Commit graph

9504 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
Todd Gamblin
650786c812 locks: improve errors and permission checking
- Clean up error messages for when a lock can't be created, or when an
  exclusive (write) lock can't be taken on a file.

- Add a number of subclasses of LockError to distinguish timeouts from
  permission issues.

- Add an explicit check to prevent the user from taking a write lock on a
  read-only file.
  - We had a check for this for when we try to *upgrade* a lock on an RO
    file, but not for an initial write lock attempt.

- Add more tests for different lock permission scenarios.
2018-07-12 19:59:53 +02:00
Todd Gamblin
ab794fa741 locks: llnl.util.lock now only writes host info when in debug mode
- write locks previously wrote information about the lock holder (host
  and pid), and read locks woudl read this in.

- This is really only for debugging, so only enable it then

- add some tests that target debug info, and improve multiproc lock test
  output
2018-07-12 19:59:53 +02:00
Todd Gamblin
b9af52a888 tests: Separate tests for llnl.util.lock and spack.util.lock
- llnl.util.lock tests are now independent of Spack
2018-07-12 19:59:53 +02:00
Todd Gamblin
7626ec4579 refactor: move spack.util.multiproc to llnl.util.multiproc
- multiproc doesn't depend on Spack
- llnl.util.lock test uses it, but shouldn't use parts of Spack.
2018-07-12 19:59:53 +02:00
Todd Gamblin
fe0fe1caa1 tests: add lib/spack/spack/test/.cache to gitignore for pytest
- this shoudl have been moved when we moved pytest.ini to lib/spack/spack/test
2018-07-12 19:59:53 +02:00
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
Massimiliano Culpo
e3a556cd2a Don't propagate version-specific URL overrides to newer versions (#8565)
When a user specifies a URL for a specific version of a package, Spack originally
would use that URL for all newer versions of the package. This behavior has
proven to be generally more harmful than useful, so this PR removes the feature
such that a version-specific URL override affects only that version.
2018-07-11 13:12:19 -07:00
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
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