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2019-05-19Add latest version of joblib (#11495)Adam J. Stewart1-4/+7
2019-05-19Add latest version of setuptools (#11493)Adam J. Stewart1-1/+2
2019-05-18Update Umpire package with new versions (#11441)David Beckingsale1-1/+17
* Update Umpire package with new versions * Fix version ordering
2019-05-18trilinos: add variant to disable chaco from seacas (#11482)Denis Davydov2-2/+23
* trilinos: add variant to disable chaco from seacas keep it OFF by default due to the presence of the global symbol "divide" that can lead to symbol clash with other libraries, for example see https://github.com/dealii/dealii/issues/8170#issuecomment-492700787 * dealii: add conflict statement for adol-c and Trilinos SEACAS Chaco
2019-05-18dyninst: rework the cmake args for version 10.1 and later (#11484)Mark W. Krentel1-22/+41
* dyninst: rework the cmake args for version 10.1 and later Add a separate when() case for the cmake args for Dyninst 10.1.0 and later. The prereq args have changed enough that this makes things easier going forward. (My previous commit 26b9369c was inaccurate and temporary.) Dyninst 10.1.0 accepts boost 1.70, but earlier dyninst are restricted to <= 1.69 (not worth back porting every boost change). Change all the dyninst versions to 3 digits for clarity and consistency. * Add version 10.1.0.
2019-05-18QMCPACK Update May 2019 (#11492)Nichols A. Romero1-7/+8
* Add QMCPACK 3.7.0 * SOA is now the default. * Add QMCPACK converter based on QE 6.4
2019-05-18Add conflicts in deal.II package between SymEngine and Trilinos variants ↵Jean-Paul Pelteret1-0/+7
(#11499)
2019-05-18Fix typo in spack executable (#11512)Adam J. Stewart1-1/+1
2019-05-18intel-tbb: fix patch for old compilers (#11371)Owen Solberg2-5/+42
* 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:
2019-05-18Typos: funciton, woudl, hm,... (#11511)George Hartzell1-3/+3
2019-05-18Execute modulecmd in bash shell (#11510)Mario Melara1-2/+4
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.
2019-05-17r-popvar: new package at 1.2.1 (#11490)Justin S1-0/+22
2019-05-17smof: new package at 2.13.1 (#11502)Justin S1-0/+29
2019-05-17r-bglr: new package at 1.0.8 (#11489)Justin S1-0/+19
2019-05-17r-rrblup: new package at 4.6 (#11488)Justin S1-0/+18
2019-05-17r-qtl: new package at 1.44-9 (#11487)Justin S1-0/+18
2019-05-17py-metasv: new package at 0.5.4 (#11476)Justin S1-0/+21
2019-05-17py-pybedtools: new package at 0.6.9 (#11475)Justin S1-0/+23
* py-pybedtools: new package at 0.6.9 * py-pybedtools: add bedtools2 dep
2019-05-17repeatmodeler: new package at 1.0.11 (#11472)Justin S1-0/+66
2019-05-17added branch multisplice to the parsplice package (#11504)Sriram Swaminarayan1-2/+7
2019-05-17gasnet: 2019.3.0 (#11503)Christoph Junghans1-0/+10
2019-05-17parsplice: needs LAMMPS_EXCEPTIONS (#11500)Christoph Junghans2-0/+5
2019-05-17Add version 2.5.1-alpha1 of MAGMA (#11486)Piotr Luszczek1-2/+3
2019-05-17cmake: default to +ownlibs to improve build times (#11483)Todd Gamblin1-2/+6
- 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.
2019-05-16OpenSpeedShop/CBTF package updates and fixes (#11470)Jim Galarowicz8-13/+18
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
2019-05-16CDO package: Fix build with gcc@9 (#11464)Michael Kuhn2-0/+212
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.
2019-05-16Kokkos package: add debug variant (#11469)Andrew Gaspar1-0/+6
2019-05-16Command extensions can import code from modules in root or cmd folder (#11209)Massimiliano Culpo4-4/+277
#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)
2019-05-17Allow command access to dump/pickle_environment from #8476 (#11434)Chris Green2-7/+56
* Allow command access to dump/pickle_environment from #8476
2019-05-16numpy: new version 1.16.3; update historical versions. (#11364)Chris Green1-0/+12
2019-05-16paraview: fix several dependency issues (#11432)Chuck Atkins1-2/+4
* Use externally provided mpi4py * Make mpi4py and numpy both build deps instead of only run deps * libxt is only on ~osmesa platform=linux
2019-05-16junit: escape remaining inputs. (#11382)Matthias Wolf1-2/+2
2019-05-16Fix CMake versions dependencies in RAJA package (#11440)David Beckingsale1-1/+2
2019-05-16Likwid: added versions 4.3.3 and 4.3.4 (#11479)Thomas Gruber1-0/+2
2019-05-16symengine: add 0.4.0, fix dependency in dealii (#11473)Denis Davydov2-1/+2
2019-05-16flake8: add exceptions for overly pedantic camelcase rules from pep8-naming ↵Todd Gamblin2-2/+4
(#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.
2019-05-15Update flecsi package.py (#11442)ktsai71-5/+14
* Update flecsi package.py * Update package.py * Update package.py * Update package.py
2019-05-15r-geonames: new package at 0.999 (#11455)Justin S1-0/+19
2019-05-15repeatscout: new package at 1.0.5 (#11409)Justin S1-0/+24
* repeatscout: new package at 1.0.5 * repeatscout: add trf runtime dependency * repeatscout: add nseg runtime dependency
2019-05-15r-phylostratr: new package (#11053)Justin S1-0/+34
2019-05-15r-taxizedb: new package at 0.1.4 (#11052)Justin S1-0/+28
2019-05-15r-rmysql: add 0.10.17, mariadb-connector-c dependency (#11044)Justin S1-2/+3
* r-rmysql: add 0.10.17, mariadb-connector-c dependency * r-rmysql: add dbi, mariadb version constraints
2019-05-15recon: new package at 1.08 (#11408)Justin S2-0/+635
* 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
2019-05-15r-rnoaa: new package at 0.8.4 (#11461)Justin S1-0/+32
2019-05-15r-isdparser: new package at 0.3.0 (#11460)Justin S1-0/+19
2019-05-15r-crul: new package at 0.7.4 (#11459)Justin S1-0/+22
2019-05-15r-httpcode: new package at 0.2.0 (#11454)Justin S1-0/+16
2019-05-15r-urltools: new package at 1.7.3 (#11458)Justin S1-0/+20
2019-05-15r-triebeard: new package at 0.3.0 (#11457)Justin S1-0/+18
2019-05-15r-curl: add 3.3 (#11456)Justin S1-0/+1
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