From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id CC2EC138200 for ; Thu, 11 Jul 2013 20:26:59 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id B99BBE0A0B; Thu, 11 Jul 2013 20:26:56 +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 427DEE0A0B for ; Thu, 11 Jul 2013 20:26:56 +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 0B92F33E907 for ; Thu, 11 Jul 2013 20:26:55 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id AF9B7E468F for ; Thu, 11 Jul 2013 20:26:53 +0000 (UTC) From: "Justin Lecher" 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" Message-ID: <1371448515.f43609fc308239ce00e3b66ad121c43dbf15b1ed.jlec@gentoo> Subject: [gentoo-commits] proj/sci:vtk commit in: / X-VCS-Repository: proj/sci X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: f43609fc308239ce00e3b66ad121c43dbf15b1ed X-VCS-Branch: vtk Date: Thu, 11 Jul 2013 20:26:53 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 13c5f309-f176-4668-b4a0-dcc09e796480 X-Archives-Hash: 7c1e2e1a22717bfec55dc97b2578e1d6 commit: f43609fc308239ce00e3b66ad121c43dbf15b1ed Author: Justin Lecher gentoo org> AuthorDate: Mon Jun 17 05:55:15 2013 +0000 Commit: Justin Lecher gentoo 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(-) From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id DF24A1381F3 for ; Mon, 17 Jun 2013 05:56:19 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 11173E09A4; Mon, 17 Jun 2013 05:55:57 +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 1CE53E0996 for ; Mon, 17 Jun 2013 05:55:56 +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 138A233E3EA for ; Mon, 17 Jun 2013 05:55:55 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id B3BCEE5465 for ; Mon, 17 Jun 2013 05:55:53 +0000 (UTC) From: "Justin Lecher" 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" Message-ID: <1371448515.f43609fc308239ce00e3b66ad121c43dbf15b1ed.jlec@gentoo> Subject: [gentoo-commits] proj/sci:jlec commit in: / X-VCS-Repository: proj/sci X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: f43609fc308239ce00e3b66ad121c43dbf15b1ed X-VCS-Branch: jlec Date: Mon, 17 Jun 2013 05:55:53 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 97662e3b-f13e-45c2-89b2-d1b7374af2c0 X-Archives-Hash: 99c8f7f8c0ebc8cfab10ad457c13bcb4 Message-ID: <20130617055553.vQcNPFDKgR2v4uuxZicRxzcdJ8Ot00M3VYuumN8xKcY@z> commit: f43609fc308239ce00e3b66ad121c43dbf15b1ed Author: Justin Lecher gentoo org> AuthorDate: Mon Jun 17 05:55:15 2013 +0000 Commit: Justin Lecher gentoo 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 +- 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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(-) From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 17342138202 for ; 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 ; 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 ; 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 ; Mon, 8 Jul 2013 12:08:01 +0000 (UTC) From: "Justin Lecher" 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" 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: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail 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 gentoo org> AuthorDate: Mon Jun 17 05:55:15 2013 +0000 Commit: Justin Lecher gentoo 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(-)