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2019-01-31py-pybigwig: fix build with python3, add numpy variant (#10444)Ricardo Silva2-2/+23
* added patch to correctly pick up non-system curl when building with Python 3 * added numpy variant * add version 0.3.12 * update checksums to sha256
2019-01-31New package: openjdk (#9861)snehring1-0/+98
Closes #2622 This retrieves and installs the binary of Oracle's OpenJDK (an open-source JDK implementation). The logic is largely based on the Spack JDK package (Oracle's closed-source JDK implementation). For now this is only supports Linux. If the download could be customized based on OS (for the same version), binaries are also available for MacOS and Windows.
2019-01-30git-lfs: add version 2.6.1, update build system (#10405)Matthias Diener1-13/+6
Build system was changed to use a Makefile. Therefore older versions (which don't support this) are removed. The new build system also supports testing by default.
2019-01-30fftw: fix include error for 2.x versions (#10039)Tom Payerle1-6/+15
Fixes #7372 Added patch method which renames config.h in the fftw subdir of the source tree. fftw 2.1.5 appears to ship with a copy of this file with all defines commented out. This gets read by the #include directives instead of the version in the build directory with the correct defines. As a result, many C preprocessor macros left undefined, including F77_FUNC_ which causes the bulk of fttwf77.c to be skipped due to an #ifdef, so fftw_reverse_int_array et al not included in library. Fixes #7372 Also fixed some inconsistencies with the handling of quad and long_double in specs between the configure method and the build, check, and install methods.
2019-01-30HDF5: Add develop Version (#10382)Axel Huebl1-0/+13
2019-01-30Mercury package: update libfabric dependency on Cray (#10408)Phil Carns1-1/+0
The Mercury package previously depended on libfabric@develop on Cray platforms in order to pick up a fix for the GNI provider that was only available in git. This is no longer needed now that the libfabric package is at 1.7.0.
2019-01-30r-pkgmaker: add 0.27, new dependencies (#10419)Justin Stanley1-0/+14
2019-01-30gobject-introspection: add 1.56.1 and fix download (#10462)Michael Kuhn1-0/+5
Define url_for_version, since Spack's default substitution is not sufficient
2019-01-30go: fix directory structure issue for 1.11.5 (#10484)Matthias Diener1-2/+9
2019-01-30cmake: Fix linker errors on Darwin when using external dependencies (#10467)Chuck Atkins2-0/+33
Adds upstream patch for a missing framework. This is anticipated to be fixed by CMake 3.13.4 so is only applied up to version 3.13.3
2019-01-30libsodium: Updates source URL. (#10483)Matt Belhorn1-1/+1
The source URL for versions 1.0.15 and older is updated to reflect where those archives are now hosted by the upstream libsodium developers.
2019-01-30ninja: Add kitware version with fortran capability (#10470)Jon Rood1-1/+3
2019-01-30New package: SLATE (#10434)G-Ragghianti1-0/+63
2019-01-30jemalloc: Add variant to prepend public api with "je_" prefix (#10356)Jason Lee1-0/+3
2019-01-30redundans: add 0.14a (#10006)Justin Stanley1-10/+15
Also update install to use globbing
2019-01-30New package: simgrid (#10076)Samuel Thibault1-0/+76
2019-01-30zoltan: detect metis int64 variant (#10051)Cameron Smith1-0/+4
Configure zoltan depending on metis int64 support
2019-01-30Package py-keras: add new versions and dependencies (#10353)dorier3-7/+70
Add new versions for py-keras. Versions of py-keras at or after 2.2.0 require keras-processing and keras-applications packages. Add these packages to Spack and add dependencies to the py-keras package.
2019-01-30cudnn package: add version 7.2 (#10481)Jimmy Tang1-0/+2
2019-01-30Update opa-psm2 package (#10344)sknigh1-8/+14
* Add version 11.2.68 * Add variant to disable AVX2 for older hardware * Change the makefile so libraries and includes are not placed under $PREFIX/usr * Updated URL and homepage
2019-01-30r-preprocesscore: add version 1.44.0 (#10389)Justin Stanley1-0/+1
2019-01-30r-impute: add version 1.56.0 (#10390)Justin Stanley1-0/+1
2019-01-30codes package: add version 1.1.0 (#10414)Abhinav Bhatele1-0/+1
2019-01-30r-runit: new package at 0.4.32 (#10416)Justin Stanley1-0/+19
2019-01-30r-bibtex: new package at 0.4.2 (#10417)Justin Stanley1-0/+22
2019-01-30r-rngtools: add 1.3.1 (#10418)Justin Stanley1-0/+1
2019-01-30ROSS package: update homepage and git url (#10429)Abhinav Bhatele1-2/+2
2019-01-30Add JDK 11.0.2_9 (#10413)Adam J. Stewart1-2/+4
Also add 11.0.1_13; remove 11.0.1, which is no longer available for download.
2019-01-30ncl package: require cairo with pdf support (#10465)Michael Kuhn1-1/+1
Needed after #10135
2019-01-30gtkplus: add gettext dependency (#10464)Michael Kuhn1-0/+1
2019-01-30New package: lm-sensors (#10443)G-Ragghianti1-0/+34
2019-01-30go: add version 1.11.5 (#10451)Matthias Diener1-0/+1
2019-01-30py-petsc4py: add version 3.10.1 (#10457)Satish Balay1-1/+3
Also update dependency version ranges
2019-01-30py-espresso package: add version 4.0.1 (#10469)Christoph Junghans1-0/+1
2019-01-30py-dask package: add version 1.1.0 (#10475)Sajid Ali1-1/+2
2019-01-30neovim package: add version 0.3.4 (#10472)Sajid Ali1-1/+2
2019-01-30geopm package: new versions, dependency updates (#10480)Matthias Maiterth1-5/+12
Added versions 1.0.0-rc1, 0.6.1, 0.6.0, 0.5.1 hwloc dependency was removed after 0.5.1, so the related configure option is not specified after 0.5.1 Require py-matplotlib dependency version 2.2.3 (version was not specified before)
2019-01-30Add Open MPI 2.1.6 (#10478)Daniel Topa1-0/+1
2019-01-30py-numexpr package: add version 2.6.9 (#10477)Sajid Ali1-1/+2
2019-01-30 modified: var/spack/repos/builtin/packages/libx11/package.py (#10473)Sajid Ali1-1/+2
2019-01-30py-pyfftw package: add version 0.11.1 (#10474)Sajid Ali1-0/+1
2019-01-29Add configparser v3.5.1, fixes backports namespace (#10433)George Hartzell1-0/+1
Fixes #8343 #4154 #7370 Closes #4155 All but one of the backports packages were using "pkgutil-style" namespacing, but configparser was using "pkg_resource-style". A namespace needs to be one style or another. This adds a new configparser version which switches to using the pkgutil-style namespace approach. With this update, one can now install flake8 with Spack and use it by loading modules.
2019-01-29debug output includes modulecmd output (#9476)Peter Scheibel1-7/+28
Debug output now includes the output of modulecmd executions. Only output module content when a failure occurs; always report when a module is loaded/unloaded.
2019-01-29rhash: Fix broken RPATH info on darwinChuck Atkins1-3/+3
The PREFIX variable in the makefiles is directly used to construct the install name on the library metadata on darwin. If not passed, the default /usr/local is used and the resulting librhash.dylib contains usage informaiton of /usr/local/lib/librhash.0.dylib. This adds the PREFIX= variable directly to the make command so the resulting usage metadata contains the correct valid library path.
2019-01-28add flux-core@0.11.0 and flux-sched@0.7.0 (#10447)Stephen Herbein2-5/+11
* flux-core: add v0.11.0 and updated dependencies libuuid hasn't been a direct dependency of flux-core since 2015 (well before any of the versions listed in the package). The yaml-cpp dependency moved to flux-sched when we moved the jobpsec library from core to sched. Some python3 incompatibilities were found in 0.11.0, so bump the python3 support back a version. * flux-sched: add v0.7.0 and make boost dependency more precise
2019-01-29llvm: various updates (#10427)Chuck Atkins1-0/+21
* llvm: Bump version to 7.0.1 * llvm: Added perl-data-dumper build dependency for openmp * llvm: Enable exception handling and RTTI Useful to have turned on in general with RTTI but also necessary to workaround some lldb stability issues with some versions of libstdc++.
2019-01-26Update the PMIx package (#10442)Ralph Castain1-27/+32
* Update the PMIx package - Add latest releases to the list. - Add dependency on hwloc for versions >= 3.0 - Flag preferred versions for libevent and hwloc - Improve the description - Point the project URL to the correct site Signed-off-by: Ralph Castain <rhc@pmix.org> * Only install the hwloc dependency for versions >= 3.0.0 Thanks to @ax3l for the suggestion Signed-off-by: Ralph Castain <rhc@pmix.org> * Add myself as a listed maintainer Signed-off-by: Ralph Castain <rhc@pmix.org>
2019-01-26add variant for a debug build (#10409)Cameron Smith1-0/+4
2019-01-26QMCPACK Update - Jan 2019 (#10252)Nichols A. Romero1-28/+98
* Add warnings for existing conflicts. New versions of QMCPACK require a compiler with C++14 support. * QMCPACK now requires a newer release of CMake. * Switch QMCPACK to using FFTW-api provider. * Relax dependencies on QMCPACK +da variant. * Add QMCPACK 3.6.0 release. * QMCPACK compiler-CUDA conflicts. * QMCPACK fix typo in expressing conflict. * Conditional needed since these variables are only used when FFTW is a dependency to QMCPACK. * QMCPACK QE variant dependency was underspecified. Must include MPI as a hard dependency on QE. * Update QMCPACK dependencies for HDF5, CMake and Boost. * QMCPACK clean-up, more consistent use of spec vs. self.spec. * Add support for collective I/O variant of QMCPACK. * Update QMCPACK conflicts for QE and PHDF5 variants. * Use built-in install method for QMCPACK starting with 3.6.0 * QMCPACK compiler C++14 conflicts were off by one version. * QMCPACK package needs to setup_environment method. * In support of PR#10252, get rid of slashes in string. * Migrate these to the CUDA package and make a seperate PR. * In support of PR#10252, get rid of join_path for nexus. * In support of PR#10252, work around concretizer limitation. * In support of PR#10252, convert to conditionals to if-else clauses for compactness. * In support of PR#10252, get rid of extra space and new line in warning messages.
2019-01-26laghos: update version (#10420)Abhinav Bhatele2-1/+2