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6344 Commits

Author SHA1 Message Date
Levi Baber
44c999e2e1 mothur: mpi not used (#8706) 2018-07-13 20:31:25 -05:00
Matthias Diener
2cf9c7955c Scotch: fix compilation of 6.0.5a (#8704) 
Prevent this error:

metis_graph_part.c:301:7: error: non-void function 'METIS_PartGraphVKway' should return a value
      [-Wreturn-type]
 2018-07-13 15:51:04 -05:00
Sajid Ali
aec91d1cca update version for numexpr (#8702) 
* 	modified:   package.py

* 	deleted:    var/spack/repos/builtin/packages/py-numexpr/numexpr-2.6.5.tar.gz
 2018-07-13 15:50:21 -05:00
Sajid Ali
4c5e4cb960 Add py-backcall (#8701) 
* 	new file:   var/spack/repos/builtin/packages/py-backcall/package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py
 2018-07-13 10:59:02 -05:00
Christoph Junghans
d569a9c124 flang: add support for llvm-6 (#8073) 
* flang: add support for llvm-6

* flang: review changes

* pgmath: make flake8 happy
 2018-07-12 18:37:50 -06:00
Tim Law
2a27a37597 Add Git development versions for Typhon and BookLeaf_Cpp. (#8694) 2018-07-12 07:37:42 -05:00
Nicolas Richart
d8921ac323 First try on pytorch (#8649) 
* initial version of the package pyTorch (#171)

* adding version 0.4

* flake8 correction

* reordering version, removing run dependecies

* Changing depends_on type to default
 2018-07-12 07:30:59 -05:00
Levi Baber
1846bc5ed6 mitofates: more deps and a patch to make it functional (#8686) 
* mitofates: more deps and a patch to make it functional
 2018-07-12 10:23:22 +02:00
Adam J. Stewart
ecff47538e Remove unnecessary version-specific URL overrides (#8693) 2018-07-12 07:28:11 +02:00
Levi Baber
2561d1d656 transdecoder: needs perl-uri-escape (#8690) 2018-07-11 17:38:58 -05:00
Levi Baber
f29c1d9096 beast1: new version (#8691) 2018-07-11 17:07:20 -05:00
Levi Baber
feb4701ae3 mothur: new version (#8692) 2018-07-11 17:07:02 -05:00
Massimiliano Culpo
10e628a5a0 py-ply: added version 3.11 (#8383) 2018-07-11 22:21:55 +02:00
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
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
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
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
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