sci-biology/gap2caf: remove -rpath-link from src/Makefile

Package-Manager: portage-2.2.7
sci-biology/Atlas-Link: noted dependence, see bug #516366
sci-biology/emboss-6.3.1_p4-r2: added a patch for 'undefined reference to c_plwid' bug #493724

Package-Manager: portage-2.2.7
sci-biology/caftools: clarified package description

Package-Manager: portage-2.2.7
sci-biology/clview: add dependency on =x11-libs/fox-1.6*

Package-Manager: portage-2.2.7
sci-biology/MaSuRCA: add dependency on sci-biology/quorum
root and root-docs: version bump
sci-physics/root: rectify license list
sci-physics/root: Backport fixes from ROOT-6 branch

Backport fixes for .credits, .demos, .license from ROOT-6 branch.
A patch was backported by upstream too.
app-doc/root-docs: backport fixes from ROOT-6 branch
dev-python/bokeh: dev-python/bokeh: Copy latest ebuild from portage

Package-Manager: portage-2.2.10
dev-python/bokeh: dev-python/bokeh: New version with python3 support for bug #516052

Package-Manager: portage-2.2.10
sci-chemistry/nmrpipe: Fix emul-linux deps for modern multilib

Package-Manager: portage-2.2.10
RepoMan-Options: --force
Merge pull request #237 from aufau/bokeh

dev-python/bokeh (in the main tree): Fix bug #516052
Merge pull request #236 from olifre/master

New live ebuild for VGM and Geant-VMC
Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/bokeh: dev-python/bokeh: New version with python3 support for bug #516052
  dev-python/bokeh: dev-python/bokeh: Copy latest ebuild from portage
  Add subslot dependency on clhep, we need to rebuild for each clhep subslot change.
  New live ebuild for VGM, adapting to fixes for cmake install paths in upstream (no need to manually install in ebuild anymore). Released VGM-4.00 does not have these fixes yet, I am discussing with upstream whether they can also provide some tarballs of released versions (as sourceforge svn-snapshotting is unusable for us) and delay packaging of VGM-4.00 until then.
  New live ebuild, using cmake-buildsystem (upstream switches to cmake for next release), add flags for g4root and mtroot. Adapt to upstream's fixes concerning install paths, we don't need to do manually installation anymore. I will skip geant-vmc-3.00b01 from packaging, it does not include those fixes yet.
InCvs

Signed-off-by: Justin Lecher <jlec@gentoo.org>
sync with gx86, fix FEATURES=test

Package-Manager: portage-2.2.8-r1
dev-util/nvidia-cuda-toolkit: dev-util/nvidia-cuda-toolkit: add version 6.5.11

Package-Manager: portage-2.2.8-r1
Merge pull request #239 from marbre/nvidia-cuda-toolkit

dev-util/nvidia-cuda-toolkit: add version 6.5.11