Commit graph

11854 commits

Author SHA1 Message Date
Adam J. Stewart
6b068a855e
Fix typo in spack executable (#11512) 2019-05-18 21:00:46 -05:00
Owen Solberg
92604ed576 intel-tbb: fix patch for old compilers (#11371)
* added patch for intel-tbb@2019.1: with old compilers

* sparately specify when @:2018 and @2019

the reason we can't say @:2019 is that would include @2019.1 where the
patch doesn't work.

* should be possible to list when constraint as @:2019

According to my reading of ["Version ranges" in the Spack
docs](https://spack.readthedocs.io/en/latest/packaging_guide.html#version-ranges),
this should apply to up to `2019` but not `2019.1:`

* @:2019.0 appears to be necessary to specify 2019 but not 2019.1

* specifying 2019.1 2019.2 2019.3 2019.4 separately and explcitly

* flake8 fixes for long lines.

* add comments to explain why so many different patch directives

* remove blank like for flake8

* revert spec %gcc@4.8.0:4.99999 -> %gcc@4.8.0:
2019-05-18 21:00:32 -05:00
George Hartzell
e592262da8 Typos: funciton, woudl, hm,... (#11511) 2019-05-18 11:39:23 -05:00
Mario Melara
9957093e53 Execute modulecmd in bash shell (#11510)
Adds executable=/bin/bash into Popen. We discovered this bug while
working in a csh/tsch environment. By executing with /bin/bash we ensure
that the module command works.
2019-05-18 01:49:19 +02:00
Justin S
c595883195 r-popvar: new package at 1.2.1 (#11490) 2019-05-17 14:45:21 -05:00
Justin S
cc6f822cb1 smof: new package at 2.13.1 (#11502) 2019-05-17 14:44:35 -05:00
Justin S
c7a28ec1d4 r-bglr: new package at 1.0.8 (#11489) 2019-05-17 14:35:38 -05:00
Justin S
719cd6741d r-rrblup: new package at 4.6 (#11488) 2019-05-17 14:34:33 -05:00
Justin S
8c5b41793c r-qtl: new package at 1.44-9 (#11487) 2019-05-17 14:33:42 -05:00
Justin S
c00ed0d942 py-metasv: new package at 0.5.4 (#11476) 2019-05-17 14:33:04 -05:00
Justin S
7a459857e7 py-pybedtools: new package at 0.6.9 (#11475)
* py-pybedtools: new package at 0.6.9

* py-pybedtools: add bedtools2 dep
2019-05-17 14:32:21 -05:00
Justin S
79a0da6098 repeatmodeler: new package at 1.0.11 (#11472) 2019-05-17 14:31:26 -05:00
Sriram Swaminarayan
0557d93080 added branch multisplice to the parsplice package (#11504) 2019-05-17 12:08:40 -06:00
Christoph Junghans
b7f2923607
gasnet: 2019.3.0 (#11503) 2019-05-17 12:02:43 -06:00
Christoph Junghans
2af7688c55
parsplice: needs LAMMPS_EXCEPTIONS (#11500) 2019-05-17 08:57:35 -06:00
Piotr Luszczek
900f8f0806 Add version 2.5.1-alpha1 of MAGMA (#11486) 2019-05-17 08:19:32 -05:00
Todd Gamblin
23c48d94d3
cmake: default to +ownlibs to improve build times (#11483)
- CMake is built *very* frequently, and the number of dependencies it has
  accumulated can take a very long time on some systems.

- Use +ownlibs by default to avoid the build overhead. This won't
  interfere with other packages by introducing conflicting libraries, as
  CMake is nearly always a build dependency.
2019-05-17 08:47:58 +02:00
Jim Galarowicz
c7f23dcd8d OpenSpeedShop/CBTF package updates and fixes (#11470)
This avoids using Boost 1.70.0, fixes library access in OpenSpeedShop
packages, adds new versions, and updates QT dependency constraints
in CBTF and OpenSpeedShop packages

- Constrain Boost dependency to 1.69.0 or earlier to avoid issues
  with 1.70.0 for Open|SpeedShop and CBTF packages
- Update DYNINSTAPI_RT_LIB environment variable to use single library
  from "find_libraries" (which returns a list) in OpenSpeedShop
  packages
  Fixes #11443
- Add version 1.9.3 for CBTF Argo Navis, CBTF Krell, CBTF LANL, and
  CBTF packages
- Add version 2.4.1 for OpenSpeedShop Utils and OpenSpeedShop
  packages
- Update QT dependency to 5.10.0 or greater for QtGraph and CBTF Argo
  Navis packages
2019-05-16 18:19:55 -07:00
Michael Kuhn
e90b4ce6fb CDO package: Fix build with gcc@9 (#11464)
This makes several changes to make CDO work with gcc@9:

- Add version 1.9.7rc2
- Add a patch to make version 1.9.7rc2 build with gcc@9:
- Add a conflict with GCC 9 for earlier versions of CDO

It also adds a pkgconfig build dependency as configure checks for it.
2019-05-16 17:53:38 -07:00
Andrew Gaspar
8675f44d45 Kokkos package: add debug variant (#11469) 2019-05-16 17:35:23 -07:00
Massimiliano Culpo
c03be0d65a Command extensions can import code from modules in root or cmd folder (#11209)
#8612 added command extensions to Spack: a command implemented in a
separate directory. This improves the implementation by allowing
the command to import additional utility code stored within the
established directory structure for commands.

This also:

* Adds tests for command extensions
* Documents command extensions (including the expected directory
  layout)
2019-05-16 17:27:42 -07:00
Chris Green
b9370bf20b Allow command access to dump/pickle_environment from #8476 (#11434)
* Allow command access to dump/pickle_environment from #8476
2019-05-17 09:15:32 +09:00
Chris Green
f90507a227 numpy: new version 1.16.3; update historical versions. (#11364) 2019-05-16 11:44:43 -05:00
Chuck Atkins
c2d6095cf3
paraview: fix several dependency issues (#11432)
* Use externally provided mpi4py
* Make mpi4py and numpy both build deps instead of only run deps
* libxt is only on ~osmesa platform=linux
2019-05-16 09:04:44 -04:00
Matthias Wolf
7fcf534b25 junit: escape remaining inputs. (#11382) 2019-05-16 14:40:07 +02:00
David Beckingsale
5ccc695bfb Fix CMake versions dependencies in RAJA package (#11440) 2019-05-16 13:54:52 +02:00
Thomas Gruber
0337170d34 Likwid: added versions 4.3.3 and 4.3.4 (#11479) 2019-05-16 13:35:25 +02:00
Denis Davydov
38a59e6e37 symengine: add 0.4.0, fix dependency in dealii (#11473) 2019-05-16 12:23:21 +02:00
Todd Gamblin
a750237532
flake8: add exceptions for overly pedantic camelcase rules from pep8-naming (#11477)
Rules N813 and N814 prevented import statements like this:

  xml.etree.ElementTree as et
  xml.etree.ElementTree as ET

But both of those seem pretty reasonable.  We see no reason to require any camelcase import to be imported "as" a camelcase word.
2019-05-16 09:47:02 +02:00
ktsai7
f68f5e3014 Update flecsi package.py (#11442)
* Update flecsi package.py

* Update package.py

* Update package.py

* Update package.py
2019-05-15 15:29:08 -06:00
Justin S
bfb0f57492 r-geonames: new package at 0.999 (#11455) 2019-05-15 16:04:50 -05:00
Justin S
11bd795ca8 repeatscout: new package at 1.0.5 (#11409)
* repeatscout: new package at 1.0.5

* repeatscout: add trf runtime dependency

* repeatscout: add nseg runtime dependency
2019-05-15 16:04:17 -05:00
Justin S
19355cafae r-phylostratr: new package (#11053) 2019-05-15 16:03:36 -05:00
Justin S
5f5616d6a2 r-taxizedb: new package at 0.1.4 (#11052) 2019-05-15 16:02:54 -05:00
Justin S
b19429159f r-rmysql: add 0.10.17, mariadb-connector-c dependency (#11044)
* r-rmysql: add 0.10.17, mariadb-connector-c dependency

* r-rmysql: add dbi, mariadb version constraints
2019-05-15 15:58:15 -05:00
Justin S
62fa813678 recon: new package at 1.08 (#11408)
* recon: new package at 1.08

* recon: add period

* recon: use proper decorators, better documentation

* recon: fix incorrect os import

* recon: add repeatmasker patch as variant
2019-05-15 15:55:10 -05:00
Justin S
80d7573df8 r-rnoaa: new package at 0.8.4 (#11461) 2019-05-15 15:52:17 -05:00
Justin S
a99454ec6d r-isdparser: new package at 0.3.0 (#11460) 2019-05-15 15:51:50 -05:00
Justin S
cdd8da7251 r-crul: new package at 0.7.4 (#11459) 2019-05-15 15:51:11 -05:00
Justin S
cfad3cd06c r-httpcode: new package at 0.2.0 (#11454) 2019-05-15 15:50:32 -05:00
Justin S
f3dd933e3f r-urltools: new package at 1.7.3 (#11458) 2019-05-15 15:48:54 -05:00
Justin S
c49017a4c5 r-triebeard: new package at 0.3.0 (#11457) 2019-05-15 15:48:17 -05:00
Justin S
230db7c880 r-curl: add 3.3 (#11456) 2019-05-15 15:47:45 -05:00
Denis Davydov
9d34326992 fix suite-sparse built with tbb from intel-parallel-studio (#11134)
* fix suite-sparse built with tbb from intel-parallel-studio

* intel: add tbb_headers, strip newline from cxx_lib

* use property
2019-05-15 11:03:19 -07:00
Justin S
5c021f5416 New package: NSEG (starting at version 1.0) (#11410)
The source is managed as a set of files in an FTP URL. Since there
are no FetchStrategy's implemented for this setup, the files are
managed as a set of Resource's
2019-05-15 10:35:38 -07:00
Leonhard Reichenbach
eae9b0908a CMake package: add dependencies (#11257)
Add dependencies to CMake and GnuTLS which would otherwise be
picked up from the system

* Add gnutls as explicit dependency of CMake
* Add new package libidn2 as explicit dependency for gnutls
2019-05-15 10:07:31 -07:00
Christoph Junghans
0226a95232
parsplice: fix build (#11462) 2019-05-15 08:18:35 -06:00
Todd Gamblin
1dc8f952a5
Use svn info --xml instead of svn info to get svn revisions (#11466)
- `svn info` prints different results depending on the system locale
  - in particular, Japanese output doesn't contain "Revision:"

- Change Spack code to use XML output instead of using the human output
2019-05-15 13:37:02 +02:00
Brian Van Essen
821b7d3b93 Added setuptools to receipe (#11463) 2019-05-15 12:19:04 +02:00
Michael Kuhn
58c5442d62 kitty: Fix pkgconfig dependency (#11465)
pkgconfig is the correct virtual dependency while pkg-config is a
specific implementation.
2019-05-15 12:18:16 +02:00