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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
2019-05-15fix suite-sparse built with tbb from intel-parallel-studio (#11134)Denis Davydov2-2/+12
* fix suite-sparse built with tbb from intel-parallel-studio * intel: add tbb_headers, strip newline from cxx_lib * use property
2019-05-15New package: NSEG (starting at version 1.0) (#11410)Justin S1-0/+81
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
2019-05-15CMake package: add dependencies (#11257)Leonhard Reichenbach3-1/+29
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
2019-05-15parsplice: fix build (#11462)Christoph Junghans1-2/+2
2019-05-15Use `svn info --xml` instead of `svn info` to get svn revisions (#11466)Todd Gamblin2-14/+8
- `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
2019-05-15Added setuptools to receipe (#11463)Brian Van Essen1-0/+1
2019-05-15kitty: Fix pkgconfig dependency (#11465)Michael Kuhn1-1/+1
pkgconfig is the correct virtual dependency while pkg-config is a specific implementation.
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