Commit graph

9385 commits

Author SHA1 Message Date
Levi Baber
aa9bb06b89 py-cutadapt: needs py-setuptools at runtime (#8689) 2018-07-11 14:53:35 -05:00
Howard Pritchard
be9dfc2d73 openmpi: add 3.1.1 (#8684)
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-07-11 12:42:00 -05:00
Jannek Squar
6a3f36c4e3 Adjusted sublime-text package (#8685) 2018-07-11 12:41:48 -05:00
Levi Baber
d27133b3cd perl-math-cephes: new package (#8671) 2018-07-11 12:40:39 -05:00
Jimmy Tang
5780eadf64 Update kaldi (#8682)
* Update kaldi

always use the --fst-version otherwise it does the wrong thing with
selecting the fst version.

also enable speex by default

* Give version a more meaningful name

* Update older version with a date string instead
2018-07-11 12:38:06 -05:00
健美猞猁
a985dc859c New packages: libbeato bwtool. (#8681) 2018-07-11 10:33:44 -05:00
Adam J. Stewart
f036f17f61
Retire the py-dev package (#8679) 2018-07-11 10:26:38 -05:00
Sergey Kosukhin
6479ec6def Patch for 'netlib-lapack'. (#8677) 2018-07-11 08:52:21 -05:00
健美猞猁
391d89a853 Bump gromacs versions. (#8676) 2018-07-11 08:05:39 -05:00
Jon Rood
a1bfa8eca0 Adding psm as a dependency of mvapich2. (#8674) 2018-07-10 19:32:50 -05:00
Kshitij Mehta
3c4ef576d9 Gtkorvo updates (#8663)
* gtkorvo-atl: Updated to version 2.2

* gtkorvo-dill: Updated to version 2.4

* gtkorvo-enet: Updated to version 1.3.14

* libevpath: Updated to version 4.4.0

* libffs: Updated to version 1.5

* gtkorvo-atl: Bugfix: Fixed cmake args

* gtkorvo-enet: Switched order of versions to have the latest version on the top

* gtkorvo-atl: Cleaned up cmake_args. Added conditional self.run_tests

* gtkorvo-dill: Cleaned up cmake_args. Added conditional self.run_tests

* libffs: Correction in dependency versions. Cleaned up cmake_args. Added conditional self.run_tests

* libevpath: Correction in dependency versions. Cleaned up cmake_args. Added conditional self.run_tests

* gtkorvo-atl: Removed unused option from cmake args
2018-07-10 12:50:10 -05:00
Matthias Diener
90042749e8 fetch: remove 'trying' when cloning repos (#8651)
* fetch: remove 'trying' when cloning repos

This makes it similar to what the URL strategy prints.

* change svn/hg names
2018-07-10 10:22:51 -05:00
Michael Kuhn
00c3331de9 libxshmfence: Update to 1.3 (#8667)
libxshmfence@1.2 does not compile with recent versions of glibc.
2018-07-10 07:58:44 -05:00
Matthias Diener
bc5168e4b1 charm: add possibility to run tests (#8665) 2018-07-09 16:16:27 -05:00
Levi Baber
4ed7931200 libnova: new package (#8666)
* libnova: new package

* libnova: flake8
2018-07-09 16:16:09 -05:00
Christoph Junghans
8bc3f7d726 Add ccache support (#3761)
If the user sets "ccache: true" in spack's config.yaml, Spack will use an available
ccache executable when compiling c/c++ code. This feature is disabled by default
(i.e. "ccache: false") and the documentation is updated with how to enable
ccache support
2018-07-09 14:06:10 -07:00
Sergey Kosukhin
8770957b7a Make 'netlib-lapack' a CMakePackage. (#8661)
* Make 'netlib-lapack' a CMakePackage.

* Add a comment.

* Some refactoring.
2018-07-09 13:21:55 -05:00
Levi Baber
25c9a5216f express: bamtools lib handling (#8552)
* express: bamtools lib handling

* express: use libs property

* express: remove old comment
2018-07-09 13:21:38 -05:00
Andrey Prokopenko
de4b6e6100 trilinos: update dtk dependencies (#8660) 2018-07-08 15:45:21 -05:00
Andreas Baumbach
21a46fb2ce fix typo in help of spack clone prefix is singular (#8658)
Change-Id: I3bfe5b4ba497fae57d5382502ea9a1b054688fdb
2018-07-08 20:28:46 +02:00
Miles Perry
53c0c5701c blasr: new package (#8367)
* blasr: new package

* blasr: changed version release, created list with 9 things, seperated make into build phase.

* blasr: fixed build phase by adding :

* blasr: fixed syntax for configure_args

* blasr: flake8 edits

* blasr-libcpp: fixed configure_args syntax

* blasr: fixed install issues resulting from PacBio changes

* blasr: removed accidental blasr-libcpp upload

* blasr: removed accidental blasr-libcpp upload

* blasr: removed blasr-libcpp

* blasr: edited out comment
2018-07-07 10:05:57 -05:00
Elsa Gonsiorowski, PhD
c907937ff4 ECP VELOC (#8581)
* kvtree package file

* MPI is default on

* proper mpi compiler

* rankstr package

* better rankstr description

* typo

* redset package

* shuffile package

* er package

* axl package

* proper pythor

* mpi is default on

* alpha releases and master versions

* veloc package with boost headers dep

* cmake version

* added C++11 requirement

* flake8

* flake8

* ecp tag

* axl: better async api option handling

* veloc package description

* prettier args list

* C++11 flag handler

* v1.0 of veloc
2018-07-07 09:56:56 -05:00
estebanpauli
891aa6ad7a Added support for uncrustify 0.67. (#8655)
* Added support for uncrustify 0.67.

Since the build system changed for uncrustify at version 0.64,
I had to change the package from an AutotoolsPackage to a plain
Package and use @when annotations to build the packages differently.

* Removed blank line at end of file

* Added support for python2.6 in uncrustify configuration.
2018-07-06 19:59:34 -05:00
George Hartzell
64d5847f05 Fix security issue in singularity + misc cleanups (#8657)
- Versions before 2.5.2 suffer from a serious security problem
  (https://nvd.nist.gov/vuln/detail/CVE-2018-12021).  Deleted all
  versions prior to v2.5.2.
- Update homepage (looks like singularity's going Freemium).
- Use release tarball instead of automagically generated archive
  tarball (digest values are more stable).
- No longer need autotools for released versions, just @devel.
- Install needs to be single-threaded, otherwise when installed as
  root the various 'chmod' operations race against the copies.
2018-07-06 19:59:17 -05:00
George Hartzell
71076bc9c5 Fix digests for git@2.17.0 and git@2.17.1 (#8652)
The entries for git@2.17.1 and git@2.17.0 were swapped.

This fixes them.
2018-07-06 14:57:45 -05:00
George Hartzell
48c0ce2b04 Update nettle package with info for v3.4 (#8653) 2018-07-06 14:57:32 -05:00
George Hartzell
7f814971a5 Clear up a bit of modules/dotkit confusion (#8650)
`use` is an overloaded word between dotkit, modules and spack.  Add additional words to make the distinction clear in the docs.
2018-07-06 12:06:53 -05:00
Adam J. Stewart
cf140b5f4c
Add url_for_version and list_url to Ruby package (#8216) 2018-07-06 07:22:38 -05:00
Mark Olesen
f946a83c8c precice: new package (issue #8643) (#8644)
preCICE (Precise Code Interaction Coupling Environment) is a
  coupling library for partitioned multi-physics simulations.
  Partitioned means that preCICE couples existing programs (solvers)
  capable of simulating a subpart of the complete physics involved in
  a simulation.

of-precice: new package

  preCICE adapter for OpenFOAM
2018-07-06 07:19:30 -05:00
Andreas Baumbach
7098937c03 switch git to kernel.org source and sha256 (#8580)
* switch git to kernel.org source and sha256

Change-Id: I5fe15689adb1163e9ed2b7127b52c95bd0d48564

* fix forgotton md5s

Change-Id: Ib01f21e20678d9aac3344b6ee311134a90b87bdd

* remove old url

Change-Id: I717a084a0357a84b83bc6c8542749aac7e04f68b
2018-07-06 07:16:54 -05:00
Adam J. Stewart
c31ac174c6
Glog: make is a function (#8648) 2018-07-06 07:15:47 -05:00
twang15
4b15391dab cleverleaf: Intel compiler fails compilation without c++11 flag (#8550) (#8598) 2018-07-05 21:54:05 -05:00
Adam J. Stewart
7fa3e7a9aa
Add missing dependencies and variants to wcslib (#8603)
* Add missing dependencies and variants to wcslib

* Add flex version requirement
2018-07-05 21:36:29 -05:00
lingnanyuan
1fa2212543 ncbitoolkit: Create new package. (#8591)
* ncbitoolkit: Create new package.

* Fix Flake8 Error.

* Add version constraints and change format.

* Fix version constraints.
2018-07-05 21:34:38 -05:00
Gregory Lee
f8f3fe5b8f added rpy2 2.9.4 and added py-jinja2 dependency (#8645) 2018-07-05 21:33:32 -05:00
Michael Kuhn
8a1bbc5d84 gcc: Fix build of older versions with recent versions of glibc (#8510) 2018-07-04 07:39:07 -05:00
Matthias Wolf
81668c524b Parquet: new packages (#8601)
* parquet: new package

Includes the following dependencies:

* arrow
* flatbuffers

Changes for compilation:

* snappy
* thrift
* zstd

* parquet: improve recipes (including dependencies)

* arrow: remove unused import in recipe

* parquet: fix line length for flake8/py27

* parquet, arrow: fix py26 format strings

* Address review comments.

* arrow: simplify recipe
2018-07-04 07:24:38 -05:00
becker33
aab5488154 disable openblas intel openmp patch for versions > 0.2.20, fixed upstream (#8638) 2018-07-03 16:25:12 -05:00
健美猞猁
9a60698ef8 Add new versions for log4cplus. (#8621)
* Add new versions for log4cplus.

* Update log4cplus versions.

* Add urls.

* Add url_for_version.

* Remove url_for_version.
2018-07-03 10:08:22 -05:00
健美猞猁
52a997208c Bump sbt to 1.1.6. (#8634) 2018-07-03 10:03:49 -05:00
Adam J. Stewart
6c24f686ce
Fix base class for py-pyserial (#8633) 2018-07-02 22:47:56 -05:00
Matthias Diener
30a6a17507 Pxz: new package (#8631) 2018-07-02 21:33:44 -05:00
Matthias Diener
c987987ca4 screen: update package (#8630) 2018-07-02 16:03:22 -05:00
Satish Balay
b0f8b7130f petsc: add in latest release 3.9.3. (#8627)
xl related fixes are 3.9.3 so remove xlc-test-3.9.0.diff
2018-07-02 15:48:13 -05:00
Matthias Diener
6f7e012cab byobu: update package (#8628) 2018-07-02 15:17:39 -05:00
健美猞猁
2601fd66f6 Bump gradle to 4.8.1. (#8625) 2018-07-02 12:46:46 -05:00
Jon Rood
f98657491d Add Amrvis package (#8590)
* First draft of amrvis package file.

* More additions to amrvis.

* Formatting.

* Forcing compiler environment variables to point to spack mpi compilers when using mpi.

* Disabling intel compiler for amrvis.

* Comments.

* Refining amrvis package file.

* Moving library and include locations variables to be inserted at the first lines of the makefile.

* Globbing amrvis binary instead of constructing its name.

* Making env variable setting consistent and fixing globbing of executable.

* Using iglob instead of glob.

* Turning MPI on by default for Amrvis.
2018-07-02 11:42:09 -05:00
Mark Olesen
a4ca2bb889 ENH: Building OpenFOAM sub-packages (issue #8579) (#8592)
* ENH: Building OpenFOAM sub-packages (issue #8579)

* Some support for packages building with OpenFOAM

- Adjust the wrappers calling the OpenFOAM Allwmake script. Have them
  look for a Allwmake-spack file first, which is assumed to contain
  special adjustments for compiling with spack.

  This file could be delivered as part of a tarball (which is unlikely)
  or generated on the fly by the spack sub-package as part of its
  patch or configure stage.

CONFIG: change the default paraview variant for openfoam to be False

- the different combinations of paraview backends, off-screen etc
  make it difficult to suggest that building with paraview as
  a standard dependency makes much sense.
  Additionally, building paraview with qt can become quite an issue.
  So it makes much more sense to only enable that upon request.

ENH: add a +vtk variant.

- for VTK with off-screen rendering to be used by the runTimePostProcessing
  function object, which is a fairly simple framework for generating images of
  some OpenFOAM derived objects (eg, sampling planes).

SPACK spec problem:

- reflect the flex restriction impose by the scotch dependency within
  the openfoam spec as well, as partial workaround for buggy or annoying
  spec resolution.

OTHER:

- updated the backstop foamEtcFile file to include args handling
  as per the OpenFOAM-v1806 updates.

* new version: OpenFOAM-v1806

- https://www.openfoam.com/releases/openfoam-v1806/
2018-07-02 10:02:48 -05:00
健美猞猁
bd3f981fbb A new package: xhmm. (#8620)
* A new package: xhmm.

* Flake8.

* Support general BLAS.
2018-07-02 07:54:41 -05:00
Adam J. Stewart
a0c13229e8
Add Python 3.7.0 (#8619) 2018-06-29 16:25:39 -05:00