From mboxrd@z Thu Jan  1 00:00:00 1970
Return-Path: <gentoo-commits+bounces-607831-garchives=archives.gentoo.org@lists.gentoo.org>
Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80])
	by finch.gentoo.org (Postfix) with ESMTP id 17342138202
	for <garchives@archives.gentoo.org>; Mon,  8 Jul 2013 12:08:08 +0000 (UTC)
Received: from pigeon.gentoo.org (localhost [127.0.0.1])
	by pigeon.gentoo.org (Postfix) with SMTP id C197BE0952;
	Mon,  8 Jul 2013 12:08:04 +0000 (UTC)
Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183])
	(using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits))
	(No client certificate requested)
	by pigeon.gentoo.org (Postfix) with ESMTPS id 306F9E0952
	for <gentoo-commits@lists.gentoo.org>; Mon,  8 Jul 2013 12:08:04 +0000 (UTC)
Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163])
	(using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits))
	(No client certificate requested)
	by smtp.gentoo.org (Postfix) with ESMTPS id E665C33E7BF
	for <gentoo-commits@lists.gentoo.org>; Mon,  8 Jul 2013 12:08:02 +0000 (UTC)
Received: from localhost.localdomain (localhost [127.0.0.1])
	by hornbill.gentoo.org (Postfix) with ESMTP id 5C5D8E468F
	for <gentoo-commits@lists.gentoo.org>; Mon,  8 Jul 2013 12:08:01 +0000 (UTC)
From: "Justin Lecher" <jlec@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Content-Transfer-Encoding: 8bit
Content-type: text/plain; charset=UTF-8
Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" <jlec@gentoo.org>
Message-ID: <1371448515.f43609fc308239ce00e3b66ad121c43dbf15b1ed.jlec@gentoo>
Subject: [gentoo-commits] proj/sci:master commit in: /
X-VCS-Repository: proj/sci
X-VCS-Committer: jlec
X-VCS-Committer-Name: Justin Lecher
X-VCS-Revision: f43609fc308239ce00e3b66ad121c43dbf15b1ed
X-VCS-Branch: master
Date: Mon,  8 Jul 2013 12:08:01 +0000 (UTC)
Precedence: bulk
List-Post: <mailto:gentoo-commits@lists.gentoo.org>
List-Help: <mailto:gentoo-commits+help@lists.gentoo.org>
List-Unsubscribe: <mailto:gentoo-commits+unsubscribe@lists.gentoo.org>
List-Subscribe: <mailto:gentoo-commits+subscribe@lists.gentoo.org>
List-Id: Gentoo Linux mail <gentoo-commits.gentoo.org>
X-BeenThere: gentoo-commits@lists.gentoo.org
X-Archives-Salt: 77bbf1e2-0e74-46cc-a8a1-56b61dfb8b13
X-Archives-Hash: 6a039b3cb125364d598fc56a0e7a3801
Message-ID: <20130708120801.nF203b_N0X-NfnhKSnGoPOP_KQbN5uHyB_0iq1mSN6w@z>

commit:     f43609fc308239ce00e3b66ad121c43dbf15b1ed
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 17 05:55:15 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 17 05:55:15 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f43609fc

Merge branch 'master' into jlec

* master: (120 commits)
  add missing masks for live ebuilds
  dev-python/healpy: Initial import
  dev-java/jhealpix: Initial import
  sci-astronomy/healpix_idl: Initial import
  sci-astronomy/healpix_cxx: Initial import
  sci-astronomy/chealpix: Initial import
  sci-biology/twinscan: Bump to EAPI=5 and fix license
  sci-biology/ssaha2-bin: Version Bump; restrict license; add QA_PREBUILT for binaries
  sci-biology/smalt-bin: Version Bump; restrict license; add QA_PREBUILT for binaries
  sci-biology/sequin: Version BUmp; restrcit license; add QA_PREBUILT for binaries; install html files into sys path
  sci-biology/quicktree: Bump to EAPI=5 and fix license
  sci-biology/gap2caf: Bump to EAPI=5 and fix license; make it build with eautoreconf
  sci-biology/erpin: Bump to EAPI=5 and respect FLAGS / AR
  sci-biology/clover: Version BUmp; fixed license; respect LDFLAGS
  sci-chemistry/shiftx2: Respect FLAGS
  Enhanced the sci-chemistry/shiftx ebuild. Still needs some love for the emake part (portage complains about LDFLAGS not respected), but should work.
  sci-chemistry/pymol-plugins-psico: Bump to EAPI=5 and distutils-r1.eclass
  sci-chemistry/smmp: Bump to EAPI=5 and python-r1.eclass
  sci-chemistry/specView: Bump to EAPI=5 and python-single-r1.eclass
  sci-chemistry/pyquante: Bump to EAPI=5 and distutils-r1.eclass
  ...


 app-benchmarks/btl/ChangeLog                       |   5 +-
 app-benchmarks/btl/btl-9999.ebuild                 |  11 +-
 app-benchmarks/btl/metadata.xml                    |  14 +-
 app-benchmarks/numbench/ChangeLog                  |   8 +-
 app-benchmarks/numbench/metadata.xml               |  14 +-
 app-benchmarks/numbench/numbench-0.2.ebuild        |  28 +-
 app-benchmarks/numbench/numbench-9999.ebuild       |  28 +-
 app-doc/blacs-docs/Manifest                        |   2 +-
 app-doc/blas-docs/Manifest                         |   6 +-
 app-doc/lapack-docs/Manifest                       |   4 +-
 app-doc/root-docs/Manifest                         |   5 -
 app-text/dgs/Manifest                              |   2 +-
 app-vim/freefem++-syntax/Manifest                  |   2 +-
 dev-cpp/growler-arch/Manifest                      |   4 +-
 dev-cpp/growler-core/Manifest                      |   2 +-
 dev-cpp/growler-math/Manifest                      |   2 +-
 dev-cpp/growler-thread/Manifest                    |   2 +-
 dev-java/jeuclid-core/Manifest                     |   2 +-
 dev-java/jgraphx/ChangeLog                         |   7 +-
 dev-java/jgraphx/Manifest                          |   3 -
 dev-java/jgraphx/jgraphx-1.2.0.7.ebuild            |  44 --
 dev-java/jgraphx/jgraphx-1.3.0.2.ebuild            |  44 --
 dev-java/jgraphx/jgraphx-1.4.1.0.ebuild            |  18 +-
 dev-java/jgraphx/jgraphx-1.4.1.2.ebuild            |  44 --
 dev-java/jgraphx/jgraphx-1.8.0.6.ebuild            |  20 +-
 dev-java/jgraphx/metadata.xml                      |   4 +-
 dev-java/jhealpix/ChangeLog                        |   9 +
 dev-java/jhealpix/Manifest                         |   1 +
 dev-java/jhealpix/jhealpix-3.11.ebuild             |  43 ++
 dev-java/jhealpix/metadata.xml                     |  11 +
 dev-java/joda-convert/Manifest                     |   2 +-
 dev-java/vecmath/Manifest                          |   4 +-
 dev-lang/ispc/ChangeLog                            |   3 +
 dev-lang/ispc/ispc-9999.ebuild                     |   2 +-
 dev-lang/julia/ChangeLog                           |   5 +-
 dev-lang/julia/julia-9999.ebuild                   |   2 +-
 dev-lang/julia/metadata.xml                        |   4 +-
 dev-lang/path64/ChangeLog                          |   6 +-
 dev-lang/path64/metadata.xml                       |  22 +-
 dev-lang/path64/path64-9999.ebuild                 |   4 +-
 dev-libs/asmjit/ChangeLog                          |   8 +-
 dev-libs/asmjit/Manifest                           |   2 +-
 ...-1.0_beta_p2.ebuild => asmjit-1.0_beta4.ebuild} |   6 +-
 dev-libs/asmjit/metadata.xml                       |  12 +-
 dev-libs/libunzip/Manifest                         |   2 +-
 dev-libs/simclist/Manifest                         |   5 +-
 dev-ml/mlgmpidl/Manifest                           |   6 +-
 dev-ml/ocamlgraph/Manifest                         |   4 -
 dev-perl/BTLib/Manifest                            |   2 +-
 dev-perl/Lab-Instrument/Manifest                   |   2 +-
 dev-perl/Lab-Tools/Manifest                        |   2 +-
 dev-perl/Lab-VISA/Manifest                         |   2 +-
 dev-perl/go-db-perl/Manifest                       |   2 +-
 dev-perl/opal-client/Manifest                      |   2 +-
 dev-python/GOGrapher/ChangeLog                     |   3 +
 dev-python/GOGrapher/GOGrapher-9999.ebuild         |  21 +-
 dev-python/astropy/ChangeLog                       |   8 +
 dev-python/astropy/astropy-9999.ebuild             |  40 +-
 dev-python/astropy/metadata.xml                    |  10 +-
 dev-python/astropysics/ChangeLog                   |   6 +-
 dev-python/astropysics/astropysics-9999.ebuild     |  55 +-
 dev-python/astropysics/metadata.xml                |   4 +-
 dev-python/coards/ChangeLog                        |   8 +-
 dev-python/coards/Manifest                         |   2 +-
 dev-python/coards/coards-0.2.2.ebuild              |  22 -
 dev-python/coards/coards-1.0.5.ebuild              |  23 +
 dev-python/coards/metadata.xml                     |  10 +-
 dev-python/coords/ChangeLog                        |   6 +-
 dev-python/coords/Manifest                         |   2 +-
 dev-python/coords/coords-0.37.ebuild               |  22 +-
 dev-python/coords/metadata.xml                     |   4 +-
 dev-python/cosmocalc/ChangeLog                     |   6 +-
 dev-python/cosmocalc/Manifest                      |   2 +-
 dev-python/cosmocalc/cosmocalc-0.1.2-r1.ebuild     |  23 +-
 dev-python/cosmocalc/metadata.xml                  |   4 +-
 dev-python/dimensionful/ChangeLog                  |   6 +-
 dev-python/dimensionful/dimensionful-9999.ebuild   |  37 +-
 dev-python/dimensionful/metadata.xml               |   8 +-
 dev-python/emcee/ChangeLog                         |   8 +-
 dev-python/emcee/Manifest                          |   2 +-
 dev-python/emcee/emcee-1.0.1.ebuild                |  35 -
 dev-python/emcee/emcee-1.2.0.ebuild                |  27 +
 dev-python/emcee/metadata.xml                      |   4 +-
 dev-python/ffc/ChangeLog                           |   8 +-
 dev-python/ffc/Manifest                            |   2 +-
 dev-python/ffc/ffc-0.9.4.ebuild                    |  23 -
 dev-python/ffc/ffc-1.2.0.ebuild                    |  18 +
 dev-python/ffc/metadata.xml                        |   4 +-
 dev-python/fiat/ChangeLog                          |   8 +-
 dev-python/fiat/Manifest                           |   2 +-
 .../fiat/{fiat-0.9.2.ebuild => fiat-1.1.ebuild}    |  14 +-
 dev-python/fiat/metadata.xml                       |   4 +-
 dev-python/go-parser/ChangeLog                     |   6 +-
 dev-python/go-parser/Manifest                      |   2 +-
 dev-python/go-parser/go-parser-9999.ebuild         |  13 +-
 dev-python/go-parser/metadata.xml                  |  10 +-
 dev-python/healpy/ChangeLog                        |   9 +
 dev-python/healpy/Manifest                         |   1 +
 dev-python/healpy/healpy-1.6.2.ebuild              |  34 +
 dev-python/healpy/metadata.xml                     |  10 +
 dev-python/inference/ChangeLog                     |   7 +-
 dev-python/inference/inference-0.4.ebuild          |  31 +-
 dev-python/inference/metadata.xml                  |   4 +-
 dev-python/instant/ChangeLog                       |   8 +-
 dev-python/instant/Manifest                        |   2 +-
 dev-python/instant/instant-0.9.8.ebuild            |  23 -
 dev-python/instant/instant-1.2.0.ebuild            |  18 +
 dev-python/instant/metadata.xml                    |   4 +-
 dev-python/meshpy/ChangeLog                        |   8 +-
 dev-python/meshpy/Manifest                         |   2 +-
 ...meshpy-0.91.2.ebuild => meshpy-2013.1.2.ebuild} |  29 +-
 dev-python/meshpy/metadata.xml                     |   5 +-
 dev-python/numpydoc/ChangeLog                      |   6 +-
 dev-python/numpydoc/Manifest                       |   2 +-
 dev-python/numpydoc/metadata.xml                   |   4 +-
 dev-python/numpydoc/numpydoc-0.4.ebuild            |  22 +-
 dev-python/omniorbpy/ChangeLog                     |   6 +-
 dev-python/omniorbpy/Manifest                      |   2 +-
 dev-python/omniorbpy/metadata.xml                  |   2 +-
 dev-python/omniorbpy/omniorbpy-3.4.ebuild          |  90 +--
 dev-python/opal-client/ChangeLog                   |   8 +-
 dev-python/opal-client/Manifest                    |   2 +-
 dev-python/opal-client/metadata.xml                |   8 +-
 dev-python/opal-client/opal-client-2.2-r1.ebuild   |  55 --
 dev-python/opal-client/opal-client-2.4.1.ebuild    |  42 ++
 dev-python/pyhdf/ChangeLog                         |   8 +
 dev-python/pyhdf/Manifest                          |   2 +-
 dev-python/pyhdf/metadata.xml                      |  16 +-
 dev-python/pyhdf/pyhdf-0.8.3.ebuild                |  29 +-
 dev-python/pythoncgns/ChangeLog                    |   6 +-
 dev-python/pythoncgns/Manifest                     |   2 +-
 dev-python/pythoncgns/metadata.xml                 |   2 +-
 dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild |  10 +-
 dev-python/ufl/ChangeLog                           |   5 +-
 dev-python/ufl/Manifest                            |   2 +-
 dev-python/ufl/metadata.xml                        |   4 +-
 dev-python/ufl/ufl-0.5.4.ebuild                    |  17 +-
 dev-python/viper/ChangeLog                         |   8 +-
 dev-python/viper/Manifest                          |   2 +-
 dev-python/viper/metadata.xml                      |   4 +-
 dev-python/viper/viper-0.4.6.ebuild                |  23 -
 dev-python/viper/viper-1.0.1.ebuild                |  18 +
 dev-tcltk/img_rotate/ChangeLog                     |   6 +-
 dev-tcltk/img_rotate/Manifest                      |   2 +-
 dev-tcltk/img_rotate/img_rotate-1.1.ebuild         |  14 +-
 dev-tcltk/img_rotate/metadata.xml                  |   8 +-
 dev-tcltk/togl/Manifest                            |   2 +-
 dev-util/smartgit/Manifest                         |   2 +-
 licenses/GRL                                       |  15 +
 licenses/HSL                                       | 222 ++++++
 licenses/Tablet                                    |   8 +-
 media-gfx/brlcad/ChangeLog                         |   6 +-
 media-gfx/brlcad/brlcad-9999.ebuild                |   2 +-
 media-gfx/brlcad/metadata.xml                      |  26 +-
 media-gfx/librecad/ChangeLog                       |   6 +
 media-gfx/librecad/librecad-9999.ebuild            |  32 +-
 media-libs/OpenMOIV/Manifest                       |   2 +-
 media-libs/avbin-bin/Manifest                      |   4 +-
 media-libs/libgfx/Manifest                         |   2 +-
 net-firewall/gcb/Manifest                          |   2 +-
 net-ftp/bbftp-client/Manifest                      |   2 +-
 net-ftp/bbftp-server/Manifest                      |   2 +-
 net-misc/bbscp/Manifest                            |   2 +-
 net-misc/dhcp/ChangeLog                            |  61 --
 net-misc/dhcp/Manifest                             |   1 -
 net-misc/dhcp/dhcp-4.2.3_p2-r1.ebuild              | 245 -------
 net-misc/dhcp/files/dhcp-3.0-fix-perms.patch       |  15 -
 net-misc/dhcp/files/dhcp-3.0.3-dhclient-dbus.patch |  84 ---
 .../dhcp/files/dhcp-3.0.3-dhclient-no-down.patch   |  70 --
 net-misc/dhcp/files/dhcp-4.0-dhclient-ntp.patch    | 216 ------
 net-misc/dhcp/files/dhcp-4.2.0-PPP.patch           | 150 -----
 .../dhcp/files/dhcp-4.2.0-errwarn-message.patch    |  31 -
 .../dhcp/files/dhcp-4.2.2-bind-build-flags.patch   |  14 -
 net-misc/dhcp/files/dhcp-4.2.2-bind-disable.patch  |  13 -
 .../files/dhcp-4.2.2-bind-parallel-build.patch     |  14 -
 .../files/dhcp-4.2.2-dhclient-resolvconf.patch     | 409 ------------
 .../files/dhcp-4.2.2-dhclient-stdin-conf.patch     | 113 ----
 net-misc/dhcp/files/dhcp-4.2.2-gpxe-cid.patch      | 132 ----
 net-misc/dhcp/files/dhcp-4.2.2-improved-xid.patch  | 138 ----
 net-misc/dhcp/files/dhcp-4.2.2-lpf-ib.patch        | 538 ---------------
 net-misc/dhcp/files/dhcp-4.2.2-nogateway.patch     |  46 --
 net-misc/dhcp/files/dhcp-4.2.2-xen-checksum.patch  | 249 -------
 net-misc/dhcp/files/dhcp-4.2.3-options.patch       | 391 -----------
 net-misc/dhcp/files/dhcpd.conf2                    |  28 -
 net-misc/dhcp/files/dhcpd.init2                    |  94 ---
 net-misc/dhcp/files/dhcpd.init5                    | 114 ----
 net-misc/dhcp/files/dhcrelay.conf                  |  13 -
 net-misc/dhcp/files/dhcrelay.init2                 |  29 -
 net-misc/dhcp/metadata.xml                         |  10 -
 perl-core/encoding-warnings/Manifest               |   2 +-
 profiles/arch/amd64/no-multilib/package.mask       |  27 -
 profiles/arch/amd64/package.use.mask               |  23 -
 profiles/package.mask                              | 118 +---
 sci-astronomy/astrometry/ChangeLog                 |  23 +-
 sci-astronomy/astrometry/Manifest                  |   2 +-
 sci-astronomy/astrometry/astrometry-0.38.ebuild    |  57 --
 sci-astronomy/astrometry/astrometry-0.43.ebuild    |  87 +++
 .../astrometry/files/0.38-array-bounds.patch       |  11 -
 .../astrometry/files/0.38-as-needed.patch          | 694 -------------------
 .../astrometry/files/0.38-missing-headers.patch    |  11 -
 .../astrometry/files/0.38-strict-aliasing.patch    |  30 -
 .../astrometry/files/0.38-system-libs.patch        |  48 --
 .../astrometry/files/0.43-as-needed.patch          | 366 ++++++++++
 ...r-flags.patch => 0.43-respect-user-flags.patch} |   3 +
 .../astrometry/files/0.43-system-libs.patch        | 742 +++++++++++++++++++++
 sci-astronomy/astrometry/metadata.xml              |   7 +-
 sci-astronomy/bpz/ChangeLog                        |   5 +-
 sci-astronomy/bpz/bpz-1.99.3.ebuild                |  57 +-
 sci-astronomy/bpz/metadata.xml                     |   4 +-
 sci-astronomy/chealpix/ChangeLog                   |   9 +
 sci-astronomy/chealpix/Manifest                    |   1 +
 sci-astronomy/chealpix/chealpix-3.11.ebuild        |  30 +
 sci-astronomy/chealpix/metadata.xml                |  11 +
 sci-astronomy/eazy/ChangeLog                       |   5 +-
 sci-astronomy/eazy/eazy-1.00.ebuild                |  16 +-
 sci-astronomy/eazy/metadata.xml                    |   4 +-
 sci-astronomy/galfit-bin/ChangeLog                 |   3 +
 sci-astronomy/galfit-bin/galfit-bin-3.0.4.ebuild   |   6 +-
 sci-astronomy/healpix_cxx/ChangeLog                |   9 +
 sci-astronomy/healpix_cxx/Manifest                 |   1 +
 sci-astronomy/healpix_cxx/healpix_cxx-3.11.ebuild  |  54 ++
 sci-astronomy/healpix_cxx/metadata.xml             |  12 +
 sci-astronomy/healpix_idl/ChangeLog                |   9 +
 sci-astronomy/healpix_idl/Manifest                 |   1 +
 sci-astronomy/healpix_idl/healpix_idl-3.11.ebuild  |  37 +
 sci-astronomy/healpix_idl/metadata.xml             |  12 +
 sci-astronomy/psfex/ChangeLog                      |   5 +-
 sci-astronomy/psfex/metadata.xml                   |  10 +-
 sci-astronomy/psfex/psfex-9999.ebuild              |   3 +-
 sci-astronomy/scamp/ChangeLog                      |   5 +-
 sci-astronomy/scamp/metadata.xml                   |  10 +-
 sci-astronomy/scamp/scamp-9999.ebuild              |   3 +-
 sci-biology/ONTO-PERL/Manifest                     |   2 +-
 sci-biology/YASRA/ChangeLog                        |   4 +
 sci-biology/YASRA/Manifest                         |   2 +-
 .../YASRA/{YASRA-2.1.ebuild => YASRA-2.32.ebuild}  |  15 +-
 sci-biology/align_to_scf/Manifest                  |   2 +-
 sci-biology/amos-short/Manifest                    |   2 +-
 sci-biology/argo-bin/Manifest                      |   2 +-
 sci-biology/argo/Manifest                          |   2 +-
 sci-biology/autoeditor/Manifest                    |   4 +-
 sci-biology/bambus/Manifest                        |   2 +-
 sci-biology/brat/Manifest                          |   2 +-
 sci-biology/caftools/ChangeLog                     |   8 +
 sci-biology/caftools/Manifest                      |   4 +-
 sci-biology/caftools/caftools-2.0.2.ebuild         |  36 +-
 sci-biology/caftools/caftools-2.0.ebuild           |  38 --
 sci-biology/caftools/metadata.xml                  |  16 +-
 sci-biology/cap3-bin/Manifest                      |   4 +-
 sci-biology/cdbfasta/Manifest                      |   2 +-
 sci-biology/clover/ChangeLog                       |   6 +-
 sci-biology/clover/Manifest                        |   4 +-
 sci-biology/clover/clover-2010.02.19.ebuild        |  43 --
 sci-biology/clover/clover-2011.10.24.ebuild        |  40 ++
 sci-biology/clover/metadata.xml                    |   6 +-
 sci-biology/clview/Manifest                        |   4 +-
 sci-biology/codonw/Manifest                        |   2 +-
 sci-biology/cutadapt/ChangeLog                     |   6 +-
 sci-biology/cutadapt/Manifest                      |   2 +-
 .../{cutadapt-1.0.ebuild => cutadapt-1.2.1.ebuild} |  13 +-
 sci-biology/cutadapt/metadata.xml                  |  10 +-
 sci-biology/dawg/Manifest                          |   2 +-
 sci-biology/embassy-cbstools/Manifest              |   2 +-
 sci-biology/embassy-domainatrix/Manifest           |   2 +-
 sci-biology/embassy-domalign/Manifest              |   2 +-
 sci-biology/embassy-domsearch/Manifest             |   2 +-
 sci-biology/embassy-emnu/Manifest                  |   2 +-
 sci-biology/embassy-esim4/Manifest                 |   2 +-
 sci-biology/embassy-hmmer/Manifest                 |   2 +-
 sci-biology/embassy-iprscan/Manifest               |   2 +-
 sci-biology/embassy-mse/Manifest                   |   2 +-
 sci-biology/embassy-phylipnew/Manifest             |   2 +-
 sci-biology/embassy-signature/Manifest             |   2 +-
 sci-biology/embassy-structure/Manifest             |   2 +-
 sci-biology/embassy-topo/Manifest                  |   2 +-
 sci-biology/embassy-vienna/Manifest                |   2 +-
 sci-biology/erpin/ChangeLog                        |   5 +-
 sci-biology/erpin/Manifest                         |   4 +-
 sci-biology/erpin/erpin-5.5b.ebuild                |  23 +-
 sci-biology/erpin/metadata.xml                     |  10 +-
 sci-biology/est2uni/Manifest                       |  10 +-
 sci-biology/fastdnaml/Manifest                     |   4 +-
 sci-biology/gap2caf/ChangeLog                      |   8 +
 sci-biology/gap2caf/Manifest                       |   4 +-
 sci-biology/gap2caf/gap2caf-2.1.0.ebuild           |  45 +-
 sci-biology/gap2caf/metadata.xml                   |  10 +-
 sci-biology/gbench/Manifest                        |   2 +-
 sci-biology/genepop/Manifest                       |   2 +-
 sci-biology/generecon/Manifest                     |   2 +-
 sci-biology/genseed/Manifest                       |   2 +-
 sci-biology/grappa/Manifest                        |   2 +-
 sci-biology/jalview/Manifest                       |   2 +-
 sci-biology/lastz/ChangeLog                        |  12 +-
 sci-biology/lastz/Manifest                         |   3 +-
 sci-biology/lastz/files/lastz-1.03.34-build.patch  |  43 ++
 .../{lastz-1.02.00.ebuild => lastz-1.03.34.ebuild} |  28 +-
 sci-biology/lastz/metadata.xml                     |  10 +-
 sci-biology/lucy/Manifest                          |   2 +-
 sci-biology/mavid/Manifest                         |   2 +-
 sci-biology/merlin/Manifest                        |   2 +-
 sci-biology/miranda/Manifest                       |   2 +-
 sci-biology/mrbayes/Manifest                       |   2 +-
 sci-biology/mreps/Manifest                         |   2 +-
 sci-biology/mrfast/Manifest                        |   2 +-
 sci-biology/mrsfast/Manifest                       |   2 +-
 sci-biology/ncbi-tools++/ChangeLog                 |   6 +
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |   3 +-
 sci-biology/nrcl/Manifest                          |   4 +-
 sci-biology/perlprimer/Manifest                    |   2 +-
 sci-biology/phylobayes/ChangeLog                   |  10 -
 sci-biology/phylobayes/Manifest                    |   2 -
 sci-biology/phylobayes/metadata.xml                |   9 -
 sci-biology/phylobayes/phylobayes-3.3b.ebuild      |  37 -
 sci-biology/proda/Manifest                         |   2 +-
 sci-biology/psx/Manifest                           |   2 +-
 sci-biology/pybrain/ChangeLog                      |   6 +-
 sci-biology/pybrain/metadata.xml                   |   2 +-
 sci-biology/pybrain/pybrain-9999.ebuild            |  25 +-
 sci-biology/quicktree/ChangeLog                    |   6 +-
 sci-biology/quicktree/Manifest                     |   2 +-
 sci-biology/quicktree/metadata.xml                 |  10 +-
 sci-biology/quicktree/quicktree-1.1-r1.ebuild      |  17 +-
 sci-biology/rnaplex/Manifest                       |   2 +-
 sci-biology/roche454ace2caf/Manifest               |   2 +-
 sci-biology/sclust/Manifest                        |   4 +-
 sci-biology/sequin/ChangeLog                       |   9 +-
 sci-biology/sequin/Manifest                        |   4 +-
 sci-biology/sequin/sequin-20090722.ebuild          |  32 -
 sci-biology/sequin/sequin-20121202.ebuild          |  44 ++
 sci-biology/sff_dump/Manifest                      |   2 +-
 sci-biology/signalp/Manifest                       |   2 +-
 sci-biology/smalt-bin/ChangeLog                    |   8 +-
 sci-biology/smalt-bin/Manifest                     |   2 +-
 sci-biology/smalt-bin/metadata.xml                 |  10 +-
 sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild       |  25 -
 sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild       |  31 +
 sci-biology/ssaha2-bin/ChangeLog                   |   6 +-
 sci-biology/ssaha2-bin/Manifest                    |   9 +-
 sci-biology/ssaha2-bin/metadata.xml                |  10 +-
 ...a2-bin-2.5.3.ebuild => ssaha2-bin-2.5.5.ebuild} |  26 +-
 sci-biology/swissknife/Manifest                    |   2 +-
 sci-biology/tablet-bin/ChangeLog                   |   9 +-
 sci-biology/tablet-bin/Manifest                    |   3 +-
 sci-biology/tablet-bin/metadata.xml                |  10 +-
 .../tablet-bin/tablet-bin-1.11.11.01.ebuild        |  73 --
 ...1.05.03.ebuild => tablet-bin-1.13.05.17.ebuild} |  57 +-
 sci-biology/tclust/Manifest                        |   4 +-
 sci-biology/tgicl/Manifest                         |   2 +-
 sci-biology/tigr-assembler/Manifest                |   2 +-
 sci-biology/tigr-foundation-libs/Manifest          |   2 +-
 sci-biology/tmhmm/Manifest                         |   2 +-
 sci-biology/twinscan/ChangeLog                     |   6 +-
 sci-biology/twinscan/Manifest                      |   2 +-
 sci-biology/twinscan/metadata.xml                  |  10 +-
 sci-biology/twinscan/twinscan-4.1.2.ebuild         |  30 +-
 sci-biology/zmsort/Manifest                        |   4 +-
 sci-chemistry/almost/Manifest                      |   2 +-
 sci-chemistry/ball/ChangeLog                       |   3 +
 sci-chemistry/ball/ball-9999.ebuild                |  11 +-
 sci-chemistry/ball/metadata.xml                    |   2 +-
 sci-chemistry/bist/Manifest                        |   2 +-
 sci-chemistry/chemBuild/ChangeLog                  |   6 +-
 sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild     |  33 +-
 sci-chemistry/chemBuild/files/chemBuild            |   2 +-
 sci-chemistry/chemBuild/metadata.xml               |   2 +-
 sci-chemistry/cnsface/ChangeLog                    |   6 +-
 sci-chemistry/cnsface/Manifest                     |   2 +-
 sci-chemistry/cnsface/cnsface-0.0.12.ebuild        |  19 +-
 sci-chemistry/cnsface/metadata.xml                 |   8 +-
 sci-chemistry/direx/Manifest                       |   2 +-
 sci-chemistry/drawxtl/Manifest                     |   4 +-
 sci-chemistry/dssp2pdb/Manifest                    |   2 +-
 sci-chemistry/hydronmr/ChangeLog                   |   3 +
 sci-chemistry/hydronmr/hydronmr-7c.ebuild          |   1 -
 sci-chemistry/jana2000/Manifest                    |   2 +-
 sci-chemistry/jmol/Manifest                        |   2 +-
 sci-chemistry/mage/Manifest                        |   2 +-
 sci-chemistry/modeller/ChangeLog                   |   6 +-
 sci-chemistry/modeller/Manifest                    |   2 +-
 sci-chemistry/modeller/metadata.xml                |   2 +-
 .../{modeller-9.8.ebuild => modeller-9.12.ebuild}  |  96 ++-
 sci-chemistry/mtz2hkl/Manifest                     |   2 +-
 sci-chemistry/mtz2sca/Manifest                     |   2 +-
 sci-chemistry/nmrpipe/ChangeLog                    |   8 +
 .../nmrpipe/nmrpipe-7.9.2013.021.23.09-r2.ebuild   |   4 +-
 sci-chemistry/nmrview/ChangeLog                    |   6 +-
 sci-chemistry/nmrview/metadata.xml                 |  10 +-
 sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild      |  15 +-
 sci-chemistry/nwchem/ChangeLog                     |   4 +
 sci-chemistry/nwchem/Manifest                      |   1 -
 sci-chemistry/nwchem/nwchem-6.1.1.ebuild           | 126 ----
 sci-chemistry/nwchem/nwchem-6.3.ebuild             |  10 +-
 sci-chemistry/phaser/ChangeLog                     |  21 -
 sci-chemistry/phaser/Manifest                      |   1 -
 sci-chemistry/phaser/files/2.1.4-sadf.patch        |  64 --
 .../phaser/files/phaser-2.1.4-chmod.patch          |  11 -
 sci-chemistry/phaser/metadata.xml                  |  30 -
 sci-chemistry/phaser/phaser-2.1.4-r1.ebuild        | 138 ----
 sci-chemistry/phaser/phaser-2.1.4.ebuild           | 114 ----
 sci-chemistry/polygon/ChangeLog                    |   7 +-
 sci-chemistry/polygon/Manifest                     |   4 +-
 .../polygon/files/{0710-db.patch => 0612-db.patch} |  20 +-
 sci-chemistry/polygon/metadata.xml                 |   8 +-
 .../{polygon-0710.ebuild => polygon-0612.ebuild}   |  18 +-
 sci-chemistry/pymol-apbs-plugin/ChangeLog          |   9 +-
 sci-chemistry/pymol-apbs-plugin/metadata.xml       |   8 +-
 .../pymol-apbs-plugin-9999.ebuild                  |  53 +-
 sci-chemistry/pymol-plugins-ezviz/ChangeLog        |   4 +
 sci-chemistry/pymol-plugins-ezviz/Manifest         |   2 +-
 .../pymol-plugins-ezviz-1.0.2005.ebuild            |  56 +-
 sci-chemistry/pymol-plugins-psico/ChangeLog        |   3 +
 .../pymol-plugins-psico-9999.ebuild                |  15 +-
 sci-chemistry/pyquante/ChangeLog                   |   6 +-
 sci-chemistry/pyquante/Manifest                    |   2 +-
 sci-chemistry/pyquante/metadata.xml                |   2 +-
 sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild    |  11 +-
 sci-chemistry/rosetta-tools/Manifest               |   2 +-
 sci-chemistry/shiftx/ChangeLog                     |   5 +-
 sci-chemistry/shiftx/Manifest                      |   2 +-
 sci-chemistry/shiftx/metadata.xml                  |   8 +-
 sci-chemistry/shiftx/shiftx-1.1.ebuild             |  24 +-
 sci-chemistry/shiftx2/ChangeLog                    |   8 +
 sci-chemistry/shiftx2/Manifest                     |   1 +
 sci-chemistry/shiftx2/files/gentoo-fixes.patch     | 194 ++++++
 sci-chemistry/shiftx2/metadata.xml                 |  39 ++
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          | 112 ++++
 sci-chemistry/smmp/ChangeLog                       |   5 +-
 sci-chemistry/smmp/Manifest                        |   2 +-
 sci-chemistry/smmp/metadata.xml                    |   8 +-
 sci-chemistry/smmp/smmp-3.0.5.ebuild               |  41 +-
 sci-chemistry/specView/ChangeLog                   |   3 +
 sci-chemistry/specView/specView-1.0.2.ebuild       |  52 +-
 sci-chemistry/ssp/ChangeLog                        |   5 +-
 sci-chemistry/ssp/metadata.xml                     |   8 +-
 sci-chemistry/ssp/ssp-09.11.ebuild                 |   6 +-
 sci-chemistry/unio/Manifest                        |   4 +-
 sci-electronics/player/Manifest                    |   2 +-
 sci-electronics/stage/Manifest                     |   2 +-
 sci-electronics/tnt/Manifest                       |   2 +-
 sci-geosciences/cdat-lite/Manifest                 |   4 +-
 sci-geosciences/congen/Manifest                    |   2 +-
 .../harmonics-dwf-free-noncomm/Manifest            |   2 +-
 sci-geosciences/harmonics-dwf-free/Manifest        |   4 +-
 sci-geosciences/libtcd/Manifest                    |   4 +-
 sci-geosciences/seawater/Manifest                  |   2 +-
 sci-geosciences/swmm/Manifest                      |   2 +-
 sci-geosciences/tappy/Manifest                     |   2 +-
 sci-geosciences/tcd-utils/Manifest                 |   4 +-
 sci-geosciences/xtide/Manifest                     |   4 +-
 sci-libs/blastdb/ChangeLog                         |   8 +
 sci-libs/blastdb/blastdb-9999.ebuild               |   8 +-
 sci-libs/blastdb/metadata.xml                      |  31 +-
 sci-libs/calculix-cgx/Manifest                     |   4 +-
 sci-libs/cgnsfoam/Manifest                         |   2 +-
 sci-libs/cgnslib/Manifest                          |   2 +-
 sci-libs/cnsface-scripts/Manifest                  |   2 +-
 sci-libs/coinhsl/ChangeLog                         |  12 +
 sci-libs/coinhsl/Manifest                          |   1 +
 sci-libs/coinhsl/coinhsl-2012.12.21.ebuild         |  36 +
 sci-libs/coinhsl/metadata.xml                      |  12 +
 sci-libs/dcmtk/Manifest                            |   6 +-
 sci-libs/driftwood/Manifest                        |   2 +-
 sci-libs/etsf_io/Manifest                          |   2 +-
 sci-libs/factory/Manifest                          |   2 +-
 sci-libs/fgsl/Manifest                             |   4 +-
 sci-libs/fox/Manifest                              |  12 +-
 sci-libs/fplll/Manifest                            |   2 +-
 sci-libs/framewave/Manifest                        |   2 +-
 sci-libs/geom/Manifest                             |   2 +-
 sci-libs/givaro/Manifest                           |   4 +-
 sci-libs/ipopt/ChangeLog                           |   9 +
 sci-libs/ipopt/Manifest                            |   2 +-
 .../{ipopt-3.10.3.ebuild => ipopt-3.11.0.ebuild}   |  19 +-
 sci-libs/ipopt/metadata.xml                        |  11 +-
 sci-libs/libcgnsoo/Manifest                        |   2 +-
 sci-libs/libfac/Manifest                           |   4 +-
 sci-libs/libxc/Manifest                            |   2 +-
 sci-libs/lwpr/Manifest                             |   2 +-
 sci-libs/m4ri/Manifest                             |   4 +-
 sci-libs/matio/Manifest                            |   2 +-
 sci-libs/mesquite/Manifest                         |   2 +-
 sci-libs/ni-visa/Manifest                          |   2 +-
 sci-libs/oasa/Manifest                             |   2 +-
 sci-libs/omalloc/Manifest                          |   2 +-
 sci-libs/symmetrica/Manifest                       |   2 +-
 sci-libs/trilinos/ChangeLog                        |   4 +
 sci-libs/trilinos/Manifest                         |   2 +-
 sci-libs/trilinos/metadata.xml                     |  56 +-
 sci-libs/trilinos/trilinos-10.10.1.ebuild          | 124 ----
 sci-libs/trilinos/trilinos-11.0.3.ebuild           |  12 +-
 sci-mathematics/Oid/Manifest                       |   4 +-
 sci-mathematics/acl2/Manifest                      |   2 +-
 sci-mathematics/algae/files/unbundle.patch         |  41 --
 sci-mathematics/apron/Manifest                     |   5 +-
 sci-mathematics/aribas/Manifest                    |   2 +-
 sci-mathematics/axiom/Manifest                     |   2 +-
 sci-mathematics/burrtools/Manifest                 |   4 +-
 sci-mathematics/cadabra/ChangeLog                  |   5 +
 sci-mathematics/cadabra/Manifest                   |   3 -
 sci-mathematics/cadabra/cadabra-1.25.ebuild        |  89 ---
 sci-mathematics/cadabra/cadabra-1.28.ebuild        |  87 ---
 sci-mathematics/cadabra/cadabra-1.29.ebuild        |  87 ---
 sci-mathematics/cadabra/cadabra-1.31.ebuild        |  14 +-
 sci-mathematics/cadabra/metadata.xml               |   4 +-
 sci-mathematics/dolfin/Manifest                    |   2 +-
 sci-mathematics/frama-c/Manifest                   |   3 -
 sci-mathematics/gap-guava/Manifest                 |   2 +-
 sci-mathematics/gap/Manifest                       |   4 +-
 sci-mathematics/gappa/Manifest                     |   3 -
 sci-mathematics/htk/Manifest                       |   4 +-
 sci-mathematics/kayali/Manifest                    |   2 +-
 sci-mathematics/libsfmt/Manifest                   |   2 +-
 sci-mathematics/lie/Manifest                       |   2 +-
 sci-mathematics/ltl2ba/Manifest                    |  25 +-
 sci-mathematics/netgen/Manifest                    |   2 +-
 sci-mathematics/open-axiom/Manifest                |   2 +-
 sci-mathematics/pest/Manifest                      |   6 +-
 sci-mathematics/ufc/Manifest                       |   2 +-
 sci-misc/finomaton/Manifest                        |   2 +-
 sci-misc/fitscut/Manifest                          |   2 +-
 sci-misc/jwnl/Manifest                             |   4 +-
 sci-misc/kotus-sanalista/Manifest                  |   2 +-
 sci-misc/nltk/Manifest                             |   2 +-
 sci-misc/omorfi/Manifest                           |   2 +-
 sci-misc/opennlp-maxent/Manifest                   |   2 +-
 sci-misc/opennlp-tools/Manifest                    |  88 +--
 sci-misc/pywordnet/Manifest                        |   2 +-
 sci-misc/salome-kernel/Manifest                    |   4 +-
 sci-misc/salome-pycalculator/Manifest              |   4 +-
 sci-misc/stanford-parser/Manifest                  |   2 +-
 sci-misc/stanford-tagger/Manifest                  |   2 +-
 sci-physics/espresso++/ChangeLog                   |   4 +
 sci-physics/espresso++/espresso++-9999.ebuild      |  22 +-
 sci-physics/espresso++/metadata.xml                |  16 +-
 sci-physics/espresso/ChangeLog                     |   4 +
 sci-physics/espresso/espresso-9999.ebuild          |  24 +-
 sci-physics/espresso/metadata.xml                  |  10 +-
 sci-physics/qcl/Manifest                           |   8 +-
 sci-visualization/gnuplot/ChangeLog                |   4 +
 sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild  |   2 +-
 sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild  |   2 +-
 sci-visualization/nodemon/Manifest                 |   2 +-
 sys-cluster/condor/ChangeLog                       |  40 --
 sys-cluster/condor/Manifest                        |   2 -
 sys-cluster/condor/condor-7.5.2.ebuild             | 160 -----
 sys-cluster/condor/condor-7.5.4.ebuild             | 160 -----
 sys-cluster/condor/files/condor.confd              |   2 -
 sys-cluster/condor/files/condor.initd              |  64 --
 sys-cluster/condor/files/condor_config.local       |  11 -
 sys-cluster/condor/metadata.xml                    |  26 -
 sys-cluster/ganglia_jobmonarch/Manifest            |   2 +-
 sys-cluster/lustre/ChangeLog                       |   4 +
 sys-cluster/lustre/lustre-9999.ebuild              |   6 +-
 sys-cluster/lustre/metadata.xml                    |  20 +-
 sys-cluster/modules/modules-3.2.9c-r1.ebuild       |   2 +-
 sys-cluster/mpe2/ChangeLog                         |  15 -
 sys-cluster/mpe2/Manifest                          |   1 -
 .../files/slog2sdk-trace_rlog-makefile-fixes.patch |  68 --
 .../slog2sdk-trace_sample-makefile-fixes.patch     |  68 --
 sys-cluster/mpe2/metadata.xml                      |  10 -
 sys-cluster/mpe2/mpe2-1.0.6_p1.ebuild              | 148 ----
 sys-cluster/nullmpi/ChangeLog                      |   6 +-
 sys-cluster/nullmpi/Manifest                       |   2 +-
 sys-cluster/nullmpi/metadata.xml                   |  10 +-
 sys-cluster/nullmpi/nullmpi-0.7.ebuild             |   4 +-
 sys-cluster/nullmpi/nullmpi-9999.ebuild            |  16 +-
 sys-cluster/pyslice/Manifest                       |   2 +-
 sys-devel/gdebugger/Manifest                       |   4 +-
 sys-infiniband/librxe/Manifest                     |   2 +-
 www-apps/py-swish-e/ChangeLog                      |   6 +-
 www-apps/py-swish-e/Manifest                       |   2 +-
 www-apps/py-swish-e/metadata.xml                   |   8 +-
 www-apps/py-swish-e/py-swish-e-0.5.ebuild          |  12 +-
 x11-libs/tr/Manifest                               |   2 +-
 x11-libs/xview-bin/ChangeLog                       |   3 +
 x11-libs/xview-bin/xview-bin-3.2_p1428.ebuild      |   2 +-
 x11-misc/envytools/ChangeLog                       |   6 +-
 x11-misc/envytools/envytools-9999.ebuild           |  18 +-
 x11-misc/envytools/metadata.xml                    |  10 +-
 579 files changed, 4325 insertions(+), 8161 deletions(-)