[gentoo-commits] proj/sci:ccp4 commit in: /

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

commit:     3833417300c4a4415fac9efa033c5a11f0bb42d7
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 30 11:39:22 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 30 11:39:22 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=38334173

Merge branch 'master' into ccp4

* master: (46 commits)
  sci-libs/msms: Version BUmp; Bump to new distutil-r1.eclass
  app-doc/root-docs: version bump
  sci-physics/root: version bump
  sys-cluster/hpl: version bump and fixes
  fixed deps
  In sci-libs/bigdft-abi-1.0.4-r1, CUDA support made compile.
  moved to gx86
  moved to gx86
  Beautify
  Beautify
  Beautify.
  Added new package: projections
  Added new package: projections
  Bashified package name mangling.
  sys-cluster/modules: Prefix keyworded. Added tests. FHS fixes. Add bunch of fedora patches
  Fixed missing use flag.
  sci-chemistry/ucsf-tools: Fix compilation with latest gcc
  sci-chemistry/modeller: Fix lib position, #474696
  sci-chemistry/pymol: Update repo uri
  sci-chemistry/pymol: Update repo uri
  ...

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

Conflicts:
	sci-chemistry/shiftx/ChangeLog
	sci-chemistry/shiftx/shiftx-1.1.ebuild


 app-admin/eselect/ChangeLog                        |   6 +
 app-admin/eselect/Manifest                         |   2 +-
 ...1.3.4-r100.ebuild => eselect-1.3.5-r100.ebuild} |   0
 app-doc/root-docs/ChangeLog                        |   6 +
 app-doc/root-docs/Manifest                         |   2 +-
 ...ocs-5.34.08.ebuild => root-docs-5.34.09.ebuild} |   2 +-
 dev-java/fits/ChangeLog                            |   9 +-
 dev-java/fits/Manifest                             |   2 +-
 .../{fits-1.08.1.ebuild => fits-1.11.0.ebuild}     |   6 +-
 dev-lang/ispc/ChangeLog                            |   3 +
 dev-lang/ispc/ispc-9999.ebuild                     |   3 +-
 sci-chemistry/ambertools/ChangeLog                 |   4 +-
 sci-chemistry/ambertools/ambertools-12.ebuild      |   2 +-
 sci-chemistry/gnome-chemistry-utils/ChangeLog      |   4 +
 .../gnome-chemistry-utils-0.14.2.ebuild            |   2 +-
 sci-chemistry/gnome-chemistry-utils/metadata.xml   |   8 +-
 sci-chemistry/modeller/ChangeLog                   |   4 +
 ...ller-9.12-r1.ebuild => modeller-9.12-r2.ebuild} |   3 +-
 sci-chemistry/pymol/ChangeLog                      |   3 +
 sci-chemistry/pymol/pymol-9999.ebuild              |   2 +-
 sci-chemistry/shiftx/ChangeLog                     |   5 +-
 sci-chemistry/shiftx/shiftx-1.1.ebuild             |   3 +
 sci-chemistry/ucsf-tools/ChangeLog                 |   3 +
 sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild    |  13 +-
 sci-libs/bigdft-abi/ChangeLog                      |  21 +++
 ...abi-1.0.4.ebuild => bigdft-abi-1.0.4-r1.ebuild} |   9 +-
 .../files/bigdft-abi-1.0.4-CUDA_gethostname.patch  |  22 +++
 sci-libs/coinor-clp/ChangeLog                      |   6 +
 sci-libs/coinor-clp/Manifest                       |   2 +-
 ...-clp-1.15.0.ebuild => coinor-clp-1.15.1.ebuild} |   4 +-
 .../files/coinor-clp-1.15.1-mpi-header.patch       |  12 ++
 sci-libs/etsf_io/ChangeLog                         |   4 +
 sci-libs/etsf_io/etsf_io-1.0.3-r2.ebuild           |   6 +-
 sci-libs/fox/ChangeLog                             |   4 +
 .../files/4.1.2-r2-install-customizations.patch    |   4 +-
 sci-libs/lwpr/ChangeLog                            |   9 +-
 sci-libs/lwpr/Manifest                             |   2 +-
 sci-libs/lwpr/files/lwpr-1.2.2-setup.py.patch      |  12 --
 sci-libs/lwpr/lwpr-1.2.2.ebuild                    |  83 ---------
 sci-libs/lwpr/lwpr-1.2.5.ebuild                    |  51 ++++++
 sci-libs/lwpr/metadata.xml                         |  10 +-
 sci-libs/msms/ChangeLog                            |  10 +-
 sci-libs/msms/Manifest                             |   3 +-
 sci-libs/msms/metadata.xml                         |   2 +-
 sci-libs/msms/msms-1.5.4-r1.ebuild                 |  54 ------
 .../{msms-1.5.6_rc2.ebuild => msms-1.5.6.ebuild}   |  19 +--
 sci-libs/trilinos/ChangeLog                        |   7 +-
 sci-libs/trilinos/metadata.xml                     |  16 ++
 sci-libs/trilinos/trilinos-11.2.3.ebuild           | 186 +++++++++++++++++++++
 sci-physics/abinit/ChangeLog                       |   4 +
 sci-physics/abinit/files/6.12.3-gui-makefiles.tbz  | Bin 0 -> 14600 bytes
 sci-physics/bigdft/ChangeLog                       |   8 +
 sci-physics/bigdft/bigdft-1.7_pre24.ebuild         |   2 +
 sci-physics/lammps/ChangeLog                       |  55 ------
 sci-physics/lammps/Manifest                        |   3 -
 sci-physics/lammps/lammps-20130512.ebuild          |  72 --------
 sci-physics/lammps/lammps-20130514.ebuild          |  75 ---------
 sci-physics/lammps/lammps-20130526.ebuild          |  75 ---------
 sci-physics/lammps/metadata.xml                    |  30 ----
 sci-physics/root/ChangeLog                         |   6 +
 sci-physics/root/Manifest                          |   5 +-
 sci-physics/root/metadata.xml                      |   1 +
 .../{root-5.34.08.ebuild => root-5.34.09.ebuild}   |  15 +-
 sys-cluster/charm/ChangeLog                        |  26 ---
 sys-cluster/charm/Manifest                         |   1 -
 sys-cluster/charm/charm-6.5.0.ebuild               | 175 -------------------
 .../charm/files/charm-6.5.0-charmc-gentoo.patch    |  25 ---
 sys-cluster/charm/metadata.xml                     |  10 --
 sys-cluster/charmdebug/ChangeLog                   |  12 ++
 sys-cluster/charmdebug/Manifest                    |   1 +
 sys-cluster/charmdebug/charmdebug-6.2.0.ebuild     |  31 ++++
 .../charmdebug}/metadata.xml                       |   0
 sys-cluster/hpl/ChangeLog                          |   8 +
 sys-cluster/hpl/Manifest                           |   3 +-
 .../hpl/{hpl-2.0-r1.ebuild => hpl-2.1.ebuild}      |  33 ++--
 sys-cluster/modules/ChangeLog                      |  10 ++
 sys-cluster/modules/files/createmodule.py          | 186 +++++++++++++++++++++
 sys-cluster/modules/files/createmodule.sh          | 166 ++++++++++++++++++
 .../modules/files/modules-3.2.10-avail.patch       |  12 ++
 .../modules/files/modules-3.2.10-bindir.patch      |  11 ++
 .../modules/files/modules-3.2.10-clear.patch       |  11 ++
 ...orline.patch => modules-3.2.10-errorline.patch} |   1 -
 .../modules/files/modules-3.2.10-versioning.patch  |  10 ++
 .../modules/files/modules-3.2.9c-errorline.patch   |   1 -
 sys-cluster/modules/files/modules.sh.in            |   7 +
 sys-cluster/modules/metadata.xml                   |  20 ++-
 sys-cluster/modules/modules-3.2.10-r1.ebuild       |  61 +++++++
 sys-cluster/modules/modules-3.2.10.ebuild          |   6 +-
 sys-cluster/projections/ChangeLog                  |  13 ++
 sys-cluster/projections/Manifest                   |   1 +
 .../projections}/metadata.xml                      |   0
 sys-cluster/projections/projections-6.2.1.ebuild   |  30 ++++
 92 files changed, 1091 insertions(+), 786 deletions(-)

diff --cc sci-chemistry/shiftx/ChangeLog
index 85e5049,f656301..2efad58
--- a/sci-chemistry/shiftx/ChangeLog
+++ b/sci-chemistry/shiftx/ChangeLog
@@@ -5,8 -8,8 +8,8 @@@
    20 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx-1.1.ebuild,
    files/1.1-Makefile.patch, +files/1.1-bfr-overflow.patch, metadata.xml:
    Fix patch and add patch for buffer overflow fix
--
    16 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx-1.1.ebuild, metadata.xml:
++
    Bump to EAPI=5 and fix license
  
  *shiftx-1.1 (14 Jun 2009)