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4808 commits

Author SHA1 Message Date
Yifan Zhu
cd4d26705e Bioconductor package url change (#5797) 2017-11-06 11:17:59 -07:00
Michael Kuhn
450f2fa034 likwid: Use external lua if possible (#6009) 2017-11-06 11:14:34 -07:00
Douglas Duckworth
47b15feec3 added new package - MotionCor2 (#6151) 2017-11-06 11:09:46 -07:00
Denis Davydov
f538b7ac3e dealii: make sure bundled libs are not used (#6106) 2017-11-06 12:38:59 +01:00
Besnard Jean-Baptiste
84c6fea32e Graphviz : Add a GTS variant (#6149) 
Enable support for the GNU Triangulated Surface Library

	- New variant +gts for graphviz
	- Optionnal dependency for GTS (already packaged)
 2017-11-05 16:55:44 -08:00
Douglas Duckworth
ccc51cea7d added relion v 2.1 (#6023) 
* added relion v 2.1

* relion 2.1 - misssed comma

* relion now pulling from master branch - removed 2.03 - added cuda 8 as dependency given 9 does not yet work with relion per https://github.com/3dem/relion/issues/296
 2017-11-05 15:01:21 -08:00
Ben Boeckel
22df09315f Re-add list_url for all R packages (#6110) 
* r-igraph: find old packages in the archive

Fixes #6104.

* r-irlba: find old packages in the archive

Fixes #6101.

* r-lazyeval: find old packages in the archive

Fixes #6102.

* packages: set list_url for all packages hosted on CRAN

* packages: consistently use the CRAN archive URLs
 2017-11-05 13:42:24 -08:00
Adam Moody
2a8c97d440 dtcmp: add v1.1.0 (#6146) 2017-11-05 09:25:03 -08:00
Satish Balay
d34d0d6cbc petsc: update to version 3.8.1 (#6150) 
* petsc: update to version 3.8.1

* petsc: add in conflict between petsc-3.8.0 & mkl
 2017-11-05 09:24:42 -08:00
Axel Huebl
5d9dd24daa ISAAC 1.3.3 (#6152) 
Add a new release of ISAAC.
 2017-11-05 09:24:18 -08:00
Todd Gamblin
05fa302655
Replace github.com/llnl/spack with github.com/spack/spack (#6142) 
We moved to a new GitHub org! Now make the code and docs reflect that.
 2017-11-04 17:08:04 -07:00
vishalkenchan
386e0af089 add rol variant (#6105) 2017-11-04 12:14:46 -07:00
Yifan Zhu
9d234c4f8e r-yapsa: created new package (#6121) 2017-11-03 14:21:00 -06:00
Yifan Zhu
fb1160d052 r-keggrest: created new package (#6120) 2017-11-03 14:20:36 -06:00
lingnanyuan
3921948b03 r-statmod: Create new package. (#6119) 2017-11-03 14:20:14 -06:00
lingnanyuan
b204c7e793 r-deseq: Create new package. (#6118) 2017-11-03 14:19:38 -06:00
lingnanyuan
f91c25ddee r-samr: Create new package. (#6117) 2017-11-03 14:19:16 -06:00
lingnanyuan
d54627659a r-impute: Create new package. (#6116) 2017-11-03 14:18:46 -06:00
lingnanyuan
95e290eaf3 r-altcdfenvs: Create new package. (#6115) 2017-11-03 14:18:17 -06:00
lingnanyuan
64689bdb01 r-makecdfenv: Create new package. (#6114) 2017-11-03 14:17:58 -06:00
lingnanyuan
b614c7970b r-hypergraph: Create new package. (#6113) 2017-11-03 14:17:36 -06:00
Axel Huebl
5a4544ab05 ISAAC 1.3.2 (#6129) 
Add a new release of ISAAC.
 2017-11-03 14:58:38 +01:00
Ben Boeckel
be01b2d5f0 aspell: refuse to work with non-global extensions 
Aspell compiles in the paths it looks for rather than looking relative
to its binary location. There are also no environment variables to
redirect it other than changing the path to the configuration file it
looks at.
 2017-11-02 18:45:40 -07:00
Ben Boeckel
a81485cb3f perl: support extensions in views 2017-11-02 18:45:40 -07:00
Oliver Breitwieser
643a28aac5 python: extensions support for easy-install.pth 2017-11-02 18:45:40 -07:00
Ben Boeckel
d5a3d9d20e view: test conflicting packages in views 2017-11-02 18:45:40 -07:00
Ben Boeckel
13b669de8e view: test that extension paths exist 2017-11-02 18:45:40 -07:00
Ben Boeckel
41dfba0ba1 extension1: add a second version 2017-11-02 18:45:40 -07:00
Ben Boeckel
a7925bb927 bdftopcf: require xproto and fontsproto at build time (#6112) 
These are technically "link" depends of libxfont, but they have no
actual libraries.

Fixes #5936.
 2017-11-02 15:47:18 -06:00
lingnanyuan
13f1781bea Add package r-reportingtools and update url for its dependencies. (#6071) 
* r-reportingtools: Create new package.

* r-go-db: Update url.

* r-gseabase: Update url.

* r-pfam-db: Update url.
 2017-11-02 14:21:32 -06:00
Michael Kuhn
d1db161aeb adios: Fix hdf5 and sz dependencies (#6016) 
- hdf5's +hl variant is required because the build uses libhdf5_hl.
- sz is only compatible up to version 1.4.10 because the library has
  been renamed to libSZ in 1.4.11.
 2017-11-02 13:41:25 -06:00
Brice Goglin
3a1b013291 hwloc: add version 1.11.8 (#6099) 
Signed-off-by: Brice Goglin <Brice.Goglin@inria.fr>
 2017-11-02 13:40:46 -06:00
Audrey Thoma
f9341857c7 arlecore: new package (#6109) 2017-11-02 13:40:03 -06:00
Christoph Junghans
c4db3d384e gromacs: add develop version (#6098) 2017-11-02 15:16:21 +01:00
Adam J. Stewart
e47ceefc43 sundials+hypre depends on hypre (#6075) 2017-11-02 08:16:43 +01:00
Denis Davydov
11ba60413b the-silver-searcher: add missing dependency (#6095) 2017-11-02 08:10:40 +01:00
Michael Kuhn
61ed583266 xqilla: Use append instead of extend (#6094) 2017-11-02 08:09:24 +01:00
Brian Van Essen
932068d725 Update candle (#6097) 2017-11-01 23:58:55 -06:00
Yifan Zhu
7d0c6361ee r-getoptlong: created new package (#6069) 2017-11-01 19:09:54 -06:00
Yifan Zhu
f15969d624 r-gtrellis: created new package (#6088) 2017-11-01 19:09:20 -06:00
Brian Van Essen
86b7b84ddf LBANN flags and OpenCV variant (#5951) 
* Fixed the datatype flag in the LBANN package.
Fixed where the datatype flag should be set.

* Added variant to OpenCV to disable building DNN support

* Fixed a bug in how the elemental package tries to find its Fortran
library.  The current method does not work with Intel compilers.

* Added necessary paths for cuDNN and CUB.

* Addressed flake8 issues in Elemental package.

* Fixed several flake8 errors.  Added variant to build with or without
support for arbitrary-precision floating point arithmetic.

* Added the proper CMake flag when MPFR support is disabled.

* Fixed a bug in how the cudnn path was being set when there was no
cudnn requested.  Also requested that OpenCV is built without eigen
support.

* Fixed another bug where a dependency may not be there and thus should
not be always checked.
 2017-11-01 17:25:28 -07:00
Michael Kuhn
0d624eac55 lua: Build a shared library (#6008) 
Patch is inspired by Arch Linux and Homebrew.
 2017-11-01 17:10:14 -06:00
Yifan Zhu
f3af8272f5 r-circlize: new package (#6087) 2017-11-01 17:08:46 -06:00
lingnanyuan
ef240f59b8 r-alsace: Create new package. (#6064) 2017-11-01 17:04:56 -06:00
Yifan Zhu
26ade0c9ae r-globaloptions: new package (#6068) 2017-11-01 17:04:38 -06:00
lingnanyuan
a05cca49d8 r-affycoretools: Create new package and its dependency r-ff. (#6082) 
* r-ff: Create new package

* r-affycoretools: Create new package.

* r-ff: update url.
 2017-11-01 17:04:17 -06:00
lingnanyuan
541818ed06 r-agimicrorna: Create new package. (#6083) 2017-11-01 17:03:48 -06:00
Yifan Zhu
616a43b76d r-complexheatmap: created new package (#6084) 2017-11-01 17:03:30 -06:00
Yifan Zhu
ebff5086d7 r-shape: created new package (#6086) 2017-11-01 17:03:15 -06:00
Yifan Zhu
7fb6fbea54 r-pmcmr: new package (#6085) 2017-11-01 17:02:58 -06:00