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2018-04-26samtools: new version (#7921)Levi Baber1-0/+4
2018-04-26XL Fortran compiler >= 16.0 is synced with C compiler version (#7887)serbanmaerean2-0/+12
* Use reported version of IBM XL Fortran compiler for compiler versions >= 16.0. Starting with the April 2018 release, the IBM XL C and Fortran compilers report the same version, 16.0. Consequently, there is no need to downgrade the Fortran compiler version to match that of the C compiler.
2018-04-26Use GitLab's API endpoint for fetching a git snapshot. (#7881)Sergey Kosukhin11-19/+44
* Use GitLab's API endpoint for fetching a git snapshot. * More GitLab packages use the API. * find_list_url for GitLab's API URLs. * Flake8 * Url for 'hacckernels'. * Check GitLab API regexps before the non-API ones.
2018-04-26add patch to get aspell to build on OSX (#7919)healther2-0/+22
2018-04-26config_args does NOT apply to CMakePackage. (#7917)健美猫1-1/+1
2018-04-26Add Trinity package (#7828)Simon Flood1-0/+74
* Add Trinity package New package to install Trinity - another odd installer (assumes installation to /usr/local/bin and doesn't copy dot files hence deleting them) * Update package.py added dependencies from https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity * Update package.py Copy tree to prefix.bin so that PATH can correctly be set for the Trinity command - can't split it off as it seems everything needs to stay together. * Update package.py Fixed over-length lines and space before comma
2018-04-26Package 'gdbm': do not set CC. (#7912)Sergey Kosukhin1-8/+1
2018-04-26mfem: add valid range of hypre version numbers (#7903)Geoffrey Oxberry1-0/+2
This commit fixes #7900. In short: in the absence of constraints to the contrary, spack will download the preferred version of a package, which is usually the most recent non-develop version. On a clean spack installation without hypre installed, `spack install mfem` will download hypre 2.14.0, which is API-incompatible with mfem 3.3.2 (and earlier versions of mfem), so spack will throw compiler errors re: the API mismatch. This commit fixes that error by restricting mfem release versions 3.3.2 and earlier to hypre version 2.10.b to 2.13.999 (only 2.13.0 currently exists, but if it has a non-2.14.x maintenance release, these versions of hypre should also be permitted).
2018-04-26adol-c: add boost optional dependency (#7905)Denis Davydov1-10/+32
2018-04-26A new package: loki. (#7908)健美猫1-0/+50
* A new package: loki. * Flake8.
2018-04-26Added the latest versions of a few packages (#7910)Massimiliano Culpo10-2/+21
* automake: added version 1.16.1 * lmod: added version 7.7.29 * git: added version 2.17.0 * tmux: added version 2.7 * scala: added version 2.12.5, fixed typo in version 2.10.6 * Added spark@2.3.0, hadoop@3.1.0, jdk@8u172-b11 * picard: added version 2.18.3 * tar: added version 1.30
2018-04-26A new package: openslide. (#7906)健美猫1-0/+40
2018-04-25Add boost 1.67.0 (#7889)Bruno Turcksin2-18/+3
* Add boost 1.67.0 * Remove boost 1.67.0 release candidate and the associated patch
2018-04-25Additional r packages (#7892)mcneish113-3/+509
* Add r-bbmisc * Add r-dicekriging * Add r-lhs * Add r-mco * Add r-misc3d * Add r-mlr * Remove boilerplate from r-mlr package * Add r-mlrMBO * Add r-parallelmap * Add r-paramhelpers * Add r-plot3d * Add r-rgenoud * Add r-smoof * Add r-rinside 0.2.14 * Fix flake8 issues * Add specific required versions * Add more up-to-date versions of r-{mco, mlr, mlrMBO, smoof}
2018-04-25Added OpenMP Variant for Kokkos (#7902)Robert Pavel1-2/+14
Added OpenMP variant for kokkos that can be disabled to build and test on platforms where OpenMP is not available or desired. Also updated version list
2018-04-25openmpi: libfabric support, ucx cleanup (#7842)Levi Baber1-11/+13
* openmpi: libfabric support, ucx cleanup * openmpi: remove unnecessary parentheses
2018-04-25Libfabric: updating fabrics & adding deps (#7838)Levi Baber1-2/+7
* libfabric: mxm deprecated, adding mlx aka ucx * libfabric: adding dependencies that we have in spack
2018-04-25ucx: needs numactl and rdma-core (#7836)Levi Baber1-0/+3
2018-04-25psm: new package (#7834)Levi Baber1-0/+46
* psm: new package * psm: setting latest stable to preferred
2018-04-25rdma-core: new package (#7835)Levi Baber1-0/+43
* rdma-core: new package * rdma-core: change to platform conflict
2018-04-25libnl: new package (#7833)Levi Baber1-0/+42
* libnl: new package * libnl: change platform constraint to a conflict
2018-04-25Added checksums for newer versions of numpy (#7853)Sajid Ali1-0/+3
* Committer: sajid <sajid@xrmlite.phys.northwestern.edu> modified: var/spack/repos/builtin/packages/py-numpy/package.py * Corrected typo * removing whitespace * remove whitespace * remove whitespace, if not will do this in vim
2018-04-25py-testinfra: Create new package (#7883)Eric1-0/+47
* py-testinfra: Create new package * py-testinfra: flake8 fixes * py-testinfra: fix pytest version dependency * py-testinfra: fix py-importlib version dependency
2018-04-25fabtests: new package (#7837)Levi Baber1-0/+37
* fabtests: new package * fabtests: fix hashes for github archive behavior & add libfabric dep * fabtests: both versions confirmed working * fabtests: use developer provided archive
2018-04-25Add a new package: gloo. (#7894)健美猫1-0/+34
* Add a new package: gloo. * Remove dependencies.
2018-04-25Add a new package: cpuinfo. (#7895)健美猫1-0/+35
2018-04-25Add a new package: fp16. (#7896)健美猫1-0/+38
2018-04-25Openmpi update multithread (#7893)Daniel Topa1-1/+1
--enable-mpi-thread-multiple option not viable in Open MPI 3.0+ Signed-off-by: Dan Topa <dantopa@lanl.gov>
2018-04-24new package: py-weblogo (#7886)Eric3-0/+114
2018-04-24environment shell: fix `spack load` (#7747)René Widera1-6/+6
Fix `spack load` with extended packe specifications those includes spaces. Solved by using perfectly parameter forwarding via temporary array. example: ``` $ spack install zlib $ spack install zlib cppflags='-O3 -march=native' $ spack install zlib cppflags='-O2 -march=native' $ spack find -d -L -f zlib ==> 3 installed packages. -- linux-linuxmint18-x86_64 / gcc@5.4.0 ------------------------- k5hg4kkxiutkfl6n53ogz5wnlbdrsdtf zlib@1.2.11%gcc mse2fyzdxciszdhiqi4b5kl6fxkps3fh zlib@1.2.11%gcc cppflags="-O2 -march=native" vrnvj2fikcbxqxrymctnlpmud7wbuahk zlib@1.2.11%gcc cppflags="-O3 -march=native" $ spack load zlib cppflags='-O3 -march=native' ==> Error: Unexpected token ['zlib', 'cppflags=-O3', '-march=native'] ```
2018-04-24petsc and slepc: add 3.9.0; hypre: add 2.14 (needed by petsc) (#7877)Denis Davydov3-2/+8
2018-04-23ARAGORN: Create new package (#7875)Eric1-0/+46
2018-04-23prinseq-lite: Create new package (#7873)Eric1-0/+60
* prinseq-lite: Create new package * prinseq-lite: set variant description and add dependency type
2018-04-237851 pmix aarch64 (#7852)Ross Miller1-0/+10
* Fix build issue with PMIx on aarch64 Work around a bug in PMIx that causes build issues on aarch64. Bug was fixed in PMIx 2.1.1, so the spack package checks both the architecture and the PMIx version. Workaround is to just not build the PMIx test and example code. * Minor code cleanups Minor corrections to make 'spack flake8' happy. * Add support for version 2.1.1
2018-04-23New colm, ragel packages (#7867)Mark Olesen2-0/+81
- Ragel is a parser and finite state machine generator that can be used as an alternative means for solving parsing problems without Flex.
2018-04-23Add a new version 5.4.1.7 for mono. (#7866)健美猫1-0/+1
2018-04-22omega-h: new package (#7861)Dan Ibanez1-0/+67
* omega-h: new package * omega-h: fix multiple package.py issues * omega-h: use tarball checksum to avoid warning * omega-h: wrap lines for flake8
2018-04-22new package: racon (bioinformatics) (#7726)Sinan1-0/+51
* new package: racon (bioinformatics) * add cmake_arg method
2018-04-21Add a new pacakage: HiC-Pro. (#7858)健美猫1-0/+80
* HiC-Pro: a new package. * Flake8. * Update. * Remove nektar.
2018-04-21A new pacakge: IMP. (#7859)健美猫1-0/+40
2018-04-21py-mg-rast-tools: Create new package and its dependencies. (#7816)lingnanyuan8-0/+316
* r-matr: Create new package. * shocklibs: Create new package. * r-biom-utils: Create new package. * r-mgraster: Create new package * py-poster: Create new package. * py-requests-toolbelt: Create new package. * perl-libwww-perl: Create new package. * py-mg-rast-tools: Create new package. * mg-rast-tools: Fix version constraints for dependencies. * Change dependency type of py-setuptools.
2018-04-21py-pymol: new package (#7823)Levi Baber1-0/+51
* py-pymol: new package * py-pymol: needs python+tk
2018-04-21add variant htmlreport to package cppcheck (#7824)healther1-0/+6
Change-Id: I31766d3ceb4fa8852b9bdc82444e36514e760f4b
2018-04-21gnuplot: add 5.2.2 (#7831)Denis Davydov1-0/+1
2018-04-21dealii: disable +slepc with ~petsc (#7832)Denis Davydov1-0/+1
2018-04-21DIAMOND: Add version 0.9.20 (#7847)Eric1-0/+2
* DIAMOND: Add version 0.9.20 * DIAMOND: add version 0.9.21
2018-04-21jellyfish: fixing url for v2 package retrieval (#7849)Levi Baber1-1/+2
2018-04-19self has no attribute named satisfies. (#7826)健美猫1-1/+1
2018-04-19openPMD-api (#7765)Axel Huebl1-0/+102
* openPMD-api Add a new package for openPMD-api. openPMD is a meta-data standard (markup, schema) for hierarchical, scientific particle and mesh based data. openPMD-api is a library wrapping the underlying backends (HDF5, ADIOS, ...) into a single, object-aware API. * Repository: https://github.com/openPMD/openPMD-api * Project: https://github.com/openPMD http://www.openPMD.org * mpi variant forwarding: fix concretization
2018-04-19libxml2: adding subdir to cpath for deps (#7819)Levi Baber1-0/+4
* libxml2: adding subdir to cpath for deps * libxml2: no join_path * libxml2: fix cpath for run_env * libxml2: typo
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