diff options
Diffstat (limited to 'sci-biology')
258 files changed, 0 insertions, 5167 deletions
diff --git a/sci-biology/AlignGraph/ChangeLog b/sci-biology/AlignGraph/ChangeLog deleted file mode 100644 index 3bce88153..000000000 --- a/sci-biology/AlignGraph/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/AlignGraph -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/AlignGraph: Add github to remote-id in metadata.xml - -*AlignGraph-9999 (25 May 2015) - - 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +AlignGraph-9999.ebuild, +metadata.xml: - sci-biology/AlignGraph: new package diff --git a/sci-biology/Atlas-Link/ChangeLog b/sci-biology/Atlas-Link/ChangeLog deleted file mode 100644 index 3a9de4e85..000000000 --- a/sci-biology/Atlas-Link/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/Atlas-Link -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*Atlas-Link-0.01 (04 Jul 2014) - - 04 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +Atlas-Link-0.01.ebuild, +metadata.xml: - sci-biology/Atlas-Link: noted dependence, see bug #516366 - diff --git a/sci-biology/Atlas/ChangeLog b/sci-biology/Atlas/ChangeLog deleted file mode 100644 index ce67a302f..000000000 --- a/sci-biology/Atlas/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/Atlas -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> Atlas-2005.ebuild: - Fix license - -*Atlas-2005 (07 Jan 2015) - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +Atlas-2005.ebuild, - +metadata.xml: - initial ebuild - diff --git a/sci-biology/Atlas2/ChangeLog b/sci-biology/Atlas2/ChangeLog deleted file mode 100644 index 834464dd5..000000000 --- a/sci-biology/Atlas2/ChangeLog +++ /dev/null @@ -1,18 +0,0 @@ -# ChangeLog for sci-biology/Atlas2 -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 25 Dec 2015; Marius Brehler <marbre@linux.sungazer.de> Atlas2-1.4.3.ebuild: - sci-biology/Atlas2: Drop ruby19, shorten description, add missing dies - - 25 Dec 2015; Marius Brehler <marbre@linux.sungazer.de> metadata.xml: - sci-biology/Atlas2: Add longdescription - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> Atlas2-1.4.3.ebuild: - sci-biology/Atlas2: Fix ruby deps - -*Atlas2-1.4.3 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +Atlas2-1.4.3.ebuild, +metadata.xml: - a skeleton for a new package, needs help from ruby team diff --git a/sci-biology/Atlas_GapFill/ChangeLog b/sci-biology/Atlas_GapFill/ChangeLog deleted file mode 100644 index 18b895350..000000000 --- a/sci-biology/Atlas_GapFill/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/Atlas_GapFill -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> Atlas_GapFill-2.2.ebuild: - sci-biology/Atlas_GapFill: drop unknown dep - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> Atlas_GapFill-2.2.ebuild: - Fix license - -*Atlas_GapFill-2.2 (07 Jan 2015) - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +Atlas_GapFill-2.2.ebuild, +metadata.xml: - initial ebuild diff --git a/sci-biology/BBmap/ChangeLog b/sci-biology/BBmap/ChangeLog deleted file mode 100644 index 15cd8fae3..000000000 --- a/sci-biology/BBmap/ChangeLog +++ /dev/null @@ -1,51 +0,0 @@ -# ChangeLog for sci-biology/BBmap -# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*BBmap-35.82 (06 Jan 2016) - - 06 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BBmap-35.82.ebuild, - -BBmap-35.68.ebuild: - sci-biology/BBmap: version bump - -*BBmap-35.68 (19 Nov 2015) - - 19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BBmap-35.68.ebuild, - -BBmap-35.66.ebuild: - sci-biology/BBmap: version bump - -*BBmap-34.97 (15 Nov 2015) - - 15 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BBmap-34.97.ebuild, - -BBmap-34.56.ebuild: - sci-biology/BBmap: version bump; apply also the UnicodeToAscii.patch - - 12 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> BBmap-34.56.ebuild: - sci-biology/BBmap: drop the call to eclipse jcompiler, added ~amd64 KEYWORD - - 12 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> BBmap-34.56.ebuild: - sci-biology/BBmap: provided bug #542700 is resolved we can use mpi.jar from - openmpi package - - 09 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> BBmap-34.56.ebuild: - new package, needs openmpi with java support to provide mpi.jar, see bug - #542700 - -*BBmap-34.56 (05 Mar 2015) - - 05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BBmap-34.56.ebuild, - -BBmap-31.40.ebuild: - version bump - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> BBmap-31.40.ebuild: - sci-biology/BBmap: fix SLOT operators - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> BBmap-31.40.ebuild: - added license - -*BBmap-31.40 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +BBmap-31.40.ebuild, +metadata.xml: - sci-biology/BBmap: a skeleton for a new package, needs help from java team - for sure diff --git a/sci-biology/BG7/ChangeLog b/sci-biology/BG7/ChangeLog deleted file mode 100644 index 19f4c7c75..000000000 --- a/sci-biology/BG7/ChangeLog +++ /dev/null @@ -1,14 +0,0 @@ -# ChangeLog for sci-biology/BG7 -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> BG7-9999.ebuild: - sci-biology/BG7: fix SLOT operators - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> BG7-9999.ebuild, +metadata.xml: - Switch from git-2 to git-r3 - -*BG7-9999 (29 Aug 2013) - - 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BG7-9999.ebuild: - Initial, not yet working ebuild. diff --git a/sci-biology/BRAKER/ChangeLog b/sci-biology/BRAKER/ChangeLog deleted file mode 100644 index 01a091838..000000000 --- a/sci-biology/BRAKER/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sci-biology/BRAKER -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*BRAKER-20150330 (27 Apr 2015) - - 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +BRAKER-20150330.ebuild, +metadata.xml: - sci-biology/BRAKER: new package; somehow RDEPENDs are installed wrongly: Can't - locate Scalar/Util/Numeric.pm in @INC (you may need to install the - Scalar::Util::Numeric module) diff --git a/sci-biology/BRANCH/ChangeLog b/sci-biology/BRANCH/ChangeLog deleted file mode 100644 index 5a53a534c..000000000 --- a/sci-biology/BRANCH/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/BRANCH -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/BRANCH: Add github to remote-id in metadata.xml - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> BRANCH-9999.ebuild: - Move from git-2 to git-r3 eclass; add HOMEPAGE; be verbose during - compilation; install docs - -*BRANCH-9999 (07 Jan 2015) - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +BRANCH-9999.ebuild, +metadata.xml: - initial ebuild diff --git a/sci-biology/BamView/ChangeLog b/sci-biology/BamView/ChangeLog deleted file mode 100644 index f41681e6d..000000000 --- a/sci-biology/BamView/ChangeLog +++ /dev/null @@ -1,21 +0,0 @@ -# ChangeLog for sci-biology/BamView -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> BamView-1.2.11.ebuild, - metadata.xml: - sci-biology/BamView: fix SLOT operators - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> +metadata.xml, - BamView-1.2.11.ebuild: - added metadata.xml - - 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - BamView-1.2.11.ebuild: - dropped KEYWORDS - -*BamView-1.2.11 (24 Mar 2014) - - 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +BamView-1.2.11.ebuild: - not sure if we need a separate package; is said to be part of Artemis bundle diff --git a/sci-biology/BlastToSam/ChangeLog b/sci-biology/BlastToSam/ChangeLog deleted file mode 100644 index 1cece175a..000000000 --- a/sci-biology/BlastToSam/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/BlastToSam -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/BlastToSam: Add github to remote-id in metadata.xml - -*BlastToSam-9999 (29 Apr 2015) - - 29 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +BlastToSam-9999.ebuild, +metadata.xml: - sci-biology/BlastToSam: new package, works diff --git a/sci-biology/CONTIGuator/ChangeLog b/sci-biology/CONTIGuator/ChangeLog deleted file mode 100644 index 655c3f07f..000000000 --- a/sci-biology/CONTIGuator/ChangeLog +++ /dev/null @@ -1,6 +0,0 @@ -# ChangeLog for sci-biology/CONTIGuator -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> CONTIGuator-2.7.ebuild: - added license diff --git a/sci-biology/DisEMBL/ChangeLog b/sci-biology/DisEMBL/ChangeLog deleted file mode 100644 index 68d62b922..000000000 --- a/sci-biology/DisEMBL/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/DisEMBL -# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*DisEMBL-1.4 (06 Jan 2016) - - 06 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +DisEMBL-1.4.ebuild, - +metadata.xml: - sci-biology/DisEMBL: new package diff --git a/sci-biology/EBARDenovo/ChangeLog b/sci-biology/EBARDenovo/ChangeLog deleted file mode 100644 index ca9f331c2..000000000 --- a/sci-biology/EBARDenovo/ChangeLog +++ /dev/null @@ -1,14 +0,0 @@ -# ChangeLog for sci-biology/EBARDenovo -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - EBARDenovo-1.2.2.ebuild: - sci-biology/EBARDenovo: added a note about non-commercial use requirement - mentioned in http://bioinformatics.oxfordjournals.org/content/29/8/1004.full - -*EBARDenovo-1.2.2 (08 Jan 2015) - - 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +EBARDenovo-1.2.2.ebuild, +metadata.xml: - sci-biology/EBARDenovo: new package diff --git a/sci-biology/ESTate/ChangeLog b/sci-biology/ESTate/ChangeLog deleted file mode 100644 index 47e53d3bd..000000000 --- a/sci-biology/ESTate/ChangeLog +++ /dev/null @@ -1,28 +0,0 @@ -# ChangeLog for sci-biology/ESTate -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild: - sci-biology/ESTate: track file collision - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> ESTate-0.5.ebuild: - Soma QA and polishing - - 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild: - improve description and emphasize the ORF finder can overcome frameshifts in - CDS - - 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild: - use 'insinto' and not 'doins' - - 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild: - add the probability matrices - - 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild: - add the PhD thesis itself as documentation - -*ESTate-0.5 (09 Jan 2015) - - 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +ESTate-0.5.ebuild, - +metadata.xml: - sci-biology/ESTate: new package diff --git a/sci-biology/FLASH/ChangeLog b/sci-biology/FLASH/ChangeLog deleted file mode 100644 index f36fbae47..000000000 --- a/sci-biology/FLASH/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/FLASH -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*FLASH-1.2.9 (16 Mar 2014) - - 16 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +FLASH-1.2.9.ebuild, - +metadata.xml: - sci/biology/FLASH: new package diff --git a/sci-biology/GAL/ChangeLog b/sci-biology/GAL/ChangeLog deleted file mode 100644 index 3cfe9d424..000000000 --- a/sci-biology/GAL/ChangeLog +++ /dev/null @@ -1,20 +0,0 @@ -# ChangeLog for sci-biology/GAL -# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 04 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> GAL-0.2.2.ebuild: - sci-biology/GAL: fix some package names in DEPEND to match actual CPAN - packages - - 02 Jan 2016; Andreas K. Huettel <dilfridge@gentoo.org> files/Build.PL.patch: - Force systemwide installation by removing all the manual build fiddling - - 02 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> GAL-0.2.2.ebuild: - sci-biology/GAL: add another perl DEPENDency - -*GAL-0.2.1 (31 Dec 2015) -*GAL-0.2.2 (31 Dec 2015) - - 31 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +GAL-0.2.1.ebuild, - +GAL-0.2.2.ebuild, +metadata.xml: - sci-biology/GAL: new package, needed by trinityrnaseq and maker diff --git a/sci-biology/Gambit/ChangeLog b/sci-biology/Gambit/ChangeLog deleted file mode 100644 index 369fd7b88..000000000 --- a/sci-biology/Gambit/ChangeLog +++ /dev/null @@ -1,8 +0,0 @@ -# ChangeLog for sci-biology/Gambit -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> Gambit-0.4.145.ebuild, - metadata.xml: - Update to new qt deps names - diff --git a/sci-biology/HTSeq/ChangeLog b/sci-biology/HTSeq/ChangeLog deleted file mode 100644 index ca0c1795c..000000000 --- a/sci-biology/HTSeq/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/HTSeq -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 14 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> HTSeq-0.6.1.ebuild: - mention also Bowtie file format - -*HTSeq-0.6.1 (14 Feb 2015) - - 14 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +HTSeq-0.6.1.ebuild, - +metadata.xml: - new python API diff --git a/sci-biology/ICC/ChangeLog b/sci-biology/ICC/ChangeLog deleted file mode 100644 index 85de47b9f..000000000 --- a/sci-biology/ICC/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/ICC -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> ICC-2.0.1.ebuild: - Fix license - -*ICC-2.0.1 (07 Jan 2015) - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +ICC-2.0.1.ebuild: - initial ebuild, perl installation steps need to be fixed - diff --git a/sci-biology/IMAGE/ChangeLog b/sci-biology/IMAGE/ChangeLog deleted file mode 100644 index f221aba9e..000000000 --- a/sci-biology/IMAGE/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/IMAGE -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 27 Oct 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> IMAGE-2.4.1.ebuild: - sci-biology/IMAGE: improve package descr - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> IMAGE-2.4.1.ebuild: - added license - -*IMAGE-2.4.1 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +IMAGE-2.4.1.ebuild, +metadata.xml: - a skeleton for a new package diff --git a/sci-biology/InterMine/ChangeLog b/sci-biology/InterMine/ChangeLog deleted file mode 100644 index 161118182..000000000 --- a/sci-biology/InterMine/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/InterMine -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/InterMine: Add github to remote-id in metadata.xml - - 10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> - InterMine-0.98.ebuild: - Fix license, homepage and move from git-2 to git-r3 - -*InterMine-0.98 (07 Jan 2015) - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +InterMine-0.98.ebuild, +metadata.xml: - initial ebuild diff --git a/sci-biology/Jannovar-bin/ChangeLog b/sci-biology/Jannovar-bin/ChangeLog deleted file mode 100644 index e548c0157..000000000 --- a/sci-biology/Jannovar-bin/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/Jannovar-bin -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*Jannovar-bin-20150503 (05 May 2015) - - 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +Jannovar-bin-20150503.ebuild, +metadata.xml: - sci-biology/Jannovar-bin: new package diff --git a/sci-biology/KaKs_Calculator/ChangeLog b/sci-biology/KaKs_Calculator/ChangeLog deleted file mode 100644 index ed7a1b8c6..000000000 --- a/sci-biology/KaKs_Calculator/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/KaKs_Calculator -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*KaKs_Calculator-1.2 (21 Mar 2015) - - 21 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +KaKs_Calculator-1.2.ebuild, +metadata.xml: - sci-biology/KaKs_Calculator: new package but code does not compile; awaiting - some answer from upstream http://cbb.big.ac.cn/Zhang_Zhang diff --git a/sci-biology/MaSuRCA/ChangeLog b/sci-biology/MaSuRCA/ChangeLog deleted file mode 100644 index 037399200..000000000 --- a/sci-biology/MaSuRCA/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/MaSuRCA -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*MaSuRCA-2.3.2b (30 Apr 2015) - - 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +MaSuRCA-2.3.2b.ebuild, -MaSuRCA-2.1.0.ebuild: - sci-biology/MaSuRCA: version bump - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> MaSuRCA-2.1.0.ebuild: - added license - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ChangeLog: - new package but with a missing LICENSE and needs tweak to get all configure's - running diff --git a/sci-biology/MagicViewer/ChangeLog b/sci-biology/MagicViewer/ChangeLog deleted file mode 100644 index 574092dc2..000000000 --- a/sci-biology/MagicViewer/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/MagicViewer -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> MagicViewer-1.2.1.ebuild, - metadata.xml: - sci-biology/MagicViewer: fix SLOT operators - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> MagicViewer-1.2.1.ebuild: - added license diff --git a/sci-biology/MeV/ChangeLog b/sci-biology/MeV/ChangeLog deleted file mode 100644 index 8265b964c..000000000 --- a/sci-biology/MeV/ChangeLog +++ /dev/null @@ -1,7 +0,0 @@ -# ChangeLog for sci-biology/MeV -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> +metadata.xml, - MeV-4.8.1.ebuild: - added metadata.xml diff --git a/sci-biology/MochiView/ChangeLog b/sci-biology/MochiView/ChangeLog deleted file mode 100644 index 482746ebb..000000000 --- a/sci-biology/MochiView/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/MochiView -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> MochiView-1.45.ebuild: - Fix license - -*MochiView-1.45 (07 Jan 2015) - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +MochiView-1.45.ebuild, +metadata.xml: - initial ebuild - diff --git a/sci-biology/MuSeqBox/ChangeLog b/sci-biology/MuSeqBox/ChangeLog deleted file mode 100644 index fefc7c842..000000000 --- a/sci-biology/MuSeqBox/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/MuSeqBox -# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*MuSeqBox-5.4 (05 Jan 2016) - - 05 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +MuSeqBox-5.4.ebuild, -MuSeqBox-5.3.ebuild: - sci-biology/MuSeqBox: corrected package version number; added a note about - github location provided by Volker Brendel - -*MuSeqBox-5.3 (05 Jan 2016) - - 05 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +MuSeqBox-5.3.ebuild, +metadata.xml: - sci-biology/MuSeqBox: new package diff --git a/sci-biology/NGSTools/ChangeLog b/sci-biology/NGSTools/ChangeLog deleted file mode 100644 index fb4ee89e4..000000000 --- a/sci-biology/NGSTools/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/NGSTools -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*NGSTools-2.0.5 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +NGSTools-2.0.5.ebuild, +metadata.xml: - new package, needs java team help - diff --git a/sci-biology/OBO-Edit/ChangeLog b/sci-biology/OBO-Edit/ChangeLog deleted file mode 100644 index a314c332e..000000000 --- a/sci-biology/OBO-Edit/ChangeLog +++ /dev/null @@ -1,40 +0,0 @@ -# ChangeLog for sci-biology/OBO-Edit -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - OBO-Edit-2.1.1.6.ebuild: - adjust PATH to point to the installation place, few comment lines changes - - 07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - OBO-Edit-2.1.1.6.ebuild: - added the addpredict() trick from tablet-bin*.ebuild to make the ACCESS DENIED - messages quiet, bugs #402507 (learned from bug #387227) - - 07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - OBO-Edit-2.1.1.6.ebuild: - added the addpredict() trick from tablet-bin*.ebuild to make the ACCESS - DENIED messages quiet, bugs #402507 (learned from bug #387227) - - 07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - OBO-Edit-2.1.1.6.ebuild: - sci-biology/OBO-Edit: more attempts to get rid of sandbox ACCESS VIOLATION - SUMMARY errors - -*OBO-Edit-2.1.1.6 (07 Feb 2012) - - 07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +OBO-Edit-2.1.1.6.ebuild, files/response.varfile: - more attempts to get rid of sandbox ACCESS VIOLATION SUMMARY errors - -*OBO-Edit-2.1.0 (26 Dec 2011) - - 26 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - -OBO-Edit-2.1_beta8.ebuild, +OBO-Edit-2.1.0.ebuild, files/response.varfile: - Sync ebuild to use install4j as in sci-biology/tablet-bin. Awaiting a fix - from upstream so that the installer really respects --destination or -dir - options. - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> OBO-Edit-2.1_beta8.ebuild: - Cleaned ebuild - diff --git a/sci-biology/ONTO-PERL/ChangeLog b/sci-biology/ONTO-PERL/ChangeLog deleted file mode 100644 index 7d1d8c96d..000000000 --- a/sci-biology/ONTO-PERL/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sci-biology/ONTO-PERL -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 24 Sep 2014; Justin Lecher <jlec@gentoo.org> -ONTO-PERL-1.31.ebuild, - +ONTO-PERL-1.41.ebuild, metadata.xml: - Version Bump; Bump to EAPI=5 - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> ONTO-PERL-1.31.ebuild: - Cleaned ebuild, 'http://search.cpan.org/CPAN' found in thirdpartymirrors - diff --git a/sci-biology/ORFcor/ChangeLog b/sci-biology/ORFcor/ChangeLog deleted file mode 100644 index e30d24600..000000000 --- a/sci-biology/ORFcor/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/ORFcor -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - ORFcor-20130507.ebuild: - sci-biology/ORFcor: more cleanup - -*ORFcor-20130507 (09 Mar 2015) - - 09 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +ORFcor-20130507.ebuild, +metadata.xml: - new package, working ebuild diff --git a/sci-biology/RADtools/ChangeLog b/sci-biology/RADtools/ChangeLog deleted file mode 100644 index 04339886e..000000000 --- a/sci-biology/RADtools/ChangeLog +++ /dev/null @@ -1,18 +0,0 @@ -# ChangeLog for sci-biology/RADtools -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - RADtools-1.2.4.ebuild, RADtools-9999.ebuild: - sci-biology/RADtools: manually install perl modules int PERL5INC path - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> RADtools-1.2.4.ebuild, - RADtools-9999.ebuild: - removed empty line - -*RADtools-1.2.4 (28 Mar 2014) -*RADtools-9999 (28 Mar 2014) - - 28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +RADtools-1.2.4.ebuild, +RADtools-9999.ebuild, +metadata.xml: - sci-biology/RADtools: new package diff --git a/sci-biology/RSeQC/ChangeLog b/sci-biology/RSeQC/ChangeLog deleted file mode 100644 index 0633f404e..000000000 --- a/sci-biology/RSeQC/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/RSeQC -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*RSeQC-2.6.1 (24 Jun 2015) - - 24 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +RSeQC-2.6.1.ebuild, - +metadata.xml: - sci-biology/RSeQC: new package diff --git a/sci-biology/Ray/ChangeLog b/sci-biology/Ray/ChangeLog deleted file mode 100644 index 271c8405a..000000000 --- a/sci-biology/Ray/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/Ray -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*Ray-2.3.0 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +Ray-2.3.0.ebuild, - +metadata.xml: - sci-biology/Ray: a new package, maybe needs decent inspection from cluster - herd and also java diff --git a/sci-biology/Rcorrector/ChangeLog b/sci-biology/Rcorrector/ChangeLog deleted file mode 100644 index 97497f22e..000000000 --- a/sci-biology/Rcorrector/ChangeLog +++ /dev/null @@ -1,18 +0,0 @@ -# ChangeLog for sci-biology/Rcorrector -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 15 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - Rcorrector-9999.ebuild: - sci-biology/Rcorrector: add einfo() message that default kmer size 23 is - suboptimal - - 15 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - Rcorrector-9999.ebuild: - sci-biology/Rcorrector: respect CXXFLAGS - -*Rcorrector-9999 (13 Nov 2015) - - 13 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +Rcorrector-9999.ebuild, +metadata.xml: - sci-biology/Rcorrector: new package diff --git a/sci-biology/SEECER/ChangeLog b/sci-biology/SEECER/ChangeLog deleted file mode 100644 index 1302cab1e..000000000 --- a/sci-biology/SEECER/ChangeLog +++ /dev/null @@ -1,39 +0,0 @@ -# ChangeLog for sci-biology/SEECER -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 15 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - SEECER-0.1.3-r2.ebuild: - sci-biology/SEECER: add einfo() message that default kmer size 17 is - suboptimal - - 13 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - SEECER-0.1.3-r2.ebuild, files/remove-hardcoded-paths.patch: - sci-biology/SEECER: patch crappy shellscripts to at leats die on error; - require jellyfish-1.1.11 - -*SEECER-0.1.3-r2 (13 Nov 2015) - - 13 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +SEECER-0.1.3-r2.ebuild, +files/remove-hardcoded-paths.patch, - -SEECER-0.1.3-r1.ebuild: - sci-biology/SEECER: remove hardcoded paths - - 12 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - SEECER-0.1.3-r1.ebuild: - sci-biology/SEECER: install also the main program wrapper - -*SEECER-0.1.3-r1 (30 Apr 2015) - - 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +SEECER-0.1.3-r1.ebuild, +files/replace_ids.cc, -SEECER-0.1.3.ebuild: - sci-biology/SEECER: added upstream 'patch'; do more proper install process - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> SEECER-0.1.3.ebuild: - Fix license - -*SEECER-0.1.3 (07 Jan 2015) - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +SEECER-0.1.3.ebuild, +metadata.xml: - initial ebuild diff --git a/sci-biology/SSAKE/ChangeLog b/sci-biology/SSAKE/ChangeLog deleted file mode 100644 index 63092d6a3..000000000 --- a/sci-biology/SSAKE/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/SSAKE -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*SSAKE-3.8.2 (17 Apr 2015) - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +SSAKE-3.8.2.ebuild, - +metadata.xml: - sci-biology/SSAKE: new package diff --git a/sci-biology/STAR/ChangeLog b/sci-biology/STAR/ChangeLog deleted file mode 100644 index 7286865a6..000000000 --- a/sci-biology/STAR/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/STAR -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*STAR-2.4.1c (05 May 2015) -*STAR-9999 (05 May 2015) - - 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +STAR-2.4.1c.ebuild, - +STAR-9999.ebuild, +metadata.xml: - sci-biology/STAR: new package diff --git a/sci-biology/SolexaQA/ChangeLog b/sci-biology/SolexaQA/ChangeLog deleted file mode 100644 index a3501fce5..000000000 --- a/sci-biology/SolexaQA/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/SolexaQA -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*SolexaQA-2.2 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +SolexaQA-2.2.ebuild, +metadata.xml: - sci-biology/SolexaQA: new package diff --git a/sci-biology/StarORF/ChangeLog b/sci-biology/StarORF/ChangeLog deleted file mode 100644 index 477e5a368..000000000 --- a/sci-biology/StarORF/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sci-biology/StarORF -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*StarORF-9999 (06 May 2015) - - 06 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +StarORF-9999.ebuild, +metadata.xml: - sci-biology/StarORF: new package, somehow build.xml needs dev- - java/jreleaseinfo but it does not see it: 'build.xml:3: taskdef class - ch.oscg.jreleaseinfo.anttask.JReleaseInfoAntTask cannot be found' diff --git a/sci-biology/TransDecoder/ChangeLog b/sci-biology/TransDecoder/ChangeLog deleted file mode 100644 index e9110b4de..000000000 --- a/sci-biology/TransDecoder/ChangeLog +++ /dev/null @@ -1,75 +0,0 @@ -# ChangeLog for sci-biology/TransDecoder -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 25 Dec 2015; Marius Brehler <marbre@linux.sungazer.de> - TransDecoder-2.0.1.ebuild: - sci-biology/TransDecoder: Fix minorsyn, add missing die - - 19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - TransDecoder-2.0.1.ebuild: - sci-biology/TransDecoder: note that Pfam-AB was discontinued - - 19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - TransDecoder-2.0.1.ebuild: - sci-biology/TransDecoder: update homepage - - 19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/TransDecoder-2.0.1__fix_paths.patch, -files/TransDecoder.patch, - TransDecoder-2.0.1.ebuild, files/pfam_runner.pl.patch: - sci-biology/TransDecoder: install properly perl modules; fix PERL5INC paths by - adding TransDecoder::, ebuild cleanup - - 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/TransDecoder: Add github to remote-id in metadata.xml - - 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - transdecoder-2.0.1.ebuild: - sci-biology/transdecoder: more ebuild cleanup - - 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - transdecoder-2.0.1.ebuild: - sci-biology/transdecoder: ebuild cleanup - - 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - -transdecoder-20140704.ebuild, transdecoder-2.0.1.ebuild: - sci-biology/transdecoder: drop old - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - transdecoder-2.0.1.ebuild, transdecoder-20140704.ebuild: - sci-biology/transdecoder: fixed installation of perl-related files - - 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - transdecoder-2.0.1.ebuild: - dropped hmmer dependency altogether, added pkg_postinst() with - usage/dependency info - -*transdecoder-2.0.1 (19 Mar 2015) - - 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +transdecoder-2.0.1.ebuild, transdecoder-20140704.ebuild: - removing KEYWORDS until the perl files are installed to some other place. At - the moment I get: 'perl-module.eclass: Suspicious environment values found. - PERL5LIB="/usr/lib64/perl5/vendor_perl/5.18.2/TransDecoder"' - - 15 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - transdecoder-20140704.ebuild: - drop hmmer-3 dependency, it is an optional dependency only - - 10 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - transdecoder-20140704.ebuild: - install *.pm into PERL5LIB/TransDecoder and pass that via env.d - - 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/TransDecoder.patch, +files/pfam_runner.pl.patch, - transdecoder-20140704.ebuild: - sci-biology/transdecoder: added patches so that we use PATH to loclate - binaries and not in a local subdirectory named 'util', drop sys- - cluster/openmpi requirement, it does not link against it all all, this is a - bunch of perl and shell scripts - -*transdecoder-20140704 (08 Jan 2015) - - 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +transdecoder-20140704.ebuild: - sci-biology/transdecoder: new package diff --git a/sci-biology/Trinotate/ChangeLog b/sci-biology/Trinotate/ChangeLog deleted file mode 100644 index d0030f93f..000000000 --- a/sci-biology/Trinotate/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/Trinotate -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 06 Jun 2015; Justin Lecher <jlec@gentoo.org> Trinotate-2.0.1.ebuild: - sci-biology/Trinotate: Fix whitespaces - - 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/Trinotate: Add github to remote-id in metadata.xml - -*Trinotate-2.0.1 (30 Apr 2015) - - 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +Trinotate-2.0.1.ebuild, +metadata.xml: - sci-biology/Trinotate: new package diff --git a/sci-biology/VarScan/ChangeLog b/sci-biology/VarScan/ChangeLog deleted file mode 100644 index d6adc5484..000000000 --- a/sci-biology/VarScan/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/VarScan -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*VarScan-2.3.7 (13 Mar 2015) - - 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +VarScan-2.3.7.ebuild, -VarScan-2.3.6.ebuild: - fix SRC_URI to fetch real source code, ebuild improvements but not working - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> VarScan-2.3.6.ebuild, - metadata.xml: - sci-biology/VarScan: fix SLOT operators - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> VarScan-2.3.6.ebuild: - fixed DESCRIPTION diff --git a/sci-biology/VelvetOptimiser/ChangeLog b/sci-biology/VelvetOptimiser/ChangeLog deleted file mode 100644 index fa985328f..000000000 --- a/sci-biology/VelvetOptimiser/ChangeLog +++ /dev/null @@ -1,17 +0,0 @@ -# ChangeLog for sci-biology/VelvetOptimiser -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - VelvetOptimiser-2.2.5.ebuild: - sci-biology/VelvetOptimiser: fixed installation of perl-related files - - 15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - VelvetOptimiser-2.2.5.ebuild: - sci-biology/VelvetOptimiser: add requirement for threaded perl - -*VelvetOptimiser-2.2.5 (15 Apr 2014) - - 15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +VelvetOptimiser-2.2.5.ebuild, +metadata.xml: - sci-biology/VelvetOptimiser: new package diff --git a/sci-biology/YASRA/ChangeLog b/sci-biology/YASRA/ChangeLog deleted file mode 100644 index 8892c1213..000000000 --- a/sci-biology/YASRA/ChangeLog +++ /dev/null @@ -1,23 +0,0 @@ -# ChangeLog for sci-biology/YASRA -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*YASRA-2.33 (28 Mar 2014) - - 28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +YASRA-2.33.ebuild, - -YASRA-2.32.ebuild: - sci-biology/YASRA: version bump to a version without compile errors when - gcc-4.8 is used - - 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -YASRA-2.1.ebuild, - +YASRA-2.32.ebuild: - Version Bump; add KEYWORDS - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> YASRA-2.1.ebuild, metadata.xml: - Drop keywords as deps are unkeyworded - -*YASRA-2.1 (17 Jan 2012) - - 17 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +YASRA-2.1.ebuild, - +metadata.xml: - initial ebuild diff --git a/sci-biology/abacas/ChangeLog b/sci-biology/abacas/ChangeLog deleted file mode 100644 index c7b77d97b..000000000 --- a/sci-biology/abacas/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/abacas -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> abacas-1.3.1.ebuild: - sci-biology/abacas: clarify description - -*abacas-1.3.1 (31 Mar 2015) - - 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +abacas-1.3.1.ebuild, +metadata.xml: - sci-biology/abacas: new package diff --git a/sci-biology/abyss/ChangeLog b/sci-biology/abyss/ChangeLog deleted file mode 100644 index 8a0502e53..000000000 --- a/sci-biology/abyss/ChangeLog +++ /dev/null @@ -1,17 +0,0 @@ -# ChangeLog for sci-biology/abyss -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*abyss-1.3.3-r1 (23 May 2015) -*abyss-1.3.4-r1 (23 May 2015) -*abyss-1.3.6-r1 (23 May 2015) - - 23 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +abyss-1.3.3-r1.ebuild, +abyss-1.3.4-r1.ebuild, +abyss-1.3.6-r1.ebuild, - +files/abyss-1.3.3-ac_prog_ar.patch, +files/abyss-1.3.3-gcc-4.7.patch, - +files/abyss-1.3.3-samtoafg.patch, +files/abyss-1.3.4-gcc-4.7.patch, - +files/abyss-1.3.4-samtoafg.patch, +files/abyss-1.3.6-ac_prog_ar.patch, - +files/abyss-1.3.6-gcc-4.7.patch, +files/abyss-1.3.6-samtoafg.patch, - +metadata.xml: - sci-biology/amos: bring in upstream patch to cope with secondary alignments - from 'bwa mem -M' diff --git a/sci-biology/aghermann/ChangeLog b/sci-biology/aghermann/ChangeLog deleted file mode 100644 index a9cbf767e..000000000 --- a/sci-biology/aghermann/ChangeLog +++ /dev/null @@ -1,21 +0,0 @@ -# ChangeLog for sci-biology/aghermann -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 15 Jun 2015; Andrei Zavada <johnhommer@gmail.com> aghermann-1.0.5.ebuild: - New upstream version. - - 10 Apr 2015; Andrei Zavada <johnhommer@gmail.com> aghermann-1.0.4.ebuild: - New upstream version. - - 28 Mar 2015; Andrei Zavada <johnhommer@gmail.com> aghermann-1.0.3-r1.ebuild: - Install binaries into /usr/bin not /bin. - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> aghermann-1.0.3.ebuild: - sci-biology/aghermann: Fix slot operators - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> aghermann-1.0.3.ebuild: - sci-biology/aghermann: Fix indention and use virtual for pkgconfig - - 17 Feb 2015; Andrei Zavada <johnhommer@gmail.com> aghermann-1.0.3.ebuild: - Initial packaging for gentoo. diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog deleted file mode 100644 index 363a52d9b..000000000 --- a/sci-biology/amos/ChangeLog +++ /dev/null @@ -1,51 +0,0 @@ -# ChangeLog for sci-biology/amos -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - amos-3.1.0-r2.ebuild, amos-9999.ebuild: - added dev-qt/qt3support:4 to DEPEND because 'scanelf -qn /usr/bin/hawkeye' - confirms libQt3Support.so is used (thanks to Davide Pesavento pesa@g.o) - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - amos-3.1.0-r2.ebuild, amos-9999.ebuild: - sci-biology/amos: fixed installation of perl-related files - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - amos-3.1.0-r2.ebuild, amos-9999.ebuild: - sci-biology/amos: use doins instead of dobin - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - amos-3.1.0-r2.ebuild, amos-9999.ebuild: - sci-biology/amos: fixed installation of perl-related files - -*amos-3.1.0-r2 (31 Mar 2015) - - 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +amos-3.1.0-r2.ebuild, +files/amos-3.1.0-gcc-4.7.patch, - +files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch, amos-9999.ebuild: - sci-biology/amos: fix installation process and dependencies - - 29 Dec 2013; Justin Lecher <jlec@gentoo.org> -amos-3.1.0-r1.ebuild, - amos-9999.ebuild, -files/amos-3.1.0-gcc-4.7.patch, - -files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch, - -files/amos.m4.patch: - Move to tree - -*amos-3.1.0-r1 (11 Sep 2013) - - 11 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +amos-3.1.0-r1.ebuild, +files/amos-3.1.0-gcc-4.7.patch, - +files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch: - Fix indentation error and remove unused import of string module (there could - be more cleanup as suggested by pychecker). Credits to - http://sourceforge.net/p/amos/support-requests/1/ - - 19 Mar 2013; Justin Lecher <jlec@gentoo.org> amos-9999.ebuild: - Bump to latest git HEAD, fixes qt problems, #348031 - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> amos-9999.ebuild, metadata.xml: - Update to new qt deps names - - 22 May 2012; Justin Lecher <jlec@gentoo.org> amos-9999.ebuild: - Bump to EAPI=4, remove unnecessary bits diff --git a/sci-biology/ampliconnoise/ChangeLog b/sci-biology/ampliconnoise/ChangeLog deleted file mode 100644 index d38581dae..000000000 --- a/sci-biology/ampliconnoise/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/ampliconnoise -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> ampliconnoise-1.27.ebuild: - sci-biology/ampliconnoise: drop Useless blank line on last line - -*ampliconnoise-1.27 (07 Jan 2015) - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +ampliconnoise-1.27.ebuild: - initial ebuild diff --git a/sci-biology/angsd/ChangeLog b/sci-biology/angsd/ChangeLog deleted file mode 100644 index 11e60db8a..000000000 --- a/sci-biology/angsd/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/angsd -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*angsd-9999 (20 Mar 2015) - - 20 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +angsd-9999.ebuild, - +metadata.xml: - sci-biology/angsd: new package, -9999 compiles fine, need a snapshot for 0.700 - version or whichever diff --git a/sci-biology/ants/ChangeLog b/sci-biology/ants/ChangeLog deleted file mode 100644 index 004b132fe..000000000 --- a/sci-biology/ants/ChangeLog +++ /dev/null @@ -1,17 +0,0 @@ -# ChangeLog for sci-biology/ants -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 28 Jul 2015; <chymera@gentoo.org> ants-9999.ebuild: - replaced explicit command by default call - - 27 Jul 2015; <chymera@gentoo.org> ants-9999.ebuild: - using multilib eclass - - 26 Jul 2015; <chymera@gentoo.org> ants-9999.ebuild: - specifying lib dir adequaltely for multilib setups - -*ants-9999 (26 Jul 2015) - - 26 Jul 2015; <chymera@gentoo.org> +ants-9999.ebuild, +metadata.xml: - new ebuild diff --git a/sci-biology/apollo/ChangeLog b/sci-biology/apollo/ChangeLog deleted file mode 100644 index 3e8b3d4a7..000000000 --- a/sci-biology/apollo/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/apollo -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> apollo-9999.ebuild, metadata.xml: - sci-biology/apollo: fix SLOT operators - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> apollo-9999.ebuild: - sci-biology/apollo: a skeleton for a new package, needs help - - 07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> apollo-9999.ebuild: - initial ebuild diff --git a/sci-biology/argo-bin/ChangeLog b/sci-biology/argo-bin/ChangeLog deleted file mode 100644 index 062eb7851..000000000 --- a/sci-biology/argo-bin/ChangeLog +++ /dev/null @@ -1,21 +0,0 @@ -# ChangeLog for sci-biology/argo-bin -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - argo-bin-1.0.31.ebuild, argo-bin-2.0.3.ebuild: - sci-biology/argo-bin: remove IUSE - -*argo-bin-2.0.3 (26 May 2015) - - 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +argo-bin-2.0.3.ebuild, argo-bin-1.0.31.ebuild: - sci-biology/argo-bin: ebuild cleanup; version bump - - 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - argo-bin-1.0.31.ebuild: - sci-biology/argo-bin: redefine S variable so we can chdir to a WORKDIR (not - sure why the jar archive must be unpacked there at all ...) - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> argo-bin-1.0.31.ebuild: - Cleaned ebuild diff --git a/sci-biology/argo/ChangeLog b/sci-biology/argo/ChangeLog deleted file mode 100644 index 8f93ca397..000000000 --- a/sci-biology/argo/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/argo -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> argo-1.0.24.ebuild: - sci-biology/argo: ebuild cleanup - - 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> argo-1.0.24.ebuild: - fix java depencies syntax diff --git a/sci-biology/artemis-bin/ChangeLog b/sci-biology/artemis-bin/ChangeLog deleted file mode 100644 index 2e85ee642..000000000 --- a/sci-biology/artemis-bin/ChangeLog +++ /dev/null @@ -1,33 +0,0 @@ -# ChangeLog for sci-biology/artemis-bin -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - artemis-bin-16.0.11.ebuild: - sci-biology/artemis-bin: EAPI bump - -*artemis-bin-16.0.11 (08 Jan 2015) - - 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +artemis-bin-16.0.11.ebuild, -artemis-bin-16.0.6.ebuild: - sci-biology/artemis-bin: version bump - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - artemis-bin-16.0.6.ebuild: - sci-biology/artemis-bin: documented dependences - -*artemis-bin-16.0.6 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +artemis-bin-16.0.6.ebuild, -artemis-bin-13.2.12.ebuild: - sci-biology/artemis-bin: version bump, added a link to INSTALL docs - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> artemis-bin-13.2.12.ebuild, - metadata.xml: - Clean whitespace errors - -*artemis-bin-13.2.12 (08 Jan 2012) - - 08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +artemis-bin-13.2.12.ebuild, +metadata.xml: - initial, not yet working ebuild diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLog deleted file mode 100644 index b22824383..000000000 --- a/sci-biology/artemis/ChangeLog +++ /dev/null @@ -1,34 +0,0 @@ -# ChangeLog for sci-biology/artemis -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 09 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> artemis-9999.ebuild: - sci-biology/artemis: ebuild cleanup; officially there is not install and one - needs to keep the structure of the source tree and execute directly from - there; therefore the ebuild does not work yet - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> artemis-9999.ebuild: - sci-biology/artemis: fix SLOT operators - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> artemis-9999.ebuild: - sci-biology/artemis: documented dependences - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> artemis-9999.ebuild: - sci-biology/artemis: fixed JVM dependency, added a link to INSTALL docs - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> artemis-9999.ebuild, - metadata.xml: - Switch from git-2 to git-r3 - - 07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> artemis-9999.ebuild: - sci-biology/artemis: adjust ebuild based on upstream providing a Makefile - - 07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - artemis-9999.ebuild: - adjust ebuild based on upstream providing a Makefile - -*artemis-9999 (08 Jan 2012) - - 08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +artemis-9999.ebuild, +metadata.xml: - initial, not yet working ebuild diff --git a/sci-biology/atsas/ChangeLog b/sci-biology/atsas/ChangeLog deleted file mode 100644 index 2f6d4e7d7..000000000 --- a/sci-biology/atsas/ChangeLog +++ /dev/null @@ -1,25 +0,0 @@ -# ChangeLog for sci-biology/atsas -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 22 Dec 2014; Justin Lecher <jlec@gentoo.org> atsas-2.6.0.ebuild: - Add missing libs to installation - - 22 Dec 2014; Justin Lecher <jlec@gentoo.org> atsas-2.6.0.ebuild: - Add libdir to rpath - - 21 Dec 2014; Justin Lecher <jlec@gentoo.org> atsas-2.6.0.ebuild: - Drop quotes - - 21 Dec 2014; Justin Lecher <jlec@gentoo.org> atsas-2.6.0.ebuild: - Add missing libpath - - 17 Dec 2014; Justin Lecher <jlec@gentoo.org> atsas-2.6.0.ebuild: - Add missing deps - -*atsas-2.6.0 (17 Dec 2014) - - 17 Dec 2014; Justin Lecher <jlec@gentoo.org> +atsas-2.6.0.ebuild, - +metadata.xml: - New addition written by me - diff --git a/sci-biology/augustus/ChangeLog b/sci-biology/augustus/ChangeLog deleted file mode 100644 index a3b813ce1..000000000 --- a/sci-biology/augustus/ChangeLog +++ /dev/null @@ -1,90 +0,0 @@ -# ChangeLog for sci-biology/augustus -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*augustus-3.1 (25 May 2015) - - 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +augustus-3.1.ebuild, -augustus-3.0.3.ebuild: - sci-biology/augustus: version bump - - 16 Apr 2015; Justin Lecher <jlec@gentoo.org> augustus-3.0.3.ebuild: - sci-biology/augustus: Switch RDEPEND - DEPEND - - 08 Apr 2015; Justin Lecher <jlec@gentoo.org> augustus-3.0.3.ebuild: - sci-biology/augustus: Drop suspect DEPEND - - 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/autoeditor/ChangeLog b/sci-biology/autoeditor/ChangeLog deleted file mode 100644 index 6755dc5ef..000000000 --- a/sci-biology/autoeditor/ChangeLog +++ /dev/null @@ -1,7 +0,0 @@ -# ChangeLog for sci-biology/autoeditor -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 24 Jun 2011; Justin Lecher <jlec@gentoo.org> autoeditor-1.20.ebuild: - Shorten Summary - diff --git a/sci-biology/bambino/ChangeLog b/sci-biology/bambino/ChangeLog deleted file mode 100644 index 42aea399b..000000000 --- a/sci-biology/bambino/ChangeLog +++ /dev/null @@ -1,23 +0,0 @@ -# ChangeLog for sci-biology/bambino -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambino-1.02.ebuild, - bambino-1.06.ebuild: - fix java dependencies syntax - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> bambino-1.02.ebuild, - bambino-1.06.ebuild: - fixed DESCRIPTION - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambino-1.02.ebuild, - bambino-1.06.ebuild: - sci-biology/bambino: added more relevant homepage with some INSTALL info - -*bambino-1.02 (23 Mar 2014) -*bambino-1.06 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +bambino-1.02.ebuild, +bambino-1.06.ebuild, +metadata.xml: - sci-biology/bambino: a new package, maybe should have -bin in its name?; needs - decent inspection from java team for sure diff --git a/sci-biology/bambus/ChangeLog b/sci-biology/bambus/ChangeLog deleted file mode 100644 index 45b16d796..000000000 --- a/sci-biology/bambus/ChangeLog +++ /dev/null @@ -1,14 +0,0 @@ -# ChangeLog for sci-biology/bambus -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambus-2.33.ebuild: - sci-biology/bambus: actually do not install the outdated *.pm files but rely - on them from sci-biology/amos - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambus-2.33.ebuild: - sci-biology/bambus: fixed installation of perl-related files - - 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambus-2.33.ebuild: - sci-biology/bambus: fix installation process and use current perl-module files - from amos package instead diff --git a/sci-biology/bamtools/ChangeLog b/sci-biology/bamtools/ChangeLog deleted file mode 100644 index 90e25bed9..000000000 --- a/sci-biology/bamtools/ChangeLog +++ /dev/null @@ -1,30 +0,0 @@ -# ChangeLog for sci-biology/bamtools -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/bamtools: Add github to remote-id in metadata.xml - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> bamtools-9999.ebuild, - metadata.xml: - Switch from git-2 to git-r3 - - 09 Nov 2012; Justin Lecher <jlec@gentoo.org> -bamtools-1.0.2.ebuild, - bamtools-9999.ebuild: - Drop tree version, merge changes into live version - -*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/barnacle/ChangeLog b/sci-biology/barnacle/ChangeLog deleted file mode 100644 index e8bbb5016..000000000 --- a/sci-biology/barnacle/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/barnacle -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*barnacle-1.0.3 (05 May 2015) - - 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +barnacle-1.0.3.ebuild, +metadata.xml: - sci-biology/barnacle: a skeleton of a messy package diff --git a/sci-biology/barrnap/ChangeLog b/sci-biology/barrnap/ChangeLog deleted file mode 100644 index f4ef00240..000000000 --- a/sci-biology/barrnap/ChangeLog +++ /dev/null @@ -1,33 +0,0 @@ -# ChangeLog for sci-biology/barrnap -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*barrnap-0.4 (27 Apr 2015) - - 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +barrnap-0.4.ebuild, - barrnap-0.3.ebuild: - sci-biology/barrnap: version bump; adjust the ebuild to new install layout - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> barrnap-0.3.ebuild: - generalized dependency on perl - - 26 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> barrnap-0.3.ebuild: - sci-biology/barrnap: working ebuild although installing a pre-compiled binary - and until somebody hacks teh main perl code it need to be installed into - /usr/share/ and modifies - /home/mmokrejs/bin:/usr/local/bin:/usr/bin:/bin:/opt/bin:/usr/x86_64-pc-linux- - gnu/gcc-bin/4.8.2:/opt/vmware/bin:/opt/ucsc-genome-browser/bin:/opt/Apollo:/op - t/Tablet:$PATH:/usr/share/cgview_comparison_tool/scripts:/opt/meme/bin:/opt/45 - 4/bin:/usr/local/pedant/PEDANT2/soft/PEDANT2/PERL:/home/mokrejs/proj/pedant- - tools/perl:/home/mokrejs/proj/mysql-tools::/usr/local/staden-linux-1-6-0 - /linux-bin/:/home/mmokrejs/software/i386_linux24/usr/local/bin:/home/mmokrejs/ - bin/SPDBV:/home/mmokrejs/bin/PDBViewer_230303:/home/mmokrejs/bin/AstexViewer2/ - bin:/usr/local/modeller9v4/bin:/usr/local/chimera/bin:/opt/454/bin:/usr/local/ - pedant/PEDANT2/soft/PEDANT2/PERL:/home/mokrejs/proj/pedant- - tools/perl:/home/mokrejs/proj/mysql-tools: accordingly - -*barrnap-0.3 (15 Apr 2014) - - 15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +barrnap-0.3.ebuild, - +metadata.xml: - sci-biology/barrnap: new package, package contains bundled binaries, untested diff --git a/sci-biology/bcftools/ChangeLog b/sci-biology/bcftools/ChangeLog deleted file mode 100644 index aceee1547..000000000 --- a/sci-biology/bcftools/ChangeLog +++ /dev/null @@ -1,22 +0,0 @@ -# ChangeLog for sci-biology/bcftools -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/bcftools: Add github to remote-id in metadata.xml - -*bcftools-1.2 (02 Mar 2015) - - 02 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +bcftools-1.2.ebuild, -bcftools-1.1.ebuild: - version bump, respect CC and CFLAGS - - 15 Jan 2015; Christoph Junghans <ottxor@gentoo.org> bcftools-1.1.ebuild: - fixed license - -*bcftools-1.1 (14 Jan 2015) - - 14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +bcftools-1.1.ebuild, +metadata.xml: - sci-biology/bcftools: new package: compiles against bundled sci- - libs/htslib-1.1 but does not install it diff --git a/sci-biology/beagle/ChangeLog b/sci-biology/beagle/ChangeLog deleted file mode 100644 index 16542b71f..000000000 --- a/sci-biology/beagle/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/beagle -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 04 Sep 2015; Marius Brehler <marbre@linux.sungazer.de> beagle-4.0.ebuild: - sci-biology/beagle: Fix dependencies and slotting - - 04 Sep 2015; Marius Brehler <marbre@linux.sungazer.de> beagle-4.0.ebuild: - sci-biology/beagle: Adjust too long DESCRIPTION - -*beagle-4.0 (10 May 2015) - - 10 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +beagle-4.0.ebuild, - +metadata.xml: - sci-biology/beagle: a skeleton for a new java package with just *.java files - provided diff --git a/sci-biology/beaglecall/ChangeLog b/sci-biology/beaglecall/ChangeLog deleted file mode 100644 index fb1c4da54..000000000 --- a/sci-biology/beaglecall/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/beaglecall -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*beaglecall-20101115 (10 May 2015) - - 10 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +beaglecall-20101115.ebuild, +metadata.xml: - sci-biology/beaglecall: a skeleton for a new java package with just *.java - files provided diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog deleted file mode 100644 index aba828a9b..000000000 --- a/sci-biology/bedtools/ChangeLog +++ /dev/null @@ -1,27 +0,0 @@ -# ChangeLog for sci-biology/bedtools -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 06 Jun 2015; Justin Lecher <jlec@gentoo.org> bedtools-2.22.1.ebuild: - sci-biology/bedtools: Bump to EAPI=5 - - 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/bedtools: Add github to remote-id in metadata.xml - -*bedtools-2.22.1 (14 Jan 2015) - - 14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +bedtools-2.22.1.ebuild, -bedtools-2.20.1.ebuild: - drop old version which already landed in main tree; add ebuild for new version - -*bedtools-2.20.1 (30 May 2014) - - 30 May 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +bedtools-2.20.1.ebuild, -bedtools-2.19.1.ebuild: - sci-biology/bedtools-2.20.1: version bump - -*bedtools-2.19.1 (15 Apr 2014) - - 15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +bedtools-2.19.1.ebuild, +metadata.xml: - sci-biology/bedtools: version bump per bug #505538 diff --git a/sci-biology/biobambam/ChangeLog b/sci-biology/biobambam/ChangeLog deleted file mode 100644 index 059db7d79..000000000 --- a/sci-biology/biobambam/ChangeLog +++ /dev/null @@ -1,6 +0,0 @@ -# ChangeLog for sci-biology/biobambam -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/biobambam: Add github to remote-id in metadata.xml diff --git a/sci-biology/biopieces/ChangeLog b/sci-biology/biopieces/ChangeLog deleted file mode 100644 index b6d8dfa1c..000000000 --- a/sci-biology/biopieces/ChangeLog +++ /dev/null @@ -1,21 +0,0 @@ -# ChangeLog for sci-biology/biopieces -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 08 Mar 2015; Justin Lecher <jlec@gentoo.org> biopieces-9999.ebuild: - Fix missing test in IUSE and missing dep in python - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> -Manifest, biopieces-9999.ebuild: - sci-biology/biopieces: fix SLOT operators; correct ruby and python deps - - 13 Nov 2014; Justin Lecher <jlec@gentoo.org> biopieces-0.51.ebuild, - biopieces-9999.ebuild: - Use perl virtuals instead of core - -*biopieces-0.51 (28 Mar 2014) -*biopieces-9999 (28 Mar 2014) - - 28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +biopieces-0.51.ebuild, +biopieces-9999.ebuild, +metadata.xml: - sci-biology/biopieces: skeleton for a new package; has it's own install.sh - script diff --git a/sci-biology/blasr/ChangeLog b/sci-biology/blasr/ChangeLog deleted file mode 100644 index 799c8b231..000000000 --- a/sci-biology/blasr/ChangeLog +++ /dev/null @@ -1,19 +0,0 @@ -# ChangeLog for sci-biology/blasr -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> blasr-9999.ebuild: - Switch from git-2 to git-r3 - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> blasr-9999.ebuild: - correct license - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> blasr-9999.ebuild, metadata.xml: - Migrate to git2 eclass and EAPI=5 - -*blasr-9999 (22 Mar 2012) - - 22 Mar 2012; Andrey Kislyuk <weaver@gentoo.org> +blasr-9999.ebuild, - +metadata.xml: - New package, ebuild written by me - diff --git a/sci-biology/blue/ChangeLog b/sci-biology/blue/ChangeLog deleted file mode 100644 index 742b710bc..000000000 --- a/sci-biology/blue/ChangeLog +++ /dev/null @@ -1,21 +0,0 @@ -# ChangeLog for sci-biology/blue -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*blue-1.1.3 (26 May 2015) - - 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +blue-1.1.3.ebuild, - blue-1.1.2.ebuild: - sci-biology/blue: version bump, updated HOMEPAGE and SRC_URI - - 17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> blue-1.1.2.ebuild: - improved comments based on email from upstream - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> blue-1.1.2.ebuild: - Fix license - -*blue-1.1.2 (07 Jan 2015) - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +blue-1.1.2.ebuild, - +metadata.xml: - Initial ebuild, does not install the *.exe.so files. Do we need them? diff --git a/sci-biology/brat/ChangeLog b/sci-biology/brat/ChangeLog deleted file mode 100644 index d317a3b18..000000000 --- a/sci-biology/brat/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/brat -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*brat-1.2.4 (06 Dec 2013) - - 06 Dec 2013; Justin Lecher <jlec@gentoo.org> -brat-1.1.13.ebuild, - +brat-1.2.4.ebuild, metadata.xml: - Version Bump - - 09 May 2010; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package, ebuild written by me - diff --git a/sci-biology/breakdancer/ChangeLog b/sci-biology/breakdancer/ChangeLog deleted file mode 100644 index 7dd30ef1a..000000000 --- a/sci-biology/breakdancer/ChangeLog +++ /dev/null @@ -1,23 +0,0 @@ -# ChangeLog for sci-biology/breakdancer -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - breakdancer-9999.ebuild: - sci-biology/breakdancer: added inherit cmake - - 18 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - breakdancer-9999.ebuild: - sci-biology/breakdancer: update homepage - -*breakdancer-9999 (18 May 2015) - - 18 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +breakdancer-9999.ebuild, -Manifest, -breakdancer-1.1.2.ebuild: - sci-biology/breakdancer: upstream moved to github - -*breakdancer-1.1.2 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +breakdancer-1.1.2.ebuild, +metadata.xml: - sci-biology/breakdancer: a skeleton for a new package, needs perl help diff --git a/sci-biology/bru2nii/ChangeLog b/sci-biology/bru2nii/ChangeLog deleted file mode 100644 index b3db4ad4b..000000000 --- a/sci-biology/bru2nii/ChangeLog +++ /dev/null @@ -1,30 +0,0 @@ -# ChangeLog for sci-biology/bru2nii -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 25 Dec 2015; Marius Brehler <marbre@linux.sungazer.de> bru2nii-9999.ebuild: - sci-biology/bru2nii: Fix minorsyn - - 05 Nov 2015; Horea Christian <h.chr@mail.ru> bru2nii-9999.ebuild: - sci-biology/bru2nii: Updated USE conditional logic again - - 04 Nov 2015; Horea Christian <h.chr@mail.ru> bru2nii-9999.ebuild: - sci-biology/bru2nii: updated conditional die implemntation - - 03 Nov 2015; Horea Christian <h.chr@mail.ru> bru2nii-9999.ebuild: - sci-biology/bru2nii: - - 03 Nov 2015; Horea Christian <h.chr@mail.ru> bru2nii-9999.ebuild: - sci-biology/bru2nii: corrected die calls - - 03 Nov 2015; Horea Christian <h.chr@mail.ru> bru2nii-9999.ebuild: - sci-biology/bru2nii: added use-flag conditioning - - 03 Nov 2015; Horea Christian <h.chr@mail.ru> bru2nii-9999.ebuild: - sci-biology/bru2nii: removed testing snippet - -*bru2nii-9999 (03 Nov 2015) - - 03 Nov 2015; Horea Christian <h.chr@mail.ru> +bru2nii-9999.ebuild, - +metadata.xml: - sci-biology/bru2nii: new ebuild diff --git a/sci-biology/bx-python/ChangeLog b/sci-biology/bx-python/ChangeLog deleted file mode 100644 index 225759702..000000000 --- a/sci-biology/bx-python/ChangeLog +++ /dev/null @@ -1,17 +0,0 @@ -# ChangeLog for sci-biology/bx-python -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/bx-python: Add bitbucket to remote-id in metadata.xml - - 13 Apr 2015; Justin Lecher <jlec@gentoo.org> bx-python-0.7.2.ebuild, - bx-python-9999.ebuild: - sci-biology/bx-python: Streamline ebuild - -*bx-python-0.7.2 (12 Apr 2015) -*bx-python-9999 (12 Apr 2015) - - 12 Apr 2015; Michael Schubert <mschu.dev@gmail.com> +bx-python-0.7.2.ebuild, - +bx-python-9999.ebuild, +metadata.xml: - sci-biology/bx-python: add bx-python diff --git a/sci-biology/caftools/ChangeLog b/sci-biology/caftools/ChangeLog deleted file mode 100644 index 53ada3142..000000000 --- a/sci-biology/caftools/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/caftools -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - caftools-2.0.2.ebuild: - sci-biology/caftools: added a link to the original publication; Simon Dear - <sd@sanger.ac.uk>: host extmail.sanger.ac.uk[193.62.203.50] said: 550 unknown - - 04 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - caftools-2.0.2.ebuild: - sci-biology/caftools: clarified package description - - 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -caftools-2.0.ebuild, - caftools-2.0.2.ebuild, metadata.xml: - Drop old; Bump to EAPI=5 and fix license diff --git a/sci-biology/cast-bin/ChangeLog b/sci-biology/cast-bin/ChangeLog deleted file mode 100644 index aff5d4a34..000000000 --- a/sci-biology/cast-bin/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/cast-bin -# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*cast-bin-20080813 (06 Jan 2016) - - 06 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +cast-bin-20080813.ebuild, +metadata.xml: - sci-biology/cast-bin: new package diff --git a/sci-biology/cd-hit-auxtools/ChangeLog b/sci-biology/cd-hit-auxtools/ChangeLog deleted file mode 100644 index fcad5d226..000000000 --- a/sci-biology/cd-hit-auxtools/ChangeLog +++ /dev/null @@ -1,14 +0,0 @@ -# ChangeLog for sci-biology/cd-hit-auxtools -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 01 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - cd-hit-auxtools-0.5.ebuild: - sci-biology/cd-hit-auxtools: added HTML manual page - -*cd-hit-auxtools-0.5 (01 Jun 2014) - - 01 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +cd-hit-auxtools-0.5.ebuild, +files/0.5-gentoo.patch, +metadata.xml: - sci-biology/cd-hit-auxtools: new package, needs gcc<=4.6.4 or some CXXFLAG to - loosen g++ strictness diff --git a/sci-biology/cd-hit/ChangeLog b/sci-biology/cd-hit/ChangeLog deleted file mode 100644 index 051ec77c9..000000000 --- a/sci-biology/cd-hit/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/cd-hit -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 01 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> cd-hit-4.6.1.ebuild: - sci-biology/cd-hit-4.6.1: forgot to re-enable the reworked patch - -*cd-hit-4.6.1 (01 Jun 2014) - - 01 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +cd-hit-4.6.1.ebuild, +files/4.6.1-gentoo.patch, +metadata.xml: - sci-biology/cd-hit-4.6.1: version bump diff --git a/sci-biology/cegma/ChangeLog b/sci-biology/cegma/ChangeLog deleted file mode 100644 index 3939e92ff..000000000 --- a/sci-biology/cegma/ChangeLog +++ /dev/null @@ -1,14 +0,0 @@ -# ChangeLog for sci-biology/cegma -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> cegma-2.5.ebuild: - sci-biology/cegma: re-added KEYWORDS because sci-biology/ncbi-tools++ is now - available; fixed installation of perl-related files; dropped hmmer from DEPEND - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> cegma-2.5.ebuild: - Fix license;drop keywords due to missing keyowrds of deps - - 10 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +cegma-2.5.ebuild, - +metadata.xml: - new package; install *.pm into PERL5LIB/cegma and pass that via env.d diff --git a/sci-biology/cgview-bin/ChangeLog b/sci-biology/cgview-bin/ChangeLog deleted file mode 100644 index 0cbb6fd1c..000000000 --- a/sci-biology/cgview-bin/ChangeLog +++ /dev/null @@ -1,17 +0,0 @@ -# ChangeLog for sci-biology/cgview-bin -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - cgview-bin-20131130.ebuild: - sci-biology/cgview-bin: fixed installation of perl-related files - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> cgview-bin-20131130.ebuild: - sci-biology/cgview-bin: fix SLOT operators; drop KEYWORDS as fetch failed - -*cgview-bin-20131130 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +cgview-bin-20131130.ebuild, +metadata.xml: - sci-biology/cgview-bin: new package, needs java team testing, maybe dev- - java/batik is misisng svg USE flag? diff --git a/sci-biology/clover/ChangeLog b/sci-biology/clover/ChangeLog deleted file mode 100644 index 3d5b69233..000000000 --- a/sci-biology/clover/ChangeLog +++ /dev/null @@ -1,26 +0,0 @@ -# ChangeLog for sci-biology/clover -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -clover-2010.02.19.ebuild, - +clover-2011.10.24.ebuild, metadata.xml: - Version Bump; fixed license; respect LDFLAGS - -*clover-2010.02.19 (23 Aug 2010) - - 23 Aug 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> - -clover-2006.07.17.ebuild, +clover-2010.02.19.ebuild: - Trivial version bump. Thanks to Martin Mokrejš. - - 23 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> - clover-2006.07.17.ebuild: - QA fixes - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> - +clover-2006.07.17.ebuild: - Mass import from sunrise - - 15 Mar 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +clover-2006.07.17.ebuild, - +metadata.xml: - new package (bug 142269) - diff --git a/sci-biology/cluster/ChangeLog b/sci-biology/cluster/ChangeLog deleted file mode 100644 index 8cf657bdf..000000000 --- a/sci-biology/cluster/ChangeLog +++ /dev/null @@ -1,30 +0,0 @@ -# ChangeLog for sci-biology/cluster -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> cluster-1.50.ebuild, - cluster-1.50-r1.ebuild, metadata.xml: - Correct motif dep naming - - 09 Jun 2012; Justin Lecher <jlec@gentoo.org> cluster-1.50.ebuild, - cluster-1.50-r1.ebuild: - Correct masking, #419999 - -*cluster-1.50-r1 (07 Jun 2012) - - 07 Jun 2012; Justin Lecher <jlec@gentoo.org> +cluster-1.50-r1.ebuild: - Rename cluster to cluster3, #419999 - -*cluster-1.50 (24 May 2012) - - 24 May 2012; Justin Lecher <jlec@gentoo.org> -cluster-1.38.ebuild, - +cluster-1.50.ebuild, metadata.xml: - Version Bump, Move to EAPI=4 - - 23 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> - cluster-1.38.ebuild: - QA fixes - - 09 Aug 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog: - Initial import of cluster-1.36 thanks to Favero Francesco - diff --git a/sci-biology/clview/ChangeLog b/sci-biology/clview/ChangeLog deleted file mode 100644 index 6103322ce..000000000 --- a/sci-biology/clview/ChangeLog +++ /dev/null @@ -1,6 +0,0 @@ -# ChangeLog for sci-biology/clview -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 04 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> clview-0.1.ebuild: - sci-biology/clview: add dependency on =x11-libs/fox-1.6* diff --git a/sci-biology/cnrun/ChangeLog b/sci-biology/cnrun/ChangeLog deleted file mode 100644 index 7264b83fd..000000000 --- a/sci-biology/cnrun/ChangeLog +++ /dev/null @@ -1,6 +0,0 @@ -# ChangeLog for sci-biology/cnrun -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 19 Feb 2015; Andrei Zavada <johnhommer@gmail.com> cnrun-2.0.2.ebuild: - sci-biology/cnrun: initial ebuild, repoman clean diff --git a/sci-biology/codonw/ChangeLog b/sci-biology/codonw/ChangeLog deleted file mode 100644 index 4bcea2c44..000000000 --- a/sci-biology/codonw/ChangeLog +++ /dev/null @@ -1,31 +0,0 @@ -# ChangeLog for sci-biology/codonw -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 15 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - codonw-1.4.4-r2.ebuild: - sci-biology/codonw: add original Thesis of John Peden describing codonw - package in more detail - - 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/codonw: Updating remote-id in metadata.xml - -*codonw-1.4.4-r2 (30 May 2015) - - 30 May 2015; Justin Lecher <jlec@gentoo.org> +codonw-1.4.4-r2.ebuild, - -codonw-1.4.4-r1.ebuild, metadata.xml: - sci-biology/codonw: Workaround file collision by appending PN to every - command, bug #344713, bug #550388 - - 10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> - condow-1.4.4-r1.ebuild: - Move to EAPI=5. - -*codonw-1.4.4-r1 (08 Nov 2010) - - 08 Nov 2010; Kacper Kowalik <xarthisius@gentoo.org> -codonw-1.4.4.ebuild, - +codonw-1.4.4-r1.ebuild: - Respect CC,CFLAGS,LDFLAGS. Add missing die. Drop empty deps. - - 28 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package sci-biology/codonw, ebuild written by me diff --git a/sci-biology/conform-gt/ChangeLog b/sci-biology/conform-gt/ChangeLog deleted file mode 100644 index d90924a04..000000000 --- a/sci-biology/conform-gt/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/conform-gt -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*conform-gt-1174 (10 May 2015) - - 10 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +conform-gt-1174.ebuild, +metadata.xml: - sci-biology/conform-gt: a skeleton for a new java package with just *.java - files provided diff --git a/sci-biology/conifer/ChangeLog b/sci-biology/conifer/ChangeLog deleted file mode 100644 index 274438939..000000000 --- a/sci-biology/conifer/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/conifer -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*conifer-0.2.2 (16 Mar 2014) - - 16 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +conifer-0.2.2.ebuild, +metadata.xml: - sci-biology/conifer: new package diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog deleted file mode 100644 index 9943dc885..000000000 --- a/sci-biology/consed/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/consed -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*consed-29 (23 Jul 2015) - - 23 Jul 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +consed-29.ebuild, - +metadata.xml: - sci-biology/consed-29.0: version bump diff --git a/sci-biology/consed2gap/ChangeLog b/sci-biology/consed2gap/ChangeLog deleted file mode 100644 index 4b92bec71..000000000 --- a/sci-biology/consed2gap/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/consed2gap -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 24 Sep 2014; Justin Lecher <jlec@gentoo.org> consed2gap-20050520.ebuild, - metadata.xml: - Bump to EAPI=5 - -*consed2gap-20050520 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +consed2gap-20050520.ebuild, +metadata.xml: - sci-biology/consed2gap: new package, works diff --git a/sci-biology/coral/ChangeLog b/sci-biology/coral/ChangeLog deleted file mode 100644 index cd6b4e0fb..000000000 --- a/sci-biology/coral/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/coral -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*coral-1.4 (17 Mar 2015) - - 17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +coral-1.4.ebuild, - +metadata.xml: - new package diff --git a/sci-biology/cortex_var/ChangeLog b/sci-biology/cortex_var/ChangeLog deleted file mode 100644 index 88e9c0af0..000000000 --- a/sci-biology/cortex_var/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/cortex_var -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - cortex_var-1.0.5.21.ebuild: - sci-biology/cortex_var: cleanup ebuild syntax - -*cortex_var-1.0.5.21 (18 Apr 2015) - - 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +cortex_var-1.0.5.21.ebuild, +metadata.xml: - sci-biology/cortex_var: new package with bundled htslib and gsl libraries diff --git a/sci-biology/cutadapt/ChangeLog b/sci-biology/cutadapt/ChangeLog deleted file mode 100644 index 55c3fb1b3..000000000 --- a/sci-biology/cutadapt/ChangeLog +++ /dev/null @@ -1,23 +0,0 @@ -# ChangeLog for sci-biology/cutadapt -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*cutadapt-1.5 (11 Sep 2014) - - 11 Sep 2014; Jauhien Piatlicki <jauhien@gentoo.org> +cutadapt-1.5.ebuild: - version bump - - 11 Sep 2014; Jauhien Piatlicki <jauhien@gentoo.org> cutadapt-1.2.1.ebuild, - cutadapt-1.4.1.ebuild: - fix SRC_URI - - 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -cutadapt-1.0.ebuild, - +cutadapt-1.2.1.ebuild, metadata.xml: - Version Bump; Bump to EAPI5 and distutils-r1.eclass - -*cutadapt-1.0 (02 Mar 2012) - - 02 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +cutadapt-1.0.ebuild, +metadata.xml: - initial ebuild - diff --git a/sci-biology/dawg/ChangeLog b/sci-biology/dawg/ChangeLog deleted file mode 100644 index a6b5302fc..000000000 --- a/sci-biology/dawg/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/dawg -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Nov 2014; Justin Lecher <jlec@gentoo.org> -dawg-1.1.1.ebuild, - +dawg-1.1.2.ebuild, -files/dawg-1.1.1-gcc43.patch, - +files/dawg-1.1.2-gcc43.patch: - Bump EAPI; version Bump - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: - Fixed herd entry in metadata.xml - - 24 Jun 2008; weaver <weaver@gentoo.org> +files/dawg-1.1.1-gcc43.patch, - +dawg-1.1.1.ebuild: - New package - diff --git a/sci-biology/dcmstack/ChangeLog b/sci-biology/dcmstack/ChangeLog deleted file mode 100644 index 333d2d37a..000000000 --- a/sci-biology/dcmstack/ChangeLog +++ /dev/null @@ -1,24 +0,0 @@ -# ChangeLog for sci-biology/dcmstack -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: - gentoo does not support python 2_6 - - 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: - corrected python compatibilities - - 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: - added python 3.3 compatibility - - 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: - removed unneeded bits, sorted eclasses - - 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: - updated deps - -*dcmstack-9999 (31 Mar 2015) - - 31 Mar 2015; Horea Christian <h.chr@mail.ru> +dcmstack-9999.ebuild, - +metadata.xml: - new package, initial draft diff --git a/sci-biology/discrover/ChangeLog b/sci-biology/discrover/ChangeLog deleted file mode 100644 index b5a30f745..000000000 --- a/sci-biology/discrover/ChangeLog +++ /dev/null @@ -1,49 +0,0 @@ -# ChangeLog for sci-biology/discrover -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/discrover: Add github to remote-id in metadata.xml - -*discrover-1.6.0 (18 Mar 2015) - - 18 Mar 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.6.0.ebuild, - -discrover-1.5.2.ebuild, discrover-9999.ebuild, metadata.xml: - sci-biology/discrover: version bump; drop USE flag - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> discrover-1.5.2.ebuild, - discrover-9999.ebuild, metadata.xml: - sci-biology/discrover: fix SLOT operators; correct ruby deps - -*discrover-1.5.2 (27 Jan 2015) - - 27 Jan 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.5.2.ebuild, - -discrover-1.4.1.ebuild, discrover-9999.ebuild, metadata.xml: - sci-biology/discrover: bump package version, add USE flag for link-time - optimization, install doc to /usr/share/doc/${PF} - -*discrover-1.4.1 (05 Jan 2015) - - 05 Jan 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.4.1.ebuild, - -discrover-1.4.0.ebuild: - Bump patch version - -*discrover-1.4.0 (04 Jan 2015) - - 04 Jan 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.4.0.ebuild, - -discrover-1.3.1.ebuild, discrover-9999.ebuild, metadata.xml: - Bump minor version to 1.4.0. Introduces a new USE flag: 'cairo'. - x11-libs/cairo is used to generate sequence logos. The USE flag 'logo' has - been renamed to 'tikzlogo'. The tikzlogo Ruby script served the purpose that - is now fulfilled by the Cairo-based code. tikzlogo requires Ruby, ImageMagick, - and a full TeX Live installation (including the large dev-texlive/texlive- - latexextra). Compared to that, the new Cairo-based code has much reduced - dependencies, and is hence the preferred way to generate sequence logos. - -*discrover-1.3.1 (15 Dec 2014) - - 15 Dec 2014; Jonas Maaskola <jonas@maaskola.de> +discrover-1.3.1.ebuild, - -discrover-1.1.2.ebuild, discrover-9999.ebuild: - sci-biology/discrover: version bump; add to RDEPEND Bump ebuild for new - release. When the USE flag "logo" is used, we also need to depend on texlive- - latexextra for the standalone package. diff --git a/sci-biology/dna2pep/ChangeLog b/sci-biology/dna2pep/ChangeLog deleted file mode 100644 index f1a8fddb3..000000000 --- a/sci-biology/dna2pep/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/dna2pep -# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 04 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> dna2pep-1.1.ebuild: - sci-biology/dna2pep: fix shebang lines - -*dna2pep-1.1 (04 Jan 2016) - - 04 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +dna2pep-1.1.ebuild, - +metadata.xml: - sci-biology/dna2pep: new package that will needed by sci-biology/Annocript diff --git a/sci-biology/ePCR/ChangeLog b/sci-biology/ePCR/ChangeLog deleted file mode 100644 index 9d6c35e70..000000000 --- a/sci-biology/ePCR/ChangeLog +++ /dev/null @@ -1,7 +0,0 @@ -# ChangeLog for sci-biology/ePCR -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> ePCR-2.3.12.ebuild: - Fix license - diff --git a/sci-biology/edena/ChangeLog b/sci-biology/edena/ChangeLog deleted file mode 100644 index 2aa261269..000000000 --- a/sci-biology/edena/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/edena -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*edena-3.131028 (15 Jan 2015) - - 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +edena-3.131028.ebuild, +metadata.xml: - sci-biology/edena: new package diff --git a/sci-biology/epga/ChangeLog b/sci-biology/epga/ChangeLog deleted file mode 100644 index 787835328..000000000 --- a/sci-biology/epga/ChangeLog +++ /dev/null @@ -1,18 +0,0 @@ -# ChangeLog for sci-biology/epga -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/epga: Add github to remote-id in metadata.xml - - 09 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> epga-9999.ebuild: - Switch from git-2 to git-r3; Cleanup - - 18 Jan 2015; Christoph Junghans <ottxor@gentoo.org> epga-9999.ebuild: - license defined - -*epga-9999 (15 Jan 2015) - - 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +epga-9999.ebuild, - +metadata.xml: - new package; no LICENSE file diff --git a/sci-biology/erpin/ChangeLog b/sci-biology/erpin/ChangeLog deleted file mode 100644 index 4d3368ae2..000000000 --- a/sci-biology/erpin/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/erpin -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 16 Jun 2013; Justin Lecher <jlec@gentoo.org> erpin-5.5b.ebuild, metadata.xml: - Bump to EAPI=5 and respect FLAGS / AR - - 23 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package, ebuild written by me - diff --git a/sci-biology/est2assembly/ChangeLog b/sci-biology/est2assembly/ChangeLog deleted file mode 100644 index 164cb7901..000000000 --- a/sci-biology/est2assembly/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/est2assembly -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - est2assembly-1.08.ebuild: - fix S variable, use PV in URI - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> est2assembly-1.08.ebuild, - est2assembly-9999.ebuild: - Bump EAPI; drop KEYWORDS from live ebuild; fix deps - diff --git a/sci-biology/estscan/ChangeLog b/sci-biology/estscan/ChangeLog deleted file mode 100644 index a495a5353..000000000 --- a/sci-biology/estscan/ChangeLog +++ /dev/null @@ -1,30 +0,0 @@ -# ChangeLog for sci-biology/estscan -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 24 Sep 2014; Justin Lecher <jlec@gentoo.org> estscan-3.0.3.ebuild: - Bump to EAPI=5 - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: - Add local USE to metadata.xml - - 12 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - estscan-3.0.3.ebuild: - remove offending double-quotes - - 12 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - estscan-3.0.3.ebuild: - ebuild cleanup, works, releasing for testing estscan-3.0.3.ebuild - - 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - estscan-3.0.3.ebuild: - some ebuild cleanup estscan-3.0.3.ebuild - - 23 Jun 2011; Justin Lecher <jlec@gentoo.org> estscan-3.0.3.ebuild, - metadata.xml: - Streamlined fortran-2 eclass usage - - 21 Jun 2011; Justin Lecher <jlec@gentoo.org> estscan-3.0.3.ebuild, - metadata.xml: - Added fortran-2.eclass support - diff --git a/sci-biology/eval/ChangeLog b/sci-biology/eval/ChangeLog deleted file mode 100644 index 5de140c76..000000000 --- a/sci-biology/eval/ChangeLog +++ /dev/null @@ -1,27 +0,0 @@ -# ChangeLog for sci-biology/eval -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> eval-2.2.8.ebuild: - sci-biology/eval: fixed installation of perl-related files - - 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> eval-2.2.8.ebuild: - removing KEYWORDS until the perl files are installed to some other place. At - the moment I get: 'perl-module.eclass: Suspicious environment values found. - PERL5LIB="/usr/lib64/perl5/vendor_perl/5.18.2/eval"' - - 13 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> eval-2.2.8.ebuild: - fix Gentoo copyright header - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> eval-2.2.8.ebuild: - clean up - - 04 Sep 2014; Jauhien Piatlicki <jauhien@gentoo.org> eval-2.2.8.ebuild: - Add HOMEPAGE and LICENSE - -*eval-2.2.8 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +eval-2.2.8.ebuild, - +metadata.xml: - new package; needs perl team help to install this evil package with Eval.pm - into PERL_PATH diff --git a/sci-biology/exomiser-bin/ChangeLog b/sci-biology/exomiser-bin/ChangeLog deleted file mode 100644 index d80f48755..000000000 --- a/sci-biology/exomiser-bin/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/exomiser-bin -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*exomiser-bin-7.0.0 (05 May 2015) - - 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +exomiser-bin-7.0.0.ebuild, +metadata.xml: - sci-biology/exomiser-bin: new package diff --git a/sci-biology/exonerate-gff3/ChangeLog b/sci-biology/exonerate-gff3/ChangeLog deleted file mode 100644 index e4ab1cc5c..000000000 --- a/sci-biology/exonerate-gff3/ChangeLog +++ /dev/null @@ -1,21 +0,0 @@ -# ChangeLog for sci-biology/exonerate-gff3 -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/exonerate-gff3: Add github to remote-id in metadata.xml - -*exonerate-gff3-9999 (02 Apr 2015) - - 02 Apr 2015; Justin Lecher <jlec@gentoo.org> +exonerate-gff3-9999.ebuild, - +files/exonerate-gff3-9999-asneeded.patch, -exonerate-gff3-2.2.0-r1.ebuild, - -files/exonerate-gff3-2.2.0-asneeded.patch, metadata.xml: - sci-biology/exonerate-gff3: Move live ebuild to 9999 - -*exonerate-gff3-2.2.0-r1 (30 Mar 2015) - - 30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +exonerate-gff3-2.2.0-r1.ebuild, +files/exonerate-gff3-2.2.0-asneeded.patch, - +metadata.xml: - sci-biology/exonerate-gff3: an improved version of exonerate-2.2.0 with GFF3 - format output support diff --git a/sci-biology/fastdnaml/ChangeLog b/sci-biology/fastdnaml/ChangeLog deleted file mode 100644 index 8105e1a0e..000000000 --- a/sci-biology/fastdnaml/ChangeLog +++ /dev/null @@ -1,14 +0,0 @@ -# ChangeLog for sci-biology/fastdnaml -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*fastdnaml-1.2.2_p10 (10 Nov 2014) - - 10 Nov 2014; Justin Lecher <jlec@gentoo.org> -fastdnaml-1.2.2.ebuild, - +fastdnaml-1.2.2_p10.ebuild, metadata.xml: - Bump EAPI; version Bump - - 07 Jul 2008; weaver <weaver@gentoo.org> +metadata.xml, - +fastdnaml-1.2.2.ebuild: - New ebuild, bug 114089 - diff --git a/sci-biology/fastqc/ChangeLog b/sci-biology/fastqc/ChangeLog deleted file mode 100644 index d69b7c382..000000000 --- a/sci-biology/fastqc/ChangeLog +++ /dev/null @@ -1,44 +0,0 @@ -# ChangeLog for sci-biology/fastqc -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - fastqc-0.11.3.ebuild: - more comments on the external dependencies - - 10 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - fastqc-0.11.3.ebuild: - add dependency on jhdf5; more ebuild cleanup - -*fastqc-0.11.3 (30 May 2015) - - 30 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +fastqc-0.11.3.ebuild, -fastqc-0.11.2.ebuild: - sci-biology/fastqc: version bump, added perl dependency, Apache ant-building - does not work still - - 05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +files/build.xml, - fastqc-0.11.2.ebuild: - added build.xml exported by author from Eclipse IDE (it doesn't work under ant - eclasses in my hands) - -*fastqc-0.11.2 (24 Feb 2015) - - 24 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +fastqc-0.11.2.ebuild, -fastqc-0.10.1.ebuild: - version bump; still missing src_compile() logic - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> fastqc-0.10.1.ebuild: - clean up - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - fastqc-0.10.1.ebuild: - sci-biology/fastqc: reverse-engineered where sam-1.32.jar is likely coming - from - -*fastqc-0.10.1 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +fastqc-0.10.1.ebuild, +metadata.xml: - sci-biology/fastqc: a skeleton for a new perl wrapper calling java libs, need - help diff --git a/sci-biology/fastx_toolkit/ChangeLog b/sci-biology/fastx_toolkit/ChangeLog deleted file mode 100644 index 530efc94f..000000000 --- a/sci-biology/fastx_toolkit/ChangeLog +++ /dev/null @@ -1,26 +0,0 @@ -# ChangeLog for sci-biology/fastx_toolkit -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/fastx_toolkit: Add github to remote-id in metadata.xml - -*fastx_toolkit-0.0.14 (20 Jan 2014) - - 20 Jan 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +fastx_toolkit-0.0.14.ebuild, -fastx_toolkit-0.0.13.2.ebuild: - Version bump, releases were moved to github - - 20 Jan 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - fastx_toolkit-0.0.13.2.ebuild: - Moved dependency on gtextlib - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> fastx_toolkit-0.0.13.2.ebuild, - +metadata.xml: - Bump to EAPI=5 and add missing metadata.xml - -*fastx_toolkit-0.0.13.2 (29 Aug 2013) - - 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +fastx_toolkit-0.0.13.2.ebuild: - New package for FASTA/FASTQ preprocessing. diff --git a/sci-biology/ffindex/ChangeLog b/sci-biology/ffindex/ChangeLog deleted file mode 100644 index a998bf29b..000000000 --- a/sci-biology/ffindex/ChangeLog +++ /dev/null @@ -1,35 +0,0 @@ -# ChangeLog for sci-biology/ffindex -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - ffindex-0.9.9.6.ebuild: - sci-biology/ffindex: install under USE=-mpi cases as well - - 19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - ffindex-0.9.9.6.ebuild: - sci-biology/ffindex: add DEPEND on virtual/mpi - - 19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - ffindex-0.9.9.6.ebuild: - sci-biology/ffindex: add optional USE=mpi - -*ffindex-0.9.9.6 (19 Nov 2015) - - 19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +ffindex-0.9.9.6.ebuild, -ffindex-0.9.9.3.ebuild: - sci-biology/ffindex: fix HOMEPAGE, version bump - - 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/ffindex: Add github to remote-id in metadata.xml - - 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - ffindex-0.9.9.3.ebuild: - sci-biology/ffindex: fix SRC_URI because TransDecoder which contains this - bundled thing has moved - -*ffindex-0.9.9.3 (08 Jan 2015) - - 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +ffindex-0.9.9.3.ebuild, +metadata.xml: - sci-biology/ffindex: new package, maybe fits better under some other herd? diff --git a/sci-biology/flexbar/ChangeLog b/sci-biology/flexbar/ChangeLog deleted file mode 100644 index 013aab784..000000000 --- a/sci-biology/flexbar/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/flexbar -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*flexbar-2.4 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +flexbar-2.4.ebuild, - +metadata.xml: - sci-biology/flexbar: new package, needs >=sci-biology/seqan-1.4.1 to appear - first in the tree diff --git a/sci-biology/freebayes/ChangeLog b/sci-biology/freebayes/ChangeLog deleted file mode 100644 index 80fa1a4bf..000000000 --- a/sci-biology/freebayes/ChangeLog +++ /dev/null @@ -1,27 +0,0 @@ -# ChangeLog for sci-biology/freebayes -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/freebayes: Add github to remote-id in metadata.xml - - 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - freebayes-9999.ebuild: - install also the vcftools binaries although it should be a separate package - - 11 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - freebayes-9999.ebuild: - added src_install() - - 11 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - freebayes-9999.ebuild: - ebuild cleanup; the git clone --recursive flag does not work - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> freebayes-9999.ebuild: - fixed DESCRIPTION - -*freebayes-9999 (24 Mar 2014) - - 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +freebayes-9999.ebuild, +metadata.xml: - a new package skeleton; need to retrive from git in a recursive way diff --git a/sci-biology/fsa/ChangeLog b/sci-biology/fsa/ChangeLog deleted file mode 100644 index 354bc8f0b..000000000 --- a/sci-biology/fsa/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/fsa -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*fsa-1.15.7 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +fsa-1.15.7.ebuild, - +metadata.xml: - sci-biology/fsa: new package, enforces its own CXXFLAGS, compiles also some - java stuff, source code does not compile diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog deleted file mode 100644 index f802c575b..000000000 --- a/sci-biology/fsl/ChangeLog +++ /dev/null @@ -1,91 +0,0 @@ -# ChangeLog for sci-biology/fsl -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 14 Nov 2015; <chymera@gentoo.org> fsl-5.0.8.ebuild: - sci-biology/fsl: added info about updating environment - - 04 Nov 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.8.ebuild: - sci-biology/fsl: new sources location (upstream removes old sources) - - 09 Apr 2015; Horea Christian <h.chr@mail.ru> - -files/fsl-5.0.4-fsldir_redux.patch: - removed 5.0.4 redux patch - - 07 Apr 2015; Horea Christian <h.chr@mail.ru> -fsl-5.0.4.ebuild, - -fsl-5.0.5.ebuild: - removed ebuilds with unavailable sources - - 07 Apr 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: - added new gentoo fsl-5.0.6 source location - - 30 Mar 2015; Horea Christian <h.chr@mail.ru> - +files/fsl-5.0.8-fsldir_redux.patch, -files/fsl-5.0.8-redux.patch, - fsl-5.0.8.ebuild: - implemented 5.0.8 fsldir redux patch - - 30 Mar 2015; Horea Christian <h.chr@mail.ru> +files/fsl-5.0.8-redux.patch: - 5.0.8 redux patch by François Bissey - - 29 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.8.ebuild: - using the 5.0.8 headers patch - - 29 Mar 2015; Horea Christian <h.chr@mail.ru> +files/fsl-5.0.8-headers.patch, - files/fsl-5.0.4-headers.patch: - reimplmented pathc fsl-5.0.4-headers - - 28 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.8.ebuild: - ported changes from 5.0.6 regarding FSLDIR - - 28 Mar 2015; Horea Christian <h.chr@mail.ru> files/fsl-5.0.4-headers.patch: - hunk implemented by upstream - - 28 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.8.ebuild: - using new setup patch file for new ebuild - - 28 Mar 2015; Horea Christian <h.chr@mail.ru> +files/fsl-5.0.8-setup.patch: - new pathc by François Bissey - - 25 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.4.ebuild, - fsl-5.0.5.ebuild, fsl-5.0.8.ebuild: - added licences to all versions - - 25 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: - added license for included gdchart - - 25 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: - set the correct licences - - 11 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: - installing fslversion - - 11 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: - sed-ing before installing - - 10 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: - changed grep wrapper - - 10 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: - reformatted tcl sed calls - - 10 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: - fixed tcl location according to instructions by kiwifb - - 10 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: - installing fsl.sh - - 05 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: - removing faulty check - - 04 Mar 2015; Horea Christian <h.chr@mail.ru> files/99fsl: - added FSLPATH - -*fsl-5.0.8 (20 Feb 2015) - - 20 Feb 2015; Horea Christian <h.chr@mail.ru> +fsl-5.0.8.ebuild: - bumped version - - 18 Oct 2013; François Bissey <francois.bissey@canterbury.ac.nz> - +files/fsl-5.0.4-headers.patch, +files/fsl-5.0.4-setup.patch, +metadata.xml, - fsl-5.0.4.ebuild: - use system package, verbose build. diff --git a/sci-biology/full_lengther_next/ChangeLog b/sci-biology/full_lengther_next/ChangeLog deleted file mode 100644 index 6ae9e1311..000000000 --- a/sci-biology/full_lengther_next/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/full_lengther_next -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 25 Dec 2015; Marius Brehler <marbre@linux.sungazer.de> - full_lengther_next-0.0.8.ebuild: - sci-biology/full_lengther_next: Fix header, remove ruby19 - -*full_lengther_next-0.0.8 (02 Dec 2015) - - 02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +full_lengther_next-0.0.8.ebuild, +metadata.xml: - sci-biology/full_lengther_next: new package diff --git a/sci-biology/gap2caf/ChangeLog b/sci-biology/gap2caf/ChangeLog deleted file mode 100644 index f747634d4..000000000 --- a/sci-biology/gap2caf/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sci-biology/gap2caf -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 04 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - gap2caf-2.1.0.ebuild: - sci-biology/gap2caf: remove -rpath-link from src/Makefile - - 16 Jun 2013; Justin Lecher <jlec@gentoo.org> gap2caf-2.1.0.ebuild, - metadata.xml: - Bump to EAPI=5 and fix license; make it build with eautoreconf diff --git a/sci-biology/gbench/ChangeLog b/sci-biology/gbench/ChangeLog deleted file mode 100644 index a0efa74eb..000000000 --- a/sci-biology/gbench/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sci-biology/gbench -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*gbench-2.3.2 (30 Jul 2011) - - 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +gbench-2.3.2.ebuild, +metadata.xml: - backbone of a new package, should probably use a lot of stuff from - ncbi-tools++ ebuild - diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog deleted file mode 100644 index 6d840a2c4..000000000 --- a/sci-biology/gbrowse/ChangeLog +++ /dev/null @@ -1,146 +0,0 @@ -# ChangeLog for sci-biology/gbrowse -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 13 Nov 2014; Justin Lecher <jlec@gentoo.org> gbrowse-2.39.ebuild, - gbrowse-2.45.ebuild, gbrowse-2.48.ebuild: - Use perl virtuals instead of core - - 24 Sep 2014; Justin Lecher <jlec@gentoo.org> gbrowse-2.39.ebuild, - gbrowse-2.45.ebuild, gbrowse-2.48.ebuild, metadata.xml: - Bump to EAPI=5 - - 22 May 2012; Justin Lecher <jlec@gentoo.org> gbrowse-2.39.ebuild, - gbrowse-2.45.ebuild, gbrowse-2.48.ebuild: - Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits - -*gbrowse-2.48 (28 Feb 2012) - - 28 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - gbrowse-2.45.ebuild, +gbrowse-2.48.ebuild: - added dependency on <=sci-biology/primer3-2, per - http://generic-model-organism-system-database.450254.n5.nabble.com/PrimerDesi - gner-working-in-2-40-tp4724773p5479669.html - -*gbrowse-2.45 (17 Jan 2012) - - 17 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +gbrowse-2.45.ebuild, +files/GBrowseInstall.pm-2.45.patch: - version bump and some fixes so that it works with webappconfig again? - - 17 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - gbrowse-2.39.ebuild: - added dev-perl/TermReadKey to dependencies - - 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - gbrowse-2.39.ebuild, +files/disable-gbrowse_metadb_config.pl.patch, - +files/gbrowse_metadb_config.pl.patch, +files/symlink.patch: - Make sure portage does not run gbrowse_metadb_config.pl otherwise sandbox - violation occurs when modifying /var/www/gbrowse2/databases/users.sqlite* - file, maybe we could copy these during src_install to the {}, fix there and - copy back to live filesystem? Improve error handling in - gbrowse_metadb_config.pl. Fix symlink creation during install procedure. - gbrowse-2.39.ebuild files/GBrowseInstall.pm-2.39.patch files/destdir.patch - files/disable-gbrowse_metadb_config.pl.patch files/fix-PNG-export.patch - files/gbrowse-slave.default files/gbrowse-slave.init.d - files/gbrowse.conf.vhosts.d files/gbrowse_metadb_config.pl.patch - files/symlink.patch - - 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - gbrowse-2.39.ebuild, +files/fix-PNG-export.patch: - sci-biology/gbrowse: add missing brackets cause a perl error while exporting - a PNG image gbrowse-2.39.ebuild files/fix-PNG-export.patch - - 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - gbrowse-2.39.ebuild, +files/destdir.patch: - added support for --destdir, patch sent to upstream gbrowse-2.39.ebuild - - 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - gbrowse-2.39.ebuild, +files/destdir.patch: - added support for --destdir, patch sent to upstream - - 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - -gbrowse-2.38.ebuild, -files/GBrowseInstall.pm-2.38.patch, - +gbrowse-2.39.ebuild, +files/GBrowseInstall.pm-2.39.patch: - version bump but still need to rewrite upstream's install procedure to - prevent 'mkdir /var/lib/gbrowse2' from happening - -*gbrowse-2.39 (30 Jul 2011) - - 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - -gbrowse-2.38.ebuild, -files/GBrowseInstall.pm-2.38.patch, - +gbrowse-2.39.ebuild, +files/GBrowseInstall.pm-2.39.patch: - version bump but still need to rewrite upstream's install procedure to - prevent 'mkdir /var/lib/gbrowse2' from happening - - 08 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - gbrowse-2.38.ebuild: - Added dependency on >=perl-gcpan/Text-ParseWords-3.27, documented requirement - of Bio::Root::Version >= 1.0069 - -*gbrowse-2.38 (26 Jun 2011) - - 26 Jun 2011; Justin Lecher <jlec@gentoo.org> -gbrowse-2.26.ebuild, - -files/GBrowseInstall.pm-2.26.patch, - -files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch, - -gbrowse-2.33.ebuild, -files/GBrowseInstall.pm-2.33.patch, - +gbrowse-2.38.ebuild, +files/GBrowseInstall.pm-2.38.patch: - Version Bump - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -gbrowse-1.70.ebuild, - -gbrowse-2.00.ebuild, gbrowse-2.26.ebuild, gbrowse-2.33.ebuild: - Cleaned ebuild, 'http://search.cpan.org/CPAN' found in thirdpartymirrors - - 05 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - Version bump - - 11 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - Version bump, rewrite and rename to gbrowse - - 29 Jul 2007; Christian Heim <phreak@gentoo.org> - generic-genome-browser-1.58.ebuild: - Fixing the DEPEND/RDEPEND for the move of net-www/apache to - www-servers/apache (#78622). - - 23 Nov 2006; Francesco Riosa <vivo@gentoo.org> - generic-genome-browser-1.58.ebuild: - dev-db/mysql => virtual/mysql - - 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Stepping down from maintaining this package. - - 13 Feb 2006; Michael Cummings <mcummings@gentoo.org> - generic-genome-browser-1.58.ebuild: - Virtuals for some perl-core deps - - 28 Nov 2005; <mcumming@gentoo.org> generic-genome-browser-1.58.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. - - 24 May 2005; Michael Cummings <mcummings@gentoo.org> - generic-genome-browser-1.58.ebuild: - dev-perl/Digest-MD5 => perl-core/Digest-MD5 - - 24 May 2005; Michael Cummings <mcummings@gentoo.org> - generic-genome-browser-1.58.ebuild: - dev-perl/CGI => perl-core/CGI - -*generic-genome-browser-1.58 (23 Dec 2004) - - 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +generic-genome-browser-1.58.ebuild: - Moved from app-sci/generic-genome-browser to - sci-biology/generic-genome-browser. - - 03 Aug 2004; David Holm <dholm@gentoo.org> - generic-genome-browser-1.58.ebuild: - Added to ~ppc. - -*generic-genome-browser-1.58 (13 Jan 2004) - - 13 Jan 2004; Stephen Diener <sediener@gentoo.org> - generic-genome-browser-1.58.ebuild: - Initial import - diff --git a/sci-biology/geneid/ChangeLog b/sci-biology/geneid/ChangeLog deleted file mode 100644 index 49ef887d3..000000000 --- a/sci-biology/geneid/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/geneid -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> geneid-1.4.4.ebuild: - clean up - -*geneid-1.4.4 (17 Jun 2014) - - 17 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/Makefile.patch, +geneid-1.4.4.ebuild, +metadata.xml: - sci-biology/geneid: new package, works diff --git a/sci-biology/genepop/ChangeLog b/sci-biology/genepop/ChangeLog deleted file mode 100644 index bd166746a..000000000 --- a/sci-biology/genepop/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/genepop -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 29 Mar 2015; Justin Lecher <jlec@gentoo.org> genepop-4.2.1.ebuild: - sci-biology/genepop: Drop unnecessary *DEPEND - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -genepop-4.0.10.ebuild, - +genepop-4.2.1.ebuild, metadata.xml: - Punt base.eclass: version bump - - 26 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package, ebuild written by me diff --git a/sci-biology/generecon/ChangeLog b/sci-biology/generecon/ChangeLog deleted file mode 100644 index c54860946..000000000 --- a/sci-biology/generecon/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/generecon -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 17 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/1.2.1-flags.patch, - generecon-1.2.1-r1.ebuild, +files/1.2.1-gcc4.patch: - Fixing compilation with gcc4, repecting CXXFLAGS/LDFLAGS, reMANIFEST, - added missing dep on dev-libs/popt - -*generecon-1.2.1 (19 Apr 2006) - - 19 Apr 2006; Lucas Chiesa <lucas.chiesa@gmail.com>: - +generecon-1.2.1.ebuild, +metadata.xml, +ChangeLog, - Initial import. Thanks to Neil <nshephard@gmail.com> - for the initial ebuild. Closes bug #128514. diff --git a/sci-biology/genometools/ChangeLog b/sci-biology/genometools/ChangeLog deleted file mode 100644 index 6c121351d..000000000 --- a/sci-biology/genometools/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/genometools -# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*genometools-1.5.7 (04 Jan 2016) - - 04 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +genometools-1.5.7.ebuild, +metadata.xml: - sci-biology/genometools: new package diff --git a/sci-biology/genomeview-bin/ChangeLog b/sci-biology/genomeview-bin/ChangeLog deleted file mode 100644 index 5d4b417c6..000000000 --- a/sci-biology/genomeview-bin/ChangeLog +++ /dev/null @@ -1,14 +0,0 @@ -# ChangeLog for sci-biology/genomeview-bin -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> - genomeview-bin-2450.ebuild: - clean up - -*genomeview-bin-2450 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +genomeview-bin-2450.ebuild, +metadata.xml: - sci-biology/genomeview-bin: a skeleton for a new Java-based package, needs - help diff --git a/sci-biology/genseed/ChangeLog b/sci-biology/genseed/ChangeLog deleted file mode 100644 index dadccc03a..000000000 --- a/sci-biology/genseed/ChangeLog +++ /dev/null @@ -1,21 +0,0 @@ -# ChangeLog for sci-biology/genseed -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - genseed-1.0.22.ebuild: - sci-biology/genseed: some cleanup - - 10 Nov 2014; Justin Lecher <jlec@gentoo.org> genseed-1.0.22.ebuild, - metadata.xml: - Bump to EAPI=5 - - 13 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - genseed-1.0.22.ebuild: - ebuild doc cleanup genseed-1.0.22.ebuild - -*genseed-1.0.22 (13 Dec 2011) - - 13 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +genseed-1.0.22.ebuild, +metadata.xml: - A seed-driven progressive assembly program genseed-1.0.22.ebuild diff --git a/sci-biology/gfftools/ChangeLog b/sci-biology/gfftools/ChangeLog deleted file mode 100644 index 5e2a6e626..000000000 --- a/sci-biology/gfftools/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/gfftools -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*gfftools-0.98d (12 Jan 2015) - - 12 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +gfftools-0.98d.ebuild, +metadata.xml: - sci-biology/gfftools: new package diff --git a/sci-biology/gffutils/ChangeLog b/sci-biology/gffutils/ChangeLog deleted file mode 100644 index a9536a393..000000000 --- a/sci-biology/gffutils/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/gffutils -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/gffutils: Add github to remote-id in metadata.xml - - 13 Apr 2015; Justin Lecher <jlec@gentoo.org> gffutils-0.8.3.ebuild: - sci-biology/gffutils: Streamline ebuild - -*gffutils-0.8.3 (12 Apr 2015) - - 12 Apr 2015; Michael Schubert <mschu.dev@gmail.com> +gffutils-0.8.3.ebuild, - +metadata.xml: - sci-biology/gffutils: add gffutils diff --git a/sci-biology/glean/ChangeLog b/sci-biology/glean/ChangeLog deleted file mode 100644 index 952b4bfca..000000000 --- a/sci-biology/glean/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/glean -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 15 Jun 2015; Justin Lecher <jlec@gentoo.org> glean-1.0.1.ebuild: - sci-biology/glean: Fix dependency problems due to recent mask of perl-core - packages - -*glean-1.0.1 (02 May 2015) - - 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +glean-1.0.1.ebuild, - +metadata.xml: - sci-biology/glean: new package diff --git a/sci-biology/grappa/ChangeLog b/sci-biology/grappa/ChangeLog deleted file mode 100644 index 99ef56f45..000000000 --- a/sci-biology/grappa/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/grappa -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 26 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> grappa-2.0.ebuild: - Bump to EAPI=5 - - 14 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package, ebuild written by Pablo Nehab-Hess <natunobilis@gentoobr.org> - and me diff --git a/sci-biology/hexamer/ChangeLog b/sci-biology/hexamer/ChangeLog deleted file mode 100644 index c693dc4ef..000000000 --- a/sci-biology/hexamer/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/hexamer -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*hexamer-19990330 (01 May 2015) - - 01 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +hexamer-19990330.ebuild, +metadata.xml: - sci-biology/hexamer: new package diff --git a/sci-biology/hmmer/ChangeLog b/sci-biology/hmmer/ChangeLog deleted file mode 100644 index 71062a091..000000000 --- a/sci-biology/hmmer/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/hmmer -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - hmmer-3.1_beta2.ebuild: - sci-biology/hmmer: fix ${S} variable - -*hmmer-3.1_beta2 (19 Nov 2015) - - 19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +hmmer-3.1_beta2.ebuild, +metadata.xml: - sci-biology/hmmer: version bump diff --git a/sci-biology/hydra-sv/ChangeLog b/sci-biology/hydra-sv/ChangeLog deleted file mode 100644 index 66892c5ca..000000000 --- a/sci-biology/hydra-sv/ChangeLog +++ /dev/null @@ -1,8 +0,0 @@ -# ChangeLog for sci-biology/hydra-sv -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> hydra-sv-0.5.3.ebuild, - +metadata.xml: - Add metadata.xml; move to EAPI=5; cleaned ebuild syntax - diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog deleted file mode 100644 index aee3a5070..000000000 --- a/sci-biology/igv/ChangeLog +++ /dev/null @@ -1,64 +0,0 @@ -# ChangeLog for sci-biology/igv -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/igv: Add github to remote-id in metadata.xml - -*igv-2.3.52 (11 May 2015) - - 11 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/2.3.52-remove-oracle.jdbc.patch, +igv-2.3.52.ebuild, igv-2.3.47.ebuild: - sci-biology/igv: added upstream patch, version bump - -*igv-2.3.47 (29 Apr 2015) - - 29 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.47.ebuild, - -igv-2.3.44.ebuild: - sci-biology/igv: version bump - - 21 Mar 2015; Johann Schmitz <ercpe@gentoo.org> igv-2.3.44.ebuild: - Fixed upstream bug https://github.com/broadinstitute/IGV/issues/114 as - requested by Martin Mokrejŝ (note: i've excluded the test code by passing - -Dnotests=true to ant so it may break at some point). Also improved the - ebuild by unbundling stuff we already have in portage. There are quite a - number of libraries which aren't used for compilation which may be needed at - runtime. I haven't tested the program in depth: it started at didn't throw - errors when i clicked around - everything else is way beyond my knowledge. - Improved the ebuild for sci-biology/igv - - 21 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.3.44.ebuild: - sci-biology/igv: fix inherit to git-r3 - - 17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.3.44.ebuild: - fix inherit to use git instead of previously used subversion - -*igv-2.3.44 (17 Mar 2015) - - 17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.44.ebuild, - -igv-2.3.40.ebuild: - version bump - -*igv-2.3.40 (05 Mar 2015) - - 05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.40.ebuild, - -igv-2.0.35.ebuild: - updated ebuild to github URLs; version bump but does not compile for me - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> -igv-2.0.32.ebuild, - igv-2.0.35.ebuild, metadata.xml: - sci-biology/igv: fix SLOT operators; drop KEYWORDS for live ebuilds - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.0.35.ebuild: - API bumped, whitespace removal - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.0.35.ebuild: - added some dev-java dependencies and removed some bundled .jar files - -*igv-2.0.35 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.0.35.ebuild: - sci-biology/igv-2.0.35: version bump - - 08 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package, ebuild written by me diff --git a/sci-biology/inGAP-bin/ChangeLog b/sci-biology/inGAP-bin/ChangeLog deleted file mode 100644 index c74ba9ea0..000000000 --- a/sci-biology/inGAP-bin/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/inGAP-bin -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 07 Aug 2015; Justin Lecher <jlec@gentoo.org> inGAP-bin-3.0.1.ebuild: - sci-biology/inGAP-bin: Fix CAT move and many more things - -*inGAP-bin-3.0.1 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +inGAP-bin-3.0.1.ebuild, +metadata.xml: - sci-biology/inGAP-bin: new package; needs java team help diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog deleted file mode 100644 index 9132f22d3..000000000 --- a/sci-biology/jellyfish/ChangeLog +++ /dev/null @@ -1,50 +0,0 @@ -# ChangeLog for sci-biology/jellyfish -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 13 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - jellyfish-1.1.11.ebuild: - sci-biology/jellyfish: fix filename generated by pkgconfig - - 04 May 2015; Justin Lecher <jlec@gentoo.org> jellyfish-1.1.11.ebuild, - jellyfish-2.1.3.ebuild, jellyfish-2.1.4.ebuild: - sci-biology/jellyfish: Correct license from HalfLICENSE to BSD as they are - identical - - 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - jellyfish-1.1.11.ebuild: - sci-biology/jellyfish: added a note - - 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - jellyfish-1.1.11.ebuild: - sci-biology/jellyfish: fixed homepage for the old version - -*jellyfish-1.1.11 (30 Apr 2015) - - 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +jellyfish-1.1.11.ebuild, jellyfish-2.1.3.ebuild, jellyfish-2.1.4.ebuild: - sci-biology/jellyfish: added older version, added HalfLICENSE to all ebuilds - - 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - jellyfish-2.1.3.ebuild, jellyfish-2.1.4.ebuild: - sci-biology/jellyfish: added missing DEPEND on virtual/pkgconfig so that the - jellyfish-2.0.pc gets installed properly - - 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - jellyfish-2.1.3.ebuild: - sci-biology/jellyfish: fix /usr/lib64/pkgconfig/jellyfish-2.0.pc - - 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - jellyfish-2.1.3.ebuild: - sci-biology/jellyfish: fix installation of header *.hpp files into - /usr/include/jellyfish-2.1.3/jellyfish/ broken somewhere in upstream's code - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - jellyfish-2.1.3.ebuild: - added a comment on old version - -*jellyfish-2.1.3 (02 Jul 2014) - - 02 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +jellyfish-2.1.3.ebuild, +metadata.xml: - sci-biology/jellyfish: new package, works diff --git a/sci-biology/jigsaw/ChangeLog b/sci-biology/jigsaw/ChangeLog deleted file mode 100644 index cc4c20466..000000000 --- a/sci-biology/jigsaw/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/jigsaw -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> jigsaw-3.2.10.ebuild: - Fix license - -*jigsaw-3.2.10 (07 Jan 2015) - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +jigsaw-3.2.10.ebuild, +metadata.xml: - initial ebuild - diff --git a/sci-biology/jtreeview/ChangeLog b/sci-biology/jtreeview/ChangeLog deleted file mode 100644 index 28156a237..000000000 --- a/sci-biology/jtreeview/ChangeLog +++ /dev/null @@ -1,6 +0,0 @@ -# ChangeLog for sci-biology/jtreeview -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> jtreeview-1.1.6.4.ebuild: - sci-biology/jtreeview: fix SLOT operators diff --git a/sci-biology/kallisto/ChangeLog b/sci-biology/kallisto/ChangeLog deleted file mode 100644 index 0542a6d4a..000000000 --- a/sci-biology/kallisto/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/kallisto -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*kallisto-0.42.1 (21 May 2015) -*kallisto-9999 (21 May 2015) - - 21 May 2015; Michael Schubert <mschu.dev@gmail.com> +kallisto-0.42.1.ebuild, - +kallisto-9999.ebuild, +metadata.xml: - sci-biology/kallisto: add kallisto diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog deleted file mode 100644 index ac1a6e3ac..000000000 --- a/sci-biology/khmer/ChangeLog +++ /dev/null @@ -1,39 +0,0 @@ -# ChangeLog for sci-biology/khmer -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/khmer: Add github to remote-id in metadata.xml - -*khmer-1.0.1 (15 May 2014) - - 15 May 2014; Justin Lecher <jlec@gentoo.org> khmer-0.8.ebuild, - +khmer-1.0.1.ebuild: - Version Bump - - 28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> khmer-9999.ebuild: - sci-biology/khmer: upstream dropped the bundled zlib/bzip2 use if it is - available system-wide, upstream https://github.com/ged-lab/khmer/pull/346 - - 24 Mar 2014; Justin Lecher <jlec@gentoo.org> khmer-0.8.ebuild, - khmer-9999.ebuild: - Also drop sphinx as build requirement - - 20 Mar 2014; Justin Lecher <jlec@gentoo.org> khmer-0.8.ebuild, - khmer-9999.ebuild: - Drop nose requirement during build - -*khmer-0.8 (18 Mar 2014) - - 18 Mar 2014; Justin Lecher <jlec@gentoo.org> +khmer-0.8.ebuild, - khmer-9999.ebuild: - Unbundle zlib and bzpi2; bump to disturils-r1; respect CFLAGS - - 16 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> khmer-9999.ebuild: - sci-biology/khmer: revert to distutils to obey sandbox violation - -*khmer-9999 (16 Mar 2014) - - 16 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +khmer-9999.ebuild, - +metadata.xml: - sci-biology/khmer: new package diff --git a/sci-biology/kmergenie/ChangeLog b/sci-biology/kmergenie/ChangeLog deleted file mode 100644 index d5337854c..000000000 --- a/sci-biology/kmergenie/ChangeLog +++ /dev/null @@ -1,25 +0,0 @@ -# ChangeLog for sci-biology/kmergenie -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 29 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - kmergenie-1.6971.ebuild: - sci-biology/kmergenie: fix installation of launcher script - -*kmergenie-1.6971 (30 Mar 2015) - - 30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +kmergenie-1.6971.ebuild, -kmergenie-1.6950.ebuild: - sci-biology/kmergenie: version bump - - 18 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - kmergenie-1.6950.ebuild: - install the real binary, add dependency of external python module; the DEPEND - line still needs a fix: DEPEND: Invalid atom (Invalid use dep: ''), token 1 - -*kmergenie-1.6950 (13 Mar 2015) - - 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +kmergenie-1.6950.ebuild, +metadata.xml: - new package; the k-mer size is set during compilation, use 'k=121 emerge - kmergenie' to set your k-mer size diff --git a/sci-biology/lastz/ChangeLog b/sci-biology/lastz/ChangeLog deleted file mode 100644 index 46d8fbdb9..000000000 --- a/sci-biology/lastz/ChangeLog +++ /dev/null @@ -1,26 +0,0 @@ -# ChangeLog for sci-biology/lastz -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*lastz-1.03.66 (02 May 2015) - - 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/lastz-1.03.66-build.patch, +lastz-1.03.66.ebuild, - -files/lastz-1.03.34-build.patch, -lastz-1.03.34.ebuild: - sci-biology/lastz: version bump - - 12 Jun 2013; Justin Lecher <jlec@gentoo.org> -lastz-1.02.00.ebuild, - +lastz-1.03.34.ebuild, +files/lastz-1.03.34-build.patch, metadata.xml: - Version Bump; fix license; bump to EAPI=5; fix buildsystem - -*lastz-1.03.34 (12 Jun 2013) - - 12 Jun 2013; Justin Lecher <jlec@gentoo.org> -lastz-1.02.00.ebuild, - +lastz-1.03.34.ebuild, +files/lastz-1.03.34-build.patch, metadata.xml: - Version Bump; fix license; bump to EAPI=5; fix buildsystem - -*lastz-1.02.00 (16 Jan 2012) - - 16 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +lastz-1.02.00.ebuild, +metadata.xml: - initial ebuild diff --git a/sci-biology/libgtextutils/ChangeLog b/sci-biology/libgtextutils/ChangeLog deleted file mode 100644 index 8d6e47a32..000000000 --- a/sci-biology/libgtextutils/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/libgtextutils -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*libgtextutils-0.6.1 (29 Aug 2013) - - 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - -libgtextutils-0.6.ebuild, +libgtextutils-0.6.1.ebuild: - Version bump. - -*libgtextutils-0.6 (16 Jan 2012) - - 16 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +libgtextutils-0.6.ebuild, +metadata.xml: - initial ebuild - diff --git a/sci-biology/lighter/ChangeLog b/sci-biology/lighter/ChangeLog deleted file mode 100644 index 6b8d9e62f..000000000 --- a/sci-biology/lighter/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/lighter -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/lighter: Add github to remote-id in metadata.xml - -*lighter-9999 (01 May 2015) - - 01 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +lighter-9999.ebuild, +metadata.xml: - sci-libs/lighter: new package; contains IUSE=threads but ... does the Makefile - need a tweak for -lpthreads ? ;-). Go ahead and fix this. diff --git a/sci-biology/mRNAmarkup/ChangeLog b/sci-biology/mRNAmarkup/ChangeLog deleted file mode 100644 index e5311ca5b..000000000 --- a/sci-biology/mRNAmarkup/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/mRNAmarkup -# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*mRNAmarkup-1.0 (05 Jan 2016) -*mRNAmarkup-1.1 (05 Jan 2016) - - 05 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +mRNAmarkup-1.0.ebuild, +mRNAmarkup-1.1.ebuild, +metadata.xml: - sci-biology/mRNAmarkup: new package diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog deleted file mode 100644 index c06e4830b..000000000 --- a/sci-biology/maker/ChangeLog +++ /dev/null @@ -1,49 +0,0 @@ -# ChangeLog for sci-biology/maker -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 31 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild: - sci-biology/maker: DEPEND on external sci-biology/GAL package; rename - 'compare' binary as agreed with upstream - - 30 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild: - sci-biology/maker: do install from a top-level directory; there is a file - collision with /usr/bin/compare from media-gfx/imagemagick and with - /usr/bin/fasta_tool from sci-biology/trinityrnaseq - - 30 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild: - sci-biology/maker: added openmpi as dependency; define our own src_install(); - add einfo message; added dev-perl/forks-shared dependency - - 30 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild: - sci-biology/maker: added dependency on dev-perl/forks - - 18 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild: - sci-biology/maker: drop duplicated Module-Build requirement - - 18 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild: - sci-biology/maker: fix Module-Build dependency - - 01 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild: - sci-biology/maker: add DEPENDency on dev-perl/Module-Build - - 20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild: - sci-biology/maker: document opened Gentoo bugzilla tickets - - 20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild: - sci-biology/maker: depend on mpich2 when USE=mpi, add back hard DEPENDency on - repeatmasker because install process does not continue without it, document - additional perl modules not available in portage - - 20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> maker-2.31.8.ebuild: - sci-biology/maker: respect USE=mpi, remove hard DEPENDency on repeatmasker- - libraries which are fetch restricted - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> MAKER-9999.ebuild: - added license - -*MAKER-9999 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +MAKER-9999.ebuild, - +metadata.xml: - a skeleton for a new package diff --git a/sci-biology/manatee-igs/ChangeLog b/sci-biology/manatee-igs/ChangeLog deleted file mode 100644 index e998238ce..000000000 --- a/sci-biology/manatee-igs/ChangeLog +++ /dev/null @@ -1,34 +0,0 @@ -# ChangeLog for sci-biology/manatee-igs -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 27 Oct 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - manatee-igs-2.23.1.ebuild: - sci-biology/manatee-igs: depend on virtual/mysql - - 15 Jun 2015; Justin Lecher <jlec@gentoo.org> manatee-igs-2.23.1.ebuild: - sci-biology/manatee-igs: Fix dependency problems due to recent mask of perl- - core packages - - 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - manatee-igs-2.23.1.ebuild: - Both versions of manatee have same license, so rename unify the license - filename. - - 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - manatee-igs-2.23.1.ebuild: - Renamed the License file. - - 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - manatee-igs-2.23.1.ebuild: - Added dev-perl/Bio-DB-Das-Chado and improved description line. - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> manatee-igs-2.23.1.ebuild, - metadata.xml: - Shorten DESCRIPTION - -*manatee-igs-2.23.1 (08 Jan 2012) - - 08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +manatee-igs-2.23.1.ebuild, +metadata.xml: - new package for prokaryotic genome annotation and editing diff --git a/sci-biology/manatee-jcvi/ChangeLog b/sci-biology/manatee-jcvi/ChangeLog deleted file mode 100644 index 503585bab..000000000 --- a/sci-biology/manatee-jcvi/ChangeLog +++ /dev/null @@ -1,21 +0,0 @@ -# ChangeLog for sci-biology/manatee-jcvi -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 27 Oct 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - manatee-jcvi-2.4.3.ebuild: - sci-biology/manatee-jcvi: depend virtual/mysql - - 13 Nov 2014; Justin Lecher <jlec@gentoo.org> manatee-jcvi-2.4.3.ebuild, - metadata.xml: - Use perl virtuals instead of core - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> manatee-jcvi-2.4.3.ebuild: - clean up - -*manatee-jcvi-2.4.3 (29 Aug 2013) - - 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +manatee-jcvi-2.4.3.ebuild, +metadata.xml: - Initial ebuild for the other version of manatee, using different database - schema. diff --git a/sci-biology/mavid/ChangeLog b/sci-biology/mavid/ChangeLog deleted file mode 100644 index 4fe4856d0..000000000 --- a/sci-biology/mavid/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/mavid -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Nov 2014; Justin Lecher <jlec@gentoo.org> mavid-2.0.4.ebuild, - metadata.xml: - Bump EAPI - - 08 Jul 2008; weaver <weaver@gentoo.org> +metadata.xml, - +mavid-2.0.4.ebuild: - New ebuild, bug 207250 - diff --git a/sci-biology/merlin/ChangeLog b/sci-biology/merlin/ChangeLog deleted file mode 100644 index bcbbb7e81..000000000 --- a/sci-biology/merlin/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sci-biology/merlin -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> - merlin-1.1.2.ebuild: - Move to EAPI=5. - - 21 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package, bug 121921, thanks to Neil <nshephard@gmail.com> - diff --git a/sci-biology/metaseq/ChangeLog b/sci-biology/metaseq/ChangeLog deleted file mode 100644 index 6bcb4fb53..000000000 --- a/sci-biology/metaseq/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/metaseq -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/metaseq: Add github to remote-id in metadata.xml - - 13 Apr 2015; Justin Lecher <jlec@gentoo.org> metaseq-0.5.3.ebuild: - sci-biology/metaseq: Streamline ebuild - -*metaseq-0.5.3 (12 Apr 2015) - - 12 Apr 2015; Michael Schubert <mschu.dev@gmail.com> +metadata.xml, - +metaseq-0.5.3.ebuild: - sci-biology/metaseq: add metaseq diff --git a/sci-biology/mgblast/ChangeLog b/sci-biology/mgblast/ChangeLog deleted file mode 100644 index bea8e9a39..000000000 --- a/sci-biology/mgblast/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/mgblast -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> mgblast-0.1.ebuild: - clean up - -*mgblast-0.1 (24 Mar 2014) - - 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +mgblast-0.1.ebuild, +metadata.xml: - initial ebuild but while it needs an old version of ncbi-tools source tree to - build ... it is not tested yet diff --git a/sci-biology/minced/ChangeLog b/sci-biology/minced/ChangeLog deleted file mode 100644 index 43149a67f..000000000 --- a/sci-biology/minced/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/minced -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/minced: Add github to remote-id in metadata.xml - - 29 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> minced-9999.ebuild: - sci-biology/minced: fixed the launcher - -*minced-9999 (27 Apr 2015) - - 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +minced-9999.ebuild: - sci-biology/minced: new package; the /usr/bin/minced wrapper for the - minced.jar does not work diff --git a/sci-biology/mip-scaffolder/ChangeLog b/sci-biology/mip-scaffolder/ChangeLog deleted file mode 100644 index c7ff337d3..000000000 --- a/sci-biology/mip-scaffolder/ChangeLog +++ /dev/null @@ -1,17 +0,0 @@ -# ChangeLog for sci-biology/mip-scaffolder -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - mip-scaffolder-0.6.ebuild: - sci-biology/mip-scaffolder: respect CXXFLAGS although the Makefile speaks - about CFLAGS - - 17 Feb 2015; Christoph Junghans <ottxor@gentoo.org> mip-scaffolder-0.6.ebuild: - fixed LICENSE - -*mip-scaffolder-0.6 (14 Feb 2015) - - 14 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +mip-scaffolder-0.6.ebuild: - new package diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog deleted file mode 100644 index 19e5978f4..000000000 --- a/sci-biology/mira/ChangeLog +++ /dev/null @@ -1,138 +0,0 @@ -# ChangeLog for sci-biology/mira -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 21 Jul 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/mira-4.9.5-fix-miramer-symlink-error.patch, mira-4.9.5.ebuild: - sci-biology/mira-4.9.5: fix missing AND in Makefile; install config files for - staden and consed viewers/editors (maybe use config protect?) - - 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/mira: Updating remote-id in metadata.xml - - 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/miranda/ChangeLog b/sci-biology/miranda/ChangeLog deleted file mode 100644 index d7cca6b15..000000000 --- a/sci-biology/miranda/ChangeLog +++ /dev/null @@ -1,18 +0,0 @@ -# ChangeLog for sci-biology/miranda -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> miranda-3.3a.ebuild, - metadata.xml: - Punt base.eclass - -*miranda-3.3a (08 Nov 2010) - - 08 Nov 2010; Kacper Kowalik <xarthisius@gentoo.org> -miranda-3.0.ebuild, - +miranda-3.3a.ebuild: - Version bump wrt bug 144316. Thanks to Joel Berendzen <joelb@lanl.gov> for - the report. - - 10 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package sci-biology/miranda, bug 144316. Ebuild written by me. - diff --git a/sci-biology/mne-python/ChangeLog b/sci-biology/mne-python/ChangeLog deleted file mode 100644 index 677d3d382..000000000 --- a/sci-biology/mne-python/ChangeLog +++ /dev/null @@ -1,8 +0,0 @@ -# ChangeLog for sci-biology/mne-python -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> mne-python-0.7.ebuild, - mne-python-9999.ebuild, +metadata.xml: - Add missing metadata.xml; drop USE=cuda; fix python deps - diff --git a/sci-biology/mosaik/ChangeLog b/sci-biology/mosaik/ChangeLog deleted file mode 100644 index d7c69a2ad..000000000 --- a/sci-biology/mosaik/ChangeLog +++ /dev/null @@ -1,43 +0,0 @@ -# ChangeLog for sci-biology/mosaik -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*mosaik-2.2.3 (15 Jan 2015) - - 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +mosaik-2.2.3.ebuild, -mosaik-2.1.33.ebuild: - version bump, masking a crappy package until at least the Makefile's - propagate an error code back to upstream caller, https://code.google.com/p - /mosaik-aligner/issues/detail?id=135 - - 07 Jan 2014; Justin Lecher <jlec@gentoo.org> mosaik-2.1.33.ebuild, - mosaik-9999.ebuild, metadata.xml: - Readd ebuild - - 01 Jun 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - mosaik-1.1.0021.ebuild: - improved die() message to inform user that gcc-4.5.3 does not work while - gcc-4.3.6 does - - 16 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - mosaik-2.1.33.ebuild, mosaik-9999.ebuild: - sci-biology/mosaik: masking mosaik-2.1.33 mosaik-9999 - -*mosaik-9999 (15 Mar 2012) - - 15 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - mosaik-2.1.33.ebuild, +mosaik-9999.ebuild: - version bump for 2.1.33 and GIT HEAD, neither compiles so far; upstream - re-contacted mosaik-2.1.33.ebuild mosaik-9999.ebuild - -*mosaik-2.1.33 (15 Mar 2012) -*mosaik-1.1.0021 (15 Mar 2012) - - 15 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +mosaik-1.1.0021.ebuild, +mosaik-2.1.33.ebuild: - version bump, added the pdf documentation to SRC_URI, the compile process - leaks through many 'Fastq.cpp:224: error: conditional expression between - distinct pointer types 'gzFile_s*' and 'FILE*' lacks a cast' messages in - Fastq.cpp:224, Fastq.cpp:226, Fasta.cpp:258, Fasta.cpp:260, Fasta.cpp:266, - Fasta.cpp:268, but the package itself installs and executes at least - mosaik-1.1.0021.ebuild diff --git a/sci-biology/mothur/ChangeLog b/sci-biology/mothur/ChangeLog deleted file mode 100644 index 7e1aa76c8..000000000 --- a/sci-biology/mothur/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/mothur -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*mothur-1.36.1 (30 Nov 2015) - - 30 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/mothur-1.36.1-makefile.patch, +metadata.xml, +mothur-1.36.1.ebuild: - sci-biology/mothur: version bump; update makefile patch, the other patch from - 1.27 series seems not necessary anymore; added few more IUSE values but the - makefile could ideally respect them before forcing boost and zlib libraries - into LIBS diff --git a/sci-biology/mreps/ChangeLog b/sci-biology/mreps/ChangeLog deleted file mode 100644 index 2ae4bfd31..000000000 --- a/sci-biology/mreps/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/mreps -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Nov 2014; Justin Lecher <jlec@gentoo.org> mreps-2.5.ebuild, metadata.xml: - Bump to EAPI=5; respect CC - - 04 Feb 2009; weaver <weaver@gentoo.org> ChangeLog: - New package sci-biology/mreps, bug 257676 - diff --git a/sci-biology/mrfast/ChangeLog b/sci-biology/mrfast/ChangeLog deleted file mode 100644 index 9c4757f04..000000000 --- a/sci-biology/mrfast/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sci-biology/mrfast -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/mrfast: Updating remote-id in metadata.xml - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mrfast-2.1.0.3.ebuild, - +mrfast-2.6.0.1.ebuild, -files/mrfast-2.1.0.3-disc_buffer_overflow.patch, - metadata.xml: - Version Bump; punt base.eclass diff --git a/sci-biology/mricron/ChangeLog b/sci-biology/mricron/ChangeLog deleted file mode 100644 index b7ec07332..000000000 --- a/sci-biology/mricron/ChangeLog +++ /dev/null @@ -1,18 +0,0 @@ -# ChangeLog for sci-biology/mricron -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 25 Dec 2015; Marius Brehler <marbre@linux.sungazer.de> mricron-9999.ebuild: - sci-biology/mricron: Fix minorsyn - - 06 Dec 2015; Horea Christian <h.chr@mail.ru> mricron-9999.ebuild: - sci-biology/mricron: added icon and gnome desktop entry - - 04 Dec 2015; Horea Christian <h.chr@mail.ru> mricron-9999.ebuild: - sci-biology/mricron: corrected binary paths - -*mricron-9999 (04 Dec 2015) - - 04 Dec 2015; Horea Christian <h.chr@mail.ru> +metadata.xml, - +mricron-9999.ebuild: - sci-biology/mricron: new ebuild diff --git a/sci-biology/mrsfast/ChangeLog b/sci-biology/mrsfast/ChangeLog deleted file mode 100644 index 7078d4878..000000000 --- a/sci-biology/mrsfast/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/mrsfast -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/mrsfast: Updating remote-id in metadata.xml - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mrsfast-2.3.0.2.ebuild, - +mrsfast-2.6.0.4.ebuild, metadata.xml: - Version Bump; punt base.eclass diff --git a/sci-biology/ncbi-blast+/ChangeLog b/sci-biology/ncbi-blast+/ChangeLog deleted file mode 100644 index 4e0171084..000000000 --- a/sci-biology/ncbi-blast+/ChangeLog +++ /dev/null @@ -1,27 +0,0 @@ -# ChangeLog for sci-biology/ncbi-blast+ -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*ncbi-blast+-2.2.31 (22 Nov 2015) - - 22 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/ncbi-blast+-2.2.30__fix_lib_deps.patch, +ncbi-blast+-2.2.31.ebuild, - -files/fix_lib_deps.patch, ncbi-blast+-2.2.30.ebuild: - sci-biology/ncbi-blast+-2.2.31: version bump, seems that some parts of the - ncbi-blast+-2.2.30__fix_lib_deps.patch could/should be re-used - - 17 Jul 2015; Andrew Savchenko <bircoph@gentoo.org> metadata.xml: - Add sqlite3 flag description. - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> ncbi-blast+-2.2.30.ebuild: - sci-biology/ncbi-blast+: fix SLOT operators; correct python deps - - 15 Jan 2015; Christoph Junghans <ottxor@gentoo.org> metadata.xml: - added use flags to metadata.xml - -*ncbi-blast+-2.2.30 (14 Jan 2015) - - 14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +ncbi-blast+-2.2.30.ebuild, +files/disable-testsuite-compilation.txt, - +files/fix_lib_deps.patch, +metadata.xml: - ebuild derived from ncbi-tools++-12.0.0.ebuild with a Debian patch diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog deleted file mode 100644 index cdfa99a34..000000000 --- a/sci-biology/ncbi-tools++/ChangeLog +++ /dev/null @@ -1,146 +0,0 @@ -# ChangeLog for sci-biology/ncbi-tools++ -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 17 Jul 2015; Andrew Savchenko <bircoph@gentoo.org> metadata.xml: - Add sqlite3 flag description. - - 23 Jun 2015; Horea Christian <h.chr@mail.ru> ncbi-tools++-12.0.0.ebuild: - added dep needed at build-time - - 11 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/ncbi-tools++-12.0.0-bdb6.patch, ncbi-tools++-12.0.0.ebuild: - sci-biology/ncbi-tools++: added upstream patch to compile against sys- - libs/db-6.0.30 - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - ncbi-tools++-12.0.0.ebuild: - sci-biology/ncbi-tools++: re-added KEYWORDS - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> ncbi-tools++-12.0.0.ebuild: - sci-biology/ncbi-tools++: fix SLOT operators; correct python deps - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> - -files/ncbi-tools++-12.0.0-as-needed.patch, - -files/ncbi-tools++-9.0.0-as-needed.patch, - -files/ncbi-tools++-9.0.0-conf-opts.patch, - -files/ncbi-tools++-9.0.0-disable_test_compress.patch, - -files/ncbi-tools++-9.0.0-fix-creaders-linking.patch, - -files/ncbi-tools++-9.0.0-fix-order-of-libs.patch, - -files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch, -files/ncbi-tools++-9.0. - 0-fix-undef-reference-to-GenBankReaders_Register_Id1.patch, - -files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch, - -ncbi-tools++-9.0.0-r1.ebuild, -ncbi-tools++-9.0.0.ebuild, metadata.xml, - ncbi-tools++-12.0.0.ebuild: - major clean, drop old version and unused patches - - 23 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ChangeLog: - add patches for 12.0.0 to support autoconf-2.60 (so far 2.59 was needed), - patches from upstream: - http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=62745 - http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=62750 - http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=62760 - - 14 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - ncbi-tools++-9.0.0-r1.ebuild: - Support at least when user passes USE="gnutls -ssl -openssl" but what we - really want is to prefer gnutls over openssl if both are available on the - system. - - 14 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - ncbi-tools++-9.0.0-r1.ebuild, - +files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch: - Add upstream ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch with - line - offset changes. - - 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - ncbi-tools++-9.0.0-r1.ebuild, ncbi-tools++-12.0.0.ebuild, - +files/ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch, - +files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch: - Fix URL to point to a public SVN repository (an upstream patch from email - list): - - Date: Sun, 28 Jul 2013 22:05:34 -0400 - CC: <cpp@ncbi.nlm.nih.gov> - Subject: Re: [C++] new project startup example needed - - 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - ncbi-tools++-12.0.0.ebuild, - files/ncbi-tools++-9.0.0-fix-creaders-linking.patch, - +files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch, - files/ncbi-tools++-12.0.0-fix-creaders-linking.patch: - Added an upstream patch from: - - Date: Wed, 28 Aug 2013 10:50:29 -0400 - List cpp <cpp@ncbi.nlm.nih.gov> - Subject: Re: [C++] error building ncbi toolkit v.12.0.0 - - Fixed line offsets in the ncbi-tools++-12.0.0-fix-creaders-linking.patch - file. - - Fixed file path in ncbi-tools++-9.0.0-fix-creaders-linking.patch header. - - The patches copied blindly from ncbi-tools++-9.0.0-r1 under 12.0.0 need to be - adjusted still to have correct line numbers. They do NOT apply cleanly at the - moment. - - 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - ncbi-tools++-9.0.0-r1.ebuild, ncbi-tools++-12.0.0.ebuild, - files/ncbi-tools++-9.0.0-as-needed.patch, - +files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1. - patch, files/ncbi-tools++-12.0.0-as-needed.patch: - files/ncbi-tools++-12.0.0-as-needed.patch - files/ncbi-tools++-9.0.0-as-needed.patch - - Remove redundant connect per message from Aaron Ucko <ucko@ncbi.nlm.nih.gov>: - - > +DLL_LIB = xncbi xutil seqset connect xconnect xnetblast - Then simply remove connect, which is redundant with xconnect. (connect - consists of code shared with NCBI's C Toolkit; xconnect adds a C++ - layer.) - - - 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - ncbi-tools++-12.0.0.ebuild, - +files/ncbi-tools++-12.0.0-fix-creaders-linking.patch: - No, the fix-creaders-linking is needed for 12.0.0 as well. - -*ncbi-tools++-12.0.0 (13 Sep 2013) - - 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +ncbi-tools++-12.0.0.ebuild, +files/ncbi-tools++-12.0.0-as-needed.patch, - +files/ncbi-tools++-12.0.0-conf-opts.patch: - Latest release which needs so far only the two Gentoo patches. Would - be better to drop ${PV} from their filename to avoid their duplication - I think. - - 13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - ncbi-tools++-9.0.0-r1.ebuild, - +files/ncbi-tools++-9.0.0-fix-creaders-linking.patch: - add glew to dependencies inferrred via mesa - fix lib/libxobjread.so: undefined reference to 'AlignmentFileFree' message by - upstream patch - - 12 Jun 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild: - Drop empty line - - 12 Jun 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild: - Drop autotools.eclass - - 01 Apr 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild: - Some Prefix love - - 01 Apr 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild: - Some Prefix love - - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: - Document USE - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0.ebuild, - ncbi-tools++-9.0.0-r1.ebuild: - Clean whitespace errors - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> +metadata.xml: - Add metadata.xml diff --git a/sci-biology/nesoni/ChangeLog b/sci-biology/nesoni/ChangeLog deleted file mode 100644 index eb6e66e28..000000000 --- a/sci-biology/nesoni/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/nesoni -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*nesoni-0.128 (08 Jan 2015) - - 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +nesoni-0.128.ebuild, -nesoni-0.117.ebuild: - sci-biology/nesoni: version bump - -*nesoni-0.117 (15 Apr 2014) - - 15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +nesoni-0.117.ebuild: - sci-biology/nesoni: new package, needs some dev-lang/R -based packages to be - installed diff --git a/sci-biology/ngs_backbone/ChangeLog b/sci-biology/ngs_backbone/ChangeLog deleted file mode 100644 index 40345640f..000000000 --- a/sci-biology/ngs_backbone/ChangeLog +++ /dev/null @@ -1,17 +0,0 @@ -# ChangeLog for sci-biology/ngs_backbone -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - ngs_backbone-9999.ebuild: - added PYTHON_USEDEP - - 12 Sep 2014; Christoph Junghans <ottxor@gentoo.org> ngs_backbone-9999.ebuild: - drop ~x86 as deps are missing - -*ngs_backbone-9999 (24 Mar 2014) - - 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +ngs_backbone-9999.ebuild, +metadata.xml: - Initial ebuild, external optional but highly recommended dependency on - blast2GO aka b2g4pipe is not resolved diff --git a/sci-biology/ngsview/ChangeLog b/sci-biology/ngsview/ChangeLog deleted file mode 100644 index f4df1d8f5..000000000 --- a/sci-biology/ngsview/ChangeLog +++ /dev/null @@ -1,21 +0,0 @@ -# ChangeLog for sci-biology/ngsview -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/ngsview: Updating remote-id in metadata.xml - - 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/ngsview: Updating remote-id in metadata.xml - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> ngsview-0.91.ebuild: - sci-biology/ngsview: fix SLOT operators - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> ngsview-0.91.ebuild: - fixed DESCRIPTION - -*ngsview-0.91 (24 Mar 2014) - - 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +ngsview-0.91.ebuild, +metadata.xml: - needs qt team help diff --git a/sci-biology/nilearn/ChangeLog b/sci-biology/nilearn/ChangeLog deleted file mode 100644 index e3359f136..000000000 --- a/sci-biology/nilearn/ChangeLog +++ /dev/null @@ -1,35 +0,0 @@ -# ChangeLog for dev-python/nilearn -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 19 Nov 2015; <chymera@gentoo.org> nilearn-0.1.4.1.ebuild, - nilearn-9999.ebuild: - dev-python/nilearn: moved deps to DEPEND - - 19 Nov 2015; <chymera@gentoo.org> nilearn-0.1.4.1.ebuild, - nilearn-9999.ebuild: - dev-python/nilearn: added test flag and test dependency - - 14 Nov 2015; Horea Christian <h.chr@mail.ru> nilearn-0.1.4.1.ebuild: - dev-python/nilearn: added test function - - 19 Oct 2015; Horea Christian <h.chr@mail.ru> nilearn-9999.ebuild: - dev-python/nilearn: plot use flag in live ebuild as well - - 19 Oct 2015; Horea Christian <h.chr@mail.ru> metadata.xml, - nilearn-0.1.4.1.ebuild: - dev-python/nilearn: added plot use flag, added MY_PV, removed deprecated - dependency version - - 19 Oct 2015; Horea Christian <h.chr@mail.ru> nilearn-9999.ebuild: - dev-python/nilearn: dropped empty IUSE, added PYTHON_USEDEP - - 19 Oct 2015; Horea Christian <h.chr@mail.ru> nilearn-0.1.4.1.ebuild: - dev-python/nilearn: corrected format, added PYTHON_USEDEP, removed emtty IUSE - -*nilearn-0.1.4.1 (19 Oct 2015) -*nilearn-9999 (19 Oct 2015) - - 19 Oct 2015; Horea Christian <h.chr@mail.ru> +metadata.xml, - +nilearn-0.1.4.1.ebuild, +nilearn-9999.ebuild: - dev-python/nilearn: new package diff --git a/sci-biology/nistats/ChangeLog b/sci-biology/nistats/ChangeLog deleted file mode 100644 index df4c8c902..000000000 --- a/sci-biology/nistats/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/nistats -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 19 Dec 2015; Horea Christian <h.chr@mail.ru> nistats-9999.ebuild: - sci-biology/nistats: no longer depending on setuptools at runtime - -*nistats-9999 (17 Dec 2015) - - 17 Dec 2015; Horea Christian <h.chr@mail.ru> +metadata.xml, - +nistats-9999.ebuild: - sci-biology/nistats: added new package diff --git a/sci-biology/nrcl/ChangeLog b/sci-biology/nrcl/ChangeLog deleted file mode 100644 index 135c271d3..000000000 --- a/sci-biology/nrcl/ChangeLog +++ /dev/null @@ -1,14 +0,0 @@ -# ChangeLog for sci-biology/nrcl -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/110625-build.patch, - -files/0.1-build.patch: - mv 0.1-build.patch 110625-build.patch - -*nrcl-110625 (25 Jun 2011) - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/0.1-build.patch, - -nrcl-0.1.ebuild, +nrcl-110625.ebuild: - Cleaned ebuild - diff --git a/sci-biology/nwalign/ChangeLog b/sci-biology/nwalign/ChangeLog deleted file mode 100644 index 925b62c9b..000000000 --- a/sci-biology/nwalign/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/nwalign -# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*nwalign-0.3.1 (04 Jan 2016) - - 04 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +nwalign-0.3.1.ebuild: - sci-biology/nwalign: new python package diff --git a/sci-biology/pairagon/ChangeLog b/sci-biology/pairagon/ChangeLog deleted file mode 100644 index 9534819bd..000000000 --- a/sci-biology/pairagon/ChangeLog +++ /dev/null @@ -1,17 +0,0 @@ -# ChangeLog for sci-biology/pairagon -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> pairagon-1.1.ebuild: - sci-biology/pairagon: fixed installation of perl-related files - - 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> pairagon-1.1.ebuild: - removing KEYWORDS until the perl files are installed to some other place. At - the moment I get: 'perl-module.eclass: Suspicious environment values found. - PERL5LIB="/usr/lib64/perl5/vendor_perl/5.18.2/pairagon"' - -*pairagon-1.1 (05 Mar 2015) - - 05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +pairagon-1.1.ebuild: - new package diff --git a/sci-biology/parafly/ChangeLog b/sci-biology/parafly/ChangeLog deleted file mode 100644 index a0b2db8aa..000000000 --- a/sci-biology/parafly/ChangeLog +++ /dev/null @@ -1,22 +0,0 @@ -# ChangeLog for sci-biology/parafly -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 31 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - parafly-20130121.ebuild: - sci-biology/parafly: note code bundled under trinity-plugins - - 31 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - parafly-20130121.ebuild: - sci-biology/parafly: updating moved SRC_URI of a last release left on - sourceforge - - 20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - parafly-20130121.ebuild: - sci-biology/parafly: document a recent upstream bugreport from github - -*parafly-20130121 (08 Jan 2015) - - 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +parafly-20130121.ebuild: - sci-biology/parafly: new package diff --git a/sci-biology/pb-honey/ChangeLog b/sci-biology/pb-honey/ChangeLog deleted file mode 100644 index bc8fe6b42..000000000 --- a/sci-biology/pb-honey/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/pb-honey -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - pb-honey-14.1.15.ebuild: - added PYTHON_USEDEP - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> pb-honey-14.1.15.ebuild: - Fix license; add missing [] diff --git a/sci-biology/pb-jelly/ChangeLog b/sci-biology/pb-jelly/ChangeLog deleted file mode 100644 index 737c55ffb..000000000 --- a/sci-biology/pb-jelly/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/pb-jelly -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> pb-jelly-14.9.9.ebuild: - Fix license; add missing [] - -*pb-jelly-14.9.9 (07 Jan 2015) - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +pb-jelly-14.9.9.ebuild, +metadata.xml: - initial ebuild - diff --git a/sci-biology/perlprimer/ChangeLog b/sci-biology/perlprimer/ChangeLog deleted file mode 100644 index bac2acc79..000000000 --- a/sci-biology/perlprimer/ChangeLog +++ /dev/null @@ -1,19 +0,0 @@ -# ChangeLog for sci-biology/perlprimer -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/perlprimer: Updating remote-id in metadata.xml - - 10 Nov 2014; Justin Lecher <jlec@gentoo.org> -perlprimer-1.1.17.ebuild, - +perlprimer-1.1.21.ebuild, metadata.xml: - Bump to EAPI=5; Version Bump - -*perlprimer-1.1.17 (30 Apr 2009) - - 30 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - -perlprimer-1.1.14.ebuild, +perlprimer-1.1.17.ebuild, -files/gcg.801, - +metadata.xml: - cleaned up ebuild - Added ~x86 as requested in bug 231230 - removed redundant database diff --git a/sci-biology/phusion/ChangeLog b/sci-biology/phusion/ChangeLog deleted file mode 100644 index 36818c593..000000000 --- a/sci-biology/phusion/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/phusion -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*phusion-2.1c (02 May 2015) - - 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +phusion-2.1c.ebuild: - sci-biology/phusion: clarified missing LICENSE, have asked upstream for - clarification diff --git a/sci-biology/pileup/ChangeLog b/sci-biology/pileup/ChangeLog deleted file mode 100644 index 935c29eda..000000000 --- a/sci-biology/pileup/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/pileup -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> pileup-0.6.ebuild: - added license - - 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> pileup-0.6.ebuild, - metadata.xml: - dropped KEYWORDS due to misisng LICENSE - -*pileup-0.6 (24 Mar 2014) - - 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +pileup-0.6.ebuild, - +metadata.xml: - new package; a pileup pipeline used along SSAHA2 diff --git a/sci-biology/plinkseq/ChangeLog b/sci-biology/plinkseq/ChangeLog deleted file mode 100644 index 4669cd9f8..000000000 --- a/sci-biology/plinkseq/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/plinkseq -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - plinkseq-0.10.ebuild: - reported a file collision to upstream - -*plinkseq-0.10 (10 May 2015) - - 10 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +plinkseq-0.10.ebuild: - sci-biology/plinkseq: new package diff --git a/sci-biology/polyphen/ChangeLog b/sci-biology/polyphen/ChangeLog deleted file mode 100644 index 29c7f9f9f..000000000 --- a/sci-biology/polyphen/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/polyphen -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*polyphen-2.2.2 (05 May 2015) - - 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +polyphen-2.2.2.ebuild: - sci-biology/polyphen: package skeleton diff --git a/sci-biology/primerD/ChangeLog b/sci-biology/primerD/ChangeLog deleted file mode 100644 index 5d7abeb58..000000000 --- a/sci-biology/primerD/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/primerD -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 13 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - primerD-1.0.0.ebuild: - edit the bundled Makefile - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> primerD-1.0.0.ebuild: - Fix license - -*primerD-1.0.0 (07 Jan 2015) - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +primerD-1.0.0.ebuild, +metadata.xml: - ebuild skeleton diff --git a/sci-biology/proda/ChangeLog b/sci-biology/proda/ChangeLog deleted file mode 100644 index ce22a87eb..000000000 --- a/sci-biology/proda/ChangeLog +++ /dev/null @@ -1,17 +0,0 @@ -# ChangeLog for sci-biology/proda -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Nov 2014; Justin Lecher <jlec@gentoo.org> proda-1.0.ebuild, - +files/proda-1.0-buildsystem.patch, +files/proda-1.0-newgcc.patch: - Bump EAPI; Update for newer compiler - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: - Fixed herd entry in metadata.xml - - 27 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +proda-1.0.ebuild: - Mass import from sunrise - - 22 Apr 2007; Andrey Kislyuk <weaver@horizon.ath.cx> +proda-1.0.ebuild, +metadata.xml: - new package (bug 175524) - diff --git a/sci-biology/prokka/ChangeLog b/sci-biology/prokka/ChangeLog deleted file mode 100644 index da69be964..000000000 --- a/sci-biology/prokka/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/prokka -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> prokka-1.11.ebuild: - sci-biology/prokka: require either of ncbi-tools++ or ncbi-blast+ - - 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> prokka-1.11.ebuild: - sci-biology/prokka: more DEPs recorded - -*prokka-1.11 (05 May 2015) - - 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +prokka-1.11.ebuild: - sci-biology/prokka: new package diff --git a/sci-biology/prot4EST/ChangeLog b/sci-biology/prot4EST/ChangeLog deleted file mode 100644 index cea842cef..000000000 --- a/sci-biology/prot4EST/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/prot4EST -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 13 Nov 2014; Justin Lecher <jlec@gentoo.org> prot4EST-3.1b.ebuild: - Use perl virtuals instead of core - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> prot4EST-3.1b.ebuild: - added license - - 24 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml: - sci-biology/prot4EST: new package, missing LICENSE, missing dev-perl/ deps diff --git a/sci-biology/psychopy/ChangeLog b/sci-biology/psychopy/ChangeLog deleted file mode 100644 index 68a3ae6b3..000000000 --- a/sci-biology/psychopy/ChangeLog +++ /dev/null @@ -1,17 +0,0 @@ -# ChangeLog for sci-biology/psychopy -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 02 Apr 2015; Justin Lecher <jlec@gentoo.org> psychopy-1.78.00.ebuild: - sci-biology/psychopy: Drop eselect dependency - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> -psychopy-1.75.01.ebuild, - -psychopy-1.77.02.ebuild, psychopy-1.78.00.ebuild, psychopy-9999.ebuild: - sci-biology/psychopy: fix SLOT operators - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> psychopy-9999.ebuild: - Switch from git-2 to git-r3 - - 10 Jun 2013; Justin Lecher <jlec@gentoo.org> psychopy-1.75.01.ebuild, - psychopy-9999.ebuild, metadata.xml: - Add missing python use dep, move to virtual/python-imaging diff --git a/sci-biology/pvmsx/ChangeLog b/sci-biology/pvmsx/ChangeLog deleted file mode 100644 index e735c1c4e..000000000 --- a/sci-biology/pvmsx/ChangeLog +++ /dev/null @@ -1,7 +0,0 @@ -# ChangeLog for sci-biology/pvmsx -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> pvmsx-0.1.ebuild, metadata.xml: - Soma QA and polishing - diff --git a/sci-biology/pybedtools/ChangeLog b/sci-biology/pybedtools/ChangeLog deleted file mode 100644 index 4b43438d8..000000000 --- a/sci-biology/pybedtools/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/pybedtools -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/pybedtools: Add github to remote-id in metadata.xml - - 13 Apr 2015; Justin Lecher <jlec@gentoo.org> pybedtools-0.6.9.ebuild: - sci-biology/pybedtools: Streamline ebuild - -*pybedtools-0.6.9 (12 Apr 2015) - - 12 Apr 2015; Michael Schubert <mschu.dev@gmail.com> +metadata.xml, - +pybedtools-0.6.9.ebuild: - sci-biology/pybedtools: add pybedtools diff --git a/sci-biology/pybrain/ChangeLog b/sci-biology/pybrain/ChangeLog deleted file mode 100644 index 12d004434..000000000 --- a/sci-biology/pybrain/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/pybrain -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> pybrain-9999.ebuild: - Switch from git-2 to git-r3 - - 13 Jun 2013; Justin Lecher <jlec@gentoo.org> pybrain-9999.ebuild, - metadata.xml: - Bump to EAPI=5 and distutils-r1.eclass - - 10 Dec 2012; Justin Lecher <jlec@gentoo.org> pybrain-9999.ebuild, - metadata.xml: - Drop comments from metadata.xml; drop keywords from live ebuild - diff --git a/sci-biology/pyfaidx/ChangeLog b/sci-biology/pyfaidx/ChangeLog deleted file mode 100644 index ae669f37b..000000000 --- a/sci-biology/pyfaidx/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/pyfaidx -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 13 Apr 2015; Justin Lecher <jlec@gentoo.org> pyfaidx-0.3.8.ebuild: - sci-biology/pyfaidx: Streamline ebuild - -*pyfaidx-0.3.8 (12 Apr 2015) - - 12 Apr 2015; Michael Schubert <mschu.dev@gmail.com> +metadata.xml, - +pyfaidx-0.3.8.ebuild: - sci-biology/pyfaidx: add pyfaidx diff --git a/sci-biology/pysam/ChangeLog b/sci-biology/pysam/ChangeLog deleted file mode 100644 index 492a5fcb1..000000000 --- a/sci-biology/pysam/ChangeLog +++ /dev/null @@ -1,27 +0,0 @@ -# ChangeLog for sci-biology/pysam -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*pysam-0.8.4 (03 Dec 2015) - - 03 Dec 2015; Ted Tanberry <ted.tanberry@gmail.com> +pysam-0.8.4.ebuild: - sci-biology/pysam: version bump to 0.8.4 - - 04 May 2015; Marius Brehler <marbre@linux.sungazer.de> pysam-0.7.5.ebuild: - Fix deps - - 04 May 2015; Marius Brehler <marbre@linux.sungazer.de> pysam-0.6-r2.ebuild: - Drop keywords due to broken deps - - 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - pysam-0.6-r2.ebuild, pysam-0.7.5.ebuild: - added PYTHON_USEDEP - -*pysam-0.6-r2 (30 Apr 2015) -*pysam-0.7.5 (30 Apr 2015) - - 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +pysam-0.6-r2.ebuild, +pysam-0.7.5.ebuild: - sci-biology/pysam: version bump; noted samtools dependencies as mentioned in - download page accessible from https://code.google.com/p/pysam/downloads/list ; - also added PYTHON_COMPAT for python3 diff --git a/sci-biology/pysurfer/ChangeLog b/sci-biology/pysurfer/ChangeLog deleted file mode 100644 index 8ae3d3a8f..000000000 --- a/sci-biology/pysurfer/ChangeLog +++ /dev/null @@ -1,24 +0,0 @@ -# ChangeLog for sci-biology/pysurfer -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 13 Oct 2015; Horea Christian <h.chr@mail.ru> files/0.6-headless_build.patch: - sci-biology/pysurfer: removed deprecated patch section - - 12 Oct 2015; Horea Christian <h.chr@mail.ru> files/0.6-headless_build.patch: - sci-biology/pysurfer: updated patch - - 30 Sep 2015; Horea Christian <h.chr@mail.ru> +files/0.6-headless_build.patch: - added correspondng patch for =sci-biology/pysurfer-0.6 - -*pysurfer-0.6 (30 Sep 2015) - - 30 Sep 2015; Horea Christian <h.chr@mail.ru> +pysurfer-0.6.ebuild: - sci-biology/pysurfer: version bump - - 30 Sep 2015; Horea Christian <h.chr@mail.ru> pysurfer-0.4.ebuild: - new manifest and archive name for sci-biology/pysurfer - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> pysurfer-0.4.ebuild, - pysurfer-9999.ebuild, +metadata.xml: - Switch from git-2 to git-r3 diff --git a/sci-biology/quast/ChangeLog b/sci-biology/quast/ChangeLog deleted file mode 100644 index 3917ad528..000000000 --- a/sci-biology/quast/ChangeLog +++ /dev/null @@ -1,21 +0,0 @@ -# ChangeLog for sci-biology/quast -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> quast-2.3.ebuild: - added a note about additional bundled package licenses - -*quast-2.3 (15 Jan 2015) - - 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +quast-2.3.ebuild, - -quast-2.2.ebuild: - version bump - - 13 Nov 2014; Justin Lecher <jlec@gentoo.org> quast-2.2.ebuild, metadata.xml: - Bump to new python eclasses - -*quast-2.2 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +quast-2.2.ebuild: - sci-biology/quast: a skeleton for a new python-based package, need help diff --git a/sci-biology/quicktree/ChangeLog b/sci-biology/quicktree/ChangeLog deleted file mode 100644 index 72f601715..000000000 --- a/sci-biology/quicktree/ChangeLog +++ /dev/null @@ -1,18 +0,0 @@ -# ChangeLog for sci-biology/quicktree -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 16 Jun 2013; Justin Lecher <jlec@gentoo.org> quicktree-1.1-r1.ebuild, - metadata.xml: - Bump to EAPI=5 and fix license - -*quicktree-1.1-r1 (08 Nov 2010) - - 08 Nov 2010; Kacper Kowalik <xarthisius@gentoo.org> -quicktree-1.1.ebuild, - +quicktree-1.1-r1.ebuild: - Respect CC,CFLAGS,LDFLAGS. Drop empty deps, add missing die. Fix SRC_URI - wrt bug 344715. Thanks to Joel Berendzen <joelb@lanl.gov> for the report. - - 11 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package, ebuild written by me - diff --git a/sci-biology/quorum/ChangeLog b/sci-biology/quorum/ChangeLog deleted file mode 100644 index dd908e23a..000000000 --- a/sci-biology/quorum/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/quorum -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> quorum-0.2.1.ebuild, - quorum-1.0.0.ebuild: - sci-biology/quorum: avoid full path on linker commandline - /usr/lib64/libjellyfish-2.0.so - -*quorum-0.2.1 (30 Apr 2015) -*quorum-1.0.0 (30 Apr 2015) - - 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +quorum-0.2.1.ebuild, +quorum-1.0.0.ebuild: - sci-biology/quorum: new package diff --git a/sci-biology/repeatmasker-libraries/ChangeLog b/sci-biology/repeatmasker-libraries/ChangeLog deleted file mode 100644 index 1c630fa9d..000000000 --- a/sci-biology/repeatmasker-libraries/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/repeatmasker-libraries -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*repeatmasker-libraries-20150807 (20 Nov 2015) - - 20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +repeatmasker-libraries-20150807.ebuild: - sci-biology/repeatmasker-libraries: version bump and improve einfo navigation - for current website layout diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog deleted file mode 100644 index 0c329e5d9..000000000 --- a/sci-biology/repeatmasker/ChangeLog +++ /dev/null @@ -1,35 +0,0 @@ -# ChangeLog for sci-biology/repeatmasker -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*repeatmasker-4.0.6-r2 (06 Dec 2015) - - 06 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +repeatmasker-4.0.6-r2.ebuild, -repeatmasker-4.0.6-r1.ebuild: - sci-biology/repeatmasker: actually the the utilities do not include Libraries/ - in the paths so install it along all other *.pm files - -*repeatmasker-4.0.6-r1 (06 Dec 2015) - - 06 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +repeatmasker-4.0.6-r1.ebuild, -repeatmasker-4.0.6.ebuild: - sci-biology/repeatmasker: fix ebuild so that it installs files in a proper - location - - 01 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/repeatmasker-4.0.6__configure.patch, - -files/RepeatMasker-open-4-0-1__configure.patch, - -files/RepeatMasker-open-4-0-6__configure.patch: - sci-biology/repeatmasker: rename and move the patch file; drop old patch for a - previous version - - 24 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - repeatmasker-4.0.1-r1.ebuild: - sci-biology/repeatmasker: improve einfo message - -*repeatmasker-4.0.1-r1 (24 Nov 2015) - - 24 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/configure.patch, +metadata.xml, +repeatmasker-4.0.1-r1.ebuild: - sci-biology/repeatmasker: heavily patch configure to return error codes and - die upon error; add more DEPENDencies diff --git a/sci-biology/reptile/ChangeLog b/sci-biology/reptile/ChangeLog deleted file mode 100644 index de729df39..000000000 --- a/sci-biology/reptile/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/reptile -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*reptile-1.1 (30 Apr 2015) - - 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +reptile-1.1.ebuild: - sci-biology/reptile: new package diff --git a/sci-biology/rnaplex/ChangeLog b/sci-biology/rnaplex/ChangeLog deleted file mode 100644 index ca7831f31..000000000 --- a/sci-biology/rnaplex/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sci-biology/rnaplex -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> - rnaplex-0.2.ebuild: - Move to EAPI=5; Update homepage and SRC_URI; Cleanup. - - 29 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package, ebuild written by me - diff --git a/sci-biology/ruffus/ChangeLog b/sci-biology/ruffus/ChangeLog deleted file mode 100644 index 39d3d96ea..000000000 --- a/sci-biology/ruffus/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/ruffus -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*ruffus-9999 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +ruffus-9999.ebuild, +metadata.xml: - new package, works but needs some versioned checkout - diff --git a/sci-biology/rum/ChangeLog b/sci-biology/rum/ChangeLog deleted file mode 100644 index bd5157757..000000000 --- a/sci-biology/rum/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/rum -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> rum-2.0.5.5.ebuild: - sci-biology/rum: Use perl virtuals, add missing die; use PN for tarball - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/rum: Add github to remote-id in metadata.xml - -*rum-2.0.5.5 (18 Apr 2015) - - 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +rum-2.0.5.5.ebuild: - sci-biology/rum: new package diff --git a/sci-biology/sabre/ChangeLog b/sci-biology/sabre/ChangeLog deleted file mode 100644 index 2d317d111..000000000 --- a/sci-biology/sabre/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/sabre -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/sabre: Add github to remote-id in metadata.xml - - 09 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> sabre-9999.ebuild: - Switch from git-2 to git-r3; Cleanup - -*sabre-9999 (15 Jan 2015) - - 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +sabre-9999.ebuild: - sci-biology/sabre: new package diff --git a/sci-biology/salmon/ChangeLog b/sci-biology/salmon/ChangeLog deleted file mode 100644 index 478ddfa79..000000000 --- a/sci-biology/salmon/ChangeLog +++ /dev/null @@ -1,28 +0,0 @@ -# ChangeLog for sci-biology/salmon -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*salmon-0.4.2 (16 Aug 2015) - - 16 Aug 2015; Michael Schubert <mschu.dev@gmail.com> +salmon-0.4.2.ebuild, - salmon-0.3.2.ebuild, salmon-9999.ebuild: - sci-biology/salmon: fix deps & version bump to 0.4.2 - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/salmon: Add github to remote-id in metadata.xml - - 23 May 2015; Michael Schubert <mschu.dev@gmail.com> - files/salmon-0.3.2-no-boost-static.patch: - sci-biology/salmon: clean patch - - 21 May 2015; Michael Schubert <mschu.dev@gmail.com> salmon-0.3.2.ebuild, - salmon-9999.ebuild: - sci-biology/salmon: streamline ebuild - -*salmon-0.3.2 (21 May 2015) -*salmon-9999 (21 May 2015) - - 21 May 2015; Michael Schubert <mschu.dev@gmail.com> - +files/salmon-0.3.2-no-boost-static.patch, +metadata.xml, - +salmon-0.3.2.ebuild, +salmon-9999.ebuild: - sci-biology/salmon: add salmon diff --git a/sci-biology/samstat/ChangeLog b/sci-biology/samstat/ChangeLog deleted file mode 100644 index 528491d9b..000000000 --- a/sci-biology/samstat/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/samstat -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> samstat-20130708.ebuild: - fixed DESCRIPTION - -*samstat-20130708 (16 Mar 2014) - - 16 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +samstat-20130708.ebuild: - sci-biology/samstat: new package diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog deleted file mode 100644 index a34a1d7ce..000000000 --- a/sci-biology/samtools/ChangeLog +++ /dev/null @@ -1,20 +0,0 @@ -# ChangeLog for sci-biology/samtools -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/samtools: Updating remote-id in metadata.xml - -*samtools-1.0-r2 (11 May 2015) -*samtools-1.1-r1 (11 May 2015) -*samtools-1.2-r1 (11 May 2015) - - 11 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/samtools-1.0-buildsystem.patch, +files/samtools-1.0-rmdup.patch, - +files/samtools-1.1-buildsystem.patch, +files/samtools-1.1-rmdup.patch, - +files/samtools-1.2-buildsystem.patch, +files/samtools-1.2-rmdup.patch, - +metadata.xml, +samtools-1.0-r2.ebuild, +samtools-1.1-r1.ebuild, - +samtools-1.2-r1.ebuild: - sci-biology/samtools: fix core dump on 'samtools rmdup' by adding - bam_get_library() from an upstream patch from - https://github.com/samtools/samtools/issues/138 diff --git a/sci-biology/scaffold_builder/ChangeLog b/sci-biology/scaffold_builder/ChangeLog deleted file mode 100644 index c3df5787b..000000000 --- a/sci-biology/scaffold_builder/ChangeLog +++ /dev/null @@ -1,29 +0,0 @@ -# ChangeLog for sci-biology/scaffold_builder -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - scaffold_builder-20131122.ebuild: - sci-biology/scaffold_builder: set proper LICENSE to the one mentioned in the - http://www.scfbm.org/content/pdf/1751-0473-8-23.pdf article and also in the - COPYING.txt file in the distribution .zip file - - 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - scaffold_builder-20131122.ebuild: - sci-biology/scaffold_builder: noted RDEPEND, added second HOMEPAGE - -*scaffold_builder-20131122 (30 Jan 2015) - - 30 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +scaffold_builder-20131122.ebuild, -scaffold_builder-20130403.ebuild: - version bump - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> - scaffold_builder-20130403.ebuild: - added license - -*scaffold_builder-20130403 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +scaffold_builder-20130403.ebuild, +metadata.xml: - new package but with a missing LICENSE diff --git a/sci-biology/scan_for_matches/ChangeLog b/sci-biology/scan_for_matches/ChangeLog deleted file mode 100644 index f8398b643..000000000 --- a/sci-biology/scan_for_matches/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/scan_for_matches -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*scan_for_matches-20121220 (28 Mar 2014) - - 28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +scan_for_matches-20121220.ebuild: - sci-biology/scan_for_matches: new package, LICENSE not explicitly avalaible - hence seems public-domain fits? diff --git a/sci-biology/scbi_blast/ChangeLog b/sci-biology/scbi_blast/ChangeLog deleted file mode 100644 index f171b82a9..000000000 --- a/sci-biology/scbi_blast/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/scbi_blast -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 25 Dec 2015; Marius Brehler <marbre@linux.sungazer.de> - scbi_blast-0.0.37.ebuild: - sci-biology/scbi_blast: Fix header, remove ruby19 - -*scbi_blast-0.0.37 (02 Dec 2015) - - 02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +scbi_blast-0.0.37.ebuild: - sci-biology/scbi_blast: new package diff --git a/sci-biology/scbi_fasta/ChangeLog b/sci-biology/scbi_fasta/ChangeLog deleted file mode 100644 index 70011e294..000000000 --- a/sci-biology/scbi_fasta/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/scbi_fasta -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 25 Dec 2015; Marius Brehler <marbre@linux.sungazer.de> - scbi_fasta-0.1.9.ebuild: - sci-biology/scbi_fasta: Fix header, remove ruby19 - -*scbi_fasta-0.1.9 (02 Dec 2015) - - 02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +scbi_fasta-0.1.9.ebuild: - sci-biology/scbi_fasta: new package diff --git a/sci-biology/scbi_mapreduce/ChangeLog b/sci-biology/scbi_mapreduce/ChangeLog deleted file mode 100644 index bf955f239..000000000 --- a/sci-biology/scbi_mapreduce/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/scbi_mapreduce -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 25 Dec 2015; Marius Brehler <marbre@linux.sungazer.de> - scbi_mapreduce-0.0.40.ebuild: - sci-biology/scbi_mapreduce: Fix header, remove ruby19 - -*scbi_mapreduce-0.0.40 (02 Dec 2015) - - 02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +scbi_mapreduce-0.0.40.ebuild: - sci-biology/scbi_mapreduce: new package diff --git a/sci-biology/scbi_plot/ChangeLog b/sci-biology/scbi_plot/ChangeLog deleted file mode 100644 index 570e5a1bd..000000000 --- a/sci-biology/scbi_plot/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/scbi_plot -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 25 Dec 2015; Marius Brehler <marbre@linux.sungazer.de> scbi_plot-0.0.7.ebuild: - sci-biology/scbi_plot: Fix header, remove ruby19 - -*scbi_plot-0.0.7 (02 Dec 2015) - - 02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +scbi_plot-0.0.7.ebuild: - sci-biology/scbi_plot: new package diff --git a/sci-biology/screed/ChangeLog b/sci-biology/screed/ChangeLog deleted file mode 100644 index 2f03f49d8..000000000 --- a/sci-biology/screed/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/screed -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/screed: Add github to remote-id in metadata.xml - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> screed-0.7.1.ebuild: - removed empty line - -*screed-0.7.1 (18 Mar 2014) - - 18 Mar 2014; Justin Lecher <jlec@gentoo.org> +screed-0.7.1.ebuild, - +metadata.xml: - New addition written by me diff --git a/sci-biology/scythe/ChangeLog b/sci-biology/scythe/ChangeLog deleted file mode 100644 index d58089e6d..000000000 --- a/sci-biology/scythe/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/scythe -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/scythe: Add github to remote-id in metadata.xml - -*scythe-0.992 (24 Mar 2014) - - 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +scythe-0.992.ebuild, +metadata.xml: - bundled Makefile forces -O3, wrong version number, but works diff --git a/sci-biology/seqclean/ChangeLog b/sci-biology/seqclean/ChangeLog deleted file mode 100644 index fea9c3957..000000000 --- a/sci-biology/seqclean/ChangeLog +++ /dev/null @@ -1,17 +0,0 @@ -# ChangeLog for sci-biology/seqclean -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - seqclean-110625.ebuild: - sci-biology/seqclean: bump EAPI - - 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - seqclean-110625.ebuild: - sci-biology/seqclean: fix language - -*seqclean-110625 (25 Jun 2011) - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -seqclean-0.1.ebuild, - +seqclean-110625.ebuild, +files/seqclean-110625-build.patch: - Cleaned ebuild diff --git a/sci-biology/seqtools/ChangeLog b/sci-biology/seqtools/ChangeLog deleted file mode 100644 index a9192f088..000000000 --- a/sci-biology/seqtools/ChangeLog +++ /dev/null @@ -1,17 +0,0 @@ -# ChangeLog for sci-biology/seqtools -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*seqtools-4.34.5 (12 May 2015) - - 12 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +seqtools-4.34.5.ebuild, -seqtools-4.34.1.ebuild: - sci-biology/seqtools: upstream fixed dependency issues so that MAKEOPTS=-j5 - works; version bump - -*seqtools-4.34.1 (09 May 2015) - - 09 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +seqtools-4.34.1.ebuild: - sci-biology/seqtools: new package, said to be derived from AceDB (watch for - file collisions?) diff --git a/sci-biology/sequin/ChangeLog b/sci-biology/sequin/ChangeLog deleted file mode 100644 index c0b830fb6..000000000 --- a/sci-biology/sequin/ChangeLog +++ /dev/null @@ -1,17 +0,0 @@ -# ChangeLog for sci-biology/sequin -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*sequin-20121202 (16 Jun 2013) - - 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -sequin-20090722.ebuild, - +sequin-20121202.ebuild: - Version Bump; restrcit license; add QA_PREBUILT for binaries; install html - files into sys path - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: - Fixed herd entry in metadata.xml - - 19 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package, ebuild written by me - diff --git a/sci-biology/sff_dump/ChangeLog b/sci-biology/sff_dump/ChangeLog deleted file mode 100644 index 1cd77142f..000000000 --- a/sci-biology/sff_dump/ChangeLog +++ /dev/null @@ -1,7 +0,0 @@ -# ChangeLog for sci-biology/sff_dump -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 24 Jun 2011; Justin Lecher <jlec@gentoo.org> sff_dump-1.04.ebuild: - Some ebuild cleaning - diff --git a/sci-biology/sga/ChangeLog b/sci-biology/sga/ChangeLog deleted file mode 100644 index 3e6b68d1f..000000000 --- a/sci-biology/sga/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/sga -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/sga: Add github to remote-id in metadata.xml - - 09 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> sga-9999.ebuild: - Switch from git-2 to git-r3; Cleanup; Add missing die - -*sga-9999 (24 Mar 2014) - - 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +sga-9999.ebuild, - +metadata.xml: - new package; forces its own optimization flags but works fine diff --git a/sci-biology/sgp2/ChangeLog b/sci-biology/sgp2/ChangeLog deleted file mode 100644 index 0bf5d5738..000000000 --- a/sci-biology/sgp2/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/sgp2 -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> sgp2-1.1.ebuild: - sci-biology/sgp2: add dobin() call - -*sgp2-1.1 (17 Jun 2014) - - 17 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/Makefile.patch, +metadata.xml, +sgp2-1.1.ebuild: - sci-biology/sgp2: new package, works diff --git a/sci-biology/sickle/ChangeLog b/sci-biology/sickle/ChangeLog deleted file mode 100644 index 80afb2cc5..000000000 --- a/sci-biology/sickle/ChangeLog +++ /dev/null @@ -1,22 +0,0 @@ -# ChangeLog for sci-biology/sickle -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/sickle: Add github to remote-id in metadata.xml - -*sickle-1.33 (09 Mar 2015) - - 09 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +sickle-1.33.ebuild, - sickle-9999.ebuild: - respect CC and CFLAGS; added an ebuild for latest release tarball, works - - 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> sickle-9999.ebuild: - correct package description - -*sickle-9999 (24 Mar 2014) - - 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +sickle-9999.ebuild, +metadata.xml: - simple ebuild, bundled Makefile forces compile flags, program version, but - works diff --git a/sci-biology/signalp/ChangeLog b/sci-biology/signalp/ChangeLog deleted file mode 100644 index b7fc490ff..000000000 --- a/sci-biology/signalp/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/signalp -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 26 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> signalp-3.0.ebuild: - Bump to EAPI=5 - - 27 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> - signalp-3.0.ebuild: - QA fixes - - 01 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package sci-biology/signalp, ebuild written by me diff --git a/sci-biology/skewer-bin/ChangeLog b/sci-biology/skewer-bin/ChangeLog deleted file mode 100644 index a67360b6b..000000000 --- a/sci-biology/skewer-bin/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/skewer-bin -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - skewer-bin-0.1.104.ebuild: - sci-biology/skewer: fix typo - -*skewer-bin-0.1.104 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +skewer-bin-0.1.104.ebuild: - sci-biology/skewer-bin: new package diff --git a/sci-biology/smalt-bin/ChangeLog b/sci-biology/smalt-bin/ChangeLog deleted file mode 100644 index f6ade7009..000000000 --- a/sci-biology/smalt-bin/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/smalt-bin -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*smalt-bin-0.7.4 (16 Jun 2013) - - 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -smalt-bin-0.5.1.ebuild, - +smalt-bin-0.7.4.ebuild, metadata.xml: - Version Bump; restrict license; add QA_PREBUILT for binaries - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> smalt-bin-0.5.1.ebuild: - Cleaned ebuild and fixed LICENSE - diff --git a/sci-biology/snap/ChangeLog b/sci-biology/snap/ChangeLog deleted file mode 100644 index 8612cc47a..000000000 --- a/sci-biology/snap/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/snap -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*snap-20131129 (30 Mar 2015) - - 30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +snap-20131129.ebuild: - sci-biology/snap: new package diff --git a/sci-biology/snphylo/ChangeLog b/sci-biology/snphylo/ChangeLog deleted file mode 100644 index 1d9fffcfb..000000000 --- a/sci-biology/snphylo/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/snphylo -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*snphylo-20140701 (11 May 2015) - - 11 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +snphylo-20140701.ebuild: - sci-biology/snphylo: new package, needs some R packages and we have to avoid - the interactive setup.sh step diff --git a/sci-biology/spm/ChangeLog b/sci-biology/spm/ChangeLog deleted file mode 100644 index fbb5c437d..000000000 --- a/sci-biology/spm/ChangeLog +++ /dev/null @@ -1,29 +0,0 @@ -# ChangeLog for sci-biology/spm -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 11 Mar 2015; Horea Christian <h.chr@mail.ru> spm-12.ebuild: - installing into octave M subdirectory - - 10 Mar 2015; Horea Christian <h.chr@mail.ru> spm-12.ebuild: - installing ALL the things - - 04 Mar 2015; Horea Christian <h.chr@mail.ru> spm-12.ebuild: - typo - - 04 Mar 2015; Horea Christian <h.chr@mail.ru> spm-12.ebuild: - fixed doins path - -*spm-12 (04 Mar 2015) - - 04 Mar 2015; Horea Christian <h.chr@mail.ru> +spm-12.ebuild, - spm-8.ebuild: - removed slots, added new version - - 17 Feb 2015; Horea Christian <h.chr@mail.ru> -spm-8.ebuild.orig, - spm-8.ebuild: - added quotation marks, removed ori file - - 17 Feb 2015; Horea Christian <h.chr@mail.ru> +metadata.xml, - +spm-8.ebuild.orig, spm-8.ebuild: - added metadata diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog deleted file mode 100644 index 96de9b3dd..000000000 --- a/sci-biology/sra_sdk/ChangeLog +++ /dev/null @@ -1,67 +0,0 @@ -# ChangeLog for sci-biology/sra_sdk -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> sra_sdk-2.1.9.ebuild, - sra_sdk-2.2.2a.ebuild, metadata.xml: - Drop useless blank line - -*sra_sdk-2.2.2a (28 Dec 2012) - - 28 Dec 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +sra_sdk-2.2.2a.ebuild: - sci-biology/sra_sdk-2.2.2a: a version bump, still requires MAKEOPTS=-j1 and - copies softlinks to binaries and libraries as files, so everything is in 3 - physical copies - - 15 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - sra_sdk-2.1.9.ebuild: - added missing insinto sra_sdk-2.1.9.ebuild - - 15 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - sra_sdk-2.1.9.ebuild: - use EAPI=4 hoping it will handle symlinks in bin/ and lib/ directories - properly (but it does not, bug #408199 sra_sdk-2.1.9.ebuild - -*sra_sdk-2.1.6 (17 Feb 2012) - - 17 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +sra_sdk-2.1.6.ebuild, sra_sdk-2.1.9.ebuild: - sci-biology/sra_sdk: updated ebuild for 2.1.6 and 2.1.9: they both - compile/install but possibly install layout is still broken, leading to non- - functional sff-dump - - 06 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - sra_sdk-2.1.9.ebuild: - preserve libs written directly into at the end of src_compile() and install - them later on sra_sdk-2.1.9.ebuild - - 06 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - sra_sdk-2.1.9.ebuild, +files/libs_sra_Makefile.patch, - +files/tools_vdb-vcopy_Makefile.patch: - two more Makefiles needed a DESTDIR patch, in conjunction with an ugly - symlink hack in one can build the stuff; dobin does not transfer symliks so - every binary appears installed 3 times; upstream bug - http://jira.be-md.ncbi.nlm.nih.gov/browse/TR-10207 - -*sra_sdk-2.1.9 (06 Feb 2012) - - 06 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - sra_sdk-2.1.6.ebuild, +sra_sdk-2.1.9.ebuild, +files/sra_sdk-destdir.patch: - version bump and almost correct DESTDIR patch - - 22 Sep 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - sra_sdk-2.1.6.ebuild: - adjust to altered source tree strcuture, add weird ncbi/ subdirs to be - installed, more comments in the ebuild - -*sra_sdk-2.1.6 (22 Sep 2011) - - 22 Sep 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - -sra_sdk-2.0.1.ebuild, +sra_sdk-2.1.6.ebuild: - version bump sra_sdk-2.1.6.ebuild - - 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - sra_sdk-2.0.1.ebuild: - backbone of a new package, should probably use a lot of stuff from - ncbi-tools++ ebuild diff --git a/sci-biology/ssaha2-bin/ChangeLog b/sci-biology/ssaha2-bin/ChangeLog deleted file mode 100644 index a2f05d5e6..000000000 --- a/sci-biology/ssaha2-bin/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sci-biology/ssaha2-bin -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -ssaha2-bin-2.5.3.ebuild, - +ssaha2-bin-2.5.5.ebuild, metadata.xml: - Version Bump; restrict license; add QA_PREBUILT for binaries - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> ssaha2-bin-2.5.3.ebuild: - Cleaned ebuild and fixed LICENSE - diff --git a/sci-biology/stacks/ChangeLog b/sci-biology/stacks/ChangeLog deleted file mode 100644 index ac16a283b..000000000 --- a/sci-biology/stacks/ChangeLog +++ /dev/null @@ -1,19 +0,0 @@ -# ChangeLog for sci-biology/stacks -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> stacks-1.16.ebuild: - sci-biology/stacks: commented out sys-cluster/openmpi DEPENDency - - 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> stacks-1.16.ebuild: - sci-biology/stacks: SRC_URI cleanup - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> stacks-1.16.ebuild: - clean up - -*stacks-1.16 (28 Mar 2014) - - 28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +stacks-1.16.ebuild: - sci-biology/stacks: skeleton for a new package; needs webapp team help, *some* - Makefile's need proper DESTDIR support diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog deleted file mode 100644 index 018eb7dd3..000000000 --- a/sci-biology/staden/ChangeLog +++ /dev/null @@ -1,53 +0,0 @@ -# ChangeLog for sci-biology/staden -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 07 Aug 2015; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta9.ebuild, - staden-9999.ebuild: - sci-biology/staden: Fix SLOT operators, bug #556946 - - 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - staden-2.0.0_beta9.ebuild, staden-9999.ebuild: - sci-biology/staden: added SLOT operator - - 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - staden-2.0.0_beta9.ebuild, staden-9999.ebuild: - added PYTHON_USEDEP - - 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> staden-9999.ebuild: - sci-biology/staden: fix ESVN_REPO_URI to include trailing 'src/' so that we do - not have to change ''. Thanks to Justin Lercher for the patch. - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta9.ebuild, - staden-9999.ebuild, metadata.xml: - Punt base.eclass; transfer changes to live ebuild - -*staden-2.0.0_beta9 (26 Nov 2012) - - 26 Nov 2012; Justin Lecher <jlec@gentoo.org> -staden-2.0.0_beta8.ebuild, - +staden-2.0.0_beta9.ebuild, +files/staden-2.0.0_beta9-ldflags.patch, - +files/staden-2.0.0_beta9-libpng-1.5.patch, - +files/staden-2.0.0_beta9-zlib.patch, -files/rpath.patch: - Version Bump, move to sane portage like building - - 12 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> staden-9999.ebuild: - fix determination of svn-based checkout number required for building - staden-9999.ebuild - - 08 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - staden-2.0.0_beta8.ebuild, staden-9999.ebuild: - Documented that we have to install somehow - /usr/share/doc/staden/manual/gap4.index which is looked up when user accesses - built-in help menu item - - 23 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild, - staden-9999.ebuild: - Streamlined fortran-2 eclass usage - - 23 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild, - staden-9999.ebuild: - Streamlined fortran-2 eclass usage - - 21 Jun 2011; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta8.ebuild, - staden-9999.ebuild: - Added fortran-2.eclass support diff --git a/sci-biology/subread/ChangeLog b/sci-biology/subread/ChangeLog deleted file mode 100644 index 382882cf7..000000000 --- a/sci-biology/subread/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/subread -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 29 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - subread-1.4.6.ebuild: - also install GTF files; added zlib dependency - -*subread-1.4.6 (29 Jan 2015) - - 29 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +subread-1.4.6.ebuild: - sci-biology/subread: new package diff --git a/sci-biology/swissknife/ChangeLog b/sci-biology/swissknife/ChangeLog deleted file mode 100644 index 677387353..000000000 --- a/sci-biology/swissknife/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sci-biology/swissknife -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 15 Jun 2015; Justin Lecher <jlec@gentoo.org> swissknife-1.70.ebuild: - sci-biology/swissknife: Fix dependency problems due to recent mask of perl- - core packages - - 24 Sep 2014; Justin Lecher <jlec@gentoo.org> -swissknife-1.67.ebuild, - +swissknife-1.70.ebuild, metadata.xml: - Version Bump; Bump to EAPI=5 diff --git a/sci-biology/symap/ChangeLog b/sci-biology/symap/ChangeLog deleted file mode 100644 index c3d9c13a1..000000000 --- a/sci-biology/symap/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/symap -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> symap-4.0.ebuild, +metadata.xml: - Fix wrong license - -*symap-4.0 (29 Aug 2013) - - 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +symap-4.0.ebuild: - Not yet working. - diff --git a/sci-biology/tablet-bin/ChangeLog b/sci-biology/tablet-bin/ChangeLog deleted file mode 100644 index e3f12de60..000000000 --- a/sci-biology/tablet-bin/ChangeLog +++ /dev/null @@ -1,56 +0,0 @@ -# ChangeLog for sci-biology/tablet-bin -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*tablet-bin-1.14.10.21 (15 Mar 2015) - - 15 Mar 2015; Ted Tanberry <ted.tanberry@gmail.com> - +tablet-bin-1.14.10.21.ebuild, - -tablet-bin-1.13.12.17.ebuild, -tablet-bin-1.14.04.10.ebuild: - Version bump, update SRC_URI, remove dead ebuilds - - 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> - tablet-bin-1.14.04.10.ebuild: - clean up - -*tablet-bin-1.14.04.10 (02 Jul 2014) - - 02 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +tablet-bin-1.14.04.10.ebuild: - sci-biology/tablet-bin: version bump; updated the license - -*tablet-bin-1.13.12.17 (20 Jan 2014) - - 20 Jan 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +tablet-bin-1.13.12.17.ebuild, -tablet-bin-1.13.05.17.ebuild: - Version bump - - 16 Jun 2013; Justin Lecher <jlec@gentoo.org> tablet-bin-1.13.05.17.ebuild: - Version Bump; Bump to EAPI5 and python-r1.eclass; drop addpredict - - 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -tablet-bin-1.11.05.03.ebuild, - -tablet-bin-1.11.11.01.ebuild, +tablet-bin-1.13.05.17.ebuild, metadata.xml: - Version Bump; Bump to EAPI5 and python-r1.eclass - - 07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - tablet-bin-1.11.11.01.ebuild: - adjust PATH to point to the installation place - - 07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - tablet-bin-1.11.11.01.ebuild: - make use of the TMPDIR variable - - 12 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - tablet-bin-1.11.11.01.ebuild: - fix sanbox violations on some systems tablet-bin-1.11.11.01.ebuild - - 12 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - tablet-bin-1.11.11.01.ebuild: - added MYPV to the ebuild to make it more easily re-usable - tablet-bin-1.11.11.01.ebuild - -*tablet-bin-1.11.11.01 (09 Dec 2011) - - 09 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - tablet-bin-1.11.05.03.ebuild, +tablet-bin-1.11.11.01.ebuild: - ebuild cleanup, version bump diff --git a/sci-biology/tablet/ChangeLog b/sci-biology/tablet/ChangeLog deleted file mode 100644 index 7ae8ed4a0..000000000 --- a/sci-biology/tablet/ChangeLog +++ /dev/null @@ -1,28 +0,0 @@ -# ChangeLog for sci-biology/tablet -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> -tablet-1.13.12.17.ebuild, - tablet-9999.ebuild: - sci-biology/tablet: fix SLOT operators and dependencies - - 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> tablet-9999.ebuild: - sci-biology/tablet: note the compilation from source is not coded into ebuild - yet - -*tablet-1.14.04.10 (02 Jul 2014) - - 02 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +tablet-1.14.04.10.ebuild, -Manifest, tablet-1.13.12.17.ebuild, - tablet-9999.ebuild: - sci-biology/tablet: cleaned up the ebuilds, they compile and install but the - bundled samtools-*.jar is not found - -*tablet-1.13.12.17 (28 Mar 2014) -*tablet-9999 (28 Mar 2014) - - 28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/response.varfile, +metadata.xml, +tablet-1.13.12.17.ebuild, - +tablet-9999.ebuild: - sci-biology/tablet: skeleton for a new package eventually to replace current - tablet-bin package diff --git a/sci-biology/tagdust/ChangeLog b/sci-biology/tagdust/ChangeLog deleted file mode 100644 index c983e5a9f..000000000 --- a/sci-biology/tagdust/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/tagdust -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*tagdust-20101028 (02 Feb 2015) - - 02 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +tagdust-20101028.ebuild: - sci-biology/tagdust: new package diff --git a/sci-biology/tclust/ChangeLog b/sci-biology/tclust/ChangeLog deleted file mode 100644 index edc5c8c65..000000000 --- a/sci-biology/tclust/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/tclust -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*tclust-110625 (25 Jun 2011) - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -tclust-0.1.ebuild, - +tclust-110625.ebuild, +files/tclust-110625-build.patch: - Cleaned ebuild - diff --git a/sci-biology/tgicl/ChangeLog b/sci-biology/tgicl/ChangeLog deleted file mode 100644 index 53942e764..000000000 --- a/sci-biology/tgicl/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/tgicl -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 15 Jun 2015; Justin Lecher <jlec@gentoo.org> tgicl-2.1.ebuild: - sci-biology/tgicl: Fix dependency problems due to recent mask of perl-core - packages - - 24 Sep 2014; Justin Lecher <jlec@gentoo.org> tgicl-2.1.ebuild, metadata.xml: - Bump to EAPI=5 diff --git a/sci-biology/tigr-foundation-libs/ChangeLog b/sci-biology/tigr-foundation-libs/ChangeLog deleted file mode 100644 index 43c770108..000000000 --- a/sci-biology/tigr-foundation-libs/ChangeLog +++ /dev/null @@ -1,8 +0,0 @@ -# ChangeLog for sci-biology/tigr-foundation-libs -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 24 Jun 2011; Justin Lecher <jlec@gentoo.org> - tigr-foundation-libs-2.0-r1.ebuild: - Some ebuild cleaning - diff --git a/sci-biology/tmhmm/ChangeLog b/sci-biology/tmhmm/ChangeLog deleted file mode 100644 index ad347f1dc..000000000 --- a/sci-biology/tmhmm/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/tmhmm -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 26 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> tmhmm-2.0c.ebuild: - Bump to EAPI=5 and cleanup - - 27 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> - tmhmm-2.0c.ebuild, -tmhmm: - QA fixes - - 21 Aug 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package, ebuild written by me diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog deleted file mode 100644 index d382557db..000000000 --- a/sci-biology/tophat/ChangeLog +++ /dev/null @@ -1,89 +0,0 @@ -# ChangeLog for sci-biology/tophat -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*tophat-2.1.0 (14 Aug 2015) - - 14 Aug 2015; Michael Schubert <mschu.dev@gmail.com> +tophat-2.1.0.ebuild: - sci-biology/tophat: tophat-2.1.0 version bump - - 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - tophat-2.0.12.ebuild, tophat-2.0.13.ebuild, tophat-2.0.14.ebuild: - added PYTHON_USEDEP - - 28 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - tophat-2.0.12.ebuild, tophat-2.0.13.ebuild, tophat-2.0.14.ebuild: - sci-biology/tophat: recorded depependencies; dropped KEYWORDS until we have - slotted samtools (or multiple static binaries with version appended to - filename), link tophat_reporter against -lsam-0.1.18 and similarly adjust - tophat_reporter - - 28 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - tophat-2.0.14.ebuild: - sci-biology/tophat: try to introduce all-recursive target to make upstream - 'make all' call happy - - 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/trans-abyss/ChangeLog b/sci-biology/trans-abyss/ChangeLog deleted file mode 100644 index 887eca9c2..000000000 --- a/sci-biology/trans-abyss/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sci-biology/trans-abyss -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> trans-abyss-1.4.8.ebuild: - Soma polishing - -*trans-abyss-1.4.8 (07 Jan 2015) - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +trans-abyss-1.4.8.ebuild, +metadata.xml: - initial ebuild - diff --git a/sci-biology/trf/ChangeLog b/sci-biology/trf/ChangeLog deleted file mode 100644 index 86855a635..000000000 --- a/sci-biology/trf/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/trf -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*trf-4.07b (22 Apr 2014) - - 22 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +trf-4.07b.ebuild: - sci-biology/trf-4.07b: version bump; install some HTML helpfiles as well diff --git a/sci-biology/trim_galore/ChangeLog b/sci-biology/trim_galore/ChangeLog deleted file mode 100644 index e0395c1e6..000000000 --- a/sci-biology/trim_galore/ChangeLog +++ /dev/null @@ -1,23 +0,0 @@ -# ChangeLog for sci-biology/trim_galore -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*trim_galore-0.4.0 (30 May 2015) - - 30 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +trim_galore-0.4.0.ebuild, -trim_galore-0.3.7.ebuild: - sci-biology/trim_galore: version bump; ajusted S variable to match current - upstream's packaging habit; still needs fastqc package to be finished - -*trim_galore-0.3.7 (24 Feb 2015) - - 24 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +trim_galore-0.3.7.ebuild, -trim_galore-0.3.3.ebuild: - version bump; installs the simple perl script and PDF doc files - -*trim_galore-0.3.3 (23 Mar 2014) - - 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +trim_galore-0.3.3.ebuild: - sci-biology/trim_galore: a skeleton for a new package, needs sci- - biology/fastqc to move ahead diff --git a/sci-biology/trimmomatic/ChangeLog b/sci-biology/trimmomatic/ChangeLog deleted file mode 100644 index 8eaa73c4d..000000000 --- a/sci-biology/trimmomatic/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/trimmomatic -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> trimmomatic-0.32.ebuild: - sci-biology/trimmomatic: fix SLOT operators - -*trimmomatic-0.32 (22 Jan 2015) - - 22 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +trimmomatic-0.32.ebuild: - sci-biology/trimmomatic: new package diff --git a/sci-biology/trinityrnaseq/ChangeLog b/sci-biology/trinityrnaseq/ChangeLog deleted file mode 100644 index ed29a10c4..000000000 --- a/sci-biology/trinityrnaseq/ChangeLog +++ /dev/null @@ -1,53 +0,0 @@ -# ChangeLog for sci-biology/trinityrnaseq -# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jan 2016; Marius Brehler <marbre@linux.sungazer.de> - trinityrnaseq-2.0.6.ebuild, trinityrnaseq-2.1.1.ebuild: - sci-biology/trinityrnaseq: Add missing die - - 05 Jan 2016; Marius Brehler <marbre@linux.sungazer.de> - trinityrnaseq-2.0.6.ebuild: - sci-biology/trinityrnaseq: Drop KEYWORDS (depends on masked package) - - 31 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - trinityrnaseq-2.0.6.ebuild, trinityrnaseq-2.1.1.ebuild: - sci-biology/trinityrnaseq: do not install bundled GAL but DEPEND on it via - external package as sci-biology/GAL - -*trinityrnaseq-2.1.1 (20 Nov 2015) - - 20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/disable_some_plugins.patch, +trinityrnaseq-2.1.1.ebuild: - sci-biology/trinityrnaseq: version bump but dropping KEYWORDS because we - relocate *.pm file into vendor_perl and all 'use blah' calls to trinity- - provided perl modules need to be changed to 'use trinityrnaseq::blah', or - PERL5INC modified? - - 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - sci-biology/trinityrnaseq: Add github to remote-id in metadata.xml - - 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - trinityrnaseq-2.0.6.ebuild: - sci-biology/trinityrnaseq: added missing quotes - - 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - trinityrnaseq-2.0.6.ebuild: - sci-biology/trinityrnaseq: added a note and removed broken symlink upon - installation - -*trinityrnaseq-2.0.6 (30 Apr 2015) - - 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +trinityrnaseq-2.0.6.ebuild, -files/r3590_chmod.patch, -files/sort.patch, - -trinityrnaseq-20140413.ebuild: - sci-biology/trinityrnaseq: version bump; dropped patches because target file - is gone; ideally should depend on <sci-biology/samtools-1.1 but lets see what - are the real requirements - -*trinityrnaseq-20140413 (30 Apr 2015) - - 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/r3590_chmod.patch, +files/sort.patch, +metadata.xml, - +trinityrnaseq-20140413.ebuild: - sci-biology/trinityrnaseq: new package (with last release on sourceforge) diff --git a/sci-biology/trowel/ChangeLog b/sci-biology/trowel/ChangeLog deleted file mode 100644 index 6e5b88c44..000000000 --- a/sci-biology/trowel/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/trowel -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*trowel-0.1.4.1 (07 Jan 2015) - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +trowel-0.1.4.1.ebuild: - new, working ebuild diff --git a/sci-biology/twinscan/ChangeLog b/sci-biology/twinscan/ChangeLog deleted file mode 100644 index da9a3364c..000000000 --- a/sci-biology/twinscan/ChangeLog +++ /dev/null @@ -1,24 +0,0 @@ -# ChangeLog for sci-biology/twinscan -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*twinscan-4.1.2-r1 (02 May 2015) - - 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +twinscan-4.1.2-r1.ebuild, -twinscan-4.1.2.ebuild: - sci-biology/twinscan: lots of tweaks to install process, install perl modules, - more perl scripts, noted optional external dependencies - - 16 Jun 2013; Justin Lecher <jlec@gentoo.org> twinscan-4.1.2.ebuild, - metadata.xml: - Bump to EAPI=5 and fix license - - 07 Mar 2011; Justin Lecher <jlec@gentoo.org> twinscan-4.1.2.ebuild: - Correct Slots for gtk 3 introduction to tree - - 27 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> - twinscan-4.1.2.ebuild: - QA fixes - - 17 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package, bug 154939, ebuild written by me diff --git a/sci-biology/ugene/ChangeLog b/sci-biology/ugene/ChangeLog deleted file mode 100644 index f5bc37cea..000000000 --- a/sci-biology/ugene/ChangeLog +++ /dev/null @@ -1,32 +0,0 @@ -# ChangeLog for sci-biology/ugene -# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 05 Jan 2016; Alexey Shvetsov <alexxy@gentoo.org> ugene-1.20.0.ebuild: - sci-biology/ugene: Fix install target - - 05 Jan 2016; Alexey Shvetsov <alexxy@gentoo.org> ugene-1.20.0.ebuild: - sci-biology/ugene: Make it actualy compile - -*ugene-1.20.0 (04 Jan 2016) - - 04 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +ugene-1.20.0.ebuild: - sci-biology/ugene: version bump, maybe the >=Qt5-5.2.1 should be specified - more properly? - -*ugene-1.16.1 (09 May 2015) - - 09 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +ugene-1.16.1.ebuild: - sci-biology/ugene: version bump - - 01 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> - ugene-1.13.3.ebuild.ebuild: - Convert sse2 to cpu_flags_x86_sse2 - -*ugene-1.13.3 (01 Jun 2014) - - 01 Jun 2014; Alexey Shvetsov <alexxy@gentoo.org> +metadata.xml, - +ugene-1.13.3.ebuild: - Add new ebuild diff --git a/sci-biology/vague-bin/ChangeLog b/sci-biology/vague-bin/ChangeLog deleted file mode 100644 index 471563796..000000000 --- a/sci-biology/vague-bin/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-biology/vague-bin -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> vague-bin-1.0.5.ebuild: - sci-biology/vague-bin: fix SLOT operators - - 09 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> epga-9999.ebuild: - Switch from git-2 to git-r3; Cleanup; Fix KEYWORDS - -*vague-bin-1.0.5 (08 Jan 2015) - - 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +files/vague.patch, - +metadata.xml, +vague-bin-1.0.5.ebuild: - sci-biology/vague-bin: new java binary package diff --git a/sci-biology/velvetk/ChangeLog b/sci-biology/velvetk/ChangeLog deleted file mode 100644 index d4838e761..000000000 --- a/sci-biology/velvetk/ChangeLog +++ /dev/null @@ -1,16 +0,0 @@ -# ChangeLog for sci-biology/velvetk -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> velvetk-20120606.ebuild: - Simplify ebuild - - 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - velvetk-20120606.ebuild: - added perl to dependencies - -*velvetk-20120606 (15 Apr 2014) - - 15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +velvetk-20120606.ebuild: - sci-biology/velvetk: new package diff --git a/sci-biology/wcd/ChangeLog b/sci-biology/wcd/ChangeLog deleted file mode 100644 index 7336100b3..000000000 --- a/sci-biology/wcd/ChangeLog +++ /dev/null @@ -1,36 +0,0 @@ -# ChangeLog for sci-biology/wcd -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> wcd-0.6.3.ebuild: - sci-biology/wcd: add note on supported MPI implementations - - 02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> wcd-0.6.3.ebuild: - sci-biology/wcd: also install some documentation, albeit probably old - - 02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/wcd-0.6.3-impl-decl.patch, +files/wcd-0.6.3-ldflags.patch, - -files/wcd-0.6.0-impl-decl.patch, -files/wcd-0.6.0-ldflags.patch: - sci-biology/wcd: renamed patch files - - 02 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> wcd-0.6.3.ebuild: - sci-biology/wcd: fix S - -*wcd-0.6.3 (09 Jan 2015) - - 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +wcd-0.6.3.ebuild, - -wcd-0.6.0.ebuild: - sci-biology/wcd: version bump, clarify package description, add comments about - addons - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> wcd-0.6.0.ebuild, - +files/wcd-0.6.0-impl-decl.patch, +files/wcd-0.6.0-ldflags.patch, - metadata.xml: - Add missing multilib.eclass; move to EAPI=5 and autotools-utils.eclass; - simplify ebuild syntax; fix for ld.gold; fix implicid declarations - -*wcd-0.6.0 (25 Jun 2011) - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -wcd-0.6.0_beta.ebuild, - +wcd-0.6.0.ebuild: - Cleaned ebuild diff --git a/sci-biology/weblogo/ChangeLog b/sci-biology/weblogo/ChangeLog deleted file mode 100644 index ec5a14c83..000000000 --- a/sci-biology/weblogo/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for sci-biology/weblogo -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*weblogo-2.8.2 (08 Sep 2015) - - 08 Sep 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +weblogo-2.8.2.ebuild: - sci-biology/weblogo: new perl utility diff --git a/sci-biology/wgs-assembler/ChangeLog b/sci-biology/wgs-assembler/ChangeLog deleted file mode 100644 index 415bd7822..000000000 --- a/sci-biology/wgs-assembler/ChangeLog +++ /dev/null @@ -1,19 +0,0 @@ -# ChangeLog for sci-biology/wgs-assembler -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*wgs-assembler-8.3_rc2 (25 May 2015) - - 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +wgs-assembler-8.3_rc2.ebuild, -wgs-assembler-8.3_rc1.ebuild: - version bump - -*wgs-assembler-8.2 (18 Apr 2015) -*wgs-assembler-8.3_rc1 (18 Apr 2015) - - 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +wgs-assembler-8.2.ebuild, +wgs-assembler-8.3_rc1.ebuild: - sci-biology/wgs-assembler: version bumps; did not check if the LDFLAGS part of - the v7.0 patch should be carried over; CFLAGS seems are already handled - properly by current code; 8.3rc1 dies at: install: cannot stat 'Linux- - amd64/bin/TIGR': No such file or directory diff --git a/sci-biology/wise/ChangeLog b/sci-biology/wise/ChangeLog deleted file mode 100644 index 36a9faaa4..000000000 --- a/sci-biology/wise/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-biology/wise -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - -*wise-2.4.1 (09 May 2015) - - 09 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +wise-2.4.1.ebuild: - sci-biology/wise: version bump, new HOMEPAGE, SRC_URI, does not compile, the - former patches need to be updated as well diff --git a/sci-biology/zmsort/ChangeLog b/sci-biology/zmsort/ChangeLog deleted file mode 100644 index b8546a39b..000000000 --- a/sci-biology/zmsort/ChangeLog +++ /dev/null @@ -1,14 +0,0 @@ -# ChangeLog for sci-biology/zmsort -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> zmsort-110625.ebuild, - metadata.xml: - Bump EAPI - -*zmsort-110625 (25 Jun 2011) - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -zmsort-0.1.ebuild, - +zmsort-110625.ebuild, +files/zmsort-110625-build.patch: - Cleaned ebuild - |