[gentoo-commits] proj/sci:vtk commit in: /

["Justin Lecher" <jlec@gentoo.org>]

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
  ...


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 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(-)