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4822 commits

Author SHA1 Message Date
lingnanyuan
241e1b56b5 r-dnacopy: Create new package. (#6183) 2017-11-08 13:57:15 -07:00
Yifan Zhu
92a582d5f8 r-mergemaid: created new package (#6182) 2017-11-08 13:56:59 -07:00
lingnanyuan
146db9adef r-bamsignals: Create new package. (#6181) 2017-11-08 13:56:34 -07:00
Yifan Zhu
87aafeb78a r-xmapbridge: created new package (#6180) 2017-11-08 13:56:15 -07:00
Sergey Kosukhin
c7a855ba57 Missing dependency for 'cdo'. (#6175) 2017-11-08 13:55:57 -07:00
baip
ed00757265 gcc: add 5.5.0 (#6171) 2017-11-08 20:27:08 +01:00
vishalkenchan
392929ba77 lammps: add more packages (#6174) 
* lammps : adding new varients and dependencies therein

* Update package.py

* removing trailing whitespaces
 2017-11-08 09:01:14 -07:00
Matthew Scott Krafczyk
00d48e60bf Fix for nghttp2 installation (#5904) 
nghttp2 depends on python, and requires the install directory to exist,
and contain the python module directory which it will eventually
install the python modules into.
 2017-11-07 15:59:15 -08:00
James Dickson
841d42b308 TyphonIO: new package + Updated MACSio package (#6177) 2017-11-07 13:13:06 -07:00
Audrey Thoma
8bae192d5c repeatmasker: new package (#6108) 2017-11-06 17:27:42 -07:00
Michael Kuhn
ca73103dac Introduce static_to_shared_library function (#6092) 
The static_to_shared_library function takes an existing static library
and produces a shared library based on it.
 2017-11-06 17:21:46 -07:00
Satish Balay
dc78e60c83 trilinos: update hdf5 dependency to use 'hdf5+hl' (#6025) 
* trilinos: update hdf5 dependency to use 'hdf5+hl'

Without this change - I get the following error [triggered by 161dca6d5 c9810f808 changes]

$ ./bin/spack install trilinos+hdf5
==> Error: An unsatisfiable variant constraint has been detected for spec:

    hdf5@1.10.1%gcc@7~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-fedora27-x86_64

while trying to concretize the partial spec:

    netcdf+mpi
        ^m4
        ^mpich@3.3a2%gcc@7 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-fedora27-x86_64
        ^zlib@1.2.11%gcc@7+optimize+pic+shared arch=linux-fedora27-x86_64

netcdf requires hdf5 variant +hl, but spec asked for ~hl

* fix flake8 warning
 2017-11-06 13:03:06 -08:00
Luigi Calori
f0d33df3a9 some missing X11 "*proto" dependencies (#6158) 
* fix xinput deps

* adding other x11 proto missing deps, see #6157
 2017-11-06 13:02:05 -08:00
Satish Balay
436ebc4490 petsc: update petsc dependency on superlu-dist (#6159) 2017-11-06 12:52:10 -08:00
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