3.0.ebuild: + Add -j1 to tests as per bug #297070. + +*meme-4.3.0 (13 Nov 2009) + + 13 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> +meme-4.3.0.ebuild: + Version bump + +*meme-4.2.0 (18 Sep 2009) + + 18 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> + +files/meme-4.0.0-Makefile.am.patch, metadata.xml, +meme-4.2.0.ebuild: + Version bump and cleanup, disable group creation, webapp still needs work + +*meme-3.5.7 (12 Sep 2008) + + 12 Sep 2008; Markus Dittrich <markusle@gentoo.org> +meme-3.5.7.ebuild: + Version bump. + + 14 Jun 2008; Markus Dittrich <markusle@gentoo.org> -meme-3.5.4.ebuild: + Removed old ebuild with bad autotools usage (fixes bug #226609). + + 31 Dec 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog, Manifest: + Fixing my email addy. + + 17 Sep 2007; <je_fro@gentoo.org> Manifest: + Used cvs manually to add patches without mangling. + +*meme-3.5.4-r1 (17 Sep 2007) + + 17 Sep 2007; <je_fro@gentoo.org> files/meme-3.5.4-patch1.patch, + files/meme-3.5.4-patch2.patch, +meme-3.5.4-r1.ebuild: + Once again, remove parallel install for amd64 boxes, and add upstream patches. + + 17 Sep 2007; <je_fro@gentoo.org> -meme-3.5.4-r1.ebuild: + Whoa...this version worked in my overlay. Pulling until I figure out what + went wrong. + + 17 Sep 2007; <je_fro@gentoo.org> +files/meme-3.5.4-patch1.patch, + +files/meme-3.5.4-patch2.patch, meme-3.5.4.ebuild: + Remove parallel install for amd64 boxes, and add upstream patches. + +*meme-3.5.4 (24 Apr 2007) + + 24 Apr 2007; Olivier Fisette <ribosome@gentoo.org> + +files/meme-3.5.4-Makefile.am.patch, +metadata.xml, +meme-3.5.4.ebuild: + Initial import. diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog new file mode 100644 index 00000000..61ec2a25 --- /dev/null +++ b/sci-biology/mira/ChangeLog @@ -0,0 +1,139 @@ +# ChangeLog for sci-biology/mira +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.34 2015/08/03 07:08:05 jlec Exp $ + + 03 Aug 2015; Justin Lecher <jlec@gentoo.org> -mira-3.9.18.ebuild: + Drop old; obsoletes bug #555044 + + 02 Aug 2015; Agostino Sarubbo <ago@gentoo.org> mira-4.0.2.ebuild: + Stable for x86, wrt bug #556138 + + 31 Jul 2015; Agostino Sarubbo <ago@gentoo.org> mira-4.0.2.ebuild: + Stable for amd64, wrt bug #556138 + + 25 Jan 2015; Justin Lecher <jlec@gentoo.org> mira-4.0.2.ebuild, + +files/mira-4.0.2-cout.patch: + Build fix for newer gcc, #537564 + +*mira-4.0.2 (23 Jan 2015) + + 23 Jan 2015; Justin Lecher <jlec@gentoo.org> +mira-4.0.2.ebuild: + Version Bump, thanks Martin Mokrejš for the work + + 23 Jan 2015; Justin Lecher <jlec@gentoo.org> mira-3.9.18.ebuild: + Add workaroung for m4 dir location, #536172 + + 14 Jan 2014; Justin Lecher <jlec@gentoo.org> -mira-3.2.1.ebuild: + Drop old + + 14 Jan 2014; Agostino Sarubbo <ago@gentoo.org> mira-3.9.18.ebuild: + Stable for x86, wrt bug #497218 + + 12 Jan 2014; Pacho Ramos <pacho@gentoo.org> mira-3.9.18.ebuild: + amd64 stable, bug #497218 + + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild: + Punt base.eclass + + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mira-3.2.1-r1.ebuild, + -mira-3.4.0.2.ebuild: + Drop old + +*mira-3.9.18 (07 Jul 2013) + + 07 Jul 2013; Justin Lecher <jlec@gentoo.org> +mira-3.9.18.ebuild: + Version Bump; fixed compilation with dev-libs/boost-1.53.0 and some libtool + versions, #450322; thanks Martin Mokrejs for all his work + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*mira-3.4.0.2 (07 Nov 2012) + + 07 Nov 2012; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild, + mira-3.2.1-r1.ebuild, +mira-3.4.0.2.ebuild, + +files/mira-3.4.0.2-boost-1.50.patch: + Version Bump, #377807 + +*mira-3.2.1-r1 (07 Nov 2012) + + 07 Nov 2012; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild, + +mira-3.2.1-r1.ebuild, +files/mira-3.2.1-boost-1.50.patch: + Fix for boost >1.50, #425468 + + 08 Jul 2012; Justin Lecher <jlec@gentoo.org> -mira-3.0.5.ebuild, + -mira-3.2.0.ebuild: + Drop old + + 25 Jun 2012; Jeff Horelick <jdhore@gentoo.org> mira-3.2.1.ebuild: + marked x86 per bug 418439 + + 24 Jun 2012; Agostino Sarubbo <ago@gentoo.org> mira-3.2.1.ebuild: + Stable for amd64, wrt bug #418439 + + 23 Jun 2012; Kacper Kowalik <xarthisius.kk@gmail.com> mira-3.2.1.ebuild: + Don't install docs that are no longer there, thanks to David Abbott for the + patch + +*mira-3.2.1 (21 May 2011) + + 21 May 2011; Andrey Kislyuk <weaver@gentoo.org> +mira-3.2.1.ebuild: + Version bump and fix bug 367921 + + 11 Feb 2011; Markos Chandras <hwoarang@gentoo.org> mira-3.2.0.ebuild: + Stable on amd64 wrt bug #353568 + + 07 Feb 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> mira-3.2.0.ebuild: + x86 stable wrt bug #353568 + + 17 Oct 2010; Andrey Kislyuk <weaver@gentoo.org> mira-3.2.0.ebuild: + Remove doc USE flag and dependency, workaround for bug 340419 + +*mira-3.2.0 (26 Sep 2010) + + 26 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> -mira-3.0.0.ebuild, + -mira-3.0.3.ebuild, +mira-3.2.0.ebuild: + Version bump, drop old + + 28 Jun 2010; Justin Lecher <jlec@gentoo.org> mira-3.0.0.ebuild, + mira-3.0.3.ebuild, mira-3.0.5.ebuild: + Prepared for prefix, #325929 + +*mira-3.0.5 (05 May 2010) + + 05 May 2010; Andrey Kislyuk <weaver@gentoo.org> +mira-3.0.5.ebuild: + Version bump + +*mira-3.0.3 (18 Mar 2010) + + 18 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> -mira-3.0.2.ebuild, + +mira-3.0.3.ebuild: + Hotfix from upstream + +*mira-3.0.2 (10 Mar 2010) + + 10 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> -mira-3.0.1.ebuild, + +mira-3.0.2.ebuild: + Hotfix from upstream + +*mira-3.0.1 (06 Mar 2010) + + 06 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> +mira-3.0.1.ebuild: + Version bump (bugfix release) + + 25 Feb 2010; Samuli Suominen <ssuominen@gentoo.org> mira-3.0.0.ebuild, + +files/mira-3.0.0-asneeded.patch: + Fix ax_lib_expat.m4 macro to not use LDFLAGS for passing libraries wrt + #305547 by Kacper Kowalik. + + 03 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> mira-3.0.0.ebuild: + add eautoreconf + + 03 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> mira-3.0.0.ebuild: + Install 3rd party files + +*mira-3.0.0 (02 Feb 2010) + + 02 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +mira-3.0.0.ebuild: + New package, ebuild written by me diff --git a/sci-biology/mosaik/ChangeLog b/sci-biology/mosaik/ChangeLog new file mode 100644 index 00000000..3f38dab0 --- /dev/null +++ b/sci-biology/mosaik/ChangeLog @@ -0,0 +1,25 @@ +# ChangeLog for sci-biology/mosaik +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mosaik/ChangeLog,v 1.5 2013/03/11 16:13:50 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*mosaik-1.0.1388 (11 Apr 2010) + + 11 Apr 2010; Andrey Kislyuk <weaver@gentoo.org> +mosaik-1.0.1388.ebuild: + Version bump, address bug 314659 + + 03 Jan 2010; Pacho Ramos <pacho@gentoo.org> mosaik-1.0.1367.ebuild: + amd64 stable, bug 298766 + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> + mosaik-1.0.1367.ebuild: + stable x86, bug 298766 + +*mosaik-1.0.1367 (20 Nov 2009) + + 20 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +mosaik-1.0.1367.ebuild: + New package, ebuild written by me + diff --git a/sci-biology/mothur/ChangeLog b/sci-biology/mothur/ChangeLog new file mode 100644 index 00000000..1a557889 --- /dev/null +++ b/sci-biology/mothur/ChangeLog @@ -0,0 +1,74 @@ +# ChangeLog for sci-biology/mothur +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mothur/ChangeLog,v 1.14 2015/08/03 12:54:49 ago Exp $ + + 03 Aug 2015; Agostino Sarubbo <ago@gentoo.org> mothur-1.27.0-r1.ebuild: + Stable for amd64, wrt bug #556066 + +*mothur-1.27.0-r1 (27 Jul 2015) + + 27 Jul 2015; Justin Lecher <jlec@gentoo.org> +mothur-1.27.0-r1.ebuild, + -files/mothur-1.13.0-makefile.patch, -files/mothur-1.13.0-overflows.patch, + -files/mothur-1.13.0-overflows2.patch, -mothur-1.13.0-r1.ebuild, + -mothur-1.13.0-r2.ebuild, -mothur-1.27.0.ebuild: + Use fortran-2.eclass, bug #543204; drop old + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*mothur-1.27.0 (14 Aug 2012) +*mothur-1.13.0-r2 (14 Aug 2012) + + 14 Aug 2012; Justin Lecher <jlec@gentoo.org> mothur-1.6.0.ebuild, + mothur-1.13.0-r1.ebuild, +mothur-1.13.0-r2.ebuild, + +files/mothur-1.13.0-overflows2.patch, +mothur-1.27.0.ebuild, + +files/mothur-1.27.0-makefile.patch, +files/mothur-1.27.0-overflows.patch: + Version Bump; fix for buffer overflows, #431258 + + 08 Jul 2011; Samuli Suominen <ssuominen@gentoo.org> mothur-1.13.0-r1.ebuild: + Convert from "useq" to "use". + +*mothur-1.13.0-r1 (05 Oct 2010) + + 05 Oct 2010; Kacper Kowalik <xarthisius@gentoo.org> + -mothur-1.7.2-r1.ebuild, -mothur-1.13.0.ebuild, +mothur-1.13.0-r1.ebuild, + +files/mothur-1.13.0-makefile.patch, +files/mothur-1.13.0-overflows.patch: + Fix buffer overflows and building with --as-needed wrt bug 339753. Thanks + to Diego for the report. Correct dependencies. Drop old. + +*mothur-1.13.0 (26 Sep 2010) + + 26 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> +mothur-1.13.0.ebuild: + Version bump + +*mothur-1.7.2-r1 (27 Aug 2010) + + 27 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org> -mothur-1.4.1.ebuild, + -mothur-1.7.2.ebuild, +mothur-1.7.2-r1.ebuild: + Respect LDFLAGS wrt bug 334781. Thanks to Diego for the report. + Remove old. + + 06 Feb 2010; Markos Chandras <hwoarang@gentoo.org> mothur-1.6.0.ebuild: + Stable on amd64 wrt bug #298777 + +*mothur-1.7.2 (29 Dec 2009) + + 29 Dec 2009; Andrey Kislyuk <weaver@gentoo.org> +mothur-1.7.2.ebuild: + Version bump + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> mothur-1.6.0.ebuild: + stable x86, bug 298777 + +*mothur-1.6.0 (31 Oct 2009) + + 31 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +mothur-1.6.0.ebuild: + Version bump + +*mothur-1.4.1 (07 Jul 2009) + + 07 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +mothur-1.4.1.ebuild: + Import from Science overlay + + 04 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: + New package, ebuild written by me diff --git a/sci-biology/mrbayes/ChangeLog b/sci-biology/mrbayes/ChangeLog new file mode 100644 index 00000000..38863e55 --- /dev/null +++ b/sci-biology/mrbayes/ChangeLog @@ -0,0 +1,104 @@ +# ChangeLog for sci-biology/mrbayes +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/ChangeLog,v 1.27 2015/04/17 06:49:59 jlec Exp $ + +*mrbayes-3.1.2-r2 (17 Apr 2015) + + 17 Apr 2015; Justin Lecher <jlec@gentoo.org> +mrbayes-3.1.2-r2.ebuild, + metadata.xml, mrbayes-3.1.2-r1.ebuild: + Import changes from science overlay + + 21 Dec 2011; Justin Lecher <jlec@gentoo.org> -mrbayes-3.1.2.ebuild: + Cleaned old + + 21 Dec 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> mrbayes-3.1.2-r1.ebuild: + x86 stable wrt bug #393969 + + 17 Dec 2011; Agostino Sarubbo <ago@gentoo.org> mrbayes-3.1.2-r1.ebuild: + Stable for AMD64, wrt bug #393969 + + 17 Dec 2011; Justin Lecher <jlec@gentoo.org> mrbayes-3.1.2-r1.ebuild: + Use mpicc with USE=mpi, #394961 + + 16 Dec 2011; Justin Lecher <jlec@gentoo.org> mrbayes-3.1.2-r1.ebuild: + Add missing dep on sys-libs/ncurses, keyworded for ~amd64-linux + +*mrbayes-3.1.2-r1 (06 Mar 2011) + + 06 Mar 2011; Justin Lecher <jlec@gentoo.org> mrbayes-3.1.2.ebuild, + +mrbayes-3.1.2-r1.ebuild: + Fix for missing LDFLAGS, #338160 + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> mrbayes-3.1.2.ebuild: + Transfer Prefix keywords + + 11 Jun 2008; Kenneth Prugh <ken69267@gentoo.org> mrbayes-3.1.2.ebuild: + amd64 stable, bug #213362 + + 17 Mar 2008; Donnie Berkholz <dberkholz@gentoo.org>; mrbayes-3.1.2.ebuild: + (#213362) Keyword ~amd64. + + 25 Mar 2007; Danny van Dyk <kugelfang@gentoo.org> mrbayes-3.1.2.ebuild: + QA: Cleaned up whitespaces. Removed redundant src_compile(). + + 06 Jan 2007; Danny van Dyk <kugelfang@gentoo.org> -mrbayes-3.1.1.ebuild: + QA: Removed unused versions. + + 03 Nov 2006; Fabian Groffen <grobian@gentoo.org> mrbayes-3.1.1.ebuild, + mrbayes-3.1.2.ebuild: + Dropped ppc-macos, see you in prefix. + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Stepping down from maintaining this package. + + 12 Sep 2006; Olivier Fisette <ribosome@gentoo.org> mrbayes-3.1.1.ebuild, + mrbayes-3.1.2.ebuild: + Removed amd64 keywords because of bad pointer arithmetics causing segfaults + in the sumt function on all 64 bit architectures (see bug #143094). + + 09 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; mrbayes-3.1.2.ebuild: + x86 stable. + +*mrbayes-3.1.2 (03 Feb 2006) + + 03 Feb 2006; Olivier Fisette <ribosome@gentoo.org> + +files/mb_readline_312.patch, +mrbayes-3.1.2.ebuild: + New version. Added readline support. Thanks to Paul van der Mark for his + work on this ebuild. + + 09 Jan 2006; Homer Parker <hparker@gentoo.org> mrbayes-3.1.1.ebuild: + Marked ~amd64. + + 09 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -mrbayes-3.0.ebuild: + Pruning old version. + + 08 Oct 2005; Lina Pezzella <j4rg0n@gentoo.org> mrbayes-3.1.1.ebuild: + Stable ppc-macos, Bug 108333 + + 08 Oct 2005; Paul Varner <fuzzyray@gentoo.org> mrbayes-3.1.1.ebuild: + Stable on x86. Bug# 108333 + +*mrbayes-3.1.1 (14 Aug 2005) + + 14 Aug 2005; Olivier Fisette <ribosome@gentoo.org> metadata.xml, + +mrbayes-3.1.1.ebuild: + New version. Added MPI support. + + 20 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> mrbayes-3.0.ebuild: + Stable x86 and ppc-macos + + 09 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> mrbayes-3.0.ebuild: + Restricted fetching because of the license. Verified with GNU lawyers + +*mrbayes-3.0 (02 Feb 2005) + + 02 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> +metadata.xml, +mrbayes-3.0.ebuild: + Moved from sci-biology/MrBayes to sci-biology/mrbayes. + +*MrBayes-3.0 (30 Jan 2005) + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> MrBayes-3.0.ebuild: + Check for "sed" exit code. + + 19 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> : + Initial commit diff --git a/sci-biology/mummer/ChangeLog b/sci-biology/mummer/ChangeLog new file mode 100644 index 00000000..bb4a62d5 --- /dev/null +++ b/sci-biology/mummer/ChangeLog @@ -0,0 +1,65 @@ +# ChangeLog for sci-biology/mummer +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mummer/ChangeLog,v 1.15 2013/03/11 16:15:21 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 31 May 2011; Markus Meier <maekke@gentoo.org> mummer-3.22-r1.ebuild: + x86 stable, bug #368341 + + 24 May 2011; Markos Chandras <hwoarang@gentoo.org> mummer-3.22-r1.ebuild: + Stable on amd64 wrt bug #368341 + +*mummer-3.22-r1 (13 Jan 2011) + + 13 Jan 2011; Justin Lecher <jlec@gentoo.org> +files/3.22-ldflags.patch, + +files/3.22-prll.patch, -mummer-3.22.ebuild, +mummer-3.22-r1.ebuild: + Respecting *FLAGS, #335447; added real 64bit support, #351502 + + 28 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> mummer-3.22.ebuild: + Set EAPI + +*mummer-3.22 (28 Oct 2009) + + 28 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +mummer-3.22.ebuild: + Version bump + + 05 Aug 2009; Markus Meier <maekke@gentoo.org> mummer-3.21.ebuild: + x86 stable, bug #279350 + + 02 Aug 2009; <chainsaw@gentoo.org> mummer-3.21.ebuild: + Marked stable on AMD64 as requested by Andrey "weaver" Kislyuk + <weaver@gentoo.org> in bug #279350. Arch-tested by Chad A. Simmons who + reports he has no test-suite; reporter confirmed and agreed compile-test + was sufficient. + + 15 Mar 2009; Markus Meier <maekke@gentoo.org> mummer-3.20.ebuild: + amd64/x86 stable, bug #261789 + + 09 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> mummer-3.21.ebuild: + QA fixes + + 09 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> mummer-3.20.ebuild, + mummer-3.21.ebuild: + QA fixes + + 09 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> mummer-3.20.ebuild, + mummer-3.21.ebuild: + QA fixes (cflags) + +*mummer-3.21 (09 Mar 2009) + + 09 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> mummer-3.20.ebuild, + +mummer-3.21.ebuild: + Revision bump and QA fixes + + 17 Jun 2008; weaver <weaver@gentoo.org> ChangeLog: + Add gcc-4.3 patch, bug 227561, thanks to Marek Miller + +*mummer-3.20 (24 May 2008) + + 24 May 2008; weaver <weaver@gentoo.org> +metadata.xml, + +mummer-3.20.ebuild: + Initial commit. New package from sunrise, bug 169793 + diff --git a/sci-biology/muscle/ChangeLog b/sci-biology/muscle/ChangeLog new file mode 100644 index 00000000..14c76a53 --- /dev/null +++ b/sci-biology/muscle/ChangeLog @@ -0,0 +1,77 @@ +# ChangeLog for sci-biology/muscle +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/ChangeLog,v 1.21 2015/04/22 06:48:54 jlec Exp $ + + 22 Apr 2015; Justin Lecher <jlec@gentoo.org> -muscle-3.7-r1.ebuild: + Drop old + + 21 Apr 2015; Pacho Ramos <pacho@gentoo.org> muscle-3.8.31.ebuild: + ppc stable wrt bug #544956 + + 19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> muscle-3.8.31.ebuild: + Stable for x86, wrt bug #544956 + + 08 Apr 2015; Agostino Sarubbo <ago@gentoo.org> muscle-3.8.31.ebuild: + Stable for amd64, wrt bug #544956 + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> -muscle-3.6.ebuild, + -muscle-3.7.ebuild, metadata.xml, muscle-3.8.31.ebuild: + Drop old + + 20 Jul 2010; Joseph Jezak <josejx@gentoo.org> muscle-3.7-r1.ebuild: + Marked ppc stable for bug #277980. + + 29 Jun 2010; Christian Faulhammer <fauli@gentoo.org> muscle-3.7-r1.ebuild: + stable x86, bug 277980 + + 28 Jun 2010; Christoph Mende <angelos@gentoo.org> muscle-3.7-r1.ebuild: + Stable on amd64 wrt bug #277980 + +*muscle-3.7-r1 (28 Jun 2010) + + 28 Jun 2010; Justin Lecher <jlec@gentoo.org> + +files/3.7-bufferoverflow.patch, +muscle-3.7-r1.ebuild: + Fix for bufferoverflow, #309341 + + 24 Jun 2010; Christoph Mende <angelos@gentoo.org> muscle-3.7.ebuild: + Stable on amd64 wrt bug #277980 + +*muscle-3.8.31 (24 Jun 2010) + + 24 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/3.8.31-make.patch, + muscle-3.6.ebuild, muscle-3.7.ebuild, +muscle-3.8.31.ebuild: + Version Bump, blocking sci-libs/libmuscle, #308707 + +*muscle-3.7 (21 Mar 2008) + + 21 Mar 2008; Donnie Berkholz <dberkholz@gentoo.org>; +muscle-3.7.ebuild: + Bump. Bug fixes and undocumented new features. + + 31 Dec 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog: + fixing my email addy + + 26 Dec 2007; Samuli Suominen <drac@gentoo.org> muscle-3.6.ebuild: + amd64 stable wrt #203185 + + 25 Dec 2007; nixnut <nixnut@gentoo.org> muscle-3.6.ebuild: + Stable on ppc wrt bug 203185 + + 21 Oct 2007; <je_fro@gentoo.org> muscle-3.6.ebuild: + Adding ~amd64 and ~ppc for seaview + + 01 Oct 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml: + Remove myself as maintainer so it goes to all of the sci-biology team. + + 20 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>; muscle-3.6.ebuild: + Stable on x86. + + 07 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml: + Update to my new email address. + +*muscle-3.6 (21 Feb 2006) + + 21 Feb 2006; Donnie Berkholz <dberkholz@gentoo.org>; +metadata.xml, + +muscle-3.6.ebuild: + New multiple sequence alignment package. Provides a great tradeoff between + runtime and quality for global alignments; quite a bit worse on local + alignments. diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog new file mode 100644 index 00000000..df35f55c --- /dev/null +++ b/sci-biology/ncbi-tools/ChangeLog @@ -0,0 +1,535 @@ +# ChangeLog for sci-biology/ncbi-tools +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.99 2015/04/07 14:33:55 jlec Exp $ + + 11 Mar 2015; Justin Lecher <jlec@gentoo.org> ncbi-tools-2.2.26-r2.ebuild: + Add missing X deps, #542558 + + 02 Mar 2015; Justin Lecher <jlec@gentoo.org> + +files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch, + +files/ncbi-tools-2.2.26-format-security.patch, ncbi-tools-2.2.26-r2.ebuild: + Fix format-security and SLOT operators + + 12 Jun 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools-2.2.26-r2.ebuild, + files/ncbirc: + Fix for prefix + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> -ncbi-tools-0.20080302.ebuild, + -ncbi-tools-0.20090809.ebuild, -ncbi-tools-2.2.26.ebuild: + Drop old + + 03 Mar 2013; Agostino Sarubbo <ago@gentoo.org> ncbi-tools-2.2.26-r2.ebuild: + Stable for ppc64, wrt bug #458112 + + 02 Mar 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools-2.2.26-r2.ebuild, + +files/ncbi-tools-2.2.26-bfr-overflow.patch: + Fix typo in sed construct, #459920; add patch to fix buffer overflows + + 01 Mar 2013; Agostino Sarubbo <ago@gentoo.org> ncbi-tools-2.2.26-r2.ebuild: + Stable for x86, wrt bug #458112 + + 01 Mar 2013; Agostino Sarubbo <ago@gentoo.org> ncbi-tools-2.2.26-r2.ebuild: + Stable for amd64, wrt bug #458112 + +*ncbi-tools-2.2.26-r2 (01 Mar 2013) + + 01 Mar 2013; Justin Lecher <jlec@gentoo.org> -ncbi-tools-2.2.26-r1.ebuild, + +ncbi-tools-2.2.26-r2.ebuild: + Fix all config files, #459720, #459726, #459878 + +*ncbi-tools-2.2.26-r1 (01 Mar 2013) + + 01 Mar 2013; Justin Lecher <jlec@gentoo.org> +ncbi-tools-2.2.26-r1.ebuild: + Clean heuristic to fix build env, #459720 and #459726 + + 18 Feb 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools-0.20080302.ebuild, + ncbi-tools-0.20090809.ebuild, ncbi-tools-2.2.26.ebuild, + -ncbi-tools-20080302.ebuild, -ncbi-tools-20090809.ebuild, metadata.xml: + Drop old; rename fmerge.1 to fmerg-ncbi.1 -> resolves collision with + dev-util/fhist, #429560 + + 24 Oct 2012; Ulrich Müller <ulm@gentoo.org> ncbi-tools-0.20080302.ebuild, + ncbi-tools-0.20090809.ebuild, ncbi-tools-2.2.26.ebuild, + ncbi-tools-20080302.ebuild, ncbi-tools-20090809.ebuild: + Update dependency after package move from x11-libs/openmotif to + x11-libs/motif. + +*ncbi-tools-0.20090809 (13 Jun 2012) +*ncbi-tools-0.20080302 (13 Jun 2012) + + 13 Jun 2012; Justin Lecher <jlec@gentoo.org> +ncbi-tools-0.20080302.ebuild, + +ncbi-tools-0.20090809.ebuild, -ncbi-tools-20100808.ebuild: + Change Version numbers from x to 0.x in order to be able to follow upstream + new versioning scheme; Drop old unstable + +*ncbi-tools-2.2.26 (22 May 2012) + + 22 May 2012; Justin Lecher <jlec@gentoo.org> +ncbi-tools-2.2.26.ebuild: + Version Bump, #416251; restructured large parts of the ebuild; move to EAPI=4 + + 26 Apr 2012; Justin Lecher <jlec@gentoo.org> ncbi-tools-20080302.ebuild, + -ncbi-tools-20090809-r2.ebuild: + Dropped old + + 15 Nov 2010; Justin Lecher <jlec@gentoo.org> ncbi-tools-20080302.ebuild, + ncbi-tools-20090809-r2.ebuild, ncbi-tools-20100808.ebuild: + QA fixes from repoman + + 15 Nov 2010; Justin Lecher <jlec@gentoo.org> + ncbi-tools-20090809-r2.ebuild, ncbi-tools-20100808.ebuild: + Use system csh instead of shebang + + 10 Oct 2010; Ulrich Mueller <ulm@gentoo.org> ncbi-tools-20080302.ebuild, + ncbi-tools-20090809.ebuild, ncbi-tools-20090809-r2.ebuild, + ncbi-tools-20100808.ebuild: + Fix openmotif dependency. + +*ncbi-tools-20100808 (30 Sep 2010) + + 30 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> + -ncbi-tools-20090809-r1.ebuild, +ncbi-tools-20100808.ebuild: + Version bump + + 24 Jun 2010; Justin Lecher <jlec@gentoo.org> -ncbi-tools-20060507.ebuild, + -ncbi-tools-20061015-r1.ebuild, -ncbi-tools-20070826.ebuild, + -ncbi-tools-20090301.ebuild: + Cleaned old version + + 29 Mar 2010; Pacho Ramos <pacho@gentoo.org> ncbi-tools-20090809.ebuild: + amd64 stable, bug 298779 + +*ncbi-tools-20090809-r2 (07 Mar 2010) + + 07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> + +ncbi-tools-20090809-r2.ebuild: + Moved to EAPI=3 for PREFIX support, keyworded for *-linux, tested by me + +*ncbi-tools-20090809-r1 (13 Feb 2010) + + 13 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org> + +ncbi-tools-20090809-r1.ebuild: + Build spidey per bug 268042 and respect LDFLAGS + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> + ncbi-tools-20090809.ebuild: + stable x86, bug 298779 + + 02 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> + ncbi-tools-20090809.ebuild: + Update description + + 22 Sep 2009; Markus Meier <maekke@gentoo.org> ncbi-tools-20090301.ebuild: + x86 stable, bug #283678 + + 06 Sep 2009; Jeremy Olexa <darkside@gentoo.org> + ncbi-tools-20090301.ebuild: + amd64 stable, bug 283678. As requested, compile tested only due to + complexity + +*ncbi-tools-20090809 (04 Sep 2009) + + 04 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> metadata.xml, + +ncbi-tools-20090809.ebuild: + Version bump, take maintainership + + 19 Apr 2009; Brent Baude <ranger@gentoo.org> ncbi-tools-20090301.ebuild: + Marking ncbi-tools-20090301 ~ppc64 for bug 266569 + + 18 Apr 2009; Tobias Klausmann <klausman@gentoo.org> + ncbi-tools-20090301.ebuild: + Keyworded on alpha, bug #266569 + +*ncbi-tools-20090301 (17 Apr 2009) + + 17 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> + +ncbi-tools-20090301.ebuild: + Version bump, minor cleanup + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 27 Jun 2008; Ulrich Mueller <ulm@gentoo.org> ncbi-tools-20060507.ebuild, + ncbi-tools-20061015-r1.ebuild, ncbi-tools-20070826.ebuild, + ncbi-tools-20080302.ebuild: + Change dependency from virtual/motif to x11-libs/openmotif, bug 224749. + + 12 May 2008; Markus Rothe <corsair@gentoo.org> ncbi-tools-20080302.ebuild: + Stable on ppc64 + + 12 May 2008; Jeff Gardner <je_fro@gentoo.org> ChangeLog: + Move pmake to DEPEND fixing bug #221441 + + 22 Apr 2008; Olivier Fisette <ribosome@gentoo.org> + -ncbi-tools-20050605.ebuild, ncbi-tools-20080302.ebuild: + Pruned old version. Added 20080302 to x86 and amd64 (fixes bug #218233). + +*ncbi-tools-20080302 (15 Apr 2008) + + 15 Apr 2008; Jeff Gardner <je_fro@gentoo.org> +ncbi-tools-20080302.ebuild: + Latest release from NCBI. + + 08 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>; Manifest: + Fix manifest, connection dropped mid-commit. + + 08 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>; + ncbi-tools-20070826.ebuild: + (#195251) Fix build with --as-needed by always linking against dynamic + libraries (Till Korten). + + 08 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>; + ncbi-tools-20070826.ebuild: + Respect CFLAGS and compiler on 64-bit systems. Apparently I'm the only + person on amd64 who actually watches it build. =) + + 31 Dec 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog: + fixing my email address + + 19 Oct 2007; Jeff Gardner <je_fro@gentoo.org> ncbi-tools-20070826.ebuild: + Commenting out any reference to USE=mpi, which is currently broken (bug + #196466). + + 14 Oct 2007; Jeff Gardner <je_fro@gentoo.org> ncbi-tools-20070826.ebuild: + Commented out a stray reference to mpi that I missed the first time. + + 13 Oct 2007; <je_fro@gentoo.org> ncbi-tools-20050605.ebuild, + +ncbi-tools-20070826.ebuild: + Added quotes to make repoman happy. + +*ncbi-tools-20070826 (13 Oct 2007) + + 13 Oct 2007; <je_fro@gentoo.org> +ncbi-tools-20070826.ebuild: + New version - mpiblast compilation broken at present. + + 05 Jun 2007; Raúl Porcel <armin76@gentoo.org> ncbi-tools-20060507.ebuild: + alpha stable wrt #152292 + + 10 Mar 2007; Olivier Fisette <ribosome@gentoo.org> + +files/ncbi-tools-extra_vib.patch: + Added missing patch. Thanks to Walter Meinl <wuno@lsvw.de> for reporting + (bug #170202). + +*ncbi-tools-20061015-r1 (09 Mar 2007) + + 09 Mar 2007; Olivier Fisette <ribosome@gentoo.org> + -ncbi-tools-20061015.ebuild, +ncbi-tools-20061015-r1.ebuild: + Install ans2all utility. Added support for compiling/installing arbitrary + NCBI utilities. Thanks to José María Fernández González + <jmfernandez@cnio.es> for his work (see bug #169822). Pruned old version. + + 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + -ncbi-tools-20050605-r2.ebuild: + Pruned old version. + +*ncbi-tools-20061015 (03 Nov 2006) + + 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + +ncbi-tools-20061015.ebuild: + New upstream version. + + 30 Oct 2006; Christian Faulhammer <opfer@gentoo.org> + ncbi-tools-20060507.ebuild: + stable x86 as requested in bug #152292 + + 25 Oct 2006; Lars Weiler <pylon@gentoo.org> ncbi-tools-20060507.ebuild: + Stable on ppc; bug #152292. + + 25 Oct 2006; Fabian Groffen <grobian@gentoo.org> + ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild: + Dropped ppc-macos, see you in prefix. + + 24 Oct 2006; Fabian Groffen <grobian@gentoo.org> + ncbi-tools-20060507.ebuild: + Dropped ppc-macos, we don't have pmake + + 24 Oct 2006; Jeff Gardner <je_fro@gentoo.org> ncbi-tools-20060507.ebuild: + Stable on amd64. + + 23 Oct 2006; Markus Rothe <corsair@gentoo.org> ncbi-tools-20060507.ebuild: + Stable on ppc64; bug #152292 + + 23 Oct 2006; Jeff Gardner <je_fro@gentoo.org> ncbi-tools-20060507.ebuild: + Stable on sparc - bug #152292 + + 27 Jun 2006; Brent Baude <ranger@gentoo.org> ncbi-tools-20060507.ebuild: + Keywording ncbi-tools-20060507 ~ppc64 for bug #138082 + + 27 Jun 2006; Olivier Fisette <ribosome@gentoo.org> + -files/ncbi-tools-20050605-lop.patch, +files/ncbi-tools-lop.patch, + ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild, + ncbi-tools-20060507.ebuild: + Fixed ppc64 lop patch (my mistake). + +*ncbi-tools-20060507 (26 Jun 2006) + + 26 Jun 2006; Olivier Fisette <ribosome@gentoo.org> + +files/ncbi-tools-asn2all.patch, +ncbi-tools-20060507.ebuild: + New upstream version. Switched from GNU make to pmake as GNU make 3.81 is + confused by some Makefiles (fixes bug #136904, thanks to Greg Wilson for + reporting). Compile and install asn2all (fixes bug #136206, thanks to José + María Fernández González for the suggestion). Minor bugfixes and ebuild + clean-up. ppc64 keyword dropped as pmake is not available for that arch. + + 01 Feb 2006; Donnie Berkholz <spyderous@gentoo.org>; + ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild: + (#121066) Port to modular X. Add some die messages to -r2 so the die's + aren't completely unhelpful. Fix the path expansion for html docs so it + doesn't break the installation -- not sure how it got committed as is: + {*.html *.gif} is missing a comma. + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> + -ncbi-tools-20050605-r1.ebuild: + Removed buggy version. + +*ncbi-tools-20050605-r2 (14 Dec 2005) + + 14 Dec 2005; Olivier Fisette <ribosome@gentoo.org> + +ncbi-tools-20050605-r2.ebuild: + Fixed file collisions with "dev-libs/libpcre" (bug #115463). + + 16 Nov 2005; Olivier Fisette <ribosome@gentoo.org> + ncbi-tools-20050605-r1.ebuild: + Readded ~sparc (closes bug #111807). + + 15 Nov 2005; Fernando J. Pereda <ferdy@gentoo.org> + ncbi-tools-20050605-r1.ebuild: + re-add ~alpha wrt bug #111807 + +*ncbi-tools-20050605-r1 (15 Nov 2005) + + 15 Nov 2005; Olivier Fisette <ribosome@gentoo.org> + +ncbi-tools-20050605-r1.ebuild: + Added MPI support for the BLAST family of programs. Thanks to Brady + Catherman <bradyc@uidaho.edu> for his work (fixes bug #111807). + + 09 Nov 2005; Jason Wever <weeve@gentoo.org> ncbi-tools-20050605.ebuild: + Stable on SPARC wrt bug #108334. + + 22 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -files/21ncbi, + -ncbi-tools-20041020-r1.ebuild, -ncbi-tools-20050429.ebuild: + Pruning old versions. + + 22 Oct 2005; Fabian Groffen <grobian@gentoo.org> + ncbi-tools-20050605.ebuild: + Marked ppc-macos per bug #108334 + + 18 Oct 2005; Aron Griffis <agriffis@gentoo.org> + ncbi-tools-20050605.ebuild: + Mark 20050605 stable on alpha + + 12 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> + ncbi-tools-20050605.ebuild: + Stable on ppc. + + 11 Oct 2005; Luis Medinas <metalgod@gentoo.org> + ncbi-tools-20050605.ebuild: + Marked Stable on amd64 + + 09 Oct 2005; Mark Loeser <halcy0n@gentoo.org> ncbi-tools-20050605.ebuild: + Stable on x86 + + 07 Oct 2005; Brent Baude <ranger@gentoo.org> ncbi-tools-20050605.ebuild: + Marking ncbi-tools-200506 ppc64 stable for bug 108334 + + 19 Sep 2005; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Maintainer changed from Stephen Diener (MIA) to Olivier Fisette. + + 16 Sep 2005; Aron Griffis <agriffis@gentoo.org> + ncbi-tools-20050429.ebuild: + Mark 20050429 stable on alpha + + 19 Aug 2005; Michael Hanselmann <hansmi@gentoo.org> + ncbi-tools-20050429.ebuild: + Removed from ppc (xlc not available). + + 09 Aug 2005; Brent Baude <ranger@gentoo.org> + +files/ncbi-tools-20050605-lop.patch, + -files/ncbi-tools-20050605-lop.patch.gz, ncbi-tools-20050605.ebuild: + For the ebuild ncbi-tools-20050605, I was asked to remove the gz patch and + submit it as plain text. This commit will remove the gz patch and replace it + with a plain text one. The patch name change is also reflected in the + ebuild. + + 08 Aug 2005; Brent Baude <ranger@gentoo.org> + +files/ncbi-tools-20050605-lop.patch.gz, ncbi-tools-20050605.ebuild: + Added patch for 20050506 which when ppc64, will patch the makefile to use + gcc instead of the default xlc (IBM compiler) which doesnt exist on gentoo. + + 08 Aug 2005; Brent Baude <ranger@gentoo.org> ncbi-tools-20050429.ebuild: + ncbi-tools-20050429.ebuild does not compile on ppc64; will fix later ebuild + +*ncbi-tools-20050605 (06 Aug 2005) + + 06 Aug 2005; Olivier Fisette <ribosome@gentoo.org> + -ncbi-tools-20040616.ebuild, ncbi-tools-20050429.ebuild, + +ncbi-tools-20050605.ebuild: + New version. Added 20050429 to x86. Removed old version. + + 09 Jun 2005; Markus Rothe <corsair@gentoo.org> + ncbi-tools-20041020-r1.ebuild: + Stable on ppc64 + + 02 Jun 2005; Olivier Fisette <ribosome@gentoo.org> ChangeLog: + Use "virtual/motif" instead of "x11-libs/openmotif". + + 16 May 2005; Olivier Fisette <ribosome@gentoo.org> + ncbi-tools-20050429.ebuild: + Fixed CFLAGS not being applied properly (bug #92564). + +*ncbi-tools-20050429 (13 May 2005) + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> + +ncbi-tools-20050429.ebuild: + New version. + + 29 Apr 2005; Markus Rothe <corsair@gentoo.org> + ncbi-tools-20041020-r1.ebuild: + Added ~ppc64 to KEYWORDS + + 24 Apr 2005; Michael Hanselmann <hansmi@gentoo.org> + ncbi-tools-20041020-r1.ebuild: + Stable on ppc. + +*ncbi-tools-20041020-r1 (06 Mar 2005) + + 06 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +files/21ncbi-r1, + +ncbi-tools-20041020-r1.ebuild, -ncbi-tools-20041020.ebuild: + Added the "BLASTMAT" environment variable to the env.d file. + + 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> ncbi-tools-20041020.ebuild: + Stable ppc-macos + + 01 Mar 2005; Olivier Fisette <ribosome@gentoo.org> + ncbi-tools-20041020.ebuild: + Added to x86. + + 02 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> ncbi-tools-20040616.ebuild: + Stable ppc-macos + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> + ncbi-tools-20041020.ebuild: + Ebuild cleanup. + +*ncbi-tools-20041020 (18 Jan 2005) + + 18 Jan 2005; Olivier Fisette <ribosome@gentoo.org> + +ncbi-tools-20041020.ebuild: + New version. + + 02 Jan 2005; Olivier Fisette <ribosome@gentoo.org> : + Added to x86. Use toolchain-funcs rather than gcc eclass. + + 29 Dec 2004; Ciaran McCreesh <ciaranm@gentoo.org> : + Change encoding to UTF-8 for GLEP 31 compliance + +*ncbi-tools-20040616 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +files/21ncbi, +files/ncbirc, +ncbi-tools-20040616.ebuild: + Moved from app-sci/ncbi-tools to sci-biology/ncbi-tools. + + 30 Nov 2004; <j4rg0n@gentoo.org> ncbi-tools-20040616.ebuild: + Keyworded ~ppc-macos. + + 22 Nov 2004; Karol Wojtaszek <sekretarz@gentoo.org> + ncbi-tools-20040616.ebuild: + Added to ~amd64 + + 14 Oct 2004; Olivier Fisette <ribosome@gentoo.org> + ncbi-tools-20040616.ebuild: + Use gcc-getCC from gcc.eclass rather than ${CC}. + + 04 Oct 2004; Olivier Fisette <ribosome@gentoo.org> + ncbi-tools-20040616.ebuild: + Fixed potential bug in "SRC_URI". + +*ncbi-tools-20040616 (03 Oct 2004) + + 03 Oct 2004; Olivier Fisette <ribosome@gentoo.org> files/21ncbi, + -files/dot-ncbirc, +files/ncbirc, -ncbi-tools-20031103.ebuild, + -ncbi-tools-20040202-r1.ebuild, +ncbi-tools-20040616.ebuild: + Updated version and new ebuild. This fixes bug #65941. + + 02 Jun 2004; Aron Griffis <agriffis@gentoo.org> ncbi-tools-20031103.ebuild, + ncbi-tools-20040202-r1.ebuild: + Fix use invocation + + 05 May 2004; Bryan Østergaard <kloeri@gentoo.org> + ncbi-tools-20040202-r1.ebuild: + Stable on alpha. + + 19 Apr 2004; Patrick Kursawe <phosphan@gentoo.org> + ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild, + ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild, + ncbi-tools-20040202.ebuild: + Cleanup, removing S=... with no effect + + 30 Mar 2004; Donnie Berkholz <spyderous@gentoo.org>; + ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild, + ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild, + ncbi-tools-20040202.ebuild: + Change x11-base/xfree dependency to virtual/x11. + + 21 Mar 2004; Martin Holzer <mholzer@gentoo.org> + ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild, + ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild, + ncbi-tools-20040202.ebuild: + adding categorie. see 45110 for details + +*ncbi-tools-20040202-r1 (06 Feb 2004) + + 06 Feb 2004; Stephen Diener <sediener@gentoo.org> + ncbi-tools-20040202-r1.ebuild: + Replaced buggy tarball with new one. Bumped revision to propogate. + +*ncbi-tools-20040202 (05 Feb 2004) + + 05 Feb 2004; Stephen Diener <sediener@gentoo.org> + ncbi-tools-04222003-r1.ebuild, ncbi-tools-04222003.ebuild, + ncbi-tools-20030422.ebuild, ncbi-tools-20031103.ebuild, + ncbi-tools-20040202.ebuild: + Bumped 20031103 to x86, removed old ebuilds, added new release 20040202 + +*ncbi-tools-20040202 (04 Feb 2004) + + 04 Feb 2004; Stephen Diener <sediener@gentoo.org> + ncbi-tools-20031103.ebuild, ncbi-tools-20040202.ebuild: + Version bump. Changes -O3 -> -O2 so X11 apps will work. + + 11 Jan 2004; Heinrich Wendel <lanius@gentoo.org> + ncbi-tools-04222003-r1.ebuild, ncbi-tools-04222003-r2.ebuild, + ncbi-tools-20030422.ebuild, ncbi-tools-20031103.ebuild: + fixed motif dep + +*ncbi-tools-20031103 (13 Dec 2003) + + 13 Dec 2003; Stephen Diener <sediener@gentoo.org> + ncbi-tools-20031103.ebuild: + Added november release of ncbi-tools (blast-2.2.6 included); + Added support for -X + +*ncbi-tools-20030422 (11 Nov 2003) + + 11 Nov 2003; <sediener@gentoo.org> ncbi-tools-20030422.ebuild: + added bl2seq to list of installed binaries; changed date format from 04222003 + to 20030422; renamed files to have date appended to not collide and changed + SRC_URI to mirror://gentoo/ + +*ncbi-tools-04222003-r2 (08 Oct 2003) + + 08 Oct 2003; Robin H. Johnson <robbat2@gentoo.org> + ncbi-tools-04222003-r2.ebuild: + modified patch from #30656, corrected two pathes in the postinst message + +*ncbi-tools-04222003-r1 (05 May 2003) + + 05 May 2003; Jon Portnoy <avenj@gentoo.org> ncbi-tools-04222003-r1.ebuild : + A few enhancements from Gontran Zepeda <gontran@gontran.net>. + +*ncbi-tools-04222003 (03 May 2003) + + 03 May 2003; Jon Portnoy <avenj@gentoo.org> ncbi-tools-04222003 : + Initial important. Ebuild submitted by Steve Diener + <sediener@unity.ncsu.edu>. diff --git a/sci-biology/newick-utils/ChangeLog b/sci-biology/newick-utils/ChangeLog new file mode 100644 index 00000000..c92cb63d --- /dev/null +++ b/sci-biology/newick-utils/ChangeLog @@ -0,0 +1,28 @@ +# ChangeLog for sci-biology/newick-utils +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/newick-utils/ChangeLog,v 1.6 2013/03/11 16:17:11 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 13 Jul 2011; Kacper Kowalik <xarthisius@gentoo.org> + newick-utils-1.3.0.ebuild, newick-utils-1.5.0.ebuild: + Add blocker for dev-games/libnw wrt #375059 + + 02 Apr 2011; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: + Version bump + + 16 Jul 2010; Markos Chandras <hwoarang@gentoo.org> + newick-utils-1.3.0.ebuild: + Stable on amd64 wrt bug #328423 + + 16 Jul 2010; Christian Faulhammer <fauli@gentoo.org> + newick-utils-1.3.0.ebuild: + stable x86, bug 328423 + +*newick-utils-1.3.0 (06 Jun 2010) + + 06 Jun 2010; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +newick-utils-1.3.0.ebuild: + New package, ebuild written by me + diff --git a/sci-biology/njplot/ChangeLog b/sci-biology/njplot/ChangeLog new file mode 100644 index 00000000..dafa15c5 --- /dev/null +++ b/sci-biology/njplot/ChangeLog @@ -0,0 +1,65 @@ +# ChangeLog for sci-biology/njplot +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/njplot/ChangeLog,v 1.13 2015/03/02 13:14:37 jlec Exp $ + +*njplot-2.3-r1 (02 Mar 2015) + + 02 Mar 2015; Justin Lecher <jlec@gentoo.org> + +files/njplot-2.3-buildsystem.patch, +files/njplot-2.3-format-security.patch, + +njplot-2.3-r1.ebuild, njplot-2.3.ebuild: + Fix dependencies, #425710; make buildsystem sane; fix format-security + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 31 Oct 2009; Markus Meier <maekke@gentoo.org> njplot-2.3.ebuild: + amd64/x86 stable, bug #290935 + +*njplot-2.3 (04 Sep 2009) + + 04 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> metadata.xml, + +njplot-2.3.ebuild, -njplot-20050109.ebuild: + Version bump, clean up, fix bug 248338, take maintainership + + 22 Jul 2007; Donnie Berkholz <dberkholz@gentoo.org>; + njplot-20050109.ebuild: + Drop virtual/x11 references. + + 22 May 2007; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Stepped down from maintaining this package. + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 02 Feb 2006; Olivier Fisette <ribosome@gentoo.org> njplot-20050109.ebuild: + Ported to modular X. + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> njplot-20050109.ebuild: + Ebuild cleanup. + + 09 Jan 2005; Olivier Fisette <ribosome@gentoo.org> njplot-20050109.ebuild: + Added to x86. + +*njplot-20050109 (09 Jan 2005) + + 09 Jan 2005; Olivier Fisette <ribosome@gentoo.org> -njplot-1.ebuild, + +njplot-20050109.ebuild: + Changed versioning scheme. (Upstream does not use version numbers.) + +*njplot-1 (09 Jan 2005) + + 09 Jan 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +njplot-1.ebuild: + Moved from sci-biology/njplot-unrooted to sci-biology/njplot. + +*njplot-unrooted-1 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +njplot-unrooted-1.ebuild: + Moved from app-sci/njplot-unrooted to sci-biology/njplot-unrooted. + +*njplot-unrooted-1 (06 Oct 2004) + + 06 Oct 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +njplot-unrooted-1.ebuild: + Initial import. diff --git a/sci-biology/pals/ChangeLog b/sci-biology/pals/ChangeLog new file mode 100644 index 00000000..ab21899f --- /dev/null +++ b/sci-biology/pals/ChangeLog @@ -0,0 +1,23 @@ +# ChangeLog for sci-biology/pals +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/pals/ChangeLog,v 1.4 2013/03/11 16:35:33 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 22 Sep 2009; Markus Meier <maekke@gentoo.org> pals-1.0.ebuild: + x86 stable, bug #283681 + + 06 Sep 2009; Jeremy Olexa <darkside@gentoo.org> pals-1.0.ebuild: + amd64 stable, bug 283681. As requested, compile tested only due to + complexity + +*pals-1.0 (25 Jul 2009) + + 25 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +pals-1.0.ebuild: + Import from Science overlay + + 18 Feb 2009; weaver <weaver@gentoo.org> ChangeLog: + New package sci-biology/pals, ebuild written by me + diff --git a/sci-biology/paml/ChangeLog b/sci-biology/paml/ChangeLog new file mode 100644 index 00000000..688564fb --- /dev/null +++ b/sci-biology/paml/ChangeLog @@ -0,0 +1,89 @@ +# ChangeLog for sci-biology/paml +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/ChangeLog,v 1.20 2015/04/20 20:25:35 jlec Exp $ + + 20 Apr 2015; Justin Lecher <jlec@gentoo.org> -paml-4.4c.ebuild: + Drop old + + 19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> paml-4.4c-r1.ebuild: + Stable for x86, wrt bug #544958 + + 08 Apr 2015; Agostino Sarubbo <ago@gentoo.org> paml-4.4c-r1.ebuild: + Stable for amd64, wrt bug #544958 + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> paml-4.4c-r1.ebuild: + Streamline ebuild layout + +*paml-4.4c-r1 (03 Mar 2015) + + 03 Mar 2015; Justin Lecher <jlec@gentoo.org> +paml-4.4c-r1.ebuild, + metadata.xml: + Bump EAPI + + 12 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org> -paml-4.3a.ebuild, + -paml-4.3b.ebuild: + Drop old buggy versions. + + 12 Sep 2010; Markos Chandras <hwoarang@gentoo.org> paml-4.4c.ebuild: + Stable on amd64 wrt bug #335649 + + 06 Sep 2010; Christian Faulhammer <fauli@gentoo.org> paml-4.4c.ebuild: + stable x86, bug 335649 + +*paml-4.4c (02 Sep 2010) + + 02 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org> -paml-4.1.ebuild, + -paml-4.2b-r1.ebuild, +paml-4.4c.ebuild: + Version bump. Fixes bug 335608. Thanks to Diego for report. + + 09 Feb 2010; Pacho Ramos <pacho@gentoo.org> paml-4.3a.ebuild: + amd64 stable, bug 298772 + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> paml-4.3a.ebuild: + stable x86, bug 298772 + +*paml-4.3b (28 Dec 2009) + + 28 Dec 2009; Andrey Kislyuk <weaver@gentoo.org> +paml-4.3b.ebuild: + Version bump + + 13 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> -paml-4.2b.ebuild, + -paml-4b.ebuild: + Drop old versions + +*paml-4.3a (13 Nov 2009) + + 13 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> +paml-4.3a.ebuild: + Version bump + +*paml-4.2b-r1 (21 Jul 2009) + + 21 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +paml-4.2b-r1.ebuild: + Remove static linking, bug 273344 + +*paml-4.2b (25 Apr 2009) + + 25 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> +paml-4.2b.ebuild: + Version bump + +*paml-4.1 (07 Sep 2008) + + 07 Sep 2008; Markus Dittrich <markusle@gentoo.org> -paml-3.15.ebuild, + +paml-4.1.ebuild, -paml-4a.ebuild: + Version bump and removed old ebuilds. + +*paml-4b (20 Apr 2008) + + 20 Apr 2008; Markus Dittrich <markusle@gentoo.org> +paml-4b.ebuild: + Version bump (fixes bug #218232). + +*paml-4a (22 Nov 2007) + + 22 Nov 2007; Markus Dittrich <markusle@gentoo.org> +paml-4a.ebuild: + Version bump. See bug #191867. + +*paml-3.15 (21 Oct 2006) + + 21 Oct 2006; Donnie Berkholz <dberkholz@gentoo.org>; +metadata.xml, + +paml-3.15.ebuild: + New package: Phylogenetic Analysis by Maximum Likelihood. diff --git a/sci-biology/phrap/ChangeLog b/sci-biology/phrap/ChangeLog new file mode 100644 index 00000000..a9bc4e43 --- /dev/null +++ b/sci-biology/phrap/ChangeLog @@ -0,0 +1,24 @@ +# ChangeLog for sci-biology/phrap +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/phrap/ChangeLog,v 1.4 2015/06/16 08:34:28 jlec Exp $ + +*phrap-1.080812-r1 (16 Jun 2015) + + 16 Jun 2015; Justin Lecher <jlec@gentoo.org> +phrap-1.080812-r1.ebuild, + -phrap-1.080812.ebuild: + Bump to EAPI=5 and fix file collision, bug #422643; thanks Martin Mokrejs + contacting upstream regarding this issue + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 17 Feb 2013; Justin Lecher <jlec@gentoo.org> phrap-1.080812.ebuild, + metadata.xml: + Add missing deps, thanks Martin Mokrejš for the patch + +*phrap-1.080812 (31 Dec 2008) + + 31 Dec 2008; weaver <weaver@gentoo.org> +metadata.xml, + +phrap-1.080812.ebuild: + Import from Science overlay, bug 114094. Thanks to Brady Catherman and Martin + Mokrejs. diff --git a/sci-biology/phred/ChangeLog b/sci-biology/phred/ChangeLog new file mode 100644 index 00000000..d9d3134b --- /dev/null +++ b/sci-biology/phred/ChangeLog @@ -0,0 +1,19 @@ +# ChangeLog for sci-biology/phred +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/phred/ChangeLog,v 1.3 2013/03/11 16:36:54 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 07 Jul 2009; Diego E. Pettenò <flameeyes@gentoo.org> phred-071220.ebuild: + Use elog for fetch error. + +*phred-071220 (26 Feb 2009) + + 26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +phred-071220.ebuild: + Import from Science overlay + + 20 Feb 2009; weaver <weaver@gentoo.org> ChangeLog: + New package, ebuild written by me, thanks to Martin Mokrejs + diff --git a/sci-biology/phylip/ChangeLog b/sci-biology/phylip/ChangeLog new file mode 100644 index 00000000..0679eac7 --- /dev/null +++ b/sci-biology/phylip/ChangeLog @@ -0,0 +1,211 @@ +# ChangeLog for sci-biology/phylip +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/ChangeLog,v 1.47 2015/04/22 06:51:38 jlec Exp $ + + 22 Apr 2015; Justin Lecher <jlec@gentoo.org> -phylip-3.67.ebuild, + -phylip-3.69.ebuild: + Drop old + + 21 Apr 2015; Pacho Ramos <pacho@gentoo.org> phylip-3.69-r1.ebuild: + ppc stable wrt bug #544946 + + 19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> phylip-3.69-r1.ebuild: + Stable for x86, wrt bug #544946 + + 08 Apr 2015; Agostino Sarubbo <ago@gentoo.org> phylip-3.69-r1.ebuild: + Stable for amd64, wrt bug #544946 + +*phylip-3.696 (29 Mar 2015) + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> +phylip-3.696.ebuild, + phylip-3.67.ebuild, phylip-3.69-r1.ebuild, phylip-3.69.ebuild: + Version Bump + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*phylip-3.69-r1 (17 Feb 2013) + + 17 Feb 2013; Justin Lecher <jlec@gentoo.org> -phylip-3.68.ebuild, + +phylip-3.69-r1.ebuild, metadata.xml: + Respect LDFLAGS, #337921 + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> phylip-3.69.ebuild: + Transfer Prefix keywords + + 31 Oct 2009; Markus Meier <maekke@gentoo.org> phylip-3.69.ebuild: + amd64/x86 stable, bug #290939 + +*phylip-3.69 (10 Sep 2009) + + 10 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> +phylip-3.69.ebuild: + Version bump + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> -phylip-3.65-r1.ebuild, + -phylip-3.66.ebuild: + Pruned old versions. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> phylip-3.68.ebuild: + Stabilised on amd64 and x86. + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*phylip-3.68 (26 Aug 2008) + + 26 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +phylip-3.68.ebuild: + New upstream version. + + 29 Jun 2008; Torsten Veller <tove@gentoo.org> phylip-3.65-r1.ebuild, + phylip-3.66.ebuild, phylip-3.67.ebuild: + Add missing die: || "..." -> || die "..." + + 17 Mar 2008; Kenneth Prugh <ken69267@gentoo.org> phylip-3.67.ebuild: + amd64 stable, bug #207095 + + 16 Feb 2008; Markus Meier <maekke@gentoo.org> phylip-3.67.ebuild: + x86 stable, bug #207095 + + 15 Feb 2008; nixnut <nixnut@gentoo.org> phylip-3.67.ebuild: + Stable on ppc wrt bug 207095 + + 07 Feb 2008; Fabian Groffen <grobian@gentoo.org> phylip-3.65-r1.ebuild, + phylip-3.66.ebuild, phylip-3.67.ebuild: + Dropped ppc-macos keyword, see you in prefix + +*phylip-3.67 (19 Sep 2007) + + 19 Sep 2007; Olivier Fisette <ribosome@gentoo.org> files/README.Gentoo, + +phylip-3.67.ebuild: + New upstream version. (Thanks to Arfrever Frehtes Taifersar Arahesis + <arfrever.fta@gmail.com> for reporting. See bug #191869) + + 30 Aug 2007; Olivier Fisette <ribosome@gentoo.org> phylip-3.66.ebuild: + Added to ~amd64. + + 22 Jul 2007; Donnie Berkholz <dberkholz@gentoo.org>; + phylip-3.65-r1.ebuild, phylip-3.66.ebuild: + Drop virtual/x11 references. + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + +*phylip-3.66 (13 Sep 2006) + + 13 Sep 2006; Olivier Fisette <ribosome@gentoo.org> +phylip-3.66.ebuild: + New upstream version. + + 02 Feb 2006; Olivier Fisette <ribosome@gentoo.org> phylip-3.65-r1.ebuild: + Ported to modular X. + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> -phylip-3.64.ebuild: + Removed obsolete version. + + 21 Jan 2006; Hasan Khalil <gongloo@gentoo.org> phylip-3.64.ebuild: + Dropping ppc-macos stable keyword as a result of X11 bug(s). #115468 + + 23 Dec 2005; Tobias Scherbaum <dertobi123@gentoo.org> + phylip-3.65-r1.ebuild: + Marked ppc stable, #115468 + + 15 Dec 2005; Joshua Jackson <tsunam@gentoo.org> phylip-3.65-r1.ebuild: + Stable on x86 for bug #115468 + + 14 Dec 2005; Olivier Fisette <ribosome@gentoo.org> phylip-3.65-r1.ebuild: + Removed dependency on "virtual/libc". + +*phylip-3.65-r1 (14 Dec 2005) + + 14 Dec 2005; Olivier Fisette <ribosome@gentoo.org> +files/README.Gentoo, + -phylip-3.65.ebuild, +phylip-3.65-r1.ebuild: + Fixed file collision with "sys-apps/coreutils" (bug #115482). Keep only + fixed ebuild. + +*phylip-3.65 (18 Oct 2005) + + 18 Oct 2005; Olivier Fisette <ribosome@gentoo.org> +phylip-3.65.ebuild: + New version. + + 17 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -phylip-3.63.ebuild: + Pruning old version. + + 17 Oct 2005; Joseph Jezak <josejx@gentoo.org> phylip-3.64.ebuild: + Marked ppc stable for bug #108335. + + 09 Oct 2005; Mark Loeser <halcy0n@gentoo.org> phylip-3.64.ebuild: + Stable on x86 + + 08 Oct 2005; Lina Pezzella <j4rg0n@gentoo.org> phylip-3.64.ebuild: + Stable ppc-macos, Bug 108335 + + 19 Sep 2005; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Maintainer changed from Stephen Diener (MIA) to Olivier Fisette. + +*phylip-3.64 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> -phylip-3.62.ebuild, + +phylip-3.64.ebuild: + New version. Removed old version. + + 18 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> phylip-3.63.ebuild: + Stable ppc-macos + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> phylip-3.63.ebuild: + Ebuild cleanup. + + 18 Jan 2005; Olivier Fisette <ribosome@gentoo.org> phylip-3.63.ebuild: + Added to x86. + + 14 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> phylip-3.62.ebuild: + Stable ppc-macos. + + 02 Jan 2005; Olivier Fisette <ribosome@gentoo.org> phylip-3.62.ebuild, + phylip-3.63.ebuild: + Use the toolchain-funcs rather than the gcc eclass. + +*phylip-3.63 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +phylip-3.62.ebuild, +phylip-3.63.ebuild: + Moved from app-sci/phylip to sci-biology/phylip. + +*phylip-3.63 (19 Dec 2004) + + 19 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +phylip-3.63.ebuild: + New version. + + 2 Nov 2004; Lina Pezzella <j4rg0n@gentoo.org> -phylip-3.62.ebuild: + Keyworded ~ppc-macos. + + 14 Oct 2004; Olivier Fisette <ribosome@gentoo.org> -phylip-3.61.ebuild, + phylip-3.62.ebuild: + Added 3.62 to x86. Removed old version. Use gcc.eclass rather than ${CC}. + +*phylip-3.62 (29 Sep 2004) + + 29 Sep 2004; Olivier Fisette <ribosome@gentoo.org> -phylip-3.5.ebuild, + -phylip-3.6.ebuild, phylip-3.61.ebuild, +phylip-3.62.ebuild: + Added 3.61 to x86. New version 3.62. Removed old versions. + +*phylip-3.61.ebuild (7 Aug 2004) + + 7 Aug 2004; Olivier Fisette <ribosome@gentoo.org> phylip-3.61.ebuild: + Version bump. The program icons are no longer part of the distribution. + + 23 Jul 2004; Jon Hood <squinky86@gentoo.org> phylip-3.6.ebuild: + Change virtual/glibc -> virtual/libc. + + 21 Jul 2004; David Holm <dholm@gentoo.org> phylip-3.6.ebuild: + Added to ~ppc. + +*phylip-3.6.ebuild (19 Jul 2004) + + 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> phylip-3.6.ebuild: + New version and a modified ebuild. Update suggested by Pablo Nehab-Hess + <natunobilis@gentoobr.org> (#38853). + +*phylip-3.5 (23 Apr 2003) + + 23 Apr 2003; Jon Portnoy <avenj@gentoo.org> phylip-3.5.ebuild : + Initial import. Ebuild submitted in bug #19856 by Stephen Diener + (sediener@unity.ncsu.edu). diff --git a/sci-biology/phyml/ChangeLog b/sci-biology/phyml/ChangeLog new file mode 100644 index 00000000..cef759e1 --- /dev/null +++ b/sci-biology/phyml/ChangeLog @@ -0,0 +1,47 @@ +# ChangeLog for sci-biology/phyml +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/phyml/ChangeLog,v 1.11 2014/01/14 15:33:23 ago Exp $ + + 14 Jan 2014; Agostino Sarubbo <ago@gentoo.org> phyml-2.4.5-r2.ebuild: + Stable for ppc, wrt bug #497216 + + 18 Feb 2013; Justin Lecher <jlec@gentoo.org> -phyml-2.4.5.ebuild, + metadata.xml: + Drop Old + + 17 Feb 2013; Agostino Sarubbo <ago@gentoo.org> phyml-2.4.5-r2.ebuild: + Stable for x86, wrt bug #328425 + + 17 Feb 2013; Agostino Sarubbo <ago@gentoo.org> phyml-2.4.5-r2.ebuild: + Stable for amd64, wrt bug #328425 + + 10 Dec 2012; Agostino Sarubbo <ago@gentoo.org> phyml-2.4.5-r2.ebuild: + Add ~ppc, wrt bug #432368 + +*phyml-2.4.5-r2 (22 Oct 2010) + + 22 Oct 2010; Kacper Kowalik <xarthisius@gentoo.org> phyml-2.4.5.ebuild, + -phyml-2.4.5-r1.ebuild, +phyml-2.4.5-r2.ebuild: + Respect LDFLAGS wrt bug 342089. Thanks to Diego for the report. Bump to + EAPI=2, add missing dies, drop empty depends. Drop old. Add missing quotes + to stable ebuild. + + 16 Jul 2010; Christian Faulhammer <fauli@gentoo.org> + phyml-2.4.5-r1.ebuild: + stable x86, bug 328425 + +*phyml-2.4.5-r1 (09 Mar 2009) + + 09 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> +phyml-2.4.5-r1.ebuild: + QA fixes + + 17 Feb 2008; Christian Faulhammer <opfer@gentoo.org> phyml-2.4.5.ebuild: + stable x86/amd64, bug 207096 + + 25 Dec 2007; Christian Heim <phreak@gentoo.org> metadata.xml: + Removing gongloo from metadata.xml as per #53935. + +*phyml-2.4.5 (18 Aug 2006) + + 18 Aug 2006; <gongloo@gentoo.org> +metadata.xml, +phyml-2.4.5.ebuild: + Initial commit. diff --git a/sci-biology/picard/ChangeLog b/sci-biology/picard/ChangeLog new file mode 100644 index 00000000..72efcb53 --- /dev/null +++ b/sci-biology/picard/ChangeLog @@ -0,0 +1,30 @@ +# ChangeLog for sci-biology/picard +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/picard/ChangeLog,v 1.5 2013/11/24 15:32:13 ercpe Exp $ + + 24 Nov 2013; Johann Schmitz <ercpe@gentoo.org> -picard-1.58.ebuild, + -picard-1.63.ebuild: + Dropped versions 1.58 and 1.63 as they don't meet the qa requirements and a + snapshotted version of the lastest version is in the tree (#491816). + +*picard-1.103 (24 Nov 2013) + + 24 Nov 2013; Johann Schmitz <ercpe@gentoo.org> +files/1.103-gentoo.patch, + +picard-1.103.ebuild, metadata.xml: + Version bump and reworked ebuild for sci-biology/picard. Uses a snapshotted + tarball from upstreams 1.103 subversion tag to meet gentoo qa requirements + (wrt #491816) + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*picard-1.63 (28 Feb 2012) + + 28 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> +picard-1.63.ebuild: + Version bump + +*picard-1.58 (04 Jan 2012) + + 04 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> +picard-1.58.ebuild, + +metadata.xml: + New package, ebuild written by me diff --git a/sci-biology/piler/ChangeLog b/sci-biology/piler/ChangeLog new file mode 100644 index 00000000..dc34e534 --- /dev/null +++ b/sci-biology/piler/ChangeLog @@ -0,0 +1,27 @@ +# ChangeLog for sci-biology/piler +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/piler/ChangeLog,v 1.5 2013/03/11 14:33:55 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 22 Sep 2009; Markus Meier <maekke@gentoo.org> piler-1.0.ebuild: + x86 stable, bug #283683 + + 06 Sep 2009; Jeremy Olexa <darkside@gentoo.org> piler-1.0.ebuild: + amd64 stable, bug 283683. As requested, compile tested only due to + complexity + + 09 Aug 2009; Samuli Suominen <ssuominen@gentoo.org> piler-1.0.ebuild, + +files/piler-1.0-glibc-2.10.patch: + Fix building with GLIBC 2.10+ wrt #279628. + +*piler-1.0 (25 Jul 2009) + + 25 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +piler-1.0.ebuild: + Import from Science overlay + + 18 Feb 2009; weaver <weaver@gentoo.org> ChangeLog: + New package sci-biology/piler, ebuild written by me + diff --git a/sci-biology/pilercr/ChangeLog b/sci-biology/pilercr/ChangeLog new file mode 100644 index 00000000..bf1d89ca --- /dev/null +++ b/sci-biology/pilercr/ChangeLog @@ -0,0 +1,30 @@ +# ChangeLog for sci-biology/pilercr +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/pilercr/ChangeLog,v 1.8 2013/03/11 16:46:48 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 26 Apr 2012; Justin Lecher <jlec@gentoo.org> pilercr-1.0.ebuild: + Move to EAPI=, remove unecessary die + + 22 Sep 2009; Markus Meier <maekke@gentoo.org> pilercr-1.0.ebuild: + x86 stable, bug #283685 + + 06 Sep 2009; Jeremy Olexa <darkside@gentoo.org> pilercr-1.0.ebuild: + amd64 stable, bug 283685. As requested, compile tested only due to + complexity + + 27 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> pilercr-1.0.ebuild: + Correct description + + 26 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> pilercr-1.0.ebuild: + Correct description + + 25 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> + +files/pilercr-1.0-gcc43.patch, +metadata.xml: + Import from Science overlay + + 18 Feb 2009; weaver <weaver@gentoo.org> ChangeLog: + New package sci-biology/pilercr, ebuild written by me + diff --git a/sci-biology/plink/ChangeLog b/sci-biology/plink/ChangeLog new file mode 100644 index 00000000..4837ece0 --- /dev/null +++ b/sci-biology/plink/ChangeLog @@ -0,0 +1,44 @@ +# ChangeLog for sci-biology/plink +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/ChangeLog,v 1.18 2015/06/09 13:37:57 jlec Exp $ + + 09 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml, + plink-1.90_pre140514.ebuild: + Fix build problems related to missing blas, bug #530670; bug #550142 + + 22 Sep 2014; Justin Lecher <jlec@gentoo.org> plink-1.90_pre140514.ebuild: + Rename USE lapack -> blas, fixing build problems, #514106 + +*plink-1.90_pre140514 (19 May 2014) + + 19 May 2014; Justin Lecher <jlec@gentoo.org> -plink-1.07.ebuild, + +plink-1.90_pre140514.ebuild: + Version Bump, #510716 + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 27 Feb 2013; Justin Lecher <jlec@gentoo.org> files/1.07-flags.patch, + plink-1.07-r1.ebuild, metadata.xml: + Use detected pkg-config instead of generic + + 04 Jul 2012; Justin Lecher <jlec@gentoo.org> plink-1.07-r1.ebuild, + +files/plink-1.07-gcc47.patch: + Moved to EAPI=4, add fix for building with gcc-4.7, #424709 + + 13 Dec 2011; Agostino Sarubbo <ago@gentoo.org> plink-1.07-r1.ebuild: + Stable for AMD64, wrt bug #392783 + + 11 Dec 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> plink-1.07-r1.ebuild: + x86 stable wrt bug #392783 + + 07 Dec 2011; Justin Lecher <jlec@gentoo.org> plink-1.07-r1.ebuild, + metadata.xml: + Added missing sys-libs/zlib to RDEPEND noted by ago, #392783 + +*plink-1.07-r1 (26 Nov 2010) + + 26 Nov 2010; Justin Lecher <jlec@gentoo.org> +files/1.07-flags.patch, + -plink-1.06.ebuild, +plink-1.07-r1.ebuild, metadata.xml: + Fixes for #335975, respecting LDFLAGS/CXXFLAGS, supporting lapack, making R + support optional diff --git a/sci-biology/poa/ChangeLog b/sci-biology/poa/ChangeLog new file mode 100644 index 00000000..3e7aac25 --- /dev/null +++ b/sci-biology/poa/ChangeLog @@ -0,0 +1,22 @@ +# ChangeLog for sci-biology/poa +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/poa/ChangeLog,v 1.5 2015/04/07 14:34:18 jlec Exp $ + + 21 Mar 2015; Justin Lecher <jlec@gentoo.org> -poa-2.ebuild, metadata.xml, + poa-2-r1.ebuild: + Drop old; Bump EAPI; handle static-libs + +*poa-2-r1 (18 Sep 2010) + + 18 Sep 2010; Justin Lecher <jlec@gentoo.org> +files/2-respect-flags.patch, + +poa-2-r1.ebuild: + Respecting LDFLAGS, 337856 + + 07 Sep 2008; Markus Dittrich <markusle@gentoo.org> poa-2.ebuild: + Fix outdated HOMEPAGE and keyword amd64. + +*poa-2 (21 Oct 2006) + + 21 Oct 2006; Donnie Berkholz <dberkholz@gentoo.org>; + +files/respect-cflags.patch, +metadata.xml, +poa-2.ebuild: + New package: Fast multiple sequence alignments using partial-order graphs. diff --git a/sci-biology/prank/ChangeLog b/sci-biology/prank/ChangeLog new file mode 100644 index 00000000..5940618c --- /dev/null +++ b/sci-biology/prank/ChangeLog @@ -0,0 +1,55 @@ +# ChangeLog for sci-biology/prank +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/prank/ChangeLog,v 1.11 2015/03/29 13:52:32 jlec Exp $ + +*prank-140603 (29 Mar 2015) + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> +prank-140603.ebuild, + prank-100701.ebuild, prank-111130.ebuild: + Version Bump + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 20 Jun 2012; Justin Lecher <jlec@gentoo.org> prank-100701.ebuild, + prank-111130.ebuild, +files/prank-111130-gcc-4.7.patch: + Fix compilation with gcc-4.7, #422581 + +*prank-111130 (28 Feb 2012) + + 28 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> -prank-081202.ebuild, + -files/prank-081202-gcc44.patch, -prank-091016.ebuild, + -prank-100311.ebuild, +prank-111130.ebuild: + Version bump, remove old + + 09 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org> prank-100701.ebuild: + Respect user FLAGS wrt bug 331799. Thanks to Diego for report. Drop perl + from src_prepare. + +*prank-100701 (15 Jul 2010) + + 15 Jul 2010; Andrey Kislyuk <weaver@gentoo.org> +prank-100701.ebuild: + Version bump + +*prank-100311 (23 Mar 2010) + + 23 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> +prank-100311.ebuild: + Version bump + + 28 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> prank-091016.ebuild: + Restore erroneously removed patch + +*prank-091016 (28 Oct 2009) + + 28 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +prank-091016.ebuild: + Version bump + + 10 Aug 2009; Samuli Suominen <ssuominen@gentoo.org> prank-081202.ebuild, + +files/prank-081202-gcc44.patch: + Fix building with GCC 4.4+ wrt #277246. + +*prank-081202 (09 Apr 2009) + + 09 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +prank-081202.ebuild: + New package, ebuild written by me diff --git a/sci-biology/primer3/ChangeLog b/sci-biology/primer3/ChangeLog new file mode 100644 index 00000000..8026b370 --- /dev/null +++ b/sci-biology/primer3/ChangeLog @@ -0,0 +1,202 @@ +# ChangeLog for sci-biology/primer3 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/ChangeLog,v 1.46 2015/04/22 06:51:36 jlec Exp $ + + 22 Apr 2015; Justin Lecher <jlec@gentoo.org> -primer3-2.3.1.ebuild: + Drop old + + 21 Apr 2015; Pacho Ramos <pacho@gentoo.org> primer3-2.3.5.ebuild: + ppc stable wrt bug #544908 + + 19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> primer3-2.3.5.ebuild: + Stable for x86, wrt bug #544908 + + 08 Apr 2015; Agostino Sarubbo <ago@gentoo.org> primer3-2.3.5.ebuild: + Stable for amd64, wrt bug #544908 + +*primer3-2.3.6 (29 Mar 2015) + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> +primer3-2.3.6.ebuild, + -primer3-2.3.4.ebuild: + Version Bump; drop old + +*primer3-2.3.5 (14 Feb 2013) + + 14 Feb 2013; Justin Lecher <jlec@gentoo.org> +primer3-2.3.5.ebuild: + Version Bump + + 17 Dec 2012; Justin Lecher <jlec@gentoo.org> -primer3-2.2.3.ebuild, + -primer3-2.3.0.ebuild: + Drop old + + 16 Dec 2012; Agostino Sarubbo <ago@gentoo.org> primer3-2.3.1.ebuild: + Stable for ppc, wrt bug #446992 + + 16 Dec 2012; Agostino Sarubbo <ago@gentoo.org> primer3-2.3.1.ebuild: + Stable for x86, wrt bug #446992 + + 12 Dec 2012; Agostino Sarubbo <ago@gentoo.org> primer3-2.3.1.ebuild: + Stable for amd64, wrt bug #446992 + + 12 Dec 2012; Justin Lecher <jlec@gentoo.org> + files/primer3-2.3.4-buildsystem.patch: + Fix buildsystem patch to respect RANLIB, #447026 + + 12 Dec 2012; Justin Lecher <jlec@gentoo.org> primer3-2.3.1.ebuild, + primer3-2.3.4.ebuild, metadata.xml: + Fix test + +*primer3-2.3.4 (12 Dec 2012) + + 12 Dec 2012; Justin Lecher <jlec@gentoo.org> -primer3-1.1.4-r2.ebuild, + +primer3-2.3.4.ebuild, +files/primer3-2.3.4-buildsystem.patch: + Version Bump, #446982; cleaned old + +*primer3-2.3.1 (19 Jul 2012) + + 19 Jul 2012; Justin Lecher <jlec@gentoo.org> primer3-2.3.0.ebuild, + +primer3-2.3.1.ebuild: + Version Bump + + 07 Mar 2012; Brent Baude <ranger@gentoo.org> primer3-2.3.0.ebuild: + Marking primer3-2.3.0 ppc for bug 402053 + +*primer3-2.3.0 (28 Feb 2012) + + 28 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> -primer3-1.1.4.ebuild, + +primer3-2.3.0.ebuild: + Version bump, remove old + + 03 Dec 2011; Markos Chandras <hwoarang@gentoo.org> primer3-2.2.3.ebuild: + convert test statement to if;fi block because || die does not work on a + subshell + + 02 Dec 2011; Markos Chandras <hwoarang@gentoo.org> primer3-2.2.3.ebuild: + add missing sed. stable on amd64. bug #391531 + + 28 Nov 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> primer3-2.2.3.ebuild: + x86 stable wrt bug #391531 + + 23 Nov 2011; Justin Lecher <jlec@gentoo.org> -primer3-1.0.0.ebuild, + primer3-1.1.4.ebuild, primer3-1.1.4-r2.ebuild, primer3-2.2.3.ebuild: + Dropped old, respect LDFLAGS, don't mix CFLAGS and CXXFLAGS, move KEYWORDS + and fixes from ver-1 to 2 + + 09 Mar 2011; Justin Lecher <jlec@gentoo.org> +primer3-1.0.0.ebuild: + Reanimate last stable version for ppc/ppc64 + +*primer3-2.2.3 (03 Feb 2011) + + 03 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> -primer3-1.0.0.ebuild, + +primer3-2.2.3.ebuild: + Version bump, drop old + +*primer3-1.1.4-r2 (31 Aug 2010) + + 31 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org> + -primer3-1.1.4-r1.ebuild, +primer3-1.1.4-r2.ebuild, + +files/primer3-1.1.4-ldflags.patch: + Respect CC and LDFLAGS wrt bug 335225. Thanks to Diego for the report. + +*primer3-1.1.4-r1 (07 Mar 2010) + + 07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> + +primer3-1.1.4-r1.ebuild: + Moved to EAPI=3 for PREFIX support, imported prefix patches from overlay, + keyworded as in overlay + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> primer3-1.1.4.ebuild: + Stabilised on x86 and amd64. + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 13 Sep 2008; Olivier Fisette <ribosome@gentoo.org> -primer3-1.0.1.ebuild, + -primer3-1.1.1.ebuild: + Pruned old versions, fixing bug #237441. + +*primer3-1.1.4 (26 Aug 2008) + + 26 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +primer3-1.1.4.ebuild: + New upstream version. + +*primer3-1.1.1 (28 Jun 2007) + + 28 Jun 2007; Olivier Fisette <ribosome@gentoo.org> +primer3-1.1.1.ebuild: + New upstream version. + + 28 Jun 2007; Olivier Fisette <ribosome@gentoo.org> primer3-1.0.0.ebuild, + primer3-1.0.1.ebuild: + Updated home page URL. + +*primer3-1.0.1 (02 Feb 2007) + + 02 Feb 2007; Olivier Fisette <ribosome@gentoo.org> +primer3-1.0.1.ebuild: + New upstream version. + + 06 Jan 2007; Danny van Dyk <kugelfang@gentoo.org> -primer3-1.0b.ebuild: + QA: Removed unused versions. + +*primer3-1.0b (03 Nov 2006) + + 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> +primer3-1.0b.ebuild: + New upstream version. + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> primer3-1.0.0.ebuild: + Dropped ppc-macos, see you in prefix. + + 18 Aug 2006; Jason Wever <weeve@gentoo.org> primer3-1.0.0.ebuild: + Added ~sparc keyword wrt bug #144241. + + 11 Oct 2005; Luis Medinas <metalgod@gentoo.org> primer3-1.0.0.ebuild: + Marked Stable on amd64. + + 04 Sep 2005; Simon Stelling <blubb@gentoo.org> primer3-1.0.0.ebuild: + added ~amd64 keyword + + 19 Jun 2005; Markus Rothe <corsair@gentoo.org> primer3-1.0.0.ebuild: + Stable on ppc64 + + 02 May 2005; Omkhar Arasaratnam <omkhar@gentoo.org> primer3-1.0.0.ebuild: + Added ~ppc64 + + 02 May 2005; Michael Hanselmann <hansmi@gentoo.org> primer3-1.0.0.ebuild: + Stable on ppc. + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> primer3-1.0.0.ebuild: + Ebuild cleanup. + + 14 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> primer3-1.0.0.ebuild: + Stable ppc-macos. + + 26 Dec 2004; Lina Pezzella <j4rg0n@gentoo.org> primer-3-1.0.0.ebuild: + Keyworded ~ppc-macos. + Modified Makefile to dynamically link on ppc-macos. + +*primer3-1.0.0 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +primer3-1.0.0.ebuild: + Moved from app-sci/primer3 to sci-biology/primer3. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> -primer3-0.9.ebuild, + primer3-1.0.0.ebuild: + Removed old version. Added 1.0 to x86. Fixed regression test. + +*primer3-1.0.0 (10 Aug 2004) + + 10 Aug 2004; Olivier Fisette <ribosome@gentoo.org> + primer3-0.9.ebuild: + Added to x86. + primer3-1.0.0.ebuild: + Updated package. Added regression test support. + + 24 Jun 2004; David Holm <dholm@gentoo.org> primer3-0.9.ebuild: + Added to ~ppc. + +*primer3-0.9 (23 Jun 2004) + + 23 Jun 2004; Olivier Fisette <ribosome@gentoo.org> + primer3-0.9.ebuild, metadata.xml : + Initial import. Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>. + Reference: Gentoo Bugzilla, bug #54036 diff --git a/sci-biology/prints/ChangeLog b/sci-biology/prints/ChangeLog new file mode 100644 index 00000000..4751456f --- /dev/null +++ b/sci-biology/prints/ChangeLog @@ -0,0 +1,114 @@ +# ChangeLog for sci-biology/prints +# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/prints/ChangeLog,v 1.30 2012/03/08 08:04:51 jlec Exp $ + + 08 Mar 2012; Justin Lecher <jlec@gentoo.org> -prints-38.0.ebuild: + Dropped old + + 07 Mar 2012; Brent Baude <ranger@gentoo.org> prints-39.0.ebuild: + Marking prints-39.0 ppc for bug 393929 + + 21 Dec 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> prints-39.0.ebuild: + x86 stable wrt bug #393929 + + 18 Dec 2011; Agostino Sarubbo <ago@gentoo.org> prints-39.0.ebuild: + Stable for AMD64, wrt bug #393929 + + 16 Dec 2011; Justin Lecher <jlec@gentoo.org> prints-38.0.ebuild, + prints-39.0.ebuild: + Add missing die, restructural to fit common-sense + + 09 Aug 2011; Kacper Kowalik <xarthisius@gentoo.org> prints-38.0.ebuild, + prints-39.0.ebuild: + ppc64 keyword dropped + + 13 Mar 2011; Raúl Porcel <armin76@gentoo.org> prints-38.0.ebuild, + prints-39.0.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> prints-39.0.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> prints-38.0.ebuild: + Q.A.: Explicit dependencies. + +*prints-39.0 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> +prints-39.0.ebuild: + New upstream version. + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> prints-38.0.ebuild: + Dropped ppc-macos, see you in prefix. + + 18 Aug 2006; Jason Wever <weeve@gentoo.org> prints-38.0.ebuild: + Added ~sparc keyword wrt bug #144241. + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> -prints-37.0.ebuild: + Removed obsolete version. + + 14 Jan 2006; Fabian Groffen <grobian@gentoo.org> prints-38.0.ebuild: + Marked ppc-macos stable for bug #115453 + + 31 Dec 2005; Simon Stelling <blubb@gentoo.org> prints-38.0.ebuild: + stable on amd64 + + 23 Dec 2005; Tobias Scherbaum <dertobi123@gentoo.org> prints-38.0.ebuild: + Marked ppc stable, #115453 + + 15 Dec 2005; Olivier Fisette <ribosome@gentoo.org> prints-38.0.ebuild: + Added to x86. + + 13 Dec 2005; Markus Rothe <corsair@gentoo.org> prints-38.0.ebuild: + Stable on ppc64; bug #115453 + + 19 Nov 2005; Simon Stelling <blubb@gentoo.org> prints-37.0.ebuild: + stable on amd64 + +*prints-38.0 (18 Oct 2005) + + 18 Oct 2005; Olivier Fisette <ribosome@gentoo.org> +prints-38.0.ebuild: + New version. + + 04 Sep 2005; Simon Stelling <blubb@gentoo.org> prints-37.0.ebuild: + added ~amd64 keyword + + 19 Jun 2005; Markus Rothe <corsair@gentoo.org> prints-37.0.ebuild: + Stable on ppc64 + + 02 May 2005; Omkhar Arasaratnam <omkhar@gentoo.org> prints-37.0.ebuild: + Added ~ppc64 + + 02 May 2005; Michael Hanselmann <hansmi@gentoo.org> prints-37.0.ebuild: + Stable on ppc. + + 22 Feb 2005; Olivier Fisette <ribosome@gentoo.org> prints-37.0.ebuild: + Added support for the "emboss" and "minimal" "USE" flags. + + 02 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> prints-37.0.ebuild: + Stable ppc-macos + + 01 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> prints-37.0.ebuild: + Unstable ppc-macos. + +*prints-37.0 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +prints-37.0.ebuild: + Moved from app-sci/prints to sci-biology/prints. + + 10 Aug 2004; Olivier Fisette <ribosome@gentoo.org> prints-37.0.ebuild: + Added to x86. + + 26 Jun 2004; David Holm <dholm@gentoo.org> prints-37.0.ebuild: + Added to ~ppc. + +*prints-37.0 (24 Jun 2004) + + 24 Jun 2004; Olivier Fisette <ribosome@gentoo.org> + prints-37.0.ebuild, metadata.xml : + Initial import. Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>. + Reference: Gentoo Bugzilla, bug #54325 + diff --git a/sci-biology/probcons/ChangeLog b/sci-biology/probcons/ChangeLog new file mode 100644 index 00000000..418fdd76 --- /dev/null +++ b/sci-biology/probcons/ChangeLog @@ -0,0 +1,65 @@ +# ChangeLog for sci-biology/probcons +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/ChangeLog,v 1.15 2015/03/29 14:58:53 jlec Exp $ + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> -files/1.10-fix-cxxflags.patch, + -probcons-1.10.ebuild, -probcons-1.12.ebuild, metadata.xml, + probcons-1.12-r1.ebuild: + Drop old + + 13 Jun 2011; Justin Lecher <jlec@gentoo.org> probcons-1.12-r1.ebuild, + +files/probcons-1.12-gcc-4.6.patch: + Make it gcc46 resistant, #370471 + + 16 Jul 2010; Markos Chandras <hwoarang@gentoo.org> + probcons-1.12-r1.ebuild: + Stable on amd64 wrt bug #328427 + + 16 Jul 2010; Christian Faulhammer <fauli@gentoo.org> + probcons-1.12-r1.ebuild: + stable x86, bug 328427 + + 17 Jun 2010; Justin Lecher <jlec@gentoo.org> probcons-1.10.ebuild, + probcons-1.12.ebuild, probcons-1.12-r1.ebuild: + Blocking sci-geosciences/gmt to resolve bug 248333 + +*probcons-1.12-r1 (15 Jun 2010) + + 15 Jun 2010; Justin Lecher <jlec@gentoo.org> +probcons-1.12-r1.ebuild, + files/probcons-1.12-cxxflags.patch: + QA and keyworded for linux prefix + + 16 Aug 2009; Donnie Berkholz <dberkholz@gentoo.org>; probcons-1.12.ebuild: + Keyword ~amd64. + + 15 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>; +files/gcc-4.3.patch, + probcons-1.12.ebuild: + Fix build with gcc 4.3. + + 07 Oct 2007; Donnie Berkholz <dberkholz@gentoo.org>; probcons-1.12.ebuild: + Add needed quotes; don't specify the default for DESTTREE; add die messages. + +*probcons-1.12 (06 Oct 2007) + + 06 Oct 2007; Markus Dittrich <markusle@gentoo.org> +files/probcons-1.12-cxxflags.patch, +probcons-1.12.ebuild: + New version (fixes bug #191874). + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 01 Oct 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml: + Remove myself as maintainer so it goes to all of the sci-biology team. + + 09 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; probcons-1.10.ebuild: + x86 stable. + + 07 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml: + Update to my new email address. + +*probcons-1.10 (21 Feb 2006) + + 21 Feb 2006; Donnie Berkholz <dberkholz@gentoo.org>; + +files/1.10-fix-cxxflags.patch, +metadata.xml, +probcons-1.10.ebuild: + New multiple sequence alignment package. Probably the best global aligner, + although it runs slower. Takes 5-10 times longer than clustalw, but about + half as long as t-coffee. diff --git a/sci-biology/prodigal/ChangeLog b/sci-biology/prodigal/ChangeLog new file mode 100644 index 00000000..1298a8bc --- /dev/null +++ b/sci-biology/prodigal/ChangeLog @@ -0,0 +1,15 @@ +# ChangeLog for sci-biology/prodigal +# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/prodigal/ChangeLog,v 1.2 2012/01/02 23:06:54 weaver Exp $ + +*prodigal-2.60 (02 Jan 2012) + + 02 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> +prodigal-2.60.ebuild: + Version bump + +*prodigal-2.50 (16 Jul 2011) + + 16 Jul 2011; Andrey Kislyuk <weaver@gentoo.org> +prodigal-2.50.ebuild, + +metadata.xml: + New package, ebuild written by me + diff --git a/sci-biology/profphd/ChangeLog b/sci-biology/profphd/ChangeLog new file mode 100644 index 00000000..5b29b3af --- /dev/null +++ b/sci-biology/profphd/ChangeLog @@ -0,0 +1,22 @@ +# ChangeLog for sci-biology/profphd +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/profphd/ChangeLog,v 1.4 2014/04/24 11:38:57 jlec Exp $ + +*profphd-1.0.40 (24 Apr 2014) + + 24 Apr 2014; Justin Lecher <jlec@gentoo.org> profphd-1.0.39.ebuild, + +profphd-1.0.40.ebuild, +files/profphd-1.0.39-perl.patch: + Fix for newer perl, version Bump + + 24 Apr 2013; Justin Lecher <jlec@gentoo.org> profphd-1.0.39.ebuild: + Updated deps + + 21 Mar 2013; Justin Lecher <jlec@gentoo.org> profphd-1.0.39.ebuild: + Add some more PREFIX love + +*profphd-1.0.39 (19 Mar 2013) + + 19 Mar 2013; Justin Lecher <jlec@gentoo.org> +profphd-1.0.39.ebuild, + +metadata.xml: + New addition + diff --git a/sci-biology/prosite/ChangeLog b/sci-biology/prosite/ChangeLog new file mode 100644 index 00000000..a9f11843 --- /dev/null +++ b/sci-biology/prosite/ChangeLog @@ -0,0 +1,522 @@ +# ChangeLog for sci-biology/prosite +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/prosite/ChangeLog,v 1.112 2011/12/13 23:20:18 ago Exp $ + + 13 Dec 2011; Agostino Sarubbo <ago@gentoo.org> prosite-20.72.ebuild: + Stable for AMD64, wrt bug #392825 + + 11 Dec 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> prosite-20.72.ebuild: + x86 stable wrt bug #392825 + + 05 Dec 2011; Justin Lecher <jlec@gentoo.org> prosite-20.36.ebuild, + prosite-20.52.ebuild, prosite-20.72.ebuild: + Resorted upper ebuild section + + 09 Aug 2011; Kacper Kowalik <xarthisius@gentoo.org> prosite-19.36.ebuild, + prosite-20.36.ebuild, prosite-20.52.ebuild, prosite-20.72.ebuild: + ppc64 keyword dropped + +*prosite-20.72 (25 Apr 2011) + + 25 Apr 2011; Justin Lecher <jlec@gentoo.org> +prosite-20.72.ebuild: + Version Bump + + 09 Mar 2011; Raúl Porcel <armin76@gentoo.org> prosite-19.36.ebuild, + prosite-20.36.ebuild, prosite-20.52.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> prosite-20.52.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> -prosite-20.16.ebuild, + -prosite-20.17.ebuild: + Pruning old versions. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> prosite-20.36.ebuild: + Stabilised on amd64 and x86. + +*prosite-20.52 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> +prosite-20.52.ebuild: + New upstream version. + +*prosite-20.36 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +prosite-20.36.ebuild: + New upstream version. + +*prosite-20.17 (20 Aug 2007) + + 20 Aug 2007; Olivier Fisette <ribosome@gentoo.org> +prosite-20.17.ebuild: + New upstream version. + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> -prosite-20.10.ebuild, + -prosite-20.12.ebuild: + Pruned older ebuilds that will never be stabilised. + +*prosite-20.16 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> +prosite-20.16.ebuild: + New upstream version. + +*prosite-20.12 (22 May 2007) + + 22 May 2007; Olivier Fisette <ribosome@gentoo.org> -prosite-20.9.ebuild, + +prosite-20.12.ebuild: + New upstream version. Pruned old version. + +*prosite-20.10 (21 Apr 2007) + + 21 Apr 2007; Olivier Fisette <ribosome@gentoo.org> -prosite-20.1.ebuild, + +prosite-20.10.ebuild: + New upstream version. Pruned old version. + +*prosite-20.9 (11 Apr 2007) + + 11 Apr 2007; Olivier Fisette <ribosome@gentoo.org> +prosite-20.9.ebuild: + New upstream version. + +*prosite-20.1 (12 Dec 2006) + + 12 Dec 2006; Olivier Fisette <ribosome@gentoo.org> -prosite-19.38.ebuild, + +prosite-20.1.ebuild: + New upstream version. Removed old version. + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> -prosite-19.18.ebuild, + -prosite-19.22.ebuild, -prosite-19.37.ebuild: + Pruned old versions. + + 20 Nov 2006; <blubb@gentoo.org> prosite-19.36.ebuild: + stable on amd64 + + 15 Nov 2006; Markus Rothe <corsair@gentoo.org> prosite-19.36.ebuild: + Stable on ppc64; bug #153766 + + 03 Nov 2006; nixnut <nixnut@gentoo.org> prosite-19.36.ebuild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> -prosite-19.25.ebuild, + -prosite-19.29.ebuild, -prosite-19.35.ebuild: + Pruned old versions. + +*prosite-19.38 (03 Nov 2006) + + 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> +prosite-19.38.ebuild: + New upstream version. + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> prosite-19.18.ebuild, + prosite-19.22.ebuild, prosite-19.25.ebuild, prosite-19.29.ebuild, + prosite-19.35.ebuild, prosite-19.36.ebuild, prosite-19.37.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> prosite-19.36.ebuild: + Added to x86. + +*prosite-19.37 (18 Oct 2006) + + 18 Oct 2006; Olivier Fisette <ribosome@gentoo.org> +prosite-19.37.ebuild: + New upstream version. + +*prosite-19.36 (08 Oct 2006) + + 08 Oct 2006; Olivier Fisette <ribosome@gentoo.org> +prosite-19.36.ebuild: + New upstream version. + +*prosite-19.35 (29 Sep 2006) + + 29 Sep 2006; Olivier Fisette <ribosome@gentoo.org> +prosite-19.35.ebuild: + New upstream version. + + 18 Aug 2006; Jason Wever <weeve@gentoo.org> prosite-19.29.ebuild: + Added ~sparc keyword wrt bug #144241. + +*prosite-19.29 (26 Jun 2006) + + 26 Jun 2006; Olivier Fisette <ribosome@gentoo.org> +prosite-19.29.ebuild: + New upstream version. + + 24 May 2006; Michael Hanselmann <hansmi@gentoo.org> prosite-19.22.ebuild: + Stable on ppc. + + 22 Apr 2006; Markus Rothe <corsair@gentoo.org> prosite-19.22.ebuild: + Stable on ppc64 + +*prosite-19.25 (19 Apr 2006) + + 19 Apr 2006; Olivier Fisette <ribosome@gentoo.org> -prosite-19.16.ebuild, + -prosite-19.17.ebuild, -prosite-19.19.ebuild, -prosite-19.20.ebuild, + prosite-19.22.ebuild, +prosite-19.25.ebuild: + Removed old versions. Added 19.22 to x86. New version. + + 08 Apr 2006; Simon Stelling <blubb@gentoo.org> prosite-19.18.ebuild: + stable on amd64 + +*prosite-19.22 (15 Mar 2006) + + 15 Mar 2006; Olivier Fisette <ribosome@gentoo.org> +prosite-19.22.ebuild: + New version. + + 22 Feb 2006; Fabian Groffen <grobian@gentoo.org> prosite-19.18.ebuild: + Marked ppc-macos stable (bug #123334) + + 22 Feb 2006; <nixnut@gentoo.org> prosite-19.18.ebuild: + Stable on ppc. bug 123334 + + 21 Feb 2006; Markus Rothe <corsair@gentoo.org> prosite-19.18.ebuild: + Stable on ppc64; bug #123334 + + 20 Feb 2006; Joshua Jackson <tsunam@gentoo.org> prosite-19.18.ebuild: + Stable on x86; bug #123334 + +*prosite-19.20 (13 Feb 2006) + + 13 Feb 2006; Olivier Fisette <ribosome@gentoo.org> +prosite-19.20.ebuild: + New version. + +*prosite-19.19 (28 Jan 2006) + + 28 Jan 2006; Olivier Fisette <ribosome@gentoo.org> +prosite-19.19.ebuild: + New version. + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> -prosite-19.10.ebuild, + -prosite-19.14.ebuild, -prosite-19.15.ebuild: + Removed obsolete versions. + + 18 Jan 2006; Markus Rothe <corsair@gentoo.org> prosite-19.16.ebuild: + Stable on ppc64; bug #118831 + + 15 Jan 2006; Marcus D. Hanwell <cryos@gentoo.org> prosite-19.16.ebuild: + Stable on amd64, bug 118831. + + 14 Jan 2006; Fabian Groffen <grobian@gentoo.org> prosite-19.16.ebuild: + Marked ppc-macos stable for bug #118831 + + 14 Jan 2006; Tobias Scherbaum <dertobi123@gentoo.org> + prosite-19.16.ebuild: + ppc stable, bug #118831 + + 13 Jan 2006; Olivier Fisette <ribosome@gentoo.org> prosite-19.16.ebuild: + Added to x86. + +*prosite-19.18 (12 Jan 2006) + + 12 Jan 2006; Olivier Fisette <ribosome@gentoo.org> +prosite-19.18.ebuild: + New version. + + 24 Dec 2005; Simon Stelling <blubb@gentoo.org> prosite-19.14.ebuild: + stable on amd64 + + 23 Dec 2005; Tobias Scherbaum <dertobi123@gentoo.org> + prosite-19.14.ebuild: + Marked ppc stable, #115435 + +*prosite-19.17 (21 Dec 2005) + + 21 Dec 2005; Olivier Fisette <ribosome@gentoo.org> +prosite-19.17.ebuild: + New version. + + 13 Dec 2005; Markus Rothe <corsair@gentoo.org> prosite-19.14.ebuild: + Stable on ppc64; bug #115435 + + 12 Dec 2005; Olivier Fisette <ribosome@gentoo.org> -prosite-19.13.ebuild, + prosite-19.14.ebuild: + Removed old version. Added newer version to x86. + +*prosite-19.16 (08 Dec 2005) + + 08 Dec 2005; Olivier Fisette <ribosome@gentoo.org> -prosite-19.11.ebuild, + -prosite-19.12.ebuild, prosite-19.13.ebuild, +prosite-19.16.ebuild: + Pruned obsolete versions. Added 19.13 to x86. New version. + +*prosite-19.15 (28 Nov 2005) + + 28 Nov 2005; Olivier Fisette <ribosome@gentoo.org> +prosite-19.15.ebuild: + New version. + + 19 Nov 2005; Olivier Fisette <ribosome@gentoo.org> + files/digest-prosite-19.14: + Fixed digest for 19.14 (fixes bug #112926). + +*prosite-19.14 (13 Nov 2005) + + 13 Nov 2005; Olivier Fisette <ribosome@gentoo.org> +prosite-19.14.ebuild: + New version + + 19 Nov 2005; Simon Stelling <blubb@gentoo.org> prosite-19.10.ebuild: + stable on amd64 + +*prosite-19.13 (07 Nov 2005) + + 07 Nov 2005; Olivier Fisette <ribosome@gentoo.org> +prosite-19.13.ebuild: + New version. + +*prosite-19.12 (18 Oct 2005) + + 18 Oct 2005; Olivier Fisette <ribosome@gentoo.org> +prosite-19.12.ebuild: + New version. + + 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -prosite-19.6.ebuild: + Removed obsolete version. + + 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> prosite-19.10.ebuild: + Stable on ppc-macos (with j4rg0n's permission, bug #102420). + + 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> prosite-19.10.ebuild: + Stable on ppc. + +*prosite-19.11 (28 Sep 2005) + + 28 Sep 2005; Olivier Fisette <ribosome@gentoo.org> +prosite-19.11.ebuild: + New version. + + 24 Sep 2005; Markus Rothe <corsair@gentoo.org> prosite-19.10.ebuild: + Stable on ppc64 + + 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> prosite-19.10.ebuild: + Added to x86. + +*prosite-19.10 (19 Sep 2005) + + 19 Sep 2005; Olivier Fisette <ribosome@gentoo.org> -prosite-19.7.ebuild, + -prosite-19.8.ebuild, -prosite-19.9.ebuild, +prosite-19.10.ebuild: + New version. Removed obsolete versions. + + 04 Sep 2005; Simon Stelling <blubb@gentoo.org> prosite-19.8.ebuild: + added ~amd64 keyword + +*prosite-19.9 (01 Sep 2005) + + 01 Sep 2005; Olivier Fisette <ribosome@gentoo.org> +prosite-19.9.ebuild: + New version. + + 31 Aug 2005; Olivier Fisette <ribosome@gentoo.org> -prosite-19.0.ebuild, + -prosite-19.1.ebuild, -prosite-19.2.ebuild, -prosite-19.3.ebuild, + -prosite-19.4.ebuild, -prosite-19.5.ebuild: + Removed obsolete versions. + + 29 Aug 2005; Lina Pezzella <j4rg0n@gentoo.org> prosite-19.6.ebuild: + Stable ppc-macos + +*prosite-19.8 (21 Aug 2005) + + 21 Aug 2005; Olivier Fisette <ribosome@gentoo.org> -prosite-18.46.ebuild, + -prosite-18.47.ebuild, -prosite-18.48.ebuild, -prosite-18.49.ebuild, + +prosite-19.8.ebuild: + New version. Removed obsolete versions. + + 19 Aug 2005; Michael Hanselmann <hansmi@gentoo.org> prosite-19.6.ebuild: + Stable on ppc. + + 08 Aug 2005; Markus Rothe <corsair@gentoo.org> prosite-19.6.ebuild: + Stable on ppc64 + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> prosite-19.7.ebuild: + Fixed bug #101667. + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> prosite-19.7.ebuild: + Fixed indexing with EMBOSS 3.0.0. + +*prosite-19.7 (06 Aug 2005) + + 06 Aug 2005; Olivier Fisette <ribosome@gentoo.org> -prosite-18.45.ebuild, + prosite-19.6.ebuild, +prosite-19.7.ebuild: + New version: 19.7. Added 19.6 to x86. Removed old version: 18.45. + + 28 Jul 2005; Lina Pezzella <j4rg0n@gentoo.org> prosite-19.5.ebuild: + Stable ppc-macos + +*prosite-19.6 (28 Jul 2005) + + 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> -prosite-18.44.ebuild, + prosite-19.5.ebuild, +prosite-19.6.ebuild: + New version: 19.6. Added 19.5 to x86. Removed old version: 18.44. + + 09 Jul 2005; Markus Rothe <corsair@gentoo.org> prosite-19.4.ebuild: + Stable on ppc64 + + 09 Jul 2005; Lina Pezzella <j4rg0n@gentoo.org> prosite-19.3.ebuild, + prosite-19.4.ebuild: + Stable ppc-macos + +*prosite-19.5 (08 Jul 2005) + + 08 Jul 2005; Olivier Fisette <ribosome@gentoo.org> -prosite-18.43.ebuild, + prosite-19.4.ebuild, +prosite-19.5.ebuild: + Removed old version: 18.43. Added 19.4 to x86. New version: 19.5 + + 27 Jun 2005; Markus Rothe <corsair@gentoo.org> prosite-19.3.ebuild: + Stable on ppc64 + +*prosite-19.4 (26 Jun 2005) + + 26 Jun 2005; Olivier Fisette <ribosome@gentoo.org> -prosite-18.42.ebuild, + prosite-19.3.ebuild, +prosite-19.4.ebuild: + New version: 19.4. Added 19.3 to x86. Removed old version. + + 19 Jun 2005; Markus Rothe <corsair@gentoo.org> prosite-19.2.ebuild: + Stable on ppc64 + +*prosite-19.3 (15 Jun 2005) + + 15 Jun 2005; Olivier Fisette <ribosome@gentoo.org> -prosite-18.41.ebuild, + prosite-19.2.ebuild, +prosite-19.3.ebuild: + Removed obsolete version. Added 19.2 to x86. New version. + + 31 May 2005; Lina Pezzella <j4rg0n@gentoo.org> prosite-18.49.ebuild, + prosite-19.0.ebuild, prosite-19.1.ebuild: + Stable ppc-macos + +*prosite-19.2 (27 May 2005) + + 27 May 2005; Olivier Fisette <ribosome@gentoo.org> -prosite-18.40.ebuild, + prosite-19.1.ebuild, +prosite-19.2.ebuild: + Removed obsolete version. Added 19.1 to x86. New version. + +*prosite-19.1 (24 May 2005) + + 24 May 2005; Olivier Fisette <ribosome@gentoo.org> -prosite-18.39.ebuild, + prosite-19.0.ebuild, +prosite-19.1.ebuild: + New version: 19.1. Added 19.0 to x86. Removed obsolete version: 18.39. + +*prosite-19.0 (10 May 2005) + + 10 May 2005; Olivier Fisette <ribosome@gentoo.org> -prosite-18.38.ebuild, + prosite-18.49.ebuild, +prosite-19.0.ebuild: + New version: 19.0. Added 18.49 to x86. Removed old version: 18.38. + + 02 May 2005; Omkhar Arasaratnam <omkhar@gentoo.org> prosite-18.49.ebuild: + Added ~ppc64 + + 02 May 2005; Michael Hanselmann <hansmi@gentoo.org> prosite-18.48.ebuild: + Stable on ppc. + + 27 Apr 2005; Lina Pezzella <j4rg0n@gentoo.org> prosite-18.47.ebuild, + prosite-18.48.ebuild: + Stable ppc-macos + +*prosite-18.49 (16 Apr 2005) + + 16 Apr 2005; Olivier Fisette <ribosome@gentoo.org> prosite-18.48.ebuild, + +prosite-18.49.ebuild: + New version: 18.49. Added 18.48 to x86. + +*prosite-18.48 (05 Apr 2005) + + 05 Apr 2005; Olivier Fisette <ribosome@gentoo.org> prosite-18.47.ebuild, + +prosite-18.48.ebuild: + New version: 14.48. Added 18.47 to x86. + + 26 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> prosite-18.45.ebuild, + prosite-18.46.ebuild: + Stable ppc-macos + +*prosite-18.47 (22 Mar 2005) + + 22 Mar 2005; Olivier Fisette <ribosome@gentoo.org> prosite-18.46.ebuild, + +prosite-18.47.ebuild: + New version: 18.47. Added 18.46 to x86. + +*prosite-18.46 (15 Mar 2005) + + 15 Mar 2005; Olivier Fisette <ribosome@gentoo.org> prosite-18.45.ebuild, + +prosite-18.46.ebuild: + New version: 18.46. Added 18.45 to x86. + + 04 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> prosite-18.44.ebuild: + Stable ppc-macos + +*prosite-18.45 (27 Feb 2005) + + 27 Feb 2005; Olivier Fisette <ribosome@gentoo.org> +prosite-18.45.ebuild: + New version. + + 23 Feb 2005; Olivier Fisette <ribosome@gentoo.org> prosite-18.38.ebuild, + prosite-18.39.ebuild, prosite-18.40.ebuild, prosite-18.41.ebuild, + prosite-18.42.ebuild, prosite-18.43.ebuild, prosite-18.44.ebuild: + Added support for the "emboss" and "minimal" "USE" flags. Added 18.44 to x86. + + 18 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> prosite-18.43.ebuild: + Stable ppc-macos + +*prosite-18.44 (02 Feb 2005) + + 02 Feb 2005; Olivier Fisette <ribosome@gentoo.org> prosite-18.43.ebuild, + +prosite-18.44.ebuild: + New version: 18.44. Added 18.43 to x86. + + 02 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> prosite-18.42.ebuild: + Stable ppc-macos + +*prosite-18.43 (18 Jan 2005) + + 18 Jan 2005; Olivier Fisette <ribosome@gentoo.org> prosite-18.42.ebuild, + +prosite-18.43.ebuild: + New version: 18.43. Added 18.42 to x86. + + 01 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> prosite-18.42.ebuild: + Unstable ppc-macos. + +*prosite-18.42 (30 Dec 2004) + + 30 Dec 2004; Olivier Fisette <ribosome@gentoo.org> prosite-18.41.ebuild, + +prosite-18.42.ebuild: + New version: 18.42. Added 18.41 to x86. + +*prosite-18.41 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +prosite-18.38.ebuild, +prosite-18.39.ebuild, +prosite-18.40.ebuild, + +prosite-18.41.ebuild: + Moved from app-sci/prosite to sci-biology/prosite. + +*prosite-18.41 (13 Dec 2004) + + 13 Dec 2004; Olivier Fisette <ribosome@gentoo.org> prosite-18.40.ebuild, + +prosite-18.41.ebuild: + New version: 18.41. Added 18.40 to x86. + +*prosite-18.40 (23 Nov 2004) + + 23 Nov 2004; Olivier Fisette <ribosome@gentoo.org> prosite-18.39.ebuild, + +prosite-18.40.ebuild: + New version: 18.40. Added 18.39 to x86. + +*prosite-18.39 (08 Nov 2004) + + 08 Nov 2004; Olivier Fisette <ribosome@gentoo.org> -prosite-18.36.ebuild, + prosite-18.38.ebuild, +prosite-18.39.ebuild: + New version (18.39). Added 18.38 to x86. Removed obsolete version. + +*prosite-18.38 (30 Oct 2004) + + 30 Oct 2004; Olivier Fisette <ribosome@gentoo.org> -prosite-18.32.ebuild, + prosite-18.36.ebuild, +prosite-18.38.ebuild: + Removed obsolete version (18.32). Added to x86 (18.36). New version (18.38). + +*prosite-18.36 (29 Sep 2004) + + 29 Sep 2004; Olivier Fisette <ribosome@gentoo.org> -prosite-18.26.ebuild, + prosite-18.32.ebuild, +prosite-18.36.ebuild: + Added x86 to 18.32. New version 18.36. Removed old version. + +*prosite-18.32 (10 Aug 2004) + + 10 Aug 2004; Olivier Fisette <ribosome@gentoo.org> + prosite-18.32.ebuild: + Updated package. + prosite-18.26.ebuild: + Added to x86. + + 26 Jun 2004; David Holm <dholm@gentoo.org> prosite-18.26.ebuild: + Added to ~ppc. + +*prosite-18.26 (24 Jun 2004) + + 24 Jun 2004; Olivier Fisette <ribosome@gentoo.org> + prosite-18.26.ebuild, metadata.xml : + Initial import. Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>. + Reference: Gentoo Bugzilla, bug #54326 + diff --git a/sci-biology/psipred/ChangeLog b/sci-biology/psipred/ChangeLog new file mode 100644 index 00000000..b8049aba --- /dev/null +++ b/sci-biology/psipred/ChangeLog @@ -0,0 +1,68 @@ +# ChangeLog for sci-biology/psipred +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/ChangeLog,v 1.13 2015/04/07 14:34:37 jlec Exp $ + + 14 May 2014; Justin Lecher <jlec@gentoo.org> psipred-3.1.ebuild, + psipred-3.2.ebuild, psipred-3.2.1.ebuild, psipred-3.3.ebuild, + psipred-3.4.ebuild, psipred-3.5.ebuild: + Add additional dep on sci-biology/update-blast + +*psipred-3.5 (07 Apr 2014) + + 07 Apr 2014; Justin Lecher <jlec@gentoo.org> +psipred-3.5.ebuild: + Version Bump + +*psipred-3.4 (05 Nov 2013) + + 05 Nov 2013; Justin Lecher <jlec@gentoo.org> +psipred-3.4.ebuild, + metadata.xml: + Version Bump + + 19 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + herd is now sci-biology + + 11 Jul 2012; Justin Lecher <jlec@gentoo.org> psipred-3.2.1.ebuild: + Cleaned SRC_URI + + 11 Jul 2012; Michael Sterrett <mr_bones_@gentoo.org> psipred-3.2.1.ebuild, + psipred-3.3.ebuild: + add missing test to IUSE + +*psipred-3.3 (10 Jul 2012) + + 10 Jul 2012; Justin Lecher <jlec@gentoo.org> psipred-3.2.1.ebuild, + +psipred-3.3.ebuild, metadata.xml: + Version Bump + +*psipred-3.2.1 (24 May 2011) + + 24 May 2011; Justin Lecher <jlec@gentoo.org> psipred-3.1.ebuild, + psipred-3.2.ebuild, +psipred-3.2.1.ebuild: + Version Bump + +*psipred-3.2 (16 Oct 2010) + + 16 Oct 2010; Justin Lecher <jlec@gentoo.org> +files/3.1-fgets.patch, + -psipred-2.6.1-r1.ebuild, psipred-3.1.ebuild, +files/3.2-fgets.patch, + -psipred-3.0.ebuild, +psipred-3.2.ebuild: + removed old, Version Bump, FORTIFY patch + +*psipred-3.1 (16 May 2010) + + 16 May 2010; Justin Lecher <jlec@gentoo.org> +files/3.1-Makefile.patch, + +psipred-3.1.ebuild, +files/3.1-path.patch: + Version bump + +*psipred-3.0 (06 May 2010) +*psipred-2.6.1-r1 (06 May 2010) + + 06 May 2010; Justin Lecher <jlec@gentoo.org> +files/3.0-path.patch, + -psipred-2.6.1.ebuild, +psipred-2.6.1-r1.ebuild, +psipred-3.0.ebuild: + Version Bump, #317977; fixed installation of shipped bins + +*psipred-2.6.1 (28 Feb 2010) + + 28 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org> + +files/2.6.1-Makefile.patch, +files/2.6.1-path.patch, + +psipred-2.6.1.ebuild, +metadata.xml: + moved from sci-chemistry to sci-biology diff --git a/sci-biology/pysam/ChangeLog b/sci-biology/pysam/ChangeLog new file mode 100644 index 00000000..c9fe4b5b --- /dev/null +++ b/sci-biology/pysam/ChangeLog @@ -0,0 +1,24 @@ +# ChangeLog for sci-biology/pysam +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/pysam/ChangeLog,v 1.5 2015/04/13 06:22:56 jlec Exp $ + + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> pysam-0.6-r1.ebuild: + Keyword for x86 + +*pysam-0.6-r1 (30 Jun 2014) + + 30 Jun 2014; Mike Gilbert <floppym@gentoo.org> +pysam-0.6-r1.ebuild, + -pysam-0.6.ebuild: + Convert to distutils-r1. Depend on setuptools. + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 25 Feb 2012; Patrick Lauer <patrick@gentoo.org> pysam-0.6.ebuild: + Restricting py 2.5, pypy and jython + +*pysam-0.6 (29 Jan 2012) + + 29 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> +pysam-0.6.ebuild, + +metadata.xml: + New package, ebuild written by me diff --git a/sci-biology/qrna/ChangeLog b/sci-biology/qrna/ChangeLog new file mode 100644 index 00000000..75dd0dbd --- /dev/null +++ b/sci-biology/qrna/ChangeLog @@ -0,0 +1,104 @@ +# ChangeLog for sci-biology/qrna +# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/qrna/ChangeLog,v 1.25 2012/12/06 10:14:12 jlec Exp $ + + 06 Dec 2012; Justin Lecher <jlec@gentoo.org> -qrna-2.0.3c.ebuild: + Drop old + + 06 Dec 2012; Pawel Hajdan jr <phajdan.jr@gentoo.org> qrna-2.0.3c-r1.ebuild: + x86 stable wrt bug #441020 + + 10 Nov 2012; <ago@gentoo.org> qrna-2.0.3c-r1.ebuild: + Stable for amd64, wrt bug #441020 + + 09 Nov 2012; Justin Lecher <jlec@gentoo.org> qrna-2.0.3c-r1.ebuild: + Move to EAPI=4 + +*qrna-2.0.3c-r1 (10 Mar 2010) + + 10 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> + +qrna-2.0.3c-r1.ebuild, +files/qrna-2.0.3c-ldflags.patch: + Respecting LDFLAGS, rebuilding all libs instead of using upstreams bundled + ones, #308703 + + 05 Aug 2009; Samuli Suominen <ssuominen@gentoo.org> qrna-2.0.3c.ebuild, + +files/qrna-2.0.3c-glibc-2.10.patch: + Fix building with GLIBC 2.10+ wrt #277098. + + 07 Sep 2008; Markus Dittrich <markusle@gentoo.org> qrna-2.0.3c.ebuild: + Fixed bad HOMEPAGE and formatting in ebuild. + + 22 Jun 2008; Jeff Gardner <je_fro@gentoo.org> qrna-2.0.3c.ebuild: + Do not install shuffle, it comes from hmmer. + + 22 Jun 2008; Jeff Gardner <je_fro@gentoo.org> qrna-2.0.3c.ebuild: + No longer compiling files in squid02 because they are newer in hmmer and + we avoid collisions. qrna now depends on hmmer. See bug #208462. + + 22 May 2007; Olivier Fisette <ribosome@gentoo.org> qrna-2.0.3c.ebuild: + Updated home page. + + 09 Apr 2007; Jeff Gardner <je_fro@gentoo.org> qrna-2.0.3c.ebuild: + Fixed to use doenvd wrt bug #173884 + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Stepping down from maintaining this package. + + 15 Mar 2006; Olivier Fisette <ribosome@gentoo.org> qrna-2.0.3c.ebuild: + Correctly rename README file (fixes bug #125502). + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> qrna-2.0.3c.ebuild: + Ebuild clean-up. + + 04 Jan 2006; Olivier Fisette <ribosome@gentoo.org> qrna-2.0.3c.ebuild: + Do not depend on "virtual/libc" (package not in system target). + + 17 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -qrna-2.0.3b.ebuild: + Pruning old version. + + 17 Oct 2005; Joseph Jezak <josejx@gentoo.org> qrna-2.0.3c.ebuild: + Marked ppc stable for bug #108336. + + 11 Oct 2005; Luis Medinas <metalgod@gentoo.org> qrna-2.0.3c.ebuild: + Marked Stable on amd64. + + 09 Oct 2005; Mark Loeser <halcy0n@gentoo.org> qrna-2.0.3c.ebuild: + Stable on x86 + +*qrna-2.0.3c (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> -qrna-2.0.2c.ebuild, + qrna-2.0.3b.ebuild, +qrna-2.0.3c.ebuild: + New version. Added 2.0.3b to x86. Removed old version. + +*qrna-2.0.3b (13 May 2005) + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> +qrna-2.0.3b.ebuild: + New version. + +*qrna-2.0.2c (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +files/26qrna, +qrna-2.0.2c.ebuild: + Moved from app-sci/qrna to sci-biology/qrna. + + 22 Nov 2004; Olivier Fisette <ribosome@gentoo.org> : + Jason Huebel <jhuebel@gentoo.org> added qrna-2.0.2c to ~amd64. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> qrna-2.0.2c.ebuild: + Added to x86. + + 23 Jul 2004; Jon Hood <squinky86@gentoo.org> qrna-2.0.2c.ebuild: + Change virtual/glibc -> virtual/libc. + + 21 Jul 2004; David Holm <dholm@gentoo.org> qrna-2.0.2c.ebuild: + Added to ~ppc. + +*qrna-2.0.2c (20 Jul 2004) + + 20 Jul 2004; Olivier Fisette <ribosome@gentoo.org> + qrna-2.0.2c.ebuild, metadata.xml, ChangeLog: + Initial import. diff --git a/sci-biology/raxml/ChangeLog b/sci-biology/raxml/ChangeLog new file mode 100644 index 00000000..38585bf2 --- /dev/null +++ b/sci-biology/raxml/ChangeLog @@ -0,0 +1,54 @@ +# ChangeLog for sci-biology/raxml +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/ChangeLog,v 1.12 2015/04/07 14:34:43 jlec Exp $ + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> raxml-7.2.6.ebuild: + Use REQUIRED_USE to constrain sse3 compatibility + + 29 Jan 2015; Michał Górny <mgorny@gentoo.org> metadata.xml, + raxml-7.2.6.ebuild: + Switch to CPU_FLAGS_X86. + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 18 Feb 2013; Justin Lecher <jlec@gentoo.org> -raxml-7.2.2.ebuild, + -raxml-7.2.5.ebuild, -raxml-7.2.5-r1.ebuild, raxml-7.2.6.ebuild, + metadata.xml: + Drop old; stop building when non sse3 capable CPU is detected, #375061 + +*raxml-7.2.6 (27 Jun 2011) + + 27 Jun 2011; Justin Lecher <jlec@gentoo.org> +raxml-7.2.6.ebuild, + +files/raxml-7.2.6-makefile.patch, metadata.xml: + Version Bump, 312897 + +*raxml-7.2.5-r1 (21 Jun 2011) + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> raxml-7.2.2.ebuild, + raxml-7.2.5.ebuild, +raxml-7.2.5-r1.ebuild, + +files/raxml-7.2.5-makefile.patch, metadata.xml: + Tweaking ebuild, respect LDFLAGS #335629 + +*raxml-7.2.5 (27 Jan 2010) + + 27 Jan 2010; Andrey Kislyuk <weaver@gentoo.org> -raxml-7.0.4.ebuild, + +raxml-7.2.5.ebuild: + Version bump + + 31 Oct 2009; Markus Meier <maekke@gentoo.org> raxml-7.2.2.ebuild: + amd64/x86 stable, bug #290929 + + 04 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> raxml-7.2.2.ebuild: + Tweak build process + +*raxml-7.2.2 (04 Sep 2009) + + 04 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> +raxml-7.2.2.ebuild: + Version bump (but no mpi support in 7.2.2) + +*raxml-7.0.4 (03 Sep 2009) + + 03 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +raxml-7.0.4.ebuild: + New package, ebuild written by me diff --git a/sci-biology/readseq/ChangeLog b/sci-biology/readseq/ChangeLog new file mode 100644 index 00000000..60eb6372 --- /dev/null +++ b/sci-biology/readseq/ChangeLog @@ -0,0 +1,80 @@ +# ChangeLog for sci-biology/readseq +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/readseq/ChangeLog,v 1.13 2014/08/10 20:31:52 slyfox Exp $ + + 10 Aug 2014; Sergei Trofimovich <slyfox@gentoo.org> + readseq-20080420-r1.ebuild, readseq-20100513.ebuild: + QA: drop trailing '.' from DESCRIPTION + +*readseq-20100513 (08 Feb 2014) + + 08 Feb 2014; Johann Schmitz <ercpe@gentoo.org> +readseq-20100513.ebuild: + Version bump of sci-biology/readseq + +*readseq-20080420-r1 (08 Feb 2014) + + 08 Feb 2014; Johann Schmitz <ercpe@gentoo.org> + +files/20080420-no-bundling.patch, +readseq-20080420-r1.ebuild, + -files/19930201-buffer.patch, -files/19930201-getline.patch, + -files/19930201-impl-dec.patch, -files/19930201-ldflags.patch, + -readseq-20080420.ebuild: + Dropped unneeded patch files and dropped unneeded dependencies (bug #500488 + and #239161) + + 01 Feb 2013; Justin Lecher <jlec@gentoo.org> -readseq-19930201.ebuild, + -readseq-19930201-r1.ebuild, readseq-20080420.ebuild, metadata.xml: + Drop old; Resolve file collision sci-biology/meme, #455010 + +*readseq-19930201-r1 (28 Nov 2010) + + 28 Nov 2010; Justin Lecher <jlec@gentoo.org> +files/19930201-buffer.patch, + +files/19930201-getline.patch, +files/19930201-ldflags.patch, + +readseq-19930201-r1.ebuild, +files/19930201-impl-dec.patch: + Fixes fo various problems, #346883 + + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 16 Jul 2008; Raúl Porcel <armin76@gentoo.org> readseq-20080420.ebuild: + Add ~x86 wrt #231945 + +*readseq-20080420 (26 Apr 2008) + + 26 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>; + +readseq-20080420.ebuild: + Add the Java version, which is actually maintained. This could possibly + use some more enhancement to add wrappers for the GUI and such, but the + ebuild is already a fully functional replacement for the old version. + + 17 Aug 2006; Jason Wever <weeve@gentoo.org> readseq-19930201.ebuild: + Added ~sparc keyword wrt bug #144246. + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> + readseq-19930201.ebuild: + Ebuild clean-up. + + 10 Nov 2005; <dang@gentoo.org> readseq-19930201.ebuild: + Marked ~amd64 + +*readseq-19930201 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +readseq-19930201.ebuild: + Moved from app-sci/readseq to sci-biology/readseq. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> readseq-19930201.ebuild: + Added to x86. Fixed bug with SRC_URI. + + 09 Aug 2004; Olivier Fisette <ribosome@gentoo.org> readseq-19930201.ebuild: + Use "mirror://debian/" syntax. + + 17 Jul 2004; David Holm <dholm@gentoo.org> readseq-19930201.ebuild: + Added to ~ppc. + +*readseq-19930201 (14 Jul 2004) + + 14 Jul 2004; Olivier Fisette <ribosome@gentoo.org> + readseq-19930201.ebuild, metadata.xml + Initial import (#51992), suggested by Koen Deforche + <koen.deforche@uz.kuleuven.ac.be>, with modifications. diff --git a/sci-biology/rebase/ChangeLog b/sci-biology/rebase/ChangeLog new file mode 100644 index 00000000..4b35227e --- /dev/null +++ b/sci-biology/rebase/ChangeLog @@ -0,0 +1,707 @@ +# 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 1.170 2015/08/02 17:28:18 jlec Exp $ + + 02 Aug 2015; Justin Lecher <jlec@gentoo.org> rebase-1507.ebuild: + Fix stable KEYWORDS + +*rebase-1508 (02 Aug 2015) + + 02 Aug 2015; Justin Lecher <jlec@gentoo.org> +rebase-1508.ebuild: + Version Bump + + 02 Aug 2015; Justin Lecher <jlec@gentoo.org> -rebase-1505.ebuild, + -rebase-1506.ebuild: + Drop old + + 02 Aug 2015; Justin Lecher <jlec@gentoo.org> rebase-1507.ebuild: + Follow stable ppc for ALLARCHES, bug #553618 + + 23 Jul 2015; Pacho Ramos <pacho@gentoo.org> rebase-1507.ebuild: + ppc stable wrt bug #553618 + +*rebase-1507 (30 Jun 2015) + + 30 Jun 2015; Justin Lecher <jlec@gentoo.org> +rebase-1507.ebuild: + Version Bump + + 15 Jun 2015; Justin Lecher <jlec@gentoo.org> -rebase-1504.ebuild: + Drop old + + 11 Jun 2015; Agostino Sarubbo <ago@gentoo.org> rebase-1505.ebuild: + Stable for ppc, wrt bug #550804 + + 09 Jun 2015; Agostino Sarubbo <ago@gentoo.org> rebase-1505.ebuild: + Stable for x86, wrt bug #550804 + + 08 Jun 2015; Agostino Sarubbo <ago@gentoo.org> rebase-1505.ebuild: + Stable for amd64, wrt bug #550804 + +*rebase-1506 (30 May 2015) + + 30 May 2015; Justin Lecher <jlec@gentoo.org> +rebase-1506.ebuild: + Version Bump + + 13 May 2015; Justin Lecher <jlec@gentoo.org> -rebase-1503.ebuild: + Drop old + + 13 May 2015; Agostino Sarubbo <ago@gentoo.org> rebase-1504.ebuild: + Stable for x86, wrt bug #548594 + + 13 May 2015; Jack Morgan <jmorgan@gentoo.org> rebase-1504.ebuild: + ppc stable wrt bug #548594 + + 12 May 2015; Agostino Sarubbo <ago@gentoo.org> rebase-1504.ebuild: + Stable for amd64, wrt bug #548594 + +*rebase-1505 (04 May 2015) + + 04 May 2015; Justin Lecher <jlec@gentoo.org> +rebase-1505.ebuild: + Version Bump + +*rebase-1503 (08 Apr 2015) + + 08 Apr 2015; Michał Górny <mgorny@gentoo.org> +rebase-1503.ebuild: + Restore -1503 that was just marked stable, bug #545982. + + 08 Apr 2015; Justin Lecher <jlec@gentoo.org> -rebase-1502.ebuild, + -rebase-1503.ebuild: + Drop old + + 08 Apr 2015; Agostino Sarubbo <ago@gentoo.org> rebase-1503.ebuild: + Stable for ppc/x86, wrt bug #545430 + + 08 Apr 2015; Agostino Sarubbo <ago@gentoo.org> rebase-1503.ebuild: + Stable for amd64, wrt bug #545430 + +*rebase-1504 (03 Apr 2015) + + 03 Apr 2015; Justin Lecher <jlec@gentoo.org> +rebase-1504.ebuild: + Version BUMP + + 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 + + 02 Mar 2015; Agostino Sarubbo <ago@gentoo.org> rebase-1502.ebuild: + Stable for ppc, wrt bug #541512 + + 28 Feb 2015; Agostino Sarubbo <ago@gentoo.org> rebase-1502.ebuild: + Stable for amd64, wrt bug #541512 + +*rebase-1503 (27 Feb 2015) + + 27 Feb 2015; Justin Lecher <jlec@gentoo.org> +rebase-1503.ebuild: + Version Bump + +*rebase-1502 (02 Feb 2015) + + 02 Feb 2015; Justin Lecher <jlec@gentoo.org> +rebase-1502.ebuild: + Version Bump + + 26 Jan 2015; Justin Lecher <jlec@gentoo.org> -rebase-1411.ebuild: + Drop old + + 26 Jan 2015; Agostino Sarubbo <ago@gentoo.org> rebase-1412.ebuild: + Stable for x86, wrt bug #534598 + + 17 Jan 2015; Agostino Sarubbo <ago@gentoo.org> rebase-1412.ebuild: + Stable for ppc, wrt bug #534598 + + 09 Jan 2015; Agostino Sarubbo <ago@gentoo.org> rebase-1412.ebuild: + Stable for amd64, wrt bug #534598 + +*rebase-1501 (04 Jan 2015) + + 04 Jan 2015; Justin Lecher <jlec@gentoo.org> -rebase-1403.ebuild, + -rebase-1406.ebuild, -rebase-1408.ebuild, -rebase-1409.ebuild, + -rebase-1410.ebuild, +rebase-1501.ebuild: + Version Bump; Drop old + + 31 Dec 2014; Agostino Sarubbo <ago@gentoo.org> rebase-1411.ebuild: + Stable for ppc, wrt bug #531422 + + 31 Dec 2014; Agostino Sarubbo <ago@gentoo.org> rebase-1410.ebuild: + Stable for ppc, wrt bug #527402 + + 28 Dec 2014; Agostino Sarubbo <ago@gentoo.org> rebase-1411.ebuild: + Stable for x86, wrt bug #531422 + + 27 Dec 2014; Agostino Sarubbo <ago@gentoo.org> rebase-1411.ebuild: + Stable for amd64, wrt bug #531422 + + 26 Dec 2014; Agostino Sarubbo <ago@gentoo.org> rebase-1410.ebuild: + Stable for x86, wrt bug #527402 + + 22 Dec 2014; Chema Alonso <nimiux@gentoo.org> rebase-1410.ebuild: + Stable for amd64 wrt bug #527402 + +*rebase-1412 (02 Dec 2014) + + 02 Dec 2014; Justin Lecher <jlec@gentoo.org> +rebase-1412.ebuild: + Version Bump + +*rebase-1411 (30 Oct 2014) + + 30 Oct 2014; Justin Lecher <jlec@gentoo.org> +rebase-1411.ebuild: + Version Bump + +*rebase-1410 (30 Sep 2014) + + 30 Sep 2014; Justin Lecher <jlec@gentoo.org> +rebase-1410.ebuild: + Version Bump + + 15 Sep 2014; Justin Lecher <jlec@gentoo.org> -rebase-1111.ebuild: + Drop ebuild with deprecated EAPI + +*rebase-1409 (15 Sep 2014) + + 15 Sep 2014; Justin Lecher <jlec@gentoo.org> +rebase-1409.ebuild: + Version Bump + + 03 Aug 2014; Agostino Sarubbo <ago@gentoo.org> rebase-1403.ebuild: + Stable for ppc, wrt bug #512118 + +*rebase-1408 (31 Jul 2014) + + 31 Jul 2014; Justin Lecher <jlec@gentoo.org> +rebase-1408.ebuild: + Version Bump + + 26 Jul 2014; Pawel Hajdan jr <phajdan.jr@gentoo.org> rebase-1403.ebuild: + x86 stable wrt bug #512118 + + 17 Jul 2014; Chema Alonso <nimiux@gentoo.org> rebase-1403.ebuild: + Stable for amd64 wrt bug #512118 + +*rebase-1406 (04 Jun 2014) + + 04 Jun 2014; Justin Lecher <jlec@gentoo.org> -rebase-1404.ebuild, + +rebase-1406.ebuild: + Version Bump, fixes broken snapshot, #512286 + +*rebase-1404 (02 Jun 2014) + + 02 Jun 2014; Justin Lecher <jlec@gentoo.org> -rebase-1202.ebuild, + -rebase-1303.ebuild, -rebase-1310.ebuild, -rebase-1311.ebuild, + -rebase-1312.ebuild, +rebase-1404.ebuild: + Version Bump; clean old + +*rebase-1403 (06 Mar 2014) + + 06 Mar 2014; Justin Lecher <jlec@gentoo.org> +rebase-1403.ebuild: + Version Bump + +*rebase-1312 (01 Dec 2013) + + 01 Dec 2013; Justin Lecher <jlec@gentoo.org> +rebase-1312.ebuild: + Version Bump + + 06 Nov 2013; Justin Lecher <jlec@gentoo.org> Manifest: + Fix tarball and ist checksum, #490360 + +*rebase-1311 (02 Nov 2013) + + 02 Nov 2013; Justin Lecher <jlec@gentoo.org> +rebase-1311.ebuild: + Version Bump + +*rebase-1310 (08 Oct 2013) + + 08 Oct 2013; Justin Lecher <jlec@gentoo.org> +rebase-1310.ebuild: + Version Bump + +*rebase-1303 (28 Feb 2013) + + 28 Feb 2013; Justin Lecher <jlec@gentoo.org> +rebase-1303.ebuild, + metadata.xml: + Version Bump + + 08 Mar 2012; Justin Lecher <jlec@gentoo.org> -rebase-1006.ebuild, + -rebase-1105.ebuild: + Dropped old + + 07 Mar 2012; Brent Baude <ranger@gentoo.org> rebase-1111.ebuild: + Marking rebase-1111 ppc for bug 402053 + + 16 Feb 2012; Pawel Hajdan jr <phajdan.jr@gentoo.org> rebase-1111.ebuild: + x86 stable wrt bug #402053 + + 03 Feb 2012; Markos Chandras <hwoarang@gentoo.org> rebase-1111.ebuild: + Stable on amd64 wrt bug #402053 + +*rebase-1202 (03 Feb 2012) + + 03 Feb 2012; Justin Lecher <jlec@gentoo.org> -rebase-1103.ebuild, + -rebase-1104.ebuild, -rebase-1106.ebuild, +rebase-1202.ebuild: + Version Bump, cleaned old + + 28 Nov 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> rebase-1105.ebuild: + x86 stable wrt bug #391615 + + 26 Nov 2011; Markos Chandras <hwoarang@gentoo.org> rebase-1105.ebuild: + Stable on amd64 wrt bug #391615 + +*rebase-1111 (02 Nov 2011) + + 02 Nov 2011; Justin Lecher <jlec@gentoo.org> +rebase-1111.ebuild: + Version Bump + + 09 Aug 2011; Kacper Kowalik <xarthisius@gentoo.org> rebase-1006.ebuild, + rebase-1103.ebuild, rebase-1104.ebuild, rebase-1105.ebuild, + rebase-1106.ebuild: + ppc64 keyword dropped + +*rebase-1106 (01 Jun 2011) + + 01 Jun 2011; Justin Lecher <jlec@gentoo.org> +rebase-1106.ebuild: + Version Bump + +*rebase-1105 (30 Apr 2011) + + 30 Apr 2011; Justin Lecher <jlec@gentoo.org> +rebase-1105.ebuild: + Version Bump + +*rebase-1104 (01 Apr 2011) + + 01 Apr 2011; Justin Lecher <jlec@gentoo.org> +rebase-1104.ebuild: + Version Bump + +*rebase-1103 (11 Mar 2011) + + 11 Mar 2011; Justin Lecher <jlec@gentoo.org> -rebase-610.ebuild, + -rebase-905.ebuild, rebase-1006.ebuild, +rebase-1103.ebuild: + Version Bump, cleaned old + + 09 Mar 2011; Raúl Porcel <armin76@gentoo.org> rebase-610.ebuild, + rebase-905.ebuild, rebase-1006.ebuild: + Drop sparc keywords + + 12 Sep 2010; Justin Lecher <jlec@gentoo.org> rebase-1006.ebuild: + fix DEPENDS for xz, 336945 + + 18 Jul 2010; <nixnut@gentoo.org> rebase-1006.ebuild: + ppc stable #325457 + + 09 Jul 2010; Samuli Suominen <ssuominen@gentoo.org> rebase-1006.ebuild: + ppc64 stable wrt #325457 + + 28 Jun 2010; Christian Faulhammer <fauli@gentoo.org> rebase-1006.ebuild: + stable x86, bug 325457 + + 26 Jun 2010; Christoph Mende <angelos@gentoo.org> rebase-1006.ebuild: + Stable on amd64 wrt bug #325457 + + 25 Jun 2010; Justin Lecher <jlec@gentoo.org> rebase-610.ebuild, + rebase-905.ebuild, rebase-1006.ebuild: + It's a db, so we will have RESTRICT=binchecks strip + +*rebase-1006 (25 Jun 2010) + + 25 Jun 2010; Justin Lecher <jlec@gentoo.org> -rebase-909.ebuild, + +rebase-1006.ebuild: + Version Bump + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> rebase-909.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*rebase-909 (01 Sep 2009) + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> +rebase-909.ebuild: + New upstream version. + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> rebase-905.ebuild: + Stabilised on amd64 and 86. + + 02 May 2009; Jeff Gardner <je_fro@gentoo.org> rebase-905.ebuild: + Fix SRC_URI + +*rebase-905 (02 May 2009) + + 02 May 2009; Jeff Gardner <je_fro@gentoo.org> +rebase-905.ebuild: + Latest from neb, with a kick from jlec. + +*rebase-808 (27 Aug 2008) + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +rebase-808.ebuild: + New upstream version. + +*rebase-708 (20 Aug 2007) + + 20 Aug 2007; Olivier Fisette <ribosome@gentoo.org> +rebase-708.ebuild: + New upstream version. + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> -rebase-704.ebuild, + -rebase-705.ebuild: + Pruned older ebuilds that will never be stabilised. + +*rebase-707 (18 Jul 2007) + + 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> +rebase-707.ebuild: + New upstream version. Ebuild updated for EMBOSS 5.0.0. + +*rebase-705 (22 May 2007) + + 22 May 2007; Olivier Fisette <ribosome@gentoo.org> -rebase-612.ebuild, + +rebase-705.ebuild: + New upstream version. Pruned old version. + +*rebase-704 (11 Apr 2007) + + 11 Apr 2007; Olivier Fisette <ribosome@gentoo.org> +rebase-704.ebuild: + New upstream version. + +*rebase-612 (12 Dec 2006) + + 12 Dec 2006; Olivier Fisette <ribosome@gentoo.org> -rebase-611.ebuild, + +rebase-612.ebuild: + New upstream version. Removed old version. + + 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> -rebase-601-r1.ebuild, + -rebase-603.ebuild: + Pruned old versions. + + 20 Nov 2006; <blubb@gentoo.org> rebase-610.ebuild: + stable on amd64 + + 15 Nov 2006; Markus Rothe <corsair@gentoo.org> rebase-610.ebuild: + Stable on ppc64; bug #153766 + + 03 Nov 2006; nixnut <nixnut@gentoo.org> rebase-610.ebuild: + Stable on ppc wrt bug 153766 + + 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> -rebase-604.ebuild, + -rebase-606.ebuild, -rebase-607.ebuild, -rebase-608.ebuild, + -rebase-609.ebuild: + Pruned old versions. + +*rebase-611 (03 Nov 2006) + + 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> +rebase-611.ebuild: + New upstream version. + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> rebase-601-r1.ebuild, + rebase-603.ebuild, rebase-604.ebuild, rebase-606.ebuild, + rebase-607.ebuild, rebase-608.ebuild, rebase-609.ebuild, + rebase-610.ebuild: + Dropped ppc-macos, see you in prefix. + + 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> rebase-610.ebuild: + Added to x86. + +*rebase-610 (08 Oct 2006) + + 08 Oct 2006; Olivier Fisette <ribosome@gentoo.org> +rebase-610.ebuild: + New upstream version. + +*rebase-609 (12 Sep 2006) + + 12 Sep 2006; Olivier Fisette <ribosome@gentoo.org> +rebase-609.ebuild: + New upstream version. + + 19 Aug 2006; Jason Wever <weeve@gentoo.org> rebase-608.ebuild: + Added ~sparc keyword. + + 18 Aug 2006; Jason Wever <weeve@gentoo.org> rebase-601-r1.ebuild: + Added ~sparc keyword wrt bug #144241. + +*rebase-608 (17 Aug 2006) + + 17 Aug 2006; Olivier Fisette <ribosome@gentoo.org> +rebase-608.ebuild: + New upstream version. + +*rebase-607 (12 Jul 2006) + + 12 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +rebase-607.ebuild: + New ustream version. + +*rebase-606 (26 Jun 2006) + + 26 Jun 2006; Olivier Fisette <ribosome@gentoo.org> +rebase-606.ebuild: + New upstream version. + + 24 May 2006; Michael Hanselmann <hansmi@gentoo.org> rebase-603.ebuild: + Stable on ppc. + + 22 Apr 2006; Markus Rothe <corsair@gentoo.org> rebase-603.ebuild: + Stable on ppc64 + + 19 Apr 2006; Olivier Fisette <ribosome@gentoo.org> -rebase-602.ebuild: + Removed old version. + +*rebase-604 (19 Apr 2006) + + 19 Apr 2006; Olivier Fisette <ribosome@gentoo.org> -rebase-512.ebuild, + rebase-603.ebuild, +rebase-604.ebuild: + New version (604). Removed old version (512). Added 603 to x86. + + 08 Apr 2006; Simon Stelling <blubb@gentoo.org> rebase-601-r1: + stable on amd64 + +*rebase-603 (15 Mar 2006) + + 15 Mar 2006; Olivier Fisette <ribosome@gentoo.org> +rebase-603.ebuild: + New version. + + 22 Feb 2006; Fabian Groffen <grobian@gentoo.org> rebase-601-r1.ebuild: + Marked ppc-macos stable (bug #123332) + + 22 Feb 2006; <nixnut@gentoo.org> rebase-601-r1.ebuild: + Stable on ppc. bug 123332 + + 21 Feb 2006; Markus Rothe <corsair@gentoo.org> rebase-601-r1.ebuild: + Stable on ppc64; bug #123332 + + 20 Feb 2006; Joshua Jackson <tsunam@gentoo.org> rebase-601-r1.ebuild: + Stable on x86; bug #123332 + +*rebase-602 (06 Feb 2006) + + 06 Feb 2006; Olivier Fisette <ribosome@gentoo.org> +rebase-602.ebuild: + New version. + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> -rebase-509.ebuild, + -rebase-511.ebuild, -rebase-601.ebuild: + Removed obsolete/buggy versions. + +*rebase-601-r1 (21 Jan 2006) + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> +rebase-601-r1.ebuild: + Install an enzymes prototypes file, replacing the one distributed with + EMBOSS. This will solve the inconsistencies reported in bug #118832. + + 18 Jan 2006; Markus Rothe <corsair@gentoo.org> rebase-512.ebuild: + Stable on ppc64; bug #118832 + + 15 Jan 2006; Marcus D. Hanwell <cryos@gentoo.org> rebase-512.ebuild: + Stable on amd64, bug 118832. + + 14 Jan 2006; Fabian Groffen <grobian@gentoo.org> rebase-512.ebuild: + Marked ppc-macos stable (bug #118832) + + 14 Jan 2006; Tobias Scherbaum <dertobi123@gentoo.org> rebase-512.ebuild: + ppc stable, bug #118832 + + 13 Jan 2006; Olivier Fisette <ribosome@gentoo.org> rebase-512.ebuild: + Added to x86. + +*rebase-601 (07 Jan 2006) + + 07 Jan 2006; Olivier Fisette <ribosome@gentoo.org> +rebase-601.ebuild: + New version. + + 24 Dec 2005; Simon Stelling <blubb@gentoo.org> rebase-511.ebuild: + stable on amd64 + + 23 Dec 2005; Tobias Scherbaum <dertobi123@gentoo.org> rebase-511.ebuild: + Marked ppc stable, #115436 + + 13 Dec 2005; Markus Rothe <corsair@gentoo.org> rebase-511.ebuild: + Stable on ppc64; bug #115436 + +*rebase-512 (08 Dec 2005) + + 08 Dec 2005; Olivier Fisette <ribosome@gentoo.org> -rebase-510.ebuild, + rebase-511.ebuild, +rebase-512.ebuild: + Pruned old version. Added 511 to x86. New version. + + 19 Nov 2005; Simon Stelling <blubb@gentoo.org> rebase-509.ebuild: + stable on amd64 + +*rebase-511 (07 Nov 2005) + + 07 Nov 2005; Olivier Fisette <ribosome@gentoo.org> +rebase-511.ebuild: + New version. + + 18 Oct 2005; Olivier Fisette <ribosome@gentoo.org> rebase-510.ebuild: + Ebuild clean-up. + + 17 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -rebase-507.ebuild, + -rebase-508.ebuild: + Pruning old versions. + + 08 Oct 2005; Lina Pezzella <j4rg0n@gentoo.org> rebase-509.ebuild: + Stable ppc-macos, Bug 108337 + + 08 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> rebase-509.ebuild: + Stable on ppc. + + 07 Oct 2005; Brent Baude <ranger@gentoo.org> rebase-509.ebuild: + Marking rebase-509 stable ppc64 for bug 108337 + + 07 Oct 2005; Olivier Fisette <ribosome@gentoo.org> rebase-509.ebuild, + rebase-510.ebuild: + 509 added to stable x86. Reverted 510 being x86 stable. + + 07 Oct 2005; Olivier Fisette <ribosome@gentoo.org> rebase-510.ebuild: + Added to stable x86. + +*rebase-510 (06 Oct 2005) + + 06 Oct 2005; Olivier Fisette <ribosome@gentoo.org> +rebase-510.ebuild: + New version. + +*rebase-509 (10 Sep 2005) + + 10 Sep 2005; Olivier Fisette <ribosome@gentoo.org> +rebase-509.ebuild: + New version. + + 31 Aug 2005; Olivier Fisette <ribosome@gentoo.org> -rebase-503.ebuild, + -rebase-504.ebuild, -rebase-505.ebuild, -rebase-506.ebuild: + Removed obsolete versions. + + 29 Aug 2005; Lina Pezzella <j4rg0n@gentoo.org> rebase-507.ebuild: + Stable ppc-macos + + 18 Aug 2005; Michael Hanselmann <hansmi@gentoo.org> rebase-507.ebuild: + Stable on ppc. + + 09 Aug 2005; Markus Rothe <corsair@gentoo.org> rebase-507.ebuild: + Stable on ppc64 + +*rebase-508 (06 Aug 2005) + + 06 Aug 2005; Olivier Fisette <ribosome@gentoo.org> rebase-507.ebuild, + +rebase-508.ebuild: + New version: 508. Added 507 to x86. + + 09 Jul 2005; Markus Rothe <corsair@gentoo.org> rebase-506.ebuild: + Stable on ppc64 + + 09 Jul 2005; Lina Pezzella <j4rg0n@gentoo.org> rebase-506.ebuild: + Stable ppc-macos + +*rebase-507 (08 Jul 2005) + + 08 Jul 2005; Olivier Fisette <ribosome@gentoo.org> rebase-506.ebuild, + +rebase-507.ebuild: + New version: 507. Added 506 to x86. + + 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> rebase-505.ebuild: + Stable ppc-macos + + 19 Jun 2005; Markus Rothe <corsair@gentoo.org> rebase-505.ebuild: + Stable on ppc64 + +*rebase-506 (03 Jun 2005) + + 03 Jun 2005; Olivier Fisette <ribosome@gentoo.org> rebase-505.ebuild, + +rebase-506.ebuild: + New version. Added 505 to x86. + + 31 May 2005; Lina Pezzella <j4rg0n@gentoo.org> rebase-504.ebuild: + Stable ppc-macos + +*rebase-505 (10 May 2005) + + 10 May 2005; Olivier Fisette <ribosome@gentoo.org> -rebase-502.ebuild, + rebase-504.ebuild, +rebase-505.ebuild: + New version: 505. Added 504 to x86. Removed old version: 502. + + 02 May 2005; Omkhar Arasaratnam <omkhar@gentoo.org> rebase-504.ebuild: + Added ~ppc64 + + 01 May 2005; Michael Hanselmann <hansmi@gentoo.org> rebase-503.ebuild: + Stable on ppc. + + 27 Apr 2005; Lina Pezzella <j4rg0n@gentoo.org> rebase-503.ebuild: + Stable ppc-macos + + 27 Apr 2005; <dams@gentoo.org> rebase-503.ebuild: + there is no emboss marked as stable, so rebase cannot be marked as stable. + Changing to ~ppc + + 24 Apr 2005; Michael Hanselmann <hansmi@gentoo.org> rebase-503.ebuild: + Stable on ppc. + +*rebase-504 (05 Apr 2005) + + 05 Apr 2005; Olivier Fisette <ribosome@gentoo.org> rebase-503.ebuild, + +rebase-504.ebuild: + New version: 504. Added 503 to x86. + + 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> rebase-502.ebuild: + Stable ppc-macos + +*rebase-503 (01 Mar 2005) + + 01 Mar 2005; Olivier Fisette <ribosome@gentoo.org> -rebase-501.ebuild, + rebase-502.ebuild, +rebase-503.ebuild: + Removed obsolete version (501). Added to x86 (502). New version (503). + + 23 Feb 2005; Olivier Fisette <ribosome@gentoo.org> -rebase-411.ebuild, + -rebase-412.ebuild, rebase-501.ebuild rebase-502.ebuild: + Added support for the "emboss" and "minimal" "USE" flags. + + 11 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> rebase-501.ebuild: + Stable ppc-macos + +*rebase-502 (02 Feb 2005) + + 02 Feb 2005; Olivier Fisette <ribosome@gentoo.org> rebase-501.ebuild, + +rebase-502.ebuild: + New version: 502. Added 501 to x86. + + 02 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> rebase-412.ebuild: + Stable ppc-macos + +*rebase-501 (02 Jan 2005) + + 02 Jan 2005; Olivier Fisette <ribosome@gentoo.org> rebase-412.ebuild, + +rebase-501.ebuild: + New version: 501. Added 412 to x86. + + 01 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> rebase-412.ebuild: + Unstable ppc-macos. + +*rebase-412 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +rebase-411.ebuild, +rebase-412.ebuild: + Moved from app-sci/rebase to sci-biology/rebase. + + 19 Dec 2004; Olivier Fisette <ribosome@gentoo.org> -rebase-409.ebuild: + Removed old version. + +*rebase-412 (13 Dec 2004) + + 13 Dec 2004; Olivier Fisette <ribosome@gentoo.org> rebase-411.ebuild, + +rebase-412.ebuild: + New version: 412. Added 411 to x86. + + 21 Nov 2004; Karol Wojtaszek <sekretarz@gentoo.org> rebase-411.ebuild: + Keyworded ~amd64, bug #71858 + +*rebase-411 (30 Oct 2004) + + 30 Oct 2004; Olivier Fisette <ribosome@gentoo.org> -rebase-408.ebuild, + rebase-409.ebuild, +rebase-411.ebuild: + Removed obsolete version (408). Added to x86 (409). New version (411). + +*rebase-409 (29 Sep 2004) + + 29 Sep 2004; Olivier Fisette <ribosome@gentoo.org> -rebase-406.ebuild, + rebase-408.ebuild, +rebase-409.ebuild: + Added x86 to 408. New version 409. Removed old version. + +*rebase-408 (10 Aug 2004) + + 10 Aug 2004; Olivier Fisette <ribosome@gentoo.org> + rebase-406.ebuild: + Added to x86. + rebase-408.ebuild: + Updated package. + + 26 Jun 2004; David Holm <dholm@gentoo.org> rebase-406.ebuild: + Added to ~ppc. + +*rebase-406 (24 Jun 2004) + + 24 Jun 2004; Olivier Fisette <ribosome@gentoo.org> + rebase-406.ebuild, metadata.xml : + Initial import. Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>. + Reference: Gentoo Bugzilla, bug #45945 diff --git a/sci-biology/recon/ChangeLog b/sci-biology/recon/ChangeLog new file mode 100644 index 00000000..3dbb812e --- /dev/null +++ b/sci-biology/recon/ChangeLog @@ -0,0 +1,25 @@ +# ChangeLog for sci-biology/recon +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/recon/ChangeLog,v 1.4 2013/03/11 16:52:42 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*recon-1.06-r2 (26 Aug 2012) + + 26 Aug 2012; Justin Lecher <jlec@gentoo.org> +recon-1.06-r2.ebuild, + +files/recon-1.06-respect.patch: + Respect CFLAGS and CC, #432660 + +*recon-1.06-r1 (10 Mar 2011) + + 10 Mar 2011; Justin Lecher <jlec@gentoo.org> + +files/1.06-buffer-overflow.patch, -recon-1.06.ebuild, +recon-1.06-r1.ebuild: + Fixes for buffer overflow, #358195, USE=examples added + +*recon-1.06 (03 Feb 2011) + + 03 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> +recon-1.06.ebuild, + +metadata.xml: + New package, dependency of sci-biology/repeatmodeler. Ebuild written by me + diff --git a/sci-biology/repeatmasker-libraries/ChangeLog b/sci-biology/repeatmasker-libraries/ChangeLog new file mode 100644 index 00000000..899409c0 --- /dev/null +++ b/sci-biology/repeatmasker-libraries/ChangeLog @@ -0,0 +1,46 @@ +# ChangeLog for sci-biology/repeatmasker-libraries +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker-libraries/ChangeLog,v 1.6 2015/04/07 14:35:04 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*repeatmasker-libraries-20120418 (07 Mar 2013) + + 07 Mar 2013; Justin Lecher <jlec@gentoo.org> + -repeatmasker-libraries-20090120.ebuild, + -repeatmasker-libraries-20090604.ebuild, + +repeatmasker-libraries-20120418.ebuild, metadata.xml: + Version Bump; cleaned old; fix license + +*repeatmasker-libraries-20090604 (20 Aug 2009) + + 20 Aug 2009; Andrey Kislyuk <weaver@gentoo.org> + +repeatmasker-libraries-20090604.ebuild: + Version bump + + 03 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> metadata.xml: + Fix metadata.xml + +*repeatmasker-libraries-20090120 (26 Feb 2009) + + 26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +repeatmasker-libraries-20090120.ebuild: + Import from Science overlay + + 19 Feb 2009; weaver <weaver@gentoo.org> ChangeLog: + Version bump + + 08 Jul 2008; weaver <weaver@gentoo.org> + -repeatmasker-libraries-20061006.ebuild, + +repeatmasker-libraries-20080611.ebuild: + Version bump + + 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> + +repeatmasker-libraries-20061006.ebuild: + Mass import from sunrise + + 20 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> + +repeatmasker-libraries-20061006.ebuild, +metadata.xml: + new package (bug 114096) + diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog new file mode 100644 index 00000000..e3f3b44a --- /dev/null +++ b/sci-biology/repeatmasker/ChangeLog @@ -0,0 +1,52 @@ +# ChangeLog for sci-biology/repeatmasker +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/ChangeLog,v 1.8 2015/04/07 14:34:58 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*repeatmasker-4.0.1 (07 Mar 2013) + + 07 Mar 2013; Justin Lecher <jlec@gentoo.org> -repeatmasker-3.2.7.ebuild, + -repeatmasker-3.2.8.ebuild, -repeatmasker-3.2.9.ebuild, + +repeatmasker-4.0.1.ebuild, metadata.xml: + Version Bump; cleaned old + +*repeatmasker-3.2.9 (03 Feb 2011) + + 03 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> + +repeatmasker-3.2.9.ebuild: + Version bump, switch over to sci-biology/rmblast + +*repeatmasker-3.2.8 (20 Aug 2009) + + 20 Aug 2009; Andrey Kislyuk <weaver@gentoo.org> + +repeatmasker-3.2.8.ebuild: + Version bump + + 17 Aug 2009; Andrey Kislyuk <weaver@gentoo.org> repeatmasker-3.2.7.ebuild: + Install symlinks to fix bug 281533 + + 03 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> metadata.xml: + Fix metadata.xml + +*repeatmasker-3.2.7 (26 Feb 2009) + + 26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +repeatmasker-3.2.7.ebuild: + Import from Science overlay, bug 114096 + + 19 Feb 2009; weaver <weaver@gentoo.org> ChangeLog: + Version bump + + 08 Jul 2008; weaver <weaver@gentoo.org> +repeatmasker-3.2.5.ebuild: + Version bump + + 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> + +repeatmasker-3.1.7.ebuild: + Mass import from sunrise + + 20 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +repeatmasker-3.1.7.ebuild, + +metadata.xml: + new package (bug 114096) + diff --git a/sci-biology/rmblast/ChangeLog b/sci-biology/rmblast/ChangeLog new file mode 100644 index 00000000..e98d9079 --- /dev/null +++ b/sci-biology/rmblast/ChangeLog @@ -0,0 +1,28 @@ +# ChangeLog for sci-biology/rmblast +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/rmblast/ChangeLog,v 1.6 2015/06/16 08:38:38 jlec Exp $ + + 16 Jun 2015; Justin Lecher <jlec@gentoo.org> -rmblast-1.2.ebuild, + rmblast-1.2-r1.ebuild: + Add missing dependency on cpio, bug #513420 + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*rmblast-1.2-r1 (18 Feb 2013) + + 18 Feb 2013; Justin Lecher <jlec@gentoo.org> rmblast-1.2.ebuild, + +rmblast-1.2-r1.ebuild, +files/rmblast-1.2-gcc47.patch, metadata.xml: + Bug fixes: Build against any boost, #356315; build with gcc-4.7, #442266 + + 31 Oct 2012; Diego E. Pettenò <flameeyes@gentoo.org> rmblast-1.2.ebuild: + QA: drop maximum boost version dep; if it fails to build, it has to be fixed. + + 02 May 2011; Justin Lecher <jlec@gentoo.org> rmblast-1.2.ebuild: + Removed redundant src_install + +*rmblast-1.2 (06 Nov 2010) + + 06 Nov 2010; Andrey Kislyuk <weaver@gentoo.org> +rmblast-1.2.ebuild, + +metadata.xml: + New package, dependency of sci-biology/repeatmasker. Ebuild written by me diff --git a/sci-biology/rnaview/ChangeLog b/sci-biology/rnaview/ChangeLog new file mode 100644 index 00000000..5241f8d0 --- /dev/null +++ b/sci-biology/rnaview/ChangeLog @@ -0,0 +1,66 @@ +# ChangeLog for sci-biology/rnaview +# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/rnaview/ChangeLog,v 1.13 2012/08/03 15:04:03 jlec Exp $ + +*rnaview-20040713-r3 (03 Aug 2012) + + 03 Aug 2012; Justin Lecher <jlec@gentoo.org> +rnaview-20040713-r3.ebuild, + files/rnaview-20040713-makefile.patch: + Respect CFLAGS, #429536; Bump to EAPI=4 + +*rnaview-20040713-r2 (06 Sep 2010) + + 06 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org> + -rnaview-20040713-r1.ebuild, +rnaview-20040713-r2.ebuild, + +files/rnaview-20040713-implicit.patch, + +files/rnaview-20040713-makefile.patch: + Respect LDFLAGS wrt bug 336196. Thanks to Diego for the report. Fix + install and implicit function declaration. Drop old. + +*rnaview-20040713-r1 (26 Aug 2008) + + 26 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + +rnaview-20040713-r1.ebuild: + Added convenience env file. + + 10 Apr 2007; Jeff Gardner <je_fro@gentoo.org> rnaview-20040713.ebuild: + Added ~amd64. + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Stepping down from maintaining this package. + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> + rnaview-20040713.ebuild: + Fixed home page URL. + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> + rnaview-20040713.ebuild: + Ebuild clean-up. + +*rnaview-20040713 (13 May 2005) + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> -rnaview-1.ebuild, + +rnaview-20040713.ebuild: + Changed versionning scheme. (Upstream does not use version numbers.) + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> rnaview-1.ebuild: + Ebuild cleanup. + + 18 Jan 2005; Olivier Fisette <ribosome@gentoo.org> rnaview-1.ebuild: + Added to x86. + +*rnaview-1 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +rnaview-1.ebuild: + Moved from app-sci/rnaview to sci-biology/rnaview. + +*rnaview-1 (07 Nov 2004) + + 07 Nov 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +rnaview-1.ebuild: + Initial import. + diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog new file mode 100644 index 00000000..54226395 --- /dev/null +++ b/sci-biology/samtools/ChangeLog @@ -0,0 +1,136 @@ +# ChangeLog for sci-biology/samtools +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.26 2015/07/01 18:30:25 zlogene Exp $ + + 01 Jul 2015; Mikle Kolyada <zlogene@gentoo.org> samtools-1.0-r1.ebuild: + x86 stable wrt bug #525630 + + 08 Apr 2015; Michał Górny <mgorny@gentoo.org> samtools-0.1.19-r2.ebuild: + Drop old Python implementations + + 28 Feb 2015; Justin Lecher <jlec@gentoo.org> + files/samtools-1.2-buildsystem.patch, samtools-1.2.ebuild: + Fix depend rules in make which break due to unbundling of htslib, #541134; use + LD_LIBRARY_PATH druing tests + +*samtools-1.2 (18 Feb 2015) + + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> + +files/samtools-1.2-buildsystem.patch, +samtools-1.2.ebuild: + Version Bump, #540356 + +*samtools-1.1 (06 Jan 2015) + + 06 Jan 2015; Justin Lecher <jlec@gentoo.org> +samtools-1.1.ebuild, + +files/samtools-1.1-buildsystem.patch: + Version Bump + +*samtools-1.0-r1 (25 Sep 2014) + + 25 Sep 2014; Justin Lecher <jlec@gentoo.org> +samtools-1.0-r1.ebuild, + +files/samtools-1.0-buildsystem.patch: + Install bam headers and create libbam.so, #523644 + + 24 Sep 2014; Justin Lecher <jlec@gentoo.org> samtools-1.0.ebuild: + Add missing build dep, #523586 + +*samtools-1.0 (20 Sep 2014) + + 20 Sep 2014; Justin Lecher <jlec@gentoo.org> -samtools-0.1.18.ebuild, + -samtools-0.1.18-r2.ebuild, -samtools-0.1.18-r3.ebuild, + samtools-0.1.19-r2.ebuild, +samtools-1.0.ebuild: + Version Bump, #523224; drop old + +*samtools-0.1.19-r2 (23 Mar 2014) + + 23 Mar 2014; Justin Lecher <jlec@gentoo.org> -samtools-0.1.19-r1.ebuild, + +samtools-0.1.19-r2.ebuild: + Fix symlink creation, thanks Martin Mokrejs telling me that + + 11 Feb 2014; Fabian Groffen <grobian@gentoo.org> samtools-0.1.19-r1.ebuild: + Reference correct library name on Darwin, thanks Linlin Yan in bug #491812 + +*samtools-0.1.19-r1 (06 Dec 2013) + + 06 Dec 2013; Justin Lecher <jlec@gentoo.org> -samtools-0.1.19.ebuild, + +samtools-0.1.19-r1.ebuild, files/samtools-0.1.19-buildsystem.patch: + Fix underlinking + + 06 Dec 2013; Justin Lecher <jlec@gentoo.org> samtools-0.1.12.ebuild, + samtools-0.1.18.ebuild, samtools-0.1.18-r2.ebuild, samtools-0.1.18-r3.ebuild, + samtools-0.1.19.ebuild: + Keyword for *-linux, tested by me + +*samtools-0.1.19 (20 Sep 2013) + + 20 Sep 2013; Justin Lecher <jlec@gentoo.org> +samtools-0.1.19.ebuild, + +files/samtools-0.1.19-buildsystem.patch: + Version Bump, #485450 + +*samtools-0.1.18-r3 (29 Mar 2013) + + 29 Mar 2013; Justin Lecher <jlec@gentoo.org> +samtools-0.1.18-r3.ebuild: + Install bcftools and vcfutils.pl pointed out by mahnmut + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*samtools-0.1.18-r2 (27 Jan 2013) + + 27 Jan 2013; Justin Lecher <jlec@gentoo.org> -samtools-0.1.18-r1.ebuild, + +samtools-0.1.18-r2.ebuild: + Add missing deps and correct sed lines, #454134; thanks Torsten Veller + +*samtools-0.1.18-r1 (23 Jan 2013) + + 23 Jan 2013; Justin Lecher <jlec@gentoo.org> -samtools-0.1.12a-r1.ebuild, + -samtools-0.1.16.ebuild, -samtools-0.1.17.ebuild, +samtools-0.1.18-r1.ebuild, + metadata.xml: + Drop old; use pkg-config to check for libncurses + +*samtools-0.1.18 (26 Sep 2011) + + 26 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +samtools-0.1.18.ebuild: + Version bump + +*samtools-0.1.17 (18 Jul 2011) + + 18 Jul 2011; Justin Lecher <jlec@gentoo.org> samtools-0.1.12.ebuild, + samtools-0.1.12a-r1.ebuild, samtools-0.1.16.ebuild, +samtools-0.1.17.ebuild: + Version Bump, #375519 + +*samtools-0.1.16 (30 Apr 2011) + + 30 Apr 2011; Justin Lecher <jlec@gentoo.org> samtools-0.1.12.ebuild, + samtools-0.1.12a-r1.ebuild, +samtools-0.1.16.ebuild: + Version Bump, #365265 + +*samtools-0.1.12a-r1 (14 Mar 2011) + + 14 Mar 2011; Kacper Kowalik <xarthisius@gentoo.org> -samtools-0.1.12a.ebuild, + +samtools-0.1.12a-r1.ebuild: + Drop empty RDEP/DEP, respect CC,LDFLAGS wrt 358563. Thanks to Diego for the + report. + +*samtools-0.1.12a (18 Feb 2011) + + 18 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> +samtools-0.1.12a.ebuild: + Address bug 354941, build library, correct versioning + + 17 Feb 2011; Thomas Kahle <tomka@gentoo.org> samtools-0.1.12.ebuild: + x86 stable per bug 353566 + + 11 Feb 2011; Markos Chandras <hwoarang@gentoo.org> samtools-0.1.12.ebuild: + Stable on amd64 wrt bug #353566 + +*samtools-0.1.12 (21 Dec 2010) + + 21 Dec 2010; Andrey Kislyuk <weaver@gentoo.org> +samtools-0.1.12.ebuild, + +metadata.xml: + Version bump, import from Science overlay + + 22 Jan 2010; root <root@onyx.(none)> + Version bump + + 26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: + New package, ebuild written by me diff --git a/sci-biology/seaview/ChangeLog b/sci-biology/seaview/ChangeLog new file mode 100644 index 00000000..37e191fb --- /dev/null +++ b/sci-biology/seaview/ChangeLog @@ -0,0 +1,256 @@ +# ChangeLog for sci-biology/seaview +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/seaview/ChangeLog,v 1.54 2014/01/14 15:39:14 jlec Exp $ + + 14 Jan 2014; Justin Lecher <jlec@gentoo.org> -seaview-4.3.3.ebuild: + Drop old + + 14 Jan 2014; Agostino Sarubbo <ago@gentoo.org> seaview-4.3.5.ebuild: + Stable for ppc, wrt bug #497216 + + 14 Jan 2014; Agostino Sarubbo <ago@gentoo.org> seaview-4.3.5.ebuild: + Stable for x86, wrt bug #497216 + + 12 Jan 2014; Pacho Ramos <pacho@gentoo.org> seaview-4.3.5.ebuild: + amd64 stable, bug #497216 + + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> seaview-4.3.3.ebuild: + Punt base.eclass + + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> seaview-4.3.5.ebuild: + Punt base.eclass; Bump EAPI to 5; add missing dep for pkg-config; Give some + PREFIX love; use tc-getPKG_CONFIG instead of plain pkg-config + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 10 Dec 2012; Agostino Sarubbo <ago@gentoo.org> seaview-4.3.5.ebuild: + Add ~ppc, wrt bug #432368 + + 18 Oct 2012; Justin Lecher <jlec@gentoo.org> -seaview-4.2.5.ebuild: + Drop old + + 17 Oct 2012; Pawel Hajdan jr <phajdan.jr@gentoo.org> seaview-4.3.3.ebuild: + x86 stable wrt bug #432366 + + 14 Sep 2012; Agostino Sarubbo <ago@gentoo.org> seaview-4.3.3.ebuild: + Stable for amd64, wrt bug #432366 + + 14 Sep 2012; Justin Lecher <jlec@gentoo.org> seaview-4.2.5.ebuild, + seaview-4.3.3.ebuild, seaview-4.3.5.ebuild: + Add missing deps, #432366 + +*seaview-4.3.5 (26 Aug 2012) + + 26 Aug 2012; Justin Lecher <jlec@gentoo.org> seaview-4.2.5.ebuild, + -seaview-4.2.12.ebuild, seaview-4.3.3.ebuild, +seaview-4.3.5.ebuild: + Version Bump; Drop overlinking, #431074 + +*seaview-4.3.3 (04 Jul 2012) + + 04 Jul 2012; Justin Lecher <jlec@gentoo.org> +seaview-4.3.3.ebuild: + Version Bump imported from sci overlay, prepared by Martin Mokrejs, #351005; + fixes also compilation with gcc47, #424727 + + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> seaview-4.2.5.ebuild, + seaview-4.2.12.ebuild: + x11-libs/fltk SLOTMOVE 1.1 -> 1, corrected ebuild accordingly + + 22 Feb 2011; Tomáš Chvátal <scarabeus@gentoo.org> -seaview-4.1.ebuild, + -seaview-4.2.3.ebuild, seaview-4.2.5.ebuild, seaview-4.2.12.ebuild, + -files/seaview-20071113-glibc-2.10.patch, -files/seaview.desktop: + Remove old. Say goodbye to pdflib pdf useflag. + + 01 Feb 2011; Jeff Gardner <je_fro@gentoo.org> seaview-4.2.12.ebuild: + Fix to use pkg-config instead of deprecated xft-config. + +*seaview-4.2.12 (01 Feb 2011) + + 01 Feb 2011; Jeff Gardner <je_fro@gentoo.org> +seaview-4.2.12.ebuild: + Adding latest version. + + 16 Jul 2010; Markos Chandras <hwoarang@gentoo.org> seaview-4.2.5.ebuild: + Stable on amd64 wrt bug #328429 + + 16 Jul 2010; Christian Faulhammer <fauli@gentoo.org> seaview-4.2.5.ebuild: + stable x86, bug 328429 + + 04 Jul 2010; Mark Loeser <halcy0n@gentoo.org> seaview-4.1.ebuild: + Change x11-libs/fltk[-noxft] dep to fltk[xft] as the useflag has been + renamed + +*seaview-4.2.5 (16 May 2010) + + 16 May 2010; Jeff Gardner <je_fro@gentoo.org> +seaview-4.2.5.ebuild: + Latest version, clean out old. + +*seaview-4.2.3 (20 Mar 2010) + + 20 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> + -files/seaview-4.2-gcc44.patch, -seaview-4.2.ebuild, + +seaview-4.2.3.ebuild: + Version bump and address bug 290900 + + 09 Mar 2010; Jonathan Callen <abcd@gentoo.org> seaview-4.1.ebuild, + seaview-4.2.ebuild: + QA: Do not use absolute path to icon when in standard dirs (in + make_desktop_entry()) + +*seaview-4.2 (18 Oct 2009) + + 18 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> + +files/seaview-4.2-gcc44.patch, +seaview-4.2.ebuild: + Version bump and gcc-4.4 patch + + 07 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> metadata.xml, + +seaview-4.1.ebuild, seaview-20071113.ebuild: + Drop keywords in seaview-20071113, will expedite 4.1 + +*seaview-4.1 (07 Oct 2009) + + 07 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> metadata.xml, + +seaview-4.1.ebuild: + Version bump, take ownership, cleanup. Thanks to Martin Mokrejs and Joel + Berendzen (bug 246778). + + 04 Sep 2009; Samuli Suominen <ssuominen@gentoo.org> + seaview-20071113.ebuild, +files/seaview-20071113-glibc-2.10.patch: + Fix building with GLIBC 2.10+ wrt #282431. + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 14 Nov 2008; Olivier Fisette <ribosome@gentoo.org> + seaview-20071113.ebuild: + Restricted dependency to x11-libs/fltk:1.1 (see bug #207107). + + 26 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + seaview-20071113.ebuild: + Added missing pdflib dependency. Fixes bug #233044. + +*seaview-20071113 (12 Feb 2008) + + 12 Feb 2008; Olivier Fisette <ribosome@gentoo.org> -seaview-2.2.ebuild, + +seaview-20071113.ebuild: + Reverting to date-based version scheme. We cannot use upstream's versions + since they keep modifying the package whilst keeping the same version. + PDFlib is no longer needed as recent versions include PDFlib lite (fixes + bug #208334). Commiting straight to stable as this is the same as 2.2, + which was stable. + + 31 Dec 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog: + Fixing my email addy in the Changelog + + 26 Dec 2007; <je_fro@gentoo.org> Manifest: + Dropping old versions. + + 26 Dec 2007; Samuli Suominen <drac@gentoo.org> seaview-2.2.ebuild: + amd64 stable wrt #203185 + + 25 Dec 2007; nixnut <nixnut@gentoo.org> seaview-2.2.ebuild: + Stable on ppc wrt bug 203185 + + 24 Dec 2007; Dawid Węgliński <cla@gentoo.org> seaview-2.2.ebuild: + Stable on x86 (bug #203185) + + 23 Dec 2007; <je_fro@gentoo.org> seaview-2.2.ebuild: + Adding menu entries. + + 22 Dec 2007; <je_fro@gentoo.org> -seaview-20060213.ebuild, + -seaview-20070919.ebuild: + Removing obsolete versions + +*seaview-2.2 (19 Dec 2007) + + 19 Dec 2007; <je_fro@gentoo.org> +seaview-2.2.ebuild: + Bump to latest version. + + 22 Oct 2007; <je_fro@gentoo.org> +files/seaview.desktop, + seaview-20070919.ebuild: + Adding desktop entry + + 21 Oct 2007; <je_fro@gentoo.org> seaview-20041220.ebuild, + seaview-20060213.ebuild, seaview-20070919.ebuild: + remove excessive quotes + + 21 Oct 2007; Jeff Gardner <je_fro@gentoo.org> seaview-20070919.ebuild: + seaview 20070919 appears to work with the latest pdflib + + 21 Oct 2007; Jeff Gardner <je_fro@gentoo.org> seaview-20070919.ebuild: + Adding sci-biology/muscle dependency + +*seaview-20070919 (21 Oct 2007) + + 21 Oct 2007; <je_fro@gentoo.org> seaview-20041220.ebuild, + seaview-20060213.ebuild, +seaview-20070919.ebuild: + Bumping to latest version which contains several new features. + + 25 Mar 2007; Danny van Dyk <kugelfang@gentoo.org> seaview-20041220.ebuild, + seaview-20060213.ebuild: + QA: Fixed assignment of CFLAGS. Makefile respects CXXFLAGS now. Fixed + include and library paths. + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> + -seaview-20050713.ebuild: + Pruned old version. + +*seaview-20060213 (08 Mar 2006) + + 08 Mar 2006; Donnie Berkholz <spyderous@gentoo.org>; + +seaview-20060213.ebuild: + Bump to most recent modification date on upstream's unversioned tarball. + Fixes problem with file-open dialog not finding files, among others. + +*seaview-20050713 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> + +seaview-20050713.ebuild: + New version. + + 24 Apr 2005; Michael Hanselmann <hansmi@gentoo.org> + seaview-20041220.ebuild: + Stable on ppc. + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> + seaview-20041220.ebuild: + Ebuild cleanup. + +*seaview-20041220 (09 Jan 2005) + + 09 Jan 2005; Olivier Fisette <ribosome@gentoo.org> -files/29seaview, + -seaview-1-r1.ebuild, +seaview-20041220.ebuild: + Changed versioning scheme. (Upstream does not use version numbers.) + +*seaview-1-r1 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +files/29seaview, +seaview-1-r1.ebuild: + Moved from app-sci/seaview to sci-biology/seaview. + + 22 Nov 2004; Karol Wojtaszek <sekretarz@gentoo.org> seaview-1-r1.ebuild: + Added to ~amd64, bug #72078 + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> seaview-1-r1.ebuild: + Added to x86. + +*seaview-1 (24 Jun 2004) + + 24 Jun 2004; Olivier Fisette <ribosome@gentoo.org> + seaview-1-r1.ebuild, metedata.xml: + Added app-sci/clustalw as a mandatory dependency. + Set maintainer (ribosome). + +*seaview-1 (24 Jun 2004) + + 24 Jun 2004; David Holm <dholm@gentoo.org> seaview-1.ebuild: + Added to ~ppc. + +*seaview-1 (23 Jun 2004) + + 23 Jun 2004; Olivier Fisette <ribosome@gentoo.org> + seaview-1.ebuild, metadata.xml, files/29seaview : + Initial import. Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>. + Reference: Gentoo Bugzilla, bug #54055 diff --git a/sci-biology/seqan/ChangeLog b/sci-biology/seqan/ChangeLog new file mode 100644 index 00000000..1dc27fe8 --- /dev/null +++ b/sci-biology/seqan/ChangeLog @@ -0,0 +1,46 @@ +# ChangeLog for sci-biology/seqan +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/seqan/ChangeLog,v 1.11 2015/04/08 18:20:42 mgorny Exp $ + + 08 Apr 2015; Michał Górny <mgorny@gentoo.org> seqan-1.3.1-r1.ebuild: + Drop old Python implementations + +*seqan-2.0.0 (24 Feb 2015) + + 24 Feb 2015; Justin Lecher <jlec@gentoo.org> +files/seqan-2.0.0-zlib.patch, + +seqan-2.0.0.ebuild: + Version Bump, #540692 + + 19 Feb 2015; Justin Lecher <jlec@gentoo.org> seqan-1.4.2.ebuild: + Prefix love, #540690; thanks Michael Schubert for the patch + + 26 Dec 2014; Justin Lecher <jlec@gentoo.org> seqan-1.4.2.ebuild: + Test for SSE4.1 support, #531876 + + 24 Oct 2014; Justin Lecher <jlec@gentoo.org> seqan-1.4.2.ebuild: + Fix file collision, #526586 + +*seqan-1.4.2 (17 Oct 2014) + + 17 Oct 2014; Justin Lecher <jlec@gentoo.org> +seqan-1.4.2.ebuild, + +files/seqan-1.4.2-include.patch, +files/seqan-1.4.2-shared.patch: + Version Bump + + 17 Jul 2013; Justin Lecher <jlec@gentoo.org> seqan-1.3.1-r1.ebuild: + Add missing dep + + 29 May 2013; Justin Lecher <jlec@gentoo.org> seqan-1.3.1-r1.ebuild: + Fix usage of new python r1 eclasses (missing PYTHON_REQUIRED_USE, + PYTHON_DEPS) + +*seqan-1.3.1-r1 (29 Mar 2013) + + 29 Mar 2013; Justin Lecher <jlec@gentoo.org> -seqan-1.3.1.ebuild, + +seqan-1.3.1-r1.ebuild: + Correct doc installation path + +*seqan-1.3.1 (13 Mar 2013) + + 13 Mar 2013; Justin Lecher <jlec@gentoo.org> +seqan-1.3.1.ebuild, + +metadata.xml: + New addition diff --git a/sci-biology/shrimp/ChangeLog b/sci-biology/shrimp/ChangeLog new file mode 100644 index 00000000..93dca7b3 --- /dev/null +++ b/sci-biology/shrimp/ChangeLog @@ -0,0 +1,101 @@ +# ChangeLog for sci-biology/shrimp +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.25 2015/04/08 18:20:42 mgorny Exp $ + + 08 Apr 2015; Michał Górny <mgorny@gentoo.org> shrimp-2.2.3.ebuild: + Drop old Python implementations + + 29 Jan 2015; Michał Górny <mgorny@gentoo.org> shrimp-2.2.3.ebuild: + Switch to CPU_FLAGS_X86. + + 05 Sep 2013; Michał Górny <mgorny@gentoo.org> shrimp-2.2.3.ebuild: + Clean up PYTHON_COMPAT from old implementations. + + 29 May 2013; Justin Lecher <jlec@gentoo.org> shrimp-2.2.3.ebuild: + Fix usage of new python r1 eclasses (missing PYTHON_REQUIRED_USE, + PYTHON_DEPS) + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 17 Feb 2013; Justin Lecher <jlec@gentoo.org> shrimp-2.2.3.ebuild: + Force sse2 support by the cpu, #337401 + + 17 Feb 2013; Justin Lecher <jlec@gentoo.org> shrimp-2.0.1.ebuild, + -shrimp-2.1.0.ebuild, shrimp-2.2.3.ebuild, metadata.xml: + Drop old; block collision with emboss, #450426; move to new python eclasses + + 05 Feb 2013; Ulrich Müller <ulm@gentoo.org> shrimp-2.0.1.ebuild, + shrimp-2.1.0.ebuild, shrimp-2.2.3.ebuild: + Specify LICENSE more precisely, see LICENSE file, bug 455566. + + 23 Jan 2013; Patrick Lauer <patrick@gentoo.org> shrimp-2.0.1.ebuild, + shrimp-2.1.0.ebuild, shrimp-2.2.3.ebuild: + Adding blocker for #453044 + +*shrimp-2.2.3 (18 Oct 2012) + + 18 Oct 2012; Justin Lecher <jlec@gentoo.org> +shrimp-2.2.3.ebuild: + Vesion Bump + + 18 Oct 2012; Justin Lecher <jlec@gentoo.org> -shrimp-1.3.1.ebuild, + shrimp-2.0.1.ebuild, shrimp-2.1.0.ebuild: + Do not install elf in usr/share, #438652 + + 07 Mar 2011; Thomas Kahle <tomka@gentoo.org> shrimp-2.0.1.ebuild: + x86 stable per bug 353563 + + 27 Feb 2011; Markos Chandras <hwoarang@gentoo.org> shrimp-2.0.1.ebuild: + Stable on amd64 wrt bug #353563 + +*shrimp-2.1.0 (03 Feb 2011) + + 03 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> -shrimp-1.2.1.ebuild, + +shrimp-2.1.0.ebuild: + Version bump, drop old + + 09 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org> shrimp-2.0.1.ebuild: + Fix dependency on openmp. + + 09 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org> shrimp-2.0.1.ebuild: + Respect LDFLAGS wrt bug 331823. Thanks to Diego for report. + +*shrimp-2.0.1 (25 Jul 2010) + + 25 Jul 2010; Andrey Kislyuk <weaver@gentoo.org> +shrimp-2.0.1.ebuild: + Version bump + + 03 Jan 2010; Pacho Ramos <pacho@gentoo.org> shrimp-1.3.1.ebuild: + amd64 stable, bug 298764 + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> shrimp-1.3.1.ebuild: + stable x86, bug 298764 + +*shrimp-1.3.1 (09 Dec 2009) + + 09 Dec 2009; Andrey Kislyuk <weaver@gentoo.org> shrimp-1.2.1.ebuild, + -shrimp-1.3.0.ebuild, +shrimp-1.3.1.ebuild: + Fix gcc-4.4 issue, bug 294811. Thanks to Martin Mokrejš. Version bump. + +*shrimp-1.3.0 (28 Oct 2009) + + 28 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +shrimp-1.3.0.ebuild: + Version bump + + 22 Sep 2009; Markus Meier <maekke@gentoo.org> shrimp-1.2.1.ebuild: + x86 stable, bug #283679 + + 06 Sep 2009; Jeremy Olexa <darkside@gentoo.org> shrimp-1.2.1.ebuild: + amd64 stable, bug 283679. As requested, compile test only + + 07 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> shrimp-1.2.1.ebuild: + Don't use versionator + +*shrimp-1.2.1 (07 Jul 2009) + + 07 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +shrimp-1.2.1.ebuild: + Import from Science overlay + + 02 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: + New package sci-biology/shrimp, ebuild written by me diff --git a/sci-biology/sibsim4/ChangeLog b/sci-biology/sibsim4/ChangeLog new file mode 100644 index 00000000..cb3d55af --- /dev/null +++ b/sci-biology/sibsim4/ChangeLog @@ -0,0 +1,33 @@ +# ChangeLog for sci-biology/sibsim4 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/sibsim4/ChangeLog,v 1.8 2013/06/18 06:33:18 jlec Exp $ + + 18 Jun 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop maintainer + + 18 Feb 2013; Justin Lecher <jlec@gentoo.org> -sibsim4-0.17.ebuild: + Drop Old + + 17 Feb 2013; Agostino Sarubbo <ago@gentoo.org> sibsim4-0.20.ebuild: + Stable for amd64, wrt bug #328431 + + 17 Feb 2013; Justin Lecher <jlec@gentoo.org> sibsim4-0.20.ebuild, + metadata.xml: + Respect CC, CFLAGS and LDFLAGS, #328431 + + 16 Jul 2010; Christian Faulhammer <fauli@gentoo.org> sibsim4-0.20.ebuild: + stable x86, bug 328431 + +*sibsim4-0.20 (05 May 2010) + + 05 May 2010; Andrey Kislyuk <weaver@gentoo.org> +sibsim4-0.20.ebuild: + Version bump + + 04 Apr 2009; Markus Meier <maekke@gentoo.org> sibsim4-0.17.ebuild: + amd64/x86 stable, bug #263770 + +*sibsim4-0.17 (27 Dec 2008) + + 27 Dec 2008; weaver <weaver@gentoo.org> +metadata.xml, + +sibsim4-0.17.ebuild: + Import from Science overlay, bug 175143 diff --git a/sci-biology/sim4/ChangeLog b/sci-biology/sim4/ChangeLog new file mode 100644 index 00000000..c5954ed8 --- /dev/null +++ b/sci-biology/sim4/ChangeLog @@ -0,0 +1,41 @@ +# ChangeLog for sci-biology/sim4 +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/sim4/ChangeLog,v 1.8 2010/09/01 15:16:59 xarthisius Exp $ + +*sim4-20030921-r1 (01 Sep 2010) + + 01 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org> + +sim4-20030921-r1.ebuild: + Respect CC,CFLAGS,LDFLAGS wrt bug 335553. Thanks to Diego for the report. + + 25 Mar 2007; Danny van Dyk <kugelfang@gentoo.org> sim4-20030921.ebuild: + QA: Removed redundant src_compile(). + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Stepping down from maintaining this package. + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> sim4-20030921.ebuild: + Ebuild clean-up. + +*sim4-20030921 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +sim4-20030921.ebuild: + Moved from app-sci/sim4 to sci-biology/sim4. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> sim4-20030921.ebuild: + Added to x86. + + 23 Jun 2004; David Holm <dholm@gentoo.org> sim4-20030921.ebuild: + Added to ~ppc. + +*sim4-20030921 (22 Jun 2004) + + 22 Jun 2004; Olivier Fisette <ribosome@gentoo.org> + sim4-20030921.ebuild, metadata.xml : + Initial import. Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>. + Reference: Gentoo Bugzilla, bug #54041 + diff --git a/sci-biology/snpfile/ChangeLog b/sci-biology/snpfile/ChangeLog new file mode 100644 index 00000000..31d2f2d7 --- /dev/null +++ b/sci-biology/snpfile/ChangeLog @@ -0,0 +1,51 @@ +# ChangeLog for sci-biology/snpfile +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/snpfile/ChangeLog,v 1.12 2013/03/12 12:09:03 jlec Exp $ + + 12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 15 Jan 2012; Justin Lecher <jlec@gentoo.org> Manifest: + Dropped old + + 15 Jan 2012; Pawel Hajdan jr <phajdan.jr@gentoo.org> snpfile-2.0.1-r1.ebuild: + x86 stable wrt bug #326455 + + 07 Jan 2012; Agostino Sarubbo <ago@gentoo.org> snpfile-2.0.1-r1.ebuild: + Stable for AMD64, wrt bug #326455 + + 07 Jan 2012; Kacper Kowalik <xarthisius@gentoo.org> snpfile-2.0.1-r1.ebuild: + Remove .la file if not static-libs + + 28 May 2011; Justin Lecher <jlec@gentoo.org> snpfile-2.0.1-r1.ebuild, + +files/snpfile-2.0.1-gold.patch: + Gold fix, #369001 + + 02 Oct 2010; Kacper Kowalik <xarthisius@gentoo.org> + files/snpfile-2.0.1-gentoo.diff: + Fix patch to compile with make-3.82 wrt bug 336542. Thanks to Diego for + the report. + +*snpfile-2.0.1-r1 (20 Jun 2010) + + 20 Jun 2010; Kacper Kowalik <xarthisius@gentoo.org> + +snpfile-2.0.1-r1.ebuild, +files/snpfile-2.0.1-gentoo.diff: + Fixing as-needed issues wrt bug 294971, provide shared libs. Thanks Diego + for reporting. + + 26 Jul 2009; Samuli Suominen <ssuominen@gentoo.org> snpfile-2.0.1.ebuild, + +files/snpfile-2.0.1-gcc44.patch: + Fix building with GCC 4.4 wrt #276196. + + 24 May 2009; Markus Meier <maekke@gentoo.org> snpfile-2.0.1.ebuild: + amd64/x86 stable, bug #269967 + +*snpfile-2.0.1 (13 Feb 2009) + + 13 Feb 2009; weaver <weaver@gentoo.org> -files/snpfile-2.0.0-gcc43.patch, + -snpfile-2.0.0.ebuild, +snpfile-2.0.1.ebuild: + Bump, drop patch + + 07 Feb 2009; weaver <weaver@gentoo.org> ChangeLog: + New package, ebuild written by me + diff --git a/sci-biology/stride/ChangeLog b/sci-biology/stride/ChangeLog new file mode 100644 index 00000000..44aaa6c1 --- /dev/null +++ b/sci-biology/stride/ChangeLog @@ -0,0 +1,74 @@ +# ChangeLog for sci-biology/stride +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/stride/ChangeLog,v 1.19 2015/04/19 06:52:08 pacho Exp $ + + 19 Apr 2015; Pacho Ramos <pacho@gentoo.org> stride-20011129-r1.ebuild: + x86 stable wrt bug #525378 + + 02 Mar 2015; Agostino Sarubbo <ago@gentoo.org> stride-20011129-r1.ebuild: + Stable for ppc, wrt bug #525378 + + 03 Nov 2014; Chema Alonso <nimiux@gentoo.org> stride-20011129-r1.ebuild: + Stable for amd64 wrt bug #525378 + + 31 Oct 2014; Justin Lecher <jlec@gentoo.org> stride-20011129-r1.ebuild: + Fix 404 on patches, #525346 + + 14 Oct 2014; Justin Lecher <jlec@gentoo.org> -stride-20011129.ebuild, + stride-20011129-r1.ebuild: + Put patches in my devspace, #525346 + + 14 Apr 2013; Justin Lecher <jlec@gentoo.org> stride-20011129.ebuild, + stride-20011129-r1.ebuild, metadata.xml: + Fix license, thanks ulm looking for correct licensing + + 08 May 2012; Christoph Junghans <ottxor@gentoo.org> + stride-20011129-r1.ebuild: + added ~x86-macos keyword + + 20 Jul 2011; Pacho Ramos <pacho@gentoo.org> metadata.xml: + Drop maintainer due retirement, bug #105599 + + 29 Jun 2011; Justin Lecher <jlec@gentoo.org> stride-20011129.ebuild, + stride-20011129-r1.ebuild: + Fix sed on *FLAGS from : to |, EAPI bump + + 07 Mar 2010; Justin Lecher <jlec@gentoo.org> + stride-20011129-r1.ebuild: + Keyworded for prefix-linux, tested by me + + 06 Nov 2009; Markus Dittrich <markusle@gentoo.org> stride-20011129.ebuild, + stride-20011129-r1.ebuild: + Updated outdated homepage (fixes bug #290795). + +*stride-20011129-r1 (06 Nov 2009) + + 06 Nov 2009; Markus Dittrich <markusle@gentoo.org> + +stride-20011129-r1.ebuild, +files/stride-LDFLAGS.patch: + Added patch to respect LDFLAGS (bug #290754). Thanks much to + Justin Lecher <jlec@gentoo.org> for providing it. + + 20 Sep 2007; Santiago M. Mola <coldwind@gentoo.org> + stride-20011129.ebuild: + Change sed separator to :, now it doesn't fail if CC contains a path. + + 22 May 2007; Olivier Fisette <ribosome@gentoo.org> stride-20011129.ebuild: + Updated home page. + + 03 Dec 2006; Steve Dibb <beandog@gentoo.org> stride-20011129.ebuild: + Add ~amd64, bug 147983 + + 01 Oct 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml: + Transfer to sci-biology herd from sci. + + 28 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; + stride-20011129.ebuild: + Keyword ~ppc. + +*stride-20011129 (23 Jul 2006) + + 23 Jul 2006; Markus Dittrich <markusle@gentoo.org> +metadata.xml, + +stride-20011129.ebuild: + Initial import. Many thanks go the the author Dmitrij Frishman + <d.frishman@wzw.tum.de> for allowing us to distribute the source + and for an updated version of the code. diff --git a/sci-biology/t-coffee/ChangeLog b/sci-biology/t-coffee/ChangeLog new file mode 100644 index 00000000..72716245 --- /dev/null +++ b/sci-biology/t-coffee/ChangeLog @@ -0,0 +1,243 @@ +# ChangeLog for sci-biology/t-coffee +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.58 2015/05/05 13:40:54 jlec Exp $ + + 05 May 2015; Justin Lecher <jlec@gentoo.org> -files/8.69-flags.patch, + -files/8.69-test.patch, -t-coffee-8.69.ebuild: + Drop old + + 26 Apr 2015; Pacho Ramos <pacho@gentoo.org> t-coffee-9.03.1318-r1.ebuild: + ppc stable wrt bug #544930 + + 19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> t-coffee-9.03.1318-r1.ebuild: + Stable for x86, wrt bug #544930 + + 08 Apr 2015; Agostino Sarubbo <ago@gentoo.org> t-coffee-9.03.1318-r1.ebuild: + Stable for amd64, wrt bug #544930 + +*t-coffee-11.00 (29 Mar 2015) + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> +t-coffee-11.00.ebuild, + -t-coffee-8.93.ebuild: + Version Bump; drop old + + 09 Feb 2015; Anthony G. Basile <blueness@gentoo.org> t-coffee-8.69.ebuild, + t-coffee-8.93.ebuild, t-coffee-9.03.1318-r1.ebuild: + Keyword ~ppc64, bug #452010. + + 12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 03 Feb 2013; Agostino Sarubbo <ago@gentoo.org> t-coffee-9.03.1318-r1.ebuild: + Add ~ppc, wrt bug #452010 + +*t-coffee-9.03.1318-r1 (14 Jan 2013) + + 14 Jan 2013; Justin Lecher <jlec@gentoo.org> -t-coffee-9.03.1318.ebuild, + +t-coffee-9.03.1318-r1.ebuild, metadata.xml: + Don't build TMalign, but depend on sci-chemistry/tm-align; fixes #451802 and + #451804 + +*t-coffee-9.03.1318 (11 Dec 2012) + + 11 Dec 2012; Justin Lecher <jlec@gentoo.org> t-coffee-8.69.ebuild, + t-coffee-8.93.ebuild, +t-coffee-9.03.1318.ebuild, + +files/t-coffee-9.03.1318-flags.patch: + Version Bump + + 15 Oct 2010; Justin Lecher <jlec@gentoo.org> -t-coffee-5.65.ebuild, + -t-coffee-8.14.ebuild: + Clean old + + 15 Oct 2010; Brent Baude <ranger@gentoo.org> t-coffee-8.69.ebuild: + stable ppc, bug 339575 + + 10 Oct 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org> t-coffee-8.69.ebuild: + x86 stable wrt bug #339575 + + 04 Oct 2010; Markos Chandras <hwoarang@gentoo.org> t-coffee-8.69.ebuild: + Stable on amd64 wrt bug #339575 + + 03 Oct 2010; Justin Lecher <jlec@gentoo.org> t-coffee-5.65.ebuild, + -t-coffee-7.54.ebuild: + QA + +*t-coffee-8.93 (03 Oct 2010) + + 03 Oct 2010; Justin Lecher <jlec@gentoo.org> +t-coffee-8.93.ebuild: + Version Bump, 338199 + + 18 Jun 2010; Justin Lecher <jlec@gentoo.org> t-coffee-8.69.ebuild: + Fix installation, #324307 + +*t-coffee-8.69 (15 Jun 2010) + + 15 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/8.69-flags.patch, + +t-coffee-8.69.ebuild, +files/8.69-test.patch: + Version bump, included test, respecting LDFLAGS and keyworded for linux + prefix + + 03 Jan 2010; Pacho Ramos <pacho@gentoo.org> t-coffee-8.14.ebuild: + amd64 stable, bug 298765 + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> t-coffee-8.14.ebuild: + stable x86, bug 298765 + + 24 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> -t-coffee-5.31.ebuild, + -t-coffee-6.82.ebuild: + Drop old versions + +*t-coffee-8.14 (24 Nov 2009) + + 24 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> metadata.xml, + +t-coffee-8.14.ebuild: + Version bump, assume maintainership + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + +*t-coffee-7.54 (01 Mar 2009) + + 01 Mar 2009; Patrick Lauer <patrick@gentoo.org> +t-coffee-7.54.ebuild: + Bump to 7.54. Closes #258081. + +*t-coffee-6.82 (06 Sep 2008) + + 06 Sep 2008; Markus Dittrich <markusle@gentoo.org> -t-coffee-4.96.ebuild, + -t-coffee-5.05.ebuild, +t-coffee-6.82.ebuild: + Version bump and removed old ebuilds (fixes bug #232323). According + to the website and docs, t-coffee is now released under the GPL-2, + hence changed the license info and uploaded the tarball to our + mirrors. + + 14 Jul 2008; nixnut <nixnut@gentoo.org> t-coffee-5.65.ebuild: + Stable on ppc wrt bug 221165 + + 08 Jul 2008; Christian Faulhammer <opfer@gentoo.org> t-coffee-5.65.ebuild: + stable x86, bug 221165 + + 06 Jul 2008; Olivier Fisette <ribosome@gentoo.org> t-coffee-5.65.ebuild: + Stable on amd64. + + 27 May 2008; Jeff Gardner <je_fro@gentoo.org> Manifest: + Fix Manifest for bug #223717 + +*t-coffee-5.65 (14 Apr 2008) + + 14 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>; + +t-coffee-5.65.ebuild: + Bump. + + 17 Feb 2008; Christian Faulhammer <opfer@gentoo.org> t-coffee-5.31.ebuild: + stable x86/amd64, bug 208416 + + 15 Feb 2008; nixnut <nixnut@gentoo.org> t-coffee-5.31.ebuild: + Stable on ppc wrt bug 208416 + + 31 Dec 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog: + Fixing my email address. + + 08 Dec 2007; <je_fro@gentoo.org> t-coffee-5.31.ebuild: + Adding ~amd64 + +*t-coffee-5.31 (07 Dec 2007) + + 07 Dec 2007; Jeff Gardner <je_fro@gentoo.org> +t-coffee-5.31.ebuild: + Latest version - thanks to Martin Mokrejs on bug #201495 + + 02 Jul 2007; Piotr Jaroszyński <peper@gentoo.org> t-coffee-4.96.ebuild, + t-coffee-5.05.ebuild: + (QA) RESTRICT clean up. + + 01 Jul 2007; Olivier Fisette <ribosome@gentoo.org> -t-coffee-3.84.ebuild: + Removed old version (sources are no longer available). There is no stable + PPC version any longer (see bug #179327). + + 22 May 2007; Christian Faulhammer <opfer@gentoo.org> t-coffee-4.96.ebuild: + x86 stable, bug 179327 + +*t-coffee-5.05 (21 May 2007) + + 21 May 2007; Olivier Fisette <ribosome@gentoo.org> -t-coffee-4.45.ebuild, + +t-coffee-5.05.ebuild: + New upstream version (5.05). Removed 4.45 as sources are no longer available. + +*t-coffee-4.96 (09 Mar 2007) + + 09 Mar 2007; Olivier Fisette <ribosome@gentoo.org> +t-coffee-4.96.ebuild: + New upstream version. + +*t-coffee-4.45 (13 Sep 2006) + + 13 Sep 2006; Olivier Fisette <ribosome@gentoo.org> +t-coffee-4.45.ebuild: + New upstream version. + + 09 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; t-coffee-3.84.ebuild: + x86/ppc stable. + + 16 Mar 2006; Olivier Fisette <ribosome@gentoo.org> -t-coffee-2.66.ebuild, + -t-coffee-3.27.ebuild, t-coffee-3.84.ebuild: + Add fno-unit-at-a-time when using GCC 3.4. Removed old versions. + +*t-coffee-3.84 (07 Mar 2006) + + 07 Mar 2006; Donnie Berkholz <spyderous@gentoo.org>; + +t-coffee-3.84.ebuild: + Bump. + + 08 Dec 2005; Olivier Fisette <ribosome@gentoo.org> -t-coffee-3.18.ebuild: + Pruning old version. + + 08 Dec 2005; Olivier Fisette <ribosome@gentoo.org> t-coffee-3.27.ebuild: + Added a warning regarding an internal compiler error (see bug #114745). + +*t-coffee-3.27 (08 Dec 2005) + + 08 Dec 2005; Olivier Fisette <ribosome@gentoo.org> +t-coffee-3.27.ebuild: + New version. + +*t-coffee-3.18 (19 Oct 2005) + + 19 Oct 2005; Olivier Fisette <ribosome@gentoo.org> +t-coffee-3.18.ebuild: + New version. + + 17 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -t-coffee-2.50.ebuild: + Pruning old version. + + 17 Oct 2005; Joseph Jezak <josejx@gentoo.org> t-coffee-2.66.ebuild: + Marked ppc stable for bug #108340. + + 13 Oct 2005; Mark Loeser <halcy0n@gentoo.org> t-coffee-2.66.ebuild: + Stable on x86 + + 08 Aug 2005; David Holm <dholm@gentoo.org> t-coffee-2.66.ebuild: + Added to ~ppc. + +*t-coffee-2.66 (07 Aug 2005) + + 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> -t-coffee-2.26.ebuild, + t-coffee-2.50.ebuild, +t-coffee-2.66.ebuild: + New version. Added 2.50 to x86. Removed old version. + +*t-coffee-2.50 (12 May 2005) + + 12 May 2005; Olivier Fisette <ribosome@gentoo.org> -t-coffee-2.03.ebuild, + t-coffee-2.26.ebuild, +t-coffee-2.50.ebuild: + Removed obsolete version. + +*t-coffee-2.50 (12 May 2005) + + 12 May 2005; Olivier Fisette <ribosome@gentoo.org> t-coffee-2.26.ebuild, + +t-coffee-2.50.ebuild: + New version: 2.50. Added 2.26 to x86. + +*t-coffee-2.26 (30 Mar 2005) + + 30 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +t-coffee-2.26.ebuild: + New version. + +*t-coffee-2.03 (03 Mar 2005) + + 03 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +t-coffee-2.03.ebuild: + Initial import. diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog new file mode 100644 index 00000000..a262a0b4 --- /dev/null +++ b/sci-biology/tophat/ChangeLog @@ -0,0 +1,69 @@ +# ChangeLog for sci-biology/tophat +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.14 2015/04/07 14:35:24 jlec Exp $ + + 17 Oct 2014; Sergey Popov <pinkbyte@gentoo.org> tophat-1.0.12.ebuild: + Non-maintainer commit: fix building, approved by Justin Lecher + +*tophat-2.0.9 (06 Mar 2014) + + 06 Mar 2014; Justin Lecher <jlec@gentoo.org> +tophat-2.0.9.ebuild, + +files/tophat-2.0.9-flags.patch: + Version Bump, #502532; thanks José María Fernández González for the new + ebuild + +*tophat-2.0.8 (13 Mar 2013) + + 13 Mar 2013; Justin Lecher <jlec@gentoo.org> +tophat-2.0.8.ebuild, + +files/tophat-2.0.8-flags.patch: + Version Bump; unbundle sci-biology/seqan + + 12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*tophat-2.0.2 (19 Jul 2012) + + 19 Jul 2012; Justin Lecher <jlec@gentoo.org> tophat-2.0.0.ebuild, + +tophat-2.0.2.ebuild, +files/tophat-2.0.2-flags.patch, metadata.xml: + Version Bump; do parallel builds; handle debug build + + 25 Apr 2012; Justin Lecher <jlec@gentoo.org> tophat-1.0.12.ebuild, + tophat-1.4.1.ebuild, tophat-2.0.0.ebuild: + Drop unnessecary die + +*tophat-2.0.0 (15 Apr 2012) + + 15 Apr 2012; Andrey Kislyuk <weaver@gentoo.org> -tophat-1.3.3.ebuild, + +tophat-2.0.0.ebuild: + version bump + +*tophat-1.4.1 (04 Feb 2012) +*tophat-1.3.3 (04 Feb 2012) + + 04 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> -tophat-1.3.2.ebuild, + +tophat-1.3.3.ebuild, +tophat-1.4.1.ebuild: + version bump + + 04 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> tophat-1.3.2.ebuild: + filter as-needed + +*tophat-1.3.2 (26 Sep 2011) + + 26 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +tophat-1.3.2.ebuild: + Version bump + + 05 Apr 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org> tophat-1.0.12.ebuild: + x86 stable wrt bug #311829 + + 29 Mar 2010; Pacho Ramos <pacho@gentoo.org> tophat-1.0.12.ebuild: + amd64 stable, bug 311829 + + 07 Dec 2009; Andrey Kislyuk <weaver@gentoo.org> tophat-1.0.12.ebuild: + Fix x86 compile issue. Thanks to Fabian Groffen. + +*tophat-1.0.12 (07 Dec 2009) + + 07 Dec 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +tophat-1.0.12.ebuild: + Import from Science overlay and version bump. Thanks to Philippe Veber. + diff --git a/sci-biology/transfac/ChangeLog b/sci-biology/transfac/ChangeLog new file mode 100644 index 00000000..72b3b4c8 --- /dev/null +++ b/sci-biology/transfac/ChangeLog @@ -0,0 +1,68 @@ +# ChangeLog for sci-biology/transfac +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/transfac/ChangeLog,v 1.17 2011/08/09 15:36:17 xarthisius Exp $ + + 09 Aug 2011; Kacper Kowalik <xarthisius@gentoo.org> transfac-3.2.ebuild: + ppc64 keyword dropped + + 09 Mar 2011; Raúl Porcel <armin76@gentoo.org> transfac-3.2.ebuild: + Drop sparc keywords + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> transfac-3.2.ebuild: + Transfer Prefix keywords + + 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> transfac-3.2.ebuild: + Dropped ppc-macos, see you in prefix. + + 18 Aug 2006; Jason Wever <weeve@gentoo.org> transfac-3.2.ebuild: + Added ~sparc keyword wrt bug #144241. + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> transfac-3.2.ebuild: + Ebuild clean-up. + + 19 Nov 2005; Simon Stelling <blubb@gentoo.org> transfac-3.2.ebuild: + stable on amd64 + + 04 Sep 2005; Simon Stelling <blubb@gentoo.org> transfac-3.2.ebuild: + added ~amd64 keyword + + 02 May 2005; Michael Hanselmann <hansmi@gentoo.org> transfac-3.2.ebuild: + Stable on ppc. + + 05 Mar 2005; Markus Rothe <corsair@gentoo.org> transfac-3.2.ebuild: + Stable on ppc64 + + 22 Feb 2005; Olivier Fisette <ribosome@gentoo.org> transfac-3.2.ebuild: + Added support for the "emboss" and "minimal" "USE" flags. + + 14 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> transfac-3.2.ebuild: + Stable ppc-macos. + + 01 Jan 2005; Markus Rothe <corsair@gentoo.org> transfac-3.2.ebuild: + Added ~ppc64 to KEYWORDS + + 01 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> transface-3.2.ebuild: + Unstable ppc-macos. + +*transfac-3.2 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +transfac-3.2.ebuild: + Moved from app-sci/transfac to sci-biology/transfac. + + 10 Aug 2004; Olivier Fisette <ribosome@gentoo.org> transfac-3.2.ebuild: + Added to x86. + + 26 Jun 2004; David Holm <dholm@gentoo.org> transfac-3.2.ebuild: + Added to ~ppc. + +*transfac-3.2 (24 Jun 2004) + + 24 Jun 2004; Olivier Fisette <ribosome@gentoo.org> + transfac-3.2.ebuild, metadata.xml : + Initial import. Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>. + Reference: Gentoo Bugzilla, bug #54327 + diff --git a/sci-biology/tree-puzzle/ChangeLog b/sci-biology/tree-puzzle/ChangeLog new file mode 100644 index 00000000..34e72f3c --- /dev/null +++ b/sci-biology/tree-puzzle/ChangeLog @@ -0,0 +1,93 @@ +# ChangeLog for sci-biology/tree-puzzle +# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/tree-puzzle/ChangeLog,v 1.19 2012/08/01 15:41:29 jlec Exp $ + + 01 Aug 2012; Justin Lecher <jlec@gentoo.org> tree-puzzle-5.2.ebuild, + +files/tree-puzzle-impl-dec.patch: + Mask stupid test, which fails due to precision reached depending on + optimization used at compile time, #297646; fix move to EAPI=4, #429354 + + 24 May 2012; Justin Lecher <jlec@gentoo.org> tree-puzzle-5.2.ebuild: + Corrected dep from sys-cluster/lam-mpi to virtual/mpi, #415765 + + 26 Apr 2012; Justin Lecher <jlec@gentoo.org> tree-puzzle-5.2.ebuild: + Add missing quotes + + 26 Apr 2012; Justin Lecher <jlec@gentoo.org> tree-puzzle-5.2.ebuild: + Move to EAPI=4 + + 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> + tree-puzzle-5.2.ebuild: + Transfer Prefix keywords + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 07 Feb 2008; Fabian Groffen <grobian@gentoo.org> tree-puzzle-5.2.ebuild: + Dropped ppc-macos keyword, see you in prefix + + 01 Jun 2007; nixnut <nixnut@gentoo.org> tree-puzzle-5.2.ebuild: + Added ~ppc wrt bug 179645 + + 21 May 2007; Olivier Fisette <ribosome@gentoo.org> + -tree-puzzle-5.1.ebuild: + Pruned old version. + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 04 Jan 2006; Olivier Fisette <ribosome@gentoo.org> tree-puzzle-5.2.ebuild: + Do not depend on "virtual/libc" (package not in system target). + + 07 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> tree-puzzle-5.1.ebuild, + tree-puzzle-5.2.ebuild: + Stripped -fast from CLAGS as it causes *too* accurate floating point arithmetic + + 03 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> tree-puzzle-5.2.ebuild: + Unstable ppc-macos + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> tree-puzzle-5.2.ebuild: + Ebuild cleanup. + + 18 Jan 2005; Jan Brinkmann <luckyduck@gentoo.org> tree-puzzle-5.2.ebuild: + added ~amd64 to KEYWORDS. fixes bug #78237 + + 14 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> tree-puzzle-5.1.ebuild: + Stable ppc-macos. + + 02 Jan 2005; Olivier Fisette <ribosome@gentoo.org> tree-puzzle-5.2.ebuild: + Use the toolchain-funcs rather than the gcc eclass. + +*tree-puzzle-5.2 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +tree-puzzle-5.1.ebuild, +tree-puzzle-5.2.ebuild: + Moved from app-sci/tree-puzzle to sci-biology/tree-puzzle. + + 14 Oct 2004; Hasan Khalil <gongloo@gentoo.org> tree-puzzle-5.1.ebuild: + Keyworded ~ppc-macos. + + 14 Oct 2004; Olivier Fisette <ribosome@gentoo.org> tree-puzzle-5.1.ebuild, + tree-puzzle-5.2.ebuild: + Added to x86. Use gcc-getCC from gcc.eclass rather than ${CC}. + + 23 Jul 2004; Jon Hood <squinky86@gentoo.org> tree-puzzle-5.2.ebuild: + Change virtual/glibc -> virtual/libc. + +*tree-puzzle-5.2 (20 Jul 2004) + + 20 Jul 2004; Olivier Fisette <ribosome@gentoo.org> + tree-puzzle-5.2.ebuild, metadata.xml: + New version and an updated ebuild supporting the compilation of the + parallelized version of the program (ppuzzle). + Set myself as maintainer. + +*tree-puzzle-5.1 (08 Jun 2004) + + 08 Jun 2004; David Holm <dholm@gentoo.org> tree-puzzle-5.1.ebuild: + Added to ~ppc. + + 17 May 2004; Patrick Kursawe <phosphan@gentoo.org> : + Initial import, ebuild by Olivier Fisette <olivier.fisette@sympatico.ca> in + bug #45938 + diff --git a/sci-biology/treeviewx/ChangeLog b/sci-biology/treeviewx/ChangeLog new file mode 100644 index 00000000..6b3df1df --- /dev/null +++ b/sci-biology/treeviewx/ChangeLog @@ -0,0 +1,117 @@ +# ChangeLog for sci-biology/treeviewx +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/treeviewx/ChangeLog,v 1.25 2010/10/26 16:18:39 dirtyepic Exp $ + + 26 Oct 2010; Ryan Hill <dirtyepic@gentoo.org> -treeviewx-0.5.1.ebuild, + -treeviewx-0.5.1-r1.ebuild: + Remove old. + + 12 Oct 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org> + treeviewx-0.5.1-r2.ebuild: + x86 stable wrt bug #340471 + + 11 Oct 2010; Markos Chandras <hwoarang@gentoo.org> + treeviewx-0.5.1-r2.ebuild: + Stable on amd64 wrt bug #340471 + +*treeviewx-0.5.1-r2 (06 Sep 2010) + + 06 Sep 2010; Ryan Hill <dirtyepic@gentoo.org> +treeviewx-0.5.1-r2.ebuild, + +files/treeviewx-0.5.1-wx28.patch: + Migrate to wxGTK-2.8 with patch from Debian. Use EAPI 2. Simplify + wxwidgets handling. + + 18 Feb 2010; Ryan Hill <dirtyepic@gentoo.org> treeviewx-0.5.1.ebuild, + treeviewx-0.5.1-r1.ebuild: + Remove unnecessary built_with_use check. + + 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Giving up maintainership of this package. + + 05 Nov 2008; Olivier Fisette <ribosome@gentoo.org> + treeviewx-0.5.1-r1.ebuild: + Stable on x86 for GCC 4.3 (bug #245699). + + 17 Jun 2008; Markus Dittrich <markusle@gentoo.org> + files/treeviewx-0.5.1-gcc4.3.patch: + Slightly modified gcc-4.3 patch since it got mangled by cvs during commit. + +*treeviewx-0.5.1-r1 (16 Jun 2008) + + 16 Jun 2008; Markus Dittrich <markusle@gentoo.org> + +files/treeviewx-0.5.1-gcc4.3.patch, +treeviewx-0.5.1-r1.ebuild: + Added new revision with fix for gcc-4.3 compile issues (bug #227245). + Thanks much to Marek Miller <mlm@shells.pl> for his patch. + + 30 Apr 2007; Ryan Hill <dirtyepic@gentoo.org> treeviewx-0.5.1.ebuild: + Use wxwidgets.eclass + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 01 Apr 2006; Scott Stoddard <deltacow@gentoo.org> treeviewx-0.5.1.ebuild: + Added ~amd64. (bug #128237) + + 13 Dec 2005; Olivier Fisette <ribosome@gentoo.org> -treeviewx-0.5.ebuild, + treeviewx-0.5.1.ebuild: + Added 0.5.1 to x86. Removed old version. (Small change to propagate the + fix for bug #112927 to the stable branch.) + + 19 Nov 2005; Olivier Fisette <ribosome@gentoo.org> treeviewx-0.5.1.ebuild: + Added check for wxGTK built with X (fixes bug #112927). + +*treeviewx-0.5.1 (01 Oct 2005) + + 01 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + +files/treeviewx-wxt.patch, +treeviewx-0.5.1.ebuild: + New version, along with a patch to compile against wxGTK-2.6. The new + version has a configure check for wxGTK-svg (fixes bug #90181). + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> + -treeviewx-0.4-r1.ebuild, treeviewx-0.5.ebuild: + Removed obsolete version. Added 0.5 to x86. + +*treeviewx-0.5 (30 Mar 2005) + + 30 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +treeviewx-0.5.ebuild: + New version. + + 01 Mar 2005; Olivier Fisette <ribosome@gentoo.org> -treeviewx-0.4.ebuild: + Keep only the patched version (solves bug #82455). + +*treeviewx-0.4-r1 (27 Feb 2005) + + 27 Feb 2005; Olivier Fisette <ribosome@gentoo.org> + +files/treeviewx-gcc-3.4.patch, +treeviewx-0.4-r1.ebuild: + GCC 3.4 fixes. This might fix bug #82455. + + 22 Feb 2005; Olivier Fisette <ribosome@gentoo.org> + -files/nodeiterator.h.patch, treeviewx-0.4.ebuild: + Removed useless patch. + + 20 Feb 2005; Olivier Fisette <ribosome@gentoo.org> + files/nodeiterator.h.patch: + Fixed dumb patch mistake. + + 19 Feb 2005; Olivier Fisette <ribosome@gentoo.org> + +files/nodeiterator.h.patch, treeviewx-0.4.ebuild: + Added a patch which might solve bug #82455. + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> treeviewx-0.4.ebuild: + Ebuild cleanup. + +*treeviewx-0.4 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +treeviewx-0.4.ebuild: + Moved from app-sci/treeviewx to sci-biology/treeviewx. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> treeviewx-0.4.ebuild: + Added to x86. + +*treeviewx-0.4 (8 Aug 2004) + + 8 Aug 2004; Olivier Fisette <ribosome@gentoo.org> + treeviewx-0.4.ebuild, ChangeLog, metadata.xml: + Initial import (suggested by Koen Deforche <koen.deforche@uz.kuleuven.ac.be> + in bug #51990). diff --git a/sci-biology/trf/ChangeLog b/sci-biology/trf/ChangeLog new file mode 100644 index 00000000..5abe4805 --- /dev/null +++ b/sci-biology/trf/ChangeLog @@ -0,0 +1,40 @@ +# ChangeLog for sci-biology/trf +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/trf/ChangeLog,v 1.9 2014/04/17 21:08:54 ulm Exp $ + + 17 Apr 2014; Ulrich Müller <ulm@gentoo.org> trf-4.04.ebuild: + Fix LICENSE, add mirror and bindist restrictions, update SRC_URI, bug 470778. + + 12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 04 Mar 2013; Justin Lecher <jlec@gentoo.org> trf-4.04.ebuild, metadata.xml: + What happens in /opt, stays in /opt + + 06 Oct 2012; Justin Lecher <jlec@gentoo.org> -trf-4.0.ebuild, + trf-4.04.ebuild: + Drop old; move to EAPI=4; use QA_PREBUILT, #436718 + + 05 Apr 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org> trf-4.04.ebuild: + x86 stable wrt bug #311833 + + 29 Mar 2010; Pacho Ramos <pacho@gentoo.org> trf-4.04.ebuild: + amd64 stable, bug 311833 + +*trf-4.04 (29 Jan 2010) + + 29 Jan 2010; Andrey Kislyuk <weaver@gentoo.org> +trf-4.04.ebuild: + Version bump + + 23 Apr 2009; Markus Meier <maekke@gentoo.org> trf-4.0: + amd64/x86 stable, bug #266871 + +*trf-4.0 (26 Feb 2009) + + 26 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +trf-4.0.ebuild: + Import from Science overlay + + 19 Feb 2009; weaver <weaver@gentoo.org> ChangeLog: + New package sci-biology/trf, ebuild written by me + diff --git a/sci-biology/trnascan-se/ChangeLog b/sci-biology/trnascan-se/ChangeLog new file mode 100644 index 00000000..e65627ee --- /dev/null +++ b/sci-biology/trnascan-se/ChangeLog @@ -0,0 +1,67 @@ +# ChangeLog for sci-biology/trnascan-se +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/trnascan-se/ChangeLog,v 1.15 2015/04/07 14:35:30 jlec Exp $ + +*trnascan-se-1.31 (08 Jan 2015) + + 08 Jan 2015; Justin Lecher <jlec@gentoo.org> -trnascan-se-1.23-r1.ebuild, + +trnascan-se-1.31.ebuild, +files/trnascan-se-1.31-ldflags.patch, + metadata.xml: + Version Bump, #532460 + + 16 Jul 2010; Markos Chandras <hwoarang@gentoo.org> + trnascan-se-1.23-r2.ebuild: + Stable on amd64 wrt bug #328435 + + 16 Jul 2010; Christian Faulhammer <fauli@gentoo.org> + trnascan-se-1.23-r2.ebuild: + stable x86, bug 328435 + +*trnascan-se-1.23-r2 (25 Jun 2010) + + 25 Jun 2010; Justin Lecher <jlec@gentoo.org> +trnascan-se-1.23-r2.ebuild, + +files/trnascan-se-1.23-ldflags.patch: + Fixed test, #318641; multilib, LDFLAGS, PREFIX awareness + + 05 Aug 2009; Samuli Suominen <ssuominen@gentoo.org> + trnascan-se-1.23-r1.ebuild, +files/trnascan-se-1.23-glibc-2.10.patch: + Fix building with GLIBC 2.10+ wrt #279574. + + 22 May 2007; Olivier Fisette <ribosome@gentoo.org> + trnascan-se-1.23-r1.ebuild: + Updated home page. + + 15 Mar 2007; Danny van Dyk <kugelfang@gentoo.org> + trnascan-se-1.23-r1.ebuild: + QA: Removed illegal use of ${ROOT}. Bug #168043 + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Stepping down from maintaining this package. + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> + trnascan-se-1.23-r1.ebuild: + Fixed home page URL. + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> + trnascan-se-1.23-r1.ebuild: + Ebuild clean-up. + +*trnascan-se-1.23-r1 (12 Aug 2005) + + 12 Aug 2005; Olivier Fisette <ribosome@gentoo.org> + -trnascan-se-1.23.ebuild, +trnascan-se-1.23-r1.ebuild: + Fixed bug #102258: Broken hard-coded paths. + + 01 Mar 2005; Olivier Fisette <ribosome@gentoo.org> + trnascan-se-1.23.ebuild: + Added to x86. + +*trnascan-se-1.23 (30 Jan 2005) + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +trnascan-se-1.23.ebuild: + Initial import. + diff --git a/sci-biology/uchime/ChangeLog b/sci-biology/uchime/ChangeLog new file mode 100644 index 00000000..f19cc30f --- /dev/null +++ b/sci-biology/uchime/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-biology/uchime +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/uchime/ChangeLog,v 1.2 2015/08/03 12:54:53 ago Exp $ + + 03 Aug 2015; Agostino Sarubbo <ago@gentoo.org> uchime-4.2.40.ebuild: + Stable for amd64, wrt bug #556066 + +*uchime-4.2.40 (14 Aug 2012) + + 14 Aug 2012; Justin Lecher <jlec@gentoo.org> +uchime-4.2.40.ebuild, + +files/CMakeLists.txt, +metadata.xml: + New addition diff --git a/sci-biology/ucsc-genome-browser/ChangeLog b/sci-biology/ucsc-genome-browser/ChangeLog new file mode 100644 index 00000000..e5a7e1a1 --- /dev/null +++ b/sci-biology/ucsc-genome-browser/ChangeLog @@ -0,0 +1,42 @@ +# ChangeLog for sci-biology/ucsc-genome-browser +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ucsc-genome-browser/ChangeLog,v 1.7 2015/04/17 06:21:51 jlec Exp $ + + 17 Apr 2015; Justin Lecher <jlec@gentoo.org> -ucsc-genome-browser-223.ebuild, + ucsc-genome-browser-260.ebuild: + Drop old; bump EAPI + + 12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*ucsc-genome-browser-260 (27 Dec 2011) + + 27 Dec 2011; Justin Lecher <jlec@gentoo.org> +ucsc-genome-browser-260.ebuild, + metadata.xml: + Version Bump, move to EAPI=4, handled static-libs, respect mostly everywhere + LDFALGS + + 24 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> + ucsc-genome-browser-223.ebuild: + Re-add parallel make workaround + +*ucsc-genome-browser-223 (08 Feb 2010) + + 08 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> + -ucsc-genome-browser-221.ebuild, +ucsc-genome-browser-223.ebuild: + Version bump and set SLOT per bug 300736 + +*ucsc-genome-browser-221 (10 Jan 2010) + + 10 Jan 2010; Andrey Kislyuk <weaver@gentoo.org> + -ucsc-genome-browser-217.ebuild, +ucsc-genome-browser-221.ebuild: + Version bump + +*ucsc-genome-browser-217 (28 Oct 2009) + + 28 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +ucsc-genome-browser-217.ebuild: + Import from Science overlay + + 23 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: + New package, bug 155780. Ebuild written by me and dawe <daweonline@gmail.com> diff --git a/sci-biology/unafold/ChangeLog b/sci-biology/unafold/ChangeLog new file mode 100644 index 00000000..1e14f170 --- /dev/null +++ b/sci-biology/unafold/ChangeLog @@ -0,0 +1,19 @@ +# ChangeLog for sci-biology/unafold +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/unafold/ChangeLog,v 1.3 2013/03/12 12:11:48 jlec Exp $ + + 12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*unafold-3.8-r1 (18 Feb 2013) + + 18 Feb 2013; Justin Lecher <jlec@gentoo.org> unafold-3.8.ebuild, + +unafold-3.8-r1.ebuild, metadata.xml: + Fix test, #358053; respect CFLAGS + +*unafold-3.8 (13 Jan 2011) + + 13 Jan 2011; Andrey Kislyuk <weaver@gentoo.org> +unafold-3.8.ebuild, + +metadata.xml: + New package, ebuild written by me + diff --git a/sci-biology/update-blastdb/ChangeLog b/sci-biology/update-blastdb/ChangeLog new file mode 100644 index 00000000..c31b0bef --- /dev/null +++ b/sci-biology/update-blastdb/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for sci-biology/update-blastdb +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/update-blastdb/ChangeLog,v 1.2 2014/05/19 10:32:30 jlec Exp $ + + 19 May 2014; Justin Lecher <jlec@gentoo.org> update-blastdb-12.0.0.ebuild: + Fix typo + +*update-blastdb-12.0.0 (14 May 2014) + + 14 May 2014; Justin Lecher <jlec@gentoo.org> +update-blastdb-12.0.0.ebuild, + +metadata.xml: + New addition, written by me + diff --git a/sci-biology/vaal/ChangeLog b/sci-biology/vaal/ChangeLog new file mode 100644 index 00000000..eda7ae83 --- /dev/null +++ b/sci-biology/vaal/ChangeLog @@ -0,0 +1,79 @@ +# ChangeLog for sci-biology/vaal +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.18 2015/04/07 14:35:35 jlec Exp $ + + 24 Mar 2015; Justin Lecher <jlec@gentoo.org> -vaal-1.6.ebuild: + Drop old + + 24 Mar 2015; Agostino Sarubbo <ago@gentoo.org> vaal-46233.ebuild: + Stable for amd64, wrt bug #543404 + + 15 Mar 2015; Justin Lecher <jlec@gentoo.org> -vaal-42179.ebuild, + -vaal-45166.ebuild: + Drop old + + 12 Nov 2013; Justin Lecher <jlec@gentoo.org> vaal-1.6.ebuild, + vaal-42179.ebuild, vaal-45166.ebuild, vaal-46233.ebuild: + Drop x86 as upstream gives no support and types are not easily fixable, + #458488, #472088 & #488550 + +*vaal-46233 (02 Jun 2013) + + 02 Jun 2013; Justin Lecher <jlec@gentoo.org> +vaal-46233.ebuild: + Version Bump + + 12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*vaal-45166 (20 Feb 2013) + + 20 Feb 2013; Justin Lecher <jlec@gentoo.org> +vaal-45166.ebuild, + metadata.xml: + Version Bump + +*vaal-42179 (25 Jun 2012) + + 25 Jun 2012; Justin Lecher <jlec@gentoo.org> +vaal-42179.ebuild: + Version Bump + + 25 Jun 2012; Justin Lecher <jlec@gentoo.org> -vaal-1.2-r1.ebuild, + vaal-1.6.ebuild, files/vaal-1.6-respect-flags.patch: + Drop old, #309127; Handle openmp, don't install license + + 25 Jun 2012; Kacper Kowalik <xarthisius@gentoo.org> + +files/vaal-1.6-gcc47.patch, files/vaal-1.6-respect-flags.patch, + vaal-1.6.ebuild: + Fix building with gcc-4.7 wrt #423497 by Diego Elio Pettenò + <flameeyes@gentoo.org>, drop -O3 -ggdb from CXXFLAGS + + 11 Feb 2011; Markos Chandras <hwoarang@gentoo.org> vaal-1.6.ebuild: + Stable on amd64 wrt bug #353572 + + 24 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> vaal-1.6.ebuild: + Drop x86 from keywords + +*vaal-1.6 (20 Sep 2010) + + 20 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> +vaal-1.6.ebuild, + +files/vaal-1.6-respect-flags.patch: + Version bump. Addresses boost problems and compilation issues + +*vaal-1.2-r1 (14 Feb 2010) + + 14 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> + +files/vaal-1.2-as-needed.patch, +files/vaal-1.2-respect-flags.patch, + -vaal-1.2.ebuild, +vaal-1.2-r1.ebuild: + Apply patches, fix bug 294738 and move binaries to libexec + + 12 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> vaal-1.2.ebuild: + Remove hardcoded version in SRC_URI + + 12 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> + +files/vaal-1.2-gcc-x86-no-autocast.patch, vaal-1.2.ebuild: + Add patch for bug 279087 + +*vaal-1.2 (07 Jul 2009) + + 07 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +vaal-1.2.ebuild: + New package, ebuild written by me diff --git a/sci-biology/vcftools/ChangeLog b/sci-biology/vcftools/ChangeLog new file mode 100644 index 00000000..85631053 --- /dev/null +++ b/sci-biology/vcftools/ChangeLog @@ -0,0 +1,43 @@ +# ChangeLog for sci-biology/vcftools +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/vcftools/ChangeLog,v 1.9 2015/04/07 14:35:41 jlec Exp $ + + 03 Apr 2015; Andreas K. Huettel <dilfridge@gentoo.org> + -vcftools-0.1.7.ebuild, -vcftools-0.1.8.ebuild, + -files/vcftools-0.1.8-buildsystem.patch: + Drop old + +*vcftools-0.1.12b (03 Apr 2015) + + 03 Apr 2015; Andreas K. Huettel <dilfridge@gentoo.org> + +vcftools-0.1.12b.ebuild, +files/vcftools-0.1.12b-buildsystem.patch: + Version bump, fixing bug 545304 + + 12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 27 Feb 2013; Justin Lecher <jlec@gentoo.org> vcftools-0.1.8.ebuild, + files/vcftools-0.1.8-buildsystem.patch, metadata.xml: + Use PKG_CONFIG instead of generic pkg-config + +*vcftools-0.1.8 (19 Jul 2012) + + 19 Jul 2012; Justin Lecher <jlec@gentoo.org> +vcftools-0.1.8.ebuild, + +files/vcftools-0.1.8-buildsystem.patch: + Version Bump, fix build system + +*vcftools-0.1.7 (02 Jan 2012) + + 02 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> -vcftools-0.1.6.ebuild, + +vcftools-0.1.7.ebuild: + Version bump + + 08 Oct 2011; Andrey Kislyuk <weaver@gentoo.org> vcftools-0.1.6.ebuild: + patch vcftools to set perl libdir properly + +*vcftools-0.1.6 (02 Oct 2011) + + 02 Oct 2011; Andrey Kislyuk <weaver@gentoo.org> +vcftools-0.1.6.ebuild, + +metadata.xml: + New package, ebuild written by me + diff --git a/sci-biology/velvet/ChangeLog b/sci-biology/velvet/ChangeLog new file mode 100644 index 00000000..0315ddd3 --- /dev/null +++ b/sci-biology/velvet/ChangeLog @@ -0,0 +1,97 @@ +# ChangeLog for sci-biology/velvet +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/ChangeLog,v 1.22 2015/04/07 14:35:47 jlec Exp $ + +*velvet-1.2.10 (28 Dec 2013) + + 28 Dec 2013; Justin Lecher <jlec@gentoo.org> +velvet-1.2.10.ebuild: + Import Version Bump from sci overlay, thanks mahn for the ebuild, #495094 + + 12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 21 Dec 2011; Justin Lecher <jlec@gentoo.org> -velvet-0.7.55.ebuild, + -velvet-0.7.62.ebuild: + Cleaned old + + 21 Dec 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> velvet-1.0.18-r1.ebuild: + x86 stable wrt bug #393981 + + 16 Dec 2011; Justin Lecher <jlec@gentoo.org> velvet-1.0.18-r1.ebuild: + Added missing dep on sys-libs/zlib requested by ago, #393981 + + 16 Dec 2011; Agostino Sarubbo <ago@gentoo.org> velvet-1.0.18-r1.ebuild: + Stable for AMD64, wrt bug #393981 + + 16 Dec 2011; Justin Lecher <jlec@gentoo.org> velvet-1.0.18-r1.ebuild: + Do not add O3, move to EAPI=4 + +*velvet-1.0.18-r1 (13 Apr 2011) + + 13 Apr 2011; Kacper Kowalik <xarthisius@gentoo.org> -velvet-1.0.18.ebuild, + +velvet-1.0.18-r1.ebuild, -files/velvet-1.0.18-gentoo.diff, + +files/velvet-1.0.18-gentoo-r1.diff: + Fix building with --as-needed wrt #363479 by Diego Elio Pettenò + <flameeyes@gentoo.org> + +*velvet-1.0.18 (03 Feb 2011) + + 03 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> +velvet-1.0.18.ebuild, + +files/velvet-1.0.18-gentoo.diff: + Version bump + + 20 Jun 2010; Kacper Kowalik <xarthisius@gentoo.org> -velvet-0.7.50.ebuild: + Remove old + + 20 Jun 2010; Kacper Kowalik <xarthisius@gentoo.org> velvet-0.7.62.ebuild, + +files/velvet-0.7.62-gentoo.diff: + Fix parallel build, respect FLAGS, fix --as-needed issues wrt bug 277938. + Thanks Diego for reporting. + +*velvet-0.7.62 (05 May 2010) + + 05 May 2010; Andrey Kislyuk <weaver@gentoo.org> +velvet-0.7.62.ebuild: + Version bump + + 31 Oct 2009; Markus Meier <maekke@gentoo.org> velvet-0.7.55.ebuild: + amd64/x86 stable, bug #290936 + + 19 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> velvet-0.7.55.ebuild: + Use elog + + 19 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> velvet-0.7.55.ebuild: + Add support for passing compile-time variables to build + +*velvet-0.7.55 (19 Sep 2009) + + 19 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> -velvet-0.7.47.ebuild, + +velvet-0.7.55.ebuild: + Version bump, drop old + +*velvet-0.7.50 (20 Aug 2009) + + 20 Aug 2009; Andrey Kislyuk <weaver@gentoo.org> -velvet-0.7.31.ebuild, + -velvet-0.7.34.ebuild, -velvet-0.7.42.ebuild, +velvet-0.7.50.ebuild: + Version bump, remove old + +*velvet-0.7.47 (27 Jul 2009) + + 27 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +velvet-0.7.47.ebuild: + Version bump + +*velvet-0.7.42 (07 Jul 2009) + + 07 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +velvet-0.7.42.ebuild: + Version bump + +*velvet-0.7.34 (21 Jun 2009) + + 21 Jun 2009; Andrey Kislyuk <weaver@gentoo.org> +velvet-0.7.34.ebuild: + Version bump + +*velvet-0.7.31 (05 Jun 2009) + + 05 Jun 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +velvet-0.7.31.ebuild: + New package, ebuild written by me + diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog new file mode 100644 index 00000000..1c08cb4c --- /dev/null +++ b/sci-biology/vienna-rna/ChangeLog @@ -0,0 +1,243 @@ +# ChangeLog for sci-biology/vienna-rna +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.55 2014/11/16 20:29:21 dilfridge Exp $ + + 16 Nov 2014; Andreas K. Huettel <dilfridge@gentoo.org> + vienna-rna-2.1.1.ebuild, vienna-rna-2.1.8.ebuild: + Replace fixlocalpod with perl_delete_localpod + +*vienna-rna-2.1.8 (15 Sep 2014) + + 15 Sep 2014; Justin Lecher <jlec@gentoo.org> +vienna-rna-2.1.8.ebuild, + +files/vienna-rna-2.1.8-bindir.patch: + Version Bump, #522850 + + 29 Aug 2014; Mikle Kolyada <zlogene@gentoo.org> -vienna-rna-1.8.5.ebuild, + vienna-rna-2.1.1.ebuild: + ppc stable wrt bug #520776; Drop old. + + 29 Aug 2014; Sergey Popov <pinkbyte@gentoo.org> vienna-rna-2.1.1.ebuild: + Stable on amd64 and x86, wrt bug #520776 + + 29 Aug 2014; Sergey Popov <pinkbyte@gentoo.org> vienna-rna-2.1.1.ebuild: + QA: move AUTOTOOLS_IN_SOURCE_BUILD definition beforce inheriting autotools + eclass, drop obsolete python 2.6 support + + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> vienna-rna-1.8.5.ebuild: + Punt base.eclass + + 05 Sep 2013; Michał Górny <mgorny@gentoo.org> vienna-rna-2.1.1.ebuild: + Clean up PYTHON_COMPAT from old implementations. + + 29 May 2013; Justin Lecher <jlec@gentoo.org> vienna-rna-2.1.1.ebuild: + Fix usage of new python r1 eclasses (missing PYTHON_REQUIRED_USE) + +*vienna-rna-2.1.1 (13 Feb 2013) + + 13 Feb 2013; Justin Lecher <jlec@gentoo.org> +vienna-rna-2.1.1.ebuild, + +files/vienna-rna-2.1.1-bindir.patch, + +files/vienna-rna-2.1.1-impl-decl.patch, +files/vienna-rna-2.1.1-prll.patch, + +files/vienna-rna-2.1.1-setup.py: + Version Bump; move to EAPI=5, new python eclasses; autotools-utils + + 31 Jan 2013; Justin Lecher <jlec@gentoo.org> vienna-rna-1.8.5.ebuild, + metadata.xml: + Only call distutils phase functions with USE=python, #422899 + + 10 Jul 2012; Justin Lecher <jlec@gentoo.org> -vienna-rna-1.8.4-r1.ebuild, + -vienna-rna-1.8.4-r2.ebuild, metadata.xml: + Cleaned old + + 10 Jul 2012; Brent Baude <ranger@gentoo.org> vienna-rna-1.8.5.ebuild: + Marking vienna-rna-1.8.5 ppc for bug 393867 + + 26 Feb 2012; Patrick Lauer <patrick@gentoo.org> vienna-rna-1.8.4-r1.ebuild, + vienna-rna-1.8.5.ebuild: + Restricting jython + + 21 Dec 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> vienna-rna-1.8.5.ebuild: + x86 stable wrt bug #393867 + + 16 Dec 2011; Agostino Sarubbo <ago@gentoo.org> vienna-rna-1.8.5.ebuild: + Stable for AMD64, wrt bug #393867 + + 16 Dec 2011; Justin Lecher <jlec@gentoo.org> vienna-rna-1.8.5.ebuild: + Add missing dep on dev-lang/swig, #394933 + + 16 Dec 2011; Justin Lecher <jlec@gentoo.org> vienna-rna-1.8.5.ebuild: + Handle static-libs + + 28 Jun 2011; Brent Baude <ranger@gentoo.org> vienna-rna-1.8.4-r1.ebuild: + Marking vienna-rna-1.8.4-r1 ppc for bug 325459 + + 03 May 2011; Justin Lecher <jlec@gentoo.org> vienna-rna-1.8.5.ebuild, + +files/vienna-rna-1.8.5-setup.py: + Added python support, #365793 + + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> vienna-rna-1.8.4-r1.ebuild, + vienna-rna-1.8.4-r2.ebuild, vienna-rna-1.8.5.ebuild: + Install Perl modules into vendor-dir, #349772 + +*vienna-rna-1.8.5 (20 Mar 2011) + + 20 Mar 2011; Justin Lecher <jlec@gentoo.org> vienna-rna-1.8.4-r1.ebuild, + vienna-rna-1.8.4-r2.ebuild, +vienna-rna-1.8.5.ebuild: + Version Bump + +*vienna-rna-1.8.4-r2 (15 Oct 2010) + + 15 Oct 2010; Kacper Kowalik <xarthisius@gentoo.org> + -files/vienna-rna-1.7.2-disable-gd.patch, + -files/vienna-rna-1.7.2-gcc4.3.patch, + -files/vienna-rna-1.7.2-gcc4.4.patch, -vienna-rna-1.8.4.ebuild, + +vienna-rna-1.8.4-r2.ebuild, +files/vienna-rna-1.8.4-implicits.patch, + +files/vienna-rna-1.8.4-overflows.patch: + Fix buffer overflows wrt bug 341089. Thanks to Diego for the report. Fix + implicit function declarations. Drop old. + + 15 Jul 2010; Christian Faulhammer <fauli@gentoo.org> + vienna-rna-1.8.4-r1.ebuild: + stable x86, bug 325459 + + 26 Jun 2010; Christoph Mende <angelos@gentoo.org> + vienna-rna-1.8.4-r1.ebuild: + Stable on amd64 wrt bug #325459 + +*vienna-rna-1.8.4-r1 (25 Jun 2010) + + 25 Jun 2010; Justin Lecher <jlec@gentoo.org> -vienna-rna-1.7.2.ebuild, + -vienna-rna-1.8.3.ebuild, +vienna-rna-1.8.4-r1.ebuild, + +files/vienna-rna-1.8.4-bindir.patch: + Install ELFs in correct place, #300012 + + 03 Apr 2010; Justin Lecher <jlec@gentoo.org> vienna-rna-1.8.4.ebuild, + +files/vienna-rna-1.8.4-jobserver-fix.patch: + jobserver fix, #304117, thanks Myckel + + 09 Feb 2010; Pacho Ramos <pacho@gentoo.org> vienna-rna-1.8.4.ebuild: + amd64 stable, bug 298769 + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> + vienna-rna-1.8.4.ebuild: + stable x86, bug 298769 + +*vienna-rna-1.8.4 (13 Nov 2009) + + 13 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> +vienna-rna-1.8.4.ebuild: + Version bump + + 02 Nov 2009; Markus Meier <maekke@gentoo.org> vienna-rna-1.8.3.ebuild: + amd64/x86 stable, bug #290926 + + 31 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> vienna-rna-1.8.3.ebuild: + Fix linking failure on x86 + + 10 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> vienna-rna-1.8.3.ebuild: + Fix gcc-4.4 patching, bug 284539 + +*vienna-rna-1.8.3 (10 Sep 2009) + + 10 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> + +files/vienna-rna-1.8.3-gcc4.3.patch, +vienna-rna-1.8.3.ebuild: + Version bump and cleanup + + 30 Jul 2009; Samuli Suominen <ssuominen@gentoo.org> + vienna-rna-1.7.2.ebuild, +files/vienna-rna-1.7.2-gcc4.4.patch: + Fix building with GCC 4.4 and GLIBC 2.10+ wrt #274044. Rename getline to + v_getline. Missing include. + + 09 Oct 2008; Markus Dittrich <markusle@gentoo.org> + vienna-rna-1.7.2.ebuild: + Remove perlocal.pod file to avoid file collisions (see bug #240358). + + 06 Oct 2008; Markus Dittrich <markusle@gentoo.org> + +files/vienna-rna-1.7.2-LDFLAGS.patch, + +files/vienna-rna-1.7.2-disable-gd.patch, vienna-rna-1.7.2.ebuild: + Fixed ignored LDFLAGS issues and bogus detection of GD support. Also + enabled the tests that come with the package. + +*vienna-rna-1.7.2 (28 Aug 2008) + + 28 Aug 2008; Markus Dittrich <markusle@gentoo.org> + +files/vienna-rna-1.7.2-gcc4.3.patch, -vienna-rna-1.6.1.ebuild, + -vienna-rna-1.6.5.ebuild, +vienna-rna-1.7.2.ebuild: + Version bump and removed old ebuilds (fixes bug #235943). Thanks much to + Chad A. Simmons <chad.simmons@member.fsf.org> for his ebuild and patches. + + 06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml: + Add USE flag description to metadata wrt GLEP 56. + +*vienna-rna-1.7.0 (01 May 2008) + + 01 May 2008; Markus Dittrich <markusle@gentoo.org> + +vienna-rna-1.7.0.ebuild: + Version bump. + +*vienna-rna-1.6.5 (24 Nov 2007) + + 24 Nov 2007; Markus Dittrich <markusle@gentoo.org> + +files/vienna-rna-1.6.5-c-fixes.patch, +vienna-rna-1.6.5.ebuild: + Version bump (fixes bug #191882). + + 29 Apr 2007; Jeff Gardner <je_fro@gentoo.org> vienna-rna-1.6.1.ebuild: + Adding ~amd64. + + 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: + Redigest for Manifest2 + + 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> -vienna-rna-1.6.ebuild: + Pruned old version. + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Stepping down from maintaining this package. + +*vienna-rna-1.6.1 (14 Sep 2006) + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> + +vienna-rna-1.6.1.ebuild: + New upstream version. + +*vienna-rna-1.6 (03 Feb 2006) + + 03 Feb 2006; Olivier Fisette <ribosome@gentoo.org> + -vienna-rna-1.5_beta.ebuild, -vienna-rna-1.6_alpha.ebuild, + +vienna-rna-1.6.ebuild: + Removed alpha and beta versions. New version. Removed dependency on X11. + +*vienna-rna-1.6_alpha (19 Oct 2005) + + 19 Oct 2005; Olivier Fisette <ribosome@gentoo.org> + +vienna-rna-1.6_alpha.ebuild: + New version. + + 30 Aug 2005; Olivier Fisette <ribosome@gentoo.org> + vienna-rna-1.5_beta.ebuild: + Added to x86. + + 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> vienna-rna-1.4.ebuild: + Ebuild cleanup. + +*vienna-rna-1.5_beta (09 Jan 2005) + + 09 Jan 2005; Olivier Fisette <ribosome@gentoo.org> + +vienna-rna-1.5_beta.ebuild: + Added new beta release (hard-masked). + +*vienna-rna-1.4 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +vienna-rna-1.4.ebuild: + Moved from app-sci/vienna-rna to sci-biology/vienna-rna. + + 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> vienna-rna-1.4.ebuild: + Added to x86. + + 23 Jun 2004; David Holm <dholm@gentoo.org> vienna-rna-1.4.ebuild: + Added to ~ppc. + +*vienna-rna-1.4 (22 Jun 2004) + + 22 Jun 2004; Olivier Fisette <ribosome@gentoo.org> + vienna-rna-1.4.ebuild, metadata.xml : + Initial import. Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>. + Reference: Gentoo Bugzilla, bug #53734 diff --git a/sci-biology/wgs-assembler/ChangeLog b/sci-biology/wgs-assembler/ChangeLog new file mode 100644 index 00000000..ca2f7495 --- /dev/null +++ b/sci-biology/wgs-assembler/ChangeLog @@ -0,0 +1,63 @@ +# ChangeLog for sci-biology/wgs-assembler +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/ChangeLog,v 1.13 2013/03/12 12:15:27 jlec Exp $ + + 12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 14 Nov 2012; Andreas Schuerch <nativemad@gentoo.org> + wgs-assembler-7.0-r1.ebuild: + x86 stable, see bug 328437 + + 11 Nov 2012; <ago@gentoo.org> wgs-assembler-7.0-r1.ebuild: + Stable for amd64, wrt bug #328437 + +*wgs-assembler-7.0-r1 (10 Nov 2012) + + 10 Nov 2012; Justin Lecher <jlec@gentoo.org> wgs-assembler-5.4.ebuild, + wgs-assembler-6.1.ebuild, wgs-assembler-7.0.ebuild, + +wgs-assembler-7.0-r1.ebuild, +files/wgs-assembler-7.0-build.patch: + Respect LDFLAGS, #331935; fix linking with gold; handle static-libs + +*wgs-assembler-7.0 (06 Feb 2012) + + 06 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> +wgs-assembler-7.0.ebuild: + Version bump + + 20 Mar 2011; Andrey Kislyuk <weaver@gentoo.org> wgs-assembler-5.4.ebuild, + wgs-assembler-6.1.ebuild: + Block x11-terms/terminator per bug 359363 + + 20 Mar 2011; Andrey Kislyuk <weaver@gentoo.org> wgs-assembler-6.1.ebuild: + Block x11-terms/terminator per bug 359363 + + 16 Jul 2010; Christian Faulhammer <fauli@gentoo.org> + wgs-assembler-6.1.ebuild: + stable x86, bug 328437 + +*wgs-assembler-6.1 (07 May 2010) + + 07 May 2010; Andrey Kislyuk <weaver@gentoo.org> -wgs-assembler-5.3.ebuild, + +wgs-assembler-6.1.ebuild: + Version bump + + 29 Mar 2010; Pacho Ramos <pacho@gentoo.org> wgs-assembler-5.4.ebuild: + amd64 stable, bug 298775 + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> + wgs-assembler-5.4.ebuild: + stable x86, bug 298775 + + 02 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> wgs-assembler-5.4.ebuild: + Fix paths generation + +*wgs-assembler-5.4 (27 Sep 2009) + + 27 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> +wgs-assembler-5.4.ebuild: + Version bump + +*wgs-assembler-5.3 (05 Jun 2009) + + 05 Jun 2009; Andrey Kislyuk <weaver@gentoo.org> +wgs-assembler-5.3.ebuild: + New package, ebuild written by me + diff --git a/sci-biology/wise/ChangeLog b/sci-biology/wise/ChangeLog new file mode 100644 index 00000000..088b9929 --- /dev/null +++ b/sci-biology/wise/ChangeLog @@ -0,0 +1,83 @@ +# ChangeLog for sci-biology/wise +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/ChangeLog,v 1.21 2015/04/20 20:25:58 jlec Exp $ + + 20 Apr 2015; Justin Lecher <jlec@gentoo.org> -wise-2.2.0.ebuild: + Drop old + + 19 Apr 2015; Agostino Sarubbo <ago@gentoo.org> wise-2.4.0_alpha.ebuild: + Stable for x86, wrt bug #544940 + + 14 Apr 2015; Agostino Sarubbo <ago@gentoo.org> wise-2.4.0_alpha.ebuild: + Stable for ia64, wrt bug #544940 + + 08 Apr 2015; Agostino Sarubbo <ago@gentoo.org> wise-2.4.0_alpha.ebuild: + Stable for amd64, wrt bug #544940 + + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> metadata.xml, + wise-2.4.0_alpha.ebuild: + Bump to EAPI=5 + + 02 Oct 2010; Andreas K. Huettel <dilfridge@gentoo.org> wise-2.2.0.ebuild, + wise-2.4.0_alpha.ebuild: + Less strict RDEPEND: ~sci-biology/hmmer-2.3.2 instead of + =sci-biology/hmmer-2.3.2-r1. Fixes bug 265534. + +*wise-2.4.0_alpha (23 Jun 2010) + + 23 Jun 2010; Justin Lecher <jlec@gentoo.org> wise-2.2.0.ebuild, + +wise-2.4.0_alpha.ebuild, +files/wise-2.4.0_alpha-cflags.patch, + +files/wise-2.4.0_alpha-glibc-2.10.patch: + Version bump, #191982 + + 05 Aug 2009; Samuli Suominen <ssuominen@gentoo.org> wise-2.2.0.ebuild, + +files/wise-2.2.0-glibc-2.10.patch: + Fix building with GLIBC 2.10+ wrt #278307. + + 09 Jun 2008; Markus Dittrich <markusle@gentoo.org> wise-2.2.0.ebuild: + Switched virtual/tetex -> virtual/latex-base and added amd64 + keyword (see bug #222501). + + 06 Jan 2007; Danny van Dyk <kugelfang@gentoo.org> -wise-2.1.23c.ebuild: + QA: Removed unused versions. + + 10 Nov 2006; Olivier Fisette <ribosome@gentoo.org> +wise-2.1.23c.ebuild, + wise-2.2.0.ebuild: + Ebuild clean-up. Readded version 2.1.23c. (I forgot we need it for threads + support.) + + 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> -wise-2.1.23c.ebuild: + Pruned old version. + + 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: + Stepping down from maintaining this package. + + 06 Apr 2006; Thomas Cort <tcort@gentoo.org> wise-2.2.0.ebuild: + Added ~alpha wrt Bug #123622. + + 29 Mar 2006; Aron Griffis <agriffis@gentoo.org> wise-2.2.0.ebuild: + Mark 2.2.0 stable on ia64 + + 23 Feb 2006; Aron Griffis <agriffis@gentoo.org> wise-2.2.0.ebuild: + Mark 2.2.0 ~ia64. #123622 + +*wise-2.1.23c (19 Feb 2006) + + 19 Feb 2006; Olivier Fisette <ribosome@gentoo.org> +wise-2.1.23c.ebuild: + Added old version for multiprocessor environements, as suggested by dawe + <daweonline@gmail.com> in bug #122338. + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> wise-2.2.0.ebuild: + Ebuild clean-up. + + 21 May 2005; Jason Wever <weeve@gentoo.org> wise-2.2.0.ebuild: + Added ~sparc keyword. + + 13 May 2005; Olivier Fisette <ribosome@gentoo.org> wise-2.2.0.ebuild: + Added to x86. + +*wise-2.2.0 (06 Mar 2005) + + 06 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +files/wise-api.tex.patch, +files/wise-env, +wise-2.2.0.ebuild: + Initial import. diff --git a/sci-biology/yass/ChangeLog b/sci-biology/yass/ChangeLog new file mode 100644 index 00000000..f95b2c3e --- /dev/null +++ b/sci-biology/yass/ChangeLog @@ -0,0 +1,19 @@ +# ChangeLog for sci-biology/yass +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/yass/ChangeLog,v 1.3 2013/03/12 12:17:12 jlec Exp $ + + 12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*yass-1.14-r1 (21 Jun 2010) + + 21 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/1.14-as-needed.patch, + +yass-1.14-r1.ebuild: + As-needed fix 324945, added threads and lowmem USE + +*yass-1.14 (18 Jun 2010) + + 18 Jun 2010; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +yass-1.14.ebuild: + New package, ebuild written by me + |