Commit graph

7440 commits

Author SHA1 Message Date
Yifan Zhu
db0fec4d09 r-biocinstaller: added versioned dependency on r (#5663) 2017-10-11 19:49:08 -06:00
Yifan Zhu
4e8ac1d525 r-matrixstats: created new package (#5682) 2017-10-11 19:48:39 -06:00
Yifan Zhu
5e41ad6fed r-biocgenerics: added version 0.22.1 and added versioned dependency on r (#5683) 2017-10-11 19:48:19 -06:00
Yifan Zhu
8d48f07de1 r-genomeinfodbdata: added versioned dependency on r (#5685) 2017-10-11 19:48:00 -06:00
Yifan Zhu
a04e95a492 r-genomeinfodb: created new package (#5695) 2017-10-11 19:47:03 -06:00
Yifan Zhu
dc95dddd61 r-genomicranges: added new package (#5697) 2017-10-11 19:45:03 -06:00
Yifan Zhu
c93ecda872 r-futile-options: created new package (#5699) 2017-10-11 19:43:53 -06:00
Yifan Zhu
4af446d7f4 r-lambda-r: created new package (#5700) 2017-10-11 19:43:33 -06:00
Yifan Zhu
f8db73d567 r-futile-logger: created new package (#5701) 2017-10-11 19:43:15 -06:00
Yifan Zhu
01e104dfcb r-rsamtools: created new package (#5702) 2017-10-11 19:42:55 -06:00
Yifan Zhu
670463e95a r-biocparallel: created new package (#5703) 2017-10-11 19:42:25 -06:00
Yifan Zhu
e08e7af34e r-delayedarray: created new package (#5704) 2017-10-11 19:42:04 -06:00
Yifan Zhu
9a2ef4c4b3 r-biomart: added versioned dependency on r (#5666) 2017-10-11 19:41:08 -06:00
George Hartzell
124bdfb910 Strelka depends on boost 1.56.0 *or newer* (#5690)
Relax/correct the constraint on the version of boost used
by Strelka to match the docs.
2017-10-11 17:21:26 -06:00
Denis Davydov
35a62f715b dealii: minor fixes (#5687)
* dealii: fix minor bug in Assimp config

* dealii: request sundials without pthreads
2017-10-11 15:09:39 -06:00
Christoph Junghans
cfc13dec9f Add a bundle package for the ECP proxy applications suite (#5689)
* Add a bundle package for the ECP proxy applications suite

* Update package.py
2017-10-11 13:39:30 -06:00
健美猫
9e95e8394e Add a package: dmlc/mxnet. (#3579)
* Add dmlc/mxnet packags.

* Build mxnet+cuda+opencv with GCC-4.8.5 and GCC-5.4.0.

* Build mxnet version 0.10.0, 0.10.0.post1 and 0.10.0.post2.

* Add component version constrain for mxnet 0.10.0.x .

* Go through flake8.

* Replace commit hash with commit date as package version.

* Go throught Travis-CI.

* Update submodule version for 0.10.0.post2.

* Add openmp variant for dmlc-core and mxnet.

* Refine variant handling.

* Fix filter_file for dmlc-core.

* Cut long strings into multiple lies due to PEP8 requirements.

* Fix for PEP8.

* Add CUB_INCLUDE.

* Add py-mxnet: Python binding for MXNet.

* Remove distutils.dir_util.

* Add the profiler variant for mxnet.

* Add a shared variant for nnvm.

* Set USE_OPENMP to OFF by default.

* Fix flake8 errors.

* Fix flake8 issues.

* flake8 issues again.
2017-10-10 13:56:26 -07:00
Christoph Junghans
ef822453b9 Adding flang - a llvm based Fortran compiler (#5459)
* flang: initial commit

* flang: added symlink to clang's flang

* add flang wrapper

* flang wrapper: inject rpath as well

* flang wrapper: PATH -> -B
2017-10-10 13:52:31 -07:00
Christoph Junghans
cb7628c9a4 compilers/clang: add flang (#5503)
* compilers/clang: add flang

* Update clang.py
2017-10-10 13:52:10 -07:00
Christoph Junghans
88b515ede8 ninja: add v1.8.2 (#5625) 2017-10-10 12:50:56 -07:00
Massimiliano Culpo
a3bbe066b3 plumed: reworked patching applications, added new version (#5680)
closes #5506

The application of patches to upstream executables has been reworked
according to the suggestions of the main developer in #5506. In
particular we are not maintaining a dictionary that maps plumed
versions to the versions of patchable executables, and we are using a
non-interactive command to patch applications.

All the comments on substituting plumed at run-time do not apply here,
since we use RPATH and we want to maintain a 1:1 relationship between
the DAG hash and the plumed library used.
2017-10-10 12:35:53 -07:00
Audrey Thoma
e3053d7425 snap-korf: new package (#5589) 2017-10-10 11:09:31 -07:00
Jon Rood
f2b49d8f66 Adding openfast variant to nalu. (#5675) 2017-10-09 20:10:47 -06:00
lingnanyuan
35583f48f4 r-adsplit: Create new package and update version for its dependencies. (#5640)
* r-adsplit: Create new package.

* r-rlang: Update version.

* r-s4vectors: Update version.
2017-10-09 17:10:29 -06:00
Audrey Thoma
a8cd92a2e4 switching downloads to git (#5659) 2017-10-09 17:07:13 -06:00
lingnanyuan
196b82f2c7 r-affycompatible: Create new package. (#5664) 2017-10-09 17:05:53 -06:00
lingnanyuan
ef1f71447e r-affydata: Create new package. (#5665) 2017-10-09 17:05:21 -06:00
lingnanyuan
1f05e9ae58 r-affycontam: Create new package. (#5668) 2017-10-09 17:04:51 -06:00
George Hartzell
ab2c7573c1 strelka: new package (#5632)
* Add package for strelka@2.8.2

* Fix flake8 complaints
2017-10-09 17:02:44 -06:00
George Hartzell
0d1c36e559 Add package for aspell and ass't dictionaries (#3890)
* Add package for aspell and ass't dictionaries

Add a package definition for aspell.

Add a handful of dictionaries to convince myself that the support for
a bunch of dictionaries works.

* Flake8 cleanup

* Use six's version of urlparse

`urlparse` is not python3 friendly.  This works around it (stolen from
`.../cmd/md5.py`).

* Fix incorrect trimming regexp

* Clean up dictionary build

- more parsimonious use of `which` (`make()` has already been made)
- use `sh` instead of `bash`

* Use a helper method to generate info for variants

I figured out my issues with static methods.  I *think* that it this
is pythonic.

* Convert aspell to an extendable package

Convert aspell to be extendable and rework the dictionaries to be
extensions.

As it stands, there's a great deal of cut and paste in the
dictionaries, I'll abstract that out next.

The {de,}activate methods copy a great deal of code out of
package.py.  Perhaps there's a better way....

* Create AspellDictPackage and use it for the dictionaries

Reduce the repeated code, pull it into a base class.

I'm confused about why 'from spack import *' wasn't more useful in the
base class.

* Oops, -de & -es should be AspellDictPackages too

* Typo: pakcage -> package

* Address some commentary

* Update copyright dates, 2016->2017
2017-10-09 14:14:19 -07:00
Aaron Fisher
5ccc9c17dc Added mfem v3.3.1-rc1 to the mfem package. (#5644) 2017-10-09 21:48:25 +02:00
Axel Huebl
4ba7359d55 libpng: zlib flags more elegant (#5656) 2017-10-09 21:46:10 +02:00
becker33
5d13f236b4 Fix setup for changes to dirty flag (#5592)
* Pass dirty arg through setup to setup_package
2017-10-09 10:01:55 -07:00
Christoph Junghans
57643ae84e espressopp: added v1.9.5 (#5652) 2017-10-08 18:16:56 -07:00
Piotr Luszczek
1b5410b87b Add PLASMA package (#5540) 2017-10-08 17:59:41 -06:00
Pramod S Kumbhar
32d183af05 Fix node-js : requires openssl min 1.0.2 (#5650) 2017-10-08 17:04:09 -06:00
Denis Davydov
5ed457759c hypre: add 2.12.1 (#5653) 2017-10-08 07:27:25 -06:00
George Hartzell
ee6d21e311 adding http2 support (#5628)
Requires nghttp2 libraries
2017-10-07 09:58:56 -06:00
lingnanyuan
73bb34ad6e r-affycomp: Create new package. (#5642) 2017-10-06 20:13:57 -06:00
lingnanyuan
a755c47fb1 r-affxparser: Create new package. (#5641) 2017-10-06 20:13:38 -06:00
Yifan Zhu
cf94e4140b r-genomeinfodbdata: created new package (#5639) 2017-10-06 20:13:09 -06:00
Yifan Zhu
62538e3d37 r-hms: created new package (#5638) 2017-10-06 20:12:59 -06:00
scheibelp
b08d457dfd Don't check package.installed in _mark_concrete if value=True (#5634)
* spec and spec.package.spec can refer to different objects in the
database. When these two instances of spec differ in terms of
the value of the 'concrete' property, Spec._mark_concrete can
fail when checking Spec.package.installed (which requires
package.spec to be concrete). This skips the check for
spec.package.installed when _mark_concrete is called with
'True' (in other words, when the database is marking all specs
as being concrete).

* add test to confirm this fixes #5293
2017-10-06 14:23:28 -07:00
William Scullin
3d8d3e8882 qmcpack: new package (#4907)
This adds QMCPACK along with patches to Quantum Espresso for using Quantum Espresso in QMCPACK workflows.
2017-10-06 13:51:18 -07:00
George Hartzell
d05f98d405 Nghttp2 new package (#5627)
* nghttp2 library package

Added for dependencies

* Update package.py

* Removed useless code

* Flake8 fix
2017-10-06 13:59:56 -06:00
George Hartzell
a659f0f8f4 Add a package for VarDictJava@1.5.1 (#5626)
This is a simple package that drops their shell wrapper into
prefix.bin and their jar files into prefix.lib.

The approach comes from the picard package.
2017-10-06 13:58:34 -06:00
George Hartzell
202c66d90c The silver searcher: new version (#5630)
* Updating ag to the latest version

* Pretty by request

* Restore url to previous value

There *is* an https version available, but I've also been told
to not just update the url when adding new version.  I'm following
the latter advice and trusting security to the digest.
2017-10-06 13:56:58 -06:00
Massimiliano Culpo
2b2a5ca7bf git + luafilesystem: minor fixes (#5635)
* git: setup_dependent_environment won't fail for external packages

* luafilesystem: relax the request on git (it seemed overly restrictive)
2017-10-06 13:56:14 -06:00
George Hartzell
68011bde39 maven: new version (#5631)
* Adding maven v3.5.0

Updating package file to include later version of maven but still signifying a preference for the older

* removing specific preference flag
2017-10-06 13:53:56 -06:00
Michael Kuhn
4065ef2106 ncl: Fix temp directory and depend on esmf (#5636)
* ncl: Fix temp directory

Currently, ncl is configured using a transient temp directory. This
leads to warnings such as this when executing ncl later on:

warning:"/tmp/ncl_ncar_xxxxxx" tmp dir does not exist or is not writable:
NCL functionality may be limited -- check TMPDIR environment variable

As this also breaks some functionality, use the system temp directory
instead (typically /tmp).

* ncl: Depend on esmf

esmf is required for some ncl scripts (such as ESMF_regridding.ncl).
2017-10-06 13:53:05 -06:00