# ChangeLog for sci-biology/bowtie
# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2
# (auto-generated from git log)

*bowtie-1.0.0 (09 Aug 2015)
*bowtie-0.12.8 (09 Aug 2015)

  09 Aug 2015; Robin H. Johnson <robbat2@gentoo.org> +bowtie-0.12.8.ebuild,
  +bowtie-1.0.0.ebuild, +files/bowtie-0.12.8-gcc-47.patch, +metadata.xml:
  proj/gentoo: Initial commit

  This commit represents a new era for Gentoo:
  Storing the gentoo-x86 tree in Git, as converted from CVS.

  This commit is the start of the NEW history.
  Any historical data is intended to be grafted onto this point.

  Creation process:
  1. Take final CVS checkout snapshot
  2. Remove ALL ChangeLog* files
  3. Transform all Manifests to thin
  4. Remove empty Manifests
  5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
  5.1. Do not touch files with -kb/-ko keyword flags.

  Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
  X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration
  tests
  X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this
  project
  X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo
  developer, wrote Git features for the migration
  X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve
  cvs2svn
  X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
  X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014
  work in migration
  X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
  X-Thanks: All of other Gentoo developers - many ideas and lots of paint on
  the bikeshed

  24 Aug 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
  Use https by default

  Convert all URLs for sites supporting encrypted connections from http to
  https

  Signed-off-by: Justin Lecher <jlec@gentoo.org>

  24 Aug 2015; Mike Gilbert <floppym@gentoo.org> metadata.xml:
  Revert DOCTYPE SYSTEM https changes in metadata.xml

  repoman does not yet accept the https version.
  This partially reverts eaaface92ee81f30a6ac66fe7acbcc42c00dc450.

  Bug: https://bugs.gentoo.org/552720

*bowtie-1.1.2 (14 Oct 2015)

  14 Oct 2015; Justin Lecher <jlec@gentoo.org> -bowtie-0.12.8.ebuild,
  -bowtie-1.0.0.ebuild, +bowtie-1.1.2.ebuild,
  -files/bowtie-0.12.8-gcc-47.patch,
  +files/bowtie-1.1.2-tbb-tinythread-missing.patch, metadata.xml:
  version bump, SLOT major version

  sci-biology/bowtie is now SLOTed, in order to allow for a
  parallel installation with bowtie2. In addition, the latest
  bowtie now supports dev-cpp/tbb with 'tbb' USE flag.

*bowtie-2.2.6 (14 Oct 2015)

  14 Oct 2015; Justin Lecher <jlec@gentoo.org> +bowtie-2.2.6.ebuild:
  Add bowtie2 in SLOT=2

  14 Oct 2015; Justin Lecher <jlec@gentoo.org> bowtie-1.1.2.ebuild:
  do not remove -Wall from CXXFLAGS

  Retain -Wall in CXXFLAGS in bowtie-1.1.2

  14 Oct 2015; Justin Lecher <jlec@gentoo.org>
  files/bowtie-1.1.2-tbb-tinythread-missing.patch:
  include descriptive header in patch

  14 Oct 2015; Justin Lecher <jlec@gentoo.org> bowtie-2.2.6.ebuild:
  remove REQUIRED_USE

  When SSE2 support is not explicitly enabled, the user is
  informed by erroring out instead of portage recommending
  enabling cpu flags.

  14 Oct 2015; Justin Lecher <jlec@gentoo.org> bowtie-1.1.2.ebuild:
  1.1.2: Enable 'tbb' USE flag by default

  14 Oct 2015; Justin Lecher <jlec@gentoo.org> bowtie-2.2.6.ebuild:
  2.2.6: Enable 'tbb' USE flag by default

*bowtie-0.12.8 (14 Oct 2015)

  14 Oct 2015; Justin Lecher <jlec@gentoo.org> +bowtie-0.12.8.ebuild,
  +files/bowtie-0.12.8-gcc-47.patch:
  bring back stable bowtie-0.12.8

  bowtie-0.12.8 is the only stable variant and removing it
  breaks the stable depgraph.

  14 Oct 2015; Justin Lecher <jlec@gentoo.org> bowtie-2.2.6.ebuild,
  metadata.xml:
  Respect CXX

  Package-Manager: portage-2.2.23
  Signed-off-by: Justin Lecher <jlec@gentoo.org>

  25 Dec 2015; Agostino Sarubbo <ago@gentoo.org> bowtie-2.2.6.ebuild:
  amd64 stable wrt bug #569708

  Package-Manager: portage-2.2.24
  RepoMan-Options: --include-arches="amd64"
  Signed-off-by: Agostino Sarubbo <ago@gentoo.org>

  25 Dec 2015; Agostino Sarubbo <ago@gentoo.org> bowtie-1.1.2.ebuild:
  amd64 stable wrt bug #569706

  Package-Manager: portage-2.2.24
  RepoMan-Options: --include-arches="amd64"
  Signed-off-by: Agostino Sarubbo <ago@gentoo.org>

  25 Dec 2015; Agostino Sarubbo <ago@gentoo.org> bowtie-2.2.6.ebuild:
  x86 stable wrt bug #569708

  Package-Manager: portage-2.2.24
  RepoMan-Options: --include-arches="x86"
  Signed-off-by: Agostino Sarubbo <ago@gentoo.org>

  25 Dec 2015; Agostino Sarubbo <ago@gentoo.org> bowtie-1.1.2.ebuild:
  x86 stable wrt bug #569706

  Package-Manager: portage-2.2.24
  RepoMan-Options: --include-arches="x86"
  Signed-off-by: Agostino Sarubbo <ago@gentoo.org>

  26 Dec 2015; Justin Lecher <jlec@gentoo.org> -bowtie-0.12.8.ebuild,
  -files/bowtie-0.12.8-gcc-47.patch:
  Drop old

  obsoletes:
  Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=564320

  Package-Manager: portage-2.2.26
  Signed-off-by: Justin Lecher <jlec@gentoo.org>

  26 Dec 2015; Justin Lecher <jlec@gentoo.org> bowtie-2.2.6.ebuild:
  Chop DESCRIPTION to 80 chars

  Package-Manager: portage-2.2.26
  Signed-off-by: Justin Lecher <jlec@gentoo.org>

  24 Jan 2016; Michał Górny <mgorny@gentoo.org> metadata.xml:
  Replace all herds with appropriate projects (GLEP 67)

  Replace all uses of herd with appropriate project maintainers, or no
  maintainers in case of herds requested to be disbanded.

  24 Jan 2016; Michał Górny <mgorny@gentoo.org> metadata.xml:
  Set appropriate maintainer types in metadata.xml (GLEP 67)

*bowtie-1.1.2-r1 (09 Apr 2016)

  09 Apr 2016; David Seifert <soap@gentoo.org> +bowtie-1.1.2-r1.ebuild,
  +files/bowtie-1.1.2-_ContextLss-1.1-1.4.patch,
  +files/bowtie-1.1.2-fix-setBegin-call.patch,
  +files/bowtie-1.1.2-seqan-popcount.patch,
  +files/bowtie-1.1.2-seqan-rename-ChunkPool.patch,
  +files/bowtie-1.1.2-seqan-rename-fill-to-resize.patch,
  +files/bowtie-1.1.2-spelling.patch,
  +files/bowtie-1.1.2-unbundle-seqan.patch:
  unbundle SeqAn, import Debian patches

  * EAPI=6

  Package-Manager: portage-2.2.28

*bowtie-2.2.8 (10 Apr 2016)

  10 Apr 2016; David Seifert <soap@gentoo.org> +bowtie-2.2.8.ebuild:
  Version bump to 2.2.8

  * EAPI=6

  Package-Manager: portage-2.2.28

*bowtie-2.2.9 (04 Jun 2016)

  04 Jun 2016; David Seifert <soap@gentoo.org> -bowtie-2.2.8.ebuild,
  +bowtie-2.2.9.ebuild:
  version bump

  Package-Manager: portage-2.3.0_rc1

  18 Sep 2016; David Seifert <soap@gentoo.org> bowtie-2.2.9.ebuild,
  +files/bowtie-2.2.9-fix-c++14.patch:
  Allow for compiling with GCC 6

  Gentoo-bug: 593966

  Package-Manager: portage-2.3.0

