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2018-05-15Format-agnostic data structure for reportsZack Galbreath2-66/+68
Replace the JUnit-specific terms 'testsuite' and 'testcase' with 'spec' and 'package', respectively.
2018-05-14patch petsc test cases for XL compiler (#8091)Serban Maerean2-0/+62
- After spack install, these test cases are built in a seperate step, outside of spack, but they need to patched after staging so users don't have to do it in a seperate step. - The test cases are installed under `<petsc install directory>/share/petsc/examples` and can be built and executed by invoking `gmake -f gmakefile.test` in that directory.
2018-05-14Added Shim to Support hdf5+mpi in Spack Silo (#8130)Robert Pavel1-1/+9
* Added Shim to Support hdf5+mpi in Spack Silo Added compatibility for hdf5+mpi to silo spackage to support spackages with dependency chains that include silo and hf5+mpi * Fixed fixable flake8 issue with silo spackage Fixed missing whitespace around operator * Setting MPI Variant to Default to True As per guidance changing variant to default to MPI builds
2018-05-14salmon: adding in version restriction for boost (#8129)snehring1-1/+1
1.67 does not work with this
2018-05-14prenek missing X.h (#8121)Cameron Smith1-0/+9
2018-05-14lordec: Create new package. (#8095)lingnanyuan1-0/+44
* lordec: Create new package. * lordec: Add homepage, change to MakefilePackage. * Modify dependency type.
2018-05-14r-fit-models: Create new package (#8122)Eric1-0/+38
2018-05-14r-vipor: Create new package (#8128)Eric1-0/+38
2018-05-14LBANN: add hydrogen as optional dependency (#8085)Brian Van Essen2-6/+188
Add Hydrogen package for fork of Elemental library. Update LBANN to use either Hydrogen or Elemental.
2018-05-14r-shinydashboard: Create new package (#8116)Eric1-0/+40
2018-05-14r-picante: Create new package (#8117)Eric1-0/+40
* r-picante: Create new package * Remove dependency already included in RPackage base class
2018-05-14r-squash: Create new package (#8118)Eric1-0/+36
* r-squash: Create new package * Remove dependency already included in RPackage base class * remove extra file
2018-05-14Update py-llvmlite to reflect llvm@6 requirement for versions >0.23.0 (#8109)Sajid Ali1-2/+5
* new file: package.py * corrected using pep8online.com * Update package.py * correct typo * as requested * modified: package.py * Update package.py
2018-05-14Aegean: new package (#8113)Levi Baber2-0/+46
* aegean: new package * genometools: set dependent env for aegean
2018-05-14charliecloud: fix copyright (#8115)Christoph Junghans1-1/+1
2018-05-14dealii: another fix for quick tests only in 9.0 and thus hash (#8114)Denis Davydov1-1/+1
2018-05-14A new pacakge: Kaiju. (#8111)健美猞猁1-0/+48
* A new package: kaiju. * Replace ftp:// with https://.
2018-05-14hisea: new package (#8112)Levi Baber1-0/+43
2018-05-14Add numexpr 3 (#8107)Sajid Ali1-0/+48
* new file: package.py * corrected using pep8online.com * Update package.py * correct typo * as requested
2018-05-14dealii: update hash due to upstream changes (#8105)Denis Davydov1-1/+1
2018-05-14add version 0.6.2 to yaml-cpp (#7931)healther1-1/+11
2018-05-13Add cmake for newer version of libjpeg-turbo (#8102)Sajid Ali1-4/+21
* modified: package.py * add official build reference. * Update package.py * Update package.py * Update package.py * fixed with pep8online.com * update make to make() * change homepage
2018-05-13charliecloud: initial commit (#8106)Christoph Junghans1-0/+38
2018-05-13boost: added the +numpy variant which enables building libboost_numpy (#8104)dorier1-0/+4
* added the +numpy variant which enables building the libboost_numpy libraries * Update package.py Added `type=('build', 'run')`
2018-05-12Create custom PATH that texlive requires in its module. (#8064)Jon Rood1-2/+7
* Create custom PATH that texlive requires in its module. * Updating texlive to 2018 distribution. * Using platform instead of sys for easier portability across linux and osx.
2018-05-12plink: new source version 1.9-beta5 (#8076)Yifan Zhu1-4/+16
* plink: new source version 1.9-beta5 * plink: replace version 1.9 with 1.07
2018-05-12Add package for "bumpversion" (#8078)George Hartzell1-0/+37
* Add package for "bumpversion" bumpversion is a tool that automagically increments version numbers for projects. It can update files and do other magic along the way. * Remove py- package prefix and use pypi.io URL Renamed the package 'bumpversion'. Fetch the package from pypi.io. * Add version info for bumpverion@0.5.3
2018-05-12r-cdcfluview: new package (#8089)Yifan Zhu1-0/+51
* r-cdcfluview: new package * updated package.py
2018-05-12nfft: added version 3.4.1 Moved package to github (#8099)Massimiliano Culpo1-2/+3
2018-05-12netcdf: added version 4.6.1 (#8098)Massimiliano Culpo1-0/+1
2018-05-12shoremap: new package (#7343)Yifan Zhu3-0/+83
2018-05-11dealii: add 9.0.0 (#8096)Denis Davydov1-6/+7
2018-05-11pmix: add 1.2.5 and 2.0.3 bug fix releases (#8097)Howard Pritchard1-0/+2
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-05-11masurca: new version (#8094)Levi Baber1-0/+1
* masurca: new version * masurca: reorder versions
2018-05-11llvm: replace @when with internal check in @run_before (#8092)scheibelp1-1/+2
Fixes #8088 #7012 added a @when condition for a @run_before check to constrain that check to only run on Darwin. @when is intended to be used to choose one of several different implementations of a given function and cannot be used to conditionally deactivate a check altogether. This replaces the external decorator with a check that executes at the beginning of the function.
2018-05-11adds new version to swiftsim (#8093)Mayeul d'Avezac1-0/+1
2018-05-11dealii: disable tpetra when +cuda; check for '' in cuda_arch (#7958)Denis Davydov1-5/+9
* dealii: disable tpetra when +cuda; check for '' in cuda_arch * trilinos: fix Kokkos CUDA * Revert "trilinos: fix Kokkos CUDA" This reverts commit 6aae894bc7d49c9e736c06f65b81b8c219443920. * update according to @aprokop comments * minor * fix flake8
2018-05-11gmsh: add netgen and tetgen (#8060)Denis Davydov3-18/+31
* gmsh: add netgen and tetgen dealii: require gmsh+netgen+tetgen netgen: use http instead of https * dealii: add oce requirement to gmsh
2018-05-10r-mmwrweek: new pacakge (#8086)Yifan Zhu1-0/+40
2018-05-10petsc: specify number of processors used for test case (#8015)David Wootton1-0/+12
For Spectrum MPI, if -np is omitted, the default behavior is to assign one process per process slot, where the default process slot allocation is one per core. On systems with many cores, the number of processes can exceed the size of the grid specified when the testcase is run and the test case fails. This specifies a small number of processes when running the test case to prevent failure.
2018-05-10wireshark: stop cmake from picking up /usr paths (#8053)healther1-2/+14
* stop cmake from picking up /usr paths if spack has corresponding packages Change-Id: I7217122562697c7a642cded2b4bfb606d2e35ffb * add libpcap dependency Change-Id: If0d5c2c94b2c2d1cbb9b19e31e44f870b71ba88b * make cmake actually pick up pcap Change-Id: I67b87fd9282c26f5ff4e0a5aedd8bbbae39a5960 * add libtool build dependency Change-Id: I5c6d14dca7ccbe457318903dd170bb19d004e952 * use .libs for pcap Change-Id: Ibe78f8765524385f9da4a8f9963f2c61632cc9f7 * explicitly add bison build dependency Change-Id: I47112778abdf4c0de81789685a7eca4dddb20f77 * add lua explicitly Change-Id: I8e306e1e4cfa0e16138f3a5109ddcfe912120946 * fix libs usage Change-Id: I8c1e03f10df69e3ef74326a13cacaf0e5498e6aa * add minimal version requirement Change-Id: I4dd181389f9a63067df541b982bc0727f974d4ce
2018-05-09Add new Sundials versions (#8075)David Gardner1-0/+3
* Add new Sundials versions, update minimum cmake version required * specify which versions require a newer cmake * revise cmake dependency * remove develop, add 4.0.0-dev version
2018-05-09Add 3.5.2; Add optional cpp implementation enable for py-protobuf (#8069)mcneish12-0/+17
* Add 3.5.2; Add optional cpp implementation enable for py-protobuf * Make flake8 happy * Give all required install_args
2018-05-09perl-extutils-pkgconfig: Add pkg-config dependency (#8045)Eric1-0/+2
* perl-extutils-pkgconfig: Add pkg-config dependency * perl-extutils-pkgconfig: fix build dependency * perl-extutils-pkgconfig: fix build dependency
2018-05-09llvm+lldb plaform=darwin: check for lldb_codesign certificate (#7012)Geoffrey Oxberry1-0/+20
* llvm+lldb plaform=darwin: check for lldb_codesign Building LLVM with LLDB requires that the "lldb_codesign" code certificate be created (see https://llvm.org/svn/llvm-project/lldb/trunk/docs/code-signing.txt for details). This commit checks for this certificate on Darwin if LLDB is to be built, and returns an informative error message if this certificate is unavailable.
2018-05-08Add gdb@8.1; add optional lzma dependency for debug information support (#8068)mcneish11-1/+4
2018-05-08opencv updates for lbann (#6502)Brian Van Essen2-32/+122
Add variants to control building of many 3rd-party modules in opencv. They are enabled by default, which matches the defaults chosen by opencv when these options are not set explicitly. This also updates the lbann opencv dependency to disable most of these new variants by default in order to build faster.
2018-05-08Packages can tune the list of files to be archived at the end of install (#7760)Massimiliano Culpo5-0/+134
Fixes #2781 This PR introduces a new attribute for packages called `archive_files`, which designates files that should be saved from a package build (e.g. the config.log generated during autotools builds). The attribute contains a list of glob expressions; Any file that matches will be archived in the `<prefix>/.spack/archived-files` directory. Errors that occur when archiving files are collected and reported in a file named `<prefix>/.spack/archived-files/errors.txt`. `AutotoolsPackage` and `CMakePackage` provide a sensible default override for this attribute.
2018-05-08Py cnvkit: updating dependencies (#8057)peetsv1-1/+3
* py-pyfaidx: adding new package * updating the url * identifying dependencies
2018-05-08intltool requires patching for newer perl versions (#8061)Gregory Lee1-0/+6
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